diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index 8f410717..ce8f0a78 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,50 +1,50 @@ -dentistry and oral medicine,bioinformatics,immunology,cardiovascular medicine,evolutionary biology,biophysics,dermatology,oncology,orthopedics,pediatrics,hiv aids,geriatric medicine,public and global health,neurology,month,occupational and environmental health,intensive care and critical care medicine,biochemistry,pharmacology and therapeutics,microbiology,primary care research,systems biology,epidemiology,health systems and quality improvement,Total,health policy,allergy and immunology,genomics,radiology and imaging,genetic and genomic medicine,respiratory medicine,obstetrics and gynecology,pathology,health economics,infectious diseases,emergency medicine,molecular biology,scientific communication and education,psychiatry and clinical psychology,health informatics,surgery,ophthalmology -,,,,,,,,,,,,2,,Feb-24,,,,,,,,1,,4,,,,,,,,,,1,,,,,,, -,,,,,,,,,,,,2,,Jan-24,1,,,,,,,,,3,,,,,,,,,,,,,,,,, -,,,1,,,,,,,,,1,1,Dec-23,1,,,,,,,4,,10,,,,,,,,,2,,,,,,,, -,,,,,,,1,,,,,,,Nov-23,,,,,,,,2,,4,,,,,,,,,,1,,,,,,, -,,1,,,,,,,,,,,,Oct-23,,,,,,,,1,,5,,,,,,1,,,,1,,,,,1,, -,,,,,,,,,,,,,,Sep-23,,,,,,,,,,1,,,,,,,,,,1,,,,,,, -,,,,,,,,,,,,1,,Aug-23,1,,,,,1,,3,,6,,,,,,,,,,,,,,,,, -,,,,,,,,,,,,1,,Jul-23,,,,,,,,2,2,6,,,,,1,,,,,,,,,,,, -,,,,,,,,1,,,,,,Jun-23,1,,,,,,,1,,7,,,,,,,,,,2,,,1,,1,, -,,1,,,,,,,,,,1,,May-23,,,,,,,,2,,6,,,,,,1,,,,1,,,,,,, -,,,,,,,,,,,,2,,Apr-23,,,,,,,,,,3,,,,,,,,,,1,,,,,,, -,,,,,,,,,,,,2,,Mar-23,1,,,,,,,2,,8,,,,,,,,,,3,,,,,,, -,,,,,,,,,,,,2,1,Feb-23,,,,,,,,2,,6,,,,,,1,,,,,,,,,,, -,,,,,,,,,,,,,,Jan-23,,,,,,,,5,,6,,,,,,,,,,1,,,,,,, -,,,,,,,,,,,,1,,Dec-22,,,,,,,,3,,12,1,,,,,2,,1,,4,,,,,,, -,,,,,,,,,,,,,,Nov-22,,,,,,,,,,4,,,,,,,,,,4,,,,,,, -,,,1,,,,,,,,,2,,Oct-22,,,,,,,,1,,6,,,,,,,,,,2,,,,,,, -,,,,,,,,,1,,,1,,Sep-22,2,,,,1,,,1,,9,,,,,,1,,,,2,,,,,,, -,,,,,,,,,,,,3,,Aug-22,,,,,,,,4,,10,,,,,,,,,,3,,,,,,, -,,1,,,,,,,1,,,,,Jul-22,,,,,,,,2,,8,,,,,,,,,,3,,,,,1,, -,,,,,,,,,,,,1,,Jun-22,,,,,,,,6,,18,,,,,1,,,,,4,,,,5,1,, -,,,,,,,,,,,,1,,May-22,,,,,1,1,,2,1,14,,,,,,,,,1,5,,,,2,,, -,,,1,,,,,,,,,1,,Apr-22,1,,,,1,,,5,2,16,,,,,,1,,,1,3,,,,,,, -,,,,1,,,,,,,,,,Mar-22,,,,,,1,,9,,17,,,,,,1,,,,4,,,,1,,, -,,,,,,,,,,,,1,1,Feb-22,,,,,,,,6,,12,,,,,,,,,,4,,,,,,, -,,1,1,,,,,,,,,1,,Jan-22,1,,,,,,,5,,14,,,,,,,,,,3,,,,,2,, -,,,1,,,,,,1,,,,1,Dec-21,,,,,,1,,10,,22,,,,,,,,,,8,,,,,,, -,,,,,1,,,,,,,3,1,Nov-21,,1,,,,1,,9,2,24,,,1,,,,,,,4,,,,1,,, -,,,,,,,,,1,,1,,,Oct-21,,,,,,,,4,,11,,,,,,,,,,3,,,,2,,, -,,,1,,,,,,,,,2,,Sep-21,,1,,1,,,,6,,16,,,,,,,,,,4,,,,,1,, -,,,1,,,,,,,,,3,,Aug-21,1,1,,,,,,2,,13,,,,,,1,,,,3,,,,,1,, -,,,,,,,,,1,,,4,,Jul-21,,1,,,,,,3,,25,,,,,1,2,,,,12,1,,,,,, -,,1,,,,,,,1,,,4,1,Jun-21,1,1,,,,1,,6,1,27,,1,,,,,,,,7,,,,1,1,, -,,,,,,1,,,,,,1,,May-21,,,,,,,,11,,22,,,,,1,,,,,7,,,,1,,, -,,,,,,,,,,,,1,,Apr-21,2,,,,1,1,,3,1,19,,1,,,,,,,,7,,,,1,1,, -,,,,,,,,,1,,2,5,1,Mar-21,,,1,,,,,5,,38,,,,1,1,,,,,17,,,,1,2,1, -,,,,,,,,,,,,1,,Feb-21,,,,,,,,9,1,23,,,,,,,,,1,9,,,,,1,1, -1,,,,,,,,,,,1,3,,Jan-21,,1,,,,1,,4,1,22,1,,,,,,,,,8,,,,1,,, -,,,2,,,,,,,,,3,,Dec-20,,,,,1,1,,4,1,23,,,2,,,,,,,4,,,,2,3,, -,1,1,,,,,,,,,,5,,Nov-20,,,,,,,,5,,26,1,,,,,,,,,12,,,,,1,, -,1,1,,,,,1,,,,1,,,Oct-20,,1,,,,1,1,6,,30,1,,,,,,,,,12,,,,3,1,, -,,,,,,,,,,1,,3,,Sep-20,,1,,,1,1,,6,,26,,,,,,,,,,8,2,,,2,1,, -,,,,,,,,,,,,2,,Aug-20,1,,,,,,,6,1,27,,,,,1,,1,,,12,2,1,,,,, -,,1,1,,,,,,,,,4,,Jul-20,,1,,,,,,10,,28,,,1,,,1,,,,8,,,,1,,, -,1,1,,,,,1,,,,1,3,,Jun-20,,3,,,,,,7,1,36,1,,,,,1,,,,10,,,,4,1,,1 -,1,,2,,,,1,,,,1,8,,May-20,1,1,,,,,,8,,36,,,,,,1,,,1,10,,,,,1,, -,,,,,,,,,,,,1,,Apr-20,,,,,,,,7,1,19,,,1,,2,,,,,7,,,,,,, -,,,,,,,,,,,,3,,Mar-20,,,,,,,,4,,8,,,,,,,,,,1,,,,,,, -,,,,,,,,,,,,2,,Feb-20,,,,,,,,4,,6,,,,,,,,,,,,,,,,, +intensive care and critical care medicine,oncology,obstetrics and gynecology,molecular biology,respiratory medicine,evolutionary biology,primary care research,month,systems biology,health economics,infectious diseases,pharmacology and therapeutics,radiology and imaging,dermatology,surgery,hiv aids,public and global health,pathology,dentistry and oral medicine,Total,allergy and immunology,genetic and genomic medicine,health systems and quality improvement,psychiatry and clinical psychology,epidemiology,neurology,scientific communication and education,emergency medicine,ophthalmology,immunology,health informatics,bioinformatics,genomics,biophysics,occupational and environmental health,orthopedics,microbiology,geriatric medicine,biochemistry,pediatrics,health policy,cardiovascular medicine +,,,,,,,Feb-24,,,1,,,,,,2,,,4,,,,,1,,,,,,,,,,,,,,,,, +,,,,,,,Jan-24,,,,,,,,,2,,,3,,,,,,,,,,,,,,,1,,,,,,, +,,,,,,,Dec-23,,2,,,,,,,1,,,10,,,,,4,1,,,,,,,,,1,,,,,,,1 +,1,,,,,,Nov-23,,,1,,,,,,,,,3,,,,,1,,,,,,,,,,,,,,,,, +,,,,1,,,Oct-23,,,1,,,,,,,,,5,,,,,1,,,,,1,1,,,,,,,,,,, +,,,,,,,Sep-23,,,1,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,, +,,,,,,1,Aug-23,,,,,,,,,1,,,6,,,,,4,,,,,,,,,,,,,,,,, +,,,,,,,Jul-23,,,,,,,,,1,,,7,,1,2,,3,,,,,,,,,,,,,,,,, +,,,,,,,Jun-23,,,2,,,,,,,,,7,,,,,1,,1,,,,1,,,,1,1,,,,,, +,,,,1,,,May-23,,,1,,,,,,1,,,6,,,,,2,,,,,1,,,,,,,,,,,, +,,,,,,,Apr-23,,,1,,,,,,2,,,3,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,Mar-23,,,3,,,,,,2,,,9,,,,1,2,,,,,,,,,,1,,,,,,, +,,,,1,,,Feb-23,,,,,,,,,2,,,8,,,,,4,1,,,,,,,,,,,,,,,, +,,,,,,,Jan-23,,,1,,,,,,,,,6,,,,,5,,,,,,,,,,,,,,,,, +,,,,2,,,Dec-22,,,4,,,,,,1,1,,12,,,,,3,,,,,,,,,,,,,,,,1, +,,,,,,,Nov-22,,,3,,,,,,,,,3,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,Oct-22,,,2,,,,,,2,,,6,,,,,1,,,,,,,,,,,,,,,,,1 +,,,,1,,,Sep-22,,,2,,,,,,1,,,9,,,,,1,,,,,,,,,,2,,1,,,1,, +,,,,,,,Aug-22,,,3,,,,,,3,,,10,,,,,4,,,,,,,,,,,,,,,,, +,,,,,,,Jul-22,,,3,,,,,,,,,8,,,,,2,,,,,1,1,,,,,,,,,1,, +,,,,,,,Jun-22,,,4,,,,,,1,,,18,,1,,5,6,,,,,,1,,,,,,,,,,, +,,,,,,1,May-22,,1,5,,,,,,1,,,14,,,1,2,2,,,,,,,,,,,,1,,,,, +,,,,1,,,Apr-22,,1,3,,,,,,1,,,16,,,2,,5,,,,,,,,,,1,,1,,,,,1 +,,,,1,1,1,Mar-22,,,5,,,,,,,,,18,,,,1,9,,,,,,,,,,,,,,,,, +,,,,,,,Feb-22,,,3,,,,,,1,,,11,,,,,6,1,,,,,,,,,,,,,,,, +,,,,,,,Jan-22,,,3,,,,,,1,,,14,,,,,5,,,,,1,2,,,,1,,,,,,,1 +,,,,,,1,Dec-21,,,8,,,,,,1,,,24,,,,,10,1,,,,,,,,,,,1,,,1,,1 +1,,,,,,1,Nov-21,,,5,,,,,,3,,,24,,,2,1,8,1,,,,,,,1,1,,,,,,,, +,,,,,,,Oct-21,,,3,,,,,,,,,11,,,,2,4,,,,,,,,,,,,,1,,1,, +1,,,,,,,Sep-21,,,5,1,,,,,2,,,17,,,,,6,,,,,,1,,,,,,,,,,,1 +1,,,,1,,,Aug-21,,,3,,,,,,3,,,13,,,,,2,,,,,,1,,,,1,,,,,,,1 +1,1,,,2,,,Jul-21,,,11,,,,,,4,,,25,,1,,,3,,,1,,,,,,,,,,,,1,, +1,,,,,,1,Jun-21,,,7,,,,,,4,,,28,1,,1,1,7,1,,,,1,1,,,,1,,,,,1,, +,,,,,,,May-21,,,7,,,1,,,1,,,22,,1,,1,10,,,,,,1,,,,,,,,,,, +,,,,,,1,Apr-21,,,6,,,,,,1,,,19,1,,1,1,4,,,,,,1,,,,2,,1,,,,, +,,,,,,,Mar-21,,,17,,1,,1,,5,,,39,,1,,1,6,1,,,,,2,,,,,,,2,1,1,, +,,,,,,,Feb-21,,1,9,,,,1,,1,,,22,,,,,8,,,,,,1,,,,,,,,,,,1 +1,,,,,,1,Jan-21,,,8,,,,,,3,,1,22,,,1,1,4,,,,,1,,,,,,,,1,,,, +,,,,,,1,Dec-20,,,4,,,,,,3,,,23,,,1,2,4,,,,,,3,,2,,,,1,,,,,2 +,,,,,,,Nov-20,,,13,,,,,,5,,,28,,,,,6,,,,,1,1,1,,,,,,,,,1, +1,1,,,,,1,Oct-20,1,,12,,,,,,,,,30,,,,3,6,,,,,1,1,1,,,,,,1,,,1, +1,,,,,,1,Sep-20,,,8,,,,,1,3,,,27,,,,2,6,,,3,,,1,,,,,,1,,,,, +,,1,1,,,,Aug-20,,,12,,,,,,2,,,27,,1,1,,6,,,2,,,,,,,1,,,,,,, +1,,,,1,,,Jul-20,,,8,,,,,,4,,,27,,,,1,9,,,,,1,,,1,,,,,,,,,1 +3,1,,,1,,,Jun-20,,,10,,,,,,3,,,36,,,1,4,7,,,,1,1,1,1,,,,,,,,,1,1 +1,1,,,1,,,May-20,,1,9,,,,,,8,,,35,,,,,8,,,,,,1,1,,,1,,,1,,,,2 +,,,,,,,Apr-20,,,5,,,,,,1,,,17,,2,1,,7,,,,,,,,1,,,,,,,,, +,,,,,,,Mar-20,,,1,,,,,,3,,,8,,,,,4,,,,,,,,,,,,,,,,, +,,,,,,,Feb-20,,,1,,,,,,2,,,7,,,,,4,,,,,,,,,,,,,,,,, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index 395a9d7f..f993c120 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -137,7 +137,6 @@ FindingsIn 1,888 participants included in the primary analysis, 1,149 received c InterpretationSystemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL one year after hospital discharge. Treatments to address this are urgently needed. Take home messageSystemic corticosteroids given for acute COVID-19 do not affect health-related quality of life or other patient reported outcomes, physical and mental health outcomes, and organ function one year after hospital discharge",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2023.11.06.23298026,2023-11-07,https://medrxiv.org/cgi/content/short/2023.11.06.23298026,"Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England",Harrison Manley; Thomas Bayley; Gabriel Danelian; Lucy Burton; Thomas Finnie; Andre Charlett; Nick Watkins; Paul Birrell; Daniela De Angelis; Matt J Keeling; Sebastian J Funk; Graham Medley; Lorenzo Pellis; Marc Baguelin; Graeme J Ackland; Johanna Hutchinson; Steven Riley; Jasmina Panovska-Griffiths,"UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Cambridge Cambridge, UK; University of Warwick, Zeeman Institute: SBIDER; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; The University of Manchester; Imperial College London; University of Edinburgh; UK Health Security Agency; UK Health Security Agency; University of Oxford","Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated Medium-Term Projections (MTPs) of possible epidemic trajectories over the future 4-6 weeks from a collection of epidemiological models.In this paper we outline this collaborative modelling approach and evaluate the accuracy of the combined and individual model projections against the data over the period November 2021-December 2022 when various Omicron subvariants were spreading across England. Using a number of statistical methods, we quantify the predictive performance of the model projections for both the combined and individual MTPs, by evaluating the point and probabilistic accuracy. Our results illustrate that the combined MTPs, produced from an ensemble of heterogeneous epidemiological models, were a closer fit to the data than the individual models during the periods of epidemic growth or decline, with the 90% confidence intervals widest around the epidemic peaks. We also show that the combined MTPs increase the robustness and reduce the biases associated with a single model projection. Learning from our experience of ensemble modelling during the COVID-19 epidemic, our findings highlight the importance of developing cross-institutional multi-model infectious disease hubs for future outbreak control.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.10.26.23297598,2023-10-26,https://medrxiv.org/cgi/content/short/2023.10.26.23297598,Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection,Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL,"IntroductionEmerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. MethodsConcentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. @@ -184,26 +183,6 @@ MethodsSurvival analysis was performed in adults (n=23,452) with community-manag FindingsIndividuals reporting baseline symptoms had longer post-COVID symptom duration (from 10 to 15 days) with baseline fatigue nearly doubling duration. Two-thirds (910 of 1350 [67.4%]) of individuals with long illness were asymptomatic beforehand. However, 440 (32.6%) had baseline symptoms, vs. 255 (18.9%) of 1350 individuals with short illness (p<0.0001). Baseline symptoms increased the odds ratio for long illness (2.14 [CI: 1.78; 2.57]). Prior comorbidities were more common in individuals with long vs. short illness. In individuals with long illness, baseline symptomatic (vs. asymptomatic) individuals were more likely to be female, younger, and have prior comorbidities; and baseline and post-acute symptoms and symptom burden correlated strongly. InterpretationIndividuals experiencing symptoms before COVID-19 have longer illness duration and increased odds of long illness. However, many individuals with long illness are well before SARS-CoV-2 infection.",infectious diseases,fuzzy,94,100 -medRxiv,10.1101/2023.08.25.23294609,2023-08-25,https://medrxiv.org/cgi/content/short/2023.08.25.23294609,Risk factors for SARS-Cov-2 infection at a United Kingdom electricity-generating company: a test-negative design case-control study,Charlotte E Rutter; Martie J Van Tongeren; Tony Fletcher; Sarah E Rhodes; Yiqun Chen; Ian Hall; Nicholas Warren; Neil Pearce,London School of Hygiene and Tropical Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Health and Safety Executive; University of Manchester; Health and Safety Executive; London School of Hygiene and Tropical Medicine,"ObjectivesIdentify workplace risk factors for SARS-Cov-2 infection, using data collected by a United Kingdom electricity-generating company. - -MethodsUsing a test-negative design case-control study we estimated the odds ratios (OR) of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage, and site COVID-19 weekly risk rating, adjusting for age, test date and test type. - -ResultsFrom an original 80,077 COVID-19 tests, there were 70,646 included in the final analysis. Most exclusions were due to being visitor tests (5,030) or tests after an individual first tested positive (2,968). - -Women were less likely to test positive than men (OR=0.71; 95% confidence interval=0.58-0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area it was a strong confounder for other variables. Compared to routine tests, tests due to symptoms were highest risk (94.99; 78.29-115.24), followed by close contact (16.73; 13.80-20.29) and broader-defined work contact 2.66 (1.99-3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model. - -ConclusionsIn general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates. - -Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIIn the United Kingdom, there is now a considerable body of evidence showing occupational differences in Covid-19 infection and severity, but with understandable focus on high-risk industries like healthcare. -C_LIO_LILess is known about differences in risk of COVID-19 infection in other industries that do not involve directly working with the general public, in particular, there is relatively little evidence on the risks of transmission in the electricity-generating industry. -C_LI - -What this study addsO_LIAt this company, infection risk was not associated with job category after adjusting for test reason; however women were less likely to test positive than men and the risk was higher when there was a power outage, requiring more staff to visit the site in person. -C_LI - -How this study might affect research, practice or policyO_LIThe site risk rating showed a consistent (but modest) dose-response with infection risk, indicating that such risk rating may be useful for identifying ""high risk"" sites. -C_LIO_LIThis analysis demonstrates the importance of adjusting for both date of and reason for test, when prevalence and testing protocols differ over time. -C_LI",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2023.08.11.23293977,2023-08-15,https://medrxiv.org/cgi/content/short/2023.08.11.23293977,"Digital Mental Health Service engagement changes during Covid-19 in children and young people across the UK: presenting concerns, service activity, and access by gender, ethnicity, and deprivation",Duleeka Knipe; Santiago de Ossorno Garcia; Louisa Salhi; Lily Mainstone-Cotton; Aaron Sefi; Ann John,University of Bristol School of Social and Community Medicine: University of Bristol Population Health Sciences; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Swansea University,"The adoption of digital health technologies accelerated during Covid-19, with concerns over the equity of access due to digital exclusion. Using data from a text-based online mental health service for children and young people we explore the impact of the pandemic on service access and presenting concerns and whether differences were observed by sociodemographic characteristics in terms of access (gender, ethnicity and deprivation). We used interrupted time-series models to assess whether there was a change in the level and rate of service use during the Covid-19 pandemic (April 2020-April 2021) compared to pre-pandemic trends (June 2019-March 2020). Routinely collected data from 61221 service users were extracted for observation, those represented half of the service population as only those with consent to share their data were used. The majority of users identified as female (74%) and White (80%), with an age range between 13 and 20 years of age. There was evidence of a sudden increase (13%) in service access at the start of the pandemic (RR 1.13 95% CI 1.02, 1.25), followed by a reduced rate (from 25% to 21%) of engagement during the pandemic compared to pre-pandemic trends (RR 0.97 95% CI 0.95,0.98). There was a sudden increase in almost all presenting issues apart from physical complaints. There was evidence of a step increase in the number of contacts for Black/African/Caribbean/Black British (38% increase; 95% CI: 1%-90%) and White ethnic groups (14% increase; 95% CI: 2%-27%)), sudden increase in service use at the start of the pandemic for the most (58% increase; 95% CI: 1%-247%) and least (47% increase; 95% CI: 6%-204%) deprived areas. During the pandemic, contact rates decreased, and referral sources change at the start. Findings on access and service activity align with other studies observing reduced service utilization. The lack of differences in deprivation levels and ethnicity at lockdown suggests exploring equity of access to the anonymous service. The study provides unique insights into changes in digital mental health use during Covid-19 in the UK.",public and global health,fuzzy,100,100 medRxiv,10.1101/2023.08.07.23293778,2023-08-09,https://medrxiv.org/cgi/content/short/2023.08.07.23293778,"Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.",Kurt Taylor; Sophie Eastwood; Venexia Walker; Genevieve Cezard; Rochelle Knight; Marwa Al Arab; Yinghui Wei; Elsie M F Horne; Lucy Teece; Harriet Forbes; Alex Walker; Louis Fisher; Jon Massey; Lisa E M Hopcroft; Tom Palmer; Jose Cuitun Coronado; Samantha Ip; Simon Davy; Iain Dillingham; Caroline Morton; Felix Greaves; John MacLeod; Ben Goldacre; Angela Wood; Nishi Chaturvedi; Jonathan A C Sterne; Rachel Denholm; - CONVALESCENCE Long-COVID study; - Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies; - OpenSAFELY collaborative,University of Bristol; University College London; University of Bristol; University of Cambridge; University of Bristol; University of Bristol; University of Plymouth; University of Bristol; University of Leicester; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Bristol; University of Bristol; University of Cambridge; University of Oxford; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Bristol; University of Oxford; University of Cambridge; University College London; University of Bristol; University of Bristol; -; -; -,"BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear. @@ -251,6 +230,27 @@ Added value of this studyThis study is the first to quantify changes in fit note Implications of all the available evidenceWhile we have likely underestimated the fit note rate due to overcounting of people in the workforce and misclassification of COVID-19 status, we still identified a substantial increased risk of receiving a fit note in people with COVID-19 compared with the general population over all years, even after adjusting for demographics and a wide range of clinical characteristics. The increased risk persisted into 2022, in an era where most people are vaccinated and the severity of COVID-19 illness is lessened. Given the high infection rates still occurring, these findings provide evidence for a substantial impact of COVID-19 on productivity and further evidence of the long-term impacts of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.08.02.23293519,2023-08-04,https://medrxiv.org/cgi/content/short/2023.08.02.23293519,Real-time epidemiological modelling during the COVID-19 emergency in Wales,Michael Gravenor; Mark Dawson; Ed Bennett; Ben Thorpe; Carla White; Alma Rahat; Daniel Archambault; Noemi Picco; Gibin Powathil; Biagio Lucini,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2023.08.01.23293491,2023-08-02,https://medrxiv.org/cgi/content/short/2023.08.01.23293491,Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study,Haowei Wang; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; David Haw; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Christl A Donnelly; Paul Elliott; Steven Riley,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","ObjectivesThe rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities across ethnic and sociodemographic subgroups. In this paper, we aimed to investigate how inequalities influence the risk of getting infected across ethnic and sociodemographic subgroups during a key period before widespread vaccination. + +DesignRepeated cross-sectional community-based study. + +MethodsWe analysed risk factors for test-positivity for SARS-CoV-2, based on self-administered throat and nose swabs in the community during rounds 5 to 10 of the REal-time Assessment of Community Transmission-1 (REACT-1) study between 18 September 2020 and 30 March 2021. + +ResultsCompared to white ethnicity, people of Asian and black ethnicity had a higher risk of infection during rounds 5 to 10, with odds of 1.46 (1.27, 1.69) and 1.35 (1.11, 1.64) respectively. Among ethnic subgroups, the highest and the second-highest odds were found in Bangladeshi and Pakistan participants at 3.29 (2.23, 4.86) and 2.15 (1.73, 2.68) respectively when compared to British whites. People in larger (compared to smaller) households had higher odds of infection. Health care workers with direct patient contact and care home workers showed higher odds of infection compared to other essential/key workers. Additionally, the odds of infection among participants in public-facing activities or settings were greater than among those not working in those activities or settings. + +ConclusionOur findings highlight the differences in the risk of SARS-CoV-2 infection in a global-north population during a period when the risk of infection was high, and there were substantial levels of social mixing. Planning for future severe waves of respiratory pathogens should include policies to reduce inequality in the risk of infection by ethnicity, household size, and occupational activity in order to reduce inequality in disease. + +Summary boxWhat is already known on this topic + +Extensive studies have described the relationship between socio-demographic factors and SARS-CoV-2 outcomes such as hospitalisations and deaths, rather than SARS-CoV-2 infection. Limited community-based studies investigated risk factors associated with SARS-CoV-2 infection, with the time frame of these studies has mainly focused on the period of the first wave of infection, or the beginning of the second wave, or the rollout of the first dose of the vaccine after the second wave period. We did not find studies that covered the critical period of the second wave in England when levels of social mixing were high, but no vaccine was available. + +What this study adds + +We show health inequalities across ethnic and sociodemographic subgroups during a key period: before widespread vaccination, but, largely, not during the period of stringent social distancing. We observed substantial ethnic and occupational differences in the risk of SARS-CoV-2 infection. Minority ethnic groups, including those of Bangladeshi and Pakistani ethnicity, had an excess risk of infection compared with the British white population. Healthcare workers, care home workers and people who work in public-facing activities or settings were associated with higher odds of infection. The risk of SARS-CoV-2 infection increased monotonically as household size increased, and more deprived neighbourhood areas were associated with a higher risk of infection. + +How this study might affect research, practice or policy + +Our findings highlight the differences in the risk of SARS-CoV-2 infection in a global-north population during a period when the risk of infection was high, and there were substantial levels of social mixing. Planning for future waves of severe respiratory infection should explicitly aim to reduce inequalities in infection in order to reduce inequality in disease.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.07.31.23293422,2023-07-31,https://medrxiv.org/cgi/content/short/2023.07.31.23293422,Associations between SARS-CoV-2 infection and subsequent economic inactivity and employment status: pooled analyses of five linked longitudinal surveys,Richard John Shaw; Rebecca Rhead; Richard J Silverwood; Jacques Wels; Jingmin Zhu; Olivia KL Hamilton; Giorgio Di Gessa; Ruth CE Bowyer; Bettina Moltrecht; Michael J Green; Evangelia Demou; Serena Pattaro; Paola Zaninotto; Andy W Boyd; Felix Greaves; Nish Chaturvedi; George B Ploubidis; Srinivasa Vittal Katikireddi,"University of Glasgow; King's College London; University College London; Centre Metices, Universite libre de Bruxelles, Brussels, BE.; University College London; University of Glasgow; University College London; King's College London; University College London; Duke University School of Medicine, Durham, NC, USA.; University of Glasgow; University of Glasgow; University College London, UK; University of Bristol; Imperial College London; University College London; University College London; University of Glasgow","IntroductionFollowing the acute phase of the COVID-19 pandemic, record numbers of people became economically inactive (i.e., neither working nor looking for work), or non-employed (including unemployed job seekers and economically inactive people). A possible explanation is people leaving the workforce after contracting COVID-19. We investigated whether testing positive for SARS-CoV-2 is related to subsequent economic inactivity and non-employment, among people employed pre-pandemic. MethodsThe data came from five UK longitudinal population studies held by both the UK Longitudinal Linkage Collaboration (UK LLC; primary analyses) and the UK Data Service (UKDS; secondary analyses). We pooled data from five long established studies (1970 British Cohort Study, English Longitudinal Study of Ageing, 1958 National Child Development Study, Next Steps, and Understanding Society). The study population were aged 25-65 years between March 2020 to March 2021 and employed pre-pandemic. Outcomes were economic inactivity and non-employment measured at the time of the last follow-up survey (November 2020 to March 2021, depending on study). For the UK LLC sample (n=8,174), COVID-19 infection was indicated by a positive SARS-CoV-2 test in NHS England records. For the UKDS sample we used self-reported measures of COVID-19 infection (n=13,881). Logistic regression models estimated odds ratios (ORs) with 95% confidence intervals (95%CIs) adjusting for potential confounders including sociodemographic variables, pre-pandemic health and occupational class. @@ -289,6 +289,11 @@ MethodsWe implemented a computer simulation model of patient flow through an int ResultsThe results from the simulation model suggest that, without mitigation, the impact of COVID-19 will be an increase in pressure on GP and specialist community based services by 50% and 50-100% respectively. Simulating the impact of possible mitigation strategies, results show that increasing capacity in lower-acuity services, such as GP, results in demand being shifted to other parts of the mental health system while decreasing length of stay in higher acuity services is insufficient to mitigate the impact of increased demand. ConclusionIn capturing the interrelation of patient flow related dynamics between various mental health care settings, we demonstrate the value of computer simulation for assessing the impact of interventions on system flow.",health systems and quality improvement,fuzzy,100,100 +medRxiv,10.1101/2023.07.16.23292705,2023-07-18,https://medrxiv.org/cgi/content/short/2023.07.16.23292705,"Community-onset urinary tract infection in females in the context of COVID-19: a longitudinal population cohort study exploring case presentation, management, and outcomes",Nina J Zhu; Benedict Hayhoe; Raheelah Ahmad; James R Price; Donna Lecky; Monsey McLeod; Elena Ferran; Timothy M Rawson; Emma Carter; Alison H Holmes; Paul Aylin,"National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Department of Primary Care and Public Health, School of Public Health, Imperial College London, London, United Kingdom; Division of Health Services Research and Management, School of Health Sciences, City, University of London, London, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom; NHS England and NHS Improvement, London, United Kingdom; Barts Health NHS Trust, London, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom","BackgroundCOVID-19 affected the epidemiology of other infectious diseases and how they were managed. Urinary tract infection (UTI) is one of the most common infections treated in the community in England. We investigated the impact of the COVID-19 pandemic on UTI primary care consultations and outcomes in female patients. + +Methods and findingsWe analysed General Practice (GP) consultation and hospital admission records using the Whole Systems Integrated Care (WSIC) data in North West London between 2016 and 2021. We quantified the changes in UTI GP consultation rates using time series analysis before and during the pandemic. We assessed the outcomes of UTI, measured by subsequent bacteraemia and sepsis within 60 days, for consultations delivered face-to-face or remotely, with or without diagnostic tests recommended by the national guidelines, and with or without antibiotic treatment. Between January 2016 and December 2021, we identified 375,859 UTI episodes in 233,450 female patients. Before the COVID-19 pandemic (January 2016 - February 2020), the UTI GP consultation rate stayed level at 522.8 cases per 100,000 population per month, with a seasonal pattern of peaking in October. Since COVID-19, (March 2020 - December 2021), monthly UTI GP consultations declined when COVID-19 cases surged and rose when COVID-19 case fell. During the pandemic, the UTI consultations delivered face-to-face reduced from 72.0% to 29.4%, the UTI consultations with appropriate diagnostic tests, including urine culture and urinalysis, reduced from 17.3% to 10.4%, and the UTI cases treated with antibiotics reduced from 52.0% to 47.8%. The likelihood of antibiotics being prescribed was not affected by whether the consultation was delivered face-to-face or remotely but associated with whether there was a diagnostic test. Regardless of whether the UTI consultation occurred before or during the pandemic, the absence of antibiotic treatment for UTI is associated with a 10-fold increase in the risk of having bacteraemia or sepsis within 60 days, though the patients who consulted GPs for UTI during the pandemic were older and more co-morbid. Across the study period (January 2016 - December 2021), nitrofurantoin remained the first-line antibiotic option for UTI. The percentage of non-prophylactic acute UTI antibiotic prescriptions with durations that exceeded the guideline recommendations was 58.7% before the pandemic, and 49.4% since. This led to 830,522 total excess days of treatment, account for 63.3% of all non-prophylactic acute antibiotics prescribed for UTI. Before the pandemic, excess antibiotic days of UTI drugs had been reducing consistently. However, this decline slowed down during the pandemic. Having a diagnostic test was associated with 0.6 less excess days of antibiotic treatment. + +ConclusionsThis analysis provides a comprehensive examination of management and outcomes of community-onset UTI in female patients, considering the changes in GP consultations during the COVID-19 pandemic. Our findings highlighted the importance of appropriate urine testing to support UTI diagnosis in symptomatic patients and initiation of antibiotic treatment with appropriate course duration. Continued monitoring is required to assess the overall impact on patients and health systems from the changed landscape of primary care delivery.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.07.06.23292295,2023-07-07,https://medrxiv.org/cgi/content/short/2023.07.06.23292295,Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern,Massimo Cavallaro; Louise Dyson; Michael J Tildesley; Daniel Todkill; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta, and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.07.03.23291596,2023-07-05,https://medrxiv.org/cgi/content/short/2023.07.03.23291596,Risk of COVID-19 death in adults who received booster COVID-19 vaccinations: national retrospective cohort study on 14.6 million people in England,Isobel L Ward; Chris Robertson; Utkarsh Agrawal; Lynsey Patterson; Declan T Bradley; Ting Shi; Simon de Lusignan; Richard Hobbs; Aziz Sheikh; Vahe Nafilyan,"Office for National Statistics, Newport, UK; Department of Mathematics and Statistics, Strathclyde University, Glasgow, Scotland and Public Health Scotland, Glasgow, Scotland; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK and Public Health Agency, Belfast, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; Office for National Statistics, Newport, UK","ImportanceThe emergence of the COVID-19 vaccination has been critical in changing the course of the COVID-19 pandemic, with estimates suggesting vaccinations have prevented millions of deaths worldwide. To ensure protection remains high in vulnerable groups booster vaccinations in the UK have been targeted based on age and clinical vulnerabilities. @@ -452,6 +457,27 @@ C_LIO_LIThe use of an additional control group from the general public for compa C_LIO_LIIn the subgroup analyses, PCR+ cases and PCR- controls were compared with the population controls to assess the risk factors for those aged 18-55 years. Hence, the results may not be generalisable to patients older than 55 years. C_LIO_LIPCR test results, rather than symptoms, were used to categorise the participants into cases or controls, and therefore risk factors for SARS-CoV-2 infection and not COVID-19 disease were assessed. C_LI",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2023.03.15.23287292,2023-03-15,https://medrxiv.org/cgi/content/short/2023.03.15.23287292,Living alone and mental health: parallel analyses in longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic,Eoin McElroy; Emily Herrett; Kishan Patel; Dominik M Piehlmaier; Giorgio Di Gessa; Charlotte Huggins; Michael J Green; Alex SF Kwong; Ellen J Thompson; Jingmin Zhu; Kathryn E Mansfield; Richard J Silverwood; Rosie Mansfield; Jane Maddock; Rohini Mathur; Ruth E Costello; Anthony A Matthews; John Tazare; Alasdair Henderson; Kevin Wing; Lucy Bridges; Sebastian Bacon; Amir Mehrkar; - OpenSafely Collaborative; Richard John Shaw; Jacques Wels; Srinivasa Vittal Katikireddi; Nishi Chaturvedi; Laurie Tomlinson; Praveetha Patalay,"School of Psychology, Ulster University, Coleraine, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; University of Sussex Business Sch; Department of Epidemiology & Public Health, University College London, London, UK; Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Twin Research and Genetic Epidemiology, Kings College London; Department of Epidemiology & Public Health, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Centre for Longitudinal Studies, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Primary Care, Wolfson Insitute of Population Health, Queen Mary, University of London, London; London School of Hygiene and Tropical Medicine, London, UK; Karolinska Institutet, Stockholm, Sweden; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; ; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK","ObjectivesTo describe the mental health gap between those who live alone and those who live with others, and to examine whether the COVID-19 pandemic had an impact on this gap. + +DesignTen population based prospective cohort studies, and a retrospective descriptive cohort study based on electronic health records (EHRs). + +SettingUK Longitudinal population-based surveys (LPS), and primary and secondary care records within the OpenSAFELY-TPP database. + +ParticipantsParticipants from the LPS were included if they had information on living status in early 2020, valid data on mental ill-health at the closest pre-pandemic assessment and at least once during the pandemic, and valid data on a key minimum set of covariates. The EHR dataset included 16 million adults registered with primary care practices in England using TPP SystmOne software on 1st February 2020, with at least three months of registration, valid address data, and living in households of <16 people. + +Main outcome measuresIn the LPS, self-reported survey measures of psychological distress and life satisfaction were assessed in the nearest pre-pandemic sweep and three periods during the pandemic: April-June 2020, July-October 2020, and November 2020-March 2021. In the EHR analyses, outcomes were morbidity codes recorded in primary or secondary care between March 2018 and January 2022 reflecting the diagnoses of depression, self-harm, anxiety, obsessive compulsive disorder, eating disorders, and severe mental illnesses. + +ResultsThe LPS consisted of 37,544 participants (15.2% living alone) and we found greater psychological distress (SMD: 0.09 (95% CI: 0.04, 0.14) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30, -0.15) in those living alone pre-pandemic, and the gap between the two groups stayed similar after the onset of the pandemic. In the EHR analysis of almost 16 million records (21.4% living alone), codes indicating mental health conditions were more common in those who lived alone compared to those who lived with others (e.g., depression 26 and severe mental illness 58 cases more per 100,000). Recording of mental health conditions fell during the pandemic for common mental health disorders and the gap between the two groups narrowed. + +ConclusionsMultiple sources of data indicate that those who live alone experience greater levels of common and severe mental illnesses, and lower life satisfaction. During the pandemic this gap in need remained, however, there was a narrowing of the gap in service use, suggesting greater barriers to healthcare access for those who live alone. + +Summary BoxO_ST_ABSWhat is already known on the topic?C_ST_ABSHouseholds with one individual are an increasing demographic, comprising over a quarter of all households in the UK in 2021. However, the mental health gap between those who live alone compared to those who live with others is not well described and even less is known about the relative gaps in need and healthcare-seeking and access. The pandemic and associated restrictive measures further increased the likelihood of isolation for this group, which may have impacted mental health. + +What this study adds?We present comprehensive evidence from both population-based surveys and electronic health records regarding the greater levels of mental health symptoms and in recorded diagnoses for common (anxiety, depression) and less common (OCD, eating disorders, SMIs) mental health conditions for people living alone compared to those living with others. + +Our analyses indicate that mental health conditions are more common among those who live alone compared to those who live with others. Although levels of reported distress increased for both groups during the pandemic, healthcare-seeking dropped in both groups, and the rates of healthcare-seeking among those who live alone converged with those who live with others for common mental health conditions. This suggests greater barriers for treatment access among those that live alone. + +The findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2023.02.26.23286474,2023-03-06,https://medrxiv.org/cgi/content/short/2023.02.26.23286474,Improving the representativeness of UKs national COVID-19 Infection Survey through spatio-temporal regression and post-stratification,Koen B Pouwels; David W Eyre; Thomas House; Ben Aspey; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Jaison Kolenchery; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; tim E peto; Ann Sarah Walker; - COVID-19 Infection Survey Team,University of Oxford; University of Oxford; University of Manchester; Office for National Statistics; The Francis Crick Institute; University of Oxford; University of Exeter; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; oxford university; University of Oxford; -,"Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially impacted by biases arising from differences in participation rates across key groups. Here, we use spatio-temporal regression and post-stratification models to UKs national COVID-19 Infection Survey (CIS) to obtain representative estimates of PCR positivity (6,496,052 tests) and antibody prevalence (1,941,333 tests) for different regions, ages and ethnicities (7-December-2020 to 4-May-2022). Not accounting for vaccination status through post-stratification led to small underestimation of PCR positivity, but more substantial overestimations of antibody levels in the population (up to 21%), particularly in groups with low vaccine uptake in the general population. There was marked variation in the relative contribution of different areas and age-groups to each wave. Future analyses of infectious disease surveys should take into account major drivers of outcomes of interest that may also influence participation, with vaccination being an important factor to consider.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2023.03.01.23286627,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286627,Effectiveness of successive booster vaccine doses against SARS-CoV-2 related mortality in residents of Long-Term Care Facilities in the VIVALDI study,Oliver Stirrup; Madhumita Shrotri; Natalie L. Adams; Maria Krutikov; Borscha Azmi; Igor Monakhov; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; UK Health Security Agency; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"We evaluated the effectiveness of 1-3 booster vaccinations against SARS-CoV-2 related mortality among a cohort of 13407 older residents of long-term care facilities (LTCFs) participating in the VIVALDI study in England in 2022. Cox regression was used to estimate relative hazards of SARS-CoV-2 related death following booster vaccination relative to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex and LTCF capacity. Each booster provided additional short-term protection relative to primary vaccination, with consistent pattern of waning to 45-75% reduction in risk beyond 112 days.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2023.03.01.23286624,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286624,Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease,Hannah Whittaker; Costantinos Kallis; Angela Wood; Thomas Bolton; Samantha Walker; Aziz Sheikh; Alex Brownrigg; Ashley Akbari; Kamil Sterniczuk; Jennifer K Quint,"Imperial College London; Imperial College London; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom; Health Data Research UK; Asthm + Lung; The University of Edinburgh College of Medicine and Veterinary Medicine; Health Data Research UK BREATHE; Swansea University; Health Data Research UK BREATHE; Imperial College London","BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people. @@ -521,6 +547,13 @@ ResultsIgG spike-protein antibodies were undetectable in 23.3%, 14.1% and 20.7% ConclusionsApproximately one in five individuals with SOT, RAIRD and LM have no detectable IgG spike-protein antibodies despite three or more vaccines, but this proportion reduces with sequential booster doses. Choice of immunosuppressant and disease-type is strongly associated with serological response. Antibody testing could enable rapid identification of individuals who are most likely to benefit from additional COVID-19 interventions. Trial registrationClinicaltrials.gov, NCT05148806",public and global health,fuzzy,100,100 +medRxiv,10.1101/2023.02.06.23285513,2023-02-06,https://medrxiv.org/cgi/content/short/2023.02.06.23285513,A Rapid review on the COVID-19 Pandemic's Global Impact on Breast Cancer Screening Participation Rates and Volumes from January-December 2020,"Reagan Lee; - UNCOVER; Wei Xu; - International Partnership for Resilience in Cancer Systems (I-PaRCS), Breast Cancer Working Group 2; Marshall Dozier; Ruth McQuillan; Evropi Theodoratou; Jonine Figueroa",University of Edinburgh; -; University of Edinburgh; -; University of Edinburgh; University of Edinburgh; The University of Edinburgh; University of Edinburgh,"BackgroundCOVID-19 has strained population breast mammography screening programs that aim to diagnose and treat breast cancers earlier. As the pandemic has affected countries differently, we aimed to quantify changes in breast screening volume and uptake during the first year of the COVID-19 pandemic. + +MethodsWe systematically searched Medline, the WHO (World Health Organization) COVID-19 database, and governmental databases. Studies covering January 2020 to March 2022 were included. We extracted and analyzed data regarding study methodology, screening volume and uptake. To assess for risk-of-bias, we used the Joanna Briggs Institute Critical Appraisal tool. + +ResultsTwenty-six cross-sectional descriptive studies were included out of 935 independent records. Reductions in screening volume and uptake rates were observed among eight countries. Changes in screening participation volume in five countries with national population-based screening ranged from -13% to -31%. Among two countries with limited population-based programs the decline ranged from -61% to -41%. Within the USA, population participation volumes varied ranging from +18% to -39% with suggestion of differences by insurance status (HMO, Medicare, and low-income programs). Almost all studies had high risk-of-bias due to insufficient statistical analysis and confounding factors. + +Discussion and ConclusionExtent of COVID-19-induced reduction in breast screening participation volume differed by region and data suggested potential differences by healthcare setting (e.g., national health insurance vs private health care). Recovery efforts should monitor access to screening and early diagnosis to determine if prevention services need strengthening to increase coverage of marginalized groups and reduce disparities.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.02.01.23285333,2023-02-02,https://medrxiv.org/cgi/content/short/2023.02.01.23285333,Associations between reported healthcare disruption due to COVID-19 and avoidable hospitalisation: Evidence from seven linked longitudinal studies for England,Mark A Green; Martin McKee; Olivia Hamilton; Richard Shaw; John MacLeod; Andrew Boyd; - The LH&W NCS Collaborative; Srinivasa Vittal Katikireddi,University of Liverpool; London School of Hygiene and Tropical Medicine; University of Glasgow; University of Glasgow; University of Bristol; University of Bristol; ; University of Glasgow,"BackgroundHealth services across the UK struggled to cope during the COVID-19 pandemic. Many treatments were postponed or cancelled, although the impact was mitigated by new models of delivery. While the scale of disruption has been studied, much less is known about if this disruption impacted health outcomes. The aim of our paper is to examine whether there is an association between individuals experiencing disrupted access to healthcare during the pandemic and risk of an avoidable hospitalisation. MethodsWe used individual-level data for England from seven longitudinal cohort studies linked to electronic health records from NHS Digital (n = 29 276) within the UK Longitudinal Linkage Collaboration trusted research environment. Avoidable hospitalisations were defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions (1st March 2020 to 25th August 2022). Self-reported measures of whether people had experienced disruption during the pandemic to appointments (e.g., visiting their GP or an outpatient department), procedures (e.g., surgery, cancer treatment) or medications were used as our exposures. Logistic regression models examined associations. @@ -528,6 +561,12 @@ MethodsWe used individual-level data for England from seven longitudinal cohort Results35% of people experienced some form of disrupted access to healthcare. Those whose access was disrupted were at increased risk of any (Odds Ratio (OR) = 1.80, 95% Confidence Intervals (CIs) = 1.34-2.41), acute (OR = 1.68, CIs = 1.13-2.53) and chronic (OR = 1.93, CIs = 1.40-2.64) ambulatory care sensitive hospital admissions. There were positive associations between disrupted access to appointments and procedures to measures of avoidable hospitalisations as well. ConclusionsOur study presents novel evidence from linked individual-level data showing that people whose access to healthcare was disrupted were more likely to have an avoidable or potentially preventable hospitalisation. Our findings highlight the need to increase healthcare investment to tackle the short- and long-term implications of the pandemic beyond directly dealing with SARS-CoV-2 infections.",public and global health,fuzzy,100,100 +medRxiv,10.1101/2023.01.31.23285232,2023-02-01,https://medrxiv.org/cgi/content/short/2023.01.31.23285232,"Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour",Thomas Edward Byrne; Jana Kovar; Sarah Beale; Isobel Braithwaite; Ellen Fragaszy; Wing Lam Erica Fong; Cyril Geismar; Susan J Hoskins; Annalan Mathew Dwight Navaratnam; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Pia Hardelid; Linda Wijlaars; Eleni Nastouli; Moira Spyer; Anna Ayree; Ingemar Cox; Vasileios Lampos; Rachel A McKendry; Tao Cheng; Anne M Johnson; Susan Fiona Michie; Jo Gibbs; Richard Gilson; Alison Rodger; Ibrahim Abubakar; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; University College London; UCL; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCLH; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL,"Key FeaturesO_LIVirus Watch is a national community cohort study of COVID-19 in households in England and Wales, established in June 2020. The study aims to provide evidence on which public health approaches are most effective in reducing transmission, and investigate community incidence, symptoms, and transmission of COVID-19 in relation to population movement and behaviours. +C_LIO_LI28,527 households and 58,628 participants of age (0-98 years, mean age 48), were recruited between June 2020 - July 2022 +C_LIO_LIData collected include demographics, details on occupation, co-morbidities, medications, and infection-prevention behaviours. Households are followed up weekly with illness surveys capturing symptoms and their severity, activities in the week prior to symptom onset and any COVID-19 test results. Monthly surveys capture household finance, employment, mental health, access to healthcare, vaccination uptake, activities and contacts. Data have been linked to Hospital Episode Statistics (HES), inpatient and critical care episodes, outpatient visits, emergency care contacts, mortality, virology testing and vaccination data held by NHS Digital. +C_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555). +C_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS. +C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.01.29.23285160,2023-01-30,https://medrxiv.org/cgi/content/short/2023.01.29.23285160,High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study,Mahan Ghafari; Matthew Hall; Tanya Golubchik; Daniel Ayoubkhani; Thomas House; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; Roberto Cahuantzi; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Jeff Barrett; Christophe Fraser; David Bonsall; Sarah Walker; Katrina A Lythgoe,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Office for National Statistics; -; -; -; Wellcome Sanger Institute; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.01.24.23284906,2023-01-25,https://medrxiv.org/cgi/content/short/2023.01.24.23284906,The impact of COVID-19 lockdown on a cohort of adults with recurrent major depressive disorder from Catalonia: a decentralized longitudinal study using remote measurement technology,Raffaele Lavalle Sr.; Elena Condominas; Josep Maria Haro; Iago Gine-Vazquez; Raquel Bailon; Estela Laporta; Ester Garcia; Spyridon Kontaxis; Gemma Riquelme; Federica Lombardini; Antonio Preti; Maria Teresa Penarrubia Maria; Marta Coromina; Belen Arranz; Elisabet Vilella; Elena Rubio Abadal; Faith Matcham; Femke Lamers; Matthew Hotopf; Brenda W.J.H Penninx; Peter Annas; Vaibhav Narayan; Sara Katherine Simblett; Sara Siddi,"Dipartimento di neuroscienze, Universita degli studi di Torino, Italia; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain; Centros de investigacion biomedica en red en el area de bioingenieria, biomateriales y nanomedicina (CIBER BBN), Madrid, Spain; Microelectronica y Sistemas Electronicos, Universidad Autonoma de Barcelona, Spain; Centros de Investigacion Biomedica en Red en el Area de Bioingenieria, Biomateriales y Nanomedicina (CIBER BBN), 28029 Madrid, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Dipartimento di neuroscienze, Universita degli studi di Torino, Italia; Health Technology Assessment in Primary Care and Mental Health (PRISMA) Research Group, Parc Sanitari Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, St; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; Hospital Universitari Institut Pere Mata, Reus, Spain Institut d'Investigacio Sanitaria Pere Virgili CERCA, Reus, Spain; Universitat Rovira i Virgili, Reus, Spa; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain; King's College London: London, GB; VU medisch centrum: Amsterdam, Noord-Holland, NL; Kings College London, Institute of Psychiatry, Psychology and Neuroscience, UK; Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Psychiatry, Boelelaan 1117, Amsterdam, The Netherlands; H. Lundbeck A/S, Valby, Denmark; Research and Development Information Technology, Janssen Research & Development, LLC, Titusville, NJ, USA; Kings College London, Institute of Psychiatry, Psychology and Neuroscience, UK; Parc Sanitari Sant Joan de Deu, Fundacio Sant Joan de Deu, CIBERSAM,Universitat de Barcelona, Barcelona, Spain","BackgroundThe present study analyzes the effects of each containment phase of the first COVID-19 wave on depression levels in a cohort of adults with a history of major depressive disorder (MDD). @@ -684,7 +723,6 @@ MethodsWith the approval of NHS England we used routine clinical data from 24 mi ResultsAmong the 2367 renal patients treated with sotrovimab (n=1852) or molnupiravir (n=515) between December 16, 2021 and August 1, 2022 in England, 38 cases (1.6%) of COVID-19 related hospitalisations/deaths were observed during the 28 days of follow-up after treatment initiation, with 21 (1.1%) in the sotrovimab group and 17 (3.3%) in the molnupiravir group. In multiple-adjusted analysis sotrovimab was associated with substantially lower risk of 28-day COVID-19 related hospitalisation/death than treatment with molnupiravir (hazard ratio, HR=0.35, 95% CI: 0.17 to 0.71; P=0.004), with results remaining robust in sensitivity analyses. In the SRR cohort, there were 19 cases (1.9%) of COVID-19 related hospitalisations/deaths during the 28 days of follow-up after treatment initiation of sotrovimab (n=723) or molnupiravir (n=270). In multiple-adjusted analysis, sotrovimab showed a trend toward lower risk of 28-day COVID-19 related hospitalisation/death than treatment with molnupiravir (HR=0.39, 95% CI: 0.13 to 1.21; P=0.106). In both datasets, sotrovimab had no evidence of association with other hospitalisation/death compared with molnupiravir (HRs ranging from 0.73-1.29; P>0.05). ConclusionsIn routine care of non-hospitalised patients with COVID-19 on kidney replacement therapy, those who received sotrovimab had substantially lower risk of severe COVID-19 outcomes than those receiving molnupiravir.",epidemiology,fuzzy,92,100 -medRxiv,10.1101/2022.11.29.22282916,2022-11-30,https://medrxiv.org/cgi/content/short/2022.11.29.22282916,Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population,Jia Wei; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Brian Marsden; Jaison Kolenchery; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; Tim E Peto; Ann Sarah Walker; Koen Pouwels; David W Eyre,University of Oxford; University of Oxford; University of Oxford; Public Health England; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Following primary SARS-CoV-2 vaccination, understanding the relative extent of protection against SARS-CoV-2 infection from boosters or from breakthrough infections (i.e. infection in the context of previous vaccination) has important implications for vaccine policy. In this study, we investigated correlates of protection against Omicron BA.4/5 infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults [≥]18y from the United Kingdom general population. We found that higher anti-spike IgG antibody levels were associated with increased protection against Omicron BA.4/5 infection and that breakthrough infections were associated with higher levels of protection at any given antibody level than booster vaccinations. Breakthrough infections generated similar antibody levels to third/booster vaccinations, and the subsequent declines in antibody levels were similar to or slightly slower than those after third/booster vaccinations. Taken together our findings show that breakthrough infection provides longer lasting protection against further infections than booster vaccinations. For example, considering antibody levels associated with 67% protection against infection, a third/booster vaccination did not provide long-lasting protection, while a Delta/Omicron BA.1 breakthrough infection could provide 5-10 months of protection against Omicron BA.4/5 reinfection. 50-60% of the vaccinated UK population with a breakthrough infection would still be protected by the end of 2022, compared to <15% of the triple-vaccinated UK population without previous infection. Although there are societal impacts and risks to some individuals associated with ongoing transmission, breakthrough infection could be an efficient immune-boosting mechanism for subgroups of the population, including younger healthy adults, who have low risks of adverse consequences from infection.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.11.29.22282899,2022-11-29,https://medrxiv.org/cgi/content/short/2022.11.29.22282899,"Performance of antigen lateral flow devices in the United Kingdom during the Alpha, Delta, and Omicron waves of the SARS-CoV-2 pandemic",David W Eyre; Matthias Futschik; Sarah Tunkel; Jia Wei; Joanna Cole-Hamilton; Rida Saquib; Nick Germanacos; Andrew Dodgson; Paul E Klapper; Malur Sudhanva; Chris Kenny; Peter Marks; Edward Blandford; Susan Hopkins; Tim Peto; Tom Fowler,University of Oxford; UK Health Security Agency; UK Health Security Agency; University of Oxford; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Manchester; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Oxford; UK Health Security Agency,"BackgroundAntigen lateral flow devices (LFDs) have been widely used to control SARS-CoV-2. Changes in LFD sensitivity and detection of infectious individuals during the pandemic with successive variants, vaccination, and changes in LFD use are incompletely understood. MethodsPaired LFD and PCR tests were collected from asymptomatic and symptomatic participants, across multiple settings in the UK between 04-November-2020 and 21-March-2022. Multivariable logistic regression was used to analyse LFD sensitivity and specificity, adjusting for viral load, LFD manufacturer, setting, age, sex, assistance, symptoms, vaccination, and variant. National contact tracing data were used to estimate the proportion of transmitting index cases (with [≥]1 PCR/LFD-positive contact) potentially detectable by LFDs over time, accounting for viral load, variant, and symptom status. @@ -1436,6 +1474,13 @@ ConclusionThere is no evidence of an association between COVID-19 vaccination an What is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination. What this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.03.23.22272804,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.23.22272804,Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records,Elsie MF Horne; William J Hulme; Ruth H Keogh; Tom M Palmer; Elizabeth J Williamson; Edward PK Parker; Amelia Green; Venexia Walker; Alex J Walker; Helen Curtis; Louis Fisher; Brian MacKenna; Richard Croker; Lisa Hopcroft; Robin Y Park; Jon Massey; Jessica Morely; Amir Mehrkar; Sebastian Bacon; David Evans; Peter Inglesby; Caroline E Morton; George Hickman; Simon Davy; Tom Ward; Iain Dillingham; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne,University of Bristol; Univeristy of Oxford; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Univeristy of Oxford; University of Bristol; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Harvard University; University of Bristol,"BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies. + +MethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death. + +FindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1. + +InterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.03.18.22272607,2022-03-21,https://medrxiv.org/cgi/content/short/2022.03.18.22272607,"Multi-organ impairment and Long COVID: a 1-year prospective, longitudinal cohort study",Andrea Dennis; Daniel J Cuthbertson; Dan Wootton; Michael Crooks; Mark Gabbay; Nicole Eichert; Sofia Mouchti; Michele Pansini; Adriana Roca-Fernandez; Helena Thomaides-Brears; Matt Kelly; Matthew Robson; Lyth Hishmeh; Emily Attree; Melissa J Heightman; Rajarshi Banerjee; Amitava Banerjee,Perspectum Ltd; University of Liverpool; University of Liverpool; University of Hull; University of Liverpool; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Diagnostics; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Long COVID SoS; UKDoctors#Longcovid; UCLH; Perspectum Ltd; University College London,"ImportanceMulti-organ impairment associated with Long COVID is a significant burden to individuals, populations and health systems, presenting challenges for diagnosis and care provision. Standardised assessment across multiple organs over time is lacking, particularly in non-hospitalised individuals. ObjectiveTo determine the prevalence of organ impairment in Long COVID patients at 6 and at 12 months after initial symptoms and to explore links to clinical presentation. @@ -1657,7 +1702,6 @@ MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. ConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.02.07.22270451,2022-02-08,https://medrxiv.org/cgi/content/short/2022.02.07.22270451,Anti-spike antibody trajectories in individuals previously immunised with BNT162b2 or ChAdOx1 following a BNT162b2 booster dose,Alexei Yavlinsky; Sarah Beale; Vincent Nguyen; Madhumita Shrotri; Thomas Edward Byrne; Cyril Geismar; Ellen Fragaszy; Susan J Hoskins; Wing Lam Erica Fong; Annalan Mathew Dwight Navaratnam; Isobel Braithwaite; Parth Patel; Jana Kovar; Andrew C Hayward; Robert W Aldridge,"Institute of Health Informatics, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, UK","The two most commonly-used SARS-CoV-2 vaccines in the UK, BNT162b2 (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca), employ different immunogenic mechanisms. Compared to BNT162b2, two-dose immunisation with ChAdOx1 induces substantially lower peak anti-spike antibody (anti-S) levels and is associated with a higher risk of breakthrough infections. To provide preliminary indication of how a third booster BNT162b2 dose impacts anti-S levels, we performed a cross-sectional analysis using capillary blood samples from vaccinated adults (aged [≥]18 years) participating in Virus Watch, a prospective community cohort study in England and Wales. Blood samples were analysed using Roche Elecsys Anti-SARS-CoV-2 S immunoassay. We analysed anti-S levels by week since the third dose for vaccines administered on or after September 1, 2021 and stratified the results by second dose vaccine type (ChAdOx1 or BNT162b2), age, sex and clinical vulnerability. Anti-S levels peaked at two weeks post-booster for BNT162b2 (22,185 U/mL; 95%CI: 21,406-22,990) and ChAdOx1 second dose recipients (19,203 U/mL; 95%CI: 18,094-20,377). These were higher than the corresponding peak antibody levels post-second dose for BNT162b2 (12,386 U/mL; 95%CI: 9,801-15,653, week 2) and ChAdOx1 (1,192 U/mL; 95%CI: 818-1735, week 3). No differences emerged by second dose vaccine type, age, sex or clinical vulnerability. Anti-S levels declined post-booster for BNT162b2 (half-life=44 days) and ChAdOx1 second dose recipients (half-life=40 days). These rates of decline were steeper than those post-second dose for BNT162b2 (half-life=54 days) and ChAdOx1 (half-life=80 days). Our findings suggest that peak anti-S levels are higher post-booster than post-second dose, but that levels are projected to be similar after six months for BNT162b2 recipients. Higher peak anti-S levels post-booster may partially explain the increased effectiveness of booster vaccination compared to two-dose vaccination against symptomatic infection with the Omicron variant. Faster waning trajectories post third-dose may have implications for the timing of future booster campaigns or four-dose vaccination regimens for the clinically vulnerable.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.02.03.22270365,2022-02-06,https://medrxiv.org/cgi/content/short/2022.02.03.22270365,Post-peak dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022,Paul Elliott; Oliver Eales; Barbara Bodinier; David Tang; Haowei Wang; Jakob Jonnerby; David Haw; Joshua Elliott; Matthew Whitaker; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alexander Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly,"School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Imperial College Healthcare NHS Trust, UK Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","BackgroundRapid transmission of the SARS-CoV-2 Omicron variant has led to the highest ever recorded case incidence levels in many countries around the world. MethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been characterising the transmission of the SARS-CoV-2 virus using RT-PCR test results from self-administered throat and nose swabs from randomly-selected participants in England at ages 5 years and over, approximately monthly since May 2020. Round 17 data were collected between 5 and 20 January 2022 and provide data on the temporal, socio-demographic and geographical spread of the virus, viral loads and viral genome sequence data for positive swabs. @@ -1844,6 +1888,7 @@ MethodTrial emulation was conducted by pooling results from six cohorts whose re ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2. DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,fuzzy,100,100 +bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,fuzzy,100,100 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. @@ -1928,6 +1973,13 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe systematically s Added value of this studyIn a diverse population of adults post-hospital admission with COVID-19, our large UK prospective multi-centre study reports several novel findings: the minority felt fully recovered at one year with minimal recovery from five months across any health domain; female sex and obesity are associated with being less likely to feel fully recovered at one year; several inflammatory mediators were increased in individuals with the most severe physical, mental health, and cognitive impairments compared to individuals with milder ongoing impairments. Implications of all the available evidenceBoth pharmacological and non-pharmacological interventions are urgently needed to improve the ongoing burden following hospitalisation for COVID-19 both for individuals and healthcare systems; our findings support the use of a precision medicine approach with potential treatable traits of systemic inflammation and obesity.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.12.13.21267368,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.13.21267368,Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations,Ingibjorg Magnusdottir; Aniko Lovik; Anna Bara Unnarsdottir; Daniel L. McCartney; Helga Ask; Kadri Koiv; Lea Arregui Nordahl Christoffersen; Sverre Urnes Johnson; Andrew M McIntosh; Anna K. Kahler; Archie Campbell; Arna Hauksdottir; Chloe Fawns-Ritchie; Christian Erikstrup; Dorte Helenius; Drew Altschul; Edda Bjork Thordardottir; Elias Eythorsson; Emma M. Frans; Gunnar Tomasson; Harpa Lind Jonsdottir; Harpa Runarsdottir; Henrik Hjalgrim; Hronn Hardardottir; Juan Gonzalez-Hijon; Karina Banasik; Khoa Manh Dinh; Li Lu; Lili Milani; Lill Trogstad; Maria Didriksen; Omid V. Ebrahimi; Patrick F. Sullivan; Per Minor Magnus; Qing Shen; Ragnar Nesvag; Reedik Magi; Runolfur Palsson; Sisse Rye Ostrowski; Thomas Werge; Asle Hoffart; David J. Porteous; Fang Fang; Johanna Jakobsdottir; Kelli Lehto; Ole A. Andreassen; Ole B.V. Pedersen; Thor Aspelund; Unnur Anna Valdimarsdottir,"Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Edinburgh, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Danish Cancer Society Research Center, Copenhagen, Denmark; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA; Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Immunology, Zealand University Hospital, Denmark; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland","BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis. + +METHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time. + +FINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period. + +CONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.",public and global health,fuzzy,100,92 medRxiv,10.1101/2021.12.14.21267460,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.14.21267460,Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales,Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase. MethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR). @@ -2037,6 +2089,13 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existin Added value of this studyUsing data from one of the largest UK citizen science epidemiological initiatives, we describe and compare illness (symptom duration, burden, profile, risk of long illness, and hospital attendance) in symptomatic community-based adults presenting when either the Alpha or Delta variant was the predominant circulating strain of SARS-CoV-2 in the UK. We assess evidence of transmission, reinfection, and vaccine effectiveness. Our data show that the seven most common symptoms with Delta infection were the same as with Alpha infection. Risks of illness duration [≥]7 days and [≥]28 days, and of requiring hospital care, were not increased. In line with previous research, we found increased transmissibility of Delta vs. previous variants; and no evidence of increased re-infection rates. Our data support high vaccine efficacy of BNT162b2 and ChAdOx1 nCoV-19 formulations against Delta variant infection. Overall, our study adds quantitative information regarding meaningful clinical differences in COVID-19 due to Delta vs. other variants. Implications of all the available evidenceOur observational data confirm that COVID-19 disease in UK in adults is generally comparable to infection with the Alpha variant, including in elderly individuals. Our data contribute to epidemiological surveillance from the wider UK population and may capture information from COVID-19 presentation within the community that might be missed in healthcare-based surveillance. Our data may be useful in informing healthcare service planning, vaccination policies, and measures for social protection.",epidemiology,fuzzy,94,100 +medRxiv,10.1101/2021.11.22.21266692,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266692,Serological responses to COVID-19 booster vaccine in England,Georgina Ireland; Heather Whitaker; Shamez N Ladhani; Frances Baawuah; Vani Subbarao; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corrine Whillock; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown,"UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre, Kilburn, London, United Kingdom; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency","IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca). + +MethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared. + +ResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants. + +ConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.11.22.21266512,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266512,Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales,Rochelle Knight; Venexia Walker; Samantha Ip; Jennifer A Cooper; Thomas Bolton; Spencer Keene; Rachel Denholm; Ashley Akbari; Hoda Abbasizanjani; Fatemeh Torabi; Efosa Omigie; Sam Hollings; Teri-Louise North; Renin Toms; Emanuele Di Angelantonio; Spiros Denaxas; Johan H Thygesen; Christopher Tomlinson; Ben Bray; Craig J Smith; Mark Barber; George Davey Smith; Nishi Chaturvedi; Cathie Sudlow; William N Whiteley; Angela Wood; Jonathan A C Sterne; - CVD-COVID-UK/COVID-IMPACT consortium; - Longitudinal Health and Wellbeing COVID-19 National Core Study,University of Bristol; University of Bristol; University of Cambridge; University of Bristol; University of Cambridge; University of Cambridge; University of Bristol; Swansea University; Swansea University; Swansea University; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University College London; University College London; University College London; Kings College London; University of Manchester; Glasgow Caledonian University; University of Bristol; University College London; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ,"ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear. ObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease. @@ -2171,19 +2230,6 @@ MethodsData were from 27,841 participants in eight UK adult longitudinal surveys ResultsCompared to stable employment, neither furlough, no longer being employed, nor stable unemployment were associated with smoking, vaping or drinking, following adjustment for pre-pandemic characteristics. However, some sex differences in these associations were observed, with stable unemployment associated with smoking for women (ARR=1.35; 95% CI: 1.00-1.82; I2: 47%) but not men (0.84; 95% CI: 0.67-1.05; I2: 0%). No longer being employed was associated with vaping among women (ARR=2.74; 95% CI: 1.59-4.72; I2: 0%) but not men (ARR=1.25; 95% CI: 0.83-1.87; I2: 0%). There was little indication of associations with drinking differing by age, gender or education. ConclusionsWe found no clear evidence of furlough or unemployment having adverse impacts on smoking, vaping or drinking behaviours during the early stages of the COVID-19 pandemic in the UK, with differences in risk compared to those who remained employed largely explained by pre-pandemic characteristics.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.11.01.21265660,2021-11-02,https://medrxiv.org/cgi/content/short/2021.11.01.21265660,"Estimating the relationship between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana",Hamish Gibbs; Yang Liu; Sam Abbott; Isaac Baffoe-Nyarko; Dennis O. Laryea; Ernest Akyereko; Patrick Kuma-Aboagye; Ivy Asante; Oriol Mitja; - LSHTM CMMID COVID-19 Working Group; William Ampofo; Franklin Asiedu-Bekoe; Michael Marks; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Ghana Health Service; Ghana Health Service; Ghana Health Service; Ghana Health Service; University of Ghana Noguchi Memorial Institute for Medical Research; Fight Against AIDS Foundation; ; University of Ghana Noguchi Memorial Institute for Medical Research; Ghana Health Service; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundGovernments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts. - -MethodsIn this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of Rt, a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana. - -FindingsWe observe a relationship between reductions in human mobility and decreases in Rt during the early stages of the COVID-19 epidemic in Ghana. We find that the strength of this relationship varies through time, decreasing after the most stringent period of interventions in the early epidemic. - -InterpretationOur findings demonstrate how the association of NPI and mobility indicators with COVID-19 transmission may vary through time. Further, we demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity and monitor the impact of NPI policies. - -Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and preprint archives for articles published in English that contained information about the COVID-19 pandemic published up to Nov 1, 2021, using the search terms ""coronavirus"", ""CoV"", ""COVID-19"", ""mobility"", ""movement"", and ""flow"". The data thus far suggests that NPI measures including physical distancing, reduction of travel, and use of personal protective equipment have been demonstrated to reduce COVID-19 transmission. Much of the existing research focuses on comparisons of NPI stringency with COVID-19 transmission among different high-income countries, or on high-income countries, leaving critical questions about the applicability of these findings to low- and middle-income settings. - -Added value of this studyWe used a detailed COVID-19 surveillance dataset from Ghana, and unique high resolution spatial data on human mobility from Vodafone Ghana as well as Google smartphone GPS location data. We show how human mobility and NPI stringency were associated with changes in the effective reproduction number (Rt). We further demonstrate how this association was strongest in the early COVID-19 outbreak in Ghana, decreasing after the relaxation of national restrictions. - -Implications of all the available evidenceThe change in association between human mobility, NPI stringency, and Rt may reflect a ""decoupling"" of NPI stringency and human mobility from disease transmission in Ghana as the COVID-19 epidemic progressed. This finding provides public health decision makers with important insights for the understanding of the utility of mobility data for predicting the spread of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.10.28.21265615,2021-10-29,https://medrxiv.org/cgi/content/short/2021.10.28.21265615,Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK,William Waites; Carl AB Pearson; Katherine M Gaskell; Thomas House; Lorenzo Pellis; Marina Johnson; Victoria Gould; Adam Hunt; Neil RH Stone; Ben Kasstan; Tracey Chantler; Sham Lal; Chrissy h Roberts; David Goldblatt; - CMMID COVID-19 Working Group; Michael Marks; Rosalind M Eggo,University of Edinburgh; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; The University of Manchester; University College London; London School of Hygiene and Tropical Medicine; University College London; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.10.22.21264701,2021-10-25,https://medrxiv.org/cgi/content/short/2021.10.22.21264701,Long-term health-related quality of life in non-hospitalised COVID-19 cases with confirmed SARS-CoV-2 infection in England: Longitudinal analysis and cross-sectional comparison with controls,Frank Sandmann; Elise Tessier; Joanne Lacy; Meaghan Kall; Edwin Van Leeuwen; Andre Charlett; Rosalind M Eggo; Gavin Dabrera; W. John Edmunds; Mary Ramsay; Helen Campbell; Gayatri Amirthalingam; Mark Jit,"Statistics, Modelling and Economics Department, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; COVID-19 National Epidemiology Cell, UK Health Security Agency, Wellington House, 133-155 Waterloo Rd, London SE1 8UG, UK; Immunisation Division, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; COVID-19 National Epidemiology Cell, UK Health Security Agency, Wellington House, 133-155 Waterloo Rd, London SE1 8UG, UK; Statistics, Modelling and Economics Department, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; Statistics, Modelling and Economics Department, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK; COVID-19 National Epidemiology Cell, UK Health Security Agency, Wellington House, 133-155 Waterloo Rd, London SE1 8UG, UK; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK; Immunisation Division, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; Immunisation Division, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; Immunisation Division, UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK","BackgroundThis study measured the long-term health-related quality of life of non-hospitalised COVID-19 cases with PCR-confirmed SARS-CoV-2(+) infection using the recommended instrument in England (the EQ-5D). @@ -2359,6 +2405,7 @@ Methods and findingsWe performed a rapid systematic review, searching Medline, E 49 observational studies (15 peer-reviewed papers and 34 preprints) reported primary outcomes for eight drug groups hypothesised to be deleterious. Meta-analysis showed that acute inpatient corticosteroid use was associated with increased mortality (OR 2.22, 95% CI 1.26-3.90), however this result appeared to have been biased by confounding via indication. One subgroup analysis indicated an association between immunosuppressant use and susceptibility to COVID-19 among case control and cross-sectional studies (OR 1.29, 95% CI 1.19-1.40) but this was not found with cohort studies (OR 1.11, 95% CI 0.86-1.43). Studies which adjusted for multiple confounders showed that people taking angiotensin-converting-enzyme inhibitors (ACEIs) or angiotensin-II-receptor blockers (ARBs) required a lower level of care (OR 0.85, 95% CI 0.74-0.98). Furthermore, studies which combined these two drug groups in their analysis demonstrated an association with a lower mortality (OR 0.68, 95% CI 0.55-0.85). ConclusionsWe found minimal high quality or consistent evidence that any drug groups increase susceptibility, severity or mortality in COVID-19. Converse to initial hypotheses, we found some evidence that regular use of ACEIs and ARBs prior to infection may be effective in reducing the level of care required, such as requiring intensive care, in patients with COVID-19.",pharmacology and therapeutics,fuzzy,100,100 +medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.09.13.21262360,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21262360,Efficacy of two doses of COVID-19 vaccine against severe COVID-19 in those with risk conditions and residual risk to the clinically extremely vulnerable: the REACT-SCOT case-control study,Paul M McKeigue; David McAllister; Chris Robertson; Sharon J Hutchinson; Stuart McGurnaghan; Diane Stockton; Helen M Colhoun,University of Edinburgh; University of Glasgow; University of Strathclyde; Glasgow Caledonian University; University of Edinburgh; Public Health Scotland; University of Edinburgh,"ObjectivesTo determine whether COVID-19 efficacy varies with clinical risk category and to investigate risk factors for severe COVID-19 in those who have received two doses of vaccine. DesignMatched case-control study (REACT-SCOT). @@ -2573,15 +2620,6 @@ MethodsAn observational cohort study using linked ambulance service data for pat ResultsOf 7549 patients in our cohort, 17.6% (95% CI:16.8% to 18.5%) experienced the primary outcome. The NEWS2, PMEWS, PRIEST tool and WHO algorithm identified patients at risk of adverse outcomes with a high sensitivity (>0.95) and specificity ranging from 0.3 (NEWS2) to 0.41 (PRIEST tool). The high sensitivity of NEWS2 and PMEWS was achieved by using lower thresholds than previously recommended. On index assessment, 65% of patients were transported to hospital and EMS decision to transfer patients achieved a sensitivity of 0.84 (95% CI 0.83 to 0.85) and specificity of 0.39 (95% CI 0.39 to 0.40). ConclusionUse of NEWS2, PMEWS, PRIEST tool and WHO algorithm could improve sensitivity of EMS triage of patients with suspected COVID-19 infection. Use of the PRIEST tool would improve sensitivity of triage without increasing the number of patients conveyed to hospital.",emergency medicine,fuzzy,100,100 -medRxiv,10.1101/2021.07.26.21261140,2021-07-28,https://medrxiv.org/cgi/content/short/2021.07.26.21261140,Higher serological responses and increased vaccine effectiveness demonstrate the value of extended vaccine schedules in combatting COVID-19 in England,Gayatri Amirthalingam; Jamie Lopez Bernal; Nick J Andrews; Heather Whitaker; Charlotte Gower; Julia Stowe; Elise Tessier; Sathyavani Subbarao; Georgina Ireland; Frances Baawuah; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corinne Whillock; Paul Moss; Shamez N Ladhani; Kevin E Brown; Mary E Ramsay,Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Brondesbury Medical Centre; Public Health England; University of Birmingham; Public Health England; Public Health England; Public Health England,"IntroductionIn January 2021, the UK decided to prioritise the delivery of the first dose of BNT162b2 (Pfizer/BioNTech) and AZD1222 (AstraZeneca) vaccines by extending the interval until the second dose up to 12 weeks. - -MethodsSerological responses were compared after BNT162b2 and AZD1222 vaccination with varying intervals in uninfected and previously-infected adults aged 50-89 years. These findings are evaluated against real-world national vaccine effectiveness (VE) estimates against COVID-19 in England. - -ResultsWe recruited 750 participants aged 50-89 years, including 126 (16.8%) with evidence of previous infection; 421 received BNT162b2 and 329 and AZD1222. For both vaccines, over 95% had seroconverted 35-55 days after dose one, and 100% seroconverted 7+ days after dose 2. Following a 65-84 day interval between two doses, geometric mean titres (GMTs) at 14-34 days were 6-fold higher for BNT162b2 (6703; 95%CI, 5887-7633) than AZD1222 (1093; 806-1483), which in turn were higher than those receiving BNT162b2 19-29 days apart (694; 540 - 893). For both vaccines, VE was higher across all age-groups from 14 days after dose two compared to one dose, but the magnitude varied with interval between doses. Higher two-dose VE was observed with >6 week intervals between BNT162b2 doses compared to the authorised 3-week schedule, including [≥]80 year-olds. - -ConclusionOur findings support the UK approach of prioritising the first dose of COVID-19 vaccines, with evidence of higher protection following extended schedules. Given global vaccine constraints, these results are relevant to policymakers, especially with highly transmissible variants and rising incidence in many countries. - -FundingPublic Health England",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.07.23.21260992,2021-07-25,https://medrxiv.org/cgi/content/short/2021.07.23.21260992,A cluster randomised trial of the impact of a policy of daily testing for contacts of COVID-19 cases on attendance and COVID-19 transmission in English secondary schools and colleges,Bernadette C Young; David W Eyre; Saroj Kendrick; Chris White; Sylvester Smith; George Beveridge; Toby Nonnenmacher; Fegor Ichofu; Joseph Hillier; Ian Diamond; Emma Rourke; Fiona Dawe; Ieuan Day; Lisa Davies; Paul Staite; Andrea Lacey; James McCrae; Ffion Jones; Joseph Kelly; Urszula Bankiewicz; Sarah Tunkel; Richard Ovens; David Chapman; Peter Marks; Nick Hicks; Tom Fowler; Susan Hopkins; Lucy Yardley; Tim EA Peto,"University of Oxford; University of Oxford; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Department of Health and Social Care, UK Government; Deloitte MCS limited; Deloitte MCS limited; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Public Health England; University of Bristol; University of Oxford","BackgroundSchool-based COVID-19 contacts in England are asked to self-isolate at home. However, this has led to large numbers of missed school days. Therefore, we trialled daily testing of contacts as an alternative, to investigate if it would affect transmission in schools. MethodsWe performed an open-label cluster randomised controlled trial in students and staff from secondary schools and further education colleges in England (ISRCTN18100261). Schools were randomised to self-isolation of COVID-19 contacts for 10 days (control) or to voluntary daily lateral flow device (LFD) testing for school contacts with LFD-negative contacts remaining at school (intervention). Household contacts were excluded from participation. @@ -2610,6 +2648,13 @@ QuestionDoes the association between BMI and COVID-19 mortality vary by ethnicit FindingsIn this study of 12.6 million adults, BMI was associated with COVID-19 in all ethnicities, but with stronger associations in ethnic minority populations such that the risk of COVID-19 mortality for a BMI of 40 kg/m2 in white ethnicities was observed at a BMI of 30.1 kg/m2, 27.0 kg/m2, and 32.2 kg/m2 in black, South Asian and other ethnicities, respectively. MeaningBMI is a stronger risk factor for COVID-19 mortality in ethnic minorities. Obesity management is therefore a priority in these populations.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.07.20.21260558,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.20.21260558,Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study,Rebecca Wilson; Harriet Quinn-Scoggins; Yvonne Moriarty; Jacqueline Hughes; Mark Goddard; Rebecca Cannings-John; Victoria Whitelock; Katriina L Whitaker; Detelina Grozeva; Julia Townson; Kirstie Osborne; Stephanie Smits; Michael Robling; Julie Hepburn; Graham Moore; Ardiana Gjini; Kate Brain; Jo Waller,"Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cancer Research UK; University of Surrey; Cardiff University; Cardiff University; Cancer Research UK; Cardiff University; Cardiff University; Public Involvement Community, Health and Care Research Wales; Cardiff University; Public Health Wales; Cardiff University; Kings College London","Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK. + +Overall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically. + +Of those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed. + +Intentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.",oncology,fuzzy,100,98 medRxiv,10.1101/2021.07.19.21260782,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.19.21260782,Does COVID-19 vaccination improve mental health? A difference-in-difference analysis of the UnderstandingCoronavirus in America study,Jonathan Koltai; Julia Raifman; Jacob Bor; Martin McKee; David Stuckler,University of New Hampshire; Boston University; Boston University; London School of Hygiene and Tropical Medicine; Bocconi University,"BackgroundMental health problems increased during the COVID-19 pandemic. Knowledge that one is less at risk after being vaccinated may alleviate distress, but this hypothesis remains unexplored. Here we test whether psychological distress declined in those vaccinated against COVID-19 in the US and whether changes in perceived risk mediated any association. MethodsA nationally-representative cohort of U.S. adults (N=5,792) in the Understanding America Study were interviewed every two weeks from March 2020 to June 2021 (28 waves). Difference-in-difference regression tested whether getting vaccinated reduced distress (PHQ-4 scores), with mediation analysis used to identify potential mechanisms, including perceived risks of infection, hospitalization, and death. @@ -2911,6 +2956,15 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed Added value of this studyImmune interference and safety are always a concern when two vaccines are administered at the same time. This is the first study to demonstrate the safety and immunogenicity profile and clinical vaccine efficacy of a COVID-19 vaccine when co-administered with a seasonal influenza vaccine. Implications of all the available evidenceThis study provides much needed information to help guide national immunisation policy decision making on the critical issue of concomitant use of COVID-19 vaccines with influenza vaccines.",allergy and immunology,fuzzy,95,100 +medRxiv,10.1101/2021.06.08.21258533,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258533,The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.,Aleksandra Kovacevic; Rosalind M Eggo; Marc Baguelin; Matthieu Domenech de Cellès; Lulla Opatowski,Institut Pasteur; London School of Hygiene & Tropical Medicine; Imperial College London; Max Planck Institute for Infection Biology; Univ Versailles Saint Quentin / Institut Pasteur / Inserm,"BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data. + +MethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality. + +ResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive. + +ConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance. + +SummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.08.21258546,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258546,Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies,Jane Maddock; Sam Parsons; Giorgio Di Gessa; Michael J Green; Ellen J Thompson; Anna J Stevenson; Alex S.F. Kwong; Eoin McElroy; Gillian Santorelli; Richard J Silverwood; Gabriella Captur; Nish Chaturvedi; Claire J Steves; Andrew Steptoe; Praveetha Patalay; George B Ploubidis; Srinivasa Vittal Katikireddi,University College London; University College London; University College London; University of Glasgow; King's College London; University of Edinburgh; University of Bristol; University of Leicester; Bradford Institute for Health Research; University College London; University College London; University College London; King's College London; University College London; University College London; University College London; University of Glasgow,"BackgroundHealth systems worldwide have faced major disruptions due to COVID-19 which could exacerbate health inequalities. The UK National Health Service (NHS) provides free healthcare and prioritises equity of delivery, but the pandemic may be hindering the achievement of these goals. We investigated associations between multiple social characteristics (sex, age, occupational social class, education and ethnicity) and self-reported healthcare disruptions in over 65,000 participants across twelve UK longitudinal studies. MethodsParticipants reported disruptions from March 2020 up to late January 2021. Associations between social characteristics and three types of self-reported healthcare disruption (medication access, procedures, appointments) and a composite of any of these were assessed in logistic regression models, adjusting for age, sex and ethnicity where relevant. Random-effects meta-analysis was conducted to obtain pooled estimates. @@ -3010,13 +3064,15 @@ MethodsWe used data from a sub-cohort (n =3761) of adults ([≥]18) tested for ResultsSeropositivity was 16.0% (113/707) amongst workers with daily close contact, compared to 12.9% (120/933) for those with intermediate-frequency contact and 9.6% (203/2121) for those with no work-related close contact. Healthcare (OR= 2.14, 95% CI 1.47,3.12), indoor trade, process and plant (2.09, 1.31,3.33), leisure and personal service (1.96, 1.004,3.84), and transport and mobile machine (2.17, 1.12,4.18) workers had elevated total odds of SARS-CoV-2 seropositivity compared to other professional and associate occupations. Frequency of workplace contact accounted for a variable part of the increased odds in different occupational groups (OR range 1.04 [1.0004,1.07] - 1.22 [1.07, 1.38]). Healthcare workers and indoor trades and process plant workers continued to have raised odds of infection after accounting for work-related contact, and also had had greater odds of frequent exposure to poorly-ventilated workplaces (respectively 2.15 [1.66, 2.79] and (1.51, [1.12, 2.04]). DiscussionMarked variations in occupational odds of seropositivity remain after accounting for age, sex, region, and household income. Close contact in the workplace appears to contribute substantially to this variation. Reducing frequency of workplace contact is a critical part of COVID-19 control measures.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.05.14.21257229,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.14.21257229,Symptom profiles and accuracy of clinical definitions for COVID-19 in the community. Results of the Virus Watch community cohort.,Ellen Fragaszy; Madhumita Shrotri; Cyril Geismar; Anna Aryee; Sarah Beale; Isobel Braithwaite; Thomas Byrne; Wing Lam Erica Fong; Jo Gibbs; Pia Hardelid; Jana Kovar; Vasileios Edward Lampos; Eleni Nastouli; Annalan Mathew Dwight Navaratnam; Vincent Grigori Nguyen; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,"Centre for Public Health Data Science, Institute of Health Informatics, University College London; Department of Infectious Disease Epidemiology, London School ; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute for Global Health, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Institute of Epidemiology and Health Care, University College London; Department of Computer Science, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Francis Crick Institute, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London; . Institute of Epidemiology and Health Care, University Colle; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College London; ","BackgroundUnderstanding the symptomatology and accuracy of clinical case definitions for COVID-19 in the community is important for the initiation of Test, Trace and Isolate (TTI) and may, in future, be important for early prescription of antivirals. +medRxiv,10.1101/2021.05.18.21257267,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.18.21257267,"Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Enti Spata; Jonathan R Emberson; Natalie Staplin; Guilherme Pessoa-Amorim; Leon Peto; Martin Wiselka; Laura Wiffen; Simon Tiberi; Ben Caplin; Caroline Wroe; Christopher Green; Paul Hine; Benjamin Prudon; Tina George; Andrew Wight; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph L Hamers; Thomas Jaki; Edmund Juszczak; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat; Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Department of Infection, Barts Health NHS Trust, London, United Kingdom; Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Course Sciences, King?s College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un","BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions. + +MethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). -MethodsVirus Watch is a large community cohort with prospective daily recording of a wide range of symptoms and self-reporting of swab results (mainly undertaken through the UK TTI system). We compared frequency, severity, timing, and duration of symptoms in test positive and test negative cases. We compared the test performance of the current UK case definition used by TTI (any one of: new continuous cough, high temperature, or loss of or altered sense of smell or taste) with a wider definition that also included muscle aches, chills, headache, or loss of appetite. +FindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47). -FindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition. +InterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death. -InterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.",epidemiology,fuzzy,100,100 +FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.17.21256818,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.17.21256818,Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data,George Nicholson; Brieuc CL Lehmann; Tullia Padellini; Koen B Pouwels; Radka Jersakova; James Lomax; Ruairidh E King; Ann-Marie Mallon; Peter J Diggle; Sylvia Richardson; Marta Blangiardo; Chris Holmes,University of Oxford; University of Oxford; Imperial College London; University of Oxford; The Alan Turing Institute; The Alan Turing Institute; MRC Harwell Institute; MRC Harwell Institute; Lancaster University; MRC Biostatistics Unit; Imperial College London; University of Oxford,"Targeted surveillance testing schemes for SARS-CoV-2 focus on certain subsets of the population, such as individuals experiencing one or more of a prescribed list of symptoms. These schemes have routinely been used to monitor the spread of SARS-CoV-2 in countries across the world. The number of positive tests in a given region can provide local insights into important epidemiological parameters, such as prevalence and effective reproduction number. Moreover, targeted testing data has been used inform the deployment of localised non-pharmaceutical interventions. However, surveillance schemes typically suffer from ascertainment bias; the individuals who are tested are not necessarily representative of the wider population of interest. Here, we show that data from randomised testing schemes, such as the REACT study in the UK, can be used to debias fine-scale targeted testing data in order to provide accurate localised estimates of the number of infectious individuals. We develop a novel, integrative causal framework that explicitly models the process underlying the selection of individuals for targeted testing. The output from our model can readily be incorporated into longitudinal analyses to provide local estimates of the reproduction number. We apply our model to characterise the size of the infectious population in England between June 2020 and January 2021. Our local estimates of the effective reproduction number are predictive of future changes in positive case numbers. We also capture local increases in both prevalence and effective reproductive number in the South East from November 2020 to December 2020, reflecting the spread of the Kent variant. Our results illustrate the complementary roles of randomised and targeted testing schemes. Preparations for future epidemics should ensure the rapid deployment of both types of schemes to accurately monitor the spread of emerging and ongoing infectious diseases.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.15.21257017,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.15.21257017,Extended interval BNT162b2 vaccination enhances peak antibody generation in older people,Helen M Parry; Rachel Bruton; Christine Stephens; Kevin Brown; Gayatri Amirthalingam; Bassam Hallis; Ashley Otter; Jianmin Zuo; Paul Moss,"University of Birmingham, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK","ObjectivesTo assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination. @@ -3131,13 +3187,9 @@ MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96 ResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4). ConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.05.10.21256912,2021-05-11,https://medrxiv.org/cgi/content/short/2021.05.10.21256912,Household overcrowding and risk of SARS-CoV-2: analysis of the Virus Watch prospective community cohort study in England and Wales,Robert W Aldridge; Helen Pineo; Ellen Fragaszy; Max Eyre; Jana Kovar; Vincent Nguyen; Sarah Beale; Thomas Byrne; Anna Aryee; Colette Smith; Delanjathan Devakumar; Jonathon Taylor; Vittal Katikireddi; Wing Lam Erica Fong; Cyril Geismar; Parth Patel; Madhumita Shrotri; Isobel Braithwaite; Annalan M D Navaratnam; Anne M Johnson; Andrew Hayward,"Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Institute for Environmental Design and Engineering, Bartlett School of Environment, Energy and Resources, University College London, London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Institute for Global Health, University College London, London, UK.; Institute for Global Health, University College London, London, UK.; Department of Civil Engineering, Tampere University, Finland.; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow Institute of Health and Wellbeing, Glasgow, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Institute for Global Health, University College London, London, UK.; Institute of Epidemiology and Health Care, University College London, London, UK","BackgroundHousehold overcrowding is associated with increased risk of infectious diseases across contexts and countries. Limited data exist linking household overcrowding and risk of COVID-19. We used data collected from the Virus Watch cohort to examine the association between overcrowded households and SARS-CoV-2. - -MethodsThe Virus Watch study is a household community cohort of acute respiratory infections in England & Wales that began recruitment in June 2020. We calculated the persons per room for each household and classified accommodation as overcrowded when the number of rooms{square}was fewer than the number of people. We considered two primary outcomes - PCR-confirmed positive SARS-CoV-2 antigen tests and laboratory confirmed SARS-CoV-2 antibodies (Roche Elecsys anti-N total immunoglobulin assay). We used mixed effects logistic regression models that accounted for household structure to estimate the association between household overcrowding and SARS-CoV-2 infection. - -ResultsThe proportion of participants with a positive SARS-CoV-2 PCR result was highest in the overcrowded group (6.6%; 73/1,102) and lowest in the under-occupied group (2.9%; 682/23,219). In a mixed effects logistic regression model that included age, sex, ethnicity, household income and geographical region, we found strong evidence of an increased odds of having a positive PCR SARS-CoV-2 antigen result (Odds Ratio 3.72; 95% CI: 1.92, 7.13; p-value < 0.001) and increased odds of having a positive SARS-CoV-2 antibody result in individuals living in overcrowded houses (2.96; 95% CI: 1.13, 7.74; p-value =0.027) compared to people living in under-occupied houses. The proportion of variation at the household level was 9.91% and 9.97% in the PCR and antibody models respectively. +medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively. -DiscussionPublic health interventions to prevent and stop the spread of SARS-CoV-2 should consider the much greater risk of infection for people living in overcrowded households and pay greater attention to reducing household transmission. There is an urgent need to better recognise housing as a leading determinant of health in the context of a pandemic and beyond.",infectious diseases,fuzzy,100,100 +Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.05.05.21256649,2021-05-08,https://medrxiv.org/cgi/content/short/2021.05.05.21256649,Illness duration and symptom profile in a large cohort of symptomatic UK school-aged children tested for SARS-CoV-2,Erika Molteni; Carole Helene Sudre; Liane Santos Canas; Sunil S Bhopal; Robert C Hughes; Michela S Antonelli; Benjamin Murray; Kerstin Klaser; Eric Kerfoot; Liyuan Chen; Jie Deng; Christina Hu; Somesh Selvachandran; Kenneth Read; Joan Capdevila Pujol; Alexander Hammers; Timothy Spector; Sebastien Ourselin; Claire J Steves; Marc Modat; Michael Absoud; Emma L Duncan,King's College London; University College London; King's College London; King's College London; Newcastle University; London School of Hygiene & Tropical Medicine; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd; Zoe Global Ltd; ZOE Global Ltd; Zoe Global Ltd; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Evelina Hospital London; King's College London,"BackgroundIn children, SARS-CoV-2 is usually asymptomatic or causes a mild illness of short duration. Persistent illness has been reported; however, its prevalence and characteristics are unclear. We aimed to determine illness duration and characteristics in symptomatic UK school-aged children tested for SARS-CoV-2 using data from the COVID Symptom Study, the largest UK citizen participatory epidemiological study to date. MethodsData from 258,790 children aged 5-17 years were reported by an adult proxy between 24 March 2020 and 22 February 2021. Illness duration and symptom profiles were analysed for all children testing positive for SARS-CoV-2 for whom illness duration could be determined, considered overall and within younger (5-11 years) and older (12-17 years) groups. Data from symptomatic children testing negative for SARS-CoV-2, matched 1:1 for age, gender, and week of testing, were also assessed. @@ -3187,6 +3239,13 @@ What this study addsO_LIIn 70,464 people with atrial fibrillation, at the thresh C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs. C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs. C_LI",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation. + +MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period. + +ResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods. + +ConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.04.24.21255968,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.24.21255968,MORTALITY OF CARE HOME RESIDENTS AND COMMUNITY-DWELLING CONTROLS DURING THE COVID-19 PANDEMIC IN 2020: MATCHED COHORT STUDY,Martin C Gulliford; A Toby Prevost; Andrew Clegg; Emma C Rezel-Potts,King's College London; King's College London; University of Leeds; King's College London,"ObjectiveTo estimate mortality of care home (CH) residents, and matched community-dwelling controls, during the Covid-19 pandemic from primary care electronic health records. DesignMatched cohort study @@ -3200,21 +3259,6 @@ Main outcome measuresAll-cause mortality. Adjusted rate ratios (RR) by negative ResultsDuring April 2020, the mortality rate of CH residents was 27.2 deaths per 1,000 patients per week, compared with 2.31 per 1,000 for controls, RR 11.1 (95% confidence interval 10.1 to 12.2). Compared with CH residents, LTCs and frailty were differentially associated with greater mortality in community-dwelling controls. During April 2020, mortality rates per 1,000 patients per week for persons with 9+ LTCs were: CH, 37.9; controls 17.7; RR 2.14 (1.18 to 3.89). In severe frailty, mortality rates were: CH, 29.6; controls 5.1; RR 6.17 (5.74 to 6.62). ConclusionsIndividual-patient data from primary care electronic health records may be used to estimate mortality in care home residents. Mortality is substantially higher than for community-dwelling comparators and showed a disproportionate increase in the first wave of the Covid-19 pandemic. Multiple morbidity and frailty were associated with greater absolute risks but lower relative risks because community-dwelling frail or multi-morbid patients also experienced high mortality.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.04.21.21255807,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.21.21255807,A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial,Timothy SC Hinks; Lucy Cureton; Ruth Knight; Ariel Wang; Jennifer L Cane; Vicki S Barber; Joanna Black; Susan J Dutton; James Melhorn; Maisha Jabeen; Phil Moss; Rajendar Garlapati; Tanya Baron; Graham Johnson; Fleur Cantle; David Clarke; Samer Elkhodair; Jonathan Underwood; Daniel Lasserson; Ian D Pavord; Sophie B Morgan; Duncan Richards,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; St George's Hospital, London; East Lancashire NHS Hospitals; Oxford University Hospitals NHS Trust; Royal Derby Hospital; Kings College Hospital, London; Royal Berkshire Hospital; University College London Hospital; Cardiff University; Oxford University Hospitals NHS Trust; University of Oxford; University of Oxford; University of Oxford","BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19. - -MethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed. - -Findings298 participants were enrolled from 3rd June 2020 to 29th January 2021. The primary outcome was assessed in 292 participants. The primary endpoint was not significantly different between the azithromycin and control groups (Adjusted OR 0{middle dot}91 [95% CI 0{middle dot}43-1{middle dot}92], p=0{middle dot}80). Rates of respiratory failure, progression to pneumonia, all-cause mortality, and adverse events, including serious cardiovascular events, were not significantly different between groups. - -InterpretationIn patients with mild-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospitalisation or death. Our findings do not support the use of azithromycin in patients with mild-moderate COVID-19. - -FundingNIHR Oxford BRC, University of Oxford and Pfizer Inc. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE and the Cochrane Central register of Controlled Trials (CENTRAL) with the terms (""azithromycin"") AND (""COVID"" OR ""COVID-19"") AND (""clinical trials""), until March 25, 2021, with no language restrictions. We identified 42 studies, among which there were four completed randomised trials of azithromycin (with or without hydroxychloroquine) in hospitalised patients with severe disease, and three completed randomised trials of azithromycin in mild COVID-19 in primary care. The four trials in hospitalised patients randomised 8,988 participants to azithromycin or standard care or hydroxychloroquine and found no evidence of a difference in mortality, duration of hospital stay or peak disease severity. Of the three trials in primary care, these randomised participants with early disease to 3 or 5 days of therapy, of which only one assessed azithromycin as standalone therapy. This large, adaptive platform trial in the UK randomised 540 participants in primary care to 3 days treatment with azithromycin versus 875 to standard care alone and found no meaningful difference in time to first reported recovery, or of rates of hospitalisation (3% versus 3%) and there were no deaths. We did not identify any randomised trials in patients with COVID-19 managed in ambulatory care. - -Added value of this studyThe ATOMIC2 trial was uniquely-designed to assess azithromycin as a standalone therapy in those with mild-moderately COVID-19 presenting to emergency care, but assessed as appropriate for initial ambulatory management without hospital admission. ATOMIC2 also uniquely assessed high-dose, long-duration treatment to investigate the efficacy of putative anti-inflammatory effects. We found that azithromycin 500 mg daily for 14 days did not reduce the proportion of participants who died or required hospital admission from any cause over the 28 days from randomisation. - -Implications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.04.22.21255949,2021-04-25,https://medrxiv.org/cgi/content/short/2021.04.22.21255949,Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study,Michael Tildesley; Anna Vassall; Steven Riley; Mark Jit; Frank Sandmann; Edward M Hill; Robin Thompson; Benjamin Atkins; John Edmunds; Louise M Dyson; Matt J Keeling,"University of Warwick; London School of Hygiene and Tropical Medicine; Dept Inf Dis Epi, Imperial College; London School of Hygiene & Tropical Medicine; Public Health England; University of Warwick; University of Warwick; University of Warwick; London School of Hygiene and Tropical Medicine; University of Warwick; University of Warwick","BackgroundEven with good progress on vaccination, SARS-CoV-2 infections in the UK may continue to impose a high burden of disease and therefore pose substantial challenges for health policy decision makers. Stringent government-mandated physical distancing measures (lockdown) have been demonstrated to be epidemiologically effective, but can have both positive and negative economic consequences. The duration and frequency of any intervention policy could, in theory, could be optimised to maximise economic benefits while achieving substantial reductions in disease. MethodsHere we use a pre-existing SARS-CoV-2 transmission model to assess the health and economic implications of different strengths of control through time in order to identify optimal approaches to non-pharmaceutical intervention stringency in the UK, considering the role of vaccination in reducing the need for future physical distancing measures. The model is calibrated to the COVID-19 epidemic in England and we carry out retrospective analysis of the optimal timing of precautionary breaks in 2020 and the optimal relaxation policy from the January 2021 lockdown, considering the willingness to pay for health improvement. @@ -3520,6 +3564,7 @@ Added value of this studyThrough prospective collection of symptom and test repo Implications of all the available evidenceDespite the UK having a simple set of symptom-based testing criteria, with tests made freely available through nationalised healthcare, a quarter of individuals with qualifying symptoms do not get tested. Our findings suggest testing uptake may be limited by individuals not acting on mild or transient symptoms, not recognising the testing criteria, and not knowing where to get tested. Improved messaging may help address this testing gap, with opportunities to target individuals of older age or fewer years of education. Messaging may prove even more valuable in countries with more fragmented testing infrastructure or more nuanced testing criteria, where knowledge barriers are likely to be greater.",public and global health,fuzzy,94,100 bioRxiv,10.1101/2021.03.14.435295,2021-03-16,https://biorxiv.org/cgi/content/short/2021.03.14.435295,3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome,Ewan Hunter; Christina Koutsothanasi; Adam Wilson; Francisco Coroado Santos; Matthew Salter; Ryan Powell; Ann Dring; Paulina Brajer; Benedict Egan; Jurjen Westra; Aroul Ramadass; William Messner; Amanda Brunton; Zoe Lyski; Rama Vancheeswaran; Andrew Barlow; Dmitri Pchejetski; Alexandre Akoulitchev,"Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; West Hertfordshire NHS Trust, Watford, UK; West Hertfordshire NHS Trust, Watford, UK; Norwich Medical School, University of East Anglia; Oxford BioDynamics Plc, Oxford UK","Human infection with the SARS-CoV-2 virus leads to coronavirus disease (COVID-19). A striking characteristic of COVID-19 infection in humans is the highly variable host response and the diverse clinical outcomes, ranging from clinically asymptomatic to severe immune reactions leading to hospitalization and death. Here we used a 3D genomic approach to analyse blood samples at the time of COVID diagnosis, from a global cohort of 80 COVID-19 patients, with different degrees of clinical disease outcomes. Using 3D whole genome EpiSwitch(R) arrays to generate over 1 million data points per patient, we identified a distinct and measurable set of differences in genomic organization at immune-related loci that demonstrated prognostic power at baseline to stratify patients with mild forms of illness and those with severe forms that required hospitalization and intensive care unit (ICU) support. Further analysis revealed both well established and new COVID-related dysregulated pathways and loci, including innate and adaptive immunity; ACE2; olfactory, G{beta}{psi}, Ca2+ and nitric oxide (NO) signalling; prostaglandin E2 (PGE2), the acute inflammatory cytokine CCL3, and the T-cell derived chemotactic cytokine CCL5. We identified potential therapeutic agents for mitigation of severe disease outcome, with several already being tested independently, including mTOR inhibitors (rapamycin and tacrolimus) and general immunosuppressants (dexamethasone and hydrocortisone). Machine learning algorithms based on established EpiSwitch(R) methodology further identified a subset of 3D genomic changes that could be used as prognostic molecular biomarker leads for the development of a COVID-19 disease severity test.",biochemistry,fuzzy,92,100 medRxiv,10.1101/2021.03.09.21253012,2021-03-15,https://medrxiv.org/cgi/content/short/2021.03.09.21253012,The local and systemic response to SARS-CoV-2 infection in children and adults,Masahiro Yoshida; Kaylee B Worlock; Ni Huang; Rik GH Lindeboom; Colin R Butler; Natsuhiko Kumasaka; Cecilia Dominguez Conde; Lira Mamanova; Liam Bolt; Laura Richardson; Krzysztof Polanski; Elo Madissoon; Josephine L Barnes; Jessica Allen-Hyttinen; Eliz Kilich; Brendan C Jones; Angus de Wilton; Anna Wilbrey-Clark; Waradon Sungnak; Jan Patrick Prett; Elena Prigmore; Henry Yung; Puja Mehta; Aarash Saleh; Anita Saigal; Vivian Chu; Jonathan M Cohen; Clare Cane; Aikaterini Iordanidou; Soichi Shibuya; Ann-Kathrin Reuschl; A. Christine Argento; Richard G Wunderink; Sean B Smith; Taylor A Poor; Catherine A Gao; Jane E Dematte; - NU SCRIPT Study Investigators; Gary Reynolds; Muzlifah Haniffa; Georgina S Bowyer; Matthew Coates; Menna R Clatworthy; Fernando J Calero-Nieto; Berthold Gottgens; Neil J Sebire; Clare Jolly; Paolo de Coppi; Claire M Smith; Alexander V Misharin; Sam M Janes; Sarah A Teichmann; Marko Z Nikolic; Kerstin B Meyer,"UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Wellcome Trust Sanger Institute; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; University College London Hospital Trust; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Division of Infection and Immunity, University College London, London, UK; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Northwestern University Feinberg School of Medicine; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; ; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; University of Cambridge, Department of Medicine; University of Cambride, Department of Medicine; Wellcome Trust & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge UK; Wellcome Trust & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge UK; NIHR Great Ormond Street BRC and Institute of Child Health, London, UK; Division of Infection and Immunity, University College London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Northwestern University; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK","While a substantial proportion of adults infected with SARS-CoV-2 progress to develop severe disease, children rarely manifest respiratory complications. Therefore, understanding differences in the local and systemic response to SARS-CoV-2 infection between children and adults may provide important clues about the pathogenesis of SARS-CoV-2 infection. To address this, we first generated a healthy reference multi-omics single cell data set from children (n=30) in whom we have profiled triple matched samples: nasal and tracheal brushings and PBMCs, where we track the developmental changes for 42 airway and 31 blood cell populations from infancy, through childhood to adolescence. This has revealed the presence of naive B and T lymphocytes in neonates and infants with a unique gene expression signature bearing hallmarks of innate immunity. We then contrast the healthy reference with equivalent data from severe paediatric and adult COVID-19 patients (total n=27), from the same three types of samples: upper and lower airways and blood. We found striking differences: children with COVID-19 as opposed to adults had a higher proportion of innate lymphoid and non-clonally expanded naive T cells in peripheral blood, and a limited interferon-response signature. In the airway epithelium, we found the highest viral load in goblet and ciliated cells and describe a novel inflammatory epithelial cell population. These cells represent a transitional regenerative state between secretory and ciliated cells; they were found in healthy children and were enriched in paediatric and adult COVID-19 patients. Epithelial cells display an antiviral and neutrophil-recruiting gene signature that is weaker in severe paediatric versus adult COVID-19. Our matched blood and airway samples allowed us to study the spatial dynamics of infection. Lastly, we provide a user-friendly interface for this data1 as a highly granular reference for the study of immune responses in airways and blood in children.",pediatrics,fuzzy,100,100 +medRxiv,10.1101/2021.03.12.21253484,2021-03-13,https://medrxiv.org/cgi/content/short/2021.03.12.21253484,Limits of lockdown: characterising essential contacts during strict physical distancing,Amy C Thomas; Leon Danon; Hannah Christensen; Kate Northstone; Daniel Smith; Emily J Nixon; Adam Trickey; Gibran Hemani; Sarah Sauchelli; Adam Finn; Nicholas J Timpson; Ellen Brooks-Pollock,"University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; NIHR Bristol Biomedical Research Centre, University of Bristol; University of Bristol; University of Bristol; University of Bristol","COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.03.10.21253173,2021-03-12,https://medrxiv.org/cgi/content/short/2021.03.10.21253173,"High household transmission of SARS-CoV-2 in the United States: living density, viral load, and disproportionate impact on communities of color",Carla Cerami; Tyler Rapp; Feng-Chang Lin; Kathleen Tompkins; Christopher Basham; Meredith Smith Muller; Maureen Whittelsey; Haoming Zhang; Srijana Bhattarai Chhetri; Judy Smith; Christy Litel; Kelly Lin; Mehal Churiwal; Salman Khan; Faith Claman; Rebecca Rubinstein; Katie Mollan; David Wohl; Lakshmanane Premkumar; Jonathan J. Juliano; Jessica T Lin,"MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; University of North Carolina School of Medicine; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA","BackgroundFew prospective studies of SARS-CoV-2 transmission within households have been reported from the United States, where COVID-19 cases are the highest in the world and the pandemic has had disproportionate impact on communities of color. Methods and FindingsThis is a prospective observational study. Between April-October 2020, the UNC CO-HOST study enrolled 102 COVID-positive persons and 213 of their household members across the Piedmont region of North Carolina, including 45% who identified as Hispanic/Latinx or non-white. Households were enrolled a median of 6 days from onset of symptoms in the index case. Secondary cases within the household were detected either by PCR of a nasopharyngeal (NP) swab on study day 1 and weekly nasal swabs (days 7, 14, 21) thereafter, or based on seroconversion by day 28. After excluding household contacts exposed at the same time as the index case, the secondary attack rate (SAR) among susceptible household contacts was 60% (106/176, 95% CI 53%-67%). The majority of secondary cases were already infected at study enrollment (73/106), while 33 were observed during study follow-up. Despite the potential for continuous exposure and sequential transmission over time, 93% (84/90, 95% CI 86%-97%) of PCR-positive secondary cases were detected within 14 days of symptom onset in the index case, while 83% were detected within 10 days. Index cases with high NP viral load (>10^6 viral copies/ul) at enrollment were more likely to transmit virus to household contacts during the study (OR 4.9, 95% CI 1.3-18 p=0.02). Furthermore, NP viral load was correlated within families (ICC=0.44, 95% CI 0.26-0.60), meaning persons in the same household were more likely to have similar viral loads, suggesting an inoculum effect. High household living density was associated with a higher risk of secondary household transmission (OR 5.8, 95% CI 1.3-55) for households with >3 persons occupying <6 rooms (SAR=91%, 95% CI 71-98%). Index cases who self-identified as Hispanic/Latinx or non-white were more likely to experience a high living density and transmit virus to a household member, translating into an SAR in minority households of 70%, versus 52% in white households (p=0.05). @@ -3788,15 +3833,6 @@ ResultsThere were 5451 COVID-19 cases within the cohort. HRT was associated with ConclusionsWomen on HRT with COVID-19 had a lower likelihood of death. Further work is needed in larger cohorts to examine the association of COCP in COVID-19. Our findings support the current hypothesis that oestrogens may contribute a protective effect against COVID-19 severity. FundingThis study was funded by a School for Primary Care National Institute for Health Research grant (SPCR2014-10043).",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.02.15.21251552,2021-02-19,https://medrxiv.org/cgi/content/short/2021.02.15.21251552,Evaluating the effect of COVID-19 on dispensing patterns: a national cohort analysis,Fatemeh Torabi; Ashley Akbari; Laura North; Daniel Harris; Gareth Davies; Mike Gravenor; Rowena Griffiths; Jane Lyons; Neil Jenkins; Andrew Morris; Julian Halcox; Ronan A. Lyons,"Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK, SwanseaUniversity; NHS Wales Shared Services Partnership; Swansea University; Population Data Science and Health Data Research UK, Swansea University; Population Data Science and Health Data Research UK, Swansea University","BackgroundMedication prescribing and dispensing often regarded as one of the most effective ways to manage and improve population health. Prescribed and dispensed medications can be monitored through data linkage for each patient. We hypothesised that changes in patient care resulting from COVID-19, changed the way patients access their prescribed medication. - -ObjectiveTo develop an efficient approach for evaluation of the impact of COVID-19 on drug dispensing patterns. - -MethodsRetrospective observational study using national patient-level dispensing records in Wales-UK. Total dispensed drug items between 01-Jan-2016 and 31-Dec-2019 (counterfactual pre-COVID-19) were compared to 2020 (COVID-19 year). We compared trends of dispensed items in three main British National Formulary (BNF) sections(Cardiovascular system, Central Nervous System, Immunological & Vaccine) using European Age-Standardized rates. We developed an online tool to enable monitoring of changes in dispensing as the pandemic evolves. - -ResultAmongst all BNF chapters, 52,357,639 items were dispensed in 2020 compared to 49,747,141 items in 2019 demonstrating a relative increase of 5.25% in 2020(95%CI[5.21,5.29]). Comparison of monthly patterns of 2020 and 2019 dispensed items showed a notable difference between the total number of dispensed drug items each month, with an average difference (D) of +290,055 and average Relative Change (RC) of +5.52%. The greatest RC was observed in a substantial March-2020 increase (D=+1,501,242 and RC=+28%), followed by second peak in June (D=+565,004, RC=+10.97%). May was characterised by lower dispensing (D=-399,244, RC=-5.9%). Cardiovascular categories were characterised, across all age groups, by dramatic March-2020 increases, at the epidemic peak, followed by months of lower than expected dispensing, and gradual recovery by September. The Central Nervous System category was similar, but with only a short decline in May, and quicker recovery. A stand-out grouping was Immunological and Vaccine, which dropped to very low levels across all age groups, and all months (including the March dispensing peak). - -ConclusionsAberration in clinical service delivery during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes",health systems and quality improvement,fuzzy,100,100 medRxiv,10.1101/2021.02.17.21251812,2021-02-19,https://medrxiv.org/cgi/content/short/2021.02.17.21251812,Changes in the rate of cardiometabolic and pulmonary events during the COVID-19 pandemic,Alex J Walker; John Tazare; George Hickman; Christopher T Rentsch; Elizabeth J Williamson; Krishnan Bhaskaran; David Evans; Kevin Wing; Rohini Mathur; Angel YS Wong; Anna Schultze; Sebastian CJ Bacon; Christopher Bates; Caroline E Morton; Helen J Curtis; Emily Nightingale; Helen I McDonald; Amir Mehrkar; Peter Inglesby; Brian MacKenna; Jonathan Cockburn; William J Hulme; Harriet Forbes; Caroline Minassian; Richard Croker; John Parry; Frank Hester; Sam Harper; Rosalind M Eggo; Stephen JW Evans; Liam Smeeth; Ian J Douglas; Laurie Tomlinson; Ben Goldacre,University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundThere has been extensive speculation about the relationship between COVID-19 and various cardiometabolic and pulmonary conditions. This a complex question: COVID-19 may cause a cardiometabolic or respiratory event; admission for a clinical event may result in hospital-acquired SARS-CoV-2 infection; both may contribute to a patient surpassing the threshold for presenting to services; and the presence of a pandemic may change whether patients present to services at all. To inform analysis of these questions, we set out to describe the overall rate of various key clinical events over time, and their relationship with COVID-19. MethodsWorking on behalf of NHS England, we used data from the OpenSAFELY platform containing data from approximately 40% of the population of England. We selected the whole adult population of 17m patients and within this identified two further mutually exclusive groups: patients who tested positive for SARS-CoV-2 in the community; and patients hospitalised with COVID-19. We report counts of death, DVT, PE, ischaemic stroke, MI, heart failure, AKI and diabetic ketoacidosis in each month between February 2019 and October 2020 within each of: the general population, community SARS-CoV-2 cases, and hospitalised patients with COVID-19. Outcome events were defined using hospitalisations, GP records and cause of death data. @@ -3812,30 +3848,6 @@ In December, we observed a large rise in the number of absences per school in se medRxiv,10.1101/2021.02.10.21251480,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.10.21251480,Symptom reporting in over 1 million people: community detection of COVID-19,Joshua Elliott; Matthew Whitaker; Barbara Bodinier; Steven Riley; Helen Ward; Graham Cooke; Ara Darzi; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London,,infectious diseases,fuzzy,96,100 medRxiv,10.1101/2021.02.11.21251587,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.11.21251587,Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study,Trystan Leng; Edward M Hill; Robin N Thompson; Michael J Tildesley; Matt J Keeling; Louise J Dyson,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,,infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.11.21249258,2021-02-11,https://medrxiv.org/cgi/content/short/2021.02.11.21249258,"Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): preliminary results of a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Natalie Staplin; Enti Spata; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Christopher E Brightling; Rahuldeb Sarkar; Koshy Thomas; Vandana Jeebun; Abdul Ashish; Redmond Tully; David Chadwick; Muhammad Sharafat; Richard Stewart; Banu Rudran; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Furst; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Medway Foundation NHS Trust, Gillingham, United Kingdom; King?s College London, London, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Royal Oldham Hospital, Northern Care Alliance, Oldham, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Luton & Dunstable University Hospital, Luton, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","Findings: Between 23 April 2020 and 25 January 2021, 4116 adults were included in the assessment of tocilizumab, including 562 (14%) patients receiving invasive mechanical ventilation, 1686 (41%) receiving non-invasive respiratory support, and. 1868 (45%) receiving no respiratory support other than oxygen. Median CRP was 143 [IQR 107-205] mg/L and 3385 (82%) patients were receiving systemic corticosteroids at randomisation. Overall, 596 (29%) of the 2022 patients allocated tocilizumab and 694 (33%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0.86; 95% confidence interval [CI] 0.77-0.96; p=0.007). Consistent results were seen in all pre-specified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital alive within 28 days (54% vs. 47%; rate ratio 1.23; 95% CI 1.12-1.34; p<0.0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (33% vs. 38%; risk ratio 0.85; 95% CI 0.78-0.93; p=0.0005). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes regardless of the level of respiratory support received and in addition to the use of systemic corticosteroids.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.02.08.21250525,2021-02-09,https://medrxiv.org/cgi/content/short/2021.02.08.21250525,"COVID-19 infection and outcomes in a population-based cohort of 17,173 adults with intellectual disabilities compared with the general population",Angela Henderson; Micheal Fleming; Sally-Ann Cooper; Jill Pell; Craig Melville; Daniel MacKay; Christopher Hatton; Deborah Kinnear,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Manchester Metropolitan University; University of Glasgow,"ObjectivesTo compare COVID-19 infection, severe infection, mortality, case-fatality, and excess deaths, among adults with intellectual disabilities and those without. - -DesignRecord-linkage of all adults recorded with intellectual disabilities in Scotlands Census, 2011, and a 5% sample of other adults, to COVID-19 test results (Electronic Communication of Surveillance in Scotland), hospitalisations (Scottish Morbidity Record 01), and deaths (National Records of Scotland). - -SettingGeneral population; 24th January 2020 - 15th August 2020 - -ParticipantsSuccessful linkage of 94.8% provided data on 17,173 adults with, and 195,859 without, intellectual disabilities. - -OutcomesCrude rates of COVID-19 infection, severe infection (hospitalisation/death), mortality, and case fatality; age-, sex- and deprivation-standardised severe infection and mortality ratios; annual all-cause mortality for 2020 and 2015-2019. - -ResultsAdults with intellectual disabilities had higher rates of COVID-19 infection (957/100,000 versus 513/100,000); severe infection (549/100,000 versus 237/100,000); mortality (259/100,000 versus 114/100,000); and case-fatality (30% versus 24%). Poorer COVID-19 outcomes remained after standardising for age, sex and deprivation: standardised severe infection ratio 2.59 (95% CI 1.80, 3.39) and mortality ratio 3.20 (95% CI 2.16, 4.25). These were higher among 55-64 year olds: 7.12 (95% CI 3.73, 10.50) and 16.16 (95% CI7.69, 24.63) respectively. Among adults with intellectual disabilities, all-cause mortality was only slightly higher in 2020 than the previous five years: standardised mortality ratios 2.49 (95% CI 2.17, 2.81) and 2.38 (95% CI 2.26, 2.49) respectively. - -ConclusionsAdults with intellectual disabilities were more likely to be infected with COVID-19, and had worse outcomes once infected, particularly those under 65 years. Non-pharmaceutical interventions directed at formal and informal carers are essential to reduce transmission and all adults with intellectual disabilities should be immediately prioritised for vaccination regardless of age. - -Summary boxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICOVID-19 mortality is higher within multi-occupancy residences. -C_LIO_LIAdults with intellectual disabilities may be at higher risk of COVID-19 mortality than other adults, but there are gaps in the evidence. -C_LIO_LICOVID-19 case-fatality may be no different, or as much as 2.75 times higher in adults with intellectual disabilities compared with other adults. -C_LI - -What this study addsO_LICompared with general population adults, adults with intellectual disabilities were almost twice as likely to become infected with COVID-19, 2.3 times as likely to have severe infection, 2.3 times as likely to have COVID-19 mortality, and had 25% higher COVID-19 case-fatality. -C_LIO_LIAfter standardising for age, sex and deprivation, people with intellectual disabilities were 3.2 times more at risk of covid-19 mortality and 2.6 times more at risk of severe infection relative to those with no intellectual disabilities -C_LIO_LICompared with general population adults, adults with intellectual disabilities had poorer outcomes among non-elderly age-groups particularly those aged 55-65 years, men, and those living in less-deprived neighbourhoods. -C_LIO_LINon-pharmaceutical initiatives are important for carers and care-provider organisations, and adults with intellectual disabilities should be prioritised in the national rollouts of COVID-19 vaccination programmes, regardless of age, sex, or neighbourhood deprivation. -C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.02.04.21251155,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251155,Impact of school closures on the health and well-being of primary school children in Wales UK; a routine data linkage study using the HAPPEN survey (2018-2020).,Michaela James; Emily Marchant; Margaret A Defeyter; Jayne V Woodside; Sinead Brophy,Swansea University; Swansea University; Northumbria University; Queen's University Belfast; Swansea University,"IntroductionIn response to the COVID-19 pandemic, school closures were implemented across the United Kingdom. This study aimed to explore the impact of school closures on childrens health by comparing health and wellbeing outcomes collected during school closures (April - June 2020) with data from the same period in 2019 and 2018. MethodsData were collected online via the HAPPEN At Home survey, which captured the typical health behaviours of children aged 8 - 11 years between April - June 2020. These data were compared with data in 2018 and 2019 also collected between April-June, from HAPPEN. Free school meal (FSM) status was used as a proxy for socio-economic deprivation. Analyses were repeated stratifying by FSM. @@ -3878,6 +3890,13 @@ ResultsWave 2 patients were younger, more ethnically diverse, had less co-morbid ConclusionPrior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21251054,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251054,Age-related heterogeneity in Neutralising antibody responses to SARS-CoV-2 following BNT162b2 vaccination,Dami Collier; Isabella Ferreira; Rawlings Datir; Prasanti Kotagiri; Eleanor Lim; Bo Meng; - The CITIID-NIHR Bioresource COVID-19 Collaboration; Anne Elmer; Nathalie Kingston; Barbara Graves; Barbara Graves; Kenneth GC Smith; John Bradley; Paul Lyons; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; Michelle Linterman; Laura McCoy; Rainer Doffinger; Mark Wills; Ravindra K Gupta,UCL; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; -; Cambridge; NIHR; NIHR; Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Babraham Institute; UCL; University of Cambridge; University of Cambridge; University of Cambridge,"Two dose mRNA vaccination provides excellent protection against SARS-CoV-2. However, there are few data on vaccine efficacy in elderly individuals above the age of 801. Additionally, new variants of concern (VOC) with reduced sensitivity to neutralising antibodies have raised fears for vulnerable groups. Here we assessed humoral and cellular immune responses following vaccination with mRNA vaccine BNT162b22 in elderly participants prospectively recruited from the community and younger health care workers. Median age was 72 years and 51% were females amongst 140 participants. Neutralising antibody responses after the first vaccine dose diminished with increasing age, with a marked drop in participants over 80 years old. Sera from participants below and above 80 showed significantly lower neutralisation potency against B.1.1.7, B.1.351 and P.1. variants of concern as compared to wild type. Those over 80 were more likely to lack any neutralisation against VOC compared to younger participants following first dose. The adjusted odds ratio for inadequate neutralisation activity against the B.1.1.7, P.1 and B.1.351 variant in the older versus younger age group was 4.3 (95% CI 2.0-9.3, p<0.001), 6.7 (95% CI 1.7-26.3, p=0.008) and 1.7 (95% CI 0.5-5.7, p=0.41). Binding IgG and IgA antibodies were lower in the elderly, as was the frequency of SARS-CoV-2 Spike specific B-memory cells. We observed a trend towards lower somatic hypermutation in participants with suboptimal neutralisation, and elderly participants demonstrated clear reduction in class switched somatic hypermutation, driven by the IgA1/2 isotype. SARS-CoV-2 Spike specific T-cell IFN{gamma} and IL-2 responses fell with increasing age, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high risk population that warrant specific measures in order to mitigate against vaccine failure, particularly where variants of concern are circulating.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.02.02.21251043,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.02.21251043,COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort,Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell,University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow,"ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE). + +Patients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally. + +ResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test. + +ConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21251004,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251004,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England,Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. MethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. @@ -4003,19 +4022,6 @@ C_LIO_LIBasal temperature is heritable, suggesting biological factors underlying C_LIO_LIOur findings support a lower temperature threshold of 37.4{degrees}C for identifying possible COVID-19 infection in older adults C_LIO_LIThis has implications for case detection, surveillance and isolation and could be incorporated into observation assessment C_LI",geriatric medicine,fuzzy,94,100 -medRxiv,10.1101/2021.01.26.21249744,2021-01-27,https://medrxiv.org/cgi/content/short/2021.01.26.21249744,The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in a higher education sample,Daniel Leightley Dr; Valentina Vitiello Dr; Alice Wickersham Ms; Katrina A.S. Davis Dr; Gabriella Bergin-Cartwright Ms; Grace Lavelle Dr; Sharon A.M. Stevelink Dr; Matthew Hotopf Prof; Reza Razavi Prof,"Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.","ObjectiveTo assess the feasibility of home antibody testing as part of large-scale study, the Kings College London Coronavirus Health and Experiences of Colleagues at Kings (KCL CHECK). - -MethodsParticipants of the KCL CHECK study were sent a SureScreen Diagnostics COVID-19 IgG/IgM Rapid Test Cassette to complete at home in June 2020 (phase 1) and September 2020 (phase 2). Participants were asked to upload a test result image to a study website. Test result images and sociodemographic information were analysed by the research team. - -ResultsA total of n=2716 participants enrolled in the KCL CHECK study, with n=2003 (73.7%) and n=1825 (69.3%) consenting and responding to phase 1 and 2. Of these, n=1882 (93.9%; phase 1) and n=1675 (91.8%; phase 2) returned a valid result. n=123 (6.5%; phase 1) and n=91 (5.4%; phase 2) tested positive for SARS-CoV-2 antibodies. A total of n=1488 participants provided a result in both phases, with n=57 (3.8%) testing positive for SARS- CoV-2 antibodies across both phases, suggesting a reduction in the number of positive antibody results over time. Initial comparisons showed variation by age group, gender and clinical role. - -ConclusionsOur study highlights the feasibility of rapid, repeated and low-cost SARS-CoV-2 serological testing without the need for face-to-face contact. - -What is already known about this subject?Higher education institutions have a duty of care to minimise the spread and transmission of COVID-19 in its campuses, and among staff and students. The reopening of higher education buildings and campuses has brought about a mass movement of students, academics and support staff from across the UK. Serological antibody studies can assist by highlighting groups of people and behaviours associated with high risk of COVID-19. - -What are the new findings?We report a framework for SARS-CoV-2 serological antibody testing in an occupational group of postgraduate research students and current members of staff at Kings College London. Over two phases of data collection, 6.5% (phase 1) and 5.4% (phase 2) tested positive for SARS-CoV-2 antibodies, with only 3.8% testing positive for antibodies in both phases, suggesting a reduction in positive antibody results over time. - -How might this impact on policy or clinical practice in the foreseeable future?Our study highlights the feasibility of rapidly deploying low-cost and repeatable SARS-CoV-2 serological testing, without the need for face-to-face contact, to support the higher education system of the UK.",health policy,fuzzy,100,100 medRxiv,10.1101/2021.01.25.21250356,2021-01-26,https://medrxiv.org/cgi/content/short/2021.01.25.21250356,"Trends, regional variation, and clinical characteristics of COVID-19 vaccine recipients: a retrospective cohort study in 23.4 million patients using OpenSAFELY.",Helen J Curtis; Peter Inglesby; Caroline E Morton; Brian MacKenna; Alex J Walker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth J Williamson; William J Hulme; Amelia Green; Anna Rowan; Louis Fisher; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Ian J Douglas; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Aaron Fowles; Nasreen Parkes; Paul Griffiths; Stephen JW Evans; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS Group; EMIS Group; EMIS Group; EMIS Group; University of Oxford; EMIS Group; EMIS Group; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundOn December 8th 2020, NHS England administered the first COVID-19 vaccination as part of an ambitious vaccination programme during a global health emergency. AimsTo describe trends and variation in vaccine coverage by key clinical and demographic groups; to create a framework for near-real-time monitoring of vaccine coverage in key subgroups. @@ -4049,6 +4055,7 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measu Added value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification. Implications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.",public and global health,fuzzy,100,100 +bioRxiv,10.1101/2021.01.25.428136,2021-01-25,https://biorxiv.org/cgi/content/short/2021.01.25.428136,mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge,Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev,"University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston","The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.",immunology,fuzzy,96,94 medRxiv,10.1101/2021.01.21.20240887,2021-01-22,https://medrxiv.org/cgi/content/short/2021.01.21.20240887,"The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.",Danielle Lamb; Sam Gnanapragasam; Neil Greenberg; Rupa Bhundia; Ewan Carr; Matthew Hotopf; Reza Razavi; Rosalind Raine; Sean Cross; Amy Dewar; Mary Docherty; Sarah Dorrington; Stephani Hatch; Charlotte Wilson-Jones; Daniel Leightley; Ira Madan; Sally Marlow; Isabel McMullen; Anne Marie Rafferty; Martin Parsons; Catherine Polling; Danai Serfioti; Helen Gaunt; Peter Aitken; Joanna Morris-Bone; Chloe Simela; Veronica French; Rachel Harris; Sharon A.M. Stevelink; Simon Wessely,"Department of Applied Health Research, UCL, 1-19 Torrington Place, London, WC1E 7HB; South London and Maudsley NHS Foundation Trust, London, UK; Health Protection Research Unit, King's College London, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ; Department of Psychological Medicine, King's College London, London, UK.; Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute of Health Research Biomedical Research Centre at the South London and Maudsley NHS Foundation Trust.; 1 Lambeth Palace Rd, South Bank, London, SE1 7EU; Dept of Applied Health Research, UCL; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Guy's and St Thomas' NHS Foundation Trust; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Guy's and St Thomas' NHS Foundation Trust, London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Department of Psychological Medicine, King's College Hospital, South London and Maudsley NHS Foundation Trust; Adult Nursing, King's College London; Mental Health Liaison Team, King's College Hospital; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, King's College London, Room 307, Weston Education Centre, 10 Cutcombe Road, London SE5 9RJ; University Hospital of Leciester NHS Trust. Groby Road Leciester LE4 9QP; Devon Partnership NHS Trust, Trust HQ, R&D, Dryden Road, Exeter, Devon, EX2 5AF; Avon & Wiltshire Mental Health Partnership NHS Trust, R&D, Fromeside, Blackberry Hill Hospital, Bristol, BS16 1EG; Guy's and St Thomas' NHS Foundation Trust, London; Nottinghamshire Healthcare NHS Foundation Trust; Cornwall Partnership Foundation NHS Trust/ Research and Innovation Team; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Department of Psychological Medicine, King's College London, Weston Education, Denmark Hill, London, SE5 9JR","ObjectivesThis study reports preliminary findings on the prevalence of, and factors associated with, mental health and wellbeing outcomes of healthcare workers during the early months (April-June) of the COVID-19 pandemic in the UK. MethodsPreliminary cross-sectional data were analysed from a cohort study (n=4,378). Clinical and non-clinical staff of three London-based NHS Trusts (UK), including acute and mental health Trusts, took part in an online baseline survey. The primary outcome measure used is the presence of probable common mental disorders (CMDs), measured by the General Health Questionnaire (GHQ-12). Secondary outcomes are probable anxiety (GAD-7), depression (PHQ-9), Post-Traumatic Stress Disorder (PTSD) (PCL-6), suicidal ideation (CIS-R), and alcohol use (AUDIT). Moral injury is measured using the Moray Injury Event Scale (MIES). @@ -4398,6 +4405,7 @@ C_LIO_LIOptimal symptom combinations maximise case capture considering available C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20233932,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20233932,REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020. MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020. @@ -4412,6 +4420,13 @@ MethodsWe use a data-driven approach to parameterise an individual-based network ResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels. ConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.11.18.20225029,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20225029,The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic,Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden,University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen,"BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic. + +MethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed. + +FindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures. + +InterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20234369,2020-11-19,https://medrxiv.org/cgi/content/short/2020.11.18.20234369,Antibodies to SARS-CoV-2 are associated with protection against reinfection,Sheila F Lumley; Nicole E Stoesser; Philippa C Matthews; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Fiona Warren; Liam J Peck; Thomas G Ritter; Zoe de Toledo; Laura Warren; David Axten; Richard J Cornall; E Yvonne Jones; David I Stuart; Gavin Screaton; Daniel Ebner; Sarah Hoosdally; Meera Chand; - Oxford University Hospitals Staff Testing Group; Derrick W Crook; Christopher P Conlon; Koen B Pouwels; A Sarah Walker; Tim EA Peto; Susan Hopkins; Tim M Walker; Katie Jeffery; David W Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; ; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford,"BackgroundIt is critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection. MethodsWe investigated the incidence of SARS-CoV-2 PCR-positive results in seropositive and seronegative healthcare workers (HCWs) attending asymptomatic and symptomatic staff testing at Oxford University Hospitals, UK. Baseline antibody status was determined using anti-spike and/or anti-nucleocapsid IgG assays and staff followed for up to 30 weeks. We used Poisson regression to estimate the relative incidence of PCR-positive results and new symptomatic infection by antibody status, accounting for age, gender and changes in incidence over time. @@ -4895,6 +4910,15 @@ MethodsIn this analysis of the Bug Watch prospective community cohort study, we ResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020. ConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. + +MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. + +ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold. + +ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. + +RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186502,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186502,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection,Thibaut Jombart; Stephane Ghozzi; Dirk Schumacher; Quentin Leclerc; Mark Jit; Stefan Flasche; Felix Greaves; Tom Ward; Rosalind M Eggo; Emily Nightingale; Sophie Meakin; Oliver J Brady; - Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Graham Medley; Michael Hohle; John Edmunds,"London School of Hygiene and Tropical Medicine (LSHTM); Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany; R Epidemics Consortium; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; Joint Biosecurity Centre; Joint Biosecurity Centre; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; LSHTM; London School of Hygiene and Tropical Medicine; ; LSHTM; Department of Mathematics, Stockholm University, Sweden; LSHTM","As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186817,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186817,Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data,John Ojal; Samuel PC Brand; Vincent Were; Emelda A Okiro; Ivy Kadzo Kombe; Caroline Mburu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Ifedayo M. O Adetifa; John Anthony Scott; Edward Otieno; Lynette I Ochola-Oyier; Charles Nyaigoti Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Edwine Barasa; Matt J Keeling; D James Nokes,"Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; KEMRI Wellcome Trust Research Programme; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK; KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK","Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.01.20183822,2020-09-02,https://medrxiv.org/cgi/content/short/2020.09.01.20183822,Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK,Luisa Enria; Naomi Waterlow; Nina Trivedy Rogers; Hannah Brindle; Sham Lal; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; UCL; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine (LSHTM),"BackgroundThe success of a governments COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK governments COVID-19 response, focusing on the relationship between trust and transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom. @@ -5142,15 +5166,6 @@ Results30-day mortality peaked for people admitted to critical care in early Apr ConclusionsThere has been a substantial mortality improvement in people admitted to critical care with COVID-19 in England, with markedly lower mortality in people admitted in mid-April and May compared to earlier in the pandemic. This trend remains after adjustment for patient demographics and comorbidities suggesting this improvement is not due to changing patient characteristics. Possible causes include the introduction of effective treatments as part of clinical trials and a falling critical care burden.",health systems and quality improvement,fuzzy,100,100 medRxiv,10.1101/2020.07.29.20164269,2020-07-30,https://medrxiv.org/cgi/content/short/2020.07.29.20164269,The potential health and economic impact of dexamethasone treatment for patients with COVID-19,RICARDO AGUAS; Adam Mahdi; RIMA SHRETTA; Peter Horby; Martin Landray; Lisa J White,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.07.29.20162701,2020-07-30,https://medrxiv.org/cgi/content/short/2020.07.29.20162701,Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England,Philippa M Wells; Katie M Doores; Simon Couvreur; Rocio Martin Martinez; Jeffrey Seow; Carl Graham; Sam Acors; Neophytos Kouphou; Stuart Neil; Richard Tedder; Pedro Matos; Kate Poulton; Maria Jose Lista; Ruth Dickenson; Helin Sertkaya; Thomas Maguire; Edward Scourfield; Ruth Bowyer; Deborah Hart; Aoife O'Byrne; Kathryn Steele; Oliver Hemmings; Carolina Rosadas; Myra McClure; Joan Capedevila-Pujol; Jonathan wolf; Sebastien Ourseilin; Matthew Brown; Michael Malim; Timothy Spector; Claire Steves,King's College London; King's College London; KCL; King's College London; KCL; KCL; KCL; KCL; KCL; Imperial; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; Imperial College London; Imperial College London; KCL; Zoe Global; Zoe Global; KCL; KCL; King's College London; King's College London,"BackgroundUnderstanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. - -MethodsWe undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. - -FindingsWe demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. - -InterpretationSeroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. - -FundingNIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC",epidemiology,fuzzy,92,100 medRxiv,10.1101/2020.07.26.20161570,2020-07-28,https://medrxiv.org/cgi/content/short/2020.07.26.20161570,"Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries",Vasilis Kontis; James E Bennett; Theo Rashid; Robbie M Parks; Jonathan Pearson-Stuttard; Michel Guillot; Perviz Asaria; Bin Zhou; Marco Battaglini; Gianni Corsetti; Martin McKee; Mariachiara Di Cesare; Colin D Mathers; Majid Ezzati,Imperial College London; Imperial College London; Imperial College London; Columbia University; Imperial College London; University of Pennsylvania; Imperial College London; Imperial College London; Italian National Institute of Statistics; Italian National Institute of Statistics; London School of Hygiene & Tropical Medicine; Middlesex University London; Independent Researcher; Imperial College London,"The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on. Taken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic. @@ -5487,21 +5502,6 @@ MethodsWe developed (i) an in vitro neutralization assay using a lentivirus expr Results45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests. ConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.06.15.20131722,2020-06-17,https://medrxiv.org/cgi/content/short/2020.06.15.20131722,"Delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults",Maria Beatrice Zazzara; Rose S. Penfold; Amy L. Roberts; Karla Lee; Hannah Dooley; Carole H. Sudre; Carly Welch; Ruth C. E. Bowyer; Alessia Visconti; Massimo Mangino; Maxim B. Freydin; Julia S. El-Sayed Moustafa; Kerrin Small; Benjamin Murray; Marc Modat; Jonathan Wolf; Sebastien Ourselin; Finbarr C. Martin; Claire J. Steves; Mary Ni Lochlainn,"Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Gerontology, Neuroscience and O; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Institute of Inflammation and Ageing, University of Birmingham, B15 2TT; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; NIHR Biomedical Research Centre at Guy's and ; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Population Health Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH","BackgroundFrailty, increased vulnerability to physiological stressors, is associated with adverse outcomes. COVID-19 exhibits a more severe disease course in older, co-morbid adults. Awareness of atypical presentations is critical to facilitate early identification. - -ObjectiveTo assess how frailty affects presenting COVID-19 symptoms in older adults. - -DesignObservational cohort study of hospitalised older patients and self-report data for community-based older adults. - -SettingAdmissions to St Thomas Hospital, London with laboratory-confirmed COVID-19. Community-based data for 535 older adults using the COVID Symptom Study mobile application. - -SubjectsHospital cohort: patients aged 65 and over (n=322); unscheduled hospital admission between March 1st, 2020-May 5th, 2020; COVID-19 confirmed by RT-PCR of nasopharyngeal swab. Community-based cohort: participants aged 65 and over enrolled in the COVID Symptom Study (n=535); reported test-positive for COVID-19 from March 24th (application launch)-May 8th, 2020. - -MethodsMultivariate logistic regression analysis performed on age-matched samples from hospital and community-based cohorts to ascertain association of frailty with symptoms of confirmed COVID-19. - -ResultsHospital cohort: significantly higher prevalence of delirium in the frail sample, with no difference in fever or cough. Community-based cohort :significantly higher prevalence of probable delirium in frailer, older adults, and fatigue and shortness of breath. - -ConclusionsThis is the first study demonstrating higher prevalence of delirium as a COVID-19 symptom in older adults with frailty compared to other older adults. This emphasises need for systematic frailty assessment and screening for delirium in acutely ill older patients in hospital and community settings. Clinicians should suspect COVID-19 in frail adults with delirium.",geriatric medicine,fuzzy,94,100 medRxiv,10.1101/2020.06.13.20130419,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.13.20130419,Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020,Robert Stewart; Evangelia Martin; Matthew Broadbent,King's College London; King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.06.12.20129056,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.12.20129056,Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app,Carole H Sudre; Karla Lee; Mary Ni Lochlainn; Thomas Varsavsky; Benjamin Murray; Mark S. Graham; Cristina Menni; Marc Modat; Ruth C.E. Bowyer; Long H Nguyen; David Alden Drew; Amit D Joshi; Wenjie Ma; Chuan Guo Guo; Chun Han Lo; Sajaysurya Ganesh; Abubakar Buwe; Joan Capdevila Pujol; Julien Lavigne du Cadet; Alessia Visconti; Maxim Freydin; Julia S. El Sayed Moustafa; Mario Falchi; Richard Davies; Maria F. Gomez; Tove Fall; M. Jorge Cardoso; Jonathan Wolf; Paul W Franks; Andrew T Chan; Timothy D Spector; Claire J Steves; Sebastien Ourselin,King's College London; Department of Twin Research and Genetic Epidemiology; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Lund University; Lund University; King's College London; Zoe Global Limited; Lund University; Massachusetts General Hospital; King's College London; King's College London; King's College London,"As no one symptom can predict disease severity or the need for dedicated medical support in COVID-19, we asked if documenting symptom time series over the first few days informs outcome. Unsupervised time series clustering over symptom presentation was performed on data collected from a training dataset of completed cases enlisted early from the COVID Symptom Study Smartphone application, yielding six distinct symptom presentations. Clustering was validated on an independent replication dataset between May 1-May 28th, 2020. Using the first 5 days of symptom logging, the ROC-AUC of need for respiratory support was 78.8%, substantially outperforming personal characteristics alone (ROC-AUC 69.5%). Such an approach could be used to monitor at-risk patients and predict medical resource requirements days before they are required. @@ -5539,6 +5539,15 @@ C_LI What do these findings mean?O_LIIndividuals with [≥]2 LTCs, especially if these are cardiometabolic in nature, should be particularly stringent in adhering to preventive measures, such as physical distancing and hand hygiene. C_LIO_LIOur findings have implications for clinicians, occupational health and employers when considering work-place environments, appropriate advice for patients, and adaptations that might be required to protect such staff, identified here, as higher risk. C_LI",epidemiology,fuzzy,100,91 +medRxiv,10.1101/2020.06.10.20127175,2020-06-11,https://medrxiv.org/cgi/content/short/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway,"University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL","BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both ""direct"", through infection, and ""indirect"", through changes in healthcare. + +MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(""direct"" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For ""indirect"" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. + +FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. + +InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. + +FundingNIHR, HDR UK, Astra Zeneca",cardiovascular medicine,fuzzy,100,100 bioRxiv,10.1101/2020.06.11.145920,2020-06-11,https://biorxiv.org/cgi/content/short/2020.06.11.145920,SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness,Kizzmekia S. Corbett; Darin Edwards; Sarah R. Leist; Olubukola M. Abiona; Seyhan Boyoglu-Barnum; Rebecca A. Gillespie; Sunny Himansu; Alexandra Schafer; Cynthia T. Ziwawo; Anthony T. DiPiazza; Kenneth H. Dinnon; Sayda M. Elbashir; Christine A. Shaw; Angela Woods; Ethan J. Fritch; David R. Martinez; Kevin W. Bock; Mahnaz Minai; Bianca M. Nagata; Geoffrey B. Hutchinson; Kapil Bahl; Dario Garcia-Dominguez; LingZhi Ma; Isabella Renzi; Wing-Pui Kong; Stephen D. Schmidt; Lingshu Wang; Yi Zhang; Laura J. Stevens; Emily Phung; Lauren A. Chang; Rebecca J. Loomis; Nedim Emil Altaras; Elisabeth Narayanan; Mihir Metkar; Vlad Presnyak; Catherine Liu; Mark K. Louder; Wei Shi; Kwanyee Leung; Eun Sung Yang; Ande West; Kendra L. Gully; Nianshuang Wang; Daniel Wrapp; Nicole A. Doria-Rose; Guillaume Stewart-Jones; Hamilton Bennett; Martha C. Nason; Tracy J. Ruckwardt; Jason S. McLellan; Mark R. Denison; James D. Chappell; Ian N. Moore; Kaitlyn M. Morabito; John R. Mascola; Ralph S. Baric; Andrea Carfi; Barney S Graham,"Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Department of Epidemiology; University of North Carolina at Chapel Hill; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Department of Epidemiology; University of North Carolina at Chapel Hill; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill; Department of Epidemiology; University of North Carolina at Chapel Hill; National Institute of Allergy and Infectious Diseases; National Institutes of Health; National Institute of Allergy and Infectious Diseases; National Institutes of Health; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Pediatrics, Vanderbilt University Medical Center; Institute for Biomedical Sciences, George Washington University; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Molecular Biosciences; University of Texas at Austin; Department of Molecular Biosciences; University of Texas at Austin; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Molecular Biosciences; University of Texas at Austin; Department of Pediatrics, Vanderbilt University Medical Center; Department of Pediatrics, Vanderbilt University Medical Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Microbiology and Immunology, School of Medicine, University of North Caro; Moderna, Inc.; Vaccine Research Center, NIAID, NIH","A SARS-CoV-2 vaccine is needed to control the global COVID-19 public health crisis. Atomic-level structures directed the application of prefusion-stabilizing mutations that improved expression and immunogenicity of betacoronavirus spike proteins. Using this established immunogen design, the release of SARS-CoV-2 sequences triggered immediate rapid manufacturing of an mRNA vaccine expressing the prefusion-stabilized SARS-CoV-2 spike trimer (mRNA-1273). Here, we show that mRNA-1273 induces both potent neutralizing antibody and CD8 T cell responses and protects against SARS-CoV-2 infection in lungs and noses of mice without evidence of immunopathology. mRNA-1273 is currently in a Phase 2 clinical trial with a trajectory towards Phase 3 efficacy evaluation.",immunology,fuzzy,96,94 medRxiv,10.1101/2020.06.08.20120584,2020-06-09,https://medrxiv.org/cgi/content/short/2020.06.08.20120584,SARS-CoV-2 virus and antibodies in front-line Health Care Workers in an acute hospital in London: preliminary results from a longitudinal study,Catherine Houlihan; Nina Vora; Thomas Byrne; Dan Lewer; Judith Heaney; David A Moore; Rebecca Matthews; Sajida Adam; Louise Enfield; Abigail Severn; Angela McBride; Moira Jane Spyer; Rupert Beale; Peter Cherepanov; Kathleen Gaertner; Maryam Shahmanesh; - The SAFER Field Study Team; Kevin Ng; Georgina Cornish; Naomi Walker; Susan Michie; Ed Manley; Fabiana Lorencatto; - The Crick-COVID-Consortium; Richard Gilson; Sonia Gandhi; Steve Gamblin; George Kassiotis; Laura McCoy; Charles Swanton; Andrew Hayward; Eleni Nastouli,University College London Hospital; UCL; UCL; University College London; UCL; Francis Crick Institute; UCL; UCL; UCL; UCL; UCL; UCL; Francis Crick Institute; Francis Crick Institute; UCL; UCL; ; Francis Crick Institute; Francis Crick Institute; UCL; UCL; Leeds University; UCL; ; UCL; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; UCL; Francis Crick Institute; UCL; University College London,"BackgroundAlthough SARS-CoV-2 infection in Healthcare Workers (HCWs) is a public health concern, there is little description of their longitudinal antibody response in the presence or absence of SARS-CoV-2 and symptoms. We followed HCWs in an acute London hospital to measure seroconversion and RNA detection at the peak of the pandemic. @@ -5773,6 +5782,9 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe interaction bet Added value of this studyData from a large UK population who are users of a symptom reporting app during the pandemic supports the hypothesis that smokers are more likely to develop symptoms consistent with COVID-19 and that they have an increased symptom burden. Implications of all the available evidenceThese population data, combined with evidence of a worse outcome in smokers hospitalised with the condition, support the contention that smoking increases individual risk from COVID-19. Support to help people to quit smoking should therefore form part of efforts to deal with the pandemic.",respiratory medicine,fuzzy,94,100 +medRxiv,10.1101/2020.05.14.20101824,2020-05-19,https://medrxiv.org/cgi/content/short/2020.05.14.20101824,Changing travel patterns in China during the early stages of the COVID-19 pandemic,Hamish Gibbs; Yang Liu; Carl AB Pearson; Christopher I Jarvis; Chris Grundy; Billy J Quilty; Charlie Diamond; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study. + +One sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.11.20098269,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.11.20098269,Accessibility and allocation of public parks and gardens during COVID-19 social distancing in England and Wales,Niloofar Shoari; Majid Ezzati; Jill Baumgartner; Diego Malacarne; Daniela Fecht,Imperial College London; Imperial College London; McGill University; Imperial College London; Imperial College London,"Visiting parks and gardens may attenuate the adverse physical and mental health impacts of social distancing implemented to reduce the spread of COVID-19. We quantified access to public parks and gardens in urban areas of England and Wales, and the potential for park crowdedness during periods of high use. We combined data from the Office for National Statistics and Ordnance Survey to quantify (i) the number of parks within 500 and 1,000 metres of urban postcodes (i.e., availability), (ii) the distance of postcodes to the nearest park (i.e., accessibility), and (iii) per-capita space in each park for people living within 1,000m. We examined how these measures vary by city and share of homes that are flats. Around 25.4 million people can access public parks or gardens within a ten-minute walk, while 3.8 million residents live farther away; of these 21% are children and 13% are elderly. Areas with a higher share of flats on average are closer to a park but people living in these areas are potentially less able to meet social distancing requirements while in parks during periods of high use. Cities in England and Wales can provide residents with access to green space that enables outdoor exercise and play during social distancing. Cities aiming to facilitate social distancing while keeping public green spaces open might require implementing measures such as dedicated park times for different age groups or entry allocation systems that, combined with smartphone apps or drones, can monitor and manage the total number of people using the park.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.12.20098921,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.12.20098921,Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.,Nina Trivedy Rogers; Naomi Waterlow; Hannah E Brindle; Luisa Enria; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,University College London (UCL); London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Bath; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"ImportanceThere are growing concerns that the UK COVID-19 lockdown has reduced opportunities to maintain health through physical activity, placing individuals at higher risk of chronic disease and leaving them more vulnerable to severe sequelae of COVID-19. @@ -5905,17 +5917,7 @@ MethodsWe present a deterministic, age-structured transmission model that uses r FindingsWe find that significant relaxation of social distancing measures from 7th May onwards can lead to a rapid resurgence of COVID-19 disease and the health system being quickly overwhelmed by a sizeable, second epidemic wave. In all considered age-shielding based strategies, we projected serious demand on critical care resources during the course of the pandemic. The reintroduction and release of strict measures on a regional basis, based on ICU bed occupancy, results in a long epidemic tail, until the second half of 2021, but ensures that the health service is protected by reintroducing social distancing measures for all individuals in a region when required. DiscussionOur work confirms the effectiveness of stringent non-pharmaceutical measures in March 2020 to suppress the epidemic. It also provides strong evidence to support the need for a cautious, measured approach to relaxation of lockdown measures, to protect the most vulnerable members of society and support the health service through subduing demand on hospital beds, in particular bed occupancy in intensive care units.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.05.07.20094557,2020-05-11,https://medrxiv.org/cgi/content/short/2020.05.07.20094557,"Early impact of the COVID-19 pandemic and social distancing measures on routine childhood vaccinations in England, January to April 2020",Helen I McDonald; Elise Tessier; Joanne M White; Matthew Woodruff; Charlotte Knowles; Chris Bates; John Parry; Jemma L Walker; J Anthony Scott; Liam Smeeth; Joanne Yarwood; Mary Ramsay; Michael Edelstein,London School of Medicine and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation; Public Health England; Public Health England; TPP (Leeds) Ltd; TPP (Leeds) Ltd; TPP (Leeds) Ltd; TPP (Leeds) Ltd; London School of Hygiene and Tropical Medicine; Public Health England; NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation; Public Health England; Public Health England; NIHR Health Protection Research Unit (HPRU) in Immunisation; Public Health England,"Electronic health records were used to assess the early impact of COVID-19 on routine childhood vaccination in England to 26 April 2020. - -MMR vaccination counts fell from February 2020, and in the three weeks after introduction of social distancing measures were 19.8% lower (95% CI -20.7 to -18.9%) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated on introduction of social distancing.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.08.20078386,2020-05-11,https://medrxiv.org/cgi/content/short/2020.05.08.20078386,"Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland",Benjamin Parcell; Kathryn Brechin; Sarah Allstaff; Meg Park; Wendy Third; Susan Bean; Chris Hind; Rajiv Farmer; James D Chalmers,NHS Tayside; NHS Tayside; NHS Tayside; NHS Tayside; NHS Tayside; NHS Tayside; NHS Tayside; NHS Tayside; University of Dundee,"It has been recognised that health and social care workers (HSCW) experience higher rates of infection with SARS-CoV-2. Widespread testing of HSCWs and their symptomatic household contacts (SHCs) has not been fully implemented in the United Kingdom. We describe the results of a testing programme for HSCWs and SHCs in a single UK region (Tayside, Scotland). The testing service was established 17 th March 2020 as the first in the country, and samples were collected at a drive-through testing hub based at a local community hospital. HSCWs with mild symptoms who were self-isolating and the SHCs of HSCWs who would therefore be absent from work attended for testing. From 17 th March 2020 to 11 th April, 1887 HSCWs and SHCs underwent testing. Clinical information was available for 1727 HSCWs and SHCs. 4/155 (2.6%) child contacts, 73/374 (19.5%) adult contacts and 325/1173 (27.7%) HSCWs tested positive for SARS-CoV-2. 15 of 188 undetermined cases were positive (8.0%). We estimate that testing prevented up to 3634 lost work days from HSCW testing, 2795 from adult SHC testing and 1402 lost work days from child SHC testing. The establishment of this testing programme has assisted the infection prevention and control team in their investigation of transmission and supported adequate staffing in health and social care sectors.",infectious diseases,fuzzy,95,100 -medRxiv,10.1101/2020.05.05.20092296,2020-05-09,https://medrxiv.org/cgi/content/short/2020.05.05.20092296,Ethnicity and risk of death in patients hospitalised for COVID-19 infection: an observational cohort study in an urban catchment area,Elizabeth Sapey; Suzy Gallier; Chris Mainey; Peter Nightingale; David McNulty; Hannah Crothers; Felicity Evison; Katharine Reeves; Domenico Pagano; Alastair K Denniston; Krishnarajah Nirantharakumar; Peter Diggle; Simon Ball,University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS FoundationTrust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Lancaster; University Hospitals Birmingham NHS Foundation Trust,"BackgroundStudies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients. - -MethodsPatients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10th March 2020-17th April 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching. - -ResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2-1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)). - -ConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.05.06.20092734,2020-05-08,https://medrxiv.org/cgi/content/short/2020.05.06.20092734,The impact of Coronavirus disease 2019 (COVID-19) on health systems and household resources in Africa and South Asia,Nicholas G Davies; Sedona Sweeney; Sergio Torres-Rueda; Fiammetta Bozzani; Nichola Kitson; Edwine Barasa; Simon Procter; Matthew Quaife; - LSHTM Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Rosalind M Eggo; Anna Vassall; Mark Jit,London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; -; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundCoronavirus disease 2019 (COVID-19) epidemics strain health systems and households. Health systems in Africa and South Asia may be particularly at risk due to potential high prevalence of risk factors for severe disease, large household sizes and limited healthcare capacity. MethodsWe investigated the impact of an unmitigated COVID-19 epidemic on health system resources and costs, and household costs, in Karachi, Delhi, Nairobi, Addis Ababa and Johannesburg. We adapted a dynamic model of SARS-CoV-2 transmission and disease to capture country-specific demography and contact patterns. The epidemiological model was then integrated into an economic framework that captured city-specific health systems and household resource use. @@ -6181,26 +6183,6 @@ One Sentence SummaryCOVID-19 symptom tracker for smartphones",epidemiology,fuzzy medRxiv,10.1101/2020.04.02.20051284,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051284,Building an International Consortium for Tracking Coronavirus Health Status,Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective),"Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ","Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease. In the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.04.01.20049908,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.01.20049908,"The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study",Nicholas G Davies; Adam J Kucharski; Rosalind M Eggo; Amy Gimma; - CMMID COVID-19 Working Group; W. John Edmunds,London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; -; London School of Hygiene & Tropical Medicine,"BackgroundNon-pharmaceutical interventions have been implemented to reduce transmission of SARS-CoV-2 in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been critical to support evidence-based policymaking during the early stages of the epidemic. - -MethodsWe used a stochastic age-structured transmission model to explore a range of intervention scenarios, including the introduction of school closures, social distancing, shielding of elderly groups, self-isolation of symptomatic cases, and extreme ""lockdown""-type restrictions. We simulated different durations of interventions and triggers for introduction, as well as combinations of interventions. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (intensive care unit, ICU) treatment, and deaths. - -FindingsWe found that mitigation measures aimed at reducing transmission would likely have decreased the reproduction number, but not sufficiently to prevent ICU demand from exceeding NHS availability. To keep ICU bed demand below capacity in the model, more extreme restrictions were necessary. In a scenario where ""lockdown""-type interventions were put in place to reduce transmission, these interventions would need to be in place for a large proportion of the coming year in order to prevent healthcare demand exceeding availability. - -InterpretationThe characteristics of SARS-CoV-2 mean that extreme measures are likely required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs. - -Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSAs countries have moved from early containment efforts to planning for the introduction of large-scale non-pharmaceutical interventions to control COVID-19 outbreaks, epidemic modelling studies have explored the potential for extensive social distancing measures to curb transmission. However, it remains unclear how different combinations of interventions, timings, and triggers for the introduction and lifting of control measures may affect the impact of the epidemic on health services, and what the range of uncertainty associated with these estimates would be. - -Added value of this studyUsing a stochastic, age-structured epidemic model, we explored how eight different intervention scenarios could influence the number of new cases and deaths, as well as intensive care beds required over the projected course of the epidemic. We also assessed the potential impact of local versus national targeting of interventions, reduction in leisure events, impact of increased childcare by grandparents, and timing of triggers for different control measures. We simulated multiple realisations for each scenario to reflect uncertainty in possible epidemic trajectories. - -Implications of all the available evidenceOur results support early modelling findings, and subsequent empirical observations, that in the absence of control measures, a COVID-19 epidemic could quickly overwhelm a healthcare system. We found that even a combination of moderate interventions - such as school closures, shielding of older groups and self-isolation - would be unlikely to prevent an epidemic that would far exceed available ICU capacity in the UK. Intermittent periods of more intensive lockdown-type measures are predicted to be effective for preventing the healthcare system from being overwhelmed.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.04.01.20047357,2020-04-04,https://medrxiv.org/cgi/content/short/2020.04.01.20047357,Detecting SARS-CoV-2 at point of care: Preliminary data comparing Loop-mediated isothermal amplification (LAMP) to PCR,Marc F Osterdahl; Karla A Lee; Mary Ni Lochlainn; Stuart Wilson; Sam Douthwaite; Rachel Horsfall; Alyce Sheedy; Simon D Goldenberg; Christoper J Stanley; Tim D Spector; Claire Steves,"Department of Ageing & Health, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; MicrosensDx Ltd, 2 Royal College Street, London, UK; Department of Infection, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Infection, Guys and St Thomas NHS Foundation Trust, London, UK; MicrosensDx Ltd, 2 Royal College Street, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK","BackgroundThe need for a fast and reliable test for COVID-19 is paramount in managing the current pandemic. A cost effective and efficient diagnostic tool as near to the point of care (PoC) as possible would be a game changer in current testing. We tested reverse transcription loop mediated isothermal amplification (RT-LAMP), a method which can produce results in under 30 minutes, alongside standard methods in a real-life clinical setting. - -MethodsThis service improvement project piloted a research RT-LAMP method on nasal and pharyngeal swabs on 21 residents in a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We calculated the sensitivity, specificity, positive and negative predictive values of a single RT-LAMP swab compared to RT-PCR, as per STARD guidelines. We also recorded vital signs of patients to correlate clinical and laboratory information. - -FindingsThe novel method accurately detected 8/10 PCR positive cases and identified a further 3 positive cases. Eight further cases were negative using both methods. Using repeated RT-PCR as a ""gold standard"", the sensitivity and specificity of the novel test were 80% and 73% respectively. Positive predictive value (PPV) was 73% and negative predictive value (NPV) was 83%. We also observed hypothermia to be a significant early clinical sign in a number of COVID-19 patients in this setting. - -InterpretationRT-LAMP testing for SARS-CoV-2 was found to be promising, fast, easy to use and to work equivalently to RT-PCR methods. Definitive studies to evaluate this method in larger cohorts are underway. RT-LAMP has the potential to transform COVID-19 detection, bringing rapid and accurate testing to the point of care. This method could be deployed in mobile testing units in the community, care homes and hospitals to detect disease early and prevent spread.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.03.27.20044925,2020-03-30,https://medrxiv.org/cgi/content/short/2020.03.27.20044925,A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage,Xianding Deng; Wei Gu; Scot Federman; Louis Du Plessis; Oliver Pybus; Nuno Faria; Candace Wang; Guixia Yu; Chao-Yang Pan; Hugo Guevara; Alicia Sotomayor-Gonzalez; Kelsey Zorn; Allan Gopez; Venice Servellita; Elaine Hsu; Steve Miller; Trevor Bedford; Alexander Greninger; Pavitra Roychoudhury; Michael Famulare; Helen Y Chu; Jay Shendure; Lea Starita; Catie Anderson; Karthik Gangavarapu; Mark Zeller; Emily Spencer; Kristian Andersen; Duncan MacCannell; Suxiang Tong; Gregory Armstrong; Clinton Paden; Yan Li; Ying Zhang; Scott Morrow; Matthew Willis; Bela Matyas; Sundari Mase; Olivia Kasirye; Maggie Park; Curtis Chan; Alexander Yu; Shua Chai; Elsa Villarino; Brandon Bonin; Debra Wadford; Charles Y Chiu,"University of Californa, San Francisco; University of California, San Francisco; University of California, San Francisco; Oxford University; University of Oxford; Oxford University; University of California, San Francisco; University of California, San Francisco; California Department of Public Health; California Department of Public Health; University of California, San Francisco; University of California, San Francisco; University of California, San Francisco; University of California, San Francisco; University of California, San Francisco; University of California, San Francisco; Fred Hutchinson Cancer Research Center; University of Washington; Fred Hutchinson Cancer Research Center; Institute for Disease Modeling; University of Washington; University of Washington; University of Washington; Scripps Institute; Scripps Institute; Scripps Institute; Scripps Institute; Scripps Institute; United States Centers for Disease Control and Prevention; United States Centers for Disease Control and Prevention; United States Centers for Disease Control and Prevention; United States Centers for Disease Control and Prevention; United States Centers for Disease Control and Prevention; United States Centers for Disease Control and Prevention; San Mateo County Department of Public Health; Marin County Division of Public Health; Solano County Department of Public Health; Sonoma County Department of Public Health; Sacramento County Division of Public Health; San Joaquin County Department of Public Health; San Francisco Department of Public Health; California Department of Public Health; California Department of Public Health; Santa Clara County Department of Public Health; Santa Clara County Department of Public Health; California Department of Public Health; University of California, San Francisco","The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.",infectious diseases,fuzzy,92,100 medRxiv,10.1101/2020.03.30.20047217,2020-03-30,https://medrxiv.org/cgi/content/short/2020.03.30.20047217,"Physical interventions to interrupt or reduce the spread of respiratory viruses. Part 1 - Face masks, eye protection and person distancing: systematic review and meta-analysis",Tom Jefferson; Mark Jones; Lubna A Al Ansari; Ghada Bawazeer; Elaine Beller; Justin Clark; John Conly; Chris Del Mar; Elisabeth Dooley; Eliana Ferroni; Paul Glasziou; Tammy Hoffman; Sarah Thorning; Mieke Van Driel,"University of Oxford; Bond University, Australia; Kind Saud University, Saudi Arabia; King Saud, University, Saudi Arabia; Bond University, Australia; Bond University, Australia; Department of Medicine, Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary and Alberta Health Services , Calgary,; Bond University, Australia; Bond University, Australia; Regione Veneto, Italy; Bond University, Australia; Bond University, Australia; Bond University, Australia; Primary Care Clinical Unit, Faculty of Medicine, University of Queensland, Australia","OBJECTIVETo examine the effectiveness of eye protection, face masks, or person distancing on interrupting or reducing the spread of respiratory viruses. @@ -6275,3 +6257,12 @@ Added value of this studyThis study uses a mathematical model to assess the feas Implications of all the available evidenceContact tracing and isolation may not contain outbreaks of 2019-nCoV unless very high levels of contact tracing are achieved. Even in this case, if there is asymptomatic transmission, or a high fraction of transmission before onset of symptoms, this strategy may not achieve control within three months.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.01.31.20019265,2020-02-02,https://medrxiv.org/cgi/content/short/2020.01.31.20019265,Effectiveness of airport screening at detecting travellers infected with 2019-nCoV,Billy Quilty; Sam Clifford; Stefan Flasche; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"As the number of novel coronavirus cases grows both inside and outside of China, public health authorities require evidence on the effectiveness of control measures such as thermal screening of arrivals at airports. We evaluated the effectiveness of exit and entry screening for 2019-nCoV infection. In our baseline scenario, we estimated that 46.5% (95%CI: 35.9 to 57.7) of infected travellers would not be detected, depending on the incubation period, sensitivity of exit and entry screening, and the proportion of cases which are asymptomatic. Airport screening is unlikely to detect a sufficient proportion of 2019-nCoV infected travellers to avoid entry of infected travellers. We developed an online tool so that results can be updated as new information becomes available.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.01.31.20019901,2020-02-02,https://medrxiv.org/cgi/content/short/2020.01.31.20019901,Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study,Adam J Kucharski; Timothy W Russell; Charlie Diamond; Yang Liu; CMMID nCoV working group; John Edmunds; Sebastian Funk; Rosalind M Eggo,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas. + +MethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas. + +FindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population. + +InterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually. + +FundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)",infectious diseases,fuzzy,100,100 diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index 3115b487..fb41e802 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -91,26 +91,6 @@ FindingsSwabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for S InterpretationSymptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity. FundingUK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.",respiratory medicine,exact,100,100 -medRxiv,10.1101/2023.08.25.23294609,2023-08-25,https://medrxiv.org/cgi/content/short/2023.08.25.23294609,Risk factors for SARS-Cov-2 infection at a United Kingdom electricity-generating company: a test-negative design case-control study,Charlotte E Rutter; Martie J Van Tongeren; Tony Fletcher; Sarah E Rhodes; Yiqun Chen; Ian Hall; Nicholas Warren; Neil Pearce,London School of Hygiene and Tropical Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Health and Safety Executive; University of Manchester; Health and Safety Executive; London School of Hygiene and Tropical Medicine,"ObjectivesIdentify workplace risk factors for SARS-Cov-2 infection, using data collected by a United Kingdom electricity-generating company. - -MethodsUsing a test-negative design case-control study we estimated the odds ratios (OR) of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage, and site COVID-19 weekly risk rating, adjusting for age, test date and test type. - -ResultsFrom an original 80,077 COVID-19 tests, there were 70,646 included in the final analysis. Most exclusions were due to being visitor tests (5,030) or tests after an individual first tested positive (2,968). - -Women were less likely to test positive than men (OR=0.71; 95% confidence interval=0.58-0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area it was a strong confounder for other variables. Compared to routine tests, tests due to symptoms were highest risk (94.99; 78.29-115.24), followed by close contact (16.73; 13.80-20.29) and broader-defined work contact 2.66 (1.99-3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model. - -ConclusionsIn general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates. - -Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIIn the United Kingdom, there is now a considerable body of evidence showing occupational differences in Covid-19 infection and severity, but with understandable focus on high-risk industries like healthcare. -C_LIO_LILess is known about differences in risk of COVID-19 infection in other industries that do not involve directly working with the general public, in particular, there is relatively little evidence on the risks of transmission in the electricity-generating industry. -C_LI - -What this study addsO_LIAt this company, infection risk was not associated with job category after adjusting for test reason; however women were less likely to test positive than men and the risk was higher when there was a power outage, requiring more staff to visit the site in person. -C_LI - -How this study might affect research, practice or policyO_LIThe site risk rating showed a consistent (but modest) dose-response with infection risk, indicating that such risk rating may be useful for identifying ""high risk"" sites. -C_LIO_LIThis analysis demonstrates the importance of adjusting for both date of and reason for test, when prevalence and testing protocols differ over time. -C_LI",occupational and environmental health,exact,100,100 medRxiv,10.1101/2023.08.11.23293977,2023-08-15,https://medrxiv.org/cgi/content/short/2023.08.11.23293977,"Digital Mental Health Service engagement changes during Covid-19 in children and young people across the UK: presenting concerns, service activity, and access by gender, ethnicity, and deprivation",Duleeka Knipe; Santiago de Ossorno Garcia; Louisa Salhi; Lily Mainstone-Cotton; Aaron Sefi; Ann John,University of Bristol School of Social and Community Medicine: University of Bristol Population Health Sciences; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Kooth Digital Health; Swansea University,"The adoption of digital health technologies accelerated during Covid-19, with concerns over the equity of access due to digital exclusion. Using data from a text-based online mental health service for children and young people we explore the impact of the pandemic on service access and presenting concerns and whether differences were observed by sociodemographic characteristics in terms of access (gender, ethnicity and deprivation). We used interrupted time-series models to assess whether there was a change in the level and rate of service use during the Covid-19 pandemic (April 2020-April 2021) compared to pre-pandemic trends (June 2019-March 2020). Routinely collected data from 61221 service users were extracted for observation, those represented half of the service population as only those with consent to share their data were used. The majority of users identified as female (74%) and White (80%), with an age range between 13 and 20 years of age. There was evidence of a sudden increase (13%) in service access at the start of the pandemic (RR 1.13 95% CI 1.02, 1.25), followed by a reduced rate (from 25% to 21%) of engagement during the pandemic compared to pre-pandemic trends (RR 0.97 95% CI 0.95,0.98). There was a sudden increase in almost all presenting issues apart from physical complaints. There was evidence of a step increase in the number of contacts for Black/African/Caribbean/Black British (38% increase; 95% CI: 1%-90%) and White ethnic groups (14% increase; 95% CI: 2%-27%)), sudden increase in service use at the start of the pandemic for the most (58% increase; 95% CI: 1%-247%) and least (47% increase; 95% CI: 6%-204%) deprived areas. During the pandemic, contact rates decreased, and referral sources change at the start. Findings on access and service activity align with other studies observing reduced service utilization. The lack of differences in deprivation levels and ethnicity at lockdown suggests exploring equity of access to the anonymous service. The study provides unique insights into changes in digital mental health use during Covid-19 in the UK.",public and global health,exact,100,100 medRxiv,10.1101/2023.08.07.23293778,2023-08-09,https://medrxiv.org/cgi/content/short/2023.08.07.23293778,"Diabetes following SARS-CoV-2 infection: Incidence, persistence, and implications of COVID-19 vaccination. A cohort study of fifteen million people.",Kurt Taylor; Sophie Eastwood; Venexia Walker; Genevieve Cezard; Rochelle Knight; Marwa Al Arab; Yinghui Wei; Elsie M F Horne; Lucy Teece; Harriet Forbes; Alex Walker; Louis Fisher; Jon Massey; Lisa E M Hopcroft; Tom Palmer; Jose Cuitun Coronado; Samantha Ip; Simon Davy; Iain Dillingham; Caroline Morton; Felix Greaves; John MacLeod; Ben Goldacre; Angela Wood; Nishi Chaturvedi; Jonathan A C Sterne; Rachel Denholm; - CONVALESCENCE Long-COVID study; - Longitudinal Health and Wellbeing and Data and Connectivity UK COVID-19 National Core Studies; - OpenSAFELY collaborative,University of Bristol; University College London; University of Bristol; University of Cambridge; University of Bristol; University of Bristol; University of Plymouth; University of Bristol; University of Leicester; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Bristol; University of Bristol; University of Cambridge; University of Oxford; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Bristol; University of Oxford; University of Cambridge; University College London; University of Bristol; University of Bristol; -; -; -,"BackgroundType 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear. @@ -239,6 +219,27 @@ C_LIO_LIThe use of an additional control group from the general public for compa C_LIO_LIIn the subgroup analyses, PCR+ cases and PCR- controls were compared with the population controls to assess the risk factors for those aged 18-55 years. Hence, the results may not be generalisable to patients older than 55 years. C_LIO_LIPCR test results, rather than symptoms, were used to categorise the participants into cases or controls, and therefore risk factors for SARS-CoV-2 infection and not COVID-19 disease were assessed. C_LI",infectious diseases,exact,100,100 +medRxiv,10.1101/2023.03.15.23287292,2023-03-15,https://medrxiv.org/cgi/content/short/2023.03.15.23287292,Living alone and mental health: parallel analyses in longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic,Eoin McElroy; Emily Herrett; Kishan Patel; Dominik M Piehlmaier; Giorgio Di Gessa; Charlotte Huggins; Michael J Green; Alex SF Kwong; Ellen J Thompson; Jingmin Zhu; Kathryn E Mansfield; Richard J Silverwood; Rosie Mansfield; Jane Maddock; Rohini Mathur; Ruth E Costello; Anthony A Matthews; John Tazare; Alasdair Henderson; Kevin Wing; Lucy Bridges; Sebastian Bacon; Amir Mehrkar; - OpenSafely Collaborative; Richard John Shaw; Jacques Wels; Srinivasa Vittal Katikireddi; Nishi Chaturvedi; Laurie Tomlinson; Praveetha Patalay,"School of Psychology, Ulster University, Coleraine, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; University of Sussex Business Sch; Department of Epidemiology & Public Health, University College London, London, UK; Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Twin Research and Genetic Epidemiology, Kings College London; Department of Epidemiology & Public Health, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Centre for Longitudinal Studies, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Primary Care, Wolfson Insitute of Population Health, Queen Mary, University of London, London; London School of Hygiene and Tropical Medicine, London, UK; Karolinska Institutet, Stockholm, Sweden; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; ; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK","ObjectivesTo describe the mental health gap between those who live alone and those who live with others, and to examine whether the COVID-19 pandemic had an impact on this gap. + +DesignTen population based prospective cohort studies, and a retrospective descriptive cohort study based on electronic health records (EHRs). + +SettingUK Longitudinal population-based surveys (LPS), and primary and secondary care records within the OpenSAFELY-TPP database. + +ParticipantsParticipants from the LPS were included if they had information on living status in early 2020, valid data on mental ill-health at the closest pre-pandemic assessment and at least once during the pandemic, and valid data on a key minimum set of covariates. The EHR dataset included 16 million adults registered with primary care practices in England using TPP SystmOne software on 1st February 2020, with at least three months of registration, valid address data, and living in households of <16 people. + +Main outcome measuresIn the LPS, self-reported survey measures of psychological distress and life satisfaction were assessed in the nearest pre-pandemic sweep and three periods during the pandemic: April-June 2020, July-October 2020, and November 2020-March 2021. In the EHR analyses, outcomes were morbidity codes recorded in primary or secondary care between March 2018 and January 2022 reflecting the diagnoses of depression, self-harm, anxiety, obsessive compulsive disorder, eating disorders, and severe mental illnesses. + +ResultsThe LPS consisted of 37,544 participants (15.2% living alone) and we found greater psychological distress (SMD: 0.09 (95% CI: 0.04, 0.14) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30, -0.15) in those living alone pre-pandemic, and the gap between the two groups stayed similar after the onset of the pandemic. In the EHR analysis of almost 16 million records (21.4% living alone), codes indicating mental health conditions were more common in those who lived alone compared to those who lived with others (e.g., depression 26 and severe mental illness 58 cases more per 100,000). Recording of mental health conditions fell during the pandemic for common mental health disorders and the gap between the two groups narrowed. + +ConclusionsMultiple sources of data indicate that those who live alone experience greater levels of common and severe mental illnesses, and lower life satisfaction. During the pandemic this gap in need remained, however, there was a narrowing of the gap in service use, suggesting greater barriers to healthcare access for those who live alone. + +Summary BoxO_ST_ABSWhat is already known on the topic?C_ST_ABSHouseholds with one individual are an increasing demographic, comprising over a quarter of all households in the UK in 2021. However, the mental health gap between those who live alone compared to those who live with others is not well described and even less is known about the relative gaps in need and healthcare-seeking and access. The pandemic and associated restrictive measures further increased the likelihood of isolation for this group, which may have impacted mental health. + +What this study adds?We present comprehensive evidence from both population-based surveys and electronic health records regarding the greater levels of mental health symptoms and in recorded diagnoses for common (anxiety, depression) and less common (OCD, eating disorders, SMIs) mental health conditions for people living alone compared to those living with others. + +Our analyses indicate that mental health conditions are more common among those who live alone compared to those who live with others. Although levels of reported distress increased for both groups during the pandemic, healthcare-seeking dropped in both groups, and the rates of healthcare-seeking among those who live alone converged with those who live with others for common mental health conditions. This suggests greater barriers for treatment access among those that live alone. + +The findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2023.02.26.23286474,2023-03-06,https://medrxiv.org/cgi/content/short/2023.02.26.23286474,Improving the representativeness of UKs national COVID-19 Infection Survey through spatio-temporal regression and post-stratification,Koen B Pouwels; David W Eyre; Thomas House; Ben Aspey; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Jaison Kolenchery; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; tim E peto; Ann Sarah Walker; - COVID-19 Infection Survey Team,University of Oxford; University of Oxford; University of Manchester; Office for National Statistics; The Francis Crick Institute; University of Oxford; University of Exeter; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; oxford university; University of Oxford; -,"Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially impacted by biases arising from differences in participation rates across key groups. Here, we use spatio-temporal regression and post-stratification models to UKs national COVID-19 Infection Survey (CIS) to obtain representative estimates of PCR positivity (6,496,052 tests) and antibody prevalence (1,941,333 tests) for different regions, ages and ethnicities (7-December-2020 to 4-May-2022). Not accounting for vaccination status through post-stratification led to small underestimation of PCR positivity, but more substantial overestimations of antibody levels in the population (up to 21%), particularly in groups with low vaccine uptake in the general population. There was marked variation in the relative contribution of different areas and age-groups to each wave. Future analyses of infectious disease surveys should take into account major drivers of outcomes of interest that may also influence participation, with vaccination being an important factor to consider.",infectious diseases,exact,100,100 medRxiv,10.1101/2023.03.01.23286627,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286627,Effectiveness of successive booster vaccine doses against SARS-CoV-2 related mortality in residents of Long-Term Care Facilities in the VIVALDI study,Oliver Stirrup; Madhumita Shrotri; Natalie L. Adams; Maria Krutikov; Borscha Azmi; Igor Monakhov; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; UK Health Security Agency; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"We evaluated the effectiveness of 1-3 booster vaccinations against SARS-CoV-2 related mortality among a cohort of 13407 older residents of long-term care facilities (LTCFs) participating in the VIVALDI study in England in 2022. Cox regression was used to estimate relative hazards of SARS-CoV-2 related death following booster vaccination relative to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex and LTCF capacity. Each booster provided additional short-term protection relative to primary vaccination, with consistent pattern of waning to 45-75% reduction in risk beyond 112 days.",infectious diseases,exact,100,100 medRxiv,10.1101/2023.03.01.23286624,2023-03-03,https://medrxiv.org/cgi/content/short/2023.03.01.23286624,Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease,Hannah Whittaker; Costantinos Kallis; Angela Wood; Thomas Bolton; Samantha Walker; Aziz Sheikh; Alex Brownrigg; Ashley Akbari; Kamil Sterniczuk; Jennifer K Quint,"Imperial College London; Imperial College London; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, United Kingdom; Health Data Research UK; Asthm + Lung; The University of Edinburgh College of Medicine and Veterinary Medicine; Health Data Research UK BREATHE; Swansea University; Health Data Research UK BREATHE; Imperial College London","BackgroundCOVID-19 is associated with a higher risk of cardiovascular outcomes in the general population, but it is unknown whether people with pre-existing chronic respiratory disease (CRD) have a higher risk of cardiovascular events post-COVID-19 compared with the general population and, if so, what respiratory-related risk factors may modify this risk in these people. @@ -300,6 +301,13 @@ ResultsIgG spike-protein antibodies were undetectable in 23.3%, 14.1% and 20.7% ConclusionsApproximately one in five individuals with SOT, RAIRD and LM have no detectable IgG spike-protein antibodies despite three or more vaccines, but this proportion reduces with sequential booster doses. Choice of immunosuppressant and disease-type is strongly associated with serological response. Antibody testing could enable rapid identification of individuals who are most likely to benefit from additional COVID-19 interventions. Trial registrationClinicaltrials.gov, NCT05148806",public and global health,exact,100,100 +medRxiv,10.1101/2023.02.06.23285513,2023-02-06,https://medrxiv.org/cgi/content/short/2023.02.06.23285513,A Rapid review on the COVID-19 Pandemic's Global Impact on Breast Cancer Screening Participation Rates and Volumes from January-December 2020,"Reagan Lee; - UNCOVER; Wei Xu; - International Partnership for Resilience in Cancer Systems (I-PaRCS), Breast Cancer Working Group 2; Marshall Dozier; Ruth McQuillan; Evropi Theodoratou; Jonine Figueroa",University of Edinburgh; -; University of Edinburgh; -; University of Edinburgh; University of Edinburgh; The University of Edinburgh; University of Edinburgh,"BackgroundCOVID-19 has strained population breast mammography screening programs that aim to diagnose and treat breast cancers earlier. As the pandemic has affected countries differently, we aimed to quantify changes in breast screening volume and uptake during the first year of the COVID-19 pandemic. + +MethodsWe systematically searched Medline, the WHO (World Health Organization) COVID-19 database, and governmental databases. Studies covering January 2020 to March 2022 were included. We extracted and analyzed data regarding study methodology, screening volume and uptake. To assess for risk-of-bias, we used the Joanna Briggs Institute Critical Appraisal tool. + +ResultsTwenty-six cross-sectional descriptive studies were included out of 935 independent records. Reductions in screening volume and uptake rates were observed among eight countries. Changes in screening participation volume in five countries with national population-based screening ranged from -13% to -31%. Among two countries with limited population-based programs the decline ranged from -61% to -41%. Within the USA, population participation volumes varied ranging from +18% to -39% with suggestion of differences by insurance status (HMO, Medicare, and low-income programs). Almost all studies had high risk-of-bias due to insufficient statistical analysis and confounding factors. + +Discussion and ConclusionExtent of COVID-19-induced reduction in breast screening participation volume differed by region and data suggested potential differences by healthcare setting (e.g., national health insurance vs private health care). Recovery efforts should monitor access to screening and early diagnosis to determine if prevention services need strengthening to increase coverage of marginalized groups and reduce disparities.",epidemiology,exact,100,100 medRxiv,10.1101/2023.02.01.23285333,2023-02-02,https://medrxiv.org/cgi/content/short/2023.02.01.23285333,Associations between reported healthcare disruption due to COVID-19 and avoidable hospitalisation: Evidence from seven linked longitudinal studies for England,Mark A Green; Martin McKee; Olivia Hamilton; Richard Shaw; John MacLeod; Andrew Boyd; - The LH&W NCS Collaborative; Srinivasa Vittal Katikireddi,University of Liverpool; London School of Hygiene and Tropical Medicine; University of Glasgow; University of Glasgow; University of Bristol; University of Bristol; ; University of Glasgow,"BackgroundHealth services across the UK struggled to cope during the COVID-19 pandemic. Many treatments were postponed or cancelled, although the impact was mitigated by new models of delivery. While the scale of disruption has been studied, much less is known about if this disruption impacted health outcomes. The aim of our paper is to examine whether there is an association between individuals experiencing disrupted access to healthcare during the pandemic and risk of an avoidable hospitalisation. MethodsWe used individual-level data for England from seven longitudinal cohort studies linked to electronic health records from NHS Digital (n = 29 276) within the UK Longitudinal Linkage Collaboration trusted research environment. Avoidable hospitalisations were defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions (1st March 2020 to 25th August 2022). Self-reported measures of whether people had experienced disruption during the pandemic to appointments (e.g., visiting their GP or an outpatient department), procedures (e.g., surgery, cancer treatment) or medications were used as our exposures. Logistic regression models examined associations. @@ -307,6 +315,12 @@ MethodsWe used individual-level data for England from seven longitudinal cohort Results35% of people experienced some form of disrupted access to healthcare. Those whose access was disrupted were at increased risk of any (Odds Ratio (OR) = 1.80, 95% Confidence Intervals (CIs) = 1.34-2.41), acute (OR = 1.68, CIs = 1.13-2.53) and chronic (OR = 1.93, CIs = 1.40-2.64) ambulatory care sensitive hospital admissions. There were positive associations between disrupted access to appointments and procedures to measures of avoidable hospitalisations as well. ConclusionsOur study presents novel evidence from linked individual-level data showing that people whose access to healthcare was disrupted were more likely to have an avoidable or potentially preventable hospitalisation. Our findings highlight the need to increase healthcare investment to tackle the short- and long-term implications of the pandemic beyond directly dealing with SARS-CoV-2 infections.",public and global health,exact,100,100 +medRxiv,10.1101/2023.01.31.23285232,2023-02-01,https://medrxiv.org/cgi/content/short/2023.01.31.23285232,"Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour",Thomas Edward Byrne; Jana Kovar; Sarah Beale; Isobel Braithwaite; Ellen Fragaszy; Wing Lam Erica Fong; Cyril Geismar; Susan J Hoskins; Annalan Mathew Dwight Navaratnam; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Pia Hardelid; Linda Wijlaars; Eleni Nastouli; Moira Spyer; Anna Ayree; Ingemar Cox; Vasileios Lampos; Rachel A McKendry; Tao Cheng; Anne M Johnson; Susan Fiona Michie; Jo Gibbs; Richard Gilson; Alison Rodger; Ibrahim Abubakar; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; University College London; UCL; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCLH; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL,"Key FeaturesO_LIVirus Watch is a national community cohort study of COVID-19 in households in England and Wales, established in June 2020. The study aims to provide evidence on which public health approaches are most effective in reducing transmission, and investigate community incidence, symptoms, and transmission of COVID-19 in relation to population movement and behaviours. +C_LIO_LI28,527 households and 58,628 participants of age (0-98 years, mean age 48), were recruited between June 2020 - July 2022 +C_LIO_LIData collected include demographics, details on occupation, co-morbidities, medications, and infection-prevention behaviours. Households are followed up weekly with illness surveys capturing symptoms and their severity, activities in the week prior to symptom onset and any COVID-19 test results. Monthly surveys capture household finance, employment, mental health, access to healthcare, vaccination uptake, activities and contacts. Data have been linked to Hospital Episode Statistics (HES), inpatient and critical care episodes, outpatient visits, emergency care contacts, mortality, virology testing and vaccination data held by NHS Digital. +C_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555). +C_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS. +C_LI",epidemiology,exact,100,100 medRxiv,10.1101/2023.01.29.23285160,2023-01-30,https://medrxiv.org/cgi/content/short/2023.01.29.23285160,High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study,Mahan Ghafari; Matthew Hall; Tanya Golubchik; Daniel Ayoubkhani; Thomas House; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; Roberto Cahuantzi; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Jeff Barrett; Christophe Fraser; David Bonsall; Sarah Walker; Katrina A Lythgoe,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Office for National Statistics; -; -; -; Wellcome Sanger Institute; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1-5, give rise to highly divergent lineages 6-8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients 11-14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.",epidemiology,exact,100,100 medRxiv,10.1101/2023.01.24.23284916,2023-01-25,https://medrxiv.org/cgi/content/short/2023.01.24.23284916,"Real-world effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab on preventing hospital admission among higher-risk patients with COVID-19 in Wales: a retrospective cohort study",Andrew Evans; Cathy Qi; Lolu Adebayo; Jonathan Underwood; James Coulson; Rowena Bailey; Gareth John; Alison Cooper; Ashley Akbari; Ronan Lyons; Adrian Edwards,"Welsh Government; Swansea University Medical School; Swansea University Medical School; School of Medicine, Cardiff University; School of Medicine, Cardiff University,; Swansea University Medical School; Digital Health and Care Wales; Wales COVID-19 Evidence Centre; Swansea University; Swansea University; Wales COVID-19 Evidence Centre","ObjectiveTo compare the effectiveness of molnupiravir, nirmatrelvir-ritonavir, and sotrovimab with no treatment in preventing hospital admission or death in higher-risk patients infected with SARS-CoV-2 in the community. @@ -383,7 +397,6 @@ MethodsWe searched the PubMed database for the keywords SARS-CoV-2 with biomar ResultsBiomarker effectiveness varies significantly in different continents. Admission CRP levels were a good prognostic marker for mortality due to wild-type virus in Asian countries, with a pooled area under curve (AUC) of 0.83 (95%CI 0.80-0.85), but only an average predictor of mortality in Europe/North America, with a pooled AUC of 0.67 (95%CI 0.63-0.71, P<0.0001). We observed the same pattern for D-dimer and IL-6. This variability explains why the proposed prognostic scores did not perform evenly. Notably, urea and troponin had pooled AUCs [≥]0.78 regardless of location, implying that end-organ damage at presentation is a key prognostic factor. The inflammatory biomarkers (CRP, D-dimer and IL-6) have generally declined in effectiveness in the vaccinated and variant cohorts. We note a significant lag from the pandemic advent to data availability and this has no doubt impacted on patient care. ConclusionsBiomarker efficacies vary considerably by region. It is imperative that the infrastructure for collecting clinical data should be put in place ahead of a future pandemic.",respiratory medicine,exact,100,100 -medRxiv,10.1101/2022.11.29.22282916,2022-11-30,https://medrxiv.org/cgi/content/short/2022.11.29.22282916,Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population,Jia Wei; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Brian Marsden; Jaison Kolenchery; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; Tim E Peto; Ann Sarah Walker; Koen Pouwels; David W Eyre,University of Oxford; University of Oxford; University of Oxford; Public Health England; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Following primary SARS-CoV-2 vaccination, understanding the relative extent of protection against SARS-CoV-2 infection from boosters or from breakthrough infections (i.e. infection in the context of previous vaccination) has important implications for vaccine policy. In this study, we investigated correlates of protection against Omicron BA.4/5 infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults [≥]18y from the United Kingdom general population. We found that higher anti-spike IgG antibody levels were associated with increased protection against Omicron BA.4/5 infection and that breakthrough infections were associated with higher levels of protection at any given antibody level than booster vaccinations. Breakthrough infections generated similar antibody levels to third/booster vaccinations, and the subsequent declines in antibody levels were similar to or slightly slower than those after third/booster vaccinations. Taken together our findings show that breakthrough infection provides longer lasting protection against further infections than booster vaccinations. For example, considering antibody levels associated with 67% protection against infection, a third/booster vaccination did not provide long-lasting protection, while a Delta/Omicron BA.1 breakthrough infection could provide 5-10 months of protection against Omicron BA.4/5 reinfection. 50-60% of the vaccinated UK population with a breakthrough infection would still be protected by the end of 2022, compared to <15% of the triple-vaccinated UK population without previous infection. Although there are societal impacts and risks to some individuals associated with ongoing transmission, breakthrough infection could be an efficient immune-boosting mechanism for subgroups of the population, including younger healthy adults, who have low risks of adverse consequences from infection.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.11.29.22282899,2022-11-29,https://medrxiv.org/cgi/content/short/2022.11.29.22282899,"Performance of antigen lateral flow devices in the United Kingdom during the Alpha, Delta, and Omicron waves of the SARS-CoV-2 pandemic",David W Eyre; Matthias Futschik; Sarah Tunkel; Jia Wei; Joanna Cole-Hamilton; Rida Saquib; Nick Germanacos; Andrew Dodgson; Paul E Klapper; Malur Sudhanva; Chris Kenny; Peter Marks; Edward Blandford; Susan Hopkins; Tim Peto; Tom Fowler,University of Oxford; UK Health Security Agency; UK Health Security Agency; University of Oxford; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Manchester; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Oxford; UK Health Security Agency,"BackgroundAntigen lateral flow devices (LFDs) have been widely used to control SARS-CoV-2. Changes in LFD sensitivity and detection of infectious individuals during the pandemic with successive variants, vaccination, and changes in LFD use are incompletely understood. MethodsPaired LFD and PCR tests were collected from asymptomatic and symptomatic participants, across multiple settings in the UK between 04-November-2020 and 21-March-2022. Multivariable logistic regression was used to analyse LFD sensitivity and specificity, adjusting for viral load, LFD manufacturer, setting, age, sex, assistance, symptoms, vaccination, and variant. National contact tracing data were used to estimate the proportion of transmitting index cases (with [≥]1 PCR/LFD-positive contact) potentially detectable by LFDs over time, accounting for viral load, variant, and symptom status. @@ -1015,6 +1028,7 @@ MethodTrial emulation was conducted by pooling results from six cohorts whose re ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2. DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,exact,100,100 +bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,exact,100,100 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. @@ -1296,6 +1310,7 @@ ResultsThe trial opened on April 2, 2020, with randomisation to colchicine start ConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community. Trial registrationISRCTN86534580.",infectious diseases,exact,100,100 +medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.09.09.21263026,2021-09-13,https://medrxiv.org/cgi/content/short/2021.09.09.21263026,The clinically extremely vulnerable to COVID: Identification and changes in health care while self-isolating (shielding) during the coronavirus pandemic,Jessica Erin Butler; Mintu Nath; Dimitra Blana; William P Ball; Nicola Beech; Corri Black; Graham Osler; Sebastien Peytrignet; Katie Wilde; Artur Wozniak; Simon Sawhney,University of Aberdeen; University of Aberdeen; University of Aberdeen; University of Aberdeen; NHS Grampian; NHS Grampian and University of Aberdeen; NHS Grampian; Health Foundation; University of Aberdeen; University of Aberdeen; NHS Grampian and University of Aberdeen,"BackgroundIn March 2020, the government of Scotland identified people deemed clinically extremely vulnerable to COVID due to their pre-existing health conditions. These people were advised to strictly self-isolate (shield) at the start of the pandemic, except for necessary healthcare. We examined who was identified as clinically extremely vulnerable, how their healthcare changed during isolation, and whether this process exacerbated healthcare inequalities. MethodsWe linked those on the shielding register in NHS Grampian, a health authority in Scotland, to healthcare records from 2015-2020. We described the source of identification, demographics, and clinical history of the cohort. We measured changes in out-patient, in-patient, and emergency healthcare during isolation in the shielding population and compared to the general non-shielding population. @@ -1551,13 +1566,6 @@ Added value of this studyFor the first time, we report the baseline characterist Implications of all the available evidenceThe significant, long-lasting health and social consequences of SARS-CoV-2 infection are not confined to those who required hospitalisation. As with other long-term conditions, care of patients experiencing Long COVID or specific end-organ effects require consistent, integrated, patient-centred approaches to investigation and management. At public health and policy level, burden of post-COVID morbidity demands renewed focus on effective infection suppression for all age groups.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.22.21257633,2021-05-26,https://medrxiv.org/cgi/content/short/2021.05.22.21257633,Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021,Harald S. Vohringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina Ariani; Sonia Goncalves; David Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; - The Wellcome Sanger Institute Covid-19 Surveillance Team; - The COVID-19 Genomics UK (COG-UK) Consortium; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung,"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC; Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Public Health England PHE; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK; ; ; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Imperial College, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany","The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.05.14.21257229,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.14.21257229,Symptom profiles and accuracy of clinical definitions for COVID-19 in the community. Results of the Virus Watch community cohort.,Ellen Fragaszy; Madhumita Shrotri; Cyril Geismar; Anna Aryee; Sarah Beale; Isobel Braithwaite; Thomas Byrne; Wing Lam Erica Fong; Jo Gibbs; Pia Hardelid; Jana Kovar; Vasileios Edward Lampos; Eleni Nastouli; Annalan Mathew Dwight Navaratnam; Vincent Grigori Nguyen; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,"Centre for Public Health Data Science, Institute of Health Informatics, University College London; Department of Infectious Disease Epidemiology, London School ; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute for Global Health, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Institute of Epidemiology and Health Care, University College London; Department of Computer Science, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Francis Crick Institute, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London; . Institute of Epidemiology and Health Care, University Colle; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College London; ","BackgroundUnderstanding the symptomatology and accuracy of clinical case definitions for COVID-19 in the community is important for the initiation of Test, Trace and Isolate (TTI) and may, in future, be important for early prescription of antivirals. - -MethodsVirus Watch is a large community cohort with prospective daily recording of a wide range of symptoms and self-reporting of swab results (mainly undertaken through the UK TTI system). We compared frequency, severity, timing, and duration of symptoms in test positive and test negative cases. We compared the test performance of the current UK case definition used by TTI (any one of: new continuous cough, high temperature, or loss of or altered sense of smell or taste) with a wider definition that also included muscle aches, chills, headache, or loss of appetite. - -FindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition. - -InterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.17.21256818,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.17.21256818,Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data,George Nicholson; Brieuc CL Lehmann; Tullia Padellini; Koen B Pouwels; Radka Jersakova; James Lomax; Ruairidh E King; Ann-Marie Mallon; Peter J Diggle; Sylvia Richardson; Marta Blangiardo; Chris Holmes,University of Oxford; University of Oxford; Imperial College London; University of Oxford; The Alan Turing Institute; The Alan Turing Institute; MRC Harwell Institute; MRC Harwell Institute; Lancaster University; MRC Biostatistics Unit; Imperial College London; University of Oxford,"Targeted surveillance testing schemes for SARS-CoV-2 focus on certain subsets of the population, such as individuals experiencing one or more of a prescribed list of symptoms. These schemes have routinely been used to monitor the spread of SARS-CoV-2 in countries across the world. The number of positive tests in a given region can provide local insights into important epidemiological parameters, such as prevalence and effective reproduction number. Moreover, targeted testing data has been used inform the deployment of localised non-pharmaceutical interventions. However, surveillance schemes typically suffer from ascertainment bias; the individuals who are tested are not necessarily representative of the wider population of interest. Here, we show that data from randomised testing schemes, such as the REACT study in the UK, can be used to debias fine-scale targeted testing data in order to provide accurate localised estimates of the number of infectious individuals. We develop a novel, integrative causal framework that explicitly models the process underlying the selection of individuals for targeted testing. The output from our model can readily be incorporated into longitudinal analyses to provide local estimates of the reproduction number. We apply our model to characterise the size of the infectious population in England between June 2020 and January 2021. Our local estimates of the effective reproduction number are predictive of future changes in positive case numbers. We also capture local increases in both prevalence and effective reproductive number in the South East from November 2020 to December 2020, reflecting the spread of the Kent variant. Our results illustrate the complementary roles of randomised and targeted testing schemes. Preparations for future epidemics should ensure the rapid deployment of both types of schemes to accurately monitor the spread of emerging and ongoing infectious diseases.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.05.12.21257123,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.12.21257123,Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults,Vahe Nafilyan; Piotr Pawelek; Daniel Ayoubkhani; Sarah Rhodes; Lucy Pembrey; Melissa Matz; Michel P Coleman; Claudia Allemani; Ben Windsor-Shellard; Martie van Tongeren; Neil Pearce,"Office for National Statistics; Office for National Statistics; Office for National Statistics; School of Health Sciences, University of Manchester; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Office for National Statistics; School of Health Sciences, University of Manchester; London School of Hygiene and Tropical Medicine","ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health. @@ -1605,6 +1613,9 @@ MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96 ResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4). ConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively. + +Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,exact,100,100 medRxiv,10.1101/2021.05.04.21256507,2021-05-06,https://medrxiv.org/cgi/content/short/2021.05.04.21256507,Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study,Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith,"St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK","BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression. ObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest. @@ -1636,21 +1647,13 @@ What this study addsO_LIIn 70,464 people with atrial fibrillation, at the thresh C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs. C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs. C_LI",epidemiology,exact,100,100 -medRxiv,10.1101/2021.04.21.21255807,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.21.21255807,A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial,Timothy SC Hinks; Lucy Cureton; Ruth Knight; Ariel Wang; Jennifer L Cane; Vicki S Barber; Joanna Black; Susan J Dutton; James Melhorn; Maisha Jabeen; Phil Moss; Rajendar Garlapati; Tanya Baron; Graham Johnson; Fleur Cantle; David Clarke; Samer Elkhodair; Jonathan Underwood; Daniel Lasserson; Ian D Pavord; Sophie B Morgan; Duncan Richards,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; St George's Hospital, London; East Lancashire NHS Hospitals; Oxford University Hospitals NHS Trust; Royal Derby Hospital; Kings College Hospital, London; Royal Berkshire Hospital; University College London Hospital; Cardiff University; Oxford University Hospitals NHS Trust; University of Oxford; University of Oxford; University of Oxford","BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19. - -MethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed. - -Findings298 participants were enrolled from 3rd June 2020 to 29th January 2021. The primary outcome was assessed in 292 participants. The primary endpoint was not significantly different between the azithromycin and control groups (Adjusted OR 0{middle dot}91 [95% CI 0{middle dot}43-1{middle dot}92], p=0{middle dot}80). Rates of respiratory failure, progression to pneumonia, all-cause mortality, and adverse events, including serious cardiovascular events, were not significantly different between groups. +medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation. -InterpretationIn patients with mild-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospitalisation or death. Our findings do not support the use of azithromycin in patients with mild-moderate COVID-19. +MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period. -FundingNIHR Oxford BRC, University of Oxford and Pfizer Inc. +ResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods. -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE and the Cochrane Central register of Controlled Trials (CENTRAL) with the terms (""azithromycin"") AND (""COVID"" OR ""COVID-19"") AND (""clinical trials""), until March 25, 2021, with no language restrictions. We identified 42 studies, among which there were four completed randomised trials of azithromycin (with or without hydroxychloroquine) in hospitalised patients with severe disease, and three completed randomised trials of azithromycin in mild COVID-19 in primary care. The four trials in hospitalised patients randomised 8,988 participants to azithromycin or standard care or hydroxychloroquine and found no evidence of a difference in mortality, duration of hospital stay or peak disease severity. Of the three trials in primary care, these randomised participants with early disease to 3 or 5 days of therapy, of which only one assessed azithromycin as standalone therapy. This large, adaptive platform trial in the UK randomised 540 participants in primary care to 3 days treatment with azithromycin versus 875 to standard care alone and found no meaningful difference in time to first reported recovery, or of rates of hospitalisation (3% versus 3%) and there were no deaths. We did not identify any randomised trials in patients with COVID-19 managed in ambulatory care. - -Added value of this studyThe ATOMIC2 trial was uniquely-designed to assess azithromycin as a standalone therapy in those with mild-moderately COVID-19 presenting to emergency care, but assessed as appropriate for initial ambulatory management without hospital admission. ATOMIC2 also uniquely assessed high-dose, long-duration treatment to investigate the efficacy of putative anti-inflammatory effects. We found that azithromycin 500 mg daily for 14 days did not reduce the proportion of participants who died or required hospital admission from any cause over the 28 days from randomisation. - -Implications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.",infectious diseases,exact,100,100 +ConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.",epidemiology,exact,100,100 medRxiv,10.1101/2021.04.22.21255911,2021-04-23,https://medrxiv.org/cgi/content/short/2021.04.22.21255911,The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom,Jia Wei; Nicole Stoesser; Philippa C Matthews; Ruth Studley; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Alison Howarth; Brian D Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W Crook; Tim EA Peto; Koen B Pouwels; David W Eyre; A Sarah Walker; - COVID-19 Infection Survey team,"University of Oxford; University of Oxford; University of Oxford; Office for National Statistics, UK; Office for National Statistics, UK; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics, UK; Office for National Statistics, UK; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; ","Real-world data on antibody response post-vaccination in the general population are limited. 45,965 adults in the UKs national COVID-19 Infection Survey receiving Pfizer-BioNTech or Oxford-AstraZeneca vaccines had 111,360 anti-spike IgG measurements. Without prior infection, seroconversion rates and quantitative antibody levels post single dose were lower in older individuals, especially >60y. Two doses achieved high responses across all ages, particularly increasing seroconversion in older people, to similar levels to those achieved after prior infection followed by a single dose. Antibody levels rose more slowly and to lower levels with Oxford-AstraZeneca vs Pfizer-BioNTech, but waned following a single Pfizer-BioNTech dose. Latent class models identified four responder phenotypes: older people, males, and those having long-term health conditions were more commonly low responders. Where supplies are limited, vaccines should be prioritised for those not previously infected, and second doses to individuals >60y. Further data on the relationship between vaccine-mediated protection and antibody responses are needed.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.04.22.21255913,2021-04-23,https://medrxiv.org/cgi/content/short/2021.04.22.21255913,Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK COVID-19 Infection Survey,Emma Pritchard; Philippa Matthews; Nicole Stoesser; David Eyre; Owen Gethings; Karina-Doris Vitha; Joel Jones; Thomas House; Harper VanSteenhouse; Iain Bell; John Bell; John Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Ruth Studley; Derrick W Crook; tim E peto; Ann Sarah Walker; Koen B Pouwels,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; University of Manchester; Glasgow Lighthouse Laboratory; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics,; Office for National Statistics; Office for National Statistics; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford","ObjectivesTo assess the effectiveness of COVID-19 vaccination in preventing SARS-CoV-2 infection in the community. @@ -1840,15 +1843,6 @@ ResultsThere were 5451 COVID-19 cases within the cohort. HRT was associated with ConclusionsWomen on HRT with COVID-19 had a lower likelihood of death. Further work is needed in larger cohorts to examine the association of COCP in COVID-19. Our findings support the current hypothesis that oestrogens may contribute a protective effect against COVID-19 severity. FundingThis study was funded by a School for Primary Care National Institute for Health Research grant (SPCR2014-10043).",epidemiology,exact,100,100 -medRxiv,10.1101/2021.02.15.21251552,2021-02-19,https://medrxiv.org/cgi/content/short/2021.02.15.21251552,Evaluating the effect of COVID-19 on dispensing patterns: a national cohort analysis,Fatemeh Torabi; Ashley Akbari; Laura North; Daniel Harris; Gareth Davies; Mike Gravenor; Rowena Griffiths; Jane Lyons; Neil Jenkins; Andrew Morris; Julian Halcox; Ronan A. Lyons,"Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK, SwanseaUniversity; NHS Wales Shared Services Partnership; Swansea University; Population Data Science and Health Data Research UK, Swansea University; Population Data Science and Health Data Research UK, Swansea University","BackgroundMedication prescribing and dispensing often regarded as one of the most effective ways to manage and improve population health. Prescribed and dispensed medications can be monitored through data linkage for each patient. We hypothesised that changes in patient care resulting from COVID-19, changed the way patients access their prescribed medication. - -ObjectiveTo develop an efficient approach for evaluation of the impact of COVID-19 on drug dispensing patterns. - -MethodsRetrospective observational study using national patient-level dispensing records in Wales-UK. Total dispensed drug items between 01-Jan-2016 and 31-Dec-2019 (counterfactual pre-COVID-19) were compared to 2020 (COVID-19 year). We compared trends of dispensed items in three main British National Formulary (BNF) sections(Cardiovascular system, Central Nervous System, Immunological & Vaccine) using European Age-Standardized rates. We developed an online tool to enable monitoring of changes in dispensing as the pandemic evolves. - -ResultAmongst all BNF chapters, 52,357,639 items were dispensed in 2020 compared to 49,747,141 items in 2019 demonstrating a relative increase of 5.25% in 2020(95%CI[5.21,5.29]). Comparison of monthly patterns of 2020 and 2019 dispensed items showed a notable difference between the total number of dispensed drug items each month, with an average difference (D) of +290,055 and average Relative Change (RC) of +5.52%. The greatest RC was observed in a substantial March-2020 increase (D=+1,501,242 and RC=+28%), followed by second peak in June (D=+565,004, RC=+10.97%). May was characterised by lower dispensing (D=-399,244, RC=-5.9%). Cardiovascular categories were characterised, across all age groups, by dramatic March-2020 increases, at the epidemic peak, followed by months of lower than expected dispensing, and gradual recovery by September. The Central Nervous System category was similar, but with only a short decline in May, and quicker recovery. A stand-out grouping was Immunological and Vaccine, which dropped to very low levels across all age groups, and all months (including the March dispensing peak). - -ConclusionsAberration in clinical service delivery during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes",health systems and quality improvement,exact,100,100 medRxiv,10.1101/2021.02.17.21251812,2021-02-19,https://medrxiv.org/cgi/content/short/2021.02.17.21251812,Changes in the rate of cardiometabolic and pulmonary events during the COVID-19 pandemic,Alex J Walker; John Tazare; George Hickman; Christopher T Rentsch; Elizabeth J Williamson; Krishnan Bhaskaran; David Evans; Kevin Wing; Rohini Mathur; Angel YS Wong; Anna Schultze; Sebastian CJ Bacon; Christopher Bates; Caroline E Morton; Helen J Curtis; Emily Nightingale; Helen I McDonald; Amir Mehrkar; Peter Inglesby; Brian MacKenna; Jonathan Cockburn; William J Hulme; Harriet Forbes; Caroline Minassian; Richard Croker; John Parry; Frank Hester; Sam Harper; Rosalind M Eggo; Stephen JW Evans; Liam Smeeth; Ian J Douglas; Laurie Tomlinson; Ben Goldacre,University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundThere has been extensive speculation about the relationship between COVID-19 and various cardiometabolic and pulmonary conditions. This a complex question: COVID-19 may cause a cardiometabolic or respiratory event; admission for a clinical event may result in hospital-acquired SARS-CoV-2 infection; both may contribute to a patient surpassing the threshold for presenting to services; and the presence of a pandemic may change whether patients present to services at all. To inform analysis of these questions, we set out to describe the overall rate of various key clinical events over time, and their relationship with COVID-19. MethodsWorking on behalf of NHS England, we used data from the OpenSAFELY platform containing data from approximately 40% of the population of England. We selected the whole adult population of 17m patients and within this identified two further mutually exclusive groups: patients who tested positive for SARS-CoV-2 in the community; and patients hospitalised with COVID-19. We report counts of death, DVT, PE, ischaemic stroke, MI, heart failure, AKI and diabetic ketoacidosis in each month between February 2019 and October 2020 within each of: the general population, community SARS-CoV-2 cases, and hospitalised patients with COVID-19. Outcome events were defined using hospitalisations, GP records and cause of death data. @@ -2111,6 +2105,7 @@ C_LIO_LIOptimal symptom combinations maximise case capture considering available C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,exact,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,exact,100,100 +medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,exact,100,100 medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,exact,100,100 medRxiv,10.1101/2020.11.03.20220699,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.03.20220699,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital,Daniel J Cooper; Sara Lear; Laura Watson; Ashley Shaw; Mark Ferris; Rainer Doffinger; Rachel Bousfield; Katherine Sharrocks; Michael Weekes; Ben Warne; Dominic Sparkes; Nick K Jones; Lucy Rivett; Matthew Routledge; Afzal Chaudhry; Katherine Dempsey; Montgomery Matson; Adil Lakha; George Gathercole; Olivia O'Connor; Emily Wilson; Orthi Shahzad; Kieran Toms; Rachel Thompson; Ian Halsall; David Halsall; Sally Houghton; Sofia Papadia; Nathalie Kingston; Kathleen Stirrups; Barbara Graves; Neil Walker; Hannah Stark; - The CITIID-NIHR BioResource COVID-19 Collaboration; Daniela De Angelis; Shaun Seaman; John Bradley; M Estée Török; Ian G. Goodfellow; Stephen Baker,"Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility.; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust; ; MRC Biostatistics Unit, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of pathology, Division of virology, University of Cambridge; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK","BackgroundThe COVID-19 pandemic continues to grow at an unprecedented rate. Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population but risk factors for HCW infection are not well described. @@ -2363,6 +2358,15 @@ At the recommended threshold, PMEWS and the WHO criteria showed good sensitivity ConclusionCURB-65, PMEWS and NEWS2 provide good but not excellent prediction for adverse outcome in suspected COVID-19, and predicted death without organ support better than receipt of organ support. PMEWS, the WHO criteria and NEWS2 (using a lower threshold than usually recommended) provide good sensitivity at the expense of specificity. +RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,exact,100,100 +medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. + +MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. + +ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold. + +ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. + RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,exact,100,100 medRxiv,10.1101/2020.08.26.20182279,2020-09-01,https://medrxiv.org/cgi/content/short/2020.08.26.20182279,COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study,William L Hamilton; Gerry Tonkin-Hill; Emily Smith; Dinesh Aggarwal; Charlotte Houldcroft; Ben Warne; Colin Brown; Luke Meredith; Myra Hosmillo; Aminu Jahun; Martin Curran; Surendra Parmar; Laura Caller; Sarah Caddy; Fahad Khokhar; Anna Yakovleva; Grant Hall; Theresa Feltwell; Malte Pinckert; Iliana Georgana; Yasmin Chaudhry; Nicholas Brown; Sonia Goncalves; Roberto Amato; Ewan Harrison; Mathew Beale; Michael Spencer Chapman; David Jackson; Ian Johnston; Alex Alderton; John Sillitoe; Cordelia Langford; Gordon Dougan; Sharon Peacock; Dominic Kwiatowski; Ian Goodfellow; M. Estee Torok; - COVID-19 Genomics Consortium UK,"University of Cambridge; Wellcome Sanger Institute; Cambridgeshire County Council, UK; Public Health England; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; University of Cambridge; University of Cambridge; ","COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1,167 residents from 337 care homes were identified from a dataset of 6,600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population. @@ -2713,6 +2717,15 @@ MethodsWe investigated staff reports regarding the impact of the COVID-19 pandem Results2,180 staff from a range of sectors, professions and specialties participated. Immediate infection control concerns were highly salient for inpatient staff, new ways of working for community staff. Multiple rapid adaptations and innovations in response to the crisis were described, especially remote working. This was cautiously welcomed but found successful in only some clinical situations. Staff had specific concerns about many groups of service users, including people whose conditions are exacerbated by pandemic anxieties and social disruptions; people experiencing loneliness, domestic abuse and family conflict; those unable to understand and follow social distancing requirements; and those who cannot engage with remote care. ConclusionThis overview of staff concerns and experiences in the early COVID-19 pandemic suggests directions for further research and service development: we suggest that how to combine infection control and a therapeutic environment in hospital, and how to achieve effective and targeted tele-health implementation in the community, should be priorities. The limitations of our convenience sample must be noted.",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2020.06.10.20127175,2020-06-11,https://medrxiv.org/cgi/content/short/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway,"University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL","BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both ""direct"", through infection, and ""indirect"", through changes in healthcare. + +MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(""direct"" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For ""indirect"" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. + +FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. + +InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. + +FundingNIHR, HDR UK, Astra Zeneca",cardiovascular medicine,exact,100,100 medRxiv,10.1101/2020.06.08.20120584,2020-06-09,https://medrxiv.org/cgi/content/short/2020.06.08.20120584,SARS-CoV-2 virus and antibodies in front-line Health Care Workers in an acute hospital in London: preliminary results from a longitudinal study,Catherine Houlihan; Nina Vora; Thomas Byrne; Dan Lewer; Judith Heaney; David A Moore; Rebecca Matthews; Sajida Adam; Louise Enfield; Abigail Severn; Angela McBride; Moira Jane Spyer; Rupert Beale; Peter Cherepanov; Kathleen Gaertner; Maryam Shahmanesh; - The SAFER Field Study Team; Kevin Ng; Georgina Cornish; Naomi Walker; Susan Michie; Ed Manley; Fabiana Lorencatto; - The Crick-COVID-Consortium; Richard Gilson; Sonia Gandhi; Steve Gamblin; George Kassiotis; Laura McCoy; Charles Swanton; Andrew Hayward; Eleni Nastouli,University College London Hospital; UCL; UCL; University College London; UCL; Francis Crick Institute; UCL; UCL; UCL; UCL; UCL; UCL; Francis Crick Institute; Francis Crick Institute; UCL; UCL; ; Francis Crick Institute; Francis Crick Institute; UCL; UCL; Leeds University; UCL; ; UCL; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; UCL; Francis Crick Institute; UCL; University College London,"BackgroundAlthough SARS-CoV-2 infection in Healthcare Workers (HCWs) is a public health concern, there is little description of their longitudinal antibody response in the presence or absence of SARS-CoV-2 and symptoms. We followed HCWs in an acute London hospital to measure seroconversion and RNA detection at the peak of the pandemic. MethodsWe enrolled 200 patient-facing HCWs between 26 March and 8 April 2020 and collected twice-weekly self-administered nose and throat swabs, symptom data and monthly blood samples. Swabs were tested for SARS-CoV-2 by PCR, and serum for antibodies to spike protein by ELISA and flow cytometry. @@ -2840,13 +2853,6 @@ Key PointsO_ST_ABSQuestionC_ST_ABSHow is the instantaneous reproduction number ( FindingsSocial distancing, temperate weather, and lower population density were associated with a decrease in Rt. Of these county-specific factors, social distancing appeared to be the most significant in reducing SARS-CoV-2 transmission. MeaningRt varies significantly across counties. The relationship between Rt and county-specific factors can inform policies to reduce SARS-CoV-2 transmission in selective and heterogeneous communities.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.05.05.20092296,2020-05-09,https://medrxiv.org/cgi/content/short/2020.05.05.20092296,Ethnicity and risk of death in patients hospitalised for COVID-19 infection: an observational cohort study in an urban catchment area,Elizabeth Sapey; Suzy Gallier; Chris Mainey; Peter Nightingale; David McNulty; Hannah Crothers; Felicity Evison; Katharine Reeves; Domenico Pagano; Alastair K Denniston; Krishnarajah Nirantharakumar; Peter Diggle; Simon Ball,University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS FoundationTrust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Lancaster; University Hospitals Birmingham NHS Foundation Trust,"BackgroundStudies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients. - -MethodsPatients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10th March 2020-17th April 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching. - -ResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2-1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)). - -ConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.05.06.20092999,2020-05-07,https://medrxiv.org/cgi/content/short/2020.05.06.20092999,OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.,- The OpenSAFELY Collaborative; Elizabeth Williamson; Alex J Walker; Krishnan J Bhaskaran; Seb Bacon; Chris Bates; Caroline E Morton; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen I Mcdonald; Brian MacKenna; Laurie Tomlinson; Ian J Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Richard Grieve; David Harrison; Harriet Forbes; Anna Schultze; Richard T Croker; John Parry; Frank Hester; Sam Harper; Rafael Perera; Stephen Evans; Liam Smeeth; Ben Goldacre,; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ICNARC; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundEstablishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary. Data sourcesPrimary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform. diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index dd003238..88da69e4 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -167,20 +167,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.08.25.23294609", - "date": "2023-08-25", - "link": "https://medrxiv.org/cgi/content/short/2023.08.25.23294609", - "title": "Risk factors for SARS-Cov-2 infection at a United Kingdom electricity-generating company: a test-negative design case-control study", - "authors": "Charlotte E Rutter; Martie J Van Tongeren; Tony Fletcher; Sarah E Rhodes; Yiqun Chen; Ian Hall; Nicholas Warren; Neil Pearce", - "affiliations": "London School of Hygiene and Tropical Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Health and Safety Executive; University of Manchester; Health and Safety Executive; London School of Hygiene and Tropical Medicine", - "abstract": "ObjectivesIdentify workplace risk factors for SARS-Cov-2 infection, using data collected by a United Kingdom electricity-generating company.\n\nMethodsUsing a test-negative design case-control study we estimated the odds ratios (OR) of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage, and site COVID-19 weekly risk rating, adjusting for age, test date and test type.\n\nResultsFrom an original 80,077 COVID-19 tests, there were 70,646 included in the final analysis. Most exclusions were due to being visitor tests (5,030) or tests after an individual first tested positive (2,968).\n\nWomen were less likely to test positive than men (OR=0.71; 95% confidence interval=0.58-0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area it was a strong confounder for other variables. Compared to routine tests, tests due to symptoms were highest risk (94.99; 78.29-115.24), followed by close contact (16.73; 13.80-20.29) and broader-defined work contact 2.66 (1.99-3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model.\n\nConclusionsIn general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIIn the United Kingdom, there is now a considerable body of evidence showing occupational differences in Covid-19 infection and severity, but with understandable focus on high-risk industries like healthcare.\nC_LIO_LILess is known about differences in risk of COVID-19 infection in other industries that do not involve directly working with the general public, in particular, there is relatively little evidence on the risks of transmission in the electricity-generating industry.\nC_LI\n\nWhat this study addsO_LIAt this company, infection risk was not associated with job category after adjusting for test reason; however women were less likely to test positive than men and the risk was higher when there was a power outage, requiring more staff to visit the site in person.\nC_LI\n\nHow this study might affect research, practice or policyO_LIThe site risk rating showed a consistent (but modest) dose-response with infection risk, indicating that such risk rating may be useful for identifying \"high risk\" sites.\nC_LIO_LIThis analysis demonstrates the importance of adjusting for both date of and reason for test, when prevalence and testing protocols differ over time.\nC_LI", - "category": "occupational and environmental health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.08.11.23293977", @@ -419,6 +405,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.03.15.23287292", + "date": "2023-03-15", + "link": "https://medrxiv.org/cgi/content/short/2023.03.15.23287292", + "title": "Living alone and mental health: parallel analyses in longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic", + "authors": "Eoin McElroy; Emily Herrett; Kishan Patel; Dominik M Piehlmaier; Giorgio Di Gessa; Charlotte Huggins; Michael J Green; Alex SF Kwong; Ellen J Thompson; Jingmin Zhu; Kathryn E Mansfield; Richard J Silverwood; Rosie Mansfield; Jane Maddock; Rohini Mathur; Ruth E Costello; Anthony A Matthews; John Tazare; Alasdair Henderson; Kevin Wing; Lucy Bridges; Sebastian Bacon; Amir Mehrkar; - OpenSafely Collaborative; Richard John Shaw; Jacques Wels; Srinivasa Vittal Katikireddi; Nishi Chaturvedi; Laurie Tomlinson; Praveetha Patalay", + "affiliations": "School of Psychology, Ulster University, Coleraine, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; University of Sussex Business Sch; Department of Epidemiology & Public Health, University College London, London, UK; Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Twin Research and Genetic Epidemiology, Kings College London; Department of Epidemiology & Public Health, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Centre for Longitudinal Studies, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Primary Care, Wolfson Insitute of Population Health, Queen Mary, University of London, London; London School of Hygiene and Tropical Medicine, London, UK; Karolinska Institutet, Stockholm, Sweden; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; ; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK", + "abstract": "ObjectivesTo describe the mental health gap between those who live alone and those who live with others, and to examine whether the COVID-19 pandemic had an impact on this gap.\n\nDesignTen population based prospective cohort studies, and a retrospective descriptive cohort study based on electronic health records (EHRs).\n\nSettingUK Longitudinal population-based surveys (LPS), and primary and secondary care records within the OpenSAFELY-TPP database.\n\nParticipantsParticipants from the LPS were included if they had information on living status in early 2020, valid data on mental ill-health at the closest pre-pandemic assessment and at least once during the pandemic, and valid data on a key minimum set of covariates. The EHR dataset included 16 million adults registered with primary care practices in England using TPP SystmOne software on 1st February 2020, with at least three months of registration, valid address data, and living in households of <16 people.\n\nMain outcome measuresIn the LPS, self-reported survey measures of psychological distress and life satisfaction were assessed in the nearest pre-pandemic sweep and three periods during the pandemic: April-June 2020, July-October 2020, and November 2020-March 2021. In the EHR analyses, outcomes were morbidity codes recorded in primary or secondary care between March 2018 and January 2022 reflecting the diagnoses of depression, self-harm, anxiety, obsessive compulsive disorder, eating disorders, and severe mental illnesses.\n\nResultsThe LPS consisted of 37,544 participants (15.2% living alone) and we found greater psychological distress (SMD: 0.09 (95% CI: 0.04, 0.14) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30, -0.15) in those living alone pre-pandemic, and the gap between the two groups stayed similar after the onset of the pandemic. In the EHR analysis of almost 16 million records (21.4% living alone), codes indicating mental health conditions were more common in those who lived alone compared to those who lived with others (e.g., depression 26 and severe mental illness 58 cases more per 100,000). Recording of mental health conditions fell during the pandemic for common mental health disorders and the gap between the two groups narrowed.\n\nConclusionsMultiple sources of data indicate that those who live alone experience greater levels of common and severe mental illnesses, and lower life satisfaction. During the pandemic this gap in need remained, however, there was a narrowing of the gap in service use, suggesting greater barriers to healthcare access for those who live alone.\n\nSummary BoxO_ST_ABSWhat is already known on the topic?C_ST_ABSHouseholds with one individual are an increasing demographic, comprising over a quarter of all households in the UK in 2021. However, the mental health gap between those who live alone compared to those who live with others is not well described and even less is known about the relative gaps in need and healthcare-seeking and access. The pandemic and associated restrictive measures further increased the likelihood of isolation for this group, which may have impacted mental health.\n\nWhat this study adds?We present comprehensive evidence from both population-based surveys and electronic health records regarding the greater levels of mental health symptoms and in recorded diagnoses for common (anxiety, depression) and less common (OCD, eating disorders, SMIs) mental health conditions for people living alone compared to those living with others.\n\nOur analyses indicate that mental health conditions are more common among those who live alone compared to those who live with others. Although levels of reported distress increased for both groups during the pandemic, healthcare-seeking dropped in both groups, and the rates of healthcare-seeking among those who live alone converged with those who live with others for common mental health conditions. This suggests greater barriers for treatment access among those that live alone.\n\nThe findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.", + "category": "psychiatry and clinical psychology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.26.23286474", @@ -517,6 +517,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.02.06.23285513", + "date": "2023-02-06", + "link": "https://medrxiv.org/cgi/content/short/2023.02.06.23285513", + "title": "A Rapid review on the COVID-19 Pandemic's Global Impact on Breast Cancer Screening Participation Rates and Volumes from January-December 2020", + "authors": "Reagan Lee; - UNCOVER; Wei Xu; - International Partnership for Resilience in Cancer Systems (I-PaRCS), Breast Cancer Working Group 2; Marshall Dozier; Ruth McQuillan; Evropi Theodoratou; Jonine Figueroa", + "affiliations": "University of Edinburgh; -; University of Edinburgh; -; University of Edinburgh; University of Edinburgh; The University of Edinburgh; University of Edinburgh", + "abstract": "BackgroundCOVID-19 has strained population breast mammography screening programs that aim to diagnose and treat breast cancers earlier. As the pandemic has affected countries differently, we aimed to quantify changes in breast screening volume and uptake during the first year of the COVID-19 pandemic.\n\nMethodsWe systematically searched Medline, the WHO (World Health Organization) COVID-19 database, and governmental databases. Studies covering January 2020 to March 2022 were included. We extracted and analyzed data regarding study methodology, screening volume and uptake. To assess for risk-of-bias, we used the Joanna Briggs Institute Critical Appraisal tool.\n\nResultsTwenty-six cross-sectional descriptive studies were included out of 935 independent records. Reductions in screening volume and uptake rates were observed among eight countries. Changes in screening participation volume in five countries with national population-based screening ranged from -13% to -31%. Among two countries with limited population-based programs the decline ranged from -61% to -41%. Within the USA, population participation volumes varied ranging from +18% to -39% with suggestion of differences by insurance status (HMO, Medicare, and low-income programs). Almost all studies had high risk-of-bias due to insufficient statistical analysis and confounding factors.\n\nDiscussion and ConclusionExtent of COVID-19-induced reduction in breast screening participation volume differed by region and data suggested potential differences by healthcare setting (e.g., national health insurance vs private health care). Recovery efforts should monitor access to screening and early diagnosis to determine if prevention services need strengthening to increase coverage of marginalized groups and reduce disparities.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.01.23285333", @@ -531,6 +545,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.01.31.23285232", + "date": "2023-02-01", + "link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285232", + "title": "Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour", + "authors": "Thomas Edward Byrne; Jana Kovar; Sarah Beale; Isobel Braithwaite; Ellen Fragaszy; Wing Lam Erica Fong; Cyril Geismar; Susan J Hoskins; Annalan Mathew Dwight Navaratnam; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Pia Hardelid; Linda Wijlaars; Eleni Nastouli; Moira Spyer; Anna Ayree; Ingemar Cox; Vasileios Lampos; Rachel A McKendry; Tao Cheng; Anne M Johnson; Susan Fiona Michie; Jo Gibbs; Richard Gilson; Alison Rodger; Ibrahim Abubakar; Andrew Hayward; Robert W Aldridge", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCLH; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL", + "abstract": "Key FeaturesO_LIVirus Watch is a national community cohort study of COVID-19 in households in England and Wales, established in June 2020. The study aims to provide evidence on which public health approaches are most effective in reducing transmission, and investigate community incidence, symptoms, and transmission of COVID-19 in relation to population movement and behaviours.\nC_LIO_LI28,527 households and 58,628 participants of age (0-98 years, mean age 48), were recruited between June 2020 - July 2022\nC_LIO_LIData collected include demographics, details on occupation, co-morbidities, medications, and infection-prevention behaviours. Households are followed up weekly with illness surveys capturing symptoms and their severity, activities in the week prior to symptom onset and any COVID-19 test results. Monthly surveys capture household finance, employment, mental health, access to healthcare, vaccination uptake, activities and contacts. Data have been linked to Hospital Episode Statistics (HES), inpatient and critical care episodes, outpatient visits, emergency care contacts, mortality, virology testing and vaccination data held by NHS Digital.\nC_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555).\nC_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS.\nC_LI", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.01.29.23285160", @@ -643,20 +671,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.11.29.22282916", - "date": "2022-11-30", - "link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282916", - "title": "Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population", - "authors": "Jia Wei; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Brian Marsden; Jaison Kolenchery; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; Tim E Peto; Ann Sarah Walker; Koen Pouwels; David W Eyre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; Public Health England; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", - "abstract": "Following primary SARS-CoV-2 vaccination, understanding the relative extent of protection against SARS-CoV-2 infection from boosters or from breakthrough infections (i.e. infection in the context of previous vaccination) has important implications for vaccine policy. In this study, we investigated correlates of protection against Omicron BA.4/5 infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults [≥]18y from the United Kingdom general population. We found that higher anti-spike IgG antibody levels were associated with increased protection against Omicron BA.4/5 infection and that breakthrough infections were associated with higher levels of protection at any given antibody level than booster vaccinations. Breakthrough infections generated similar antibody levels to third/booster vaccinations, and the subsequent declines in antibody levels were similar to or slightly slower than those after third/booster vaccinations. Taken together our findings show that breakthrough infection provides longer lasting protection against further infections than booster vaccinations. For example, considering antibody levels associated with 67% protection against infection, a third/booster vaccination did not provide long-lasting protection, while a Delta/Omicron BA.1 breakthrough infection could provide 5-10 months of protection against Omicron BA.4/5 reinfection. 50-60% of the vaccinated UK population with a breakthrough infection would still be protected by the end of 2022, compared to <15% of the triple-vaccinated UK population without previous infection. Although there are societal impacts and risks to some individuals associated with ongoing transmission, breakthrough infection could be an efficient immune-boosting mechanism for subgroups of the population, including younger healthy adults, who have low risks of adverse consequences from infection.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.11.29.22282899", @@ -1539,6 +1553,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.12.17.473248", + "date": "2021-12-21", + "link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "authors": "Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge", + "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "category": "microbiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268098", @@ -1959,6 +1987,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.13.21263487", + "date": "2021-09-16", + "link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "authors": "Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.09.21263026", @@ -2421,20 +2463,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.14.21257229", - "date": "2021-05-18", - "link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257229", - "title": "Symptom profiles and accuracy of clinical definitions for COVID-19 in the community. Results of the Virus Watch community cohort.", - "authors": "Ellen Fragaszy; Madhumita Shrotri; Cyril Geismar; Anna Aryee; Sarah Beale; Isobel Braithwaite; Thomas Byrne; Wing Lam Erica Fong; Jo Gibbs; Pia Hardelid; Jana Kovar; Vasileios Edward Lampos; Eleni Nastouli; Annalan Mathew Dwight Navaratnam; Vincent Grigori Nguyen; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative", - "affiliations": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; Department of Infectious Disease Epidemiology, London School ; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute for Global Health, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Institute of Epidemiology and Health Care, University College London; Department of Computer Science, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Francis Crick Institute, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London; . Institute of Epidemiology and Health Care, University Colle; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College London; ", - "abstract": "BackgroundUnderstanding the symptomatology and accuracy of clinical case definitions for COVID-19 in the community is important for the initiation of Test, Trace and Isolate (TTI) and may, in future, be important for early prescription of antivirals.\n\nMethodsVirus Watch is a large community cohort with prospective daily recording of a wide range of symptoms and self-reporting of swab results (mainly undertaken through the UK TTI system). We compared frequency, severity, timing, and duration of symptoms in test positive and test negative cases. We compared the test performance of the current UK case definition used by TTI (any one of: new continuous cough, high temperature, or loss of or altered sense of smell or taste) with a wider definition that also included muscle aches, chills, headache, or loss of appetite.\n\nFindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition.\n\nInterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.17.21256818", @@ -2533,6 +2561,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.05.21256668", + "date": "2021-05-09", + "link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "authors": "Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz", + "affiliations": "The University of Edinburgh; The University of Edinburgh; The University of Edinburgh", + "abstract": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "category": "health informatics", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.04.21256507", @@ -2563,14 +2605,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.04.21.21255807", - "date": "2021-04-27", - "link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255807", - "title": "A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial", - "authors": "Timothy SC Hinks; Lucy Cureton; Ruth Knight; Ariel Wang; Jennifer L Cane; Vicki S Barber; Joanna Black; Susan J Dutton; James Melhorn; Maisha Jabeen; Phil Moss; Rajendar Garlapati; Tanya Baron; Graham Johnson; Fleur Cantle; David Clarke; Samer Elkhodair; Jonathan Underwood; Daniel Lasserson; Ian D Pavord; Sophie B Morgan; Duncan Richards", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; St George's Hospital, London; East Lancashire NHS Hospitals; Oxford University Hospitals NHS Trust; Royal Derby Hospital; Kings College Hospital, London; Royal Berkshire Hospital; University College London Hospital; Cardiff University; Oxford University Hospitals NHS Trust; University of Oxford; University of Oxford; University of Oxford", - "abstract": "BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19.\n\nMethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed.\n\nFindings298 participants were enrolled from 3rd June 2020 to 29th January 2021. The primary outcome was assessed in 292 participants. The primary endpoint was not significantly different between the azithromycin and control groups (Adjusted OR 0{middle dot}91 [95% CI 0{middle dot}43-1{middle dot}92], p=0{middle dot}80). Rates of respiratory failure, progression to pneumonia, all-cause mortality, and adverse events, including serious cardiovascular events, were not significantly different between groups.\n\nInterpretationIn patients with mild-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospitalisation or death. Our findings do not support the use of azithromycin in patients with mild-moderate COVID-19.\n\nFundingNIHR Oxford BRC, University of Oxford and Pfizer Inc.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE and the Cochrane Central register of Controlled Trials (CENTRAL) with the terms (\"azithromycin\") AND (\"COVID\" OR \"COVID-19\") AND (\"clinical trials\"), until March 25, 2021, with no language restrictions. We identified 42 studies, among which there were four completed randomised trials of azithromycin (with or without hydroxychloroquine) in hospitalised patients with severe disease, and three completed randomised trials of azithromycin in mild COVID-19 in primary care. The four trials in hospitalised patients randomised 8,988 participants to azithromycin or standard care or hydroxychloroquine and found no evidence of a difference in mortality, duration of hospital stay or peak disease severity. Of the three trials in primary care, these randomised participants with early disease to 3 or 5 days of therapy, of which only one assessed azithromycin as standalone therapy. This large, adaptive platform trial in the UK randomised 540 participants in primary care to 3 days treatment with azithromycin versus 875 to standard care alone and found no meaningful difference in time to first reported recovery, or of rates of hospitalisation (3% versus 3%) and there were no deaths. We did not identify any randomised trials in patients with COVID-19 managed in ambulatory care.\n\nAdded value of this studyThe ATOMIC2 trial was uniquely-designed to assess azithromycin as a standalone therapy in those with mild-moderately COVID-19 presenting to emergency care, but assessed as appropriate for initial ambulatory management without hospital admission. ATOMIC2 also uniquely assessed high-dose, long-duration treatment to investigate the efficacy of putative anti-inflammatory effects. We found that azithromycin 500 mg daily for 14 days did not reduce the proportion of participants who died or required hospital admission from any cause over the 28 days from randomisation.\n\nImplications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.", - "category": "infectious diseases", + "doi": "10.1101/2021.04.26.21255732", + "date": "2021-04-28", + "link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "authors": "Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative", + "affiliations": "University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", + "abstract": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "category": "epidemiology", "match_type": "exact", "author_similarity": 100, "affiliation_similarity": 100 @@ -2869,20 +2911,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.15.21251552", - "date": "2021-02-19", - "link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251552", - "title": "Evaluating the effect of COVID-19 on dispensing patterns: a national cohort analysis", - "authors": "Fatemeh Torabi; Ashley Akbari; Laura North; Daniel Harris; Gareth Davies; Mike Gravenor; Rowena Griffiths; Jane Lyons; Neil Jenkins; Andrew Morris; Julian Halcox; Ronan A. Lyons", - "affiliations": "Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK, SwanseaUniversity; NHS Wales Shared Services Partnership; Swansea University; Population Data Science and Health Data Research UK, Swansea University; Population Data Science and Health Data Research UK, Swansea University", - "abstract": "BackgroundMedication prescribing and dispensing often regarded as one of the most effective ways to manage and improve population health. Prescribed and dispensed medications can be monitored through data linkage for each patient. We hypothesised that changes in patient care resulting from COVID-19, changed the way patients access their prescribed medication.\n\nObjectiveTo develop an efficient approach for evaluation of the impact of COVID-19 on drug dispensing patterns.\n\nMethodsRetrospective observational study using national patient-level dispensing records in Wales-UK. Total dispensed drug items between 01-Jan-2016 and 31-Dec-2019 (counterfactual pre-COVID-19) were compared to 2020 (COVID-19 year). We compared trends of dispensed items in three main British National Formulary (BNF) sections(Cardiovascular system, Central Nervous System, Immunological & Vaccine) using European Age-Standardized rates. We developed an online tool to enable monitoring of changes in dispensing as the pandemic evolves.\n\nResultAmongst all BNF chapters, 52,357,639 items were dispensed in 2020 compared to 49,747,141 items in 2019 demonstrating a relative increase of 5.25% in 2020(95%CI[5.21,5.29]). Comparison of monthly patterns of 2020 and 2019 dispensed items showed a notable difference between the total number of dispensed drug items each month, with an average difference (D) of +290,055 and average Relative Change (RC) of +5.52%. The greatest RC was observed in a substantial March-2020 increase (D=+1,501,242 and RC=+28%), followed by second peak in June (D=+565,004, RC=+10.97%). May was characterised by lower dispensing (D=-399,244, RC=-5.9%). Cardiovascular categories were characterised, across all age groups, by dramatic March-2020 increases, at the epidemic peak, followed by months of lower than expected dispensing, and gradual recovery by September. The Central Nervous System category was similar, but with only a short decline in May, and quicker recovery. A stand-out grouping was Immunological and Vaccine, which dropped to very low levels across all age groups, and all months (including the March dispensing peak).\n\nConclusionsAberration in clinical service delivery during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes", - "category": "health systems and quality improvement", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.17.21251812", @@ -3275,6 +3303,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234849", + "date": "2020-11-22", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "authors": "Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.06.20227108", @@ -3737,6 +3779,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.01.20185793", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "authors": "Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter", + "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust", + "abstract": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "category": "emergency medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.26.20182279", @@ -4311,6 +4367,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.10.20127175", + "date": "2020-06-11", + "link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "authors": "Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL", + "abstract": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "category": "cardiovascular medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.06.08.20120584", @@ -4493,20 +4563,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.05.20092296", - "date": "2020-05-09", - "link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092296", - "title": "Ethnicity and risk of death in patients hospitalised for COVID-19 infection: an observational cohort study in an urban catchment area", - "authors": "Elizabeth Sapey; Suzy Gallier; Chris Mainey; Peter Nightingale; David McNulty; Hannah Crothers; Felicity Evison; Katharine Reeves; Domenico Pagano; Alastair K Denniston; Krishnarajah Nirantharakumar; Peter Diggle; Simon Ball", - "affiliations": "University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS FoundationTrust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Lancaster; University Hospitals Birmingham NHS Foundation Trust", - "abstract": "BackgroundStudies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients.\n\nMethodsPatients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10th March 2020-17th April 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching.\n\nResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2-1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)).\n\nConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.06.20092999", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 30035418..5e4f163b 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -279,20 +279,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.11.06.23298026", - "date": "2023-11-07", - "link": "https://medrxiv.org/cgi/content/short/2023.11.06.23298026", - "title": "Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England", - "authors": "Harrison Manley; Thomas Bayley; Gabriel Danelian; Lucy Burton; Thomas Finnie; Andre Charlett; Nick Watkins; Paul Birrell; Daniela De Angelis; Matt J Keeling; Sebastian J Funk; Graham Medley; Lorenzo Pellis; Marc Baguelin; Graeme J Ackland; Johanna Hutchinson; Steven Riley; Jasmina Panovska-Griffiths", - "affiliations": "UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; University of Cambridge Cambridge, UK; University of Warwick, Zeeman Institute: SBIDER; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; The University of Manchester; Imperial College London; University of Edinburgh; UK Health Security Agency; UK Health Security Agency; University of Oxford", - "abstract": "Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated Medium-Term Projections (MTPs) of possible epidemic trajectories over the future 4-6 weeks from a collection of epidemiological models.In this paper we outline this collaborative modelling approach and evaluate the accuracy of the combined and individual model projections against the data over the period November 2021-December 2022 when various Omicron subvariants were spreading across England. Using a number of statistical methods, we quantify the predictive performance of the model projections for both the combined and individual MTPs, by evaluating the point and probabilistic accuracy. Our results illustrate that the combined MTPs, produced from an ensemble of heterogeneous epidemiological models, were a closer fit to the data than the individual models during the periods of epidemic growth or decline, with the 90% confidence intervals widest around the epidemic peaks. We also show that the combined MTPs increase the robustness and reduce the biases associated with a single model projection. Learning from our experience of ensemble modelling during the COVID-19 epidemic, our findings highlight the importance of developing cross-institutional multi-model infectious disease hubs for future outbreak control.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.10.26.23297598", @@ -377,20 +363,6 @@ "author_similarity": 94, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.08.25.23294609", - "date": "2023-08-25", - "link": "https://medrxiv.org/cgi/content/short/2023.08.25.23294609", - "title": "Risk factors for SARS-Cov-2 infection at a United Kingdom electricity-generating company: a test-negative design case-control study", - "authors": "Charlotte E Rutter; Martie J Van Tongeren; Tony Fletcher; Sarah E Rhodes; Yiqun Chen; Ian Hall; Nicholas Warren; Neil Pearce", - "affiliations": "London School of Hygiene and Tropical Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; Health and Safety Executive; University of Manchester; Health and Safety Executive; London School of Hygiene and Tropical Medicine", - "abstract": "ObjectivesIdentify workplace risk factors for SARS-Cov-2 infection, using data collected by a United Kingdom electricity-generating company.\n\nMethodsUsing a test-negative design case-control study we estimated the odds ratios (OR) of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage, and site COVID-19 weekly risk rating, adjusting for age, test date and test type.\n\nResultsFrom an original 80,077 COVID-19 tests, there were 70,646 included in the final analysis. Most exclusions were due to being visitor tests (5,030) or tests after an individual first tested positive (2,968).\n\nWomen were less likely to test positive than men (OR=0.71; 95% confidence interval=0.58-0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area it was a strong confounder for other variables. Compared to routine tests, tests due to symptoms were highest risk (94.99; 78.29-115.24), followed by close contact (16.73; 13.80-20.29) and broader-defined work contact 2.66 (1.99-3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model.\n\nConclusionsIn general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIIn the United Kingdom, there is now a considerable body of evidence showing occupational differences in Covid-19 infection and severity, but with understandable focus on high-risk industries like healthcare.\nC_LIO_LILess is known about differences in risk of COVID-19 infection in other industries that do not involve directly working with the general public, in particular, there is relatively little evidence on the risks of transmission in the electricity-generating industry.\nC_LI\n\nWhat this study addsO_LIAt this company, infection risk was not associated with job category after adjusting for test reason; however women were less likely to test positive than men and the risk was higher when there was a power outage, requiring more staff to visit the site in person.\nC_LI\n\nHow this study might affect research, practice or policyO_LIThe site risk rating showed a consistent (but modest) dose-response with infection risk, indicating that such risk rating may be useful for identifying \"high risk\" sites.\nC_LIO_LIThis analysis demonstrates the importance of adjusting for both date of and reason for test, when prevalence and testing protocols differ over time.\nC_LI", - "category": "occupational and environmental health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.08.11.23293977", @@ -461,6 +433,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.08.01.23293491", + "date": "2023-08-02", + "link": "https://medrxiv.org/cgi/content/short/2023.08.01.23293491", + "title": "Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study", + "authors": "Haowei Wang; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; David Haw; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Christl A Donnelly; Paul Elliott; Steven Riley", + "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc", + "abstract": "ObjectivesThe rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities across ethnic and sociodemographic subgroups. In this paper, we aimed to investigate how inequalities influence the risk of getting infected across ethnic and sociodemographic subgroups during a key period before widespread vaccination.\n\nDesignRepeated cross-sectional community-based study.\n\nMethodsWe analysed risk factors for test-positivity for SARS-CoV-2, based on self-administered throat and nose swabs in the community during rounds 5 to 10 of the REal-time Assessment of Community Transmission-1 (REACT-1) study between 18 September 2020 and 30 March 2021.\n\nResultsCompared to white ethnicity, people of Asian and black ethnicity had a higher risk of infection during rounds 5 to 10, with odds of 1.46 (1.27, 1.69) and 1.35 (1.11, 1.64) respectively. Among ethnic subgroups, the highest and the second-highest odds were found in Bangladeshi and Pakistan participants at 3.29 (2.23, 4.86) and 2.15 (1.73, 2.68) respectively when compared to British whites. People in larger (compared to smaller) households had higher odds of infection. Health care workers with direct patient contact and care home workers showed higher odds of infection compared to other essential/key workers. Additionally, the odds of infection among participants in public-facing activities or settings were greater than among those not working in those activities or settings.\n\nConclusionOur findings highlight the differences in the risk of SARS-CoV-2 infection in a global-north population during a period when the risk of infection was high, and there were substantial levels of social mixing. Planning for future severe waves of respiratory pathogens should include policies to reduce inequality in the risk of infection by ethnicity, household size, and occupational activity in order to reduce inequality in disease.\n\nSummary boxWhat is already known on this topic\n\nExtensive studies have described the relationship between socio-demographic factors and SARS-CoV-2 outcomes such as hospitalisations and deaths, rather than SARS-CoV-2 infection. Limited community-based studies investigated risk factors associated with SARS-CoV-2 infection, with the time frame of these studies has mainly focused on the period of the first wave of infection, or the beginning of the second wave, or the rollout of the first dose of the vaccine after the second wave period. We did not find studies that covered the critical period of the second wave in England when levels of social mixing were high, but no vaccine was available.\n\nWhat this study adds\n\nWe show health inequalities across ethnic and sociodemographic subgroups during a key period: before widespread vaccination, but, largely, not during the period of stringent social distancing. We observed substantial ethnic and occupational differences in the risk of SARS-CoV-2 infection. Minority ethnic groups, including those of Bangladeshi and Pakistani ethnicity, had an excess risk of infection compared with the British white population. Healthcare workers, care home workers and people who work in public-facing activities or settings were associated with higher odds of infection. The risk of SARS-CoV-2 infection increased monotonically as household size increased, and more deprived neighbourhood areas were associated with a higher risk of infection.\n\nHow this study might affect research, practice or policy\n\nOur findings highlight the differences in the risk of SARS-CoV-2 infection in a global-north population during a period when the risk of infection was high, and there were substantial levels of social mixing. Planning for future waves of severe respiratory infection should explicitly aim to reduce inequalities in infection in order to reduce inequality in disease.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.07.31.23293422", @@ -503,6 +489,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.07.16.23292705", + "date": "2023-07-18", + "link": "https://medrxiv.org/cgi/content/short/2023.07.16.23292705", + "title": "Community-onset urinary tract infection in females in the context of COVID-19: a longitudinal population cohort study exploring case presentation, management, and outcomes", + "authors": "Nina J Zhu; Benedict Hayhoe; Raheelah Ahmad; James R Price; Donna Lecky; Monsey McLeod; Elena Ferran; Timothy M Rawson; Emma Carter; Alison H Holmes; Paul Aylin", + "affiliations": "National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Department of Primary Care and Public Health, School of Public Health, Imperial College London, London, United Kingdom; Division of Health Services Research and Management, School of Health Sciences, City, University of London, London, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom; NHS England and NHS Improvement, London, United Kingdom; Barts Health NHS Trust, London, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial ; Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom", + "abstract": "BackgroundCOVID-19 affected the epidemiology of other infectious diseases and how they were managed. Urinary tract infection (UTI) is one of the most common infections treated in the community in England. We investigated the impact of the COVID-19 pandemic on UTI primary care consultations and outcomes in female patients.\n\nMethods and findingsWe analysed General Practice (GP) consultation and hospital admission records using the Whole Systems Integrated Care (WSIC) data in North West London between 2016 and 2021. We quantified the changes in UTI GP consultation rates using time series analysis before and during the pandemic. We assessed the outcomes of UTI, measured by subsequent bacteraemia and sepsis within 60 days, for consultations delivered face-to-face or remotely, with or without diagnostic tests recommended by the national guidelines, and with or without antibiotic treatment. Between January 2016 and December 2021, we identified 375,859 UTI episodes in 233,450 female patients. Before the COVID-19 pandemic (January 2016 - February 2020), the UTI GP consultation rate stayed level at 522.8 cases per 100,000 population per month, with a seasonal pattern of peaking in October. Since COVID-19, (March 2020 - December 2021), monthly UTI GP consultations declined when COVID-19 cases surged and rose when COVID-19 case fell. During the pandemic, the UTI consultations delivered face-to-face reduced from 72.0% to 29.4%, the UTI consultations with appropriate diagnostic tests, including urine culture and urinalysis, reduced from 17.3% to 10.4%, and the UTI cases treated with antibiotics reduced from 52.0% to 47.8%. The likelihood of antibiotics being prescribed was not affected by whether the consultation was delivered face-to-face or remotely but associated with whether there was a diagnostic test. Regardless of whether the UTI consultation occurred before or during the pandemic, the absence of antibiotic treatment for UTI is associated with a 10-fold increase in the risk of having bacteraemia or sepsis within 60 days, though the patients who consulted GPs for UTI during the pandemic were older and more co-morbid. Across the study period (January 2016 - December 2021), nitrofurantoin remained the first-line antibiotic option for UTI. The percentage of non-prophylactic acute UTI antibiotic prescriptions with durations that exceeded the guideline recommendations was 58.7% before the pandemic, and 49.4% since. This led to 830,522 total excess days of treatment, account for 63.3% of all non-prophylactic acute antibiotics prescribed for UTI. Before the pandemic, excess antibiotic days of UTI drugs had been reducing consistently. However, this decline slowed down during the pandemic. Having a diagnostic test was associated with 0.6 less excess days of antibiotic treatment.\n\nConclusionsThis analysis provides a comprehensive examination of management and outcomes of community-onset UTI in female patients, considering the changes in GP consultations during the COVID-19 pandemic. Our findings highlighted the importance of appropriate urine testing to support UTI diagnosis in symptomatic patients and initiation of antibiotic treatment with appropriate course duration. Continued monitoring is required to assess the overall impact on patients and health systems from the changed landscape of primary care delivery.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.07.06.23292295", @@ -825,6 +825,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.03.15.23287292", + "date": "2023-03-15", + "link": "https://medrxiv.org/cgi/content/short/2023.03.15.23287292", + "title": "Living alone and mental health: parallel analyses in longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic", + "authors": "Eoin McElroy; Emily Herrett; Kishan Patel; Dominik M Piehlmaier; Giorgio Di Gessa; Charlotte Huggins; Michael J Green; Alex SF Kwong; Ellen J Thompson; Jingmin Zhu; Kathryn E Mansfield; Richard J Silverwood; Rosie Mansfield; Jane Maddock; Rohini Mathur; Ruth E Costello; Anthony A Matthews; John Tazare; Alasdair Henderson; Kevin Wing; Lucy Bridges; Sebastian Bacon; Amir Mehrkar; - OpenSafely Collaborative; Richard John Shaw; Jacques Wels; Srinivasa Vittal Katikireddi; Nishi Chaturvedi; Laurie Tomlinson; Praveetha Patalay", + "affiliations": "School of Psychology, Ulster University, Coleraine, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; University of Sussex Business Sch; Department of Epidemiology & Public Health, University College London, London, UK; Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Twin Research and Genetic Epidemiology, Kings College London; Department of Epidemiology & Public Health, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Centre for Longitudinal Studies, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Primary Care, Wolfson Insitute of Population Health, Queen Mary, University of London, London; London School of Hygiene and Tropical Medicine, London, UK; Karolinska Institutet, Stockholm, Sweden; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; ; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; London School of Hygiene and Tropical Medicine, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK", + "abstract": "ObjectivesTo describe the mental health gap between those who live alone and those who live with others, and to examine whether the COVID-19 pandemic had an impact on this gap.\n\nDesignTen population based prospective cohort studies, and a retrospective descriptive cohort study based on electronic health records (EHRs).\n\nSettingUK Longitudinal population-based surveys (LPS), and primary and secondary care records within the OpenSAFELY-TPP database.\n\nParticipantsParticipants from the LPS were included if they had information on living status in early 2020, valid data on mental ill-health at the closest pre-pandemic assessment and at least once during the pandemic, and valid data on a key minimum set of covariates. The EHR dataset included 16 million adults registered with primary care practices in England using TPP SystmOne software on 1st February 2020, with at least three months of registration, valid address data, and living in households of <16 people.\n\nMain outcome measuresIn the LPS, self-reported survey measures of psychological distress and life satisfaction were assessed in the nearest pre-pandemic sweep and three periods during the pandemic: April-June 2020, July-October 2020, and November 2020-March 2021. In the EHR analyses, outcomes were morbidity codes recorded in primary or secondary care between March 2018 and January 2022 reflecting the diagnoses of depression, self-harm, anxiety, obsessive compulsive disorder, eating disorders, and severe mental illnesses.\n\nResultsThe LPS consisted of 37,544 participants (15.2% living alone) and we found greater psychological distress (SMD: 0.09 (95% CI: 0.04, 0.14) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30, -0.15) in those living alone pre-pandemic, and the gap between the two groups stayed similar after the onset of the pandemic. In the EHR analysis of almost 16 million records (21.4% living alone), codes indicating mental health conditions were more common in those who lived alone compared to those who lived with others (e.g., depression 26 and severe mental illness 58 cases more per 100,000). Recording of mental health conditions fell during the pandemic for common mental health disorders and the gap between the two groups narrowed.\n\nConclusionsMultiple sources of data indicate that those who live alone experience greater levels of common and severe mental illnesses, and lower life satisfaction. During the pandemic this gap in need remained, however, there was a narrowing of the gap in service use, suggesting greater barriers to healthcare access for those who live alone.\n\nSummary BoxO_ST_ABSWhat is already known on the topic?C_ST_ABSHouseholds with one individual are an increasing demographic, comprising over a quarter of all households in the UK in 2021. However, the mental health gap between those who live alone compared to those who live with others is not well described and even less is known about the relative gaps in need and healthcare-seeking and access. The pandemic and associated restrictive measures further increased the likelihood of isolation for this group, which may have impacted mental health.\n\nWhat this study adds?We present comprehensive evidence from both population-based surveys and electronic health records regarding the greater levels of mental health symptoms and in recorded diagnoses for common (anxiety, depression) and less common (OCD, eating disorders, SMIs) mental health conditions for people living alone compared to those living with others.\n\nOur analyses indicate that mental health conditions are more common among those who live alone compared to those who live with others. Although levels of reported distress increased for both groups during the pandemic, healthcare-seeking dropped in both groups, and the rates of healthcare-seeking among those who live alone converged with those who live with others for common mental health conditions. This suggests greater barriers for treatment access among those that live alone.\n\nThe findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.26.23286474", @@ -951,6 +965,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.02.06.23285513", + "date": "2023-02-06", + "link": "https://medrxiv.org/cgi/content/short/2023.02.06.23285513", + "title": "A Rapid review on the COVID-19 Pandemic's Global Impact on Breast Cancer Screening Participation Rates and Volumes from January-December 2020", + "authors": "Reagan Lee; - UNCOVER; Wei Xu; - International Partnership for Resilience in Cancer Systems (I-PaRCS), Breast Cancer Working Group 2; Marshall Dozier; Ruth McQuillan; Evropi Theodoratou; Jonine Figueroa", + "affiliations": "University of Edinburgh; -; University of Edinburgh; -; University of Edinburgh; University of Edinburgh; The University of Edinburgh; University of Edinburgh", + "abstract": "BackgroundCOVID-19 has strained population breast mammography screening programs that aim to diagnose and treat breast cancers earlier. As the pandemic has affected countries differently, we aimed to quantify changes in breast screening volume and uptake during the first year of the COVID-19 pandemic.\n\nMethodsWe systematically searched Medline, the WHO (World Health Organization) COVID-19 database, and governmental databases. Studies covering January 2020 to March 2022 were included. We extracted and analyzed data regarding study methodology, screening volume and uptake. To assess for risk-of-bias, we used the Joanna Briggs Institute Critical Appraisal tool.\n\nResultsTwenty-six cross-sectional descriptive studies were included out of 935 independent records. Reductions in screening volume and uptake rates were observed among eight countries. Changes in screening participation volume in five countries with national population-based screening ranged from -13% to -31%. Among two countries with limited population-based programs the decline ranged from -61% to -41%. Within the USA, population participation volumes varied ranging from +18% to -39% with suggestion of differences by insurance status (HMO, Medicare, and low-income programs). Almost all studies had high risk-of-bias due to insufficient statistical analysis and confounding factors.\n\nDiscussion and ConclusionExtent of COVID-19-induced reduction in breast screening participation volume differed by region and data suggested potential differences by healthcare setting (e.g., national health insurance vs private health care). Recovery efforts should monitor access to screening and early diagnosis to determine if prevention services need strengthening to increase coverage of marginalized groups and reduce disparities.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.01.23285333", @@ -965,6 +993,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.01.31.23285232", + "date": "2023-02-01", + "link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285232", + "title": "Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour", + "authors": "Thomas Edward Byrne; Jana Kovar; Sarah Beale; Isobel Braithwaite; Ellen Fragaszy; Wing Lam Erica Fong; Cyril Geismar; Susan J Hoskins; Annalan Mathew Dwight Navaratnam; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Pia Hardelid; Linda Wijlaars; Eleni Nastouli; Moira Spyer; Anna Ayree; Ingemar Cox; Vasileios Lampos; Rachel A McKendry; Tao Cheng; Anne M Johnson; Susan Fiona Michie; Jo Gibbs; Richard Gilson; Alison Rodger; Ibrahim Abubakar; Andrew Hayward; Robert W Aldridge", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCLH; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL", + "abstract": "Key FeaturesO_LIVirus Watch is a national community cohort study of COVID-19 in households in England and Wales, established in June 2020. The study aims to provide evidence on which public health approaches are most effective in reducing transmission, and investigate community incidence, symptoms, and transmission of COVID-19 in relation to population movement and behaviours.\nC_LIO_LI28,527 households and 58,628 participants of age (0-98 years, mean age 48), were recruited between June 2020 - July 2022\nC_LIO_LIData collected include demographics, details on occupation, co-morbidities, medications, and infection-prevention behaviours. Households are followed up weekly with illness surveys capturing symptoms and their severity, activities in the week prior to symptom onset and any COVID-19 test results. Monthly surveys capture household finance, employment, mental health, access to healthcare, vaccination uptake, activities and contacts. Data have been linked to Hospital Episode Statistics (HES), inpatient and critical care episodes, outpatient visits, emergency care contacts, mortality, virology testing and vaccination data held by NHS Digital.\nC_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555).\nC_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS.\nC_LI", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.01.29.23285160", @@ -1217,20 +1259,6 @@ "author_similarity": 92, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.11.29.22282916", - "date": "2022-11-30", - "link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282916", - "title": "Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population", - "authors": "Jia Wei; Philippa C Matthews; Nicole Stoesser; John Newton; Ian Diamond; Ruth Studley; Nick Taylor; John Bell; Jeremy Farrar; Brian Marsden; Jaison Kolenchery; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick Crook; Tim E Peto; Ann Sarah Walker; Koen Pouwels; David W Eyre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; Public Health England; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", - "abstract": "Following primary SARS-CoV-2 vaccination, understanding the relative extent of protection against SARS-CoV-2 infection from boosters or from breakthrough infections (i.e. infection in the context of previous vaccination) has important implications for vaccine policy. In this study, we investigated correlates of protection against Omicron BA.4/5 infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults [≥]18y from the United Kingdom general population. We found that higher anti-spike IgG antibody levels were associated with increased protection against Omicron BA.4/5 infection and that breakthrough infections were associated with higher levels of protection at any given antibody level than booster vaccinations. Breakthrough infections generated similar antibody levels to third/booster vaccinations, and the subsequent declines in antibody levels were similar to or slightly slower than those after third/booster vaccinations. Taken together our findings show that breakthrough infection provides longer lasting protection against further infections than booster vaccinations. For example, considering antibody levels associated with 67% protection against infection, a third/booster vaccination did not provide long-lasting protection, while a Delta/Omicron BA.1 breakthrough infection could provide 5-10 months of protection against Omicron BA.4/5 reinfection. 50-60% of the vaccinated UK population with a breakthrough infection would still be protected by the end of 2022, compared to <15% of the triple-vaccinated UK population without previous infection. Although there are societal impacts and risks to some individuals associated with ongoing transmission, breakthrough infection could be an efficient immune-boosting mechanism for subgroups of the population, including younger healthy adults, who have low risks of adverse consequences from infection.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.11.29.22282899", @@ -2449,6 +2477,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.23.22272804", + "date": "2022-03-23", + "link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272804", + "title": "Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records", + "authors": "Elsie MF Horne; William J Hulme; Ruth H Keogh; Tom M Palmer; Elizabeth J Williamson; Edward PK Parker; Amelia Green; Venexia Walker; Alex J Walker; Helen Curtis; Louis Fisher; Brian MacKenna; Richard Croker; Lisa Hopcroft; Robin Y Park; Jon Massey; Jessica Morely; Amir Mehrkar; Sebastian Bacon; David Evans; Peter Inglesby; Caroline E Morton; George Hickman; Simon Davy; Tom Ward; Iain Dillingham; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne", + "affiliations": "University of Bristol; Univeristy of Oxford; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Univeristy of Oxford; University of Bristol; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Harvard University; University of Bristol", + "abstract": "BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies.\n\nMethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death.\n\nFindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1.\n\nInterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.18.22272607", @@ -2729,20 +2771,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.02.07.22270451", - "date": "2022-02-08", - "link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270451", - "title": "Anti-spike antibody trajectories in individuals previously immunised with BNT162b2 or ChAdOx1 following a BNT162b2 booster dose", - "authors": "Alexei Yavlinsky; Sarah Beale; Vincent Nguyen; Madhumita Shrotri; Thomas Edward Byrne; Cyril Geismar; Ellen Fragaszy; Susan J Hoskins; Wing Lam Erica Fong; Annalan Mathew Dwight Navaratnam; Isobel Braithwaite; Parth Patel; Jana Kovar; Andrew C Hayward; Robert W Aldridge", - "affiliations": "Institute of Health Informatics, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Institute of Health Informatics, University College London, UK", - "abstract": "The two most commonly-used SARS-CoV-2 vaccines in the UK, BNT162b2 (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca), employ different immunogenic mechanisms. Compared to BNT162b2, two-dose immunisation with ChAdOx1 induces substantially lower peak anti-spike antibody (anti-S) levels and is associated with a higher risk of breakthrough infections. To provide preliminary indication of how a third booster BNT162b2 dose impacts anti-S levels, we performed a cross-sectional analysis using capillary blood samples from vaccinated adults (aged [≥]18 years) participating in Virus Watch, a prospective community cohort study in England and Wales. Blood samples were analysed using Roche Elecsys Anti-SARS-CoV-2 S immunoassay. We analysed anti-S levels by week since the third dose for vaccines administered on or after September 1, 2021 and stratified the results by second dose vaccine type (ChAdOx1 or BNT162b2), age, sex and clinical vulnerability. Anti-S levels peaked at two weeks post-booster for BNT162b2 (22,185 U/mL; 95%CI: 21,406-22,990) and ChAdOx1 second dose recipients (19,203 U/mL; 95%CI: 18,094-20,377). These were higher than the corresponding peak antibody levels post-second dose for BNT162b2 (12,386 U/mL; 95%CI: 9,801-15,653, week 2) and ChAdOx1 (1,192 U/mL; 95%CI: 818-1735, week 3). No differences emerged by second dose vaccine type, age, sex or clinical vulnerability. Anti-S levels declined post-booster for BNT162b2 (half-life=44 days) and ChAdOx1 second dose recipients (half-life=40 days). These rates of decline were steeper than those post-second dose for BNT162b2 (half-life=54 days) and ChAdOx1 (half-life=80 days). Our findings suggest that peak anti-S levels are higher post-booster than post-second dose, but that levels are projected to be similar after six months for BNT162b2 recipients. Higher peak anti-S levels post-booster may partially explain the increased effectiveness of booster vaccination compared to two-dose vaccination against symptomatic infection with the Omicron variant. Faster waning trajectories post third-dose may have implications for the timing of future booster campaigns or four-dose vaccination regimens for the clinically vulnerable.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.02.03.22270365", @@ -3093,6 +3121,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.12.17.473248", + "date": "2021-12-21", + "link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "authors": "Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge", + "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "category": "microbiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268098", @@ -3219,6 +3261,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.13.21267368", + "date": "2021-12-15", + "link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267368", + "title": "Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations", + "authors": "Ingibjorg Magnusdottir; Aniko Lovik; Anna Bara Unnarsdottir; Daniel L. McCartney; Helga Ask; Kadri Koiv; Lea Arregui Nordahl Christoffersen; Sverre Urnes Johnson; Andrew M McIntosh; Anna K. Kahler; Archie Campbell; Arna Hauksdottir; Chloe Fawns-Ritchie; Christian Erikstrup; Dorte Helenius; Drew Altschul; Edda Bjork Thordardottir; Elias Eythorsson; Emma M. Frans; Gunnar Tomasson; Harpa Lind Jonsdottir; Harpa Runarsdottir; Henrik Hjalgrim; Hronn Hardardottir; Juan Gonzalez-Hijon; Karina Banasik; Khoa Manh Dinh; Li Lu; Lili Milani; Lill Trogstad; Maria Didriksen; Omid V. Ebrahimi; Patrick F. Sullivan; Per Minor Magnus; Qing Shen; Ragnar Nesvag; Reedik Magi; Runolfur Palsson; Sisse Rye Ostrowski; Thomas Werge; Asle Hoffart; David J. Porteous; Fang Fang; Johanna Jakobsdottir; Kelli Lehto; Ole A. Andreassen; Ole B.V. Pedersen; Thor Aspelund; Unnur Anna Valdimarsdottir", + "affiliations": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Edinburgh, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Danish Cancer Society Research Center, Copenhagen, Denmark; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA; Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Immunology, Zealand University Hospital, Denmark; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland", + "abstract": "BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis.\n\nMETHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time.\n\nFINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.\n\nCONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 92 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.14.21267460", @@ -3387,6 +3443,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.11.22.21266692", + "date": "2021-11-24", + "link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266692", + "title": "Serological responses to COVID-19 booster vaccine in England", + "authors": "Georgina Ireland; Heather Whitaker; Shamez N Ladhani; Frances Baawuah; Vani Subbarao; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corrine Whillock; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown", + "affiliations": "UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre, Kilburn, London, United Kingdom; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency", + "abstract": "IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca).\n\nMethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared.\n\nResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants.\n\nConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.22.21266512", @@ -3639,20 +3709,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.01.21265660", - "date": "2021-11-02", - "link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265660", - "title": "Estimating the relationship between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana", - "authors": "Hamish Gibbs; Yang Liu; Sam Abbott; Isaac Baffoe-Nyarko; Dennis O. Laryea; Ernest Akyereko; Patrick Kuma-Aboagye; Ivy Asante; Oriol Mitja; - LSHTM CMMID COVID-19 Working Group; William Ampofo; Franklin Asiedu-Bekoe; Michael Marks; Rosalind M Eggo", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Ghana Health Service; Ghana Health Service; Ghana Health Service; Ghana Health Service; University of Ghana Noguchi Memorial Institute for Medical Research; Fight Against AIDS Foundation; ; University of Ghana Noguchi Memorial Institute for Medical Research; Ghana Health Service; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundGovernments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts.\n\nMethodsIn this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of Rt, a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana.\n\nFindingsWe observe a relationship between reductions in human mobility and decreases in Rt during the early stages of the COVID-19 epidemic in Ghana. We find that the strength of this relationship varies through time, decreasing after the most stringent period of interventions in the early epidemic.\n\nInterpretationOur findings demonstrate how the association of NPI and mobility indicators with COVID-19 transmission may vary through time. Further, we demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity and monitor the impact of NPI policies.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and preprint archives for articles published in English that contained information about the COVID-19 pandemic published up to Nov 1, 2021, using the search terms \"coronavirus\", \"CoV\", \"COVID-19\", \"mobility\", \"movement\", and \"flow\". The data thus far suggests that NPI measures including physical distancing, reduction of travel, and use of personal protective equipment have been demonstrated to reduce COVID-19 transmission. Much of the existing research focuses on comparisons of NPI stringency with COVID-19 transmission among different high-income countries, or on high-income countries, leaving critical questions about the applicability of these findings to low- and middle-income settings.\n\nAdded value of this studyWe used a detailed COVID-19 surveillance dataset from Ghana, and unique high resolution spatial data on human mobility from Vodafone Ghana as well as Google smartphone GPS location data. We show how human mobility and NPI stringency were associated with changes in the effective reproduction number (Rt). We further demonstrate how this association was strongest in the early COVID-19 outbreak in Ghana, decreasing after the relaxation of national restrictions.\n\nImplications of all the available evidenceThe change in association between human mobility, NPI stringency, and Rt may reflect a \"decoupling\" of NPI stringency and human mobility from disease transmission in Ghana as the COVID-19 epidemic progressed. This finding provides public health decision makers with important insights for the understanding of the utility of mobility data for predicting the spread of COVID-19.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.10.28.21265615", @@ -3891,6 +3947,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.13.21263487", + "date": "2021-09-16", + "link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "authors": "Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.13.21262360", @@ -4241,20 +4311,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.26.21261140", - "date": "2021-07-28", - "link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261140", - "title": "Higher serological responses and increased vaccine effectiveness demonstrate the value of extended vaccine schedules in combatting COVID-19 in England", - "authors": "Gayatri Amirthalingam; Jamie Lopez Bernal; Nick J Andrews; Heather Whitaker; Charlotte Gower; Julia Stowe; Elise Tessier; Sathyavani Subbarao; Georgina Ireland; Frances Baawuah; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corinne Whillock; Paul Moss; Shamez N Ladhani; Kevin E Brown; Mary E Ramsay", - "affiliations": "Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Brondesbury Medical Centre; Public Health England; University of Birmingham; Public Health England; Public Health England; Public Health England", - "abstract": "IntroductionIn January 2021, the UK decided to prioritise the delivery of the first dose of BNT162b2 (Pfizer/BioNTech) and AZD1222 (AstraZeneca) vaccines by extending the interval until the second dose up to 12 weeks.\n\nMethodsSerological responses were compared after BNT162b2 and AZD1222 vaccination with varying intervals in uninfected and previously-infected adults aged 50-89 years. These findings are evaluated against real-world national vaccine effectiveness (VE) estimates against COVID-19 in England.\n\nResultsWe recruited 750 participants aged 50-89 years, including 126 (16.8%) with evidence of previous infection; 421 received BNT162b2 and 329 and AZD1222. For both vaccines, over 95% had seroconverted 35-55 days after dose one, and 100% seroconverted 7+ days after dose 2. Following a 65-84 day interval between two doses, geometric mean titres (GMTs) at 14-34 days were 6-fold higher for BNT162b2 (6703; 95%CI, 5887-7633) than AZD1222 (1093; 806-1483), which in turn were higher than those receiving BNT162b2 19-29 days apart (694; 540 - 893). For both vaccines, VE was higher across all age-groups from 14 days after dose two compared to one dose, but the magnitude varied with interval between doses. Higher two-dose VE was observed with >6 week intervals between BNT162b2 doses compared to the authorised 3-week schedule, including [≥]80 year-olds.\n\nConclusionOur findings support the UK approach of prioritising the first dose of COVID-19 vaccines, with evidence of higher protection following extended schedules. Given global vaccine constraints, these results are relevant to policymakers, especially with highly transmissible variants and rising incidence in many countries.\n\nFundingPublic Health England", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.23.21260992", @@ -4283,6 +4339,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.07.20.21260558", + "date": "2021-07-22", + "link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260558", + "title": "Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study", + "authors": "Rebecca Wilson; Harriet Quinn-Scoggins; Yvonne Moriarty; Jacqueline Hughes; Mark Goddard; Rebecca Cannings-John; Victoria Whitelock; Katriina L Whitaker; Detelina Grozeva; Julia Townson; Kirstie Osborne; Stephanie Smits; Michael Robling; Julie Hepburn; Graham Moore; Ardiana Gjini; Kate Brain; Jo Waller", + "affiliations": "Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cancer Research UK; University of Surrey; Cardiff University; Cardiff University; Cancer Research UK; Cardiff University; Cardiff University; Public Involvement Community, Health and Care Research Wales; Cardiff University; Public Health Wales; Cardiff University; Kings College London", + "abstract": "Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK.\n\nOverall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically.\n\nOf those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed.\n\nIntentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.", + "category": "oncology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 98 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.19.21260782", @@ -4829,6 +4899,20 @@ "author_similarity": 95, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.06.08.21258533", + "date": "2021-06-12", + "link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258533", + "title": "The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.", + "authors": "Aleksandra Kovacevic; Rosalind M Eggo; Marc Baguelin; Matthieu Domenech de Cell\u00e8s; Lulla Opatowski", + "affiliations": "Institut Pasteur; London School of Hygiene & Tropical Medicine; Imperial College London; Max Planck Institute for Infection Biology; Univ Versailles Saint Quentin / Institut Pasteur / Inserm", + "abstract": "BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data.\n\nMethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality.\n\nResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive.\n\nConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.\n\nSummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.08.21258546", @@ -5027,14 +5111,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.05.14.21257229", + "doi": "10.1101/2021.05.18.21257267", "date": "2021-05-18", - "link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257229", - "title": "Symptom profiles and accuracy of clinical definitions for COVID-19 in the community. Results of the Virus Watch community cohort.", - "authors": "Ellen Fragaszy; Madhumita Shrotri; Cyril Geismar; Anna Aryee; Sarah Beale; Isobel Braithwaite; Thomas Byrne; Wing Lam Erica Fong; Jo Gibbs; Pia Hardelid; Jana Kovar; Vasileios Edward Lampos; Eleni Nastouli; Annalan Mathew Dwight Navaratnam; Vincent Grigori Nguyen; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative", - "affiliations": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; Department of Infectious Disease Epidemiology, London School ; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute for Global Health, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Institute of Epidemiology and Health Care, University College London; Department of Computer Science, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Francis Crick Institute, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London; . Institute of Epidemiology and Health Care, University Colle; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College London; ", - "abstract": "BackgroundUnderstanding the symptomatology and accuracy of clinical case definitions for COVID-19 in the community is important for the initiation of Test, Trace and Isolate (TTI) and may, in future, be important for early prescription of antivirals.\n\nMethodsVirus Watch is a large community cohort with prospective daily recording of a wide range of symptoms and self-reporting of swab results (mainly undertaken through the UK TTI system). We compared frequency, severity, timing, and duration of symptoms in test positive and test negative cases. We compared the test performance of the current UK case definition used by TTI (any one of: new continuous cough, high temperature, or loss of or altered sense of smell or taste) with a wider definition that also included muscle aches, chills, headache, or loss of appetite.\n\nFindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition.\n\nInterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.", - "category": "epidemiology", + "link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257267", + "title": "Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", + "authors": "Peter W Horby; Mark Campbell; Enti Spata; Jonathan R Emberson; Natalie Staplin; Guilherme Pessoa-Amorim; Leon Peto; Martin Wiselka; Laura Wiffen; Simon Tiberi; Ben Caplin; Caroline Wroe; Christopher Green; Paul Hine; Benjamin Prudon; Tina George; Andrew Wight; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph L Hamers; Thomas Jaki; Edmund Juszczak; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray", + "affiliations": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat; Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Department of Infection, Barts Health NHS Trust, London, United Kingdom; Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Course Sciences, King?s College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un", + "abstract": "BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions.\n\nMethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47).\n\nInterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.", + "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -5195,14 +5279,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.05.10.21256912", - "date": "2021-05-11", - "link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256912", - "title": "Household overcrowding and risk of SARS-CoV-2: analysis of the Virus Watch prospective community cohort study in England and Wales", - "authors": "Robert W Aldridge; Helen Pineo; Ellen Fragaszy; Max Eyre; Jana Kovar; Vincent Nguyen; Sarah Beale; Thomas Byrne; Anna Aryee; Colette Smith; Delanjathan Devakumar; Jonathon Taylor; Vittal Katikireddi; Wing Lam Erica Fong; Cyril Geismar; Parth Patel; Madhumita Shrotri; Isobel Braithwaite; Annalan M D Navaratnam; Anne M Johnson; Andrew Hayward", - "affiliations": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Institute for Environmental Design and Engineering, Bartlett School of Environment, Energy and Resources, University College London, London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Institute for Global Health, University College London, London, UK.; Institute for Global Health, University College London, London, UK.; Department of Civil Engineering, Tampere University, Finland.; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow Institute of Health and Wellbeing, Glasgow, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Institute for Global Health, University College London, London, UK.; Institute of Epidemiology and Health Care, University College London, London, UK", - "abstract": "BackgroundHousehold overcrowding is associated with increased risk of infectious diseases across contexts and countries. Limited data exist linking household overcrowding and risk of COVID-19. We used data collected from the Virus Watch cohort to examine the association between overcrowded households and SARS-CoV-2.\n\nMethodsThe Virus Watch study is a household community cohort of acute respiratory infections in England & Wales that began recruitment in June 2020. We calculated the persons per room for each household and classified accommodation as overcrowded when the number of rooms{square}was fewer than the number of people. We considered two primary outcomes - PCR-confirmed positive SARS-CoV-2 antigen tests and laboratory confirmed SARS-CoV-2 antibodies (Roche Elecsys anti-N total immunoglobulin assay). We used mixed effects logistic regression models that accounted for household structure to estimate the association between household overcrowding and SARS-CoV-2 infection.\n\nResultsThe proportion of participants with a positive SARS-CoV-2 PCR result was highest in the overcrowded group (6.6%; 73/1,102) and lowest in the under-occupied group (2.9%; 682/23,219). In a mixed effects logistic regression model that included age, sex, ethnicity, household income and geographical region, we found strong evidence of an increased odds of having a positive PCR SARS-CoV-2 antigen result (Odds Ratio 3.72; 95% CI: 1.92, 7.13; p-value < 0.001) and increased odds of having a positive SARS-CoV-2 antibody result in individuals living in overcrowded houses (2.96; 95% CI: 1.13, 7.74; p-value =0.027) compared to people living in under-occupied houses. The proportion of variation at the household level was 9.91% and 9.97% in the PCR and antibody models respectively.\n\nDiscussionPublic health interventions to prevent and stop the spread of SARS-CoV-2 should consider the much greater risk of infection for people living in overcrowded households and pay greater attention to reducing household transmission. There is an urgent need to better recognise housing as a leading determinant of health in the context of a pandemic and beyond.", - "category": "infectious diseases", + "doi": "10.1101/2021.05.05.21256668", + "date": "2021-05-09", + "link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "authors": "Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz", + "affiliations": "The University of Edinburgh; The University of Edinburgh; The University of Edinburgh", + "abstract": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "category": "health informatics", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -5265,13 +5349,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.04.24.21255968", - "date": "2021-04-27", - "link": "https://medrxiv.org/cgi/content/short/2021.04.24.21255968", - "title": "MORTALITY OF CARE HOME RESIDENTS AND COMMUNITY-DWELLING CONTROLS DURING THE COVID-19 PANDEMIC IN 2020: MATCHED COHORT STUDY", - "authors": "Martin C Gulliford; A Toby Prevost; Andrew Clegg; Emma C Rezel-Potts", - "affiliations": "King's College London; King's College London; University of Leeds; King's College London", - "abstract": "ObjectiveTo estimate mortality of care home (CH) residents, and matched community-dwelling controls, during the Covid-19 pandemic from primary care electronic health records.\n\nDesignMatched cohort study\n\nSettingGeneral practices contributing to the Clinical Practice Research Datalink Aurum Database in England.\n\nParticipantsThere were 83,627 CH residents contributing data in 2020, with 26,923 deaths; 80,730 (97%) were matched on age, gender and general practice with 300,445 community-dwelling adults.\n\nMain outcome measuresAll-cause mortality. Adjusted rate ratios (RR) by negative binomial regression were adjusted for age, gender, number of long-term conditions (LTCs), frailty category, region, calendar month or week, and clustering by general practice.\n\nResultsDuring April 2020, the mortality rate of CH residents was 27.2 deaths per 1,000 patients per week, compared with 2.31 per 1,000 for controls, RR 11.1 (95% confidence interval 10.1 to 12.2). Compared with CH residents, LTCs and frailty were differentially associated with greater mortality in community-dwelling controls. During April 2020, mortality rates per 1,000 patients per week for persons with 9+ LTCs were: CH, 37.9; controls 17.7; RR 2.14 (1.18 to 3.89). In severe frailty, mortality rates were: CH, 29.6; controls 5.1; RR 6.17 (5.74 to 6.62).\n\nConclusionsIndividual-patient data from primary care electronic health records may be used to estimate mortality in care home residents. Mortality is substantially higher than for community-dwelling comparators and showed a disproportionate increase in the first wave of the Covid-19 pandemic. Multiple morbidity and frailty were associated with greater absolute risks but lower relative risks because community-dwelling frail or multi-morbid patients also experienced high mortality.", + "doi": "10.1101/2021.04.26.21255732", + "date": "2021-04-28", + "link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "authors": "Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative", + "affiliations": "University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", + "abstract": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", "category": "epidemiology", "match_type": "fuzzy", "author_similarity": 100, @@ -5279,14 +5363,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.04.21.21255807", + "doi": "10.1101/2021.04.24.21255968", "date": "2021-04-27", - "link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255807", - "title": "A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial", - "authors": "Timothy SC Hinks; Lucy Cureton; Ruth Knight; Ariel Wang; Jennifer L Cane; Vicki S Barber; Joanna Black; Susan J Dutton; James Melhorn; Maisha Jabeen; Phil Moss; Rajendar Garlapati; Tanya Baron; Graham Johnson; Fleur Cantle; David Clarke; Samer Elkhodair; Jonathan Underwood; Daniel Lasserson; Ian D Pavord; Sophie B Morgan; Duncan Richards", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; St George's Hospital, London; East Lancashire NHS Hospitals; Oxford University Hospitals NHS Trust; Royal Derby Hospital; Kings College Hospital, London; Royal Berkshire Hospital; University College London Hospital; Cardiff University; Oxford University Hospitals NHS Trust; University of Oxford; University of Oxford; University of Oxford", - "abstract": "BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19.\n\nMethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed.\n\nFindings298 participants were enrolled from 3rd June 2020 to 29th January 2021. The primary outcome was assessed in 292 participants. The primary endpoint was not significantly different between the azithromycin and control groups (Adjusted OR 0{middle dot}91 [95% CI 0{middle dot}43-1{middle dot}92], p=0{middle dot}80). Rates of respiratory failure, progression to pneumonia, all-cause mortality, and adverse events, including serious cardiovascular events, were not significantly different between groups.\n\nInterpretationIn patients with mild-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospitalisation or death. Our findings do not support the use of azithromycin in patients with mild-moderate COVID-19.\n\nFundingNIHR Oxford BRC, University of Oxford and Pfizer Inc.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE and the Cochrane Central register of Controlled Trials (CENTRAL) with the terms (\"azithromycin\") AND (\"COVID\" OR \"COVID-19\") AND (\"clinical trials\"), until March 25, 2021, with no language restrictions. We identified 42 studies, among which there were four completed randomised trials of azithromycin (with or without hydroxychloroquine) in hospitalised patients with severe disease, and three completed randomised trials of azithromycin in mild COVID-19 in primary care. The four trials in hospitalised patients randomised 8,988 participants to azithromycin or standard care or hydroxychloroquine and found no evidence of a difference in mortality, duration of hospital stay or peak disease severity. Of the three trials in primary care, these randomised participants with early disease to 3 or 5 days of therapy, of which only one assessed azithromycin as standalone therapy. This large, adaptive platform trial in the UK randomised 540 participants in primary care to 3 days treatment with azithromycin versus 875 to standard care alone and found no meaningful difference in time to first reported recovery, or of rates of hospitalisation (3% versus 3%) and there were no deaths. We did not identify any randomised trials in patients with COVID-19 managed in ambulatory care.\n\nAdded value of this studyThe ATOMIC2 trial was uniquely-designed to assess azithromycin as a standalone therapy in those with mild-moderately COVID-19 presenting to emergency care, but assessed as appropriate for initial ambulatory management without hospital admission. ATOMIC2 also uniquely assessed high-dose, long-duration treatment to investigate the efficacy of putative anti-inflammatory effects. We found that azithromycin 500 mg daily for 14 days did not reduce the proportion of participants who died or required hospital admission from any cause over the 28 days from randomisation.\n\nImplications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.", - "category": "infectious diseases", + "link": "https://medrxiv.org/cgi/content/short/2021.04.24.21255968", + "title": "MORTALITY OF CARE HOME RESIDENTS AND COMMUNITY-DWELLING CONTROLS DURING THE COVID-19 PANDEMIC IN 2020: MATCHED COHORT STUDY", + "authors": "Martin C Gulliford; A Toby Prevost; Andrew Clegg; Emma C Rezel-Potts", + "affiliations": "King's College London; King's College London; University of Leeds; King's College London", + "abstract": "ObjectiveTo estimate mortality of care home (CH) residents, and matched community-dwelling controls, during the Covid-19 pandemic from primary care electronic health records.\n\nDesignMatched cohort study\n\nSettingGeneral practices contributing to the Clinical Practice Research Datalink Aurum Database in England.\n\nParticipantsThere were 83,627 CH residents contributing data in 2020, with 26,923 deaths; 80,730 (97%) were matched on age, gender and general practice with 300,445 community-dwelling adults.\n\nMain outcome measuresAll-cause mortality. Adjusted rate ratios (RR) by negative binomial regression were adjusted for age, gender, number of long-term conditions (LTCs), frailty category, region, calendar month or week, and clustering by general practice.\n\nResultsDuring April 2020, the mortality rate of CH residents was 27.2 deaths per 1,000 patients per week, compared with 2.31 per 1,000 for controls, RR 11.1 (95% confidence interval 10.1 to 12.2). Compared with CH residents, LTCs and frailty were differentially associated with greater mortality in community-dwelling controls. During April 2020, mortality rates per 1,000 patients per week for persons with 9+ LTCs were: CH, 37.9; controls 17.7; RR 2.14 (1.18 to 3.89). In severe frailty, mortality rates were: CH, 29.6; controls 5.1; RR 6.17 (5.74 to 6.62).\n\nConclusionsIndividual-patient data from primary care electronic health records may be used to estimate mortality in care home residents. Mortality is substantially higher than for community-dwelling comparators and showed a disproportionate increase in the first wave of the Covid-19 pandemic. Multiple morbidity and frailty were associated with greater absolute risks but lower relative risks because community-dwelling frail or multi-morbid patients also experienced high mortality.", + "category": "epidemiology", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -5809,6 +5893,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.12.21253484", + "date": "2021-03-13", + "link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253484", + "title": "Limits of lockdown: characterising essential contacts during strict physical distancing", + "authors": "Amy C Thomas; Leon Danon; Hannah Christensen; Kate Northstone; Daniel Smith; Emily J Nixon; Adam Trickey; Gibran Hemani; Sarah Sauchelli; Adam Finn; Nicholas J Timpson; Ellen Brooks-Pollock", + "affiliations": "University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; NIHR Bristol Biomedical Research Centre, University of Bristol; University of Bristol; University of Bristol; University of Bristol", + "abstract": "COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.10.21253173", @@ -6145,20 +6243,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.15.21251552", - "date": "2021-02-19", - "link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251552", - "title": "Evaluating the effect of COVID-19 on dispensing patterns: a national cohort analysis", - "authors": "Fatemeh Torabi; Ashley Akbari; Laura North; Daniel Harris; Gareth Davies; Mike Gravenor; Rowena Griffiths; Jane Lyons; Neil Jenkins; Andrew Morris; Julian Halcox; Ronan A. Lyons", - "affiliations": "Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK,Swansea University; Swansea University; Population Data Science and Health Data Research UK,Swansea University; Population Data Science and Health Data Research UK, SwanseaUniversity; NHS Wales Shared Services Partnership; Swansea University; Population Data Science and Health Data Research UK, Swansea University; Population Data Science and Health Data Research UK, Swansea University", - "abstract": "BackgroundMedication prescribing and dispensing often regarded as one of the most effective ways to manage and improve population health. Prescribed and dispensed medications can be monitored through data linkage for each patient. We hypothesised that changes in patient care resulting from COVID-19, changed the way patients access their prescribed medication.\n\nObjectiveTo develop an efficient approach for evaluation of the impact of COVID-19 on drug dispensing patterns.\n\nMethodsRetrospective observational study using national patient-level dispensing records in Wales-UK. Total dispensed drug items between 01-Jan-2016 and 31-Dec-2019 (counterfactual pre-COVID-19) were compared to 2020 (COVID-19 year). We compared trends of dispensed items in three main British National Formulary (BNF) sections(Cardiovascular system, Central Nervous System, Immunological & Vaccine) using European Age-Standardized rates. We developed an online tool to enable monitoring of changes in dispensing as the pandemic evolves.\n\nResultAmongst all BNF chapters, 52,357,639 items were dispensed in 2020 compared to 49,747,141 items in 2019 demonstrating a relative increase of 5.25% in 2020(95%CI[5.21,5.29]). Comparison of monthly patterns of 2020 and 2019 dispensed items showed a notable difference between the total number of dispensed drug items each month, with an average difference (D) of +290,055 and average Relative Change (RC) of +5.52%. The greatest RC was observed in a substantial March-2020 increase (D=+1,501,242 and RC=+28%), followed by second peak in June (D=+565,004, RC=+10.97%). May was characterised by lower dispensing (D=-399,244, RC=-5.9%). Cardiovascular categories were characterised, across all age groups, by dramatic March-2020 increases, at the epidemic peak, followed by months of lower than expected dispensing, and gradual recovery by September. The Central Nervous System category was similar, but with only a short decline in May, and quicker recovery. A stand-out grouping was Immunological and Vaccine, which dropped to very low levels across all age groups, and all months (including the March dispensing peak).\n\nConclusionsAberration in clinical service delivery during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes", - "category": "health systems and quality improvement", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.17.21251812", @@ -6229,20 +6313,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.08.21250525", - "date": "2021-02-09", - "link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250525", - "title": "COVID-19 infection and outcomes in a population-based cohort of 17,173 adults with intellectual disabilities compared with the general population", - "authors": "Angela Henderson; Micheal Fleming; Sally-Ann Cooper; Jill Pell; Craig Melville; Daniel MacKay; Christopher Hatton; Deborah Kinnear", - "affiliations": "University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Manchester Metropolitan University; University of Glasgow", - "abstract": "ObjectivesTo compare COVID-19 infection, severe infection, mortality, case-fatality, and excess deaths, among adults with intellectual disabilities and those without.\n\nDesignRecord-linkage of all adults recorded with intellectual disabilities in Scotlands Census, 2011, and a 5% sample of other adults, to COVID-19 test results (Electronic Communication of Surveillance in Scotland), hospitalisations (Scottish Morbidity Record 01), and deaths (National Records of Scotland).\n\nSettingGeneral population; 24th January 2020 - 15th August 2020\n\nParticipantsSuccessful linkage of 94.8% provided data on 17,173 adults with, and 195,859 without, intellectual disabilities.\n\nOutcomesCrude rates of COVID-19 infection, severe infection (hospitalisation/death), mortality, and case fatality; age-, sex- and deprivation-standardised severe infection and mortality ratios; annual all-cause mortality for 2020 and 2015-2019.\n\nResultsAdults with intellectual disabilities had higher rates of COVID-19 infection (957/100,000 versus 513/100,000); severe infection (549/100,000 versus 237/100,000); mortality (259/100,000 versus 114/100,000); and case-fatality (30% versus 24%). Poorer COVID-19 outcomes remained after standardising for age, sex and deprivation: standardised severe infection ratio 2.59 (95% CI 1.80, 3.39) and mortality ratio 3.20 (95% CI 2.16, 4.25). These were higher among 55-64 year olds: 7.12 (95% CI 3.73, 10.50) and 16.16 (95% CI7.69, 24.63) respectively. Among adults with intellectual disabilities, all-cause mortality was only slightly higher in 2020 than the previous five years: standardised mortality ratios 2.49 (95% CI 2.17, 2.81) and 2.38 (95% CI 2.26, 2.49) respectively.\n\nConclusionsAdults with intellectual disabilities were more likely to be infected with COVID-19, and had worse outcomes once infected, particularly those under 65 years. Non-pharmaceutical interventions directed at formal and informal carers are essential to reduce transmission and all adults with intellectual disabilities should be immediately prioritised for vaccination regardless of age.\n\nSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICOVID-19 mortality is higher within multi-occupancy residences.\nC_LIO_LIAdults with intellectual disabilities may be at higher risk of COVID-19 mortality than other adults, but there are gaps in the evidence.\nC_LIO_LICOVID-19 case-fatality may be no different, or as much as 2.75 times higher in adults with intellectual disabilities compared with other adults.\nC_LI\n\nWhat this study addsO_LICompared with general population adults, adults with intellectual disabilities were almost twice as likely to become infected with COVID-19, 2.3 times as likely to have severe infection, 2.3 times as likely to have COVID-19 mortality, and had 25% higher COVID-19 case-fatality.\nC_LIO_LIAfter standardising for age, sex and deprivation, people with intellectual disabilities were 3.2 times more at risk of covid-19 mortality and 2.6 times more at risk of severe infection relative to those with no intellectual disabilities\nC_LIO_LICompared with general population adults, adults with intellectual disabilities had poorer outcomes among non-elderly age-groups particularly those aged 55-65 years, men, and those living in less-deprived neighbourhoods.\nC_LIO_LINon-pharmaceutical initiatives are important for carers and care-provider organisations, and adults with intellectual disabilities should be prioritised in the national rollouts of COVID-19 vaccination programmes, regardless of age, sex, or neighbourhood deprivation.\nC_LI", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.04.21251155", @@ -6299,6 +6369,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.02.02.21251043", + "date": "2021-02-05", + "link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251043", + "title": "COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort", + "authors": "Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell", + "affiliations": "University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow", + "abstract": "ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE).\n\nPatients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally.\n\nResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test.\n\nConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.", + "category": "cardiovascular medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.02.03.21251004", @@ -6425,20 +6509,6 @@ "author_similarity": 94, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.01.26.21249744", - "date": "2021-01-27", - "link": "https://medrxiv.org/cgi/content/short/2021.01.26.21249744", - "title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in a higher education sample", - "authors": "Daniel Leightley Dr; Valentina Vitiello Dr; Alice Wickersham Ms; Katrina A.S. Davis Dr; Gabriella Bergin-Cartwright Ms; Grace Lavelle Dr; Sharon A.M. Stevelink Dr; Matthew Hotopf Prof; Reza Razavi Prof", - "affiliations": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.", - "abstract": "ObjectiveTo assess the feasibility of home antibody testing as part of large-scale study, the Kings College London Coronavirus Health and Experiences of Colleagues at Kings (KCL CHECK).\n\nMethodsParticipants of the KCL CHECK study were sent a SureScreen Diagnostics COVID-19 IgG/IgM Rapid Test Cassette to complete at home in June 2020 (phase 1) and September 2020 (phase 2). Participants were asked to upload a test result image to a study website. Test result images and sociodemographic information were analysed by the research team.\n\nResultsA total of n=2716 participants enrolled in the KCL CHECK study, with n=2003 (73.7%) and n=1825 (69.3%) consenting and responding to phase 1 and 2. Of these, n=1882 (93.9%; phase 1) and n=1675 (91.8%; phase 2) returned a valid result. n=123 (6.5%; phase 1) and n=91 (5.4%; phase 2) tested positive for SARS-CoV-2 antibodies. A total of n=1488 participants provided a result in both phases, with n=57 (3.8%) testing positive for SARS- CoV-2 antibodies across both phases, suggesting a reduction in the number of positive antibody results over time. Initial comparisons showed variation by age group, gender and clinical role.\n\nConclusionsOur study highlights the feasibility of rapid, repeated and low-cost SARS-CoV-2 serological testing without the need for face-to-face contact.\n\nWhat is already known about this subject?Higher education institutions have a duty of care to minimise the spread and transmission of COVID-19 in its campuses, and among staff and students. The reopening of higher education buildings and campuses has brought about a mass movement of students, academics and support staff from across the UK. Serological antibody studies can assist by highlighting groups of people and behaviours associated with high risk of COVID-19.\n\nWhat are the new findings?We report a framework for SARS-CoV-2 serological antibody testing in an occupational group of postgraduate research students and current members of staff at Kings College London. Over two phases of data collection, 6.5% (phase 1) and 5.4% (phase 2) tested positive for SARS-CoV-2 antibodies, with only 3.8% testing positive for antibodies in both phases, suggesting a reduction in positive antibody results over time.\n\nHow might this impact on policy or clinical practice in the foreseeable future?Our study highlights the feasibility of rapidly deploying low-cost and repeatable SARS-CoV-2 serological testing, without the need for face-to-face contact, to support the higher education system of the UK.", - "category": "health policy", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.01.25.21250356", @@ -6481,6 +6551,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.01.25.428136", + "date": "2021-01-25", + "link": "https://biorxiv.org/cgi/content/short/2021.01.25.428136", + "title": "mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge", + "authors": "Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev", + "affiliations": "University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston", + "abstract": "The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 96, + "affiliation_similarity": 94 + }, { "site": "medRxiv", "doi": "10.1101/2021.01.21.20240887", @@ -7055,6 +7139,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234849", + "date": "2020-11-22", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "authors": "Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20233932", @@ -7083,6 +7181,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.18.20225029", + "date": "2020-11-20", + "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20225029", + "title": "The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic", + "authors": "Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen", + "abstract": "BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic.\n\nMethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed.\n\nFindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures.\n\nInterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20234369", @@ -8077,6 +8189,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.01.20185793", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "authors": "Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter", + "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust", + "abstract": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "category": "emergency medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.02.20186502", @@ -8539,20 +8665,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.29.20162701", - "date": "2020-07-30", - "link": "https://medrxiv.org/cgi/content/short/2020.07.29.20162701", - "title": "Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England", - "authors": "Philippa M Wells; Katie M Doores; Simon Couvreur; Rocio Martin Martinez; Jeffrey Seow; Carl Graham; Sam Acors; Neophytos Kouphou; Stuart Neil; Richard Tedder; Pedro Matos; Kate Poulton; Maria Jose Lista; Ruth Dickenson; Helin Sertkaya; Thomas Maguire; Edward Scourfield; Ruth Bowyer; Deborah Hart; Aoife O'Byrne; Kathryn Steele; Oliver Hemmings; Carolina Rosadas; Myra McClure; Joan Capedevila-Pujol; Jonathan wolf; Sebastien Ourseilin; Matthew Brown; Michael Malim; Timothy Spector; Claire Steves", - "affiliations": "King's College London; King's College London; KCL; King's College London; KCL; KCL; KCL; KCL; KCL; Imperial; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; KCL; Imperial College London; Imperial College London; KCL; Zoe Global; Zoe Global; KCL; KCL; King's College London; King's College London", - "abstract": "BackgroundUnderstanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms.\n\nMethodsWe undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million.\n\nFindingsWe demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive.\n\nInterpretationSeroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response.\n\nFundingNIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 92, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.26.20161570", @@ -9113,20 +9225,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.15.20131722", - "date": "2020-06-17", - "link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131722", - "title": "Delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults", - "authors": "Maria Beatrice Zazzara; Rose S. Penfold; Amy L. Roberts; Karla Lee; Hannah Dooley; Carole H. Sudre; Carly Welch; Ruth C. E. Bowyer; Alessia Visconti; Massimo Mangino; Maxim B. Freydin; Julia S. El-Sayed Moustafa; Kerrin Small; Benjamin Murray; Marc Modat; Jonathan Wolf; Sebastien Ourselin; Finbarr C. Martin; Claire J. Steves; Mary Ni Lochlainn", - "affiliations": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Gerontology, Neuroscience and O; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Institute of Inflammation and Ageing, University of Birmingham, B15 2TT; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; NIHR Biomedical Research Centre at Guy's and ; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Population Health Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH", - "abstract": "BackgroundFrailty, increased vulnerability to physiological stressors, is associated with adverse outcomes. COVID-19 exhibits a more severe disease course in older, co-morbid adults. Awareness of atypical presentations is critical to facilitate early identification.\n\nObjectiveTo assess how frailty affects presenting COVID-19 symptoms in older adults.\n\nDesignObservational cohort study of hospitalised older patients and self-report data for community-based older adults.\n\nSettingAdmissions to St Thomas Hospital, London with laboratory-confirmed COVID-19. Community-based data for 535 older adults using the COVID Symptom Study mobile application.\n\nSubjectsHospital cohort: patients aged 65 and over (n=322); unscheduled hospital admission between March 1st, 2020-May 5th, 2020; COVID-19 confirmed by RT-PCR of nasopharyngeal swab. Community-based cohort: participants aged 65 and over enrolled in the COVID Symptom Study (n=535); reported test-positive for COVID-19 from March 24th (application launch)-May 8th, 2020.\n\nMethodsMultivariate logistic regression analysis performed on age-matched samples from hospital and community-based cohorts to ascertain association of frailty with symptoms of confirmed COVID-19.\n\nResultsHospital cohort: significantly higher prevalence of delirium in the frail sample, with no difference in fever or cough. Community-based cohort :significantly higher prevalence of probable delirium in frailer, older adults, and fatigue and shortness of breath.\n\nConclusionsThis is the first study demonstrating higher prevalence of delirium as a COVID-19 symptom in older adults with frailty compared to other older adults. This emphasises need for systematic frailty assessment and screening for delirium in acutely ill older patients in hospital and community settings. Clinicians should suspect COVID-19 in frail adults with delirium.", - "category": "geriatric medicine", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.06.13.20130419", @@ -9211,6 +9309,20 @@ "author_similarity": 100, "affiliation_similarity": 91 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.10.20127175", + "date": "2020-06-11", + "link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "authors": "Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL", + "abstract": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "category": "cardiovascular medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2020.06.11.145920", @@ -9575,6 +9687,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.05.14.20101824", + "date": "2020-05-19", + "link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101824", + "title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic", + "authors": "Hamish Gibbs; Yang Liu; Carl AB Pearson; Christopher I Jarvis; Chris Grundy; Billy J Quilty; Charlie Diamond; Rosalind M Eggo", + "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", + "abstract": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.\n\nOne sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.05.11.20098269", @@ -9715,20 +9841,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.07.20094557", - "date": "2020-05-11", - "link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094557", - "title": "Early impact of the COVID-19 pandemic and social distancing measures on routine childhood vaccinations in England, January to April 2020", - "authors": "Helen I McDonald; Elise Tessier; Joanne M White; Matthew Woodruff; Charlotte Knowles; Chris Bates; John Parry; Jemma L Walker; J Anthony Scott; Liam Smeeth; Joanne Yarwood; Mary Ramsay; Michael Edelstein", - "affiliations": "London School of Medicine and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation; Public Health England; Public Health England; TPP (Leeds) Ltd; TPP (Leeds) Ltd; TPP (Leeds) Ltd; TPP (Leeds) Ltd; London School of Hygiene and Tropical Medicine; Public Health England; NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation; Public Health England; Public Health England; NIHR Health Protection Research Unit (HPRU) in Immunisation; Public Health England", - "abstract": "Electronic health records were used to assess the early impact of COVID-19 on routine childhood vaccination in England to 26 April 2020.\n\nMMR vaccination counts fell from February 2020, and in the three weeks after introduction of social distancing measures were 19.8% lower (95% CI -20.7 to -18.9%) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated on introduction of social distancing.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.08.20078386", @@ -9743,20 +9855,6 @@ "author_similarity": 95, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.05.20092296", - "date": "2020-05-09", - "link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092296", - "title": "Ethnicity and risk of death in patients hospitalised for COVID-19 infection: an observational cohort study in an urban catchment area", - "authors": "Elizabeth Sapey; Suzy Gallier; Chris Mainey; Peter Nightingale; David McNulty; Hannah Crothers; Felicity Evison; Katharine Reeves; Domenico Pagano; Alastair K Denniston; Krishnarajah Nirantharakumar; Peter Diggle; Simon Ball", - "affiliations": "University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS FoundationTrust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Lancaster; University Hospitals Birmingham NHS Foundation Trust", - "abstract": "BackgroundStudies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients.\n\nMethodsPatients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10th March 2020-17th April 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching.\n\nResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2-1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)).\n\nConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.06.20092734", @@ -10163,34 +10261,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.01.20049908", - "date": "2020-04-06", - "link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049908", - "title": "The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study", - "authors": "Nicholas G Davies; Adam J Kucharski; Rosalind M Eggo; Amy Gimma; - CMMID COVID-19 Working Group; W. John Edmunds", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; -; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundNon-pharmaceutical interventions have been implemented to reduce transmission of SARS-CoV-2 in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been critical to support evidence-based policymaking during the early stages of the epidemic.\n\nMethodsWe used a stochastic age-structured transmission model to explore a range of intervention scenarios, including the introduction of school closures, social distancing, shielding of elderly groups, self-isolation of symptomatic cases, and extreme \"lockdown\"-type restrictions. We simulated different durations of interventions and triggers for introduction, as well as combinations of interventions. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (intensive care unit, ICU) treatment, and deaths.\n\nFindingsWe found that mitigation measures aimed at reducing transmission would likely have decreased the reproduction number, but not sufficiently to prevent ICU demand from exceeding NHS availability. To keep ICU bed demand below capacity in the model, more extreme restrictions were necessary. In a scenario where \"lockdown\"-type interventions were put in place to reduce transmission, these interventions would need to be in place for a large proportion of the coming year in order to prevent healthcare demand exceeding availability.\n\nInterpretationThe characteristics of SARS-CoV-2 mean that extreme measures are likely required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSAs countries have moved from early containment efforts to planning for the introduction of large-scale non-pharmaceutical interventions to control COVID-19 outbreaks, epidemic modelling studies have explored the potential for extensive social distancing measures to curb transmission. However, it remains unclear how different combinations of interventions, timings, and triggers for the introduction and lifting of control measures may affect the impact of the epidemic on health services, and what the range of uncertainty associated with these estimates would be.\n\nAdded value of this studyUsing a stochastic, age-structured epidemic model, we explored how eight different intervention scenarios could influence the number of new cases and deaths, as well as intensive care beds required over the projected course of the epidemic. We also assessed the potential impact of local versus national targeting of interventions, reduction in leisure events, impact of increased childcare by grandparents, and timing of triggers for different control measures. We simulated multiple realisations for each scenario to reflect uncertainty in possible epidemic trajectories.\n\nImplications of all the available evidenceOur results support early modelling findings, and subsequent empirical observations, that in the absence of control measures, a COVID-19 epidemic could quickly overwhelm a healthcare system. We found that even a combination of moderate interventions - such as school closures, shielding of older groups and self-isolation - would be unlikely to prevent an epidemic that would far exceed available ICU capacity in the UK. Intermittent periods of more intensive lockdown-type measures are predicted to be effective for preventing the healthcare system from being overwhelmed.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.01.20047357", - "date": "2020-04-04", - "link": "https://medrxiv.org/cgi/content/short/2020.04.01.20047357", - "title": "Detecting SARS-CoV-2 at point of care: Preliminary data comparing Loop-mediated isothermal amplification (LAMP) to PCR", - "authors": "Marc F Osterdahl; Karla A Lee; Mary Ni Lochlainn; Stuart Wilson; Sam Douthwaite; Rachel Horsfall; Alyce Sheedy; Simon D Goldenberg; Christoper J Stanley; Tim D Spector; Claire Steves", - "affiliations": "Department of Ageing & Health, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; MicrosensDx Ltd, 2 Royal College Street, London, UK; Department of Infection, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Infection, Guys and St Thomas NHS Foundation Trust, London, UK; MicrosensDx Ltd, 2 Royal College Street, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK", - "abstract": "BackgroundThe need for a fast and reliable test for COVID-19 is paramount in managing the current pandemic. A cost effective and efficient diagnostic tool as near to the point of care (PoC) as possible would be a game changer in current testing. We tested reverse transcription loop mediated isothermal amplification (RT-LAMP), a method which can produce results in under 30 minutes, alongside standard methods in a real-life clinical setting.\n\nMethodsThis service improvement project piloted a research RT-LAMP method on nasal and pharyngeal swabs on 21 residents in a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We calculated the sensitivity, specificity, positive and negative predictive values of a single RT-LAMP swab compared to RT-PCR, as per STARD guidelines. We also recorded vital signs of patients to correlate clinical and laboratory information.\n\nFindingsThe novel method accurately detected 8/10 PCR positive cases and identified a further 3 positive cases. Eight further cases were negative using both methods. Using repeated RT-PCR as a \"gold standard\", the sensitivity and specificity of the novel test were 80% and 73% respectively. Positive predictive value (PPV) was 73% and negative predictive value (NPV) was 83%. We also observed hypothermia to be a significant early clinical sign in a number of COVID-19 patients in this setting.\n\nInterpretationRT-LAMP testing for SARS-CoV-2 was found to be promising, fast, easy to use and to work equivalently to RT-PCR methods. Definitive studies to evaluate this method in larger cohorts are underway. RT-LAMP has the potential to transform COVID-19 detection, bringing rapid and accurate testing to the point of care. This method could be deployed in mobile testing units in the community, care homes and hospitals to detect disease early and prevent spread.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.03.27.20044925", @@ -10386,5 +10456,19 @@ "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 + }, + { + "site": "medRxiv", + "doi": "10.1101/2020.01.31.20019901", + "date": "2020-02-02", + "link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019901", + "title": "Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study", + "authors": "Adam J Kucharski; Timothy W Russell; Charlie Diamond; Yang Liu; CMMID nCoV working group; John Edmunds; Sebastian Funk; Rosalind M Eggo", + "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", + "abstract": "BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.\n\nMethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.\n\nFindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.\n\nInterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.\n\nFundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 } ] \ No newline at end of file diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index 7d343ea6..ccac9b0c 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,4 +1,1110 @@ [ + { + "rel_doi": "10.1101/2024.02.28.582665", + "rel_title": "Peptide Mold: A Novel Strategy for Mapping Potential Binding Sites in Protein Targets", + "rel_date": "2024-02-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.28.582665", + "rel_abs": "A novel concept titled Peptide Mold for mapping potential binding sites in protein targets is presented. A large multiconformer tetrapeptide library comprising of 32 million conformations of all possible combinations of naturally-occurring amino acids was constructed and used for molecular docking analysis in the substrate-binding site of SARS-CoV-2 PLpro enzyme. The top-ranking, structurally-diverse tetrapeptide docked conformations (symbolizing peptide mold, analogous to a clay mold) were used then for elucidating a five-point pharmacophore. Ligand-based virtual screening of a large, multiconformer library of phytoconstituents using the derived five-point pharmacophore led to identification of potential binders for SARS-CoV-2 PLpro at its substrate-binding site. The approach is based on generating the imprint of a macromolecular binding site (cavity) using tetrapeptides (clay), thereby generating a reverse mold (with definitive shape and size), which can further be used for identifying small-molecule ligands matching the captured features of the target binding site. The approach is based on the fact that the individual amino acids in the tetrapeptide represent all possible drug-receptor interaction features (electrostatic, H-bonding, van der Waals, dispersion and hydrophobic among others). The peptide mold approach can be extended to any protein target for mapping the binding site(s), and further use of the generated pharmacophore model for virtual screening of potential binders. The peptide mold approach is a robust, hybrid computational screening strategy, overcoming the present limitations of structure-based methods, e.g., molecular docking and the ligand-based methods such as pharmacophore search. Exploration of the peptide mold strategy is expected to yield high-quality, reliable and interesting virtual hits in the computational screening campaigns during the hit and lead identification stages.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Pritam Bagwe Bagwe", + "author_inst": "Institute of Chemical Technology, Mumbai" + }, + { + "author_name": "Yogesh Jagtap", + "author_inst": "Institute of Chemical Technology, Mumbai" + }, + { + "author_name": "Vaibhav Ghegade", + "author_inst": "Institute of Chemical Technology, Mumbai" + }, + { + "author_name": "Janvhi S Machhar", + "author_inst": "Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY 14203, USA" + }, + { + "author_name": "Elvis Martis", + "author_inst": "Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Vakola, Santacruz East, Mumbai 400 098, India" + }, + { + "author_name": "Shreerang V Joshi", + "author_inst": "Institute of Chemical Technology, Mumbai" + }, + { + "author_name": "Prashant S Kharkar", + "author_inst": "Institute of Chemical Technology, Mumbai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, + { + "rel_doi": "10.1101/2024.02.28.582613", + "rel_title": "Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination", + "rel_date": "2024-02-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.28.582613", + "rel_abs": "Neutralizing antibodies correlate with protection against SARS-CoV-2. Recent studies, however, show that binding antibody titers, in the absence of robust neutralizing activity, also correlate with protection from disease progression. Non-neutralizing antibodies cannot directly protect from infection but may recruit effector cells thus contribute to the clearance of infected cells. Also, they often bind conserved epitopes across multiple variants. We characterized 42 human mAbs from COVID-19 vaccinated individuals. Most of these antibodies exhibited no neutralizing activity in vitro but several non-neutralizing antibodies protected against lethal challenge with SARS-CoV-2 in different animal models. A subset of those mAbs showed a clear dependence on Fc-mediated effector functions. We determined the structures of three non-neutralizing antibodies with two targeting the RBD, and one that targeting the SD1 region. Our data confirms the real-world observation in humans that non-neutralizing antibodies to SARS-CoV-2 can be protective.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Jordan Clark", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Irene Hoxie", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Daniel Adelsberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Iden Sapse", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert Andreata-Santos", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jeremy Yong", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Johnstone Tcheou", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ariel Raskin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Gagandeep Singh", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Irene Gonzalez-Dominguez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Julia Edgar", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Stylianos Bournazos", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Weina Sun", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan Manuel Carreno", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Ali Ellebedy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Goran Bajic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2024.02.28.582480", + "rel_title": "Discovery of anti-SARS-CoV-2 S2 protein antibody CV804 with broad-spectrum reactivity with various beta coronaviruses and analysis of its pharmacological properties in vitro and in vivo", + "rel_date": "2024-02-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.28.582480", + "rel_abs": "SARS-CoV-2 pandemic alerts us that spillovers of various animal coronaviruses to human in the future may bring us enormous damages. Thus, there is a significant need of antibody-based drugs to treat patients infected with previously unseen coronaviruses. CV804 against the S2 domain of the spike protein, which is less prone to mutations. CV804 shows not only broad cross-reactivities with representative 20 animal-origin coronaviruses but also with diseases-associated human beta coronaviruses including SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-HKU1 and mutant strains of SARS-CoV-2. Other than that, the main characteristics of CV804 are that it has strong antibody-dependent cellular cytotoxicity (ADCC) activity to SARS-CoV2 spike protein-expressed cells in vitro and completely lacks virus-neutralization activity. Comprehensively in animal models, CV804 suppressed disease progression by SARS-CoV-2 infection. Structural studies using HDX-MS and point mutations of recombinant spike proteins revealed that CV804 binds to a unique epitope within the highly conserved S2 domain of the spike proteins of various coronaviruses. Based on the overall data, we suggest that the non-neutralizing CV804 antibody recognizes the conformational structure of the spike protein expressed on the surface of the infected cells and weakens the viral virulence by supporting host immune cells attack through ADCC activity in vivo. CV804 epitope identified in this study is not only useful for the design of pan-corona antibody therapeutics but also to design next-generation coronavirus vaccines and antiviral drugs.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Yoji Tsugawa", + "author_inst": "Shionogi and Co Ltd Pharmaceutical Research Center: Shionogi Seiyaku Kabushiki Kaisha Iyaku Kenkyu Center" + }, + { + "author_name": "Kentaro Furukawa", + "author_inst": "Shionogi and Co Ltd Pharmaceutical Research Center: Shionogi Seiyaku Kabushiki Kaisha Iyaku Kenkyu Center" + }, + { + "author_name": "Tomoko Ise", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Masahiro Takayama", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Takeshi Ota", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Takayuki Kuroda", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Shinya Shano", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Takashi Hashimoto", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Haruyo Konishi", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Takeshi Ishihara", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Masaaki Sato", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Haruhiko Kamada", + "author_inst": "National Institutes of Biomedicak Innovation, Health and Nutrition" + }, + { + "author_name": "Keita Fukao", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Takao Shishido", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Tatsuya Takahashi", + "author_inst": "Shionogi and Co Ltd" + }, + { + "author_name": "Satoshi Nagata", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, + { + "rel_doi": "10.1101/2024.02.27.582433", + "rel_title": "Virus-derived Synthetic Riboswitches for Real-time Coronaviruses Sensing in Live Cells", + "rel_date": "2024-02-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.27.582433", + "rel_abs": "Real-time sensing of viral infection in live cells are crucial for virology research and antiviral development. However, existing methods face challenges of low signal sensitivity and the necessity for viral manipulation and cell fixation. Here, we develop a viral riboswitch (vRibo) approach that employs the viral replicase to induce transgene expression upon viral infection. The vRibo is designed to detect viral real-time transcription and replication in live cells, which in response triggers the translation of reporter and therapeutic genes. By integrating a viral packaging sequence, vRibo can be transmitted to neighboring cells through progeny virions, effectively acting as a \"Trojan Horse\". The negative-strand vRibo elements demonstrated effective detection of several coronaviruses, including 229E and OC43, due to the conservation of cis-acting RNA structures across coronaviruses. Notably, vRibo functions as a dual-purpose system, acting both as an infection detector and inducible antiviral system. vRibo has the potential for basic virology research applications and can be adopted in improving the inducible expression of mRNA medicines for future coronaviruses.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Leiping Zeng", + "author_inst": "Stanford University" + }, + { + "author_name": "Lei S Qi", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, + { + "rel_doi": "10.1101/2024.02.28.24303516", + "rel_title": "Neutrophil-to-Lymphocyte Ratio as a Prognostic Indicator in COVID-19: Evidence from a Northern Tanzanian Cohort", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.28.24303516", + "rel_abs": "Background: COVID-19 caused a profound global impact, resulting in significant cases and deaths. The progression of COVID-19 clinical manifestations is influenced by a dysregulated inflammatory response. Early identification of the subclinical progression is crucial for timely intervention and improved patient outcomes. While there are various biomarkers to predict disease severity and outcomes, their accessibility and affordability pose challenges in resource-limited settings. We explored the potentiality of the neutrophil-to-lymphocyte ratio (NLR) as a cost-effective inflammatory marker to predict disease severity, clinical deterioration, and mortality in affected patients. Methodology: A hospital-based retrospective cohort study was conducted at KCMC Hospital among COVID-19 patients followed from admission to discharge between 1st March 2020 and 31st March 2022. NLR was calculated as the absolute neutrophil count in {micro}L divided by the absolute lymphocyte count in L. The NLR cut-off value was determined using Receiver Operating Characteristic (ROC) analysis and assessed its predictive ability at admission for in-hospital mortality. The Chi-square test compared the proportion of NLR by patient characteristics. The association of NLR with disease severity and mortality was analyzed using the modified Poisson and Cox regression models, respectively. Results: The study included 504 patients, with a median age of 64 years, 57.1% were males, and 68.3% had severe COVID-19. The in-hospital COVID-19 mortality rate was 37.7%. An NLR cutoff value of 6.1 or higher had a sensitivity of 92.1% (95% CI 89.2%-94.0%) and a specificity of 92.0% (95% CI 89.7%-94.4%). Additionally, 39.5% of patients with an NLR value of 6.1 or higher had increased risk of severe disease, subsequent clinical deterioration, and mortality. Conclusion and recommendation: An NLR value of 6.1 or higher at the time of hospital admission associated with severe disease, clinical deterioration, and mortality in patients with COVID-19. Integration of NLR as a prognostic parameter in COVID-19 prognosis scales could improve risk assessment and guide appropriate management strategies for COVID-19 patients, as well as for potential future viral-related pneumonias. Further prospective studies are necessary to validate these findings and evaluate the clinical utility of NLR in larger cohorts of patients.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Norman Jonas Kyala", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Innocent Mboya", + "author_inst": "Lund University: Lunds Universitet" + }, + { + "author_name": "Elichilia Shao", + "author_inst": "Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Francis Sakita", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Kajiru Gadiel Kilonzo", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Laura Shirima", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Abid Sadiq", + "author_inst": "Kilimanjaro Christian Medical Centre" + }, + { + "author_name": "Elifuraha Mkwizu", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Nyasatu Chamba", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Annette Marandu", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Sophia Muhali", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Faryal Raza", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Eliasa Ndale", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Damas Bayo", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Daniel Mujuni", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + }, + { + "author_name": "Furaha Lyamuya", + "author_inst": "Kilimanjaro Christian Medical College: Kilimanjaro Christian Medical University College" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2024.02.28.24303518", + "rel_title": "A structured course of disease dataset with contact tracing information in Taiwan for COVID-19 modelling", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.28.24303518", + "rel_abs": "The COVID-19 pandemic has flooded open databases with population-level data. However, individual-level structured data, such as the course of disease and contact tracing information, is almost non-existent in open databases. Publish a structured and cleaned COVID-19 dataset with the course of disease and contact tracing information for easy benchmarking of COVID-19 models. We gathered data from Taiwanese open databases and daily news reports. The outcome is a structured quantitative dataset encompassing the course of the disease of Taiwanese individuals, alongside their contact tracing information. Our dataset comprises 579 confirmed cases covering the period from January 21, to November 9, 2020, when the original SARS-CoV-2 virus was most prevalent in Taiwan. The data include features such as travel history, age, gender, symptoms, contact types between cases, date of symptoms onset, confirmed, critically ill, recovered, and dead. We also include the daily summary data at population-level from January 21, 2020, to May 23, 2022. Our data can help enhance epidemiological modelling.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yu-Heng Wu", + "author_inst": "National Cheng Kung University" + }, + { + "author_name": "Torbj\u00f6rn E. M. Nordling", + "author_inst": "National Cheng Kung University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2024.02.28.24303505", + "rel_title": "Implementation and Adherence to Regular Asymptomatic Testing in a COVID-19 Vaccine Trial", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.28.24303505", + "rel_abs": "Background For pathogens which cause infections that present asymptomatically, evaluating vaccine efficacy (VE) against asymptomatic infection is important for understanding a vaccine's potential epidemiological impact. Regular testing for subclinical infections is a potentially valuable strategy but its success hinges on participant adherence and minimising false positives. This paper describes the implementation and adherence to weekly testing in a COVID-19 vaccine trial. Methods COV002 was a phase 2/3 trial assessing the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2. Asymptomatic infections were detected using weekly self-administered swabs for RT-PCR testing. We analysed adherence using mixed-effects regression models and estimated the probability of true and false positive asymptomatic infections using estimates of adherence and testing characteristics. Findings 356,551 tests were self-administered by 10,811 participants during the 13-month follow-up. Median adherence was 75.0% (IQR 42.6-90.9), which translated to a 74.5% (IQR 50.9-78.8) probability of detecting a positive asymptomatic infection during the swabbing period, and between 21 and 96 false positives during VE evaluation. The odds of returning a swab declined by 8% per week and further after testing positive and unblinding. Adherence was higher in older age groups, females and non-healthcare workers. Interpretation The COV002 trial demonstrated the feasibility of running a long-term regular asymptomatic testing strategy. This information could be valuable for designing future phase III vaccine trials in which infection is an outcome. Funding UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, AstraZeneca.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Lucy R Williams", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Katherine RW Emary", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom 3 NIHR Oxford Biomedical Research Centre, Oxford United Kingdom a" + }, + { + "author_name": "Daniel J Phillips", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford United Kingdom" + }, + { + "author_name": "Jodie Hay", + "author_inst": "Paul O'Gorman Leukaemia Research Centre, University of Glasgow, Glasgow, United Kingdom" + }, + { + "author_name": "Jessica PJ Larwood", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford United Kingdom" + }, + { + "author_name": "Maheshi N Ramasamy", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom, NIHR Oxford Biomedical Research Centre, Oxford United Kingdom, an" + }, + { + "author_name": "Andrew J Pollard", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford United Kingdom" + }, + { + "author_name": "Nicholas C Grassly", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Merryn Voysey", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.02.27.24303454", + "rel_title": "COVID-19 vaccine uptake and associated risk factors among first antenatal care attendees in Zambia, 2021-2022: a repeated cross-sectional study", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.27.24303454", + "rel_abs": "Introduction Pregnant women are considered a high-risk group for COVID-19, and a priority for vaccination. Routine antenatal (ANC) care provides an opportunity to track trends and factors associated with vaccine uptake. We sought to evaluate COVID-19 vaccine uptake among pregnant women attending ANC in Zambia. Methods We conducted a repeated cross-sectional study in 39 public health facilities in four districts in Zambia from September 2021 to September 2022. Pregnant women who were aged 15-49 years were enrolled during their first ANC visit. Every month, ~20 women per facility were interviewed during individual HIV testing and counseling. We estimated vaccine uptake as the proportion of eligible participants who self-reported having received the COVID-19 vaccine. Results A total of 9,203 pregnant women were screened, of which 9,111 (99%) were eligible and had vaccination status. Of the 9,111 included in the analysis, 1,818 (20%) had received the COVID-19 vaccine during the study period, with a trend of increasing coverage with time (0.5% in September 2020, 27% in September 2022). Conversely, 3,789 (42%) reported not being offered a COVID-19 vaccine. We found that older age, education, employment status, and prior COVID-19 infection were significantly associated with vaccine uptake. Conclusion COVID-19 vaccine uptake among pregnant women was lower than estimates from the general population (27% across the four districts in September 2022), pointing to missed opportunities to protect this high-risk group. ANC visits were a viable point for conducting COVID-19 surveillance. Incorporating the vaccine as part of the routine ANC package might increase coverage in this group.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Tannia Tembo", + "author_inst": "CIDRZ: Center for Infectious Disease Research in Zambia" + }, + { + "author_name": "Elizabeth Heilmann", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Paul Somwe", + "author_inst": "CIDRZ: Center for Infectious Disease Research in Zambia" + }, + { + "author_name": "Samuel Bosomprah", + "author_inst": "CIDRZ: Center for Infectious Disease Research in Zambia" + }, + { + "author_name": "Kalubi Kalenga", + "author_inst": "CIDRZ: Center for Infectious Disease Research in Zambia" + }, + { + "author_name": "Nyembezi Moyo", + "author_inst": "CIDRZ: Center for Infectious Disease Research in Zambia" + }, + { + "author_name": "Bupe Kabamba", + "author_inst": "PATH" + }, + { + "author_name": "Victoria Seffren", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sombo Fwoloshi", + "author_inst": "University of Zambia University Teaching Hospital" + }, + { + "author_name": "Marie-Reine Rutagwera", + "author_inst": "PATH" + }, + { + "author_name": "Maximillian Musunse", + "author_inst": "PATH" + }, + { + "author_name": "Linos Mwiinga", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Julie R. Gutman", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jonas Z. Hines", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Izukanji Sikazwe", + "author_inst": "CIDRZ: Center for Infectious Disease Research in Zambia" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2024.02.28.24303487", + "rel_title": "Evaluating the impacts of tiered restrictions introduced in England in December 2020 on covid-19 hospitalisations: a synthetic control study.", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.28.24303487", + "rel_abs": "Objectives To assess the impact of Tier 3 covid-19 restrictions implemented in December 2020 in England on covid-19 hospital admissions compared to Tier 2 restrictions, and its potential variations by neighbourhood deprivation levels and the prevalence of the Alpha variant (B.1.1.7). Design Observational study utilising a synthetic control approach. Comparison of changes in weekly hospitalisation rates in Tier 3 areas to a synthetic control group derived from Tier 2 areas. Setting England between 4th October 2020 and 21st February 2021. Participants 23 million people under Tier 3 restrictions, compared to a synthetic control group derived from 29 million people under Tier 2 restrictions. Interventions Implementation of Tier 3 covid-19 restrictions in designated areas on 7th December 2020, with additional constraints on indoor and outdoor meetings and the hospitality sector compared to less stringent Tier 2 restrictions. Main Outcome Measures Weekly covid-19 related hospital admissions for neighbourhoods in England over a 12-week period following the interventions. Results The introduction of Tier 3 restrictions was associated with a 17% average reduction in hospital admissions compared to Tier 2 areas (95% CI 13% to 21%; 8158 (6286 to 9981) in total)). The effects were similar across different levels of neighbourhood deprivation and prevalence of the Alpha variant (B.1.1.7). Conclusions Regionally targeted Tier 3 restrictions in England had a moderate but significant effect on reducing hospitalisations. The impact did not exacerbate socioeconomic inequalities during the pandemic. Our findings suggest that regionally targeted restrictions can be effective in managing infectious diseases.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Xingna Zhang", + "author_inst": "UNIVERSITY OF LIVERPOOL" + }, + { + "author_name": "Daniel Hungerford", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Mark Green", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marta Garcia-Finana", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Iain Buchan", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Ben Barr", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2024.02.27.24303073", + "rel_title": "Implementing remote monitoring for COVID-19 patients in primary care", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.27.24303073", + "rel_abs": "Background In Germany, most patients with coronavirus disease 2019 (COVID-19) are treated in an outpatient setting. To improve assessments of the health status of COVID-19 outpatients, various remote monitoring models have been developed. However, little information exists on experiences acquired with remote monitoring in an outpatient setting, particularly from a patient perspective. The aim of our 'COVID-19@home' study was therefore to implement and evaluate an app-based remote monitoring concept for acute and post-acute COVID-19-patients in primary care. In this paper, we focus on the patients' evaluation of our remote monitoring approach. Methods Patients with acute COVID-19 measured heart rate, blood pressure, oxygen saturation, and body temperature daily for 28 days. Patients with post-acute COVID-19 determined the same parameters for 12 weeks, supplemented by lung parameters and daily step count. The data were documented using the 'SaniQ' smartphone app. COVID-19 symptoms were assessed daily using an app-based questionnaire. Patients' GPs could access the data on the 'SaniQ Praxis' telemedicine platform. We used an app-based questionnaire consisting of 11 questions presented with a 4-point Likert scale to evaluate patient satisfaction. Data were analyzed descriptively. Results Of the 51 patients aged 19-77 years that participated in the study, 42 completed the questionnaire. All patients rated home monitoring as 'very good' or 'rather good' and were able to integrate the measuring processes into their daily routines. Overall, 93% would recommend the app and the measuring devices to their family and friends. About 60% felt that their COVID-19 treatment had benefited from home monitoring. Only few patients were unsettled by the app and use of the measuring devices. During the course of the study, the implementation process was optimized. Conclusions The use of remote monitoring in COVID-19 patients is feasible and was evaluated positively by most study patients. However, it is difficult to imagine how general practices could cope with monitoring patients with acute diseases without any further organizational support. Future research should address cost-effectiveness and changes in such clinical outcomes as hospitalization and mortality.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Susanne M. Koehler", + "author_inst": "Goethe University Frankfurt, Institute of General Practice, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Svea Holtz", + "author_inst": "Goethe University Frankfurt, Institute of General Practice, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Peter Jan Chabiera", + "author_inst": "Goethe University Frankfurt, Institute of General Practice, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Nurlan Dauletbaev", + "author_inst": "Department of Internal, Respiratory and Critical Care Medicine, Philipps University of Marburg, 35043 Marburg, Germany" + }, + { + "author_name": "Kim Deutsch", + "author_inst": "Department of Digital Medicine, Medical Faculty OWL, Bielefeld University, 33615 Bielefeld, Germany" + }, + { + "author_name": "Zoe S. Oftring", + "author_inst": "Institute of Digital Medicine, Philipps University of Marburg, Germany" + }, + { + "author_name": "Dennis Lawin", + "author_inst": "Department of Cardiology and Intensive Care Medicine, University hospital OWL of Bielefeld University, Campus Klinikum Bielefeld, Bielefeld, Germany" + }, + { + "author_name": "Lukas Niekrenz", + "author_inst": "Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, 52074 Aachen, Germany" + }, + { + "author_name": "Teresa Euler", + "author_inst": "Goethe University Frankfurt, University Hospital, Medical Clinic 1, Department of Respiratory Medicine, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Rainer Gloeckl", + "author_inst": "Schoen Clinic Berchtesgadener Land, Institute for Pulmonary Rehabilitation Research, 83471 Schoenau am Koenigssee, Germany" + }, + { + "author_name": "Rembert Koczulla", + "author_inst": "Schoen Clinic Berchtesgadener Land, Institute for Pulmonary Rehabilitation Research, 83471 Schoenau am Koenigssee, Germany" + }, + { + "author_name": "Gernot Rohde", + "author_inst": "Goethe University Frankfurt, University Hospital, Medical Clinic 1, Department of Respiratory Medicine, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Michael Dreher", + "author_inst": "Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, 52074 Aachen, Germany" + }, + { + "author_name": "Claus F. Vogelmeier", + "author_inst": "Department of Internal, Respiratory and Critical Care Medicine, Philipps University of Marburg, 35043 Marburg, Germany" + }, + { + "author_name": "Sebastian Kuhn", + "author_inst": "Institute of Digital Medicine, Philipps University of Marburg, 35043 Marburg, Germany" + }, + { + "author_name": "Beate Sigrid Mueller", + "author_inst": "Institute of General Practice, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, + { + "rel_doi": "10.1101/2024.02.27.24303356", + "rel_title": "Ineffectiveness of international travel restrictions to contain spread of the SARS-CoV-2 Omicron BA.1 variant: a continent-wide laboratory-based observational study from Africa", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.27.24303356", + "rel_abs": "Background: In mid-November 2021, the SARS-CoV-2 Omicron BA.1 variant was detected in Southern Africa, prompting international travel restrictions of unclear effectiveness that exacted a substantial economic toll. Methods: Amidst the BA.1 wave, we tested 13,294 COVID-19 patients in 24 African countries between mid-2021 to early 2022 for BA.1 and Delta variants using real-time reverse transcription-PCR tests. The diagnostic precision of the assays was evaluated by high-throughput sequencing in four countries. The observed BA.1 spread was compared to mobility-based mathematical simulations. Findings: By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a median Rt of 2.4 up to 30 days before BA.1 became predominant. PCR-based South-North spread was in agreement with phylogeographic reconstructions relying on 939 SARS-CoV-2 genomes from GISAID. PCR-based reconstructions of country-level BA.1 predominance correlated significantly in time with the emergence of BA.1 genomic sequences on GISAID (p=0.0035, cor=0.70). First BA.1 detections in affluent settings beyond Africa were predicted adequately in time by mobility-based mathematical simulations (p<0.0001). BA.1-infected inbound travelers departing from five continents were identified in five Western countries and one Northern African country by late November/early December 2021, highlighting fast global BA.1 spread aided by international travel. Interpretation: Unilateral travel bans were poorly effective because by the time they came into effect, BA.1 was already widespread in Africa and beyond. PCR-based variant typing combined with mobility-based mathematical modelling can inform rapidly and cost-efficiently on Rt, spread to inform non-pharmaceutical interventions.", + "rel_num_authors": 94, + "rel_authors": [ + { + "author_name": "Carlo Fischer", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Virology, Berlin, Germany" + }, + { + "author_name": "Tongai Gibson Maponga", + "author_inst": "Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa; National Health Laboratory Service Tyger" + }, + { + "author_name": "Anges Yadouleton", + "author_inst": "Laboratoire des fievres hemorragiques virales de Cotonou, Akpakpa, Benin" + }, + { + "author_name": "Nuro Abilio", + "author_inst": "Instituto Nacional de Saude, Maputo, Mozambique" + }, + { + "author_name": "Emmanuel Aboce", + "author_inst": "MBN Clinical Laboratories, Kampala, Uganda" + }, + { + "author_name": "Praise Adewumi", + "author_inst": "Laboratoire des fievres hemorragiques virales de Cotonou, Akpakpa, Benin" + }, + { + "author_name": "Pedro Afonso", + "author_inst": "Instituto Nacional de Investigacao em Saude (INIS), Luanda, Angola" + }, + { + "author_name": "Jewelna Akorli", + "author_inst": "Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana" + }, + { + "author_name": "Soa Fy Andriamandimby", + "author_inst": "Institut Pasteur de Madagascar, Antananarivo, Madagascar" + }, + { + "author_name": "Latifa Anga", + "author_inst": "Institut Pasteur du Maroc, Casablanca, Morocco" + }, + { + "author_name": "Yvonne Ashong", + "author_inst": "Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana" + }, + { + "author_name": "Mohamed Amine Beloufa", + "author_inst": "Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria" + }, + { + "author_name": "Aicha Bensalem", + "author_inst": "Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria" + }, + { + "author_name": "Richard Birtles", + "author_inst": "Gulu University Multifunctional Laboratories, Gulu, Uganda; School of Science, Engineering and Environment, University of Salford, United Kingdom, Salford, Unit" + }, + { + "author_name": "Anicet Luc Magloire Boumba", + "author_inst": "Marien Ngouabi University, Pointe-Noire, Congo; Molecular diagnostic Laboratory HDL, Pointe-Noire, Congo" + }, + { + "author_name": "Freddie Bwanga", + "author_inst": "MBN Clinical Laboratories, Kampala, Uganda; Makerere University College of Health Sciences, Kampala, Uganda" + }, + { + "author_name": "Mike Chaponda", + "author_inst": "Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia" + }, + { + "author_name": "Paradzai Chibukira", + "author_inst": "University of Zimbabwe, Faculty of Medicine and Health Sciences, National Virology Laboratory, Avondale, Zimbabwe" + }, + { + "author_name": "R Matthew Chico", + "author_inst": "London School of Hygiene & Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Justin Chileshe", + "author_inst": "Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia" + }, + { + "author_name": "Wonderful Choga", + "author_inst": "Botswana Harvard AIDS Institute Partnership Gaborone, Botswana; Department of Medical Laboratory Sciences, School of Allied Health Professions, University of Bo" + }, + { + "author_name": "Gershom Chongwe", + "author_inst": "Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia" + }, + { + "author_name": "Assana Cisse", + "author_inst": "Laboratoire National de Reference-Grippes, Ouagadougou, Burkina Faso" + }, + { + "author_name": "Fatoumata Cisse", + "author_inst": "Institut Pasteur de Guinee, Conakry, Guinee" + }, + { + "author_name": "Umberto D Alessandro", + "author_inst": "Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia" + }, + { + "author_name": "Xavier de Lamballerie", + "author_inst": "Aix Marseille Universite-Inserm-IRD, Unite des Virus Emergents, Marseille, France" + }, + { + "author_name": "Joana F.M. de Morais", + "author_inst": "Instituto Nacional de Investigacao em Saude (INIS), Luanda, Angola" + }, + { + "author_name": "Fawzi Derrar", + "author_inst": "Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria" + }, + { + "author_name": "Ndongo Dia", + "author_inst": "Institut Pasteur de Dakar (IPD), Dakar, Senegal" + }, + { + "author_name": "Youssouf Diarra", + "author_inst": "Universite des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali" + }, + { + "author_name": "Lassina Doumbia", + "author_inst": "Universite des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Virology, Berlin, Germany" + }, + { + "author_name": "Philippe Dussart", + "author_inst": "Institut Pasteur de Madagascar, Antananarivo, Madagascar" + }, + { + "author_name": "Richard Echodu", + "author_inst": "Gulu University Multifunctional Laboratories, Gulu, Uganda" + }, + { + "author_name": "Tom Luedde", + "author_inst": "Hirsch Institute of Tropical Medicine, Asella, Ethiopia; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, He" + }, + { + "author_name": "Abdelmajid Eloualid", + "author_inst": "Institut Pasteur du Maroc, Casablanca, Morocco" + }, + { + "author_name": "Ousmane Faye", + "author_inst": "Institut Pasteur de Dakar (IPD), Dakar, Senegal" + }, + { + "author_name": "Torsten Feldt", + "author_inst": "Hirsch Institute of Tropical Medicine, Asella, Ethiopia; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, He" + }, + { + "author_name": "Anna Fruehauf", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Virology, Berlin, Germany" + }, + { + "author_name": "Simani Gaseitsiwe", + "author_inst": "Botswana Harvard AIDS Institute Partnership Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Bos" + }, + { + "author_name": "Afiwa Halatoko", + "author_inst": "Institut National d Hygiene, Lome, Togo" + }, + { + "author_name": "Pauliana-Vanessa Ilouga", + "author_inst": "Centre Pasteur du Cameroun, Yaounde, Cameroon" + }, + { + "author_name": "Nalia Ismael", + "author_inst": "Instituto Nacional de Saude, Maputo, Mozambique" + }, + { + "author_name": "Ronan Jambou", + "author_inst": "Centre de Recherche Medicale et Sanitaire (CERMES), Niamey, Niger" + }, + { + "author_name": "Sheikh Jarju", + "author_inst": "Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia" + }, + { + "author_name": "Antje Kamprad", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Virology, Berlin, Germany" + }, + { + "author_name": "Ben Katowa", + "author_inst": "Macha Research Trust, Choma, Zambia; University of Zambia, School of Veterinary Medicine, Lusaka, Zambia" + }, + { + "author_name": "John Kayiwa", + "author_inst": "Uganda Virus Research Institute, Entebbe, Uganda" + }, + { + "author_name": "Leonard Kingwara", + "author_inst": "Ministry of Health, National Public Health Reference Laboratory, Nairobi, Kenya" + }, + { + "author_name": "Ousmane Koita", + "author_inst": "Universite des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali" + }, + { + "author_name": "Vincent Lacoste", + "author_inst": "Institut Pasteur de Madagascar, Antananarivo, Madagascar" + }, + { + "author_name": "Adamou Lagare", + "author_inst": "Centre de Recherche Medicale et Sanitaire (CERMES), Niamey, Niger" + }, + { + "author_name": "Olfert Landt", + "author_inst": "TIB-Molbiol Syntheselabor GmbH, Berlin, Germany" + }, + { + "author_name": "Sonia Etenna Lekana-Douki", + "author_inst": "Centre Interdisciplinaire de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon" + }, + { + "author_name": "Jean-Bernard Lekana-Douki", + "author_inst": "Centre Interdisciplinaire de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon" + }, + { + "author_name": "Etuhole Iipumbu", + "author_inst": "University of Namibia, School of Medicine, Windhoek, Namibia" + }, + { + "author_name": "Hugues Loemba", + "author_inst": "Molecular diagnostic Laboratory HDL, Pointe-Noire, Congo; University of Ottawa, Faculty of Medicine, Ottawa, Canada" + }, + { + "author_name": "Julius Lutwama", + "author_inst": "Uganda Virus Research Institute, Entebbe, Uganda" + }, + { + "author_name": "Santou Mamadou", + "author_inst": "Centre de Recherche Medicale et Sanitaire (CERMES), Niamey, Niger" + }, + { + "author_name": "Issaka Maman", + "author_inst": "Institut National d Hygiene, Lome, Togo" + }, + { + "author_name": "Brendon Manyisa", + "author_inst": "University of Zimbabwe, Faculty of Medicine and Health Sciences, National Virology Laboratory, Avondale, Zimbabwe" + }, + { + "author_name": "Pedro A. Martinez", + "author_inst": "Instituto Nacional de Investigacao em Saude (INIS), Luanda, Angola" + }, + { + "author_name": "Japhet Matoba", + "author_inst": "Macha Research Trust, Choma, Zambia; University of Zambia, School of Veterinary Medicine, Lusaka, Zambia" + }, + { + "author_name": "Lusia Mhuulu", + "author_inst": "University of Namibia, School of Medicine, Windhoek, Namibia" + }, + { + "author_name": "Andres Moreira-Soto", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Virology, Berlin, Germany" + }, + { + "author_name": "Sikhulile Moyo", + "author_inst": "Botswana Harvard AIDS Institute Partnership Gaborone, Botswana; Department of Medical Laboratory Sciences, School of Allied Health Professions, University of Bo" + }, + { + "author_name": "Judy Mwangi", + "author_inst": "Gulu University Multifunctional Laboratories, Gulu, Uganda; School of Science, Engineering and Environment, University of Salford, United Kingdom, Salford, Unit" + }, + { + "author_name": "Nadine Ndilimabaka", + "author_inst": "Centre Interdisciplinaire de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon" + }, + { + "author_name": "Charity Angella Nassuna", + "author_inst": "Uganda Virus Research Institute, Entebbe, Uganda" + }, + { + "author_name": "Mamadou Ousmane Ndiath", + "author_inst": "Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia" + }, + { + "author_name": "Emmanuel Nepolo", + "author_inst": "University of Namibia, School of Medicine, Windhoek, Namibia" + }, + { + "author_name": "Richard Njouom", + "author_inst": "Centre Pasteur du Cameroun, Yaounde, Cameroon" + }, + { + "author_name": "Jalal Nourlil", + "author_inst": "Institut Pasteur du Maroc, Casablanca, Morocco" + }, + { + "author_name": "Steven Ger Nyanjom", + "author_inst": "Jomo Kenyatta University of Agriculture and Technology, School of Biomedical Sciences, Nairobi, Kenya" + }, + { + "author_name": "Eddy Okoth Odari", + "author_inst": "Jomo Kenyatta University of Agriculture and Technology, School of Biomedical Sciences, Nairobi, Kenya" + }, + { + "author_name": "Alfred Okeng", + "author_inst": "MBN Clinical Laboratories, Kampala, Uganda" + }, + { + "author_name": "Jean Bienvenue Ouoba", + "author_inst": "Laboratoire National de Reference-Grippes, Ouagadougou, Burkina Faso" + }, + { + "author_name": "Michael Owusu", + "author_inst": "Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST, Kumasi, Ghana" + }, + { + "author_name": "Irene Owusu Donkor", + "author_inst": "Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana" + }, + { + "author_name": "Karabo Kristen Phadu", + "author_inst": "Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa" + }, + { + "author_name": "Richard Odame Phillips", + "author_inst": "Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST, Kumasi, Ghana" + }, + { + "author_name": "Wolfgang Preiser", + "author_inst": "Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa; National Health Laboratory Service Tyger" + }, + { + "author_name": "Pierre Roques", + "author_inst": "Institut Pasteur de Guinee, Conakry, Guinee; Commissariat a l Energie Atomique, Institut de Biologie Francois Jacob, Fontenay-aux-Roses, France" + }, + { + "author_name": "Vurayai Ruhanya", + "author_inst": "University of Zimbabwe, Faculty of Medicine and Health Sciences, National Virology Laboratory, Avondale, Zimbabwe" + }, + { + "author_name": "Fortune Salah", + "author_inst": "Institut National d Hygiene, Lome, Togo" + }, + { + "author_name": "Sourakatou Salifou", + "author_inst": "Ministere de la Sante, Akpakpa, Benin" + }, + { + "author_name": "Amadou Alpha Sall", + "author_inst": "Institut Pasteur de Dakar (IPD), Dakar, Senegal" + }, + { + "author_name": "Augustina Angelina Sylverken", + "author_inst": "Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST, Kumasi, Ghana; Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana" + }, + { + "author_name": "Paul Alain Tagnouokam-Ngoupo", + "author_inst": "Centre Pasteur du Cameroun, Yaounde, Cameroon" + }, + { + "author_name": "Zekiba Tarnagda", + "author_inst": "Laboratoire National de Reference-Grippes, Ouagadougou, Burkina Faso" + }, + { + "author_name": "Francis Olivier Tchikaya", + "author_inst": "Molecular diagnostic Laboratory HDL, Pointe-Noire, Congo" + }, + { + "author_name": "Noel Tordo", + "author_inst": "Institut Pasteur de Guinee, Conakry, Guinee" + }, + { + "author_name": "Tafese Beyene Tufa", + "author_inst": "Hirsch Institute of Tropical Medicine, Asella, Ethiopia; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, He" + }, + { + "author_name": "Jan Felix Drexler", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Virology, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.02.27.24303438", + "rel_title": "Inflammatory proteins as strong predictors of death in COVID-19 patients with coexisting neurological diseases", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.27.24303438", + "rel_abs": "Background: Although many studies published so far on COVID-19 have examined its clinical prognosis, there is still no universal laboratory test that can assess the risk of a fatal outcome in patients with coexisting neurological diseases. Methods: The plasma concentrations of C-reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), ferritin, interleukin 6 (IL-6), D-dimers, and highly sensitive troponin I (hsTnI) were determined in a group of 400 consecutive in-patients with COVID-19 and concomitant neurological comorbidities. Results: The median concentration levels of most of the inflammatory mediators/indicators, calculated for the whole group of patients, remained above the normal reference ranges, whereas the median concentrations of these substances were much higher in the sub-group of patients who died. Backward stepwise logistic regression confirmed the statistically significant predictors of death in a descending order of odds ratios as follows: LDH (3.8), ferritin (2.8), hsTnI (2.0), IL-6 (1.7), and age (1.01). A concentration of hsTnI > 64 ng/L appeared to constitute a strong predictor of an unfavorable prognosis. Patients who were treated with lopinavir and ritonavir, who required mechanical ventilation, and treatment with dexamethasone presented with significant increase in the concentrations of all the studied inflammatory proteins and increased odds ratio for death. Conclusion: High plasma concentrations of pro-inflammatory proteins in patients suffering from COVID-19 and concomitant neurological diseases were associated with a more serious clinical course and an increased risk of death. The presence of these substances is worth monitoring as a valuable indicator of the current clinical condition of COVID-19 patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Justyna Zieli\u0144ska-Turek", + "author_inst": "National Medical Institute of the Ministry of the Interior and Administration" + }, + { + "author_name": "Grzegorz Turek", + "author_inst": "Brodnowski Hospital of the Mazovian Region in Warsaw: Mazowiecki Szpital Brodnowski w Warszawie Sp zoo" + }, + { + "author_name": "Tomasz Lyson", + "author_inst": "Medical University of Bialystok: Uniwersytet Medyczny w Bialymstoku" + }, + { + "author_name": "Jan Gajewski", + "author_inst": "J\u00f3zef Pi\u0142sudski University of Physical Education in Warsaw: Akademia Wychowania Fizycznego Jozefa Pilsudskego w Warszawie" + }, + { + "author_name": "Miros\u0142aw Z\u0105bek", + "author_inst": "Brodnowski Hospital of the Mazovian Region in Warsaw: Mazowiecki Szpital Brodnowski w Warszawie Sp zoo" + }, + { + "author_name": "Ma\u0142gorzata Dorobek", + "author_inst": "National Medical Institute of the Ministry of the Interior and Administration" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, + { + "rel_doi": "10.1101/2024.02.29.24303532", + "rel_title": "Oro-faecal transmission of SARS-CoV-2: A systematic review of studies employing viral culture from gastrointestinal and other potential sources", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.29.24303532", + "rel_abs": "Background. The extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established. Methods: We systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28th of November 2023. Results: We included 13 studies involving 328 COVID-19 subjects - providing 314 faecal or rectal swab SARS-CoV2 positive samples tested also with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (2 cohorts and 1 case-series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 314 faecal samples subjected to cell culture showed replication-competent virus. One study found replication competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans. Conclusions: Our review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed, using standardized cell culture methods, control groups, adequate follow-up and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Sara Gandini", + "author_inst": "Department of Experimental Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy" + }, + { + "author_name": "John Conly", + "author_inst": "University of Calgary and Alberta Health Services, Calgary, Canada" + }, + { + "author_name": "Elizabeth A Spencer", + "author_inst": "Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" + }, + { + "author_name": "David Evans", + "author_inst": "Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada" + }, + { + "author_name": "Elena Cecilia Rosca", + "author_inst": "Department of Neurology, Victor Babes University of Medicine and Pharmacy, Piata Eftimie Murgu 2, Timisoara 300041, Romania" + }, + { + "author_name": "Jon Brassey", + "author_inst": "Trip Database Ltd, Bristol, United Kingdom." + }, + { + "author_name": "Susanna Maltoni", + "author_inst": "Research and Innovation Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy" + }, + { + "author_name": "Igho Onakpoya", + "author_inst": "Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" + }, + { + "author_name": "Annette Pluddemann", + "author_inst": "Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" + }, + { + "author_name": "Tom Jefferson", + "author_inst": "Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" + }, + { + "author_name": "Carl Heneghan", + "author_inst": "Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX2 6GG, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.02.29.24303559", + "rel_title": "Long COVID and kidney function: A scoping review protocol", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.29.24303559", + "rel_abs": "Introduction: The coronavirus disease 2019 (COVID-19) pandemic had catastrophic repercussions worldwide, including short- and long-term effects on multiple organs. The term long COVID encompasses signs and symptoms associated with COVID that persist for more than two months. However, the effects of long COVID on kidney function remain poorly understood. Objective: This scoping review aims to describe the effects of long COVID on kidney function and/or kidney-related outcomes. Methods: We will follow the Joanna Briggs Institute methodology and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Based on the PCC framework, we will include studies that investigated long COVID survivors (Participants); describing kidney function and/or kidney-related outcomes (Concept); in all settings and designs (Context). A comprehensive literature search was performed using the MEDLINE, Embase, and LILACS databases without date or language restrictions from inception until August 2023. Websites, books, and guidelines will also be searched. Observational studies with retrospective, prospective, and case-control designs will be considered. Two independent reviewers will screen titles and abstracts and perform the full-text review. Data extraction will be done by the main reviewer and checked by a second one. Data about the diagnosis of COVID, follow-up time for long symptoms, and kidney function assessment and outcomes will be extracted from selected evidence. The quantitative results will be synthesized and presented in tables and figures along with a narrative summary. Ethics and dissemination: There is no requirement for ethical approval for this scoping review. On completion, it will be published in a peer-reviewed academic journal and presented at a conference.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marcella Frediani", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Heitor S. Ribeiro", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Geraldo Busatto", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Carlos Carvalho", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Emmanuel A Burdmann", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2024.02.28.582510", "rel_title": "Attenuated replication and damaging effects of SARS-CoV-2 Omicron in an intestinal epithelial barrier model", @@ -303,7 +1409,7 @@ "rel_date": "2024-02-28", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.26.582219", - "rel_abs": "The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of Spike, such as the S2 subdomain. Here, we describe a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in the S2 subdomain and can be grouped into at least five epitope classes. Most did not neutralize SARS-CoV-2 with the exception of C20.119, which bound to a highly conserved epitope in the fusion peptide and showed broad binding and neutralization activity across SARS-CoV-2, SARS-CoV-1, and closely related zoonotic sarbecoviruses. Several of the S2 mAbs tested mediated antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1 mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Three of the mAbs with ADCC function also bound to spike trimers from HCoVs, such as MERS-CoV and HCoV-HKU1. Our findings suggest there are diverse epitopes in S2, including functional S2 mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response.", + "rel_abs": "The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of Spike, such as the S2 subdomain. Here, we describe a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in the S2 subdomain and can be grouped into at least five epitope classes. Most did not neutralize SARS-CoV-2 with the exception of C20.119, which bound to a highly conserved epitope in the fusion peptide and showed broad binding and neutralization activity across SARS-CoV-2, SARS-CoV-1, and closely related zoonotic sarbecoviruses. Several of the S2 mAbs tested mediated antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1 mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Three of the mAbs with ADCC function also bound to spike trimers from HCoVs, such as MERS-CoV and HCoV-HKU1. Our findings suggest there are diverse epitopes in S2, including functional S2 mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response.\n\nAUTHOR SUMMARYThe early successes of vaccines and antibody therapies against SARS-CoV-2, the virus responsible for the COVID-19 global pandemic, leveraged the considerable antibody response to the viral entry protein, spike, after vaccination or infection. These initial interventions were highly effective at protecting from infection and reducing severe disease or death. However, SARS-CoV-2 has shown no sign of abating, with the continued rise of new variants that have escaped some of the antibody defense due to distinct alterations most significantly in regions of the spike protein that elicit most of the anti-viral, functional antibody response. These findings suggest a critical need to identify vaccine approaches and therapies that provide the broadest possible antibody responses, focused on regions of spike critical for SARS-CoV-2 infection and, therefore, do not undergo changes that could lead to immune evasion. Our study describes a panel of functional antibodies, from individuals after SARS-CoV-2 infection, that recognize the S2 spike subdomain that is responsible for carrying out viral fusion with host cells. These regions in S2 are generally well conserved across SARS-CoV-2 variants and other closely related viruses and thus, could guide more effective vaccine design in the face of continued viral evolution.", "rel_num_authors": 13, "rel_authors": [ { @@ -498,6 +1604,347 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2024.02.26.24302674", + "rel_title": "Single cell sequencing reveals cellular landscape alterations in the airway mucosa of patients with pulmonary long COVID", + "rel_date": "2024-02-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.26.24302674", + "rel_abs": "To elucidate the important cellular and molecular drivers of pulmonary long COVID, we generated a single-cell transcriptomic map of the airway mucosa using bronchial brushings from patients with long COVID who reported persistent pulmonary symptoms.\n\nAdults with and without long COVID were recruited from the general community in greater Vancouver, Canada. The cohort was divided into those with pulmonary long COVID (PLC), which was defined as persons with new or worsening respiratory symptoms following at least one year from their initial acute SARS-CoV-2 infection (N=9); and control subjects defined as SARS-CoV-2 infected persons whose acute respiratory symptoms had fully resolved or individuals who had not experienced acute COVID-19 (N=9). These participants underwent bronchoscopy from which a single cell suspension was created from bronchial brush samples and then sequenced.\n\nA total of 56,906 cells were recovered for the downstream analysis, with 34,840 cells belonging to the PLC group. A dimensionality reduction plot shows a unique cluster of neutrophils in the PLC group (p<.05). Ingenuity Pathway Analysis revealed that neutrophil degranulation pathway was enriched across epithelial cells. Differential gene expression analysis between the PLC and control groups demonstrated upregulation of mucin genes in secretory cell clusters.\n\nA single-cell transcriptomic landscape of the small airways shows that the PLC airways harbors a dominant neutrophil cluster and an upregulation in the neutrophil-associated activation signature with increased expression of MUC genes in the secretory cells. Together, they suggest that pulmonary symptoms of long COVID may be driven by chronic small airway inflammation.\n\nTake home messageSingle cell profiling shows the infiltration of neutrophils with upregulation of mucin genes in the airway mucosa of patients with pulmonary long COVID, indicating persistent small airway inflammation in pulmonary long COVID.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Firoozeh V.Gerayeli", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Hye Yun Park", + "author_inst": "Samsung Medical Center, Sungkyunkwan University School of Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine" + }, + { + "author_name": "Stephen Milne", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Xuan Li", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Chen Xi Yang", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Josie Tuong", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Rachel Eddy", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Elizabeth Guinto", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Chung Y Cheung", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Julia Shun-Wei Yang", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Cassie Gilchrist", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Dina Yehia", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Tara Stach", + "author_inst": "UBC Biomedical Research Centre" + }, + { + "author_name": "Tawimas Shaipanich", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jonathon Leipsic", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Graeme Koelwyn", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Janice Leung", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Don D Sin", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, + { + "rel_doi": "10.1101/2024.02.27.24303385", + "rel_title": "Dispersal history of SARS-CoV-2 in Galicia, Spain", + "rel_date": "2024-02-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.27.24303385", + "rel_abs": "The dynamics of SARS-CoV-2 transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron variants of concern in Galicia, northwest Spain. For this, we leveraged genomic data collected by the EPICOVIGAL Consortium and from the GISAID database, along with mobility information from other Spanish regions and foreign countries. Our analysis indicates that initial introductions during the Alpha phase were predominantly from other Spanish regions and France. However, as the pandemic progressed, introductions from Portugal and the USA became increasingly significant. Notably, Galicias major coastal cities emerged as critical hubs for viral transmission, highlighting their role in sustaining and spreading the virus. This research emphasizes the critical role of regional connectivity in the spread of SARS-CoV-2 and offers essential insights for enhancing public health strategies and surveillance measures.", + "rel_num_authors": 51, + "rel_authors": [ + { + "author_name": "Pilar Gallego-Garc\u00eda", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain ; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO" + }, + { + "author_name": "Nuria Est\u00e9vez-G\u00f3mez", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain ; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO" + }, + { + "author_name": "Loretta De Chiara", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain ; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO ; Department of Biochemistry, Genetics, " + }, + { + "author_name": "Pilar Alvari\u00f1o", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" + }, + { + "author_name": "Pedro M. Juiz-Gonz\u00e1lez", + "author_inst": "Servicio de Microbiolog\u00eda del Complejo Hospitalario Universitario de Ferrol, 15405 Ferrol" + }, + { + "author_name": "Isabel Torres-Beceiro", + "author_inst": "Servicio de Microbiolog\u00eda del Complejo Hospitalario Universitario de Ferrol, 15405 Ferrol" + }, + { + "author_name": "Margarita Poza", + "author_inst": "Microbiology Research Group, Institute of Biomedical Research (INIBIC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coru\u00f1a (UDC)-CI" + }, + { + "author_name": "Juan A. Vallejo", + "author_inst": "Microbiology Research Group, Institute of Biomedical Research (INIBIC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coru\u00f1a (UDC)-CI" + }, + { + "author_name": "Soraya Rumbo-Feal", + "author_inst": "Microbiology Research Group, Institute of Biomedical Research (INIBIC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coru\u00f1a (UDC)-CI" + }, + { + "author_name": "Kelly Conde-P\u00e9rez", + "author_inst": "Microbiology Research Group, Institute of Biomedical Research (INIBIC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coru\u00f1a (UDC)-CI" + }, + { + "author_name": "Pablo Aja-Macaya", + "author_inst": "Microbiology Research Group, Institute of Biomedical Research (INIBIC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coru\u00f1a (UDC)-CI" + }, + { + "author_name": "Susana Ladra", + "author_inst": "Database Laboratory, Research Center for Information and Communication Technologies (CITIC), University of A Coru\u00f1a (UDC), Campus de Elvi\u00f1a, 15071 A Coru\u00f1a, Spa" + }, + { + "author_name": "Antonio Moreno-Flores", + "author_inst": "Servicio de Microbiolog\u00eda, Hospital Universitario Lucus Augusti, Lugo, Spain" + }, + { + "author_name": "Mar\u00eda J. Gude-Gonz\u00e1lez", + "author_inst": "Servicio de Microbiolog\u00eda, Hospital Universitario Lucus Augusti, Lugo, Spain" + }, + { + "author_name": "Amparo Coira", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (" + }, + { + "author_name": "Antonio Aguilera", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (" + }, + { + "author_name": "Jos\u00e9 J. Costa-Alcalde", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (" + }, + { + "author_name": "Roc\u00edo Trastoy", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (" + }, + { + "author_name": "Gema Barbeito-Casti\u00f1eiras", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (" + }, + { + "author_name": "Daniel Garc\u00eda-Souto", + "author_inst": "CiMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. - Department of Zoology, Genetics and Physic Anthropology, 15782, Santiago " + }, + { + "author_name": "Jos\u00e9 M. C. Tub\u00edo", + "author_inst": "CiMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. - Department of Zoology, Genetics and Physic Anthropology, 15782, Santiago " + }, + { + "author_name": "Matilde Trigo-Daporta", + "author_inst": "Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain" + }, + { + "author_name": "Pablo Camacho-Zamora", + "author_inst": "Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain" + }, + { + "author_name": "Juan Garc\u00eda Costa", + "author_inst": "Servicio de Microbiolog\u00eda. Complejo Hospitalario Universitario de Ourense, 32005, Ourense, Spain" + }, + { + "author_name": "Mar\u00eda Gonz\u00e1lez-Dom\u00ednguez", + "author_inst": "Servicio de Microbiolog\u00eda. Complejo Hospitalario Universitario de Ourense, 32005, Ourense, Spain" + }, + { + "author_name": "Luis Canoura-Fern\u00e1ndez", + "author_inst": "Servicio de Microbiolog\u00eda. Complejo Hospitalario Universitario de Ourense, 32005, Ourense, Spain" + }, + { + "author_name": "Daniel Glez-Pe\u00f1a", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain ; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO" + }, + { + "author_name": "Sonia P\u00e9rez-Castro", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo 36213, Spain ; Microbiology and Infectology Research Group, Galicia S" + }, + { + "author_name": "Jorge J. Cabrera", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo 36213, Spain ; Microbiology and Infectology Research Group, Galicia S" + }, + { + "author_name": "Carlos Davi\u00f1a-N\u00fa\u00f1ez", + "author_inst": "Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain" + }, + { + "author_name": "Montserrat Godoy-Diz", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo 36213, Spain" + }, + { + "author_name": "Ana Bel\u00e9n Treinta-\u00c1lvarez", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo 36213, Spain" + }, + { + "author_name": "Mar\u00eda Isabel Veiga", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal - ICVS/3B's-PT Government " + }, + { + "author_name": "Jo\u00e3o Carlos Sousa", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal - ICVS/3B's-PT Government " + }, + { + "author_name": "Nuno S. Os\u00f3rio", + "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal - ICVS/3B's-PT Government " + }, + { + "author_name": "I\u00f1aki Comas", + "author_inst": "Tuberculosis Genomics Unit, Biomedicine Institute of Valencia, Spanish Research Council (CSIC), Valencia, Spain ; CIBER in Epidemiology and Public Health, Spain" + }, + { + "author_name": "Fernando Gonz\u00e1lez-Candelas", + "author_inst": "CIBER in Epidemiology and Public Health, Spain; Joint Research Unit \"Infection and Public Health\" FISABIO-University of Valencia, Valencia, Spain ; Institute fo" + }, + { + "author_name": "Samuel L. Hong", + "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuve" + }, + { + "author_name": "Nena Bollen", + "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuve" + }, + { + "author_name": "Simon Dellicour", + "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuve" + }, + { + "author_name": "Guy Baele", + "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuve" + }, + { + "author_name": "Marc A. Suchard", + "author_inst": "Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA - Department of Human Genetics, " + }, + { + "author_name": "Philippe Lemey", + "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven - University of Leuve" + }, + { + "author_name": "Andr\u00e9s Agulla", + "author_inst": "Servicio de Microbiolog\u00eda del Complejo Hospitalario Universitario de Ferrol, 15405 Ferrol" + }, + { + "author_name": "Germ\u00e1n Bou", + "author_inst": "Microbiology Research Group, Institute of Biomedical Research (INIBIC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coru\u00f1a (UDC)-CI" + }, + { + "author_name": "Pilar Alonso-Garc\u00eda", + "author_inst": "Servicio de Microbiolog\u00eda, Hospital Universitario Lucus Augusti, Lugo, Spain" + }, + { + "author_name": "Mar\u00eda Luisa P\u00e9rez-del-Molino", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research " + }, + { + "author_name": "Marta Garc\u00eda-Campello", + "author_inst": "Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain" + }, + { + "author_name": "Isabel Paz-Vidal", + "author_inst": "Servicio de Microbiolog\u00eda. Complejo Hospitalario Universitario de Ourense, 32005, Ourense, Spain" + }, + { + "author_name": "Benito Regueiro", + "author_inst": "Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo 36213, Spain ; Microbiology and Infectology Research Group, Galicia S" + }, + { + "author_name": "David Posada", + "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain ; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO ; Department of Biochemistry, Genetics, " + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.02.26.24303208", + "rel_title": "Machine Learning for COVID-19 Patient Management: Predictive Analytics and Decision Support", + "rel_date": "2024-02-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.26.24303208", + "rel_abs": "BackgroundThe global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has profoundly affected economies and healthcare systems around the world, including Lebanon. While numerous meta-analyses have explored the systemic manifestations of COVID-19, few have linked them to patient history. Our study aims to fill this gap by using cluster analysis to identify distinct clinical patterns among patients, which could aid prognosis and guide tailored treatments.\n\nMethodsWe conducted a retrospective cohort study at Beiruts largest teaching hospital on 556 patients with SARS-CoV-2. We performed cluster analyses using K-prototypes, KAMILA and LCM algorithms based on 26 variables, including laboratory results, demographics and imaging findings. Silhouette scores, concordance index and signature variables helped determine the optimal number of clusters. Subsequent comparisons and regression analyses assessed survival rates and treatment efficacy according to clusters.\n\nResultsOur analysis revealed three distinct clusters: \"resilient recoverees\" with varying disease severity and low mortality rates, \"vulnerable veterans\" with severe to critical disease and high mortality rates, and \"paradoxical patients\" with a late presentation but eventual recovery.\n\nConclusionsThese clusters offer insights for prognosis and treatment selection. Future studies should include vaccination data and various COVID-19 strains for a comprehensive understanding of the diseases dynamics.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christopher El Hadi", + "author_inst": "Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon." + }, + { + "author_name": "Rindala El Hadi", + "author_inst": "Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon." + }, + { + "author_name": "Moussa Riachy", + "author_inst": "Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon." + }, + { + "author_name": "Georges Maalouly", + "author_inst": "Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon." + }, + { + "author_name": "Ghassan Sleilaty", + "author_inst": "Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2024.02.25.581989", "rel_title": "TISSUE-SPECIFIC METABOLOMIC REPROGRAMMING DETERMINES THE DISEASE PATHOPHYSIOLOGY OF SARS-COV-2 VARIANTS IN HAMSTER MODEL", @@ -545,6 +1992,172 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2024.02.20.24303089", + "rel_title": "Risk of Adverse Events Following Monovalent Third or Booster Dose of COVID-19 mRNA Vaccination in U.S. Adults Ages 18 Years and Older", + "rel_date": "2024-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.20.24303089", + "rel_abs": "BackgroundThe U.S. FDA authorized the monovalent third primary series or booster doses of COVID-19 mRNA vaccines in August 2021 for persons 18 years and older. Monitoring of outcomes following updated authorizations is critical to evaluate vaccine safety and can provide early detection of rare adverse events (AEs) not identified in pre-licensure trials.\n\nMethodsWe evaluated the risk of 17 AEs following third doses of COVID-19 mRNA vaccines from August 2021 through early 2022 among adults aged 18-64 years in three commercial databases (Optum, Carelon Research, CVS Health) and adults aged >65 years in Medicare Fee-For-Service. We compared observed AE incidence rates to historical (expected) rates prior to the pandemic, estimated incidence rate ratios (IRRs) for the Medicare database and pooled IRR across the three commercial databases. Analyses were also stratified by prior history of COVID-19 diagnosis. Estimates exceeding a pre-defined threshold were considered statistical signals.\n\nResultsFour AEs met the threshold for statistical signals for BNT162b2 and mRNA-1273 vaccines including Bells Palsy and pulmonary embolism in Medicare, and anaphylaxis and myocarditis/pericarditis in commercial databases. Nine AEs and three AEs signaled among adults with and without prior COVID-19 diagnosis, respectively.\n\nConclusionsThis early monitoring study identified statistical signals for AEs following third doses of COVID-19 mRNA vaccination. Since this method is intended for screening purposes and generates crude results, results do not establish a causal association between the vaccines and AEs. FDAs public health assessment remains consistent that the benefits of COVID-19 vaccination outweigh the risks of vaccination.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Azadeh Shoaibi", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Kathryn Matuska", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Patricia C. Lloyd", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Hui Lee Wong", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Joann F. Gruber", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Tainya C. Clarke", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Sylvia Cho", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Emily Lassman", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Hai Lyu", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Rowan McEvoy", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Zhiruo Wan", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Mao Hu", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Sandia Akhtar", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Yixin Jiao", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Yoganand Chillarige", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Daniel Beachler", + "author_inst": "Carelon Research" + }, + { + "author_name": "Alex Secora", + "author_inst": "IQVIA" + }, + { + "author_name": "Nandini Selvam", + "author_inst": "IQVIA" + }, + { + "author_name": "Djeneba A Djibo", + "author_inst": "CVS Health" + }, + { + "author_name": "Cheryl N. McMahill Walraven", + "author_inst": "CVS Health" + }, + { + "author_name": "John D. Seeger", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Kandace L Amend", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Jennifer N Song", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Robin Clifford", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Jeffrey A Kelman", + "author_inst": "Centers for Medicare and Medicaid Services" + }, + { + "author_name": "Richard A Forshee", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Steven A Anderson", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.02.25.24303335", + "rel_title": "Telemedicine's Impact on Diabetes Care during the COVID-19 Pandemic: A Cohort Study in a Large Integrated Healthcare System", + "rel_date": "2024-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.25.24303335", + "rel_abs": "IntroductionTo examine if patients exposed to primary care telemedicine (telephone or video) early in the COVID-19 pandemic had higher rates of downstream HbA1c measurement and improved HbA1c levels in the second year of the pandemic.\n\nResearch Design and MethodsIn a cohort of 242, 848 Kaiser Permanente Northern California patients with diabetes, we examined associations between early-pandemic patient-initiated telemedicine visit and downstream HbA1c monitoring and results during the second year of the pandemic.\n\nResultsAdjusted HbA1c measurement rates were significantly higher among patients with telemedicine exposure in the early-pandemic prior year than those with no visits in the prior year (91.0% testing for patients with video visits, 90.5% for telephone visits, visits, 86.7% for no visits, p < 0.05). Among those with HbA1c measured, the rates of having an HbA1c < 8% in the second year of the COVID-19 pandemic were also statistically significantly higher among patients with telemedicine exposure in the early-pandemic prior year than those with no visits in the prior year (68.5% with HbA1c< 8% for video visits, 67.3% for telephone visits, 66.6% for no visits, p < 0.05).\n\nConclusionsAccess to telephone and video telemedicine throughout the early COVID-19 pandemic was associated with patients continued engagement in recommended diabetes care. Although our study analyzed telemedicine use during a pandemic, telemedicine visits may continue to support ongoing health care access and positive clinical outcomes.\n\nKEY MESSAGESThe pandemic significantly increased telemedicine adoption, providing an opportunity to maintain health care access for patients with diabetes. Our study investigates the impact of telemedicine, including both telephone and video visits, on diabetes care during the early COVID-19 period. The results demonstrate that patients utilizing telemedicine exhibit higher rates of HbA1c measurement and at-goal HbA1c. These findings suggest that telemedicine can be a valuable tool in supporting clinical outcomes in the management of chronic health conditions.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Reysha Patel", + "author_inst": "UC Riverside" + }, + { + "author_name": "Jie Huang", + "author_inst": "Division of Research, Kaiser Permanente Medical Care Program" + }, + { + "author_name": "Loretta Hsueh", + "author_inst": "Division of Research, Kaiser Permanente Medical Care Program" + }, + { + "author_name": "Anjali Gopalan", + "author_inst": "Division of Research, Kaiser Permanente Medical Care Program" + }, + { + "author_name": "Andrea Millman", + "author_inst": "Division of Research, Kaiser Permanente Medical Care Program" + }, + { + "author_name": "Isabelle Franklin", + "author_inst": "Kaiser Permanente Bernard J. Tyson School of Medicine" + }, + { + "author_name": "Mary Reed", + "author_inst": "Division of Research, Kaiser Permanente Medical Care Program" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2024.02.24.581855", "rel_title": "Biochemical characterization of naturally occurring mutations in SARS-CoV-2 RNA-dependent RNA polymerase", @@ -596,61 +2209,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2024.02.24.581861", - "rel_title": "Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing", - "rel_date": "2024-02-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.24.581861", - "rel_abs": "Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Mxyococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle. This immunogen elicited conformationally-relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.\n\nTable of Contents graphic\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC=\"FIGDIR/small/581861v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@114bccdorg.highwire.dtl.DTLVardef@776051org.highwire.dtl.DTLVardef@1547a98org.highwire.dtl.DTLVardef@13cac82_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sonia Bhattacharya", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Matthew C. Jenkins", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Parisa Keshavarz-Joud", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Alisyn Retos Bourque", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Keiyana White", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Amina M. Alvarez Barkane", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Anton V. Bryksin", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Carolina Hernandez", - "author_inst": "New York Structural Biology Center" - }, - { - "author_name": "Mykhailo Kopylov", - "author_inst": "New York Structural Biology Center" - }, - { - "author_name": "M.G. Finn", - "author_inst": "Georgia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2024.02.23.581160", "rel_title": "Deep plasma proteomics with data-independent acquisition: A fastlane towards biomarkers identification.", @@ -2165,6 +3723,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2024.02.19.581112", + "rel_title": "Characterization of the SARS-CoV-2 BA.5 Variants in H11-K18-hACE2 Hamsters", + "rel_date": "2024-02-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.19.581112", + "rel_abs": "This study aims to comprehensively characterize the SARS-CoV-2 BA.5 variants using K18 hACE2 transgenic mice and golden hamsters as model organisms. Previous research on SARS-CoV-2 has utilized both mouse and hamster models, leading to conflicting results concerning the viruss lethality. In our study, the finding suggests that H11-K18 hACE2 golden hamsters closely mimic the disease progression observed in human COVID-19 cases caused by BA.5 variants, demonstrating consistent severity and symptoms comparable to severe infections.\n\nAdditionally, hamsters exhibit heightened respiratory viral replication, accurately reflecting the clinical viral kinetics observed in humans. The study emphasizes the critical importance of selecting an appropriate animal model for SARS-CoV-2 research, while also providing robust support for the hypothesis that BA.5 variants contribute to fatal outcomes in COVID-19 cases. These findings highlight the pivotal role of the golden hamster model in advancing our understanding of the pathogenic mechanisms underlying SARS-CoV-2 variants, as well as in the development of targeted therapeutic strategies.\n\nSignificance StatementOur research work explores groundbreaking insights that could reshape our understanding of COVID-19 and pave the way for targeted therapies. We use golden hamster models to express the possibility of different animal models could contribute to human diseases. We hope this finding could clarify some conflicts existed, and help further development of medication for COVID.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Mei Dong", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Haofeng Lin", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Margaret Pan", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Minghong Huang", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Meiqi Liu", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Rendi Jiang", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Yana Lai", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Aimin Shi", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Bing Yao", + "author_inst": "Nanjing University" + }, + { + "author_name": "Ben Hu", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Zhengli Shi", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Aihua Zhang", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yun Gao", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Wentao Zeng", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Jianmin Li", + "author_inst": "Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2024.02.19.24302823", "rel_title": "Real-world Effectiveness and Causal Mediation Study of BNT162b2 on Long COVID Risks in Children and Adolescents", @@ -2910,41 +4543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.02.15.24302863", - "rel_title": "Impact of COVID-19 on Emergency Medical Services Utilization and Severity in the U.S. Upper Midwest", - "rel_date": "2024-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.15.24302863", - "rel_abs": "The COVID-19 pandemic has claimed nearly one million lives and has drastically changed how patients interact with the healthcare system. Emergency medical services (EMS) are essential for emergency response, disaster preparedness, and responding to everyday emergencies. We therefore examined differences in EMS utilization and call severity in 2020 (pandemic period) compared to trends from 2015-2019 (pre-pandemic period) in a large, multi-state advanced life support EMS agency serving the U.S. Upper Midwest. Specifically, we analyzed all 911 calls made to Mayo Clinic Ambulance, the sole advanced life support EMS provider serving a large area in Minnesota and Wisconsin, in 2020 compared to those made between 2015-2019. We compared the number of emergency calls made in 2020 to the number of calls expected based on trends from 2015-2019. We similarly compared caller demographics, call severity, and proportions of calls made for overdose/intoxication, behavioral health, and motor vehicle accidents. Subgroup analyses were performed for rural vs. urban areas. We identified 262,232 emergent EMS calls in the pre-pandemic period and 53,909 calls in the pandemic period, corresponding to a decrease of 28.7% in call volume during the pandemic period. Caller demographics shifted towards older patients (mean age 59.7 [SD, 23.0] vs. 59.1 [SD, 23.7] years; p<0.001) and to rural areas (20.4% vs. 20.0%; p=0.007). Call severity increased, with 95.3% of calls requiring transport (vs. 93.8%; p<0.001) and 1.9% resulting in death (vs. 1.6%; p<0.001). The proportion of calls for overdose/intoxication increased from 4.8% to 5.5% (p<0.001), while the proportion of calls for motor vehicle collisions decreased from 3.9% to 3.0% (p<0.001). All changes were more pronounced in urban areas. These findings underscore the extent to which the COVID-19 pandemic impacted healthcare utilization, particularly in urban areas, and suggest that patients may have delayed calling EMS with potential implications on disease severity and risk of death.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Brett Boggust", - "author_inst": "Creighton University School of Medicine" - }, - { - "author_name": "Rozalina McCoy", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Moshe Shalom", - "author_inst": "Tel Aviv University Sackler Faculty of Medicine" - }, - { - "author_name": "Lucas Myers", - "author_inst": "Mayo Clinic in Rochester" - }, - { - "author_name": "Carson Rogerson IV", - "author_inst": "Mayo Clinic in Rochester" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2024.02.15.24302762", "rel_title": "Barriers in accessing healthcare during the COVID-19 pandemic: analysis of the Virus Watch community cohort study", @@ -3509,7 +5107,7 @@ "rel_date": "2024-02-15", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.14.24302808", - "rel_abs": "BackgroundThe COVID-19 pandemics global impact was mitigated through rapid vaccine development, leading to a mix of natural and vaccination-derived immunity. Immunological profile in hybrid immunity remains less studies, especially in regions where non-mRNA vaccines were used. This study focuses on the immunological profiles and predictors of immune response in one such population.\n\nMethodsThis was a cross-sectional study to assess their humoral and cellular immune responses based on vaccination and infection history. Immunological assays were performed to measure anti-spike protein and neutralizing antibodies as well as interferon-{gamma} release assay. Multivariable linear regression model was used to estimate predictors of immune response.\n\nResultsThe study revealed significant differences in immune response among participants based on their hybrid immunity status, vaccination, and infection history. Higher antibody titres and cellular responses were observed in individuals with hybrid immunity, especially those with dual pre-Omicron and Omicron infections (3326 BAU/ml, IQR: 770.25-5678.25 and 4.92 IU of IFN-{gamma}/mL, IQR:3.74-16.98 respectively, p <0.001). Age and comorbidities such as diabetes and hypertension were associated with lower antibody levels and cellular response, while vaccination and hybrid immunity correlated with higher immune responses.\n\nConclusionThe prevalence of hybrid immunity was high, yet a substantial portion of the population lacks it, indicating the necessity for targeted immunization strategies. The findings underscore the importance of prioritizing high-risk individuals, such as elderly and individuals with comorbidities, for booster vaccinations to enhance community-level protection against COVID-19.", + "rel_abs": "BackgroundThe COVID-19 pandemics global impact was mitigated through rapid vaccine development, leading to a mix of natural and vaccination-derived immunity. Immunological pro[fi]le in hybrid immunity remains less studies, especially in regions where non-mRNA vaccines were used. This study focuses on the immunological pro[fi]les and predictors of immune response in one such population.\n\nMethodsThis was a cross-sectional study to assess their humoral and cellular immune responses based on vaccination and infection history. Immunological assays were performed to measure antispike protein and neutralizing antibodies as well as interferon-{gamma} release assay. Multivariable linear regression model was used to estimate predictors of immune response.\n\nResultsThe study revealed signi[fi]cant differences in immune response among participants based on their hybrid immunity status, vaccination, and infection history. Higher antibody titres and cellular responses were observed in individuals with hybrid immunity, especially those with dual pre-Omicron and Omicron infections (3326 BAU/ml, IQR: 770.25-5678.25 and 4.92 IU of IFN-{gamma}/mL, IQR:3.74-16.98 respectively, p <0.001). Age and comorbidities such as diabetes and hypertension were associated with lower antibody levels and cellular response, while vaccination and hybrid immunity correlated with higher immune responses.\n\nConclusionThe prevalence of hybrid immunity was high, yet a substantial portion of the population lacks it, indicating the necessity for targeted immunization strategies. The [fi]ndings underscore the importance of prioritizing high-risk individuals, such as elderly and individuals with comorbidities, for booster vaccinations to enhance community-level protection against COVID-19.", "rel_num_authors": 10, "rel_authors": [ { @@ -3995,6 +5593,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "forensic medicine" }, + { + "rel_doi": "10.1101/2024.02.13.24301472", + "rel_title": "Serologic evidence for early SARS-CoV-2 circulation in Lima, Peru, 2020.", + "rel_date": "2024-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.13.24301472", + "rel_abs": "During early 2021, Peru had the highest COVID-19-associated per-capita mortality rate globally. Socioeconomic inequality and insufficiently prepared healthcare and surveillance systems likely contributed to high mortality, potentially coupled with early SARS-CoV-2 introduction. We tested 1,441 individuals with fever sampled during August 2019-May 2021 in Lima, Peru, for SARS-CoV-2-specific antibodies. Serologic testing included a chemiluminescence immunoassay and confirmatory surrogate virus neutralization testing. Early positive samples (n=24) from January-March 2020 were further tested using a plaque-reduction neutralization and avidity tests based on SARS-CoV-2 spike and nucleoprotein antigens. None of the early samples were PRNT-confirmed, in contrast to 81.8% (18/22) of a subsample from April 2020 onwards (Fischer-exact test, p<0.0001). SARS-CoV-2 antibody detection rate was 0.9% in mid-April 2020 (1/104; 95% confidence interval (CI), 0.1-5.8%), suggesting onset of viral circulation in early-mid March 2020, consistent with the first molecular detection of SARS-CoV-2 in Peru on March 6th. Mean avidity increase of 62-77% to 81-94% from all PRNT-confirmed samples during early 2020, were consistent with onset of SARS-CoV-2 circulation during late February/March 2020. Early circulation of SARS-CoV-2 was confirmed in a Susceptible, Exposed, Infected and Recovered mathematical model that projected an effective reproduction number >1, during February-March 2020. Robust serologic testing thus confirmed that early SARS-CoV-2 introduction contributed to high COVID-19 mortality in Peru. Emphasizing the role of diagnostic confirmation, our study highlights the importance of early detection and accurate testing in managing infectious disease outbreaks.\n\nImportanceLatin America was hard hit by the COVID-19 pandemic. Reasons include inadequate healthcare preparation and socio-economic vulnerabilities, likely exacerbated by early undetected SARS-CoV-2 circulation. Diagnostic testing for early SARS-CoV-2 circulation requires exhaustive diagnostic validation due to unspecific reactivity. We used a cohort of circa 1400 febrile patients from August 2019 until May 2021, months earlier than the first seroprevalence study in Lima, Peru, using a two-step diagnostic algorithm. Early 2020 positive samples were further tested with neutralization tests and avidity testing. We confirmed SARS-CoV-2-specific antibodies from April 2020 onwards, suggesting undetected viral circulation circa March 2020, consistent with the first SARS-CoV-2-detection. Early circulation was further confirmed by the significant increase in avidity in positive samples during early 2020 and the modeled peak of reproduction number of >1 during February-March 2020. Using exhaustive diagnostic validation, we detected early SARS-CoV-2 circulation that likely contributed to the severe impact of COVID-19 in Peru.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Andres Moreira-Soto", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Mar\u00eda Paquita Garc\u00eda Mendoza", + "author_inst": "National Institute of Health-INS (Instituto Nacional de Salud-INS), Lima, Peru" + }, + { + "author_name": "Gloria Ang\u00e9lica Arotinco Garayar", + "author_inst": "National Institute of Health-INS (Instituto Nacional de Salud-INS), Lima, Peru" + }, + { + "author_name": "Maribel Dana Figueroa Romero", + "author_inst": "National Institute of Health-INS (Instituto Nacional de Salud-INS), Lima, Peru" + }, + { + "author_name": "Nancy Susy Merino Sarmiento", + "author_inst": "National Institute of Health-INS (Instituto Nacional de Salud-INS), Lima, Peru" + }, + { + "author_name": "Adolfo Ismael Marcelo \u00d1ique", + "author_inst": "National Institute of Health-INS (Instituto Nacional de Salud-INS), Lima, Peru" + }, + { + "author_name": "Edward M\u00e1laga-Trillo", + "author_inst": "Universidad Peruana Cayetano Heredia, Facultad de Ciencias y Filosof\u00eda, Laboratorios de Investigaci\u00f3n y Desarrollo, Lima, Peru" + }, + { + "author_name": "C\u00e9sar Augusto Cabezas S\u00e1nchez", + "author_inst": "National Institute of Health-INS (Instituto Nacional de Salud-INS), Lima, Peru" + }, + { + "author_name": "Jan Felix Drexler", + "author_inst": "Charite - Universitatmedizin Berlin Institut fur Virologie" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2024.02.13.24302781", "rel_title": "Characteristics and Determinants of Pulmonary Long COVID", @@ -4632,141 +6281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2024.02.11.24302594", - "rel_title": "A Phase II Study Integrating a Single-Blind Safety Phase with a Double-Blind, Placebo-Controlled Randomized Phase, Assessing Single-Dose Intramuscular or Intranasal Administration to Evaluate the Safety and Immunogenicity of the Recombinant Vaccine Against COVID-19 (AVX/COVID-12 \"Patria\") Based on an Active Newcastle Disease Viral Vector as a Heterologous Booster in Subjects with Evidence of Previous Immunity to SARS-CoV-2.", - "rel_date": "2024-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.11.24302594", - "rel_abs": "BackgroundThe global inequity in coronavirus disease 2019 (COVID-19) vaccine distribution, primarily affecting low- and middle-income countries (LMICs), highlights the urgent need for innovative and cost-effective vaccine technologies to address availability disparities. This is crucial for achieving and sustaining widespread immunity and protecting vulnerable populations during future booster campaigns.\n\nMethodsTo address this need, we conducted a phase II clinical trial evaluating the safety and immunogenicity of the AVX/COVID-12 \"Patria\" vaccine as a booster dose. The vaccine was administered through both intramuscular (IM) and intranasal (IN) routes to participants who had previously received severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines based on adenoviral technology, inactivated virus, or mRNA technology. The inclusion criterion involved individuals with initial anti-spike IgG titers below 1,200 U/mL, allowing observation of the booster effect induced by vaccination.\n\nResultsImmunization with AVX/COVID-12 resulted in a significant (>2.5 times) increase in neutralizing antibodies against the original Wuhan strain and variants of concern (VOCs) such as Alpha, Beta, Delta, and Omicron (BA.2 and BA.5). This immune response was accompanied by cellular interferon-gamma (IFN-{gamma}) production, indicating a robust and multifaceted reaction.\n\nConclusionsThe administration of AVX/COVID-12 as a booster dose, whether through IM or IN routes, was safe and well-tolerated. The vaccine extended immune responses not only against the original Wuhan-1 strain but also against various VOCs. Its ability to enhance preexisting immune responses suggests a potential contribution to expanding and sustaining herd immunity within the population.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Constantino L\u00f3pez-Mac\u00edas", - "author_inst": "Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Martha Torres", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Brenda Armenta-Copca", - "author_inst": "iLS Clinical Research, S.C., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Niels H. Wacher", - "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Epidemiolog\u00eda Cl\u00ednica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Laura Castro-Castrezana", - "author_inst": "CAIMED Investigaci\u00f3n en Salud, S. A. de C. V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Andrea Alicia Colli-Dom\u00ednguez", - "author_inst": "Oaxaca Site Management Organization (OSMO) S.C., Oaxaca, M\u00e9xico." - }, - { - "author_name": "Tania Rivera-Hern\u00e1ndez", - "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, IMSS, Ciudad de M\u00e9xico, M\u00e9xico. CONAHCYT, Ci" - }, - { - "author_name": "Alejandro Torres-Flores", - "author_inst": "Posgrado en Inmunolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Luis Ram\u00edrez-Mart\u00ednez", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Georgina Paz-De la Rosa", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Oscar Rojas-Mart\u00ednez", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Jes\u00fas Alejandro Su\u00e1rez-Mart\u00ednez", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Gustavo Peralta-S\u00e1nchez", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Claudia Carranza", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Esmeralda Ju\u00e1rez", - "author_inst": "Departamento de Investigaci\u00f3n en Microbiolog\u00eda, Instituto Nacional de Enfermedades Respiratorias, Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Horacio Zamudio-Meza", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Laura E. Carreto-Binaghi", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Mercedes Viettri", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Damaris Romero-Rodr\u00edguez", - "author_inst": "Unidad de Citometr\u00eda, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Andrea Palencia", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Edgar Reyna-Rosas", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Jos\u00e9 E. M\u00e1rquez-Garc\u00eda", - "author_inst": "Laboratorio de Inmunobiolog\u00eda de la Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "David Sarfati-Mizrahi", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Weina Sun", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA." - }, - { - "author_name": "H\u00e9ctor El\u00edas Chagoya-Cort\u00e9s", - "author_inst": "Consultora Mextrategy, S.A.S. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Felipa Castro-Peralta", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - }, - { - "author_name": "Peter Palese", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA." - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Garc\u00eda-Sastre", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Department of Pathology, Molecular and Cell-Based Medicine, Icahn School" - }, - { - "author_name": "Bernardo Lozano-Dubernard", - "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2024.02.12.24302698", "rel_title": "Long-term cardiovascular safety of COVID-19 vaccination according to brand, dose and combinations: Cohort study of 46 million adults in England", @@ -6037,6 +7551,37 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2024.02.07.579420", + "rel_title": "Discovering and overcoming the bias in neoantigen identification by unified machine learning models", + "rel_date": "2024-02-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.07.579420", + "rel_abs": "Neoantigens, formed by genetic mutations in tumor cells, are abnormal peptides that can trigger immune responses. Precisely identifying neoantigens from vast mutations is the key to tumor immunotherapy design. There are three main steps in the neoantigen immune process, i.e., binding with MHCs, extracellular presentation, and induction of immunogenicity. Various machine learning methods have been developed to predict the probability of one of the three events, but the overall accuracy of neoantigen identification remains far from satisfactory. To gain a systematic understanding of the key factors of neoantigen identification, we developed a unified transformer-based machine learning framework ImmuBPI that comprised three tasks and achieved state-of-the-art performance. Through cross-task model interpretation, we have discovered an underestimation of data bias for immunogenicity prediction, which has led to skewed discriminatory boundaries of current machine learning models. We designed a mutual information-based debiasing strategy that performed well on mutation variants immunogenicity prediction, a task where current methods fell short. Clustering immunogenic peptides with debiased representations uncovers unique preferences for biophysical properties, such as hydrophobicity and polarity. These observations serve as an important complement to the past understanding that accurately predicting neoantigen is constrained by limited data, highlighting the necessity of bias control. We expect this study will provide novel and insightful perspectives for neoantigen prediction methods and benefit future neoantigen-mediated immunotherapy designs.\n\nAvailabilityThe code of our work is available at https://github.com/WangLabTHU/ImmuBPI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ziting Zhang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Wenxu Wu", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Lei Wei", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Xiaowo Wang", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2024.02.08.24302489", "rel_title": "Impact of Shifting University Policies During the COVID-19 Pandemic on Self-Reported Employee Social Networks", @@ -6658,101 +8203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.02.05.24302348", - "rel_title": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission during the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study using Genomic Epidemiology", - "rel_date": "2024-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.05.24302348", - "rel_abs": "BackgroundHouseholds are a major setting for SARS-CoV-2 infections, but there remains a lack of knowledge regarding the dynamics of viral transmission, particularly in the setting of widespread pre-existing SARS-CoV-2 immunity and evolving variants.\n\nMethodsWe conducted a prospective, case-ascertained household transmission study in the greater Boston area in March-July 2022. Anterior nasal swabs, along with clinical and demographic data, were collected for 14 days. Nasal swabs were tested for SARS-CoV-2 by PCR. Whole genome sequencing was performed on high-titer samples.\n\nResultsWe enrolled 33 households in a primary analysis set, with a median age of participants of 25 years old (range 2-66); 98% of whom had received at least 2 doses of a COVID-19 vaccine. 58% of households had a secondary case during follow up and the secondary attack rate (SAR) for contacts infected was 39%. We further examined a strict analysis set of 21 households that had only 1 PCR+ case at baseline, finding an SAR of 22.5%. Genomic epidemiology further determined that there were multiple sources of infection for household contacts, including the index case and outside introductions. When limiting estimates to only highly probable transmissions given epidemiologic and genomic data, the SAR was 18.4%.\n\nConclusionsHousehold contacts of a person newly diagnosed with COVID-19 are at high risk for SARS-CoV-2 infection in the following 2 weeks. This is, however, not only due to infection from the household index case, but also because the presence of an infected household member implies increased SARS-CoV-2 community transmission. Further studies to understand and mitigate household transmission are needed.\n\nKey PointsWhen community transmission of SARS-CoV-2 is high, distinguishing household transmissions from independent introductions is difficult with either epidemiologic or genomic data alone. Here, we conducted daily nasal sampling with genomic sequencing to understand the dynamics of viral transmission within households.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Jaspreet Banga", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Taylor Brock-Fisher", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Brittany A Petros", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Eric Y. Dai", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Ariana T. Leonelli", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Sabrina T. Dobbins", - "author_inst": "Broad Institute of MGH and Harvard" - }, - { - "author_name": "Katelyn S. Messer", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Audrey B. Nathanson", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Amelia A. Capone", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Nancy A. Littlehale", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Viola Appiah-Danquah", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Siang Dim", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Gage K. Moreno", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Maura Crowther", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Kannon A. Lee", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Katherine C. DeRuff", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Bronwyn L. MacInnis", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Michael Springer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Pardis C. Sabeti", - "author_inst": "Harvard University; The Broad Institute or MIT and Harvard; Howard Hughes Medical Institute" - }, - { - "author_name": "Kathryn E. Stephenson", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2024.02.05.24302338", "rel_title": "Clinical evaluation of the Roche distributed SD Biosensor SARS-CoV-2 & Flu A/B Rapid Antigen Test amongst mild symptomatic people during the 2022/2023 winter season.", @@ -7951,6 +9401,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2024.02.02.24302188", + "rel_title": "Effects of COVID-19 on the provision of Water, Sanitation, and Hygiene (WASH) services in health care facilities in the Far-North Region of Cameroon", + "rel_date": "2024-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.02.24302188", + "rel_abs": "Worldwide, the Joint Monitoring Program reports that one in four health care facilities (HCFs) lack functional water supply on premises, one in three lack hand hygiene facilities, and one in three lack adequate infectious waste disposal. The COVID-19 pandemics shed light on the lack of investments, the absence of infrastructures, education and policies related to WASH as well as revealed insufficient investment in healthcare safety and has brought WASH services as non-negotiable for HCFs. This study used a cross-sectional pre-post COVID-19 framework to determine the proportion of HCFs: meeting basic WASH services and, which WASH services improved post-COVID-19 in the Far-North Region of Cameroon. A total of 97 (23.04%) HCFs among the 421 that are found in the Far-North region were surveyed and located in eight (25%) of the 32 Health Districts. They corresponded to the integrated health centers category (79.4%) and the surveys respondent was the chief of the HCF (92.8%). Approximately 75.3%, 0.0%, 48.5%, 46.4%, and 6.2% of HCFs respectively met thresholds for basic water, sanitation, hygiene, waste management, and environment cleaning services. When comparing pre- vs. post COVID-19 periods, a significant increase (8%) was noted in the proportion of HCFs as of optimal handwashing practices-related services (P=0.0026). There was also a significant increase (p=0.007) in the proportion of HCFs with cleaning protocols available. Further, none of the HCFs fulfilled all the criteria to meet basic services for all the five WASH services. In conclusion, the response to the COVID-19 pandemics only partially improved WASH services-related infrastructures in HCFs of the Far-North Region of Cameroon. The COVID-19 pandemics was a missed opportunity to strengthen WASH services. There should be a continuing encouragement of governments and funding agencies in planning and budgeting WASH in healthcare-related research and issues, and enabling the maintenance of existing WASH infrastructures in healthcare settings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Carole Debora Nounkeu", + "author_inst": "Regional Delegation of Public Health of Littoral, Douala, Cameroon" + }, + { + "author_name": "Giequel Corniche Noumbissi Massop", + "author_inst": "University of Yaounde I: Universite de Yaounde I" + }, + { + "author_name": "Donato Koyalta", + "author_inst": "University of N'Djamena: Universite de N'Djamena" + }, + { + "author_name": "Chanceline Bilounga Ndongo", + "author_inst": "University of Douala Faculty of Medicine and Pharmaceutical Sciences: Universite de Douala Faculte de Medecine et Sciences Pharmaceutiques" + }, + { + "author_name": "Florent Kamkumo Ouabo", + "author_inst": "BTU Cottbus-Senftenberg: Brandenburgische Technische Universitat Cottbus-Senftenberg" + }, + { + "author_name": "Bertin Nono", + "author_inst": "Delta Airlines" + }, + { + "author_name": "Marie Nicole Ngoufack", + "author_inst": "Challenges Initiative Solutions" + }, + { + "author_name": "Jigna Morarji Dharod", + "author_inst": "UNC Greensboro: University of North Carolina at Greensboro" + }, + { + "author_name": "Catherine Juillard", + "author_inst": "University of San Francisco" + }, + { + "author_name": "Alain Chichom-Mefire", + "author_inst": "University of Buea Faculty of Health Sciences" + }, + { + "author_name": "Georges Nguefack-Tsague", + "author_inst": "University of Yaounde I" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2024.02.01.24302037", "rel_title": "Treadmill Exercise Stress Echocardiography Exposes Impaired Left Ventricular Function in Patients Recovering from Hospitalization with COVID-19 Without Overt Myocarditis Versus Historical Controls", @@ -8596,53 +10105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2024.01.30.24302015", - "rel_title": "Real-World Effectiveness of a Third Dose of mRNA-1273 versus BNT162b2 on Inpatient and Medically Attended COVID-19 among Immunocompromised Adults in the United States", - "rel_date": "2024-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.30.24302015", - "rel_abs": "Recent data have shown elevated infection rates in several subpopulations at risk of SARS-CoV-2 infection and COVID-19, including immunocompromised (IC) individuals. Previous research suggests that IC persons have reduced risks of hospitalization and medically-attended COVID-19 with 2 doses of mRNA-1273 (SpikeVax; Moderna) compared to two doses of BNT162b2 (Comirnaty; Pfizer/BioNTech). The main objective of this retrospective cohort study was to compare real-world effectiveness of third doses of mRNA-1273 versus BNT162b2 at multiple time points on occurrence of COVID-19 hospitalization and medically-attended COVID-19 among IC adults in the US. The HealthVerity (HV) medical and pharmacy claims database, which contains data from >330 million patients, was the data source. Both subgroup and sensitivity analyses were conducted in addition to the core comparisons noted. In propensity score-adjusted analyses, receiving mRNA-1273 vs BNT162b2 as third dose was associated with 32% (relative risk [RR] 0.68; 95% confidence interval [CI] 0.51-0.89), 29% (0.71; 0.57-0.86), and 23% (0.77; 0.62-0.93) lower risk of COVID-19 hospitalization after 90, 180, and 270 days, respectively. Corresponding reductions in medically-attended COVID-19 were 8% (0.92; 0.86-0.98), 6% (0.94; 0.90-0.98), and 2% (0.98; 0.94-1.02), respectively. Our findings suggest a third dose of mRNA-1273 is more effective than a third dose of BNT162b2 in preventing COVID-19 hospitalization and breakthrough medically-attended COVID-19 among IC adults in the US.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Tianyu Sun", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Linwei Li", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Katherine Mues", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "Mihaela Georgieva", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Brenna Kirk", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "James Mansi", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Nicolas Van de Velde", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Ekkehard Beck", - "author_inst": "Moderna, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2024.01.30.24301978", "rel_title": "LESSONS LEARNED FROM COVID-19 MODELLING EFFORTS FOR POLICY DECISION-MAKING IN LOWER- AND MIDDLE-INCOME COUNTRIES", @@ -9821,6 +11283,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2024.01.24.23300025", + "rel_title": "Predicting COVID-19 cases across a large university campus using complementary built environment and wastewater surveillance approaches", + "rel_date": "2024-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.24.23300025", + "rel_abs": "BackgroundEnvironmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance. Built environment sampling may provide complementary spatially-refined detection for viral surveillance in congregate settings such as universities.\n\nMethodsWe conducted a prospective environmental surveillance study at the University of Ottawa between September 2021 and April 2022. Floor surface samples were collected twice weekly from six university buildings. Samples were analyzed for the presence of SARS-CoV-2 using RT-qPCR. A Poisson regression was used to model the campus-wide COVID-19 cases predicted from the fraction of floor swabs positive for SARS-CoV-2 RNA, building CO2 levels, Wi-Fi usage, and SARS-CoV-2 RNA levels in regional wastewater. We used a mixed-effects Poisson regression analysis to model building-level cases using viral copies detected in floor samples as a predictor. A random intercepts logistic regression model tested whether floor samples collected in high-traffic areas were more likely to have SARS-CoV-2 present than low-traffic areas.\n\nResultsOver the 32-week study period, we collected 554 floor swabs at six university buildings. Overall, 13% of swabs were PCR-positive for SARS-CoV-2, with positivity ranging between 4.8% and 32.7% among university buildings. Both floor swab positivity (Spearman r = 0.74, 95% CI: 0.53-0.87) and regional wastewater signal (Spearman r = 0.50, 95% CI: 0.18-0.73) were positively correlated with on-campus COVID-19 cases. In addition, built environment detection was a predictor of cases linked to individual university buildings (IRlog10(copies) + 1 = 17, 95% CI: 7-44). There was no significant difference in detection between floors sampled in high-traffic versus low-traffic areas (OR = 1.3, 95% CI: 0.8-2.1).\n\nConclusionsDetection of SARS-CoV-2 RNA on floors and viral RNA levels found in wastewater were strongly associated with the incidence of COVID-19 cases on a university campus. These data suggest a potential role for institutional built environment sampling, used together with wastewater surveillance, for predicting COVID-19 cases at both campus-wide and building level scales.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Aaron Hinz", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Jason A Moggridge", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Hanna Ke", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Alexandra M. A. Hicks", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Evgueni Doukhanine", + "author_inst": "DNA Genotek Incorporated" + }, + { + "author_name": "Michael Fralick", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Laura Hug", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Derek MacFadden", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Hebah Mejbel", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Caroline Nott", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Ashley Raudanskis", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Nisha Thampi", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Alex Wong", + "author_inst": "Carleton University" + }, + { + "author_name": "Rees Kassen", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2024.01.24.577015", "rel_title": "Interferon-\u03b3 as a Potential Inhibitor of SARS-CoV-2 ORF6 Accessory Protein", @@ -10460,101 +11993,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.01.23.24301671", - "rel_title": "Longitudinal study of immunity to SARS-CoV2 in Ocrelizumab-treated multiple sclerosis patients up to 2 years after COVID-19 vaccination", - "rel_date": "2024-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.23.24301671", - "rel_abs": "Objectives1 To plot the trajectory of humoral and cellular immune responses to the primary (two-dose) COVID-19 mRNA series and the third/booster dose in B-cell-depleted multiple sclerosis (MS) patients up to 2 years post-vaccination; 2. to identify predictors of immune responses to vaccination; and 3. to assess the impact of intercurrent COVID-19 infections on SARS CoV-2-specific immunity.\n\nMethods60 Ocrelizumab-treated MS patients were enrolled from NYU (New York) and University of Colorado (Anschutz) MS Centers. Samples were collected pre-vaccination, and then 4, 12, 24, and 48 weeks post-primary series, and 4, 12, 24, and 48 weeks post-booster. Binding anti-Spike antibody responses were assessed with multiplex bead-based immunoassay (MBI) and electrochemiluminescence (Elecsys(R), Roche Diagnostics), and neutralizing antibody responses with live-virus immunofluorescence-based microneutralization assay. Spike-specific cellular responses were assessed with IFN{gamma}/IL-2 ELISpot (Invitrogen) and, in a subset, by sequencing complementary determining regions (CDR)-3 within T-cell receptors (Adaptive Biotechnologies). A linear mixed effect model was used to compare antibody and cytokine levels across time points. Multivariate analyses identified predictors of immune responses.\n\nResultsThe primary vaccination induced an 11-208-fold increase in binding and neutralizing antibody levels and a 3-4-fold increase in IFN{gamma}/IL-2 responses, followed by a modest decline in antibody but not cytokine responses. Booster dose induced a further 3-5-fold increase in binding antibodies and 4-5-fold increase in IFN{gamma}/IL-2, which were maintained for up to 1 year. Infections had a variable impact on immunity.\n\nInterpretationHumoral and cellular benefits of COVID-19 vaccination in B-cell-depleted MS patients were sustained for up to 2 years when booster doses were administered.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Ilya Kister", - "author_inst": "NYU Multiple Sclerosis Comprehensive Care Center" - }, - { - "author_name": "Ryan Curtin", - "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology" - }, - { - "author_name": "Amanda L Piquet", - "author_inst": "Rocky Mountain MS Center, University of Colorado School of Medicine" - }, - { - "author_name": "Tyler Borko", - "author_inst": "Rocky Mountain MS Center, University of Colorado School of Medicine" - }, - { - "author_name": "Jinglan Pei", - "author_inst": "Genentech, Inc." - }, - { - "author_name": "Barbara L Banbury", - "author_inst": "Adaptive Biotechnologies" - }, - { - "author_name": "Tamar E Bacon", - "author_inst": "NYU Multiple Sclerosis Comprehensive Care Center, NYU Grossman School of Medicine" - }, - { - "author_name": "Angie Kim", - "author_inst": "NYU Multiple Sclerosis Comprehensive Care Center, NYU Grossman School of Medicine" - }, - { - "author_name": "Michael Tuen", - "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" - }, - { - "author_name": "Yogambigai Velmurugu", - "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine" - }, - { - "author_name": "Samantha Nyovanie", - "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine" - }, - { - "author_name": "Sean Selva", - "author_inst": "Rocky Mountain MS Center, University of Colorado School of Medicine" - }, - { - "author_name": "Marie I Samanovic", - "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine" - }, - { - "author_name": "Yury Patskovsky", - "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine" - }, - { - "author_name": "Jessica Priest", - "author_inst": "Genentech, Inc." - }, - { - "author_name": "Mark Cabatingan", - "author_inst": "Genentech, Inc." - }, - { - "author_name": "Ryan C Winger", - "author_inst": "Genentech, Inc." - }, - { - "author_name": "Michelle Krogsgaard", - "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine" - }, - { - "author_name": "Gregg J Silverman", - "author_inst": "Division of Rheumatology, Department of Medicine, NYU Grossman School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2024.01.20.576353", "rel_title": "Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission", @@ -11669,6 +13107,41 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2024.01.16.575911", + "rel_title": "Persistence and Free Chlorine Disinfection of Human Coronaviruses and Their Surrogates in Water", + "rel_date": "2024-01-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.16.575911", + "rel_abs": "The COVID-19 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied depending on virus and water matrix. In drinking water prior to disinfectant addition, MHV showed the largest decay rate constant (2.25 day-1) followed by HCoV-OC43 (0.99 day-1) and TGEV (0.65 day-1); while in phosphate buffer, HCoV-OC43 (0.51 day-1) had a larger decay rate constant than MHV (0.28 day-1) and TGEV (0.24 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 mg-1 min-1 L, followed by MHV (81.33 mg-1 min-1 L) and HCoV-OC43 (59.42 mg-1 min-1 L).\n\nImportanceThis study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mengyang Zhang", + "author_inst": "Stanford University" + }, + { + "author_name": "Michelle Leong", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "William Mitch", + "author_inst": "Stanford University" + }, + { + "author_name": "Catherine A. Blish", + "author_inst": "Stanford" + }, + { + "author_name": "Alexandria B Boehm", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2024.01.16.24301337", "rel_title": "Antiviral efficacy of fluoxetine in early symptomatic COVID-19: an open-label, randomised, controlled, adaptive platform trial (PLATCOV)", @@ -12422,145 +13895,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2024.01.15.575741", - "rel_title": "Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody", - "rel_date": "2024-01-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.15.575741", - "rel_abs": "SUMMARY/ABSTRACTThree coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Nicole V. Johnson", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Steven Wall", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Kevin Kramer", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Clinton Holt", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Sivakumar Periasamy", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Simone Richardson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service" - }, - { - "author_name": "Naveenchandra Suryadevara", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Emanuele Andreano", - "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences" - }, - { - "author_name": "Ida Paciello", - "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences" - }, - { - "author_name": "Giulio Pierleoni", - "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences" - }, - { - "author_name": "Giulia Piccini", - "author_inst": "VisMederi Research S.r.l., Siena 53100, Italy" - }, - { - "author_name": "Ying Huang", - "author_inst": "Florida Research and Innovation Center, Cleveland Clinic" - }, - { - "author_name": "Pan Ge", - "author_inst": "Florida Research and Innovation Center, Cleveland Clinic" - }, - { - "author_name": "James Allen", - "author_inst": "Florida Research and Innovation Center, Cleveland Clinic" - }, - { - "author_name": "Naoko Uno", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Andrea Shiakolas", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Kelsey Pilewski", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Rachel Nargi", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Alexandria Abu-Shmais", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Rachel Sutton", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Robert Parks", - "author_inst": "Duke Human Vaccine Institute" - }, - { - "author_name": "Barton Haynes", - "author_inst": "Duke Human Vaccine Institute" - }, - { - "author_name": "Robert Carnahan", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "James Crowe Jr.", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Emanuele Montomoli", - "author_inst": "VisMederi Research S.r.l., Siena 53100, Italy" - }, - { - "author_name": "Rino Rappuoli", - "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences" - }, - { - "author_name": "Alexander Bukreyev", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Ted Ross", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Giuseppe Sautto", - "author_inst": "Florida Research and Innovation Center, Cleveland Clinic" - }, - { - "author_name": "Ivelin Georgiev", - "author_inst": "Vanderbilt Vaccine Center" - }, - { - "author_name": "Jason McLellan", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2024.01.15.24301331", "rel_title": "Social inequalities in COVID-19 deaths by area-level income: patterns over time and the mediating role of vaccination in a population of 11.2 million people in Ontario, Canada", @@ -13919,6 +15253,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2024.01.11.24301106", + "rel_title": "The pandemic, COVID-19 disease and perinatal health", + "rel_date": "2024-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.11.24301106", + "rel_abs": "Adverse effects of COVID-19 on perinatal health have been documented, however there is a lack of research that separates individual disease from other changing risks during the pandemic period. We linked California statewide birth and hospital discharge data for 2019-2020, and compared health indicators among 3 groups of pregnancies: [a] 2020 delivery with COVID-19, [b] 2020 delivery with no documented COVID-19, and [c] 2019 pre-pandemic delivery. We aimed to quantify the links between COVID-19 and perinatal health, separating individual COVID-19 disease (a vs b) from the pandemic period (b vs c). We examined the following health indicators: preterm birth, hypertensive disorders of pregnancy, gestational diabetes mellitus and severe maternal morbidity. We applied model based standardization to estimate \"average effect of treatment on the treated\" risk differences (RD), and adjusted for individual and community-level confounders. Among pregnancies in 2020, those with COVID-19 disease had higher burdens of preterm birth (RD[95% confidence interval (CI)]=2.8%[2.1,3.5]), hypertension (RD[95% CI]=3.3%[2.4,4.1]), and severe maternal morbidity (RD[95% CI]=2.3%[1.9,2.7]) compared with pregnancies without COVID-19 (a vs b) adjusted for confounders. Pregnancies in 2020 without COVID-19 had a lower burden of preterm birth (RD[95% CI]=-0.4%[-0.6,-0.3]), particularly spontaneous preterm, and a higher burden of hypertension (RD[95% CI]=1.0%[0.9,1.2]) and diabetes RD[95%CI]=0.9%[0.8,1.1] compared with pregnancies in 2019 (b vs c) adjusted for confounders. Protective associations of the pandemic period for spontaneous preterm birth may be explained by socioenvironmental and behavioral modifications, while increased maternal conditions may be due to stress and other behavioral changes. To our knowledge, our study is the first to distinguish between individual COVID-19 disease and the pandemic period in connection with perinatal outcomes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shelley Jung", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Emily F Liu", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Dana E Goin", + "author_inst": "Columbia University" + }, + { + "author_name": "Kara E Rudolph", + "author_inst": "Columbia University" + }, + { + "author_name": "Mahasin S Mujahid", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "William H Dow", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Jennifer Ahern", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2024.01.10.575114", "rel_title": "SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain", @@ -14712,33 +16089,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.01.09.24301062", - "rel_title": "Patient experiences of UK primary care online triage and consultation platforms during COVID-19: A systematic review", - "rel_date": "2024-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.09.24301062", - "rel_abs": "BackgroundOnline triage and consultation platforms are being increasingly used by healthcare providers in the UK for patient/clinician interactions. COVID-19 accelerated the shift towards the use of these platforms to maintain healthcare provision and reduce transmission. Strict directives were introduced by the UK Government to avoid in-person contact wherever possible in March 2020.\n\nAimTo examine patients experiences of online triage and consultation in UK primary care during the COVID-19 pandemic and offer considerations for their continued use.\n\nDesignThis study follows the PRISMA framework and includes qualitative studies conducted in UK primary care based on the experiences of patient users of any such online platform during the period of March 2020 to April 2023. Studies were included using the PICO format. Three literature databases were searched for relevant studies: PubMed, Science Direct and EMBASE. CASP is used to assess data quality.\n\nResults540 studies were reviewed and reduced to 12 studies that met the inclusion criteria. Study characteristics were identified as: year of study, study population, disease types/conditions, patient response themes and the studys data capture method. A thematic inductive approach identifies three overarching themes (Accessibility, Care delivery, System functionality) and 10 sub-themes (Affordability, IT literacy, Communication, Convenience, Care quality, Patient safety/privacy, Usability, Continuity of care, Inequality and Media influence).\n\nConclusionThis review highlights aspects of patient satisfaction and benefit but also those most concerning for patients. This study reviews the rapid, compulsory adoption of these systems during COVID-19 with implications for their future implementation beyond the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Christopher Roberts", - "author_inst": "Swansea University" - }, - { - "author_name": "Jomin George", - "author_inst": "Swansea University" - }, - { - "author_name": "Judy Jenkins", - "author_inst": "Swansea University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2024.01.09.24301069", "rel_title": "Protection afforded by post-infection SARS-CoV-2 vaccine doses: a cohort study in Shanghai", @@ -15905,6 +17255,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2024.01.02.573936", + "rel_title": "Longitudinal transcriptional changes reveal genes from the natural killer cell-mediated cytotoxicity pathway as critical players underlying COVID-19 progression", + "rel_date": "2024-01-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.02.573936", + "rel_abs": "Patients present a wide range of clinical severities in response SARS-CoV-2 infection, but the underlying molecular and cellular reasons why clinical outcomes vary so greatly within the population remains unknown. Here, we report that negative clinical outcomes in severely ill patients were associated with divergent RNA transcriptome profiles in peripheral immune cells compared with mild cases during the first weeks after disease onset. Protein-protein interaction analysis indicated that early-responding cytotoxic NK cells were associated with an effective clearance of the virus and a less severe outcome. This innate immune response was associated with the activation of select cytokine-cytokine receptor pathways and robust Th1/Th2 cell differentiation profiles. In contrast, severely ill patients exhibited a dysregulation between innate and adaptive responses affiliated with divergent Th1/Th2 profiles and negative outcomes. This knowledge forms the basis of clinical triage that may be used to preemptively detect high-risk patients before life-threatening outcomes ensue.\n\nHighlights- Mild COVID-19 patients presented an early compromise with NK cell function, whereas severe patients do so with neutrophil function.\n- The identified co-expressed genes give insights into a coordinated transcriptional program of NK cell cytotoxic activity being associated with mild patients.\n- Key checkpoints of NK cell cytotoxicity that were enriched in mild patients include: KLRD1, CD247, and IFNG.\n- The early innate immune response related to NK cells connects with the Th1/Th2 adaptive immune responses, supporting their relevance in COVID-19 progression.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Matias A Medina", + "author_inst": "San Sebasti\u00e1n University" + }, + { + "author_name": "Francisco Fuentes-Villalobos", + "author_inst": "Universidad de Concepci\u00f3n" + }, + { + "author_name": "Claudio Quevedo", + "author_inst": "Universidad de Concepci\u00f3n" + }, + { + "author_name": "Felipe Aguilera", + "author_inst": "University of Concepci\u00f3n" + }, + { + "author_name": "Raul Riquelme", + "author_inst": "Hospital Dr. Eduardo Sch\u00fctz Schroeder" + }, + { + "author_name": "Maria Luisa Rioseco", + "author_inst": "Hospital Puerto Montt Dr. Eduardo Sch\u00fctz Schroeder" + }, + { + "author_name": "Sebastian Barria", + "author_inst": "Hospital Dr. Eduardo Sch\u00fctz Schroeder" + }, + { + "author_name": "Yazmin Pinos", + "author_inst": "Hospital Base San Jose" + }, + { + "author_name": "Mario Calvo", + "author_inst": "Hospital Base Valdivia" + }, + { + "author_name": "Ian Burbulis", + "author_inst": "Universidad San Sebastian" + }, + { + "author_name": "Raymond A Alvarez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jose Luis Garrido", + "author_inst": "Universidad San Sebastian" + }, + { + "author_name": "Maria Ines Barria", + "author_inst": "Universidad San Sebastian" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2024.01.04.574272", "rel_title": "Antigen-display exosomes provide adjuvant-free protection against SARS-CoV-2 disease at nanogram levels of spike protein", @@ -16502,85 +17919,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2024.01.02.573939", - "rel_title": "Stably-Inverted Apical-Out Human Upper Airway Organoids for SARS-CoV-2 Infection and Therapeutic Testing", - "rel_date": "2024-01-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.02.573939", - "rel_abs": "Apical-out organoids produced through eversion triggered by extra-organoid extracellular matrix (ECM) removal or degradation are generally small, structurally variable, and limited for viral infection and therapeutics testing. This work describes ECM-encapsulating, stably-inverted apical-out human upper airway organoids (AORBs) that are large ([~]500 {micro}m diameter), consistently spherical, recapitulate in vivo-like cellular heterogeneity, and maintain their inverted morphology for over 60 days. Treatment of AORBs with IL-13 skews differentiation towards goblet cells and the apical-out geometry allows extra-organoid mucus collection. AORB maturation for 14 days induces strong co-expression of ACE2 and TMPRSS2 to allow high-yield infection with five SARS-CoV-2 variants. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds [remdesivir, bemnifosbuvir (AT-511), and nirmatrelvir] shows AORB antiviral assays to be comparable to gold-standard air-liquid interface cultures, but with higher throughput ([~]10-fold) and fewer cells ([~]100-fold). While this work focuses on SARS-CoV-2 applications, the consistent AORB shape and size, and one-organoid-per-well modularity broadly impacts in vitro human cell model standardization efforts in line with economic imperatives and recently updated FDA regulation on therapeutic testing.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ji-Hoon Lee", - "author_inst": "Georgia Insitute of Technology" - }, - { - "author_name": "Julia C LeCher", - "author_inst": "Emory University" - }, - { - "author_name": "Eric Parigoris", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Noriyuki Shinagawa", - "author_inst": "Georgia Insitute of Technology" - }, - { - "author_name": "Jason Sentosa", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Candela Manfredi", - "author_inst": "Emory University" - }, - { - "author_name": "Shu Ling Goh", - "author_inst": "Emory University" - }, - { - "author_name": "Ramyani De", - "author_inst": "Emory University" - }, - { - "author_name": "Sijia Tao", - "author_inst": "Emory University" - }, - { - "author_name": "Keivan Zandi", - "author_inst": "Emory University" - }, - { - "author_name": "Franck Amblard", - "author_inst": "Emory University" - }, - { - "author_name": "Eric J Sorscher", - "author_inst": "Emory University" - }, - { - "author_name": "Jason R Spence", - "author_inst": "University of Michigan" - }, - { - "author_name": "Rabindra Tirouvanziam", - "author_inst": "Emory University" - }, - { - "author_name": "Raymond F Schinazi", - "author_inst": "Emory University" - }, - { - "author_name": "Shuichi Takayama", - "author_inst": "Georgia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2024.01.04.574161", "rel_title": "Antiviral action of different molecules obtained from invertebrates against coronavirus", @@ -17679,6 +19017,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2023.12.27.23300586", + "rel_title": "Health literacy, information access and COVID-19 vaccination hesitancy among foreign-born persons in Sweden - a focus group interview-study", + "rel_date": "2023-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.27.23300586", + "rel_abs": "BackgroundLower rates of COVID-19 vaccination have been observed in individuals with an immigrant background, yet if this relates to barriers to obtaining reliable information is unknown. This exploratory interview study investigated health literacy and information access as determinants for vaccination hesitancy towards the COVID-19 vaccine among foreign-born individuals in Sweden.\n\nMethods and findingsWe used purposive sampling to recruit foreign-born adults from low- and middle-income countries and health guides and doulas who were assigned to spread COVID-19 related information in immigrant-dense urban areas. Data were collected using semi-structured focus group interviews, which were transcribed verbatim and analysed according to systematic text condensation.\n\nTen participants were included who were gainfully employed as health guides/doulas, or in other jobs, full-time students, or housewives. Four main themes emerged: 1) Limited health literacy, 2) Consequences of not using official Swedish information, 3) Decision-making on COVID-19 vaccination, and 4) Suggestions to improve information dissemination effectiveness. The lack of health literacy in official institutions, health care personnel and recipients alike led to little use of official information. Instead, most participants relied on social media, social contacts and international media, through which a lot of contradictive and negative information about the vaccine was spread. The decision to get vaccinated or not was a process fraught with insecurities about the effectiveness and side effects of the vaccine, which was balanced against wishing to be protected and contributing to the battle against COVID-19. Suggestions for information dissemination improvements from the participants were to produce multilingual information and to increase the use of transmission through social interaction with trusted persons and platforms.\n\nConclusionsAn inadequately adapted information outreach prevented some members of the society from making fact-based decisions about getting vaccinated. Several suggestions for improving dissemination were brought forth that can be tested in future communication strategies.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSPeople with an immigrant background have consistently displayed a lower vaccination uptake than the general population. This study investigated aspects of health literacy, information access and vaccination hesitancy in foreign-born individuals in Sweden.\n\nWhat did the researchers do and find?Few participants accessed official information about the COVID-19 vaccine, mainly because of poorly adapted information outreach, language barriers and not knowing Swedish institutions. Instead, they turned to a multitude of other sources from which conflicting and inaccurate information was spread, lowering their confidence in the COVID-19 vaccine.\n\nWhat do these findings mean?In the case of national emergencies, important public health information does not reach everyone equally, obstructing the possibility for some to make an information-based decision on how to protect their health.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mia S\u00f6derberg", + "author_inst": "Goteborgs universitet Sahlgrenska Akademin" + }, + { + "author_name": "Juhaina Swaid", + "author_inst": "Goteborgs universitet Sahlgrenska Akademin" + }, + { + "author_name": "Kristina Aurelius", + "author_inst": "Sahlgrenska Sjukhuset: Sahlgrenska universitetssjukhuset" + }, + { + "author_name": "Annika Rosengren", + "author_inst": "Sahlgrenska University Hospital: Sahlgrenska universitetssjukhuset" + }, + { + "author_name": "Kristina Jakobsson", + "author_inst": "Sahlgrenska University Hospital: Sahlgrenska universitetssjukhuset" + }, + { + "author_name": "Maria Magnusson", + "author_inst": "Hopsitals West" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.12.28.23300622", "rel_title": "Changes in the medical admissions and mortality amongst children in four South African hospitals following the COVID -19 pandemic: A five-year review.", @@ -18276,61 +19653,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.12.22.23300447", - "rel_title": "Predicting poor mental health amongst older Syrian refugees in Lebanon during the COVID-19 pandemic: a multi-wave longitudinal study", - "rel_date": "2023-12-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.22.23300447", - "rel_abs": "BackgroundThe COVID-19 pandemic has worsened pre-existing vulnerabilities among older Syrian refugees in Lebanon, potentially impacting their mental health. This study aimed to identify predictors of poor mental health amongst older Syrian refugees living in Lebanon during the pandemic.\n\nMethodsThis study used repeated cross-sectional data from a multi-wave telephone survey (September 2020-March 2022). It was conducted among Syrian refugees aged 50 years or older from households that received assistance from a humanitarian organization. Poor mental health was defined as a Mental Health Inventory-5 score of 60 or less. Its trend over time was assessed using growth curve model; and, its predictors were identified using wave one data, through backwards stepwise logistic regression. The models internal validation was conducted using bootstrapping.\n\nFindingsThere were 3,229 participants (median age=56 [IQR=53-62]) and 47.5% were female. At wave one, 76.7% had poor mental health, and this increased to 89.2% and to 92.7% at waves three and five, respectively ({beta}=0{middle dot}52; 95% CI: 0{middle dot}44-0{middle dot}63; p-value<0.001). Predictors for poor mental health were younger age, food insecurity, water insecurity, lack of legal status documentation, irregular employment, higher intensity of bodily pain, having debt, and having chronic illnesses. The final model demonstrated good discriminative ability and calibration.\n\nInterpretationMental health predictors were related to basic needs, rights and financial barriers. These allow humanitarian organizations to identify high risk individuals, organizing interventions, and addressing root causes to boost resilience and well-being among older Syrian refugees in Lebanon.\n\nFundingELRHAs Research for Health in Humanitarian Crisis Programme.\n\nResearch in context\n\nEvidence before this studyA search was conducted on PubMed and Google Scholar for studies published between February 1, 2020 and June 20, 2023, using the search terms \"Syrian Refugees\", \"Mental Health\", and \"Prediction Model\", including all article types with no time constraints or language restrictions. We found that few previous prognostic models for Syrian refugees have been developed exclusively among participants at high risk of poor mental health, such as widowed women, Syrian refugees with post-traumatic stress disorder, or those who experienced ambiguous loss. Older adults were underrepresented in these studies, which had small sample sizes and focused primarily on inter-relational factors. Therefore, their effectiveness in predicting outcomes for this highly vulnerable group, which faces distinct circumstances, may be constrained due to their development based on incomparable samples and contexts. Furthermore, none were developed during the COVID-19 pandemic. Overall, the search highlighted the need for research into the specific vulnerabilities and risk factors for mental health faced by the community of older Syrian refugees in Lebanon, as the existing models do not appear to be applicable to this group.\n\nAdded value of this studyThe study developed a prognostic model to predict the risk of poor mental health amongst older Syrian refugees in Lebanon during the COVID-19 pandemic, using predictors that covered economic, social and health factors. Data were collected using a multi-wave panel study. Most participants had poor mental health that increased over the course of the study. Younger age, food insecurity, water insecurity, lack of legal status documentation, irregular employment, higher intensity of bodily pain, having debt, and having multiple chronic illnesses were predictors of poor mental health. These findings are consistent with previous literature on associations between these vulnerabilities and poor mental health amongst refugees.\n\nImplications of all the available evidenceThe study provides evidence that the population of older Syrian refugees in Lebanon faces multiple vulnerabilities and were largely at risk for poor mental health, which increased during the COVID-19 pandemic. Vulnerabilities identified in this study as predictors of poor mental health indicate that it will be necessary to engage with humanitarian sectors outside of health such as food assistance, water, sanitation and hygiene (WASH) and legal assistance programs in order to support mental health in older Syrian refugees.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Berthe Abi Zeid", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Leen Farouki", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Tanya El Khoury", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Abla Sibai", - "author_inst": "Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Carlos F. Mendes de Leon", - "author_inst": "Georgetown University School of Medicine, Washington DC, USA" - }, - { - "author_name": "Marwan Alawieh", - "author_inst": "Norwegian Refugee Council" - }, - { - "author_name": "Zeinab Ramadan", - "author_inst": "Norwegian Refugee Council" - }, - { - "author_name": "Sawsan Abdulrahim", - "author_inst": "Department of Health Promotion and Community Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Hala Ghattas", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Stephen J McCall", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.12.21.23300125", "rel_title": "Social determinants of recovery from ongoing symptoms following COVID-19 in two UK longitudinal studies: a prospective cohort study", @@ -19457,6 +20779,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.12.20.572680", + "rel_title": "Deciphering Abnormal Platelet Subpopulations in Inflammatory Diseases through Machine Learning and Single-Cell Transcriptomics", + "rel_date": "2023-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.20.572680", + "rel_abs": "IntroductionThe transcriptional heterogeneity of activated platelets, play a significant role in contributing to negative outcomes in sepsis, COVID-19, and autoimmune diseases such as systemic lupus erythematosus (SLE). Despite this, our understanding of these heterogeneous platelet responses remains limited. In this study, we aim to investigate the diverse transcriptional profiles of activated platelets in these diseases, with the goal of deciphering this platelet heterogeneity for new therapeutic strategies to target abnormal and pathogenic platelet subtypes.\n\nMaterials and methodsWe obtained the single cell transcriptional profiles of blood platelets from patients with COVID-19, sepsis, and SLE. Utilizing machine learning algorithms, Deep Neural Network (DNN) and eXtreme Gradient Boosting (XGB), we discerned the distinct transcriptomic signatures indicative of fatal versus survival clinical outcomes. Our methodological framework incorporated source data annotations and platelet markers and used SingleR and Seurat for detailed profiling. Additionally, we implemented Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and visualization, aiding in the detection of various platelet subtypes and their correlation with disease status and patient outcomes.\n\nResultsOur study identified distinct platelet subpopulations that are associated with disease severity. We demonstrated that alterations in platelet transcription patterns can exacerbate endotheliopathy, potentially heightening the risk of coagulation in fatal patients. Moreover, these changes can also influence lymphocyte function, indicating a more extensive role for platelets in inflammatory and immune responses.\n\nConclusionsEnhanced transcriptional heterogeneity in activated platelets is linked to adverse outcomes in conditions such as sepsis, COVID-19, and autoimmune diseases. The discovery of these unique platelet subpopulations paves the way for innovative therapeutic strategies targeting platelet activation, which could potentially improve patient outcomes.\n\nSummary sentenceSingle-Cell RNA Sequencing Analysis of Platelets from COVID-19, Sepsis, and SLE Reveals Disease Signatures and Treatment Options to Prevent Patient Mortality.\n\nGraphical AbstractsO_LIThe platelet to T cell ratio proportion in PBMC was identified as the most potent predictor for distinguishing survivors from fatal patients, underscores the potential of this ratio as a prognostic biomarker.\nC_LIO_LIThe discovery of different platelet subgroups, especially active coagulation, hypoxic, and quiescent clusters, in fatal COVID-19 patients, indicates potential targeted treatment strategies.\nC_LIO_LIIn patients with severe and fatal conditions, we observed three key phenomena: the aggregation of platelets with monocytes, the amplification of endothelial dysfunction by platelets, and a decrease in lymphocyte activation and differentiation due to platelets.\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC=\"FIGDIR/small/572680v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (64K):\norg.highwire.dtl.DTLVardef@141ca55org.highwire.dtl.DTLVardef@4ad1aborg.highwire.dtl.DTLVardef@b400forg.highwire.dtl.DTLVardef@9ad44e_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xinru Qiu", + "author_inst": "Division of Biomedical Sciences, University of California Riverside School of Medicine." + }, + { + "author_name": "Meera G. Nair", + "author_inst": "Division of Biomedical Sciences, University of California Riverside School of Medicine." + }, + { + "author_name": "Lukasz Jaroszewski", + "author_inst": "Division of Biomedical Sciences, University of California Riverside School of Medicine." + }, + { + "author_name": "Adam Godzik", + "author_inst": "Division of Biomedical Sciences, University of California Riverside School of Medicine." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.12.20.572426", "rel_title": "Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data", @@ -20162,69 +21515,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.12.18.572180", - "rel_title": "Neuropathological assessment of the olfactory bulb and tract in individuals with COVID-19", - "rel_date": "2023-12-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.18.572180", - "rel_abs": "The majority of patients with Parkinson disease (PD) experience a loss in their sense of smell and accumulate insoluble -synuclein aggregates in their olfactory bulbs (OB). Subjects affected by a SARS-CoV-2-linked illness (COVID-19) frequently experience hyposmia. We previously hypothesized that -synuclein and tau misprocessing could occur following host responses to microbial triggers. Using semiquantitative measurements of immunohistochemical signals, we examined OB and olfactory tract specimens collected serially at autopsies between 2020 and 2023. Deceased subjects comprised 50 adults, which included COVID19+ patients (n=22), individuals with Lewy body disease (e.g., PD and dementia with Lewy bodies (DLB; n=6)), Alzheimer disease (AD; n=3), other non-synucleinopathy-linked degenerative diseases (e.g., progressive supranuclear palsy (PSP; n=2) and multisystem atrophy (MSA; n=1)). Further, we included neurologically healthy controls (HCO; n=9) and those with an inflammation-rich brain disorder as neurological controls (NCO; n=7). When probing for inflammatory changes focusing on anterior olfactory nuclei (AON) using anti-CD68 immunostaining, scores were consistently elevated in NCO and AD cases. In contrast, inflammation on average was not significantly altered in COVID19+ patients relative to controls, although anti-CD68 reactivity in their OB and tracts declined with progression in age. Mild-to-moderate increases in phospho-Syn and phospho-tau signals were detected in the AON of tauopathy-and synucleinopathy-afflicted brains, respectively, consistent with mixed pathology, as described by others. Lastly, when both sides were available for comparison in our case series, we saw no asymmetry in the degree of pathology of the left versus right OB and tracts. We concluded from our autopsy series that after a fatal course of COVID-19, microscopic changes -when present-in the rostral, intracranial portion of the olfactory circuitry generally reflected neurodegenerative processes seen elsewhere in the brain. In general, inflammation correlated best with the degree of Alzheimers-linked tauopathy and declined with progression of age in COVID19+ patients.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Nathalie A Lengacher", - "author_inst": "Ottawa Hospital Research Institute" - }, - { - "author_name": "Julianna J Tomlinson", - "author_inst": "Ottawa Hospital Research Institute" - }, - { - "author_name": "Ann-Kristin Jochum", - "author_inst": "Institute of Pathology, Kantonsspital St. Gallen" - }, - { - "author_name": "Jonas Franz", - "author_inst": "Neuropathology Institute, University of Goettingen Medical Centre" - }, - { - "author_name": "Omar Hasan Ali", - "author_inst": "Department of Life Sciences, University of British Columbia" - }, - { - "author_name": "Lukas Flatz", - "author_inst": "Department of Dermatology, University Hospital Tubingen" - }, - { - "author_name": "Wolfram Jochum", - "author_inst": "Institute of Pathology, Kantonsspital St. Gallen" - }, - { - "author_name": "Josef Penninger", - "author_inst": "Department of Life Sciences, University of British Columbia" - }, - { - "author_name": "- aSCENT-PD Investigators", - "author_inst": "-" - }, - { - "author_name": "Christine Stadelmann-Nessler", - "author_inst": "Neuropathology Institute, University of Goettingen Medical Centre" - }, - { - "author_name": "John M Woulfe", - "author_inst": "Neuroscience Program, Ottawa Hospital Research Institute" - }, - { - "author_name": "Michael G Schlossmacher", - "author_inst": "Ottawa Hospital Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2023.12.19.572363", "rel_title": "Comparison of mitochondrial response to SARS-CoV-2 spike protein receptor binding domain in human lung microvascular, coronary artery endothelial and bronchial epithelial cells", @@ -21531,6 +22821,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2023.12.16.23300086", + "rel_title": "Retrospective analysis of Covid-19 hospitalization modelling scenarios which guided policy response in France", + "rel_date": "2023-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.16.23300086", + "rel_abs": "Epidemiological modelling has played a key role in proposing, analyzing and justifying non-pharmaceuticals interventions in response to the COVID-19 pandemic. Despite its importance, evaluations of models ability to accurately anticipate the evolution of the disease remain scarce. Thus, robust, systematic, and pre-specified evaluation criteria are needed to assess the relevance of modelling scenarios that guided policy response during the pandemic. We conduct a retrospective assessment of modelling reports which guided policy response in France from April 2020 to April 2022. After systematically verifying the scenarios hypotheses (e.g., exclusion of no-lockdown scenarios when a lockdown was effectively in place), we find that epidemiological models were (a) uncertain, (b) unaccurate, and (c) biased towards an overestimation of predicted COVID-19 related hospitalizations. In more than half of the reports, reality is below or equal to even the best-case scenario. To our knowledge, this is the only national systematic retrospective assessment of COVID-19 pandemic scenarios; such an approach should be reproduced in other countries whenever possible.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC=\"FIGDIR/small/23300086v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@ecc198org.highwire.dtl.DTLVardef@199e6bborg.highwire.dtl.DTLVardef@fb383aorg.highwire.dtl.DTLVardef@1289994_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract: Comparison of Pasteur Institutes scenarios to reality. Forecasting errors of scenarios (colors) compared to reality (black line) are expressed as a percentage of the maximum Intensive Care Units occupancy reached during the covid-19 pandemic in France (horizontal dashed line).\n\nC_FIG", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Maxime Langevin", + "author_inst": "Independent researcher" + }, + { + "author_name": "Thomas Starck", + "author_inst": "Independent researcher" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.12.15.23298521", "rel_title": "Adiposity and Sex Influence on SARS-CoV-2 Antibody Response in University Students. An ESFUERSO cross-sectional study.", @@ -22140,49 +23453,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.13.571570", - "rel_title": "Inactivation of the Niemann Pick C1 cholesterol transporter 1 (NPC1) restricts SARS-CoV-2 infection", - "rel_date": "2023-12-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.13.571570", - "rel_abs": "The Niemann Pick C1 (NPC1) protein is an intracellular cholesterol transporter located in the late endosome/lysosome (LE/Ly) and is involved in cholesterol mobilization. Loss-of-function mutations of the NPC1 gene lead to accumulation of cholesterol and sphingolipids in LE/Ly, resulting in severe fatal NPC1 disease. Cellular alterations associated with NPC1 inactivation affect both the integrity of lipid rafts and the endocytic pathway. Because the angiotensin-converting enzyme 2 (ACE2) and type 2 serine transmembrane protease (TMPRSS2) of the SARS-CoV-2 Spike (S) protein also localize to lipid rafts, we sought to investigate the hypothesis that NPC1 inactivation would generate an intrinsically unfavorable barrier to SARS-CoV-2 entry. In this study, we demonstrate that NPC1 pharmacological inactivation or CRISP/R-Cas mediated ablation of NPC1 dramatically reduced SARS-CoV-2 infectivity. More specifically, our findings demonstrate that pharmacological inactivation of NPC1 results in massive accumulation of ACE2 in the autophagosomal/lysosomal compartment. A >40-fold decrease in virus titer indicates that this effectively prevents VSV-Spike-GFP infection by impeding virus binding and entry. A similarly marked decrease in viral infectivity is observed in cells that had NPC1 expression genetically abrogated. These observations were further confirmed in a de novo SARS-CoV-2 infection paradigm, where cells were infected with the naturally pathogenic SARS-CoV-2. Overall, this work offers strong evidence that NPC1 function is essential for successful SARS-CoV-2 infection, thus implicating NPC1 as a potential therapeutic target in COVID-19 management.\n\nSignificanceA significant convergence exists between the cellular alterations associated with NPC1 inactivation and the mechanistic processes of SARS-CoV-2 infectivity. These alterations affect the integrity of lipid-enriched plasma membrane microdomains and the endocytic pathway. Furthermore, the cholesterol-regulated ACE2 receptor protein that facilitates SARS-Cov-2 viral binding and entry is targeted to the autophagolysosomal compartment upon NPC1 inactivation, thus hindering virus-host cell interaction. To our knowledge, this study provides the first evidence that NPC1 function represents a crucial factor for SARS-CoV-2 infection and suggests therapeutic opportunities.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Piergiorgio La Rosa", - "author_inst": "University La Sapienza" - }, - { - "author_name": "Jessica Tiberi", - "author_inst": "University La Sapienza" - }, - { - "author_name": "Enrico Palermo", - "author_inst": "Istituto Pasteur Italia-Cenci Bolognetti Foundation" - }, - { - "author_name": "Sofia Tiano", - "author_inst": "Telethon Institute of Genetics and Medicine" - }, - { - "author_name": "Mirko Cortese", - "author_inst": "Telethon Institute of Genetics and Medicine" - }, - { - "author_name": "John Hiscott", - "author_inst": "Istituto Pasteur Italia-Cenci Bolognetti Foundation" - }, - { - "author_name": "Maria Teresa Fiorenza", - "author_inst": "University La Sapienza" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.12.12.23299822", "rel_title": "Comparative transcriptomic analyses of peripheral blood mononuclear cells of patients with non-pneumonia and severe pneumonia at 1 year-Long-COVID-19", @@ -23201,6 +24471,37 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.12.09.23299681", + "rel_title": "Autonomous and policy-induced behavior change during the COVID-19 pandemic: Towards understanding and modeling the interplay of behavioral adaptation", + "rel_date": "2023-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.09.23299681", + "rel_abs": "Changes in human behaviors, such as reductions of physical contacts and the adoption of preventive measures, impact the transmission of infectious diseases considerably. Behavioral adaptations may be the result of individuals aiming to protect themselves or mere responses to public containment measures, or a combination of both. What drives autonomous and policy-induced adaptation, how they are related and change over time is insufficiently understood. Here, we develop a framework for more precise analysis of behavioral adaptation, focusing on confluence, interactions and time variance of autonomous and policy-induced adaptation. We carry out an empirical analysis of Germany during the fall of 2020 and beyond. Subsequently, we discuss how behavioral adaptation processes can be better represented in behavioral-epidemiological models. We find that our framework is useful to understand the interplay of autonomous and policy-induced adaptation as a \"moving target\". Our empirical analysis suggests that mobility patterns in Germany changed significantly due to both autonomous and policy-induced adaption, with potentially weaker effects over time due to decreasing risk signals, diminishing risk perceptions and an erosion of trust in the government. We find that while a number of simulation and prediction models have made great efforts to represent behavioral adaptation, the interplay of autonomous and policy-induced adaption needs to be better understood to construct convincing counterfactual scenarios for policy analysis. The insights presented here are of interest to modelers and policy makers aiming to understand and account for behaviors during a pandemic response more accurately.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Heinrich Zozmann", + "author_inst": "Helmholtz-Zentrum fur Umweltforschung UFZ" + }, + { + "author_name": "Lennart Sch\u00fcler", + "author_inst": "Helmholtz-Zentrum f\u00fcr Umweltforschung UFZ: Helmholtz-Zentrum fur Umweltforschung UFZ" + }, + { + "author_name": "Xiaoming Fu", + "author_inst": "Helmholtz-Zentrum Dresden-Rossendorf" + }, + { + "author_name": "Erik Gawel", + "author_inst": "Helmholtz-Zentrum f\u00fcr Umweltforschung UFZ: Helmholtz-Zentrum fur Umweltforschung UFZ" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.12.11.23299052", "rel_title": "Changes in internalizing and externalizing problems in Dutch children and adolescents receiving youth care before and during the COVID-19 pandemic", @@ -23942,33 +25243,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.12.06.23299628", - "rel_title": "Investigating the Determinants of COVID-19 Vaccine Uptake and Attitudes in Iraq: A Study Unveiling the Negative Impact of Misinformation and Vaccine Conspiracy", - "rel_date": "2023-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.06.23299628", - "rel_abs": "Vaccine hesitancy is a major barrier challenging the control of infectious diseases. Previous studies demonstrated high rates of COVID-19 vaccine hesitancy in the Middle East. The current study aimed to investigate the attitudes towards COVID-19 vaccination and COVID-19 vaccine uptake among the adult population in Iraq. This cross-sectional self-administered survey-based study was conducted in August-September 2022. Recruitment of possible participants was done using chain-referral sampling. The survey instrument assessed participants demographics, attitudes toward COVID-19 vaccination, beliefs in COVID-19 misinformation, vaccine conspiracy beliefs, and sources of information regarding the vaccine. The study sample comprised a total of 2544 individuals, with the majority reporting the uptake of at least one dose of COVID-19 vaccination (n=2226, 87.5%). Positive attitudes towards COVID-19 vaccination were expressed by the majority of participants (n=1966, 77.3%), while neutral attitudes were expressed by 345 participants (13.6%), and negative attitudes were expressed by 233 participants (9.2%). Strong, moderate, slight, and absence of COVID-19 misinformation were expressed by 12.4%, 22.6%, 36.2%, and 28.7% participants, respectively. The majority of participants showed a neutral attitude towards COVID-19 vaccine conspiracies (n=1464, 57.5%), while 607 participants embraced these conspiracies (23.9%), and 473 disagreed with such beliefs (18.6%). In the multivariate analysis, factors associated with positive attitudes towards COVID-19 vaccination included disbelief in COVID-19 misinformation and disagreement with vaccine conspiracies. Higher COVID-19 vaccine uptake was significantly associated with history of COVID-19 infection, higher income, residence outside the capital, disbelief in COVID-19 misinformation, disagreement with vaccine conspiracies, and reliance on reputable information sources. COVID-19 vaccine coverage prevailed among the participants, with a majority having positive attitudes towards COVID-19 vaccination. Disbelief in COVID- 19 misinformation and disagreement with vaccine conspiracies were correlated with positive vaccine attitudes and higher vaccine uptake. These insights can inform targeted interventions to enhance vaccination campaigns.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Malik Sallam", - "author_inst": "University of Jordan" - }, - { - "author_name": "Nariman Kareem", - "author_inst": "University of Jordan" - }, - { - "author_name": "Mohammed Alkurtas", - "author_inst": "University of Baghdad" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.12.07.23298951", "rel_title": "Fungal pleural infection due to Microascus gracilis with pulmonary aspergillosis after COVID-19 pneumonia", @@ -25107,6 +26381,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.11.30.23299157", + "rel_title": "Influenza Mortality as an Indicator of the Efficacy of COVID-Related, Non-pharmaceutical Interventions to Reduce the Spread of Respiratory Infections", + "rel_date": "2023-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.30.23299157", + "rel_abs": "BackgroundNon-pharmaceutical interventions (NPIs) have been criticized as ineffective in preventing COVID. Because it is a new disease with NPIs introduced almost immediately, we have no way to evaluate the counterfactual of non-intervention easily and directly. We do, however, have historic data on influenza, a respiratory disease with similar patterns of transmission and a well-established CDC surveillance system in the US. These data provide us with an excellent way to indirectly evaluate the efficacy of these interventions.\n\nResultsDuring the three seasons prior to COVID from 2016-17 to 2018-19, the mean total US influenza mortality was 9,917 deaths per season. During the pandemic, total influenza mortality declined by 80 percent relative to historical levels. Pediatric influenza morality decreased by 85 percent. At the state level, the average drop in mortality over the two flu seasons of the pandemic was strongly correlated with the percent of the 2020 presidential votes cast for Joe Biden (r2=0.39).\n\nConclusionsThese data provide strong evidence that COVID NPIs dramatically reduced the spread of influenza. Given its similar routes of transmission, these results support the assertion that these NPIs also substantially reduced COVID transmission, morbidity, and mortality. The effectiveness of NPIs was highly correlated with the political leanings of each state, suggesting that politics influenced the effectiveness of and/or compliance with NPI strategies.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Robert D Morris", + "author_inst": "Research Now Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.12.05.23299475", "rel_title": "COVID-19 vaccination uptake among healthcare workers in Ghana: A comprehensive analysis of knowledge, attitude, perceived vaccine effectiveness, and health belief model constructs", @@ -25760,49 +27053,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2023.12.03.23299330", - "rel_title": "Effect of mRNA vaccination on pulmonary sequelae after mild COVID-19", - "rel_date": "2023-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.03.23299330", - "rel_abs": "BackgroundPrevious studies indicate a protective role for SARS-CoV-2 vaccination against development of pulmonary post-acute sequelae of COVID (PASC). We compared clinical, imaging, histopathology and ultrastructural features of pulmonary PASC with and without prior vaccination in a consecutive cohort of 54 unvaccinated, 17 partially vaccinated and 28 fully vaccinated patients who presented with dyspnea on exertion after mild COVID-19 (without hospitalization).\n\nMethodsPatients underwent full clinical evaluation including autoantibody (ANA/ENA) serology, high-resolution computed tomography (HRCT), bronchioloalveolar lavage fluid (BAL) analysis and transbronchial biopsy followed by histopathological and ultrastructural analysis and SARS-CoV-2 immunohistochemistry.\n\nResultsWhile vaccinated patients were younger (p=0.0056), included more active smokers (p=0.0135) and a longer interval since infection (35 vs. 17 weeks, p=0.0002), dyspnea on exertion and impaired lung function were not different between vaccinated and unvaccinated patients. Ground glass opacities in HRCT and centrilobular fibrosis were more frequent in unvaccinated patients (p=0.0154 and p=0.0353), but presence of autoantibodies, BAL lymphocytosis and bronchiolitis were common findings in all groups. While vaccination against SARS-CoV-2 is associated with a longer time span between infection and consultation along with a reduced frequency of ground glass opacities and centrilobular fibrosis, impaired lung function, bronchiolitis and presence of autoantibodies are comparable between vaccinated and unvaccinated patients. Residual virus was not detected in lung tissue in all but 1 patient.\n\nConclusionWhile differences between the investigated groups with regard to age, smoking status and SARS-CoV-2 variants have to be taken into account, a proposed protective role of SARS-CoV-2 vaccination against pulmonary PASC is so far not fully explained by clinical and histopathology findings.\n\nKEY MESSAGESThe role of SARS-CoV-2 vaccination in the protection against pulmonary post-acute sequelae of COVID-19 (PASC) is unclear. Using a multidimensional approach integrating clinical, serological, imaging and histopathology data as well as ultrastructural analyses, we show here that previous vaccination has no impact on lung function, bronchiolitis or the detection of autoantibodies or residual virus in a previously healthy cohort of 99 PASC patients after mild COVID-19. While a higher frequency of ground glass opacities in unvaccinated patients might be due to the longer interval between infection and consultation, the observed fibrotic remodeling should prompt further investigation of a possible pro-fibrotic role of SARS-CoV-2 infection in the lung.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniel Gagiannis", - "author_inst": "Bundeswehrkrankenhaus Ulm" - }, - { - "author_name": "Carsten Hackenbroch", - "author_inst": "Bundeswehrkrankenhaus Ulm" - }, - { - "author_name": "Fabian Zech", - "author_inst": "University of Ulm" - }, - { - "author_name": "Frank Kirchhoff", - "author_inst": "Ulm University" - }, - { - "author_name": "Wilhelm Bloch", - "author_inst": "German Sports University Cologne" - }, - { - "author_name": "Katharina Junghans", - "author_inst": "Bundeswehrkrankenhaus Ulm" - }, - { - "author_name": "Konrad Steinestel", - "author_inst": "Bundeswehrkrankenhaus Ulm" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.12.03.23299331", "rel_title": "Long COVID is associated with severe cognitive slowing", @@ -26853,6 +28103,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.11.28.568639", + "rel_title": "Mechanism-based classification of SARS-CoV-2 Variants by Molecular Dynamics Resembles Phylogenetic Tree", + "rel_date": "2023-11-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.28.568639", + "rel_abs": "The COVID-19 pandemics has demonstrated the vulnerability of our societies to viral infectious disease. The mitigation of COVID-19 was complicated by the emergence of Variants of Concern (VOCs) with varying properties including increased transmissibility and immune evasion. Traditional population sequencing proved to be slow and not conducive for timely action. To tackle this challenge, we introduce the Persistence Score (PS) that assesses the pandemic potential of VOCs based on molecular dynamics of the interactions between the SARS-CoV-2 Receptor Binding Domain (RBD) and the ACE2 residues. Our mechanism-based classification approach successfully grouped VOCs into clinically relevant subgroups with higher sensitivity than classical affinity estimations and allows for risk assessment of hypothetical new VOCs. The PS-based interaction analysis across VOCs resembled the phylogenetic tree of SARS-Cov-2 demonstrating its predictive relevance for pandemic preparedness. Thus, PS allows for early detection of a variants pandemic potential, and an early risk evaluation for data-driven policymaking.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Thais Arns", + "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg" + }, + { + "author_name": "Aymeric Fouquier dHerouel", + "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg." + }, + { + "author_name": "Patrick May", + "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg" + }, + { + "author_name": "Alexandre Tkatchenko", + "author_inst": "Department of Physics and Material Science, University of Luxembourg, 6, avenue de la Faiencerie, L-2311, Limpertsberg, Luxembourg." + }, + { + "author_name": "Alexander Skupin", + "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.11.28.569052", "rel_title": "copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling", @@ -27358,69 +28643,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.11.24.568354", - "rel_title": "Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection.", - "rel_date": "2023-11-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.24.568354", - "rel_abs": "Pathogen encounter results in long-lasting epigenetic imprinting that shapes diseases caused by heterologous pathogens. The breadth of this innate immune memory is of particular interest in the context of respiratory pathogens with increased pandemic potential and wide-ranging impact on global health. Here, we investigated epigenetic imprinting across cell lineages in a disease relevant murine model of SARS-CoV-2 recovery. Past SARS-CoV-2 infection resulted in increased chromatin accessibility of type I interferon (IFN-I) related transcription factors in airway-resident macrophages. Mechanistically, establishment of this innate immune memory required viral pattern recognition and canonical IFN-I signaling and augmented secondary antiviral responses. Past SARS-CoV-2 infection ameliorated disease caused by the heterologous respiratory pathogen influenza A virus. Insights into innate immune memory and how it affects subsequent infections with heterologous pathogens to influence disease pathology could facilitate the development of broadly effective therapeutic strategies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Alexander Lercher", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Jin-Gyu Cheong", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Chenyang Jiang", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Hans-Heinrich Hoffmann", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Alison W Ashbrook", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Yue S Yin", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Corrine Quirk", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Emma J DeGrace", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Luis Chiriboga", - "author_inst": "NYU Langone" - }, - { - "author_name": "Brad R Rosenberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Steven Z Josefowicz", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Charles M Rice", - "author_inst": "The Rockefeller University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.11.25.568685", "rel_title": "The antiviral potential of the antiandrogen enzalutamide and the viral-androgen interplay in seasonal coronaviruses", @@ -28519,6 +29741,221 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.11.27.23299044", + "rel_title": "Genomic epidemiology of SARS-CoV-2 in Sudan: A retrospective analysis 2020-2022", + "rel_date": "2023-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.27.23299044", + "rel_abs": "SARS-CoV-2 was first detected in Sudan on 13th March 2020. Here, we describe the genomic epidemiology of SARS-CoV-2 in Sudan between May 2020 and April 2022 to understand the introduction and transmission of SARS-CoV-2 variants in the country. A total of 667 SARS-CoV-2 positive samples were successfully sequenced using the nCoV-19 Artic protocol on the Oxford Nanopore Technology ([≥]70% genome completeness). The genomes were compared with a select contemporaneous global dataset to determine genetic relatedness and estimate import/export events. The genomes were classified into 37 Pango lineages within the ancestral strain (107 isolates across 13 Pango lineages), Eta variant of interest (VOI) (78 isolates in 1 lineage), Alpha variant of concern (VOC) (10 isolates in 2 lineages), Beta VOC (26 isolates in 1 lineage), Delta VOC (171 isolates across 8 lineages) and Omicron VOC (242 isolates across 12 lineages). We estimated a total of 144 introductions of the observed variants from different countries across the globe. Multiple introductions of the Eta VOI, Beta VOC and Omicron VOC were observed in Sudan mainly from Europe and Africa. These findings suggest a need for continuous genomic surveillance of SARS-CoV-2 to monitor their introduction and spread consequently inform public health measures to combat SARS-CoV-2 transmission.", + "rel_num_authors": 50, + "rel_authors": [ + { + "author_name": "Maureen W Mburu", + "author_inst": "KEMRI Wellcome Trust Research Programme" + }, + { + "author_name": "Arnold W Lambisia", + "author_inst": "KEMRI Wellcome Trust Research Programme" + }, + { + "author_name": "Musab Elnegoumi", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Eman O. M. Nour", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Osama M. M. Khair", + "author_inst": "Department of Molecular Biology, National University Biomedical Research Institute." + }, + { + "author_name": "Elamin Abualas", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Rehab M Elhassan", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Muatsim A. M. Adam", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Khadija Said Mohammed", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "John Mwita Morobe", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research" + }, + { + "author_name": "Leonard Ndwiga", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Edidah O Moraa", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Timothy O Makori", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Nickson Murunga", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Esther Nyadzua Katama", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Dorcas W Waruguru", + "author_inst": "Africa Centre for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia." + }, + { + "author_name": "George Githinji", + "author_inst": "KEMRI-Wellcome Trust Research Programme" + }, + { + "author_name": "Sarah Mwangi", + "author_inst": "Africa Centre for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia." + }, + { + "author_name": "Sofonias K. Tessema", + "author_inst": "Africa Centre for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia." + }, + { + "author_name": "Mawahib H. E. Adam", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Iman Mahmoud", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Hanan SalmanBabikir Mohamed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Yousif A. A. Mustafa", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Mohamedtaha M. A. Mohamed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Rasheeda H.A. Ahmed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Nuha Y.I. Mohamed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Rahma H. Ali", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Rasha S.M. Ebraheem", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Huda H.H. Ahmed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Hamadelniel E. Abdalla", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Izdihar Mukhtar", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Abdalkhalig E. M. W. Alla", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Omer H. A. Elsheikh", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Abdualmoniem O. Musa", + "author_inst": "General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan" + }, + { + "author_name": "Mahmoud Taha Faki", + "author_inst": "General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan" + }, + { + "author_name": "Gada Mustfa Ahmed", + "author_inst": "General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan" + }, + { + "author_name": "Thoyba E. R. Ahmed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Mohammed A. O. Abdalla", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Mujtaba O. K. Mohamed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Rayan A. A. Ahmed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Samah M. M. AwadElkarim", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan." + }, + { + "author_name": "Basamat A. E. M. Ahmed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Zainab A. I. Shumo", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Eiman N. A. Ahmed", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + }, + { + "author_name": "Samia S. A. Rushwan", + "author_inst": "Port Sudan Public Health Laboratory, Red Sea State, Sudan" + }, + { + "author_name": "Phillip Bejon", + "author_inst": "KEMRI-Wellcome Trust Research Programme: Centre for Geographic Medicine Research Coast" + }, + { + "author_name": "James Nokes", + "author_inst": "Kemri-Wellcome Trust" + }, + { + "author_name": "Lynette Isabella Ochola-Oyier", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Charles N. Agoti", + "author_inst": "Kenya Medical Research Institute-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya." + }, + { + "author_name": "Shahinaz A. Bedri", + "author_inst": "National Public Health Laboratory, Khartoum, Sudan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2023.11.24.23296021", "rel_title": "Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination", @@ -29176,53 +30613,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.11.21.568093", - "rel_title": "Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2", - "rel_date": "2023-11-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.21.568093", - "rel_abs": "Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ai Nguyen", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, NIH" - }, - { - "author_name": "Huaying Zhao", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, NIH" - }, - { - "author_name": "Dulguun Myagmarsuren", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, NIH" - }, - { - "author_name": "Sanjana Srinivasan", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, NIH" - }, - { - "author_name": "Di Wu", - "author_inst": "National Heart, Lung, and Blood Institute, NIH" - }, - { - "author_name": "Jiji Chen", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Grzegorz Piszczek", - "author_inst": "National Heart, Lung, and Blood Institute, NIH" - }, - { - "author_name": "Peter Schuck", - "author_inst": "National Institutes of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.11.21.568132", "rel_title": "SARS-CoV-2 infects neurons, astrocytes, choroid plexus epithelial cells and pericytes of the human central nervous system", @@ -30357,6 +31747,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.11.20.567927", + "rel_title": "Human coronavirus OC43 infection remodels Connexin 43 mediated gap junction intercellular communication in vitro", + "rel_date": "2023-11-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.20.567927", + "rel_abs": "{beta}-coronaviruses cause acute infection in the upper respiratory tract, resulting in various symptoms and clinical manifestations. OC43 is a human {beta}-coronavirus that induces mild clinical symptoms and can be safely studied in the BSL2 laboratory. Due to its low risk, OC43 can be a valuable and accessible model for understanding {beta}-coronavirus pathogenesis. One potential target for limiting virus infectivity could be gap junction-mediated communication. This study aims to unveil the status of cell-to-cell communications through gap junctions in human {beta}-coronavirus infection. Infection with OC43 leads to reduced expression of Cx43 in A549, a lung epithelial carcinoma cell line. Infection with this virus also showed a significant ER and oxidative stress increase. Internal localization of Cx43 is observed post OC43 infection in the ERGIC region, which impairs the gap junction communication between two adjacent cells, confirmed by Lucifer yellow dye transfer assay. It also affects hemichannel formation, as depicted by the EtBr uptake assay. Altogether, these results suggest that several physiological changes accompany OC43 infection in A549 cells and can be considered an appropriate model system for understanding the differences in gap junction communication post-viral infections. This model system can provide valuable insights for developing therapies against human {beta}-coronavirus infections.\n\nImportanceThe enduring impact of the recent SARS-CoV-2 pandemic underscores the importance of studying human {beta}-coronaviruses, advancing our preparedness for future coronavirus infections. Due to SARS-CoV-2 being highly infectious, another human {beta}-coronavirus OC43 can be considered as an experimental model. One of the crucial pathways that can be considered is gap junction communication, as it is vital for cellular homeostasis. Our study seeks to understand the change in Cx43-mediated cell-to-cell communication during human {beta}-coronavirus OC43 infection. In vitro studies showed the downregulation of the gap junction protein Cx43 and the upregulation of endoplasmic reticulum and oxidative stress markers post-OC43 infection. Furthermore, OC43 infection causes impairment of functional hemichannel and gap junction formation. Overall, this current study infers that OC43 infection reshapes intercellular communication, suggesting that this pathway may be a promising target for designing highly effective therapeutics against human coronaviruses by regulating Cx43 expression.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Souvik Karmakar", + "author_inst": "Indian Institute of Science Education and Research Kolkata" + }, + { + "author_name": "Jayasri Das Sarma", + "author_inst": "Indian Institute of Science Education and Research Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2023.11.18.567697", "rel_title": "Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling", @@ -30970,65 +32383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2023.11.18.23298731", - "rel_title": "Social contact patterns during the early COVID-19 pandemic in Norway: insights from a panel study, April to September 2020", - "rel_date": "2023-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.18.23298731", - "rel_abs": "BackgroundDuring the COVID-19 pandemic, many countries adopted social distance measures and lockdowns of varying strictness. Social contact patterns are essential in driving the spread of respiratory infections, and country-specific measurements are needed. This study aimed to gain insights into changes in social contacts and behaviour during the early pandemic phase in Norway.\n\nMethodsWe conducted an online survey among a nationally representative sample of Norwegian adults, including six data collections/waves between April and September 2020, and used survey data from 2017 as baseline. We calculated mean daily contacts, and estimated age-stratified contact matrices that were used to estimate reproduction numbers during the study period.\n\nResultsThe mean daily number of contacts varied between 3.2 (95% CI 3.0-3.4) to 3.9 (95% CI 3.6-4.2) across waves, representing a 67-73% decline compared to pre-pandemic levels. Fewer contacts in the community setting largely drove the reduction; the drop was most prominent among younger adults. Despite gradual easing of social distance measures during the survey period, population contact matrices remained relatively stable and displayed more inter-age group mixing than at baseline. Contacts within households and the community outside schools and workplaces contributed most to social encounters.\n\nConclusionSocial contacts experienced a significant decline during the months following the March 2020 lockdown in Norway, aligning with the implementation of stringent social distancing measures. The findings contribute valuable empirical information into the social behaviour of the Norwegian population during the early pandemic, which can be used to enhance policy-relevant models for addressing future crises when mitigation measures might be implemented.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lamprini Veneti", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Bjarne Robberstad", - "author_inst": "University of Bergen" - }, - { - "author_name": "Anneke Steens", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Frode Forland", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Brita Winje", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Didrik Vestrheim", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Christopher Jarvis", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Amy Gimma", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "John Edmunds", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Kevin Van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Birgitte Freiesleben de Blasio", - "author_inst": "Norwegian Institute of Public Health; University of Oslo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.11.16.23298658", "rel_title": "Impact of State Telehealth Parity Laws for Private Payers on Hypertension Management before and during the COVID-19 Pandemic", @@ -32227,6 +33581,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.11.14.566985", + "rel_title": "Virological characteristics of the SARS-CoV-2 Omicron HK.3 variant harboring the \"FLip\" substitution", + "rel_date": "2023-11-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.14.566985", + "rel_abs": "In November 2023, SARS-CoV-2 XBB descendants, including EG.5.1 (XBB.1.9.2.5.1), the currently predominant lineage, are circulating worldwide according to Nextstrain. EG.5.1 has a characteristic amino acid substitution in the spike protein (S), S:F456L, which contributes to its escape from humoral immunity. EG.5.1 has further evolved, and its descendant lineage harboring S:L455F (i.e., EG.5.1+S:L455F) emerged and was named HK.3 (XBB.1.9.2.5.1.1.3). HK.3 was initially discovered in East Asia and is rapidly spreading worldwide. Notably, the XBB subvariants bearing both S:L455F and S:F456L substitutions, including HK.3, are called the \"FLip\" variants. These FLip variants, such as JG.3 (XBB.1.9.2.5.1.3.3), JF.1 (XBB.1.16.6.1) and GK.3 (XBB.1.5.70.3), have emerged convergently, suggesting that the acquisition of these two substitutions confers a growth advantage to XBB in the human population. Here, we investigated the virological properties of HK.3 as a representative of the FLip variants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Yusuke Kosugi", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Arnon Plianchaisuk", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Olivia Putri", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Yu Kaku", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Alfredo A Hinay Jr.", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Luo Chen", + "author_inst": "University of Tokyo" + }, + { + "author_name": "Jin Kuramochi", + "author_inst": "Interpark Kuramochi Clinic" + }, + { + "author_name": "Kenji Sadamasu", + "author_inst": "Tokyo Metropolitan Institute of Public Health" + }, + { + "author_name": "Kazuhisa Yoshimura", + "author_inst": "Tokyo Metropolitan Institute of Public Health" + }, + { + "author_name": "Hiroyuki Asakura", + "author_inst": "Tokyo Metropolitan Institute of Public Health" + }, + { + "author_name": "Mami Nagashima", + "author_inst": "Tokyo Metropolitan Institute of Public Health" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "-" + }, + { + "author_name": "Jumpei Ito", + "author_inst": "The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.11.14.566998", "rel_title": "COVID-19-related research data availability and quality according to the FAIR principles: A meta-research study", @@ -32696,61 +34125,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.11.10.566576", - "rel_title": "The SARS-CoV-2 Omicron sub-variant BA.2.86 is attenuated in hamsters", - "rel_date": "2023-11-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.10.566576", - "rel_abs": "SARS-CoV-2 variants have emerged throughout the COVID-19 pandemic. There is a need to risk-assess newly emerged variants in near \"real-time\" to estimate their potential threat to public health. The recently emerged Omicron sub-variant BA.2.86 raised concerns as it carries a high number of mutations compared to its predecessors. Here, we assessed the virulence of BA.2.86 in hamsters. We compared the pathogenesis of BA.2.86 and BA.2.75, as the latter is one of the most virulent Omicron sub-variants in this animal model. Using digital pathology pipelines, we quantified the extent of pulmonary lesions measuring T cell and macrophage infiltrates, in addition to alveolar epithelial hyperplasia. We also assessed body weight loss, clinical symptoms, virus load in oropharyngeal swabs, and virus replication in the respiratory tract. Our data show that BA.2.86 displays an attenuated phenotype in hamsters, suggesting that it poses no greater risk to public health than its parental Omicron sub-variants.\n\nArticle summary lineThe newly emerged Omicron sub-variant BA.2.86 is attenuated in hamsters.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Vanessa Herder", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Diogo Correa Mendonca", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Nicole Upfold", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Wilhelm Furnon", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Karen Kerr", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Georgios Ilia", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Jay Allan", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute, University of KwaZulu-Natal" - }, - { - "author_name": "Arvind H. Patel", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Massimo Palmarini", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.11.11.566634", "rel_title": "Recreating the Biological Steps of Viral Infection on a Bioelectronic Platform to Profile Viral Variants of Concern", @@ -34049,6 +35423,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.11.05.565350", + "rel_title": "Universal protection against SARS-CoV-2 viruses by multivalent mRNA vaccine in mice", + "rel_date": "2023-11-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.05.565350", + "rel_abs": "The ongoing emergence of new strains of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges available SARS-CoV-2 vaccines for adequate control of outbreaks. Currently, there is a lack of universal vaccines for SARS-CoV-2 variants that do not necessitate strain matching between mRNA vaccines and the viruses. In this study, a nucleoside-modified twenty-valent lipid nanoparticle mRNA vaccine was designed and manufactured. The primary objective is to provide protection against various recent variants via the twenty-valent mRNA vaccine after efficacy assessment. Furthermore, the protection efficiency of bivalent and quadrivalent mRNA vaccines was compared with the universal vaccine. The neutralizing antibody activity against BA.4/5, XBB.1.5, BQ.1.1, and EG.5.1 was evaluated using enzyme-linked immunosorbent assay, pseudovirus neutralization test, and a rapid fiber-optic biolayer interferometry-based biosensor. Our universal multivalent vaccine provided robust protection against both prevailing and emerging, previously unidentified SARS-CoV-2 strains.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Zhengyang Lei", + "author_inst": "Tsinghua university" + }, + { + "author_name": "Sumin Bian", + "author_inst": "Westlake University" + }, + { + "author_name": "Shiyao Zhai", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Xi Yuan", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Runming Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Pengyun Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Vijay Pandey", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Cang Yang Zhang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Dongmei Yu", + "author_inst": "Shandong University" + }, + { + "author_name": "Zhenglin Chen", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Peiwu Qin", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.11.07.566110", "rel_title": "Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles", @@ -34786,93 +36219,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.11.06.23298026", - "rel_title": "Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England", - "rel_date": "2023-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.06.23298026", - "rel_abs": "Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated Medium-Term Projections (MTPs) of possible epidemic trajectories over the future 4-6 weeks from a collection of epidemiological models.In this paper we outline this collaborative modelling approach and evaluate the accuracy of the combined and individual model projections against the data over the period November 2021-December 2022 when various Omicron subvariants were spreading across England. Using a number of statistical methods, we quantify the predictive performance of the model projections for both the combined and individual MTPs, by evaluating the point and probabilistic accuracy. Our results illustrate that the combined MTPs, produced from an ensemble of heterogeneous epidemiological models, were a closer fit to the data than the individual models during the periods of epidemic growth or decline, with the 90% confidence intervals widest around the epidemic peaks. We also show that the combined MTPs increase the robustness and reduce the biases associated with a single model projection. Learning from our experience of ensemble modelling during the COVID-19 epidemic, our findings highlight the importance of developing cross-institutional multi-model infectious disease hubs for future outbreak control.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Harrison Manley", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Thomas Bayley", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Gabriel Danelian", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Lucy Burton", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Thomas Finnie", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Andre Charlett", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Nick Watkins", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Paul Birrell", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Daniela De Angelis", - "author_inst": "University of Cambridge Cambridge, UK" - }, - { - "author_name": "Matt J Keeling", - "author_inst": "University of Warwick, Zeeman Institute: SBIDER" - }, - { - "author_name": "Sebastian J Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Graham Medley", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Lorenzo Pellis", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Marc Baguelin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graeme J Ackland", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Johanna Hutchinson", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Steven Riley", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Jasmina Panovska-Griffiths", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.11.06.23298151", "rel_title": "Text Augmentations with R-drop for Classification of Tweets Self-Reporting Covid-19", @@ -36047,6 +37393,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.11.02.23297831", + "rel_title": "Serum Antibody Fingerprinting for SARS-CoV-2 Variants in Infected and Vaccinated Subjects by Label-Free Microarray Biosensor", + "rel_date": "2023-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.02.23297831", + "rel_abs": "Both viral infection and vaccination affect the antibody repertoire of a person. Here we demonstrate that the analysis of serum antibodies carries information not only on the virus type that caused the infection, but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants, based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fraction. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed larger quantity of total Ig and lower fraction of IgA relative to the population of convalescent unvaccinated subjects.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Thomas Carzaniga", + "author_inst": "University of Milan" + }, + { + "author_name": "Luca Casiraghi", + "author_inst": "University of Milan" + }, + { + "author_name": "Giovanni Nava", + "author_inst": "University of Milan" + }, + { + "author_name": "Giuliano Zanchetta", + "author_inst": "University of Milan" + }, + { + "author_name": "Tommaso Inzani", + "author_inst": "University of Milan" + }, + { + "author_name": "Marcella Chiari", + "author_inst": "National Research Council of Italy (SCITEC-CNR)" + }, + { + "author_name": "Valentina Bollati", + "author_inst": "University of Milan" + }, + { + "author_name": "Sara Epis", + "author_inst": "University of Milan" + }, + { + "author_name": "Claudio Bandi", + "author_inst": "University of Milan" + }, + { + "author_name": "Alessia Lai", + "author_inst": "University of Milan" + }, + { + "author_name": "Gianguglielmo Zehender", + "author_inst": "University of Milan" + }, + { + "author_name": "Tommaso Bellini", + "author_inst": "University of Milan" + }, + { + "author_name": "Marco Buscaglia", + "author_inst": "University of Milan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2023.11.01.23297908", "rel_title": "Gods Lockdown: the effect of the April 2022 Colorado low blizzard on SARS-Cov-2 transmission in the midwest United States", @@ -36632,45 +38045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.26.23297643", - "rel_title": "Menstrual cycle changes increased following COVID-19 mRNA vaccination: Social media validation and self-controlled case series analysis.", - "rel_date": "2023-10-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297643", - "rel_abs": "ObjectivesTo investigate if there was an increase in menstrual abnormality related presentation post COVID-19 vaccination.\n\nDesignBERTopic machine learning, with a guided topic modelling option was used to analyse mentions of menstrual change in relation to COVID-19 vaccination on the social media platform Reddit. Self-controlled case series (SCCS) analysis using general practice data collected via the POpulation Level Analysis and Reporting (POLAR) tool with permission from Primary Health Networks (PHNs) as the de-identified dataset owners in Victoria and New South Wales.\n\nSettingGlobally for social media analysis. Victoria and New South Wales (NSW), Australia for POLAR\n\nParticipantsFor social media analysis, people who made a Reddit post about menstrual concerns post COVID-19 vaccine. For the SCCS analysis, people who presented to a POLAR GP registered practice with a new menstrual abnormality diagnosis.\n\nExposuresCOVID-19 vaccination with adenovirus vector [AstraZenecas Vaxzervria(R) ChadOx1-S], mRNA [Pfizer-BioNTechs Comirnaty(R) BNT162b2 and Modernas Spikevax(R)] or protein-subunit [Novavaxs Nuvaxovid(R)]).\n\nOutcomes and MeasuresScraped social media posts were pre-processed, analysed for positive, negative, and neutral sentiments and topic modelled. Menstrual abnormality presentations of interest were isolated from the general practice dataset aggregated by POLAR, by searching for relevant SNOMED CT codes. Similarly, relative incidence (RI) was calculated for all COVID-19 vaccine types.\n\nResultsSocial media analysis saw peaks in menstrual change posts on Reddit since the global COVID-19 vaccine rollout. The SCCS analysis demonstrates an increase in general practice presentations of menstrual abnormality diagnosis following mRNA vaccines (RI= 1.14, 95% CI: 1.07 to 1.22, P <0.001).\n\nConclusions and RelevanceThis study demonstrates an increase in menstrual abnormality presentations following COVID-19 mRNA vaccination. Our findings validate the concerns raised on social media so people who are vaccinated or are considering future vaccines feel heard, supported, and validated. Our analysis highlights the importance of using large real-world datasets to gather reliable evidence for public health decision making.\n\nSummary box O_TEXTBOXSection 1: What is already known on this topic?O_LISurveys and spontaneous surveillance systems suggested and association of menstrual cycle changes with COVID-19 vaccination.\nC_LIO_LIHeavy menstrual bleeding was added to the product information for mRNA vaccines in the European Union\nC_LI\n\nSection 2: What this study adds?O_LIOur study is the first to prove an increase in menstrual abnormality related presentations post mRNA COVID-19 vaccines using routinely collected general practice data.\nC_LIO_LIOur findings validate the concerns raised by people who menstruate and help them with their future decision to vaccinate.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Aishwarya N Shetty", - "author_inst": "Centre for Health Analytics, Melbourne Childrens Campus, Australia 3052" - }, - { - "author_name": "Gonzalo Sepulveda Kattan", - "author_inst": "Centre for Health Analytics, Melbourne Childrens Campus, Australia 3052" - }, - { - "author_name": "Muhammad Javed", - "author_inst": "Centre for Health Analytics, Melbourne Childrens Campus, Australia 3052" - }, - { - "author_name": "Christopher Pearce", - "author_inst": "Aurora Primary Care Research Institute, Blackburn, Australia 3130" - }, - { - "author_name": "Hazel J Clothier", - "author_inst": "Vaccine Safety Surveillance and Signal Detection, SAEFVIC, Murdoch Childrens Research Institute, Australia 3052" - }, - { - "author_name": "Jim P Buttery", - "author_inst": "Health Informatics, Centre for Health Analytics, Melbourne Childrens Campus, Australia 3052" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.27.23297682", "rel_title": "Influenza vaccine effectiveness against hospitalized SARS-CoV-2 infection", @@ -37577,6 +38951,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2023.10.27.23297663", + "rel_title": "Mental health conditions and COVID-19 vaccine outcomes: a scoping review", + "rel_date": "2023-10-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.27.23297663", + "rel_abs": "BackgroundThe COVID-19 pandemic has had a profound impact on the mental health of people worldwide. Mental health also impacts on physical health. In the context of viral illnesses, viral challenge studies have shown that indices of mental health are associated with susceptibility to viral infections, including coronaviruses. Research conducted during the pandemic has shown that people with a history of mental health conditions were at increased risk of infection, hospitalisation, and mortality. However, the relationship between mental health conditions and vaccine outcomes such as vaccine intentions, uptake, and vaccine breakthrough is not yet well-understood.\n\nMethodsWe conducted a systematic search on the topics of COVID-19 vaccine intentions, vaccine uptake, and vaccine breakthrough, in relation to mental health conditions, in four databases: PubMed, MEDLINE, SCOPUS, and PsychINFO, as well as the publication lists of Clinical Practice Research Datalink (CPRD), The Health Improvement Network (THIN), OpenSAFELY, and QResearch. Inclusion criteria focus on studies reporting either of the aforementioned COVID-19 vaccine outcomes among people with mental health conditions.\n\nResultsThirty-three out of 251 publications met our inclusion criteria for this review. Overall, the evidence is inconclusive regarding the level of intention to accept the COVID-19 vaccine among people with mental health conditions. However, people with mental health conditions were more likely to have lower uptake of the COVID-19 vaccine, compared to people without. Common barriers to COVID-19 vaccine uptake include concerns about the safety, effectiveness, and side effects of the vaccines. Limited evidence also suggests that vaccine breakthrough may be a particular risk for those with substance use disorder.\n\nConclusionsOur findings revealed a possible intention-behaviour gap for receiving the COVID-19 vaccine among people with mental health conditions, yielding interventions to encourage vaccine uptake in this population. There is also the need to enhance our understanding of COVID-19 vaccine breakthrough in people with mental health conditions.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ru Jia", + "author_inst": "University of Oxford" + }, + { + "author_name": "Carol Coupland", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Yana Vinogradova", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Nadeem Qureshi", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Emma Turner", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kavita Vedhara", + "author_inst": "Cardiff University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2023.10.26.23297608", "rel_title": "Understanding COVID-19 testing behaviour in England through a sociodemographic lens", @@ -38290,57 +39703,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.10.25.563806", - "rel_title": "Reduced Monocyte Proportions and Responsiveness in Convalescent COVID-19 Patients", - "rel_date": "2023-10-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.563806", - "rel_abs": "The clinical manifestations of acute severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection and COVID-19 suggest a dysregulation of the host immune response that leads to inflammation, thrombosis, and organ dysfunction. It is less clear whether these dysregulated processes persist during the convalescent phase of disease or during long COVID. We investigated the effects of SARS-CoV-2 infection on the proportions of classical, intermediate, and non-classical monocytes, their activation status, and their functional properties in convalescent COVID-19 patients and uninfected control subjects. We found that the percentage of total monocytes was decreased in convalescent COVID-19 patients compared to uninfected controls. This was due to decreased intermediate and non-classical monocytes. Classical monocytes from convalescent COVID-19 patients demonstrated a decrease in activation markers, such as CD56, in response to stimulation with bacterial lipopolysaccharide (LPS). In addition, classical monocytes from convalescent COVID-19 patients showed decreased expression of CD142 (tissue factor), which can initiate the extrinsic coagulation cascade, in response to LPS stimulation. Finally, we found that monocytes from convalescent COVID-19 patients produced less TNF- and IL-6 in response to LPS stimulation, than those from uninfected controls. In conclusion, SARS-CoV-2 infection exhibits a clear effect on the relative proportions of monocyte subsets, the activation status of classical monocytes, and proinflammatory cytokine production that persists during the convalescent phase of disease.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Eugene Ravkov", - "author_inst": "ARUP Laboratories" - }, - { - "author_name": "Elizabth S C P Williams", - "author_inst": "University of Utah" - }, - { - "author_name": "Marc Elgort", - "author_inst": "ARUP Laboratories" - }, - { - "author_name": "Adam Spivak", - "author_inst": "University of Utah" - }, - { - "author_name": "Adam P Barker", - "author_inst": "University of Utah and ARUP Laboratories" - }, - { - "author_name": "Vicente Planelles", - "author_inst": "University of Utah" - }, - { - "author_name": "Julio Delgado", - "author_inst": "ARUP Laboratories" - }, - { - "author_name": "Leo Lin", - "author_inst": "University of Utah" - }, - { - "author_name": "Timothy Hanley", - "author_inst": "University of Utah" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.10.25.564079", "rel_title": "Integrating population-level and cell-based signatures for drug repositioning", @@ -39715,6 +41077,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.10.24.23297114", + "rel_title": "Plasma-based antigen persistence in the post-acute phase of SARS-CoV-2 infection", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.24.23297114", + "rel_abs": "BACKGROUNDPersistent symptoms among some persons who develop COVID-19 has led to the hypothesis that SARS-CoV-2 may, in some form or location, persist for long periods following acute infection. Several studies have shown data in this regard but are limited by non-representative and small study populations, short duration since acute infection, and lack of a true-negative comparator group to assess assay specificity.\n\nMETHODSWe evaluated adults with RNA-confirmed COVID-19 at multiple time points following acute infection (pandemic-era participants) and adults with specimens collected prior to 2020 (pre-pandemic era). Using once-thawed plasma, we employed the Simoa(R) (Quanterix) single molecule array detection platform to measure SARS-CoV-2 spike, S1, and nucleocapsid antigens.\n\nRESULTSCompared to 250 pre-pandemic participants who had 2% assay positivity, detection of any SARS-CoV-2 antigen was significantly more frequent among 171 pandemic-era participants at three different time periods in the post-acute phase of infection. The absolute difference in SARS-CoV-2 plasma antigen prevalence was +11% (95% CI: +5.0% to +16%) at 3.0-6.0 months post-onset of COVID-19; +8.7% (95% CI: +3.1% to +14%) at 6.1 to 10.0 months; and +5.4% (95% CI: +0.42% to +10%) at 10.1-14.1 months. Hospitalization for acute COVID-19 and, among the non-hospitalized, worse self-reported health during acute COVID-19 were associated with greater post-acute phase antigen detection.\n\nCONCLUSIONSCompared to uninfected persons, there is an excess prevalence of SARS-CoV-2 antigenemia in SARS-CoV-2-infected individuals up to 14 months after acute COVID-19. These findings motivate an urgent research agenda regarding the short-term and long-term clinical manifestations of this viral persistence.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Michael J. Peluso", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Zoe N. Swank", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Sarah A. Goldberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Scott Lu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Thomas Dalhuisen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ella Borberg", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Yasmeen Senussi", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Michael A. Luna", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Celina Chang Song", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alexus Clark", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andhy Zamora", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Megan Lew", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Badri Viswanathan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Beatrice Huang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Khamal Anglin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Priscilla Y. Hsue", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew S. Durstenfeld", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A. Spinelli", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David V. Glidden", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Timothy J. Henrich", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "J. D. Kelly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steven G. Deeks", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David R. Walt", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jeffrey N. Martin", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.10.24.23297192", "rel_title": "COVID-19 vaccination-induced antibody responses and waning by age and comorbidity status in a large population-based prospective cohort study", @@ -40360,57 +41837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.23.563427", - "rel_title": "A bioactive peptide from the pearl has dual roles in resisting SARS-CoV-2 infection and its complications", - "rel_date": "2023-10-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563427", - "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is a critical receptor for the entry of the SARS-CoV-2 virus into cells. Moreover, a decrease in ACE2 level and its activity due to SARS-CoV-2 infection is considered a crucial reason for the development of Covid-19-associated complications. Here, we report a bioactive peptide derived from the seawater pearl oyster Pinctada fucata, named SCOL polypeptide, which binds strongly to ACE2 and effectively inhibits 65% of the binding of the SARS-CoV-2 S protein to ACE2; thus, this peptide can be used as a blocker to enable cells to resist SARS-CoV-2 infection. The SCOL polypeptide also increases ACE2 enzyme activity by 3.76 times. Previous studies have shown that ACE2 deficiency is associated with inflammation, pain, cardiovascular diseases, insulin resistance, and nervous system injury. Therefore, the SCOL polypeptide can be used to treat or alleviate complications such as lung inflammation, pain, diabetes, cardiovascular diseases, and loss of taste or smell caused by SARS-CoV-2 infection. Thus, the SCOL polypeptide can play a dual role in resisting SARS-CoV-2 infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xiaojun Liu", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Yayu Wang", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Zehui Yin", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Qin Wang", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Xinjiani Chen", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Bailei Li", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Liping Yao", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Zhen Zhang", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - }, - { - "author_name": "Rongqing Zhang", - "author_inst": "Yangtze Delta Region Institute of Tsinghua University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.10.22.563490", "rel_title": "Screening Peptide Drug Candidates to Neutralize Whole Viral Agents : A Case study with SARS-CoV-2 Virus", @@ -41685,6 +43111,41 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2023.10.19.563051", + "rel_title": "FAKHRAVAC and BBIBP-CorV vaccine seeds' binding to angiotensin-converting enzyme 2: A comparative molecular dynamics study", + "rel_date": "2023-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.19.563051", + "rel_abs": "BackgroundSafety and efficacy of the SARS-CoV-2 inactivated vaccines have been question since the emergence of SARS-CoV-2 variants of concern (VOCs). Using residue fluctuations and statistically comparing RMSF values, have escalated the understanding of the binding dynamics of the viral proteins to their receptors and here in this study, we compared the interaction between inactivated spike proteins (representing FAKHRAVAC and BBIBP-CorV vaccines seed) and the human Angiotensin-Converting Enzyme 2 (hACE2) receptor.\n\nMethodologyThrough 100 set of accelerated 1 ns comparative molecular dynamics simulations, we analyze the binding dynamics and energy components of these interactions and compared residue backbone fluctuations using entropy and statistics including KL-Divergence and KS-test.\n\nPrincipal FindingsOur results reveal that FAKHRAVAC and Sinopharm exhibit similar binding dynamics and affinity to hACE2. Further examination of residue-wise fluctuations highlights the common behavior of binding key residues and mutation sites between the two vaccines. However, subtle differences in residue fluctuations, especially at critical sites like Q24, Y435, L455, S477, Y505, and F486, raise the possibility of distinct efficacy profiles.\n\nConclusionThese variations may influence vaccine immunogenicity and safety in response to evolving SARS-CoV-2 variants. The study underscores the importance of considering residue-wise fluctuations for understanding vaccine-pathogen interactions and their implications for vaccine design.\n\nAuthor summaryIt is fundamentally important to ensure the safety and efficacy of the FAKHRAVAC, as an inactivated vaccine candidate for SARS-CoV-2. Considering the previously published pre-clinical and clinical findings about the similarity of the FAKHRAVACs safety and efficacy in comparison to the BBIBP-CorV vaccine seed (which is recalled as Sinopharm), it is necessary to gain more insights into structure and function of this vaccine at the molecular level, as well. Since the binding dynamics of the viral proteins to their receptor can imply the vaccines immunogenicity and mechanism-of-action, binding dynamics of a vaccine candidate must be studied comprehensively. Hereby, we have compared binding dynamics of the FAKHRAVAC and Sinopharm vaccine seeds to the SARS-CoV-2 spike proteins receptor, the ACE2. We took advantage of a comparative molecular dynamics simulation approach to effectively compare binding dynamics using atom fluctuations and at the residue level to ensure the resolution of this study. We have found similar binding dynamics and binding mechanics between these two vaccines, validating the pre-clinical and clinical findings computationally, as well as highlighting residues with different fluctuations and discussed their potential roles.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Soroush Setareh", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Iman Rad", + "author_inst": "stem cell technology research center" + }, + { + "author_name": "Jafar Meghdadi", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Kaveh Khodayari", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Ahmad Karimi Rahjerdi", + "author_inst": "Iran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "confirmatory results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.10.19.563184", "rel_title": "Divergent spike mutations impact the activation of the fusion core in Delta and Omicronvariants of SARS-CoV-2", @@ -42158,57 +43619,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.10.13.562192", - "rel_title": "Cross-sector collaboration reduces SARS-CoV-2 risk in deer", - "rel_date": "2023-10-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.13.562192", - "rel_abs": "One Health helps achieve optimal health outcomes for people, animals, plants, and their shared environments. We describe a multidisciplinary effort to better understand and mitigate SARS-CoV-2 spread in white-tailed deer across One Health sectors. We first framed the risk problem with three governance sectors that manage captive and wild deer and human public health. The framing included the objectives for each sector, interactions that facilitate human-to-deer and deer-to-deer transmission, and alternatives intended to reduce risk. We then developed a dynamic compartmental model that linked wild and captive deer herds and humans and simulated SARS-CoV-2 dynamics. For baseline conditions, we estimated that median SARS-CoV-2 prevalence in wild and captive herds varied between 0.03 - 0.07, incidence between 0.68 - 1.46, and probability of persistence between 0.64 - 0.97 across 120-day simulations. We then tested single-sector alternatives alone and in combination with other sector actions. We found that single sector alternatives varied in their ability to reduce transmission and that the best performing alternative required collaborative actions among wildlife management, agricultural management, and public health agencies.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jonathan D Cook", - "author_inst": "U.S. Geological Survey" - }, - { - "author_name": "Elias Rosenblatt", - "author_inst": "University of Vermont" - }, - { - "author_name": "Graziella V DiRenzo", - "author_inst": "U.S. Geological Survey" - }, - { - "author_name": "Evan H Campbell Grant", - "author_inst": "U.S. Geological Survey" - }, - { - "author_name": "Brittany Mosher", - "author_inst": "University of Vermont" - }, - { - "author_name": "Fernando Arce", - "author_inst": "University of Massachusetts" - }, - { - "author_name": "Sonja Christensen", - "author_inst": "Michigan State University" - }, - { - "author_name": "Ria Ghai", - "author_inst": "US Centers for Disease Control and Prevention" - }, - { - "author_name": "Michael Runge", - "author_inst": "U.S. Geological Survey" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2023.10.17.562739", "rel_title": "Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE)", @@ -43331,6 +44741,49 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.10.12.561935", + "rel_title": "Hidden evolutionary constraints dictate the retention of coronavirus accessory genes", + "rel_date": "2023-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.12.561935", + "rel_abs": "Genetic innovation is fundamental to the ability of viruses to adapt in the face of host immunity. Coronaviruses exhibit many mechanisms of innovation given flexibility in genomic composition relative to most RNA virus families1-5. Examples include the acquisition of unique accessory genes that can originate by capture of cellular genes or through duplication and divergence of existing viral genes6,7. Accessory genes may be influential in dictating viral host range and cellular tropism, but little is known about how selection acts on these variable regions of virus genomes. We used experimental evolution of mouse hepatitis virus (MHV) with an inactive native phosphodiesterase, NS2, that encodes a complementing cellular AKAP7 gene9, to simulate the capture of a host gene and found hidden patterns of constraint that determine the fate of coronavirus accessory genes. After courses of serial infection, AKAP7 was retained under strong selection but rapidly lost under relaxed selection. In contrast, the gene encoding inactive NS2, ORF2, remained intact, suggesting it is under cryptic evolutionary constraint. Guided by the retention of ORF2 and hints of similar patterns in related betacoronaviruses, we analyzed the evolution of SARS-CoV-2 ORF8, which arose via gene duplication6 and contains premature stop codons in several globally successful lineages. As with MHV ORF2, the coding-defective SARS- CoV-2 ORF8 gene remains largely intact, mirroring patterns observed during MHV experimental evolution and extending these findings to viruses currently adapting to humans. Retention of inactive genes challenges assumptions on the dynamics of gene loss in virus genomes and can help guide evolutionary analysis of emerging and pandemic coronaviruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Stephen A. Goldstein", + "author_inst": "University of Utah" + }, + { + "author_name": "Teagan M. Feeley", + "author_inst": "University of Utah" + }, + { + "author_name": "Kristina M. Babler", + "author_inst": "University of Utah" + }, + { + "author_name": "Zoe A. Hilbert", + "author_inst": "University of Utah" + }, + { + "author_name": "Diane M. Downhour", + "author_inst": "University of Utah" + }, + { + "author_name": "Niema Moshiri", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Nels C. Elde", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2023.10.12.23296928", "rel_title": "Evolution of SARS-CoV-2 in the RhineNeckar/Heidelberg Region 01/2021 07/2023", @@ -44036,41 +45489,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.11.23296911", - "rel_title": "Reproducibility of COVID-era infectious disease models", - "rel_date": "2023-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.11.23296911", - "rel_abs": "Infectious disease modelling has been prominent throughout the COVID-19 pandemic, helping to understand the virus transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the computational reproducibility of infectious disease modelling articles from the COVID era. We found that only four out of 100 randomly sampled studies released between January 2020 and August 2022 could be computationally reproduced using the resources provided (e.g., code, data, instructions). For the 100 most highly cited articles from the same period we found that only 11 were reproducible. Reflecting on our experience, we discuss common issues affecting computational reproducibility and how these might be addressed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alec S Henderson", - "author_inst": "James Cook University" - }, - { - "author_name": "Roslyn I Hickson", - "author_inst": "Commonwealth Scientific Industrial Research Organisation (CSIRO)" - }, - { - "author_name": "Morgan Morgan", - "author_inst": "James Cook University" - }, - { - "author_name": "Emma S McBryde", - "author_inst": "James Cook University" - }, - { - "author_name": "Michael T Meehan", - "author_inst": "James Cook University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.10.11.23296866", "rel_title": "SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort", @@ -45345,6 +46763,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.10.09.23296737", + "rel_title": "Covid-19 vaccine safety in pregnancy, a nested case-control study in births from April 2021 to March 2022, England", + "rel_date": "2023-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.09.23296737", + "rel_abs": "IntroductionVaccine safety in pregnancy is always of paramount importance. Current evidence of COVID-19 vaccine safety in pregnancy has been reassuring with no association found with negative maternal and neonatal outcomes. However, very few safety studies are conducted on a national level and investigate dosage, timing of vaccination as well as vaccine manufacturer. To fill this knowledge gap, we conducted a population based COVID-19 vaccine safety evaluation in England, including timing of vaccination by trimester, dosage and vaccine manufacturer received in pregnancy.\n\nMethodA matched case control study nested in a retrospective cohort where adverse maternal and neonatal pregnancy outcomes were compared across several COVID-19 vaccine exposures using conditional multivariable logistic regression, adjusting for a range of demographic and health characteristics. Eligible participants were identified from the national maternity services dataset (MSDS) and records were linked to hospital admission, national COVID-19 vaccine and COVID-19 testing databases. Matching criteria differed by outcome but included participants age and estimated week of conception.\n\nResults514,013 pregnant individuals aged between 18 and 50 years were identified during the study period (births from 16th of April 2021-31st March 2022). Receiving at least one dose of COVID-19 vaccine during pregnancy conferred lower odds of giving birth to a baby who was low birthweight (aOR=0.86, 95% CI: 0.79 - 0.93), preterm (aOR=0.89, 95% CI: 0.85 - 0.92) or who had an Apgar score less than 7 at five mins of age (aOR=0.89, 95% CI: 0.80 - 0.98). There was no association between vaccination in pregnancy and stillbirth (aOR=0.90, 95% CI: 0.76 - 1.07), neonatal death (aOR=1.27, 95% CI: 0.91 - 1.77) perinatal death (aOR=0.98, 95% CI: 0.83 - 1.16), and maternal venous thromboembolism in pregnancy (aOR=0.82, 95% CI: 0.43 - 1.56). The odds of maternal admission to intensive care unit were lower in vaccinated pregnant women (aOR=0.85, 95% CI: 0.76 - 0.95).\n\nConclusionCOVID-19 vaccines are safe to use in pregnancy and they confer protection against SARS-CoV-2 infection which can lead to adverse outcomes for both the mother and the infant. Our findings generated important information to communicate to pregnant women and health professionals to support COVID-19 maternal vaccination programmes.\n\nWhat is already known on this topicCurrent evidence shows that COVID-19 vaccines are safe to use in pregnancy. However, few studies investigate the timing of vaccination in pregnancy including the first trimester for late pregnancy outcomes. Most studies are geographically limited, and few are population based allowing inclusion of participants representative of the countrys inhabitants.\n\nWhat this study addsThis is the first population-based study in England investigating COVID-19 vaccine safety in pregnancy. We used the national maternity services dataset and national English health services data enabling inclusion of a huge numbers of participants across the country. As such, we were able to investigate relevant safety research questions such as the timing of vaccine administration in pregnancy by trimester and before pregnancy, the number of doses received and vaccine manufacturer.\n\nHow this study might affect research, practice or policyThis national study adds to further existing evidence demonstrating that all COVID-19 vaccines are safe to use in pregnancy at any point in time and gives pregnant individuals confidence in the COVID-19 maternal vaccine programme. We demonstrated that receiving multiple doses of COVID-19 vaccine in pregnancy is not associated with adverse pregnancy outcomes and additionally it was reassuring that there was no evidence of an increased risk by vaccine type.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Anna A Mensah", + "author_inst": "UKHSA" + }, + { + "author_name": "Julia Stowe", + "author_inst": "UKHSA" + }, + { + "author_name": "Jennifer E Jardine", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Freja CM Kirsebom", + "author_inst": "UKHSA" + }, + { + "author_name": "Tom Clare", + "author_inst": "UKHSA" + }, + { + "author_name": "Meaghan Kall", + "author_inst": "UKHSA" + }, + { + "author_name": "Helen Campbell", + "author_inst": "UKHSA" + }, + { + "author_name": "Jamie Lopez-Bernal", + "author_inst": "UKHSA" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UKHSA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.09.23296728", "rel_title": "Impact of sampling site on diagnostic test accuracy of RT-PCR in diagnosing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection since the emergence of omicron: a systematic review and meta-analysis", @@ -45986,85 +47455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.10.04.23296430", - "rel_title": "The Trajectory of Depression and Anxiety Among Children and Adolescents over Two Years of the COVID-19 Pandemic", - "rel_date": "2023-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.04.23296430", - "rel_abs": "Longitudinal research examining childrens mental health (MH) over the course of the COVID-19 pandemic is scarce. We examined trajectories of depression and anxiety over two pandemic years among children with and without MH disorders. Parents and children 2-18 years completed surveys at seven timepoints (April 2020 to June 2022). Parents completed validated measures of depression and anxiety for children 8-18 years, and validated measures of emotional/behavioural symptoms for children 2-7 years old; children [≥]10 years completed validated measures of depression and anxiety. Latent growth curve analysis determined depression and anxiety trajectories, accounting for demographics, child and parent MH. Data were available on 1315 unique children (1259 parent-reports; 550 child-reports). Trajectories were stable across the study period, however individual variation in trajectories was statistically significant. Of included covariates, only initial symptom level predicted symptom trajectories. Among participants with pre-COVID data, a significant increase in depression symptoms relative to pre-pandemic levels was observed. Children and adolescents experienced elevated and sustained levels of depression and anxiety during the two-year period. Findings have direct policy implications in the prioritization and of maintenance of educational, recreational, and social activities with added MH supports in the face of future events.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Daphne J Korczak", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Ronda F Lo", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Jala Rizek", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Jennifer Crosbie", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Alice Charach", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Evdokia Anagnostou", - "author_inst": "Holland Bloorview Research Institute" - }, - { - "author_name": "Catherine Birken", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Suneeta Monga", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Elizabeth Kelley", - "author_inst": "Queen's University" - }, - { - "author_name": "Rob Nicolson", - "author_inst": "Western University" - }, - { - "author_name": "Paul Arnold", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jonathon Maguire", - "author_inst": "St Michaels Hospital" - }, - { - "author_name": "Russell James Schachar", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Stelios Georgeadis", - "author_inst": "McMaster University" - }, - { - "author_name": "Christie L Burton", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Katherine Cost", - "author_inst": "Hospital for Sick Children" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.10.04.23296537", "rel_title": "Development and validation of automated methods for COVID-19 PCR MasterMix preparation.", @@ -47163,6 +48553,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.30.560318", + "rel_title": "Synthesis, Insertion and Characterization of SARS-CoV-2 Membrane Protein Within Lipid Bilayers", + "rel_date": "2023-10-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.30.560318", + "rel_abs": "SUMMARY/ABSTRACTThe membrane protein (M) is the most abundant structural protein in the SARS-CoV-2 virus and functions exclusively as a membrane-embedded homodimer. M protein is required for the formation of the SARS-CoV-2 virus particle and has been shown to interact with the Spike and Envelope proteins, as well as the RNA-packaging Nucleocapsid protein. Our knowledge of M protein is very limited due to its small size and challenges in expressing enough protein for use in structural and biophysical experiments. We report the successful development of a SUMO tag-based expression system to produce and purify significant quantities of M protein, and a method to insert the synthesized dimers into a suspended lipid membrane in a homogeneous orientation. We used AFM and Cryo-EM to image individual membrane-bound M protein dimers and characterize the configurations that they can assume. Our experimental results are in agreement with our molecular dynamics simulations which predict thinning of the membrane around the M protein and a propensity to induce local membrane curvature. Taken together, our results shed new light on M protein properties within the lipid bilayer and suggest mechanisms that could contribute to viral assembly and budding.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuanzhong Zhang", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Sara Anbir", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Joseph Mctiernan", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Siyu Li", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Michael Worcester", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Pratyasha Mishra", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Michael E Colvin", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Ajay Gopinathan", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Umar Mohideen", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Roya Zandi", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Thomas Edward Kuhlman", + "author_inst": "University of California Riverside" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.09.30.23296175", "rel_title": "Simulation of COVID-19 Epidemic from Potential Viral Loads in Saudi Arabian Wastewater Treatment Plants", @@ -47804,77 +49253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2023.09.28.559966", - "rel_title": "SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants", - "rel_date": "2023-09-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.28.559966", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional NSP14 enzyme, possessing exonuclease and mRNA capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscores the dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Sk. Sarif Hassan", - "author_inst": "Pingla Thana Mahavidyalaya" - }, - { - "author_name": "Tanishta Bhattacharya", - "author_inst": "Indian Institute of Science Education and Research, Berhampur" - }, - { - "author_name": "Debaleena Nawn", - "author_inst": "Indian Statistical Institute, Kolkata" - }, - { - "author_name": "Ishana Jha", - "author_inst": "Pondicherry University" - }, - { - "author_name": "Pallab Basu", - "author_inst": "University of Wits" - }, - { - "author_name": "Elrashdy M. Redwan", - "author_inst": "King Abdulaziz University" - }, - { - "author_name": "Kenneth Lundstrom", - "author_inst": "PanTherapeutics" - }, - { - "author_name": "Debmalya Barh", - "author_inst": "Institute of Integrative Omics and Applied Biotechnology (IIOAB)" - }, - { - "author_name": "Bruno Andrade", - "author_inst": "Universidade Estadual do Sudoeste da Bahia" - }, - { - "author_name": "Murtaza M. Tambuwala", - "author_inst": "University of Lincoln" - }, - { - "author_name": "Alaa A. Aljabali", - "author_inst": "Yarmouk University" - }, - { - "author_name": "Altijana Hromic-Jahjefendic", - "author_inst": "International University of Sarajevo" - }, - { - "author_name": "Wagner Baetas-da-Cruz", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Vladimir N Uversky", - "author_inst": "University of South Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.09.29.560110", "rel_title": "Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases.", @@ -48653,6 +50031,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.09.26.559550", + "rel_title": "Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2 in vivo", + "rel_date": "2023-09-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.26.559550", + "rel_abs": "The rapid evolution of SARS-CoV-2 variants highlights the need for new therapies to prevent disease spread. SARS-CoV-2, like SARS-CoV-1, uses the human cell surface protein angiotensin-converting enzyme 2 (ACE2) as its native receptor. Here, we design and characterize a mutant ACE2 that enables rapid affinity purification of a dimeric protein by altering the active site to prevent autoproteolytic digestion of a C-terminal His10 epitope tag. In cultured cells, mutant ACE2 competitively inhibits lentiviral vectors pseudotyped with spike from multiple SARS-CoV-2 variants, and infectious SARS-CoV-2. Moreover, the protein can be nebulized and retains virus-binding properties. We developed a system for delivery of aerosolized ACE2 to K18-hACE2 mice and demonstrate protection by our modified ACE2 when delivered as a prophylactic agent. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2 and other ACE2-dependent viruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Daniel L. Kober", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Marley C. Caballero Van Dyke", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Jennifer L. Eitson", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Ian N. Boys", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Matthew B. McDougal", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Daniel Rosenbaum", + "author_inst": "UT Southwestern, Dallas, Texas" + }, + { + "author_name": "John W Schoggins", + "author_inst": "UT Southwestern Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.09.26.559599", "rel_title": "survInTime - Exploring surveillance methods and data analysis on Brazilian respiratory syndrome dataset and community mobility changes", @@ -49466,85 +50887,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2023.09.25.559391", - "rel_title": "Using a function-first \"scout fragment\"-based approach to develop allosteric covalent inhibitors of conformationally dynamic helicase mechanoenzymes", - "rel_date": "2023-09-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.25.559391", - "rel_abs": "Helicases, classified into six superfamilies, are mechanoenzymes that utilize energy derived from ATP hydrolysis to remodel DNA and RNA substrates. These enzymes have key roles in diverse cellular processes, such as genome replication and maintenance, ribosome assembly and translation. Helicases with essential functions only in certain cancer cells have been identified and helicases expressed by certain viruses are required for their pathogenicity. As a result, helicases are important targets for chemical probes and therapeutics. However, it has been very challenging to develop selective chemical inhibitors for helicases, enzymes with highly dynamic conformations. We envisioned that electrophilic scout fragments, which have been used for chemical proteomic based profiling, could be leveraged to develop covalent inhibitors of helicases. We adopted a function-first approach, combining enzymatic assays with enantiomeric probe pairs and mass spectrometry, to develop a covalent inhibitor that selectively targets an allosteric site in SARS-CoV-2 nsp13, a superfamily-1 helicase. Further, we demonstrate that scout fragments inhibit the activity of two human superfamily-2 helicases, BLM and WRN, involved in genome maintenance. Together, our findings suggest a covalent inhibitor discovery approach to target helicases and potentially other conformationally dynamic mechanoenzymes.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jared R Ramsey", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Patrick M M Shelton", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Tyler K. Heiss", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Paul Dominic B Olinares", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Lauren E Vostal", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Heather Soileau", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Michael Grasso", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Sara Warrington", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Stephanie Adaniya", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Michael Miller", - "author_inst": "Sanders Tri-Institutional Therapeutics Discovery Institute" - }, - { - "author_name": "Shan Sun", - "author_inst": "Sanders Tri-Institutional Therapeutics Discovery Institute" - }, - { - "author_name": "David J Huggins", - "author_inst": "Sanders Tri-Institutional Therapeutics Discovery Institute" - }, - { - "author_name": "Robert W Myers", - "author_inst": "Sanders Tri-Institutional Therapeutics Discovery Institute" - }, - { - "author_name": "Brian T Chait", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Ekaterina V Vinogradova", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Tarun M Kapoor", - "author_inst": "The Rockefeller University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.09.24.558358", "rel_title": "RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variants Monitoring, and Risk Pre-warning", @@ -50435,7 +51777,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@c67fe1org.highwire.dtl.DTLVardef@1f59875org.highwire.dtl.DTLVardef@ec4b27org.highwire.dtl.DTLVardef@13a202e_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@7b6aeorg.highwire.dtl.DTLVardef@6a7952org.highwire.dtl.DTLVardef@432e19org.highwire.dtl.DTLVardef@878d4b_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -50563,6 +51905,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.09.21.23295905", + "rel_title": "Liver abnormalities following SARS-CoV-2 infection in children under 10 years of age", + "rel_date": "2023-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.21.23295905", + "rel_abs": "ObjectiveBeginning in October 2021 in the US and elsewhere, cases of severe pediatric hepatitis of unknown etiology were identified in young children. While the adenovirus and adenovirus-associated virus have emerged as leading etiologic suspects, we attempted to investigate a potential role for SARS-CoV-2 in the development of subsequent liver abnormalities.\n\nDesignWe conducted a study utilizing retrospective cohorts of de-identified, aggregated data from the electronic health records of over 100 million patients contributed by US health care organizations.\n\nResultsCompared to propensity-score-matched children with other respiratory infections, children aged 1-10 years with COVID-19 had a higher risk of elevated transaminases (Hazard ratio (HR) (95% Confidence interval (CI)) 2.16 (1.74-2.69)) or total bilirubin (HR (CI) 3.02 (1.91-4.78)), or new diagnoses of liver diseases (HR (CI) 1.67 (1.21-2.30)) from one to six months after infection. Patients with pre-existing liver abnormalities, liver abnormalities surrounding acute infection, younger age (1-4 years), or illness requiring hospitalization all had similarly elevated risk. Children who developed liver abnormalities following COVID-19 had more pre-existing conditions than those who developed abnormalities following other infections.\n\nConclusionThese results indicate that SARS-CoV-2 may prime the patient for subsequent development of liver infections or non-infectious liver diseases. While rare ([~]1 in 1,000), SARS-CoV-2 is a risk for subsequent abnormalities in liver function or the diagnosis of diseases of the liver.\n\nWhat is already known on this topicClusters of severe hepatitis in children in 2022 coincident with the increase in COVID-19 infections in children raised the question of the contribution of SARS-CoV-2 to the hepatitis outbreak, though it was soon determined that SARS-CoV-2 was not the primary etiologic agent.\n\nWhat this study addsSARS-CoV-2 may prime the patient for subsequent development of liver infections or non-infectious liver diseases.\n\nHow this study might affect research, practice or policyDespite the mild initial disease in children, there may be longer term consequences of COVID-19, such as liver abnormalities, that warrants further investigation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Pauline Terebuh", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Veronica R Olaker", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Ellen K Kendall", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "David C Kaelber", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Rong Xu", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Pamela B Davis", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.21.23295919", "rel_title": "Anti-SARS-CoV-2 Antibody Levels Associated with COVID-19 Protection in Outpatients Tested for SARS-CoV-2, US Flu VE Network, October 2021 to June 2022", @@ -51284,57 +52665,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.18.23295717", - "rel_title": "Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater", - "rel_date": "2023-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.18.23295717", - "rel_abs": "Deep sequencing of wastewater to detect SARS-Cov-2 has been used during the COVID-19 pandemic to monitor viral variants as they appear and circulate in communities. SARS-CoV-2 lineages of an unknown source that have not been detected in clinical samples, referred to as cryptic lineages, are sometimes repeatedly detected in specific locations. We have continued to detect one such lineage previously seen in a Missouri site. This cryptic lineage has continued to evolve, indicating continued selective pressure similar to that observed in Omicron lineages.\n\nAuthor SummaryMonitoring sewage for SARS-CoV-2 has been an important part of understanding the dynamics of the viruss spread and persistence within and across communities during the pandemic. We and others have also observed variants appearing in wastewater that do not appear in clinical sampling. Many of these variants not only possess genomic changes identical to or at the same position as those that have been observed in variants of concern, particularly currently circulating Omicron variants, but often acquire the changes before they have been observed in clinical samples. We report here the continued observation of a variant in Missouri wastewater, but not in clinical sampling, that has continued to evolve, gaining genomic changes that often are the same and predate changes seen in clinical samples. These observation add to our understanding of the selective pressures driving the evolution of SAR-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Devon Gregory", - "author_inst": "University of Missouri" - }, - { - "author_name": "Clayton Rushford", - "author_inst": "University of Missouri School of Medicine" - }, - { - "author_name": "Chung-Ho Lin", - "author_inst": "University of Missouri School of Natural Resources" - }, - { - "author_name": "Christie Darby", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Nicole Niehues", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Elizabeth Semkiw", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Melissa Reynolds", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Jeff Wenzel", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Marc C Johnson", - "author_inst": "University of Missouri School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.19.23295776", "rel_title": "Analysis of SARS-CoV-2 Ig seroprevalence in Northern Ireland", @@ -52461,6 +53791,101 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.09.14.557682", + "rel_title": "Enhanced neutralization of SARS-CoV-2 XBB sub-lineages and BA.2.86 by a tetravalent COVID-19 vaccine booster", + "rel_date": "2023-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.14.557682", + "rel_abs": "As the SARS-CoV-2 virus continues to evolve, novel XBB sub-lineages such as XBB.1.5, XBB.1.16, EG.5, HK.3 (FLip), and XBB.2.3, as well as the most recent BA.2.86, have been identified and aroused global concern. Understanding the efficacy of current vaccines and the immune systems response to these emerging variants is critical for global public health. In this study, we evaluated the neutralization activities of sera from participants who received COVID-19 inactivated vaccines, or a booster vaccination of the recently approved tetravalent protein vaccine in China (SCTV01E), or had contracted a breakthrough infection with BA.5/BF.7/XBB virus. Comparative analysis of their neutralization profiles against a broad panel of 30 SARS-CoV-2 sub-lineage viruses revealed that strains such as BQ.1.1, CH.1.1, and all the XBB sub-lineages exhibited heightened resistance to neutralization than previous variants, however, despite the extra mutations carried by emerging XBB sub-lineages and BA.2.86, they did not demonstrate significantly increased resistance to neutralization compared to XBB.1.5. Encouragingly, the SCTV01E booster vaccination consistently induced robust and considerably higher neutralizing titers against all these variants than breakthrough infection did. Cellular immunity assays also showed that the SCTV01E booster vaccination elicited a higher frequency of virus-specific memory B cells but not IFN-{gamma} secreting T cells. Our findings underline the importance of developing novel multivalent vaccines to more effectively combat future viral variants.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Xun Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Shujun Jiang", + "author_inst": "Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine" + }, + { + "author_name": "Wentai Ma", + "author_inst": "Beijing Institute of Genomics" + }, + { + "author_name": "Xiangnan Li", + "author_inst": "Fudan University" + }, + { + "author_name": "Kaifeng Wei", + "author_inst": "Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine" + }, + { + "author_name": "Faren Xie", + "author_inst": "Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine" + }, + { + "author_name": "Chaoyue Zhao", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaoyu Zhao", + "author_inst": "Fudan University" + }, + { + "author_name": "Chen Li", + "author_inst": "Fudan University" + }, + { + "author_name": "Rui Qiao", + "author_inst": "Fudan university" + }, + { + "author_name": "Yuchen Cui", + "author_inst": "Fudan University" + }, + { + "author_name": "Yanjia Chen", + "author_inst": "Fudan University" + }, + { + "author_name": "Jiayan Li", + "author_inst": "Fudan University" + }, + { + "author_name": "Guonan Cai", + "author_inst": "Fudan University" + }, + { + "author_name": "Changyi Liu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zixin Hu", + "author_inst": "Fudan University" + }, + { + "author_name": "Wenhong Zhang", + "author_inst": "Huashan Hospital, Fudan University" + }, + { + "author_name": "Mingkun Li", + "author_inst": "Beijing Institute of Genomics" + }, + { + "author_name": "Yanliang Zhang", + "author_inst": "Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine" + }, + { + "author_name": "Pengfei Wang", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.15.557899", "rel_title": "The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes", @@ -53070,69 +54495,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2023.09.13.23295521", - "rel_title": "Factors associated with teenage pregnancies during the Covid-19 period in Pakwach district, Northern Uganda: a case-control study", - "rel_date": "2023-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.13.23295521", - "rel_abs": "BackgroundTeenage pregnancy rates have globally decreased over the years, but remain high, especially in low- and middle-income countries (LMICs). Among girls aged 15-19, teenage pregnancy remains the leading cause of death and a significant barrier to education and productivity. Its prevalence underscores concern about the sexual and reproductive health of youth. However, limited data exist regarding factors contributing to its rise during the COVID-19 pandemic in Uganda. This study explores the factors associated with teenage pregnancy in Pakwach district during this period.\n\nMethodsWe conducted a matched case-control study, enrolling 362 teenage girls aged 10-19 years, divided into two groups: 181 pregnant teenagers and 181 not pregnant teenagers. We collected exposure data from both groups using questionnaires to evaluate factors associated with teenage pregnancy. The study period covered March 2020 to January 2021, coinciding with lockdown measures.\n\nResultsDuring the COVID-19 lockdown, teenage pregnancies were only associated with having exclusively female peers (AOR 3.0, 95% CI: 0.1-104.4). Conversely, having a Radio/TV at home (AOR 0.2, 95% CI: 0.1-0.6), age at first sexual encounter (AOR 0.1, 95% CI: 0.03-0.9), considering teenage pregnancy as sexual abuse (AOR 0.1, 95% CI: 0.02-0.4), feeling comfortable asking questions during consultations (AOR 0.5, 95% CI: 0.2-1.3), and ensuring sufficient privacy during consultations were protective against teenage pregnancy.\n\nConclusionThe factors contributing to increased teenage pregnancies during the COVID-19 pandemic were consistent with long-standing contextual factors associated with teenage pregnancy. The lockdown environment may have slightly exacerbated these factors, but no direct association was observed. Only having female peers was linked to teenage pregnancy during the lockdown. Conversely, having access to a radio/TV at home and other healthcare system-related factors offered protection. Therefore, interventions should prioritize providing comprehensive information on the risks of teenage pregnancy during any lockdown scenario.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jimmy Patrick Alunyo", - "author_inst": "Busitema University" - }, - { - "author_name": "David Mukunya", - "author_inst": "Busitema University" - }, - { - "author_name": "Agnes Napyo", - "author_inst": "Busitema University" - }, - { - "author_name": "Joseph KB Matovu", - "author_inst": "Busitema University" - }, - { - "author_name": "David Okia", - "author_inst": "Busitema University" - }, - { - "author_name": "Benon Wanume", - "author_inst": "Busitema University" - }, - { - "author_name": "Francis Okello", - "author_inst": "Busitema University" - }, - { - "author_name": "Ally Hassan Tuwa", - "author_inst": "Busitema University" - }, - { - "author_name": "Daniel Wenani", - "author_inst": "Busitema University" - }, - { - "author_name": "Ambrose Okibure", - "author_inst": "Makerere University College of Health Sciences" - }, - { - "author_name": "Godfrey Omara", - "author_inst": "Busitema University" - }, - { - "author_name": "Peter Olupot Olupot", - "author_inst": "Busitema University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2023.09.14.23295542", "rel_title": "How COVID-19 continues to affect contraception in Scotland: a retrospective analysis of Scottish prescribing data between 2016 and 2023.", @@ -53903,6 +55265,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.09.11.557219", + "rel_title": "Dual inhibition of coronavirus Mpro and PLpro enzymes by phenothiazines and their antiviral activity", + "rel_date": "2023-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.11.557219", + "rel_abs": "Coronavirus (CoV) replication requires efficient cleavage of viral polyproteins into an array of non-structural proteins involved in viral replication, organelle formation, viral RNA synthesis, and host shutoff. Human CoVs (HCoVs) encode two viral cysteine proteases, main protease (Mpro) and papain-like protease (PLpro), that mediate polyprotein cleavage. Using a structure-guided approach, a phenothiazine urea derivative that inhibits both SARS-CoV-2 Mpro and PLpro protease activity in vitro was identified. In silico docking studies also predicted binding of the phenothiazine to the active sites of Mpro and PLpro from distantly related alphacoronavirus, HCoV-229E (229E) and the betacoronavirus, HCoV-OC43 (OC43). The lead phenothiazine urea derivative displayed broad antiviral activity against all three HCoVs tested in cell culture infection models. It was further demonstrated that the compound inhibited 229E and OC43 at an early stage of viral replication, with diminished formation of viral replication organelles and the RNAs that are made within them, as expected following viral protease inhibition. These observations suggest that the phenothiazine urea derivative inhibits viral replication and may broadly inhibit proteases of diverse coronaviruses.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/557219v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@fa2c92org.highwire.dtl.DTLVardef@844484org.highwire.dtl.DTLVardef@1ae5d5aorg.highwire.dtl.DTLVardef@730133_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICoronavirus cysteine proteases Mpro and PLpro are targets for novel antiviral agents\nC_LIO_LIPhenothiazine ureas inhibit SARS-CoV-2 Mpro and PLpro protease activity\nC_LIO_LISome phenothiazine ureas inhibit replication of diverse coronaviruses with minimal cytotoxicity\nC_LIO_LIPhenothiazine ureas inhibit early stages of coronavirus replication consistent with failure of viral polyprotein cleavage\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Katrina L. Forrestall", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Eric S. Pringle", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Dane Sands", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Brett Duguay", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Brett Farewell", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Tekeleselassie Woldemariam", + "author_inst": "Vaccine and Infectious Disease Organization" + }, + { + "author_name": "Darryl Falzarano", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Ian R. Pottie", + "author_inst": "Mount Saint Vincent University" + }, + { + "author_name": "Craig McCormick", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Sultan Darvesh", + "author_inst": "Dalhousie University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.09.11.557190", "rel_title": "Compartmentalized SARS-CoV-2 replication in upper versus lower respiratory tract after intranasal inoculation or aerosol exposure", @@ -54532,85 +55949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2023.09.12.23295354", - "rel_title": "Childhood maltreatment and subsequent risk of hospitalization or death due to COVID-19: a cohort study in the UK Biobank", - "rel_date": "2023-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295354", - "rel_abs": "Childhood maltreatment has been associated with some infection-related outcomes, yet its potential role in severe COVID-19 outcomes has not been addressed. Therefore, leveraging longitudinal data from the population-based UK Biobank (N=151,427), our study aimed to explore the association between childhood maltreatment and severe COVID-19 outcomes (i.e., hospitalization or death due to COVID-19) and its underlying mechanisms. Our results suggest that childhood maltreatment, particularly physical neglect, is associated with a 54.0% increased risk of severe COVID-19 outcomes (i.e., hospitalization or death due to COVID-19), which was not modified by genetic predisposition to severe COVID-19 outcomes. We found that 50.9% of this association was mediated by suboptimal socioeconomic status, lifestyle and prepandemic somatic diseases or psychiatric disorders. These findings highlight the role of early life adversities in severe health consequences across the lifespan and call for increased clinical surveillance of people exposed to childhood maltreatment in COVID-19 outbreaks and future pandemics.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Yue Wang", - "author_inst": "University of Iceland" - }, - { - "author_name": "Fenfen Ge", - "author_inst": "University of Iceland" - }, - { - "author_name": "Thor Aspelund", - "author_inst": "University of Iceland" - }, - { - "author_name": "Helga Ask", - "author_inst": "University of Oslo" - }, - { - "author_name": "Arna Hauksdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Kejia Hu", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Johanna Jakobsdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Helga Zoega", - "author_inst": "University of Iceland" - }, - { - "author_name": "Qing Shen", - "author_inst": "Tongji University" - }, - { - "author_name": "Heather C Whalley", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Ole Birger Vesterager Pedersen", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Kelli Lehto", - "author_inst": "University of Tartu" - }, - { - "author_name": "Ole A Andreassen", - "author_inst": "University of Oslo" - }, - { - "author_name": "Fang Fang", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Huan Song", - "author_inst": "Sichuan University" - }, - { - "author_name": "Unnur A Valdimarsdottir", - "author_inst": "University of Iceland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.09.11.23295259", "rel_title": "Finding Long-COVID: Temporal Topic Modeling of Electronic Health Records from the N3C and RECOVER Programs", @@ -55821,6 +57159,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.09.08.23295136", + "rel_title": "Pre-dominance of dengue non-cross-reacting SARS-CoV-2 spike antibodies during the Omicron era and their role in the ADE-mediated surge of Dengue virus serotype 3", + "rel_date": "2023-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.08.23295136", + "rel_abs": "In India, the SARS-CoV-2 Delta wave (2020-21) gradually faded away with the advent of the Omicron variants (2021-present). Dengue incidences were observably less in Southeast Asia during the active years of the pandemic (2020-21). However, Dengue virus type 3 (DV3) cases were increasingly reported in India and many other dengue-endemic countries concurrent with the progression of the Omicron wave since 2022. This observation prompted us to investigate the current state of cross-reactivity between prevalent SARS-CoV-2 variants and different DV serotypes.\n\nFifty-five COVID-19 serum samples (collected between January-September, 2022) and three pre-pandemic healthy serum samples were tested for DV or SARS-CoV-2 Immunoglobulin G/Immunoglobulin M (IgG/IgM) using the lateral flow immunoassays (LFIAs). The SARS-CoV-2 antibody (Ab)-positive samples were further tested for their ability to cross-neutralize DV types 1-4 (DV1-4) in Huh7 cell lines.\n\nCross-reactivity between SARS-CoV-2 and DV diminished with the shift from Delta to Omicron prevalence. COVID-19 serum samples that were DV cross-reactive neutralized all DV serotypes, including DV3. However, Omicron wave serum samples were predominantly DV non-cross-reactive (about 70%) in LFIAs and coincided with the prevalence of BA.2 Omicron variant. They also cross-neutralized DV1, 2 and 4 but enhanced DV3 infectivity as evident from increased DV3 titres in virus neutralization test (VNT) compared to control serum samples.\n\nIn conclusion, DV non-cross-reactive COVID-19 serum samples are becoming increasingly prominent in the present times. These non-cross-reactive serums could neutralize DV1, 2 and 4 but they are contributing to the surge in DV3 cases worldwide by means of ADE.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Supratim Sarker", + "author_inst": "CSIR-Indian Institute of Chemical Biology, West Bengal, India" + }, + { + "author_name": "Chiroshri Dutta", + "author_inst": "CSIR-Indian Institute of Chemical Biology, West Bengal, India" + }, + { + "author_name": "Abinash Mallick", + "author_inst": "CSIR-Indian Institute of Chemical Biology, West Bengal, India" + }, + { + "author_name": "Sayantan Das", + "author_inst": "CSIR-Indian Institute of Chemical Biology, West Bengal, India" + }, + { + "author_name": "Chandrika Das Chowdhury", + "author_inst": "CSIR-Indian Institute of Chemical Biology, West Bengal, India" + }, + { + "author_name": "Abhishek De", + "author_inst": "Department of Dermatology, Calcutta National Medical College and Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Surajit Gorai", + "author_inst": "Department of Dermatology, Apollo Multispeciality Hospital, Kolkata, West Bengal, India." + }, + { + "author_name": "Subhajit Biswas", + "author_inst": "CSIR-Indian Institute of Chemical Biology; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.08.23295267", "rel_title": "Prevalence and predictors of self-medication for COVID-19 among slum dwellers in Jinja City, Uganda", @@ -56666,77 +58051,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.09.07.23295194", - "rel_title": "Effect of the 2022 COVID-19 booster vaccination campaign in 50 year olds in England: regression discontinuity analysis in OpenSAFELY", - "rel_date": "2023-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.07.23295194", - "rel_abs": "BackgroundSARS-CoV-2 vaccines are highly effective in preventing severe COVID-19 but require boosting to maintain protection. Changes to circulating variants and prevalent natural immunity may impact on real-world effectiveness of boosters in different time periods and in different populations.\n\nMethodsWith NHS England approval, we used linked routine clinical data from >24 million patients to evaluate the effectiveness of the 2022 combined COVID-19 autumn booster and influenza vaccine campaign in non-clinically vulnerable 50-year-olds in England using a regression discontinuity design. Our primary outcome was a composite of 6-week COVID-19 emergency attendance, COVID-19 unplanned hospitalisation, or death. The secondary outcomes were: respiratory hospitalisations or death; any unplanned hospitalisation; and any death.\n\nResultsOur study included 1,917,375 people aged 45-54 years with no evidence of being in a high-risk group prioritised for vaccination. By 26 November 2022, booster vaccine coverage was 11.1% at age 49.75 years increasing to 39.7% at age 50.25 years. The estimated effect of the campaign on the risk of the primary outcome in 50-year-olds during weeks 7-12 after the campaign start was -0.4 per 100,000 (95% CI -7.8, 7.1). For the secondary outcomes the estimated effects were: -0.6 per 100,000 (95%CI -13.5, 12.3) for respiratory outcomes; 5.0 per 100,000 (95%CI -40.7, 50.8) for unplanned hospitalisations; and 3.0 per 100,000 (95%CI -2.7, 8.6) for any death. The results were similar when using different follow-up start dates, different bandwidths, or when estimating the effect of vaccination (rather than the campaign).\n\nConclusionThis study found little evidence that the autumn 2022 vaccination campaign in England was associated with a reduction in severe COVID-19-related outcomes among non-clinically vulnerable 50-year-olds. Possible explanations include the low risk of severe outcomes due to substantial pre-existing vaccine- and infection-induced immunity. Modest booster coverage reduced the precision with which we could estimate effectiveness. The booster campaign may have had effects beyond those estimated, including reducing virus transmission and incidence of mild or moderate COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Andrea L Schaffer", - "author_inst": "University of Oxford" - }, - { - "author_name": "William J Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elsie M F Horne", - "author_inst": "University of Bristol" - }, - { - "author_name": "Edward P K Parker", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Venexia Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "Catherine Stables", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sebastian C J Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "" - }, - { - "author_name": "Miguel A Hern\u00e1n", - "author_inst": "Harvard University" - }, - { - "author_name": "Johnathan A C Sterne", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.06.23295138", "rel_title": "Quantity of SARS-CoV-2 RNA copies exhaled per minute during natural breathing over the course of COVID-19 infection", @@ -57807,6 +59121,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.09.05.23295025", + "rel_title": "Bivalent mRNA vaccine effectiveness against COVID-19 infections, hospitalisations and deaths in Portugal: a cohort study based on electronic health records, September 2022 to May 2023", + "rel_date": "2023-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.05.23295025", + "rel_abs": "In Portugal, a bivalent COVID-19 vaccine booster was recommended for those with complete primary COVID-19 vaccination, starting on September 6 2022. This study aims to estimate the mRNA bivalent vaccine effectiveness (VE) against COVID-19 infection, hospitalisation and death in the Portuguese population aged 65 and more years with a follow-up of more than six months.\n\nMethodsWe used a cohort approach to analyse six electronic health registries using deterministic linkage. The follow-up period comprehend September 2022 to May 2023. The outcomes included SARS-CoV-2 infection, COVID-19-related hospitalisation and death. Individuals were considered vaccinated 14 days following a bivalent mRNA COVID-19 vaccine uptake. For each outcome, COVID-19 bivalent VE was estimated as one minus the confounder adjusted hazard ratio of bivalent vaccine vs no bivalent vaccine, estimated by Cox regression with time-dependent vaccine exposure.\n\nResultsIn the [≥] 80 year-olds, bivalent VE was 23.2 (95%CI: 20.1 to 26.2), 41.3 (95%CI: 34.5 to 47.5) and 50.3 (44.6 to 55.3), against infection, COVID-19-related hospitalisation and death, respectively. In the 65-79 year-old, bivalent VE against infection was 37.7 (35.5 to 39.8), 58.5 (95%CI: 51.9 to 64.2) against hospitalisation and 65.1 (95%CI: 59 to 70.4) against death. Vaccine effectiveness decay was observed for both age groups and in all outcomes, up to 6 months of vaccine uptake.\n\nConclusionsIn a population with a high risk of SARS-CoV-2 complications, we observed moderate bivalent VE estimates against severe COVID-19 and low protection against infection. The lower VE estimates observed in the [≥] 80 year-olds should be interpreted in light of the reference group used for the estimation, i.e., individuals with high vaccine coverage (both primary series and multiple boosters). Significant VE decay was observed up to six months of vaccine uptake, which should be considered when preparing future vaccination campaigns.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ausenda Machado", + "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Irina Kislaya", + "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Patricia Soares", + "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Sarah Magalhaes", + "author_inst": "Servicos Partilhados do Ministerio da Saude, Lisbon, Portugal" + }, + { + "author_name": "Ana Paula Rodrigues", + "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Rafael Franco", + "author_inst": "Servicos Partilhados do Ministerio da Saude, Lisbon, Portugal" + }, + { + "author_name": "Pedro Pinto Leite", + "author_inst": "Direcao de Servicos de Informacao e Analise, Direcao-Geral da Saude, Lisbon, Portugal" + }, + { + "author_name": "Carlos Matias Dias", + "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Baltazar Nunes", + "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge, Lisbon, Portugal" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.08.30.23294845", "rel_title": "A Literature Review and Meta-Analysis of the Effects of Lockdowns on COVID-19 Mortality - II", @@ -58344,61 +59709,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.01.23293209", - "rel_title": "A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory", - "rel_date": "2023-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.01.23293209", - "rel_abs": "BackgroundTimely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic surveillance response playbook for the early detection and surveillance of emerging SARS-CoV-2 variants.\n\nMethodsThe playbook outlines modifications to sampling strategies, laboratory workflows, and communication processes based on the emerging variants predicted viral characteristics, observed public health impact in other jurisdictions and local community risk level. The playbook outlines procedures for implementing and reporting enhanced and accelerated genomic surveillance, including supplementing whole genome sequencing (WGS) with variant screening by quantitative PCR (qPCR).\n\nResultsThe ability of the playbook to improve the response to an emerging variant was tested for SARS-CoV-2 Omicron BA.1. Increased submission of clinical remnant samples from local hospital laboratories enabled detection of a new variant at 1% prevalence with 95% confidence rather than 2% at baseline. Genotyping qPCR concurred with WGS lineage assignments in 99.9% of 1541 samples with results by both methods, and was more sensitive, providing lineage results in 90.4% of 1833 samples rather than 85.1% for WGS, while reducing the time to lineage result from 27 to 7 days.\n\nConclusionsThe genomic surveillance response playbook provides a structured, stepwise, and data-driven approach to responding to emerging SARS-CoV-2 variants. These pre-defined processes can streamline workflows and expedite the detection and public health response to emerging variants. Based on the processes piloted during the Omicron BA.1 response, this method has been applied to subsequent Omicron subvariants and can be readily applied to future SARS-CoV-2 emerging variants and other public health surveillance activities.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Hannah J Barbian", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Alyse Kittner", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Richard Teran", - "author_inst": "Chicago Department of Public Health" - }, - { - "author_name": "Sofiya Bobrovska", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Xueting Qiu", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Kayla English", - "author_inst": "Chicago Department of Public Health" - }, - { - "author_name": "Stefan J Green", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Isaac Ghinai", - "author_inst": "Chicago Department of Public Health" - }, - { - "author_name": "Massimo Pacilli", - "author_inst": "Chicago Department of Public Health" - }, - { - "author_name": "Mary K Hayden", - "author_inst": "Rush University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.08.31.23294891", "rel_title": "Application of MALDI-MS and Machine Learning to Detection of SARS-CoV-2 and non-SARS-CoV-2 Respiratory Infections.", @@ -59517,6 +60827,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.29.23294791", + "rel_title": "How will COVID-19 persist in the future? Simulating future dynamics of COVID-19 using an agent-based network model", + "rel_date": "2023-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.29.23294791", + "rel_abs": "Despite the United States Center for Disease Control (CDC)s May 2023 expiration of the declared public health emergency pertaining to the COVID-19 pandemic (Silk 2023), approximately 3 years after the first cases of SARS-CoV-2 appeared in the United Sates, thousands of new cases persist daily. Many questions persist about the future dynamics of SARS-CoV-2s in the United States, including: will COVID continue to circulate as a seasonal disease like influenza, and will annual vaccinations be required to prevent outbreaks? In response, we present an Agent Based Networked Simulation of COVID-19 transmission to evaluate recurrent future outbreaks of the disease, accounting for contact heterogeneity and waning vaccine-derived and natural immunity. Our model is parameterized with data collected as part of the Berkeley Interpersonal Contact Survey (BICS; Feehan and Mahmud 2021) and is used to simulate time series of confirmed cases of and deaths due to SARS-CoV-2, paying special attention to seasonal forces and waning immunity (Kronfeld-Schor et al. 2021; X. Liu et al. 2021; Nichols et al. 2021). From the BICS ABM model we simulate SARS-CoV-2 dynamics over the 10-year period beginning in 2021 with waning immunity and inclusion of annual booster doses under a variety of transmission scenarios. We find that SARS-CoV-2 outbreaks are likely to occur frequently, and that distribution of booster doses during certain times of the year--notably in the late winter/early spring--may reduce the severity of a wintertime outbreak depending on the seasonal epidemiology of the pathogen.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ethan Roubenoff", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.30.555506", "rel_title": "Explainable machine learning for the identification of proteome states via the data processing kitchen sink", @@ -60294,97 +61623,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2023.08.29.555437", - "rel_title": "Molecular Property Diagnostic Suite for COVID-19 (MPDSCOVID-19): An open access disease specific drug discovery portal", - "rel_date": "2023-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.29.555437", - "rel_abs": "Computational drug discovery is intrinsically interdisciplinary and has to deal with the multifarious factors which are often dependent on the type of disease. Molecular Property Diagnostic Suite (MPDS) is a Galaxy based web portal which was conceived and developed as a disease specific web portal, originally developed for tuberculosis (MPDSTB). As specific computational tools are often required for a given disease, developing a disease specific web portal is highly desirable. This paper emphasises on the development of the customised web portal for COVID-19 infection and is referred to as MPDSCOVID-19. Expectedly, the MPDS suites of programs have modules which are essentially independent of a given disease, whereas some modules are specific to a particular disease. In the MPDSCOVID-19 portal, there are modules which are specific to COVID-19, and these are clubbed in SARS-COV-2 disease library. Further, the new additions and/or significant improvements were made to the disease independent modules, besides the addition of tools from galaxy toolshed. This manuscript provides a latest update on the disease independent modules of MPDS after almost 6 years, as well as provide the contemporary information and tool-shed necessary to engage in the drug discovery research of COVID-19. The disease independent modules include file format converter and descriptor calculation under the data processing module; QSAR, pharmacophore, scaffold analysis, active site analysis, docking, screening, drug repurposing tool, virtual screening, visualisation, sequence alignment, phylogenetic analysis under the data analysis module; and various machine learning packages, algorithms and in-house developed machine learning antiviral prediction model are available. The MPDS suite of programs are expected to bring a paradigm shift in computational drug discovery, especially in the academic community, guided through a transparent and open innovation approach. The MPDSCOVID-19 can be accessed at http://mpds.neist.res.in:8085.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "G. Narahari Sastry", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Lipsa Priyadarsinee", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Esther Jamir", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Selvaraman Nagamani", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Hridoy Jyoti Mahanta", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Nandan Kumar", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Lijo John", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Himakshi Sarma", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Asheesh Kumar", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "Anamika Singh Gaur", - "author_inst": "CSIR Indian Institute of Toxicology Research" - }, - { - "author_name": "Rosaleen Sahoo", - "author_inst": "CSIR National Chemical Laboratory" - }, - { - "author_name": "S Vaikundamani", - "author_inst": "CSIR North East Institute of Science and Technology" - }, - { - "author_name": "N Arul Murugan", - "author_inst": "IIIT Delhi" - }, - { - "author_name": "U Deva Priyakumar", - "author_inst": "IIIT Hyderabad" - }, - { - "author_name": "Gajendra P.S. Raghava", - "author_inst": "Indraprastha Institute of Information Technology" - }, - { - "author_name": "PV Bharatam", - "author_inst": "NIPER Mohali" - }, - { - "author_name": "Parthasarathi Ramakrishnan", - "author_inst": "CSIR Indian Institute of Toxicology Research" - }, - { - "author_name": "V Subramanian", - "author_inst": "IIT Madras" - }, - { - "author_name": "G Madhavi Sastry", - "author_inst": "Schrodinger Inc Hyderabad" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.08.29.555356", "rel_title": "Robust acidic pH and digestive enzyme stability of anti-SarsCov2 IgY antibodies: Implications for treatment of viral transmission thru gastrointestinal, ocular, nasal and skin tissues", @@ -61539,6 +62777,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.08.26.23294658", + "rel_title": "Limited impact of lifting universal masks on SARS-COV-2 transmission in schools: The crucial role of outcome measurements", + "rel_date": "2023-08-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.26.23294658", + "rel_abs": "As the pandemics dynamics changed, many municipalities lifted face wearing requirement in school which was initially implemented to mitigate the transmission of COVID-19. This study examines the effects of lifting mask mandates on COVID-19 transmission within Massachusetts school districts. We first replicated previous research by Cowger et al. (2022) utilizing a Difference-in-Difference (DID) model. Then, we back project the case infection and calculate the Rt value to redo the DID analysis. However, when shifting the outcome measurement to the reproductive number (Rt), our findings suggest that lifting mask mandates can only significantly influence the Rt first two weeks post-intervention. This implies that while mask mandate plays a role in mitigation, its lifting does not drastically influence COVID-19 transmissibility in the long term.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mingwei Li", + "author_inst": "The University of Hong Kong; Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park" + }, + { + "author_name": "Bingyi Yang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Benjamin J Cowling", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.28.23294549", "rel_title": "Environmental surveillance for SARS-CoV-2 for outbreak detection in hospital: A single centre prospective study", @@ -62148,53 +63413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2023.08.25.23294609", - "rel_title": "Risk factors for SARS-Cov-2 infection at a United Kingdom electricity-generating company: a test-negative design case-control study", - "rel_date": "2023-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.25.23294609", - "rel_abs": "ObjectivesIdentify workplace risk factors for SARS-Cov-2 infection, using data collected by a United Kingdom electricity-generating company.\n\nMethodsUsing a test-negative design case-control study we estimated the odds ratios (OR) of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage, and site COVID-19 weekly risk rating, adjusting for age, test date and test type.\n\nResultsFrom an original 80,077 COVID-19 tests, there were 70,646 included in the final analysis. Most exclusions were due to being visitor tests (5,030) or tests after an individual first tested positive (2,968).\n\nWomen were less likely to test positive than men (OR=0.71; 95% confidence interval=0.58-0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area it was a strong confounder for other variables. Compared to routine tests, tests due to symptoms were highest risk (94.99; 78.29-115.24), followed by close contact (16.73; 13.80-20.29) and broader-defined work contact 2.66 (1.99-3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model.\n\nConclusionsIn general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIIn the United Kingdom, there is now a considerable body of evidence showing occupational differences in Covid-19 infection and severity, but with understandable focus on high-risk industries like healthcare.\nC_LIO_LILess is known about differences in risk of COVID-19 infection in other industries that do not involve directly working with the general public, in particular, there is relatively little evidence on the risks of transmission in the electricity-generating industry.\nC_LI\n\nWhat this study addsO_LIAt this company, infection risk was not associated with job category after adjusting for test reason; however women were less likely to test positive than men and the risk was higher when there was a power outage, requiring more staff to visit the site in person.\nC_LI\n\nHow this study might affect research, practice or policyO_LIThe site risk rating showed a consistent (but modest) dose-response with infection risk, indicating that such risk rating may be useful for identifying \"high risk\" sites.\nC_LIO_LIThis analysis demonstrates the importance of adjusting for both date of and reason for test, when prevalence and testing protocols differ over time.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Charlotte E Rutter", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Martie J Van Tongeren", - "author_inst": "University of Manchester" - }, - { - "author_name": "Tony Fletcher", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sarah E Rhodes", - "author_inst": "University of Manchester" - }, - { - "author_name": "Yiqun Chen", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Ian Hall", - "author_inst": "University of Manchester" - }, - { - "author_name": "Nicholas Warren", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2023.08.24.23294503", "rel_title": "Protection conferred by COVID-19 vaccination, prior SARS-CoV-2 infection, or hybrid immunity against Omicron-associated severe outcomes among community-dwelling adults", @@ -63129,6 +64347,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2023.08.23.23294470", + "rel_title": "Risk Factors for Post-Traumatic Stress Disorder (PTSD) in COVID Survivors A Cross-Sectional Study", + "rel_date": "2023-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.23.23294470", + "rel_abs": "The study aimed to investigate the impact of demographic, socio-economic, health, and lifestyle variables on the development of PTSD symptoms in COVID survivors. The study used a cross-sectional design, and data were collected via a standard set of questionnaires from 228 COVID survivors, who required oxygen support and were admitted to Damak COVID hospital from April to October 2021.\n\nDescriptive statistics such as frequency and percentage were used to summarize the data and inferential statistics such as chi-square test, Fishers exact test, and Binary logistic regression were used to analyze the data and to infer the overall result from the taken sample. The study found that only three variables, i.e., gender, diabetes, and chronic obstructive pulmonary disorder (COPD), were significant factors that posed a higher threat of PTSD in COVID survivors. Additionally, the study uses model adequacy tests such as Pseudo R2 test, Reliability test and Hosmer and Lemeshow test to validate the model fitted.\n\nThe study found that only three variables had significant impact PTSD symptoms in COVID survivors. Male patients were more likely to have PTSD symptoms than female patients. The presence of diabetes before or after the infection increased the risk of PTSD. The patients with high blood pressure before COVID and those who developed chronic obstructive pulmonary disorder (COPD) after COVID were more likely to experience PTSD symptoms. The study provides valuable information on the risk factors for developing PTSD symptoms in COVID survivors. This study can contribute to the understanding and growing body of research on the psychological impact of COVID and help healthcare professionals identify patients who are at risk of developing PTSD and provide them with appropriate interventions to prevent or treat PTSD.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Surakshaya Dhakal", + "author_inst": "Tribhuvan University" + }, + { + "author_name": "Ram Prasad Khatiwada", + "author_inst": "Tribhuvan University Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.08.23.23294474", "rel_title": "COVID-19 self-testing: Countries accelerating policies ahead of WHO guidelines during pandemics: A Global Survey.", @@ -63850,33 +65091,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2023.08.21.554193", - "rel_title": "Ensemble-Based Modeling of the SARS-CoV-2 Omicron BA.1 and BA.2 Spike Trimers and Systematic Characterization of Cryptic Binding Pockets in Distinct Functional States : Emergence of Conformation-Sensitive and Variant-Specific Allosteric Binding Sites", - "rel_date": "2023-08-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.21.554193", - "rel_abs": "A significant body of experimental structures of the SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and emergence of druggable cryptic pockets. Understanding of the interplay of conformational dynamics changes induced by Omicron variants and identification of cryptic dynamic binding pockets in the S protein are of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study we explore conformational landscapes and characterize the universe of cryptic binding pockets in multiple open and closed functional spike states of the Omicron BA.1 and BA.2 variants. By using a combination of atomistic simulations, dynamics network analysis, and allostery-guided network screening of cryptic pockets in the conformational ensembles of BA.1 and BA.2 spike conformations, we identified all experimentally known allosteric sites and discovered significant variant-specific differences in the distribution of cryptic binding sites in the BA.1 and BA.2 trimers. This study provided in-depth structural analysis of the predicted allosteric site in the context of all available experimental information, revealing a critical role and effect of conformational plasticity on the distribution and function of allosteric binding sites. The results detailed how mutational and conformational changes in the BA.1 and BA.2 pike trimers can modulate the functional role of druggable allosteric pockets across different functional regions of the spike protein. The results of this study are particularly significant for understanding the universe of cryptic bindings sites and variant-specific preferences for druggable pockets. Exploring predicted druggable sites can present a new and previously underappreciated opportunity for therapeutic intervention of Omicron variants through conformation-selective and variant-specific targeting of functional sites involved in allosteric changes.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Mohammed Alshahrani", - "author_inst": "Chapman University" - }, - { - "author_name": "Grace Gupta", - "author_inst": "Chapman University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.08.22.554362", "rel_title": "Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects", @@ -64859,6 +66073,77 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.08.19.23294311", + "rel_title": "Seroepidemiology of COVID-19 in pregnant women and their infants in Uganda and Malawi across multiple waves 2020-2022", + "rel_date": "2023-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.19.23294311", + "rel_abs": "Data on SARS-CoV-2 infection in pregnancy and infancy has accumulated throughout the course of the pandemic. However, limited information is available from countries in sub-Saharan Africa (SSA). Evidence regarding asymptomatic SARS-CoV-2 infection and adverse birth outcomes are also scarce in these countries. The pregnant woman and infant COVID in Africa study (PeriCOVID Africa) is a South-South-North partnership involving hospitals and health centres in five countries: Malawi, Uganda, Mozambique, The Gambia, and Kenya. The study leveraged data from three ongoing prospective cohort studies: Preparing for Group B Streptococcal Vaccines (GBS PREPARE), SARS-CoV-2 infection and COVID-19 in women and their infants in Kampala and Mukono (COMAC) and Pregnancy Care Integrating Translational Science Everywhere (PRECISE). In this paper we describe the seroepidemiology of SARS-CoV-2 infection in pregnant women enrolled in sites in Uganda and Malawi, and the impact of SARS-CoV-2 infection on pregnancy and infant outcomes.\n\nThe PeriCOVID study is a prospective mother-infant cohort study that recruited pregnant women at any gestation antenatally or on the day of delivery. A nasopharyngeal swab was taken from mothers at enrolment for RT-PCR confirmation of SARS-CoV-2 infection, and maternal and cord blood samples were tested for SARS-CoV-2 antibodies using Wantai and Euroimmune ELISA. The primary outcome was seroprevalence of SARS-CoV-2 antibodies in maternal blood, reported as the proportion of seropositive women by study site and wave of COVID-19 within each country. Placental transfer of antibodies was described using the geometric mean ratio (GMR). We also estimated the proportion of asymptomatic or subclinical COVID-19 infections in pregnant women using serological testing and collected adverse pregnancy and infancy outcomes (e.g. still-birth, prematurity, maternal or infant death).\n\nIn total, 1379 women were enrolled, giving birth to 1387 infants. Overall, 63% of pregnant women had a SARS-CoV-2 positive serology. Over subsequent waves (delta and omicron), in the absence of vaccination, seropositivity rose from 20% to over 80%. The placental transfer GMR was 1.7, indicating active placental transfer of anti-spike IgG. There was no association between SARS-CoV-2 antibody positivity and adverse pregnancy or infancy outcomes. This study describes the increasing prevalence of SARS CoV-2 antibodies in pregnant woman in Uganda and Malawi across waves of SARS-CoV-2 infection. Our study adds to existing evidence that suggests under-reporting of infection if based solely on cases with clinical disease, or a positive RT-PCR for SARS-CoV-2, as most of the women in our study had asymptomatic infections and did not seek medical care. This has implications for screening in subsequent outbreaks and pandemics where protection of pregnant women and effect of infection in pregnancy on the infant are unknown.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Lauren Hookham", + "author_inst": "St George's University of London" + }, + { + "author_name": "Liberty Cantrell", + "author_inst": "University of Oxford" + }, + { + "author_name": "Stephen Cose", + "author_inst": "London School of Hygiene & Tropical Medicine Centre of Global Change and Health: London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Bridget Freyne", + "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme" + }, + { + "author_name": "Luis Gadama", + "author_inst": "Kamuzu University of Health Sciences: University of Malawi College of Medicine" + }, + { + "author_name": "Esther Imede", + "author_inst": "MRC/UVRI Uganda Research Unit On AIDS: MRC/UVRI and LSHTM Uganda Research Unit" + }, + { + "author_name": "Kondwani Kawaza", + "author_inst": "Kamuzu University of Health Sciences: University of Malawi College of Medicine" + }, + { + "author_name": "Sam Lissauer", + "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme" + }, + { + "author_name": "Phillipa Musoke", + "author_inst": "Makerere University" + }, + { + "author_name": "Victoria Nankabirwa", + "author_inst": "Makerere University" + }, + { + "author_name": "Musa Sekikubo", + "author_inst": "Makerere University" + }, + { + "author_name": "Halvor Sommerfelt", + "author_inst": "University of Bergen: Universitetet i Bergen" + }, + { + "author_name": "Merryn Voysey", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kirsty Le Doare", + "author_inst": "St George's University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.18.23293746", "rel_title": "Emergence of neutralizing antibodies associates with clearance of SARS-CoV-2 during HIV-mediated immunosuppression", @@ -65436,45 +66721,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.16.553557", - "rel_title": "Molecular evolution and adaptation of SARS-CoV-2 omicron XBB sub-lineage Spike protein under African selection pressure.", - "rel_date": "2023-08-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.16.553557", - "rel_abs": "The SARS-CoV-2 Omicron variant of concern (VOC) has multiple mutations in the spike (S) protein, which mediates viral infection and immunity. We analysed a sub-lineage of Omicron, designated XBB, that showed structural and functional changes in the S protein in response to the African selection pressures. We used molecular modelling to compare the S protein structures of Omicron and XBB and found that XBB had a reduced receptor-binding domain (RBD) due to the loss of some {beta}-sheets, which may increase its affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. We also used Fast Unconstrained Bayesian AppRoximation (FUBAR) and Recombination Detection Program 4 (RDP 4) to perform selection and recombination analysis of the S protein sequences of Omicron and XBB and detected signals of positive selection and recombination in the N-terminal domain (NTD) of the S1 subunit, which contains antibody-binding epitopes, and the RBD, which is involved in viral entry. Our results reveal the structural and functional adaptation of the Omicron XBB variant in Africa and its potential implications for viral pathogenesis and immunity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Milton Simbarashe Kambarami Sr.", - "author_inst": "Department of Molecular Diagnostics and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe" - }, - { - "author_name": "Godwins Ngorima", - "author_inst": "National Pathology Research and Diagnostic Centre, Midlands State University" - }, - { - "author_name": "Praise Khulani Moyo", - "author_inst": "Department of Applied Biosciences and Biotechnology, Faculty of Science and Technology, Midlands State University" - }, - { - "author_name": "Lucy Mabaya", - "author_inst": "National Pathology Research and Diagnostic Centre, Midlands State University" - }, - { - "author_name": "Tawanda Mushiri", - "author_inst": "Department of Biomedical Informatics and Biomedical Engineering, Faculty of Medicine and Health Sciences, University of Zimbabwe" - }, - { - "author_name": "Justen Manasa", - "author_inst": "Department of Molecular Diagnostics and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.08.16.553581", "rel_title": "Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein", @@ -66505,6 +67751,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.10.23293942", + "rel_title": "A Susceptible Vaccinated Exposed Infected Hospitalised and Removed/Recovered (SVEIHR) Model Framework for COVID-19", + "rel_date": "2023-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.10.23293942", + "rel_abs": "In reaction to the severe socio-economic effects and upheavals that the Covid-19 sickness had on the world within the first few weeks of its introduction, everyone involved had to act quickly to look for possible solutions for preventing the ensuing epidemics. A prompt response is more critical given Nigerias subpar social, economic, and healthcare infrastructure. Investigated was the efficacy of various pharmacological, non-pharmaceutical, or a combination of both therapies in flattening the Covid-19 incidence curve. In order to investigate the impact of these interventions, a deterministic SVEIHR model was created and applied. The Nigerian Center for Disease Control (NCDC) portals Covid-19 data were used to parametrize the model. For simulations using a system dynamic simulation, estimated parameters were employed. The fundamental reproduction number, R0, was used to evaluate the success of our suggested intervention in effectively managing COVID-19 transmission. The simulation results demonstrated that the use of only non-pharmaceutical interventions, such as the use of face masks, a light lockdown, and hand washing at baseline or high levels, is insufficient, with the R0 varying from vaccination at the vaccination rate of 0.5% with non-pharmaceutical interventions at any level of compliance, and a combination of vaccination at 0.05% and high hygiene level were effective in flattening the Covid-19 disease incidence curve in Nigeria, returning a R0 less than 0. Furthermore, maintaining a high level of cleanliness, which includes hand washing and the use of a face mask, would be sufficient to stop the spread of Covid-19 disease and eventually flatten Covid-19 disease incidence curve in Nigeria, given a low turnout of 0.05% for vaccination and the easing of lockdown.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Oluwafemi S Oyamakin", + "author_inst": "University of Ibadan" + }, + { + "author_name": "John I Popoola", + "author_inst": "University of Ibadan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.10.23293869", "rel_title": "A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA", @@ -67010,49 +68279,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2023.08.11.552998", - "rel_title": "Impact of age and sex on neuroinflammation following SARS-CoV-2 infection in a murine model", - "rel_date": "2023-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.11.552998", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent for the worldwide COVID-19 pandemic, is known to infect people of all ages and both sexes. Senior populations have the greatest risk of severe disease, and sexual dimorphism in clinical outcomes has been reported in COVID-19. SARS-CoV-2 infection in humans can cause damage to multiple organ systems, including the brain. Neurological symptoms are widely observed in patients with COVID-19, with many survivors suffering from persistent neurological and cognitive impairment, potentially accelerating Alzheimers disease. The present study aims to investigate the impact of age and sex on the neuroinflammatory response to SARS-CoV-2 infection using a mouse model. Wild-type C57BL/6 mice were inoculated, by intranasal route, with SARS-CoV-2 lineage B.1.351 variant known to infect mice. Older animals and in particular males exhibited a significantly greater weight loss starting at 4 dpi. In addition, male animals exhibited higher viral RNA loads and higher titers of infectious virus in the lung, which was particularly evident in males at 16 months of age. Notably, no viral RNA was detected in the brains of infected mice, regardless of age or sex. Nevertheless, expression of IL-6, TNF-, and CCL-2 in the lung and brain was increased with viral infection. An unbiased brain RNA-seq/transcriptomic analysis showed that SARS-CoV-2 infection caused significant changes in gene expression profiles in the brain, with innate immunity, defense response to virus, cerebravascular and neuronal functions, as the major molecular networks affected. The data presented in this study show that SARS-CoV-2 infection triggers a neuroinflammatory response despite the lack of detectable virus in the brain. Age and sex have a modifying effect on this pathogenic process. Aberrant activation of innate immune response, disruption of blood-brain barrier and endothelial cell integrity, and supression of neuronal activity and axonogenesis underlie the impact of SARS-CoV-2 infection on the brain. Understanding the role of these affected pathways in SARS-CoV-2 pathogenesis helps identify appropriate points of therapeutic interventions to alleviate neurological dysfunction observed during COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Venkatramana D Krishna", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Allison Chang", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Holly Korthas", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Susanna R Var", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Walter C Low", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ling Li", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Maxim C-J. Cheeran", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.13.553148", "rel_title": "SARS-CoV-2 Neutralizing Antibodies Following a Second BA.5 Bivalent Booster", @@ -67843,6 +69069,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.07.23293747", + "rel_title": "Young Healthcare Workers' Employment Status and Mental Distress over SARS-CoV-2 in Bolivia", + "rel_date": "2023-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293747", + "rel_abs": "BackgroundHealthcare workers (HCW) have been particularly affected by the SARS-CoV-2 pandemic as it influenced employment conditions and unemployment/insecure employment. Their deterioration is associated with mental distress.\n\nObjectiveThe aim of the study was to assess the trajectory of mental distress among HCW graduates during the COVID-19 pandemic in relation to their employment status.\n\nMethodsWe compared the change in mental distress over time among recent HCW graduates who were formally employed, to those who were unemployed/insecurely employed during the pandemic. In 2018 and 2022, we prospectively surveyed HCW who were in their final year of study in 2018 in Bolivia. Information was collected on socio-demographic characteristics, employment status, and mental distress. Mental distress was assessed using the 12-item General Health Questionnaire. Generalized Estimating Equations were implemented to examine changes in mental distress over time and the role of employment status in this development. Of the 663 HCW at baseline, 116 could be followed up.\n\nFindingsOver the course of the pandemic, formal employment after graduation did not change the odds of mental distress (odds ratio (OR)=0.93 [95% confidence interval (CI) 0.13-6.83]). In contrast, unemployment/insecure employment statistically significantly increased the odds of mental distress (OR=2.10 [CI 1.05-4.24]) over time.\n\nConclusionsEspecially in countries with limited social support for unemployed/insecurely employed citizens, interventions and policies to prevent mental distress among newly graduated HCW are important. This is particularly relevant in the face of crises such as the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Lea John", + "author_inst": "Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich" + }, + { + "author_name": "Katja Radon", + "author_inst": "Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich" + }, + { + "author_name": "Mira Muehlhaeusser", + "author_inst": "Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich" + }, + { + "author_name": "Maria Teresa Solis-Soto", + "author_inst": "OH TARGET Competence Center, Universidad San Francisco Xavier de Chuquisaca, Calle Junin esq. Estudiantes" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.05.23293566", "rel_title": "SARS-CoV-2 Pandemic Non-Pharmacologic Interventions Temporally Associated with Reduced Pediatric Infections Due to Mycoplasma pneumoniae and Co-Infecting Respiratory Viruses in Arkansas", @@ -68452,41 +69709,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.08.03.23293619", - "rel_title": "Infant and Neonatal Mortality During the Covid-19 Pandemic: An Interrupted Time Series Analysis From Five Low- and Middle-Income Countries", - "rel_date": "2023-08-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.03.23293619", - "rel_abs": "BackgroundThe Covid-19 pandemic led to widespread changes to health and social institutions. The effects of the pandemic on neonatal and infant health outcomes in low- and middle-income countries (LMICs) are poorly understood, and nationally representative data characterizing changes to health care and outcomes is only now emerging.\n\nMethodsWe used nationally representative survey data with vital status and perinatal care information on 2,959,203 children born in India, Madagascar, Cambodia, Nepal, and the Philippines. Using interrupted time series models, we estimated the change in neonatal mortality (death in first 30 days of life) and infant mortality (death in first year of life) following the start of the Covid-19 pandemic, controlling for granular location fixed-effects and seasonality.\n\nFindingsWe analyzed 2,935,052 births (146,820 deaths) before March 2020 and 24,151 births (799 deaths) after March 2020. We estimated that infant mortality increased by 9.9 deaths per 1,000 live births after March 2020 (95% CI 5.0, 15.0; p<0.01; 22% increase) and neonatal mortality increased by 6.7 deaths per 1,000 live births (95% CI 2.4, 11.1; p<0.01; 27% increase). We observe increased mortality in all study countries. We also estimated a 3.8 percentage point reduction in antenatal care use (95% CI -4.9, -2.7; p<0.01) and a 5.6 percentage point reduction in facility deliveries (95% CI -7.2, -4.0; p<0.01) during the pandemic.\n\nInterpretationSince the start of the Covid-19 pandemic, neonatal and infant mortality are higher than expected in five LMICs. Helping LMICs resume pre-pandemic declines in neonatal and infant mortality should be a major global priority.\n\nFundingNational Institute of Child Health and Development (R01HD104835 PI Wagner)\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe impact of the Covid-19 pandemic on infant and neonatal mortality in low- and middle-income countries (LMICs) is not well-understood. We searched PubMed using the terms \"COVID\" AND ((\"child\" OR \"infant\" OR \"neonatal\") AND \"mortality\")) AND (\"low- and middle-income countries\" OR \"developing countries\") on May 10, 2023, without language restrictions. The existing evidence is mixed. Increased mortality rates have been documented in Ghana, Nigeria, Uganda, and Nepal while decreased rates documented in South Africa and Guinea. Prior analyses were mainly based on clinic and hospital administrative data and were often confined to a selection of facilities or geographic areas, hampering the generalizability of the existing evidence. We found no published article that leveraged nationally representative data sources to provide a general assessment of infant or neonatal mortality in LMICs following the start of the Covid-19 pandemic.\n\nAdded value of this studyTo our knowledge, this study provides the most comprehensive and generalizable investigation of the impact of the Covid-19 pandemic on infant and neonatal mortality in LMICs to date. Using nationally representative survey data from five LMICs that were recently released, we estimated an increase of 9.9 and 6.7 deaths per 1,000 live births in infant and neonatal mortality, respectively, during the Covid-19 pandemic. We also found significant reductions in antenatal care use and facility deliveries, which could partly explain the changes in mortality we document.\n\nImplications of the available evidenceOur study highlights significant increases in infant and neonatal mortality rates in five LMICs following the start of the Covid-19 pandemic, which sets back about a decades worth of progress. The decline in antenatal care services and facility births documented in our study suggests mortality increases were partly driven by disruptions in health service access induced by Covid-19 control measures. Helping to get reductions in neonatal and infant mortality back on track in LMICs should be a major global priority.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zachary Wagner", - "author_inst": "RAND Corporation" - }, - { - "author_name": "Sam Heft-Neal", - "author_inst": "Stanford University" - }, - { - "author_name": "Zetianyu Wang", - "author_inst": "Pardee RAND Graduate School" - }, - { - "author_name": "Renzhi Jing", - "author_inst": "Stanford University" - }, - { - "author_name": "Eran Bendavid", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.08.04.23293551", "rel_title": "Genetic Variant rs1205 is Associated with COVID-19 Outcomes: The Strong Heart Study and Strong Heart Family Study.", @@ -69405,6 +70627,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.03.23293586", + "rel_title": "COVID-19 among migrants, refugees, and internally displaced persons: systematic review, meta-analysis and qualitative synthesis of the global empirical literature", + "rel_date": "2023-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.03.23293586", + "rel_abs": "BackgroundPandemic response and preparedness plans aim at mitigating the spread of infectious diseases and protecting public health, but migrants are often side-lined. Evidence amounted early that migrants are disproportionately affected by the COVID-19 pandemic and its consequences. However, synthesised evidence is lacking that quantifies the inequalities in infection risk and disease outcomes, or contextualises the consequences of pandemic measures and their underlying mechanisms.\n\nMethodsSystematic review searching 25 databases and grey literature (12/2019 to 11/2021). We considered empirical articles covering migrants, refugees, asylum-seekers, and internally displaced persons reporting SARS-CoV-2 cases, hospitalisation, ICU admission, mortality, COVID-19 vaccination rates or health consequences of pandemic measures. Random-effects meta-analysis of observational studies and qualitative analysis were performed for evidence synthesis. A Protocol was registered with PROSPERO (CRD42021296952).\n\nFindingsOut of 6956 studies, we included 241 in the review. For the quantitative studies (n=46), meta-analysis with over 40 million study participants showed that compared to non-migrants, migrants have an elevated risk of infection (RR = 2{middle dot}33; 95%-CI: 1{middle dot}88-2{middle dot}89) but similar risk for hospitalisation (RR = 1{middle dot}05; 0{middle dot}80-1{middle dot}37), while the likelihood of ICU admission was higher (RR = 1{middle dot}36; 1{middle dot}04-1{middle dot}78). Among those hospitalised, migrants had a lower risk of mortality (RR = 0{middle dot}47; 0{middle dot}30-0{middle dot}73), while their population-based excess mortality tended to be higher (RR = 1{middle dot}31; 0{middle dot}95-1{middle dot}80). The qualitative synthesis (n=44) highlighted the complex interplay of social and COVID-19-related factors at different levels. This involved increased exposure, risk, and impact of pandemic measures that compromised the health of migrants.\n\nInterpretationEven in the advanced stages of the pandemic, migrants faced higher infection risks and disproportionately suffered from the consequences of COVID-19 disease, including deaths. Population-level interventions in future health emergencies must better consider socio-economic, structural and community-level exposures to mitigate risks among migrants and enhance health information systems, to close coverage gaps in migrant groups.\n\nFundingNone.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Maren Hintermeier", + "author_inst": "University Hospital Heidelberg; Bielefeld School of Public Health, Germany" + }, + { + "author_name": "Nora Dalia Gottlieb", + "author_inst": "Bielefeld School of Public Health, Germany" + }, + { + "author_name": "Sven Rohleder", + "author_inst": "Bielefeld School of Public Health; University Hospital Heidelberg, Germany" + }, + { + "author_name": "Jan Oppenberg", + "author_inst": "Bielefeld School of Public Health, Germany" + }, + { + "author_name": "Mazen Baroudi", + "author_inst": "Umea University, Sweden" + }, + { + "author_name": "Sweetmavourneen Pernitez-Agan", + "author_inst": "International Organization for Migration, Manila, Philippines" + }, + { + "author_name": "Janice Lopez", + "author_inst": "International Organisation for Migration, Manila, Philippines" + }, + { + "author_name": "Sergio Flores", + "author_inst": "Uppsala University, Sweden" + }, + { + "author_name": "Amir Mohsen Mohsenpour", + "author_inst": "Bielefeld School of Public Health, Germany" + }, + { + "author_name": "Kolitha Wickramage", + "author_inst": "UN Migration Agency Global Data Institute, Migration Health Division, International Organization for Migration, Berlin, Germany" + }, + { + "author_name": "Kayvan Bozorgmehr", + "author_inst": "Bielefeld School of Public Health; University Hospital Heidelberg, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.08.01.23293449", "rel_title": "Impact of Adjustment for Differential Testing by Age and Sex on Apparent Epidemiology of SARS-CoV-2 Infection in Ontario, Canada", @@ -70038,33 +71319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.03.551813", - "rel_title": "Single-linkage molecular clustering of viral pathogens", - "rel_date": "2023-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.03.551813", - "rel_abs": "IntroductionPublic health faces the ongoing mission of safeguarding the populations health against various infectious diseases caused by a great number of pathogens. Epidemiology is an essential discipline in this field. With the rise of more advanced technologies, new tools are emerging to enhance the capability to intervene and control an epidemic. Among these approaches, molecular clustering comes forth as a promising option. However, appropriate genetic distance thresholds for defining clusters are poorly explored in contexts outside of Human Immunodeficiency Virus-1 (HIV-1).\n\nMethodsIn this work, using the well-used pairwise Tamura-Nei 93 (TN93) distance threshold of 0.015 for HIV-1 as a point of reference for molecular cluster properties of interest, we perform molecular clustering on whole genome sequence datasets from HIV-1, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Zaire ebolavirus, and Mpox virus, to explore potential pairwise distances thresholds for these other viruses.\n\nResultsWe found the following pairwise TN93 distance thresholds as potential candidates for use in molecular clustering: 0.00016 (3 mutations) for Ebola, 0.00014 (4 mutations) for SARS-CoV-2, and 0.0000051 (1 mutation) for Mpox.\n\nConclusionThis study provides valuable information for epidemic control strategies, and public health efforts in managing infectious diseases caused by these viruses. The identified pairwise distance thresholds for molecular clustering can serve as a foundation for future research and intervention to combat epidemics effectively.\n\nAvailability and implementationAll relevant data and results can be found in the following repository: https://github.com/Niema-Lab/ENLACE-2023", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maryelba Soto Miranda", - "author_inst": "Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Ramiro Narv\u00e1ez Romo", - "author_inst": "Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Niema Moshiri", - "author_inst": "Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.08.03.551784", "rel_title": "Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny", @@ -70995,6 +72249,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2023.08.01.23293491", + "rel_title": "Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study", + "rel_date": "2023-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.01.23293491", + "rel_abs": "ObjectivesThe rapid spread of SARS-CoV-2 infection caused high levels of hospitalisation and deaths in late 2020 and early 2021 during the second wave in England. Severe disease during this period was associated with marked health inequalities across ethnic and sociodemographic subgroups. In this paper, we aimed to investigate how inequalities influence the risk of getting infected across ethnic and sociodemographic subgroups during a key period before widespread vaccination.\n\nDesignRepeated cross-sectional community-based study.\n\nMethodsWe analysed risk factors for test-positivity for SARS-CoV-2, based on self-administered throat and nose swabs in the community during rounds 5 to 10 of the REal-time Assessment of Community Transmission-1 (REACT-1) study between 18 September 2020 and 30 March 2021.\n\nResultsCompared to white ethnicity, people of Asian and black ethnicity had a higher risk of infection during rounds 5 to 10, with odds of 1.46 (1.27, 1.69) and 1.35 (1.11, 1.64) respectively. Among ethnic subgroups, the highest and the second-highest odds were found in Bangladeshi and Pakistan participants at 3.29 (2.23, 4.86) and 2.15 (1.73, 2.68) respectively when compared to British whites. People in larger (compared to smaller) households had higher odds of infection. Health care workers with direct patient contact and care home workers showed higher odds of infection compared to other essential/key workers. Additionally, the odds of infection among participants in public-facing activities or settings were greater than among those not working in those activities or settings.\n\nConclusionOur findings highlight the differences in the risk of SARS-CoV-2 infection in a global-north population during a period when the risk of infection was high, and there were substantial levels of social mixing. Planning for future severe waves of respiratory pathogens should include policies to reduce inequality in the risk of infection by ethnicity, household size, and occupational activity in order to reduce inequality in disease.\n\nSummary boxWhat is already known on this topic\n\nExtensive studies have described the relationship between socio-demographic factors and SARS-CoV-2 outcomes such as hospitalisations and deaths, rather than SARS-CoV-2 infection. Limited community-based studies investigated risk factors associated with SARS-CoV-2 infection, with the time frame of these studies has mainly focused on the period of the first wave of infection, or the beginning of the second wave, or the rollout of the first dose of the vaccine after the second wave period. We did not find studies that covered the critical period of the second wave in England when levels of social mixing were high, but no vaccine was available.\n\nWhat this study adds\n\nWe show health inequalities across ethnic and sociodemographic subgroups during a key period: before widespread vaccination, but, largely, not during the period of stringent social distancing. We observed substantial ethnic and occupational differences in the risk of SARS-CoV-2 infection. Minority ethnic groups, including those of Bangladeshi and Pakistani ethnicity, had an excess risk of infection compared with the British white population. Healthcare workers, care home workers and people who work in public-facing activities or settings were associated with higher odds of infection. The risk of SARS-CoV-2 infection increased monotonically as household size increased, and more deprived neighbourhood areas were associated with a higher risk of infection.\n\nHow this study might affect research, practice or policy\n\nOur findings highlight the differences in the risk of SARS-CoV-2 infection in a global-north population during a period when the risk of infection was high, and there were substantial levels of social mixing. Planning for future waves of severe respiratory infection should explicitly aim to reduce inequalities in infection in order to reduce inequality in disease.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Oliver Eales", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "David Haw", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Christina Atchinson", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Claudio Fronterre", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Peter J. Diggle", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Steven Riley", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.07.27.23293244", "rel_title": "Prevalence of long-term symptoms varies by using different post-COVID-19 definitions in positively and negatively tested adults: the PRIME post-COVID study", @@ -71752,77 +73085,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2023.07.31.551223", - "rel_title": "Immunities Specific to Both of the M Protein Ectodomain and RBD Synergize to Confer Cross-protection against SARS-CoV-2 Infections", - "rel_date": "2023-07-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.31.551223", - "rel_abs": "The effectiveness of the prototypic SARS-CoV-2 vaccine largely decreased overtime against the emerging virus strains, necessitating the universal vaccine development. The most abundant structural membrane (M) protein is highly conserved in amino acid sequence, which arouses our research interests in developing a universal immunogen based on it. Serological analysis showed that IgG responses specific to its N-terminal peptides can be strongly detected in many serum samples from both convalescent patients and vaccinees receiving inactivated vaccines, indicating the potential existence of human B-cell epitopes in reactive peptides. Microneutralization assays showed that the N-terminal peptide S2M2-30-specific hyperimmune serum was capable of cross-neutralizing the authentic viruses including wild-type HKU-001a, B.1.617.2/Delta, and Omicron subvariant BQ.1.1, and synergized with RBD-specific serum in reinforcing antiviral activities. Strong S2M2-30-specific immunities elicited in hACE2-transgenic mice could effectively inhibit B.1.1.7/Alpha (UK) infections. Our results suggest the potentiality of conserved M peptides as vaccine targets for conferring cross-protections against sarbecoviruses.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Yibo Tang", - "author_inst": "Hunan University" - }, - { - "author_name": "Kaiming Tang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yunqi Hu", - "author_inst": "Sun Yat-Sen University" - }, - { - "author_name": "Zi-Wei Ye", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Wanyu Luo", - "author_inst": "Sun Yat-Sen University" - }, - { - "author_name": "Cuiting Luo", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hehe Cao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ran Wang", - "author_inst": "Capital Medical University" - }, - { - "author_name": "Dejian Liu", - "author_inst": "Hunan University" - }, - { - "author_name": "Cuicui Liu", - "author_inst": "Hunan University" - }, - { - "author_name": "Xingyi Ge", - "author_inst": "Hunan University" - }, - { - "author_name": "Yaoqing Chen", - "author_inst": "Sun Yat-Sen University" - }, - { - "author_name": "Shuofeng Yuan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lei Deng", - "author_inst": "Hunan University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.07.30.23293233", "rel_title": "QJHong Model for Novel Coronavirus Disease 2019 (COVID-19) in the United States", @@ -73005,6 +74267,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.07.26.550660", + "rel_title": "Interaction of SCoV-2 NSP7 or NSP8 alone may cause constriction of the RNA entry channel in NSP12: Implications for novel RdRp inhibitor drug discovery", + "rel_date": "2023-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.26.550660", + "rel_abs": "RNA-dependent RNA polymerase (RdRP) is a critical component of the RNA virus life cycle, including SCoV-2. Among the Coronavirus-encoded proteins, non-structural protein 12 (NSP12) exhibits polymerase activity in collaboration with one unit of NSP7 and two units of NSP8, constituting the RdRp holoenzyme. While there is abundant information on SCoV-2 RdRp-mediated RNA replication, the influence of interplay among NSP12, NSP7, and NSP8 on template RNA binding and primer extension activity remains relatively unexplored and poorly understood. Here, we recreated a functional RdRp holoenzyme in vitro using recombinant SCoV-2 NSP12, NSP7, and NSP8, and established its functional activity. Subsequently, molecular interactions among the NSPs in the presence of a variety of templates and their effects on polymerase activity were studied, wherein we found that NSP12 alone exhibited notable polymerase activity that increased significantly in the presence of NSP7 and NSP8. However, this activity was completely shut down, and the template RNA-primer complex was detached from NSP12 when one of the two cofactors was present. Through computational analysis, we found that the template RNA entry channel was more constricted in the presence of one of the two cofactors, which was relatively more constricted in the presence of NSP8 compared to that in the presence of NSP7. In conclusion, we report that NSP7 and NSP8 together synergise to enhance the activity of NSP12, but antagonise when present alone. Our findings have implications for novel drug development, and compounds that obstruct the binding of NSP7 or NSP8 to NSP12 can have lethal effects on viral RNA replication.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Deepa Singh", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India" + }, + { + "author_name": "Tushar Kushwaha", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India." + }, + { + "author_name": "Rajkumar Kulandaisamy", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India" + }, + { + "author_name": "Vikas Kumar", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India" + }, + { + "author_name": "Kamal Baswal", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India." + }, + { + "author_name": "Saras H Tiwari", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India." + }, + { + "author_name": "Arkadyuti Ghorai", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India." + }, + { + "author_name": "Manoj Kumar", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India." + }, + { + "author_name": "Saroj Kumar", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India" + }, + { + "author_name": "Aparoy Polamarasetty", + "author_inst": "Faculty of Biology, Indian Institute of Petroleum & Energy, Visakhapatnam, Andhra Pradesh, India." + }, + { + "author_name": "Deepak Sehgal", + "author_inst": "Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India." + }, + { + "author_name": "Madhumohan R Katika", + "author_inst": "ESIC Medical College and Hospital, Sanath Nagar, Hyderabad, Telangana, India." + }, + { + "author_name": "Suresh Gadde", + "author_inst": "Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada." + }, + { + "author_name": "Marceline C\u00f4t\u00e9", + "author_inst": "Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada" + }, + { + "author_name": "Sarala R Kayampeta", + "author_inst": "R & D Division, Srikara Biologicals Private Limited, Tirupati, Andhra Pradesh, India." + }, + { + "author_name": "Mohan B Appaiahgari", + "author_inst": "R & D Division, Srikara Biologicals Private Limited, Tirupati, Andhra Pradesh, India." + }, + { + "author_name": "Krishna K Inampudi", + "author_inst": "Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.07.24.23293101", "rel_title": "WEIRD or not: A Cross-Cultural Behavioral Economic Assessment of Demand for HIV and COVID-19 Vaccines", @@ -73621,7 +74966,7 @@ "rel_date": "2023-07-26", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.21.23292785", - "rel_abs": "In early 2020, the Coronavirus Disease 19 (COVID-19) rapidly spread across the United States, exhibiting significant geographic variability. While several studies have examined the predictive relationships of differing factors on COVID-19 deaths, few have looked at spatiotemporal variation at refined geographic scales. The objective of this analysis is to examine spatiotemporal variation of COVID-19 deaths in association with socioeconomic, health, demographic, and political factors, using regionalized multivariate regression as well as nationwide county-level geographically weighted random forest (GWRF) models. Analyses were performed on data from three sepearate timeframes: pandemic onset until May 2021, May 2021 through November 2021, and December 2021 until April 2022.Regionalized regression results across three time windows suggest that existing measures of social vulnerability for disaster preparedness (SVI) are associated with a higher degree of mortality from COVID-19. In comparison, GWRF models provide a more robust evaluation of feature importance and prediction, exposing the importance of local features, such as obesity, which is obscured by regional delineation. Overall, GWRF results indicate a more nuanced modeling strategy is useful for capturing the diverse spatial and temporal nature of the COVID-19 pandemic.", + "rel_abs": "In early 2020, the Coronavirus Disease 19 (COVID-19) rapidly spread across the United States (US), exhibiting significant geographic variability. While several studies have examined the predictive relationships of differing factors on COVID-19 deaths, few have looked at spatiotemporal variation at refined geographic scales. The objective of this analysis is to examine this spatiotemporal variation in COVID-19 deaths with respect to association with socioeconomic, health, demographic, and political factors. We use multivariate regression applied to Health and Human Services (HHS) regions as well as nationwide county-level geographically weighted random forest (GWRF) models. Analyses were performed on data from three separate time frames which correspond to the spread of distinct viral variants in the US: pandemic onset until May 2021, May 2021 through November 2021, and December 2021 until April 2022. Multivariate regression results for all regions across three time windows suggest that existing measures of social vulnerability for disaster preparedness (SVI) are predictive of a higher degree of mortality from COVID-19. In comparison, GWRF models provide a more robust evaluation of feature importance and prediction, exposing the value of local features for prediction, such as obesity, which is obscured by coarse-grained analysis. Overall, GWRF results indicate that this more nuanced modeling strategy is useful for determining the spatial variation in the importance of sociodemographic risk factors for predicting COVID-19 mortality.", "rel_num_authors": 4, "rel_authors": [ { @@ -73646,45 +74991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.07.20.23292901", - "rel_title": "The impact of COVID-19 on community-dwelling people post-stroke and informal caregivers: a qualitative study", - "rel_date": "2023-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.20.23292901", - "rel_abs": "Background/ aimsLittle is known about the experience of people post-stroke and their informal caregivers during the COVID-19 pandemic. The aim of this study was to understand the challenges faced by people post-stroke and informal caregivers during the pandemic, as well as the impact on their healthcare support, lifestyle, and self-care behaviors.\n\nMethodsA multi-perspective qualitative study was undertaken, with semi-structured interviews being carried out to sixteen participants: eight stroke patients and eight informal caregivers, mostly performed online. Reflexive thematic analysis was used, with data being independently coded and categorized before consolidated into themes and subthemes.\n\nFindingsThree themes were derived from the data analysis: i) Perceived impact of COVID-19 pandemic, ii) What helped? - strategies to manage the distress provoked by COVID-19, and iii) The value of rehabilitation and physical activity, with findings highlighting the negative psychological impact of the pandemic. In response to the perceived lack of support and access to health and social services, participants highlighted the use of digital approaches and professional support.\n\nConclusionsFindings suggest the importance of self-management support and/or digital content in order to mitigate the impact of COVID-19. The involvement of peers, family members, friends or others seems to be an important strategy to increase motivation in remote rehabilitation and physical activity.\n\nKey points- Due to the impact of COVID-19 on people post-stroke and informal caregivers daily routines, both highlighted the importance of finding new and alternative ways of communicating, which included the use of digital approaches.\n- For some informal caregivers the pandemic was perceived as an opportunity to spend more time with the family and with the person with stroke.\n- People post-stroke admit having decreased their levels of physical activity during COVID-19 and increased the value given to rehabilitation and physical activity.\n- Involving peers or others, digitally or in-person, seems to be an important strategy when planning physical activity recommendations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Teresa Dias", - "author_inst": "School of Health at Polytechnic Institute of Setubal, Portugal" - }, - { - "author_name": "Patricia Cravo", - "author_inst": "School of Health at Polytechnic Institute of Setubal, Portugal" - }, - { - "author_name": "Joana Santos", - "author_inst": "School of Health at Polytechnic Institute of Setubal, Portugal" - }, - { - "author_name": "Catarina Gomes", - "author_inst": "School of Health at Polytechnic Institute of Setubal, Portugal" - }, - { - "author_name": "Marta Assis Santiago", - "author_inst": "School of Health at Polytechnic Institute of Setubal, Portugal" - }, - { - "author_name": "Carla Mendes Pereira", - "author_inst": "School of Health at Polytechnic Institute of Setubal, Portugal" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2023.07.20.23292883", "rel_title": "Impact of COVID-19 on recorded blood pressure screening and hypertension management in England: An analysis of monthly changes in Quality and Outcomes Framework indicators in OpenSAFELY", @@ -74647,6 +75953,49 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2023.07.24.550324", + "rel_title": "Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS-CoV-2", + "rel_date": "2023-07-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.24.550324", + "rel_abs": "SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex consisting of nsp12, nsp7, and nsp8 as the key enzyme for viral genome replication and is a proven antiviral drug target. In this study, molecular interactions of nsp7 and nsp8 with nsp12 and the active site of nsp12 were coterminously targeted using in-silico screening of small molecule libraries to identify potential antivirals. Surface plasmon resonance (SPR) based assay using purified nsp7 and nsp8 proteins was developed, and the binding of identified molecules to targets was validated. The antiviral efficacy of identified small molecules was evaluated using cell-based assays, and potent antiviral effect with EC50 values of 0.56 M, 0.73 M, and 2.8 M was demonstrated by fangchinoline, cepharanthine, and sennoside B, respectively. Further in vivo, investigation using hACE2 mice is being conducted. This is the first study that targets multiple sites in the RdRp complex of SARS-CoV-2 using a structure-based molecular repurposing approach and suggests potential therapeutic options for emerging variants of SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ruchi Rani", + "author_inst": "Indian Institute of Technology, Roorkee, Uttarakhand, India" + }, + { + "author_name": "Sanketkumar Nehul", + "author_inst": "Indian Institute of Technology, Roorkee, Uttarakhand, India" + }, + { + "author_name": "Shweta Choudhary", + "author_inst": "Indian Institute of Technology, Roorkee, Uttarakhand, India" + }, + { + "author_name": "Anushka Upadhyay", + "author_inst": "Indian Institute of Technology, Roorkee, Uttarakhand, India" + }, + { + "author_name": "Gaurav Kumar Sharma", + "author_inst": "ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India" + }, + { + "author_name": "Pravindra Kumar", + "author_inst": "Indian Institute of Technology, Roorkee, Uttarakhand, India" + }, + { + "author_name": "Shailly Tomar", + "author_inst": "Indian Institute of Technology Roorkee, Uttarakhand, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.07.24.550379", "rel_title": "The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 on Intracellular Trafficking, Autophagy, and Apoptosis", @@ -75188,45 +76537,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.07.19.23292841", - "rel_title": "Admissions for eating disorders and other mental health diagnoses during the COVID-19 pandemic", - "rel_date": "2023-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292841", - "rel_abs": "ObjectiveTo examine how hospital admissions for mental health and eating disorders changed at the beginning of the COVID-19 pandemic and with the return to fully in-person school with increased vaccine availability.\n\nMethodsData from a tertiary care childrens hospital were examined for admissions to the hospital from March 2018 through March 2022, including children 6-20 years old admitted with ICD-10 codes for mental health and eating disorders. Interrupted time series (ITS) analyses were used to examine for changes at specific time points.\n\nResultsIn the time between March 2018 through March 2022, 851 admissions met inclusion criteria for eating disorders and 1,505 admissions for other mental health diagnoses. In the first year of the pandemic, the ITS analysis showed a significant increase in admissions per month for eating disorders with a slope of 1.2 (95% CI: 0.2, 2.2) and for other mental health diagnoses, a slope of 1.9 (95% CI: 1.1, 2.7). In a longer-term ITS analysis, return to fully in-person school was associated with a subsequent decrease in admissions over time at -1.0 per month (95% CI: - 2.1, 0.1). For other mental health diagnoses, return to school was associated with an initial drop and then an increase in admissions over time, slope of 2.2 (95% CI: -0.5, 3.8).\n\nConclusionThe COVID-19 pandemic had an initial impact on admissions for eating disorders and other mental health that attenuated over time. We note differences in the association of return to school on eating disorders compared with other mental health diagnoses.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sydney C Jones", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Megan Jacobs", - "author_inst": "Department of Pediatrics, Oregon Health and Science University" - }, - { - "author_name": "Emile Latour", - "author_inst": "Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University" - }, - { - "author_name": "Rebecca Marshall", - "author_inst": "Department of Psychiatry, Oregon Health & Science University" - }, - { - "author_name": "Michelle Noelck", - "author_inst": "Department of Pediatrics, Oregon Health & Science University" - }, - { - "author_name": "Byron A Foster", - "author_inst": "Department of Pediatrics, Oregon Health & Science University and OHSU-PSU School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2023.07.17.23292791", "rel_title": "Exploring COVID-19 vaccine uptake among healthcare workers in Zimbabwe: A mixed methods study", @@ -76297,6 +77607,65 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2023.07.16.23292705", + "rel_title": "Community-onset urinary tract infection in females in the context of COVID-19: a longitudinal population cohort study exploring case presentation, management, and outcomes", + "rel_date": "2023-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.16.23292705", + "rel_abs": "BackgroundCOVID-19 affected the epidemiology of other infectious diseases and how they were managed. Urinary tract infection (UTI) is one of the most common infections treated in the community in England. We investigated the impact of the COVID-19 pandemic on UTI primary care consultations and outcomes in female patients.\n\nMethods and findingsWe analysed General Practice (GP) consultation and hospital admission records using the Whole Systems Integrated Care (WSIC) data in North West London between 2016 and 2021. We quantified the changes in UTI GP consultation rates using time series analysis before and during the pandemic. We assessed the outcomes of UTI, measured by subsequent bacteraemia and sepsis within 60 days, for consultations delivered face-to-face or remotely, with or without diagnostic tests recommended by the national guidelines, and with or without antibiotic treatment. Between January 2016 and December 2021, we identified 375,859 UTI episodes in 233,450 female patients. Before the COVID-19 pandemic (January 2016 - February 2020), the UTI GP consultation rate stayed level at 522.8 cases per 100,000 population per month, with a seasonal pattern of peaking in October. Since COVID-19, (March 2020 - December 2021), monthly UTI GP consultations declined when COVID-19 cases surged and rose when COVID-19 case fell. During the pandemic, the UTI consultations delivered face-to-face reduced from 72.0% to 29.4%, the UTI consultations with appropriate diagnostic tests, including urine culture and urinalysis, reduced from 17.3% to 10.4%, and the UTI cases treated with antibiotics reduced from 52.0% to 47.8%. The likelihood of antibiotics being prescribed was not affected by whether the consultation was delivered face-to-face or remotely but associated with whether there was a diagnostic test. Regardless of whether the UTI consultation occurred before or during the pandemic, the absence of antibiotic treatment for UTI is associated with a 10-fold increase in the risk of having bacteraemia or sepsis within 60 days, though the patients who consulted GPs for UTI during the pandemic were older and more co-morbid. Across the study period (January 2016 - December 2021), nitrofurantoin remained the first-line antibiotic option for UTI. The percentage of non-prophylactic acute UTI antibiotic prescriptions with durations that exceeded the guideline recommendations was 58.7% before the pandemic, and 49.4% since. This led to 830,522 total excess days of treatment, account for 63.3% of all non-prophylactic acute antibiotics prescribed for UTI. Before the pandemic, excess antibiotic days of UTI drugs had been reducing consistently. However, this decline slowed down during the pandemic. Having a diagnostic test was associated with 0.6 less excess days of antibiotic treatment.\n\nConclusionsThis analysis provides a comprehensive examination of management and outcomes of community-onset UTI in female patients, considering the changes in GP consultations during the COVID-19 pandemic. Our findings highlighted the importance of appropriate urine testing to support UTI diagnosis in symptomatic patients and initiation of antibiotic treatment with appropriate course duration. Continued monitoring is required to assess the overall impact on patients and health systems from the changed landscape of primary care delivery.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nina J Zhu", + "author_inst": "National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial " + }, + { + "author_name": "Benedict Hayhoe", + "author_inst": "Department of Primary Care and Public Health, School of Public Health, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Raheelah Ahmad", + "author_inst": "Division of Health Services Research and Management, School of Health Sciences, City, University of London, London, United Kingdom" + }, + { + "author_name": "James R Price", + "author_inst": "National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial " + }, + { + "author_name": "Donna Lecky", + "author_inst": "Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom" + }, + { + "author_name": "Monsey McLeod", + "author_inst": "NHS England and NHS Improvement, London, United Kingdom" + }, + { + "author_name": "Elena Ferran", + "author_inst": "Barts Health NHS Trust, London, United Kingdom" + }, + { + "author_name": "Timothy M Rawson", + "author_inst": "National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial " + }, + { + "author_name": "Emma Carter", + "author_inst": "National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial " + }, + { + "author_name": "Alison H Holmes", + "author_inst": "National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial " + }, + { + "author_name": "Paul Aylin", + "author_inst": "Primary Care and Interventions Unit, United Kingdom Health Security Agency (UKHSA), Gloucestershire, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.07.17.23292714", "rel_title": "The impact of frailty on the outcomes of COVID-19 patients with persistent critical illness: A population-based cohort study.", @@ -76774,41 +78143,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.07.16.549184", - "rel_title": "Using big sequencing data to identify chronic SARS-Coronavirus-2 infections", - "rel_date": "2023-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.16.549184", - "rel_abs": "The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants, many of which may have arisen during chronic infections of immunocompromised individuals. Here, we harness a global phylogeny of [~]11.7 million SARS-CoV-2 genomes and search for clades composed of sequences with identical metadata (location, age, and sex) spanning more than 21 days. We postulate that such clades represent repeated sampling from the same chronically infected individual. A set of 271 such chronic-like clades was inferred, and displayed signatures of an elevated rate of adaptive evolution, in line with validated chronic infections. More than 70% of adaptive mutations present in currently circulating variants are found in BA.1 chronic-like clades that predate the circulating variants by months, demonstrating the predictive nature of such clades. We find that in chronic-like clades the probability of observing adaptive mutations is approximately 10-20 higher than that in global transmission chains. We next employ language models to find mutations most predictive of chronic infections and use them to infer hundreds of additional chronic-like clades in the absence of metadata and phylogenetic information. Our proposed approach presents an innovative method for mining extensive sequencing data and providing valuable insights into future evolutionary patterns.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sheri Harari", - "author_inst": "Tel-Aviv University" - }, - { - "author_name": "Danielle Miller", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Shay Fleishon", - "author_inst": "Israeli Health Intelligence Agency, Ministry of Health" - }, - { - "author_name": "David Burstein", - "author_inst": "Tel-Aviv University" - }, - { - "author_name": "Adi Stern", - "author_inst": "Tel-Aviv University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2023.07.15.549135", "rel_title": "Pre-existing interferon gamma conditions the lung to mediate early control of SARS-CoV-2", @@ -77859,6 +79193,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.07.13.23292597", + "rel_title": "Booster dose of self-amplifying SARS-CoV-2 RNA vaccine vs. mRNA vaccine: a phase 3 comparison of ARCT-154 with Comirnaty", + "rel_date": "2023-07-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.13.23292597", + "rel_abs": "BackgroundLicensed mRNA vaccines demonstrated initial effectiveness against COVID-19 but require booster doses to broaden the anti-SARS-CoV-2 response. There is an unmet need for novel highly immunogenic and broadly protective vaccines. We compared immunogenicity and tolerability of ARCT-154, a novel self-amplifying mRNA vaccine with the mRNA vaccine, Comirnaty(R).\n\nMethodsWe compared immune responses to ARCT-154 and Comirnaty booster doses in healthy 18- 77-year-old Japanese adults initially immunised with two doses of mRNA COVID-19 vaccine (Comirnaty or Spikevax(R)) then a third dose of Comirnaty at least 3 months previously. Neutralising antibodies were measured before and 28 days after booster vaccination. The primary objective was to demonstrate non-inferiority of the immune response against Wuhan-Hu-1 SARS-CoV-2 virus as geometric mean titre (GMT) ratios and seroresponse rates (SRR) of neutralising antibodies; key secondary endpoints included the immune response against the Omicron BA.4/5 variant and vaccine tolerability assessed using participant-completed electronic diaries.\n\nFindingsBetween December 13, 2022 and February 25, 2023 we enrolled 828 participants randomised 1:1 to receive ARCT-154 (n = 420) or Comirnaty (n = 408) booster doses. Four weeks after boosting, ARCT-154 induced higher Wuhan-Hu-1 neutralising antibodies GMTs than Comirnaty (5641 [95% CI: 4321, 7363] and 3934 [2993, 5169], respectively), a GMT ratio of 1{middle dot}43 (95% CI: 1{middle dot}26-1{middle dot}63), with SRR of 65{middle dot}2% (60{middle dot}2-69{middle dot}9) and 51{middle dot}6% (46{middle dot}4-56{middle dot}8) meeting the non-inferiority criteria. Respective anti-Omicron BA.4/5 GMTs were 2551 (1687-3859) and 1958 (1281-2993), a GMT ratio of 1{middle dot}30 (95% CI: 1{middle dot}07-1{middle dot}58), with SRR of 69{middle dot}9% (65{middle dot}0-74{middle dot}4) and 58{middle dot}0% (52{middle dot}8-63{middle dot}1), meeting the superiority criteria for ARCT-154 over Comirnaty. Booster doses of either ARCT-154 or Comirnaty were equally well-tolerated with no causally-associated severe or serious adverse events; 94{middle dot}8% and 96{middle dot}8% of ARCT-154 and Comirnaty vaccinees reported local reactions and 65{middle dot}7% and 62{middle dot}5% had solicited systemic adverse events. Events were mainly mild in severity, occurring and resolving within 3-4 days of vaccination.\n\nInterpretationImmune responses four weeks after an ARCT-154 booster dose in mRNA-immunised adults were higher than after a Comirnaty booster, meeting non-inferiority criteria against the prototype Wuhan-Hu-1 virus, and superiority criteria against the Omicron BA.4/5 variant.\n\nFundingThe study was funded by the Japanese Ministry of Health, Labour, and Welfare following a public invitation to bid for an urgent improvement project for vaccine manufacturing systems, fourth invitation, Grant number: 1212-3.\n\nClinical Trials registration and identifierThe study was registered on the Japan Registry for Clinical Trials (jRCT 2071220080).", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yoshiaki Oda", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Yuji Kumagai", + "author_inst": "Kitasato University Kitasato Institute Hospital" + }, + { + "author_name": "Manabu Kanai", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Yasuhiro Iwama", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Iori Okura", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Takeshi Minamida", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Yukihiro Yagi", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Toru Kurosawa", + "author_inst": "Meiji Seika Pharma Co., Ltd." + }, + { + "author_name": "Benjamin Greener", + "author_inst": "Arcturus Therapeutics, Inc., San Diego, CA, USA" + }, + { + "author_name": "Ye Zhang", + "author_inst": "Arcturus Therapeutics, Inc., San Diego, CA, USA" + }, + { + "author_name": "Judd L. Walson", + "author_inst": "Arcturus Therapeutics, Inc., San Diego, CA, USA." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.12.23292576", "rel_title": "Comparative Effectiveness of the Bivalent (Original/Omicron BA.4/BA.5) mRNA COVID-19 Vaccines mRNA-1273.222 and BNT162b2 Bivalent in Adults in the United States", @@ -78368,37 +79761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2023.07.09.23292326", - "rel_title": "Impact of COVID-19 on the cascade of care for tuberculosis: A systematic review", - "rel_date": "2023-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.09.23292326", - "rel_abs": "ObjectivesTo describe the impact of the COVID-19 pandemic on the TB care cascade.\n\nMethodsIn this systematic review, the Cochrane library, Scopus, CINAHL, Ebscohost, and PubMed databases were comprehensively searched from the onset of the pandemic, till May 5th, 2022. Eligible studies were those reporting on changes in the TB cascade of care one year before and one year during the COVID-19 pandemic. Due to the expected differences in the contexts of the included studies, a narrative synthesis was conducted.\n\nResultsTwenty-seven studies, from Asia, North America, Africa, South America, and Europe were included. TB screening decreased by between 1% - 50%, and multidrug resistance tuberculosis (MDR-TB) screening decreased by between 15%-17%. Diagnostic delay increased by between 35 - 45 days, contact tracing decreased by up to 36.1%, and case notification decreased by between 3%-63%. TB treatment enrolment decreased by between 16%-35.0%, treatment completion decreased by around 8.0% and treatment success decreased by up to 17.0%.\n\nConclusionCOVID-19 had a detrimental impact on the TB care cascade and these findings suggest a need for policies to protect healthcare systems for TB and other communicable diseases in future health emergencies.\n\nProtocol registration - PROSPERO: CRD42021272456\n\nEthics approvalThis systematic review used data from published studies and aggregated data, thus, ethics approval was not required.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tomiwa Fapohunda", - "author_inst": "Stellenbosch University, Cape Town, South Africa" - }, - { - "author_name": "Lovemore Mapahla", - "author_inst": "Stellenbosch University - Tygerberg Campus: Stellenbosch University Faculty of Medicine and Health Sciences" - }, - { - "author_name": "Reham Taha", - "author_inst": "Qatar University" - }, - { - "author_name": "Tawanda Chivese", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.07.10.23292473", "rel_title": "Risk-based prediction for optimal timing of booster vaccination for COVID-19 to prevent severe disease", @@ -79469,6 +80831,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.07.05.547902", + "rel_title": "SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection", + "rel_date": "2023-07-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.05.547902", + "rel_abs": "A better mechanistic understanding of virus-host interactions can help reveal vulnerabilities and identify opportunities for therapeutic interventions. Of particular interest are essential interactions that enable production of viral proteins, as those could target an early step in the virus lifecycle. Here, we use subcellular proteomics, ribosome profiling analyses and reporter assays to detect changes in polysome composition and protein synthesis during SARS-CoV-2 (CoV2) infection. We identify specific translation factors and molecular chaperones whose inhibition impairs infectious particle production without major toxicity to the host. We find that CoV2 non-structural protein Nsp1 selectively enhances virus translation through functional interactions with initiation factor EIF1A. When EIF1A is depleted, more ribosomes initiate translation from an upstream CUG start codon, inhibiting translation of non-structural genes and reducing viral titers. Together, our work describes multiple dependencies of CoV2 on host biosynthetic networks and identifies druggable targets for potential antiviral development.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ranen Aviner", + "author_inst": "CZ Biohub: Chan Zuckerberg Biohub" + }, + { + "author_name": "Peter V Lidsky", + "author_inst": "UCSF: University of California San Francisco" + }, + { + "author_name": "Yinghong Xiao", + "author_inst": "UCSF: University of California San Francisco" + }, + { + "author_name": "Michel Tasseto", + "author_inst": "UCSF: University of California San Francisco" + }, + { + "author_name": "Lichao Zhang", + "author_inst": "CZ Biohub: Chan Zuckerberg Biohub" + }, + { + "author_name": "Patrick L McAlpine", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Joshua Elias", + "author_inst": "CZ Biohub: Chan Zuckerberg Biohub" + }, + { + "author_name": "Judith Frydman", + "author_inst": "Stanford University" + }, + { + "author_name": "Raul Andino", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.06.547945", "rel_title": "In vitro broad-spectrum antiviral activity of MIT-001, a mitochondria-targeted reactive oxygen species scavenger, against severe acute respiratory syndrome coronavirus 2 and multiple zoonotic viruses", @@ -80206,45 +81619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.03.23292119", - "rel_title": "DECLINE OF HANDWASHING AND MASKING AMONG THE GENERAL POPULATION IN POST COVID-19 PANDEMIC: INSIGHTS FROM A MIXED METHODS STUDY IN GHANA", - "rel_date": "2023-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.03.23292119", - "rel_abs": "COVID-19 has now entered the endemic stage where the virus is widespread with less fatality than it was in 2020. Restrictions and mandates such as handwashing and masking are eased although the pandemic is not yet over. Many have concluded that we have reached a point that marks the end of the pandemic spurring changes in public behavior. However, SARS-CoV-2 is still causing deaths every day and cases have not plateaued at low level. Better knowledge on why people have relented in handwashing and masking is needed to guide the development of effective interventions against future waves of the infection. In this study, we explored factors contributing to this pattern of behavior in Ghana. Questionnaires were administered to 350 respondents, via social media (WhatsApp, LinkedIn, Twitter, Facebook, reedit,) and these were used to determine the level of handwashing and masking at the first stage of study. Screening and scoring of the questionnaires were used to estimate the level of these activities at the second stage. Among all respondents, we identified and selected 279 participants at the second stage: 95 as decliners, 120 non-regulars, and 64 maintainers according to their level of these activities and adapted scoring criteria. For each category, a group of 5 participants were randomly selected to take part in an in-depth interview. The theory of planned behavior guided our analysis. Six themes emerged from the analysis with the acronym, IMPASE; inconvenience and contamination, Mass population, pandemic patterns and regulations, Availability, Safety and infection prevention, environment and activity. These themes appeared to have elements relating to another component of the theory of planned behavior. Collectively, the environment (Subjective norms) and pattern of pandemic and regulation (Perceived behavioral control) interact with each other to ultimately influence handwashing and masking. Declining and non-regularity were associated with inconvenience and contamination. Maintenance is associated with the environment and activity. Thus, public educational campaigns must be intensified to highlight and address these themes. The public health authorities, employers and, essential services could play an important role in enforcing and disseminating such information.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Emmanuel Lamptey", - "author_inst": "KAAF University" - }, - { - "author_name": "Stanley Yaidoo", - "author_inst": "St.Gregory Catholic Hospital, Central Region Gomoa East District" - }, - { - "author_name": "Moses tia Banoya", - "author_inst": "Methodist University Ghana" - }, - { - "author_name": "Evans osei Boakye", - "author_inst": "Department of Social Work, University of Ghana, Legon" - }, - { - "author_name": "Dooshima Aki Benita", - "author_inst": "Department of Psychology, Benue State University Makurdi Nigeria" - }, - { - "author_name": "Ephraim Kumi Senkyire", - "author_inst": "Ga-West Municipal Hospital, Ghana Health Service Accra Ghana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.07.03.23291596", "rel_title": "Risk of COVID-19 death in adults who received booster COVID-19 vaccinations: national retrospective cohort study on 14.6 million people in England", @@ -81527,6 +82901,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.29.23291797", + "rel_title": "Community Antibiotic Prescribing in Patients with COVID-19 Across Three Pandemic Waves: A Population-Based Cohort Study", + "rel_date": "2023-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.29.23291797", + "rel_abs": "BackgroundReported changes in antibiotic prescribing during the COVID-19 pandemic have focused on hospital prescribing or community population trends. Community antibiotic prescribing for individuals with COVID-19 are less well described.\n\nMethodsData covering a complete geographic population ([~]800,000) were utilised. SARS-CoV-2 virus test results from February 1, 2020-March 31, 2022 were included. Anonymised data were linked to prescription data +/-28 days of the test, GP data for high-risk comorbidities, and demographic data. Multivariate binary logistic regression examined associations between patient factors and the odds of antibiotic prescription.\n\nResultsData included 768,206 tests for 184,954 individuals, identifying 16,240 COVID-19 episodes involving 16,025 individuals. There were 3,263 antibiotic prescriptions +/-28 days for 2,385 patients. 35.6% of patients had a prescription only before the test date, 52.5% of patients after, and 11.9% before and after. Antibiotic prescribing reduced over time: 20.4% of episodes in wave one, 17.7% in wave two, and 12.0% in wave three. In multivariate logistic regression, being female (OR 1.31, 95% CI 1.19,1.45), older (OR 3.02, 95% CI 2.50, 3.68 75+ vs <25 years), having a high-risk comorbidity (OR 1.45, 95% CI 1.31, 1.61), a hospital admission +/-28 days of an episode (OR 1.58, 95% CI 1.42, 1.77), and health board region (OR 1.14, 95% CI 1.03, 1.25, board B versus A) increased the odds of receiving an antibiotic.\n\nConclusionCommunity antibiotic prescriptions in COVID-19 episodes were uncommon in this population and likelihood was associated with patient factors. The reduction over pandemic waves may represent increased knowledge regarding COVID-19 treatment and/or evolving symptomatology.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laura Ciaccio", + "author_inst": "Division of Population Health and Genomics, School of Medicine, University of Dundee" + }, + { + "author_name": "Peter T Donnan", + "author_inst": "Division of Population Health and Genomics, School of Medicine, University of Dundee" + }, + { + "author_name": "Benjamin J Parcell", + "author_inst": "Department of Medical Microbiology, Ninewells Hospital and School of Medicine" + }, + { + "author_name": "Charis A Marwick", + "author_inst": "Division of Population Health and Genomics, School of Medicine, University of Dundee" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.29.23292061", "rel_title": "Intention to be vaccinated against COVID-19 in Benin and Senegal: a structural equation modelling (SEM)", @@ -82544,61 +83949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.29.23292050", - "rel_title": "The Colloido Osmotic Pressure as a useful biomarker of fatal outcome in pregnant COVID-19 patients", - "rel_date": "2023-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.29.23292050", - "rel_abs": "BackgroundPregnancy was considering a health condition that could support high severity in COVID-19, among others the cardiologic and respiratory systems express some physiologic change in the pregnant women and could specially affected in COVID-19. Pregnant women characteristically have an increase volume of blood, with a higher cardiac output and lower peripheral vascular resistance, these could be negative affected by hypoalbuminemia frequently observed in COVID-19. Then, an early recognition of hypoalbuminemia in pregnant women with COVID-19 would help us to predict fatal outcome.\n\nObjectiveWe conduct a study to analyzed the demographic, clinical, blood gas test results, laboratory and ultrasonographic doppler data in pregnant women with COVID-19 that demand medical attention for labor. Study design: Ninety-two pregnant women with COVID-19 were included in our study from may 30th 2020 to august 12th 2022, and data was analyzed in survival and fatal outcome patients. Normality test were applied to data and parametric or non-parametric test were used to determine statistical difference between or among data.\n\nResultsDemographic and clinical data were quite similar between survival and fatal outcome pregnant patients with COVID-19. Also, blood gas test shown similar results among groups (asymptomatic, mild, or severe patients who survive COVID-19 or fatal outcome patients). We observed that serum albumin was consistently low in pregnant patients with fatal outcome by COVID-19, then based on Total Protein concentration in serum we calculated the colloido-osmotic pressure and we evaluate its utility as predictor of fatal outcome. ROC analysis and Kaplan-Meier of survival curves suggest that the colloido-osmotic pressure could be a potential predictor. Also, we observed an association of low colloido-osmotic pressure and low amniotic fluid index.\n\nConclusionOur study suggests that early evaluation of pregnant with COVID-19 must include the calculation of colloido-osmotic pressure and the doppler analysis to early recognition of fatal outcome in pregnant women with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Berenice Zavala-Barrios", - "author_inst": "Hospital General de Mexico Dr. Eduardo Liceaga. Ciudad de Mexico, Mexico" - }, - { - "author_name": "Arturo Cerbulo-Vazquez", - "author_inst": "Hospital General de Mexico Dr. Eduardo Liceaga. Ciudad de Mexico, Mexico" - }, - { - "author_name": "Maritza Garcia-Espinosa", - "author_inst": "UMAE Hospital de Gineco Obstetricia No. 4 Dr. Luis Castelazo Ayala. Instituto Mexicano del Seguro Social (IMSS). Ciudad de Mexico, Mexico." - }, - { - "author_name": "Felipe Caldino-Soto", - "author_inst": "UMAE Hospital de Gineco Obstetricia No. 4 Dr. Luis Castelazo Ayala. Instituto Mexicano del Seguro Social (IMSS). Ciudad de Mexico, Mexico." - }, - { - "author_name": "Ruth L. Madera-Sandoval", - "author_inst": "UMAE Hospital de Especialidades, Centro Medico Nacional Siglo XXI. IMSS. Ciudad de Mexico, Mexico." - }, - { - "author_name": "Luz A. Ramirez-Garcia", - "author_inst": "UMAE Hospital de Gineco Obstetricia No. 4 Dr. Luis Castelazo Ayala. Instituto Mexicano del Seguro Social (IMSS). Ciudad de Mexico, Mexico." - }, - { - "author_name": "Itzel C. Elaceo-Fernandez", - "author_inst": "Hospital General de Mexico Dr. Eduardo Liceaga. Ciudad de Mexico, Mexico" - }, - { - "author_name": "Oscar Moreno-Alvarez", - "author_inst": "UMAE Hospital de Gineco Obstetricia No. 4 Dr. Luis Castelazo Ayala. Instituto Mexicano del Seguro Social (IMSS). Ciudad de Mexico, Mexico." - }, - { - "author_name": "Guadalupe M.L. Guerrero-Avendano", - "author_inst": "Hospital General de Mexico Dr. Eduardo Liceaga. Ciudad de Mexico, Mexico" - }, - { - "author_name": "Jesus C. Briones-Garduno", - "author_inst": "Hospital General de Mexico Dr. Eduardo Liceaga. Ciudad de Mexico, Mexico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2023.06.27.546805", "rel_title": "Identification of cross-reacting IgG hotspots to prevent immune evasion of SARS-CoV-2 variants", @@ -83889,6 +85239,57 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2023.06.28.23291948", + "rel_title": "Targeting Multiple Conserved T-Cell Epitopes for Protection against COVID-19 Moderate-Severe Disease by a Pan-Sarbecovirus Vaccine", + "rel_date": "2023-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.28.23291948", + "rel_abs": "BackgroundMost of current approved vaccines, based on a Spike-only as single immunogen, fall short of producing a full-blown T-cell immunity. SARS-CoV-2 continues to evolve with ever-emergent higher-contagious mutants that may take a turn going beyond Omicron to bring about a new pandemic outbreak. New recombinant SARS-CoV-2 species could be man-made through genetic manipulation to infect systemically. Development of composition-innovated, pan-variant COVID-19 vaccines to prevent from hospitalization and severe disease, and to forestall the next pandemic catastrophe, is an urgent global objective.\n\nMethods and findingsIn a retrospective, e-questionnaire Observational Study, extended from a clinical Phase-2 trial conducted in Taiwan, during the prime time of Omicron outbreak dominated by BA.2 and BA.5 variants, we investigated the preventive effects against COVID-19 moderate-severe disease (hospitalization and ICU admission) by a pan-Sarbecovirus vaccine UB-612 that targets monomeric S1-RBD-focused subunit protein and five designer peptides comprising sequence-conserved, non-mutable helper and cytotoxic T lymphocyte (Th/CTL) epitopes derived from Spike (S2), Membrane (M) and Nucleocapsid (N) proteins. Per UB-612 vaccination, there were no hospitalization and ICU admission cases (0% rate, 6 months after Omicron outbreak) reported [≥]14 months post-2nd dose of primary series, and [≥]10 months post-booster (3rd dose), to which the potent memory cytotoxic CD8 T cell immunity may be the pivotal in control of the infection disease severity. Six months post-booster, the infection rate (asymptomatic and symptomatic mild) was only 1.2%, which increased to 27.8% observed [≥]10 months post-booster. The notable protection effects are in good alignment with a preliminary Phase-3 heterologous booster trial report showing that UB-612 can serve as a competent booster substitute for other EUA-approved vaccine platforms to enhance their seroconversion rate and viral-neutralizing titer against Omicron BA.5.\n\nConclusionsUB-612, a universal multitope vaccine promoting full-blown T cell immunity, may work as a competent primer and booster for persons vulnerable to Sarbecovirus infection.\n\nTrial RegistrationClinicalTrials.gov ID: NCT04773067.\n\nAUTHOR SUMMARYA COVID-19 vaccine based on a Spike-only single immunogen would fall short of producing a full-blown, escape-proof T cell immunity. In Omicron era plagued with ever-evolving and higher-contagious SARS-CoV-2 mutants, immune antibodies against variants beyond BA.5 are seen on a cliff drop, rendering the viral-neutralizing titer strength an increasingly less relevant immunity parameter. The true, urgent issue at heart in vaccine development has not been updating variant component to increase antibody titer for prevention of infection, but to validate universal vaccines that would have a potential to head off hospitalization, severe disease and ultimately reinfection altogether, and so to forestall a new catastrophe of pandemic outbreak. To reach the ideal goals, a universal vaccine able to produce potent, broadly recognizing and durable memory T cell immunity would be essential. UB-612, a pan-Sarbecovirus T cell immunity-promoting mutitope vaccine, has been shown to provide strong and long-lasting [≥]10 month protective effect against COVID-19 moderate-severe disease (0% cases of hospitalization and ICU admission). UB-612 is a unique S1-RBD subunit protein vaccine armed with five designer peptides comprising sequence-conserved helper and cytotoxic T lymphocyte (Th/CTL) epitopes derived from Spike (S2x3), Membrane (M) and Nucleocapsid (N) proteins across Sarbecovirus species.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Chang Yi Wang", + "author_inst": "UBI Asia" + }, + { + "author_name": "Be-Sheng Kuo", + "author_inst": "UBI Asia" + }, + { + "author_name": "Yu-Hsiang Lee", + "author_inst": "UBI Asia" + }, + { + "author_name": "Yu-Hsin Ho", + "author_inst": "UBI Asia" + }, + { + "author_name": "Yi-Hua Pan", + "author_inst": "UBI Asia" + }, + { + "author_name": "Ya-Ting Yang", + "author_inst": "UBI Asia" + }, + { + "author_name": "Hsi-Chi Chang", + "author_inst": "UBI Asia" + }, + { + "author_name": "Lin-Fang Fu", + "author_inst": "UBI Asia" + }, + { + "author_name": "Wen-Jiun Peng", + "author_inst": "UBI Asia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.26.23291891", "rel_title": "SARS-CoV-2 testing in the Slovak Republic from March 2020 to September 2022 - summary of the pandemic trends", @@ -84462,49 +85863,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.06.27.546764", - "rel_title": "Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern", - "rel_date": "2023-06-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.27.546764", - "rel_abs": "With the SARS-CoV-2 virus still circulating and evolving, there remains an outstanding question if variant-specific vaccines represent the optimal path forward, or if other strategies might be more efficacious towards providing broad protection against emerging variants. Here, we examine the efficacy of strain-specific variants of our previously reported, pan-sarbecovirus vaccine candidate, DCFHP-alum, a ferritin nanoparticle functionalized with an engineered form of the SARS-CoV-2 spike protein. In non-human primates, DCFHP-alum elicits neutralizing antibodies against all known VOCs that have emerged to date and SARS-CoV-1. During development of the DCFHP antigen, we investigated the incorporation of strain-specific mutations from the major VOCs that had emerged to date: D614G, Epsilon, Alpha, Beta, and Gamma. Here, we report the biochemical and immunological characterizations that led us to choose the ancestral Wuhan-1 sequence as the basis for the final DCFHP antigen design. Specifically, we show by size exclusion chromatography and differential scanning fluorimetry that mutations in the VOCs adversely alter the antigens structure and stability. More importantly, we determined that DCFHP without strain-specific mutations elicits the most robust, cross-reactive response in both pseudovirus and live virus neutralization assays. Our data suggest potential limitations to the variant-chasing approach in the development of protein nanoparticle vaccines, but also have implications for other approaches including mRNA-based vaccines.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Payton A Weidenbacher", - "author_inst": "Stanford University" - }, - { - "author_name": "Natalia Friedland", - "author_inst": "Stanford University" - }, - { - "author_name": "Mrinmoy Sanyal", - "author_inst": "Stanford University" - }, - { - "author_name": "Mary Kate Morris", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jonathan Do", - "author_inst": "Stanford University" - }, - { - "author_name": "Carl Hanson", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Peter S. Kim", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.06.27.546719", "rel_title": "DENetwork: Unveiling Regulatory and Signaling Networks Behind Differentially-Expressed Genes", @@ -85315,6 +86673,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.06.20.23291688", + "rel_title": "Evaluating the buffering role of perceived social support and coping resources against the adult mental health impacts of COVID-19 psychosocial stress: a cross-sectional study in South Africa", + "rel_date": "2023-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.20.23291688", + "rel_abs": "ObjectiveswGrowing evidence has highlighted the global mental health impacts of the COVID- 19 pandemic and lockdown, particularly in societies with pre-existing socioeconomic adversities and public health concerns. Despite the sudden and prolonged nature of many psychosocial stressors during the pandemic, recent studies have shown that communities utilized several coping mechanisms to buffer the mental health consequences of COVID-related stress. This paper examines the extent to which coping resources and social support buffered against the mental health effects of COVID-19 psychosocial stress among adults in South Africa.\n\nMaterials & MethodsAdult participants (n=117) completed an online survey during the second and third waves of the COVID-19 pandemic in South Africa (January-July 2021), which assessed experiences of stress, coping resources, social support, and four mental health outcomes: depression, anxiety, post-traumatic stress disorder, and bipolar disorder. Moderation analyses examined the potential buffering role of coping resources and social support against the mental health effects of COVID-19 stress.\n\nResultsAdults reported elevated rates of psychiatric symptoms. Coping resources buffered against the poor mental health effects of COVID-19 psychosocial stress, whereas perceived social support did not significantly moderate the association between COVID-19 stress and adult mental health.\n\nDiscussionThese results suggest that adults in our sample utilized a variety of coping resources to protect their mental health against psychosocial stress experienced during the COVID-19 lockdown and pandemic in South Africa. Additionally, existing mental health conditions and strained social relationships may have attenuated the potential stress-buffering effect of perceived social support on adult mental health.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrew Wooyoung Kim", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Someleze Swana", + "author_inst": "Witwatersrand Health Sciences: University of the Witwatersrand Johannesburg Faculty of Health Sciences" + }, + { + "author_name": "Mallika Sarma", + "author_inst": "Johns Hopkins Medical Institutions: Johns Hopkins Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.06.18.545480", "rel_title": "Identification of a novel HKU4-related coronavirus in single-cell datasets and clade viral host analysis", @@ -85908,133 +87293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.16.23291515", - "rel_title": "Real-world Effectiveness of BNT162b2 in Children and Adolescents in Preventing Infection and Severe Diseases with SARS-CoV-2 During the Delta and Omicron Periods: Findings from Trial Emulation Using an EHR-based Cohort", - "rel_date": "2023-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291515", - "rel_abs": "BackgroundThe efficacy of the BNT162b2 vaccine in pediatrics was assessed by randomized trials before the Omicron variants emergence. The long-term durability of vaccine protection in this population during the Omicron period remains limited.\n\nObjectiveTo assess the effectiveness of BNT162b2 in preventing infection and severe diseases with various strains of the SARS-CoV-2 virus in previously uninfected children and adolescents.\n\nDesignComparative effectiveness research accounting for underreported vaccination in three study cohorts: adolescents (12 to 20 years) during the Delta phase, children (5 to 11 years) and adolescents (12 to 20 years) during the Omicron phase.\n\nSettingA national collaboration of pediatric health systems (PEDSnet).\n\nParticipants77,392 adolescents (45,007 vaccinated) in the Delta phase, 111,539 children (50,398 vaccinated) and 56,080 adolescents (21,180 vaccinated) in the Omicron period.\n\nExposuresFirst dose of the BNT162b2 vaccine vs. no receipt of COVID-19 vaccine.\n\nMeasurementsOutcomes of interest include documented infection, COVID-19 illness severity, admission to an intensive care unit (ICU), and cardiac complications. The effectiveness was reported as (1-relative risk)*100% with confounders balanced via propensity score stratification.\n\nResultsDuring the Delta period, the estimated effectiveness of BNT162b2 vaccine was 98.4% (95% CI, 98.1 to 98.7) against documented infection among adolescents, with no significant waning after receipt of the first dose. An analysis of cardiac complications did not find an increased risk after vaccination. During the Omicron period, the effectiveness against documented infection among children was estimated to be 74.3% (95% CI, 72.2 to 76.2). Higher levels of effectiveness were observed against moderate or severe COVID-19 (75.5%, 95% CI, 69.0 to 81.0) and ICU admission with COVID-19 (84.9%, 95% CI, 64.8 to 93.5). Among adolescents, the effectiveness against documented Omicron infection was 85.5% (95% CI, 83.8 to 87.1), with 84.8% (95% CI, 77.3 to 89.9) against moderate or severe COVID-19, and 91.5% (95% CI, 69.5 to 97.6)) against ICU admission with COVID-19. The effectiveness of the BNT162b2 vaccine against the Omicron variant declined after 4 months following the first dose and then stabilized. The analysis revealed a lower risk of cardiac complications in the vaccinated group during the Omicron variant period.\n\nLimitationsObservational study design and potentially undocumented infection.\n\nConclusionsOur study suggests that BNT162b2 was effective for various COVID-19-related outcomes in children and adolescents during the Delta and Omicron periods, and there is some evidence of waning effectiveness over time.\n\nPrimary Funding SourceNational Institutes of Health", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Qiong Wu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jiayi Tong", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Bingyu Zhang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Dazheng Zhang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jiajie Chen", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Yuqing Lei", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Yiwen Lu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Yudong Wang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Lu Li", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Yishan Shen", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jie Xu", - "author_inst": "University of Florida" - }, - { - "author_name": "Charles Bailey", - "author_inst": "The Children's Hospital of Philadelphia" - }, - { - "author_name": "Jiang Bian", - "author_inst": "University of Florida" - }, - { - "author_name": "Dimitri Christakis", - "author_inst": "Seattle Children's Research Institute" - }, - { - "author_name": "Megan L. Fitzgerald", - "author_inst": "New York University" - }, - { - "author_name": "Kathryn Hirabayashi", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Ravi Jhaveri", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Alka Khaitan", - "author_inst": "Indiana University" - }, - { - "author_name": "Tianchen Lyu", - "author_inst": "University of Florida" - }, - { - "author_name": "Suchitra Rao", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Hanieh Razzaghi", - "author_inst": "The Children's Hospital of Philadelphia" - }, - { - "author_name": "Hayden Schwenk", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Fei Wang", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Margot Gage Witvliet", - "author_inst": "Lamar University" - }, - { - "author_name": "Eric J. Tchetgen Tchetgen", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jeffrey S. Morris", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Christopher B. Forrest", - "author_inst": "The Children's Hospital of Philadelphia" - }, - { - "author_name": "Yong Chen", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2023.06.16.23291455", "rel_title": "Anti-SARS-CoV-2 IgG profile of protein subunit, adenovector and mRNA vaccines", @@ -87305,6 +88563,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.15.545172", + "rel_title": "SARS-CoV-2 Delta Variant Remains Viable in Environmental Biofilms found in Meat Packaging Plants", + "rel_date": "2023-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.15.545172", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a coronavirus that directly infects human airway epithelial cells and caused the COVID-19 pandemic. At the start of the pandemic in 2020, meat-packaging plants saw a surge in SARS-CoV-2 cases, which forced many to temporarily close. To determine why SARS-CoV-2 appears to thrive specifically well in meat packaging plants, we used SARS-CoV-2 Delta variant and meat packaging plant drain samples to develop mixed-species biofilms on materials commonly found within meat packaging plants (stainless steel (SS), PVC, and ceramic tile). Our data provides evidence that SARS-CoV-2 Delta variant remained viable on all the surfaces tested with and without an environmental biofilm. We observed that SARS-CoV-2 Delta variant was able to remain infectious with each of the environmental biofilms, however, we detected a significant reduction in viability post-exposure to Plant B biofilm on SS, PVC, and on ceramic tile chips, and to Plant C biofilm on SS and PVC chips. The numbers of viable SARS-CoV-2 Delta viral particles was 1.81 - 4.57-fold high than the viral inoculum incubated with the Plant B and Plant C environmental biofilm on SS, and PVC chips. We did not detect a significant difference in viability when SARS-CoV-2 Delta variant was incubated with the biofilm obtained from Plant A on any of the materials tested and SARS-CoV-2 Delta variant had higher plaque numbers when inoculated with Plant C biofilm on tile chips, with a 2.75-fold difference compared to SARS-CoV-2 Delta variant on tile chips by itself. In addition, we detected an increase in the biofilm biovolume in response to SARS-CoV-2 Delta variant which is also a concern for food safety due to the potential for foodborne pathogens to respond likewise when they come into contact with the virus. These results indicate a complex virus-environmental biofilm interaction which correlates to the different bacteria found in each biofilm. Our results also indicate that there is the potential for biofilms to protect SARS-CoV-2 from disinfecting agents and remaining prevalent in meat packaging plants. With the highly infectious nature of some SARS-CoV-2 variants such as Delta, and more so with the Omicron variant, even a minimal amount of virus could have serious health implications for the spread and reoccurrence of SARS-CoV-2 outbreaks in meat packaging plants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sapna Chitlapilly Dass", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Austin B Featherstone", + "author_inst": "Texas A&M" + }, + { + "author_name": "Arnold JTM Mathijssen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amanda C Brown", + "author_inst": "Tarleton State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "ecology" + }, { "rel_doi": "10.1101/2023.06.16.545251", "rel_title": "High-confidence placement of difficult-to-fit fragments into electron density by using anomalous signals - a case study using hits targeting SARS-CoV-2 non-structural protein 1", @@ -88014,77 +89303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.06.14.23291395", - "rel_title": "Inflammatory profiles are associated with long COVID up to 6 months after illness onset: a prospective cohort study of individuals with mild to critical COVID-19", - "rel_date": "2023-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.14.23291395", - "rel_abs": "BackgroundAfter initial COVID-19 disease, immune dysregulation may persist and drive post-acute sequelae of COVID-19 (PASC). We described longitudinal trajectories of cytokines in adults up to 6 months following SARS-CoV-2 infection and explored early predictors of PASC.\n\nMethodsRECoVERED is a prospective cohort of individuals with laboratory-confirmed SARS-CoV-2 infection between May 2020 and June 2021 in Amsterdam, the Netherlands. Serum was collected at weeks 4, 12 and 24 of follow-up. Monthly symptom questionnaires were completed from month 2 after illness onset onwards; lung diffusion capacity (DLCO) was tested at 6 months. Cytokine concentrations were analysed by human magnetic Luminex screening assay. We used a linear mixed-effects model to study log-concentrations of cytokines over time, assessing their association with socio-demographic and clinical characteristics that were included in the model as fixed effects.\n\nResults186/349 (53%) participants had [≥]2 serum samples and were included. Of these, 101 (54%: 45/101[45%] female, median age 55 years [IQR=45-64]) reported PASC at 12 and 24 weeks after illness onset. We included 37 reference samples (17/37[46%] female, median age 49 years [IQR=40-56]). PASC was associated with raised CRP and abnormal diffusion capacity with raised IL10, IL17, IL6, IP10 and TNF at 24 weeks in the multivariate model. Early (0-4 week) IL-1{beta} and BMI at illness onset were predictive of PASC at 24 weeks.\n\nConclusionsOur findings indicate that immune dysregulation plays an important role in PASC pathogenesis, especially among those individuals with reduced pulmonary function. Early IL-1{beta} shows promise as predictors of PASC.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Elke Wynberg", - "author_inst": "Public Health Service of Amsterdam" - }, - { - "author_name": "Alvin X. Han", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Hugo D.G. van Willigen", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Anouk Verveen", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Lisa van Pul", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Irma Maurer", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Ester M. van Leeuwen", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Joost G. van den Aardweg", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Menno de Jong", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Pythia T. Nieuwkerk", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Maria Prins", - "author_inst": "Public Health Service of Amsterdam" - }, - { - "author_name": "Neeltje A. Kootstra", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Godelieve J. de Bree", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "- The RECoVERED Study Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.14.544560", "rel_title": "AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor", @@ -89119,6 +90337,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.06.12.23291266", + "rel_title": "Global seasonal activities of respiratory syncytial virus before the COVID-19 pandemic: a systematic review", + "rel_date": "2023-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.12.23291266", + "rel_abs": "BackgroundVaried seasonal patterns of respiratory syncytial virus (RSV) have been reported worldwide. We aimed to review the patterns of RSV activity globally before the COVID-19 pandemic and to explore factors potentially associated with RSV seasonality.\n\nMethodsWe conducted a systematic review on articles identified in PubMed reporting RSV seasonality based on data collected before 1 January 2020. Information on the timing of the start, peak, and end of an RSV season, study location, study period, and details in study methods were extracted. RSV seasonal patterns were examined by geographic location, calendar month, analytic method and meteorological factors including temperature and absolute humidity. Correlation and regression analyses were conducted to explore the relationship between RSV seasonality and study methods and characteristics of study locations.\n\nResultsRSV seasons were reported in 209 articles published in 1973-2023 for 317 locations in 77 countries. Variations were identified in types of data, data collection and analytical methods across the studies. Regular RSV seasons were similarly reported in countries in temperate regions, with highly variable seasons identified in subtropical and tropical countries. Durations of RSV seasons were relatively longer in subtropical and tropical regions than from temperate regions. Longer durations of RSV seasons were associated with a higher daily average mean temperature and daily average mean absolute humidity.\n\nConclusionsThe global seasonal patterns of RSV provided important information for optimizing interventions against RSV infection. Heterogeneity in study methods highlighted the importance of developing and applying standardized approaches in RSV surveillance and data reporting.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Songwei Shan", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Weixin Zhang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Huizhi Gao", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Pei-Yu Huang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Zhanwei Du", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Yuan Bai", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Yiu-Chung Lau", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Dongxuan Chen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Eric HY Lau", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Joshua Nealon", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Peng Wu", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.06.08.23291183", "rel_title": "Assessment of the relationship between Google Trend search data on clinical symptoms and cases reported during the first wave of the COVID-19 outbreak in India.", @@ -89660,37 +90937,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.08.23291136", - "rel_title": "Importation models for travel-related SARS-CoV-2 cases reported in Newfoundland and Labrador during the COVID-19 pandemic", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.08.23291136", - "rel_abs": "During the COVID-19 pandemic, the World Health Organization (WHO) updated guidelines advising that a risk-assessment framework considering local epidemiology and health services capacity be used to determine if travel measures should be implemented. Data, analysis, and models are needed to support these updated WHO guidelines. In 2020 and 2021, the Canadian province of Newfoundland and Labrador (NL) implemented travel measures that affected most travelers, including non-residents of NL, and NL residents that work outside the province. We used multiple data sources to estimate the total travel volume arriving in NL before and during the pandemic. We found that during the pandemic, travel to NL decreased by 82%, and the percentage of travelers arriving from given origins changed with Quebec decreasing from 14 to 4%, and Alberta increasing from 7 to 17%. We formulated an importation model including many epidemiological details, however, a less detailed statistical model considering the product of infection prevalence and travel volume for each Canadian province and the territories better predicted daily travel-related cases of Canadian origin (R2 = 0.55). We conclude that the accuracy of importation models are limited more by data availability, particularly travel-related case data, and data quality, particularly between-country differences in infection reporting, than by the complexity and details of importation models. Our results are evidence that will inform future risk-assessment frameworks to support travel measure implementation decisions during public health emergencies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zahra Mohammadi", - "author_inst": "University of Guelph" - }, - { - "author_name": "Monica Gabriela Cojocaru", - "author_inst": "University of Guelph" - }, - { - "author_name": "Julien Arino", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Amy Hurford", - "author_inst": "Memorial University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.06.09.544432", "rel_title": "RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways", @@ -90765,6 +92011,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2023.06.06.23290982", + "rel_title": "Estimating the effectiveness of COVID-19 vaccination against COVID-19 hospitalisation and death: a cohort study based on the 2021 Census, England.", + "rel_date": "2023-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.06.23290982", + "rel_abs": "ObjectiveTo estimate the effectiveness of COVID-19 vaccination against hospitalisation for COVID-19 and death involving COVID-19 in England using linked population level data sources including the 2021 Census.\n\nDesignRetrospective cohort study.\n\nSettingEngland, 21 March 2021 to 20 March 2022.\n\nParticipantsIndividuals alive and aged 16+ on 21 March 2021, resident in England, enumerated in the 2021 Census as a usual resident, and able to link to an NHS number. A sample of 583,840 individuals was used for the analysis.\n\nExposuresCOVID-19 vaccination: first dose, second dose and third dose/first booster dose, with categories for time since each dose.\n\nMain outcome measuresHospitalisation for COVID-19 or death involving COVID-19. An adjusted Cox proportional hazard model was used to estimate the hazard ratio for the outcomes for vaccinated participants for different doses and time since dose compared to unvaccinated individuals. Vaccine effectiveness was estimated as (1-hazard ratio)x100%. A control outcome of non-COVID-19 death was also assessed.\n\nResultsVaccine effectiveness against hospitalisation for COVID-19 was 52.1% (95% confidence interval 51.3% to 52.8%) for a first dose, 55.6% (55.2% to 56.1%) for a second dose and 77.6% (77.3% to 78.0%) for a third dose, with a decrease in vaccine effectiveness 3+ months after the third dose.\n\nVaccine effectiveness against COVID-19 mortality was 58.7% (52.7% to 63.9%) for a first dose, 88.5% (87.5% to 89.5%) for a second dose and 93.2% (92.9% to 93.5%) for a third dose, with evidence of waning 3+ months after the second and third doses.\n\nFor the second dose, which is the most comparable across the different time-periods, vaccine effectiveness was higher against COVID-19 hospitalisation but slightly lower against COVID-19 mortality in the Omicron dominant period than the period before the Omicron variant became dominant. Vaccine effectiveness against both COVID-19 hospitalisation and mortality was higher in general for mRNA vaccines than non mRNA vaccines, however this could be influenced by the different populations given each vaccine vector. Non-zero VE against non-COVID-19 mortality indicates that residual confounding may impact the results, despite the inclusion of up-to-date socio-demographic adjustments and various sources of health data, with possible frailty bias, confounding by indication and a healthy vaccinee effect observed.\n\nConclusionsThe vaccine effectiveness estimates show increased protection with number of doses and a high level of protection against both COVID-19 hospitalisation and mortality for the third/booster dose, as would be expected from previous research. However, despite the various sources of health data used to adjust the models, the estimates for different breakdowns and for non-COVID-19 mortality expose residual confounding by health status, which should be considered when interpreting estimates of vaccine effectiveness.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Charlotte Bermingham", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Owen Gethings", + "author_inst": "Office for National Statistics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.06.06.23291015", "rel_title": "Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study", @@ -91322,45 +92599,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.06.03.23289684", - "rel_title": "A flexible and high-throughput genotyping workflow tracked the emergence of SARS-CoV-2 variants in the UK in 2022", - "rel_date": "2023-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.03.23289684", - "rel_abs": "In late 2021, the Omicron SARS-CoV-2 variant spread rapidly worldwide. To track its emergence, and the continued evolution of SARS-CoV-2 while giving actionable epidemiological data that informs public health policy, we developed a high-throughput, automated, genotyping workflow that pairs flexible liquid handling with a re-configurable LIMS system. This workflow facilitated the real-time monitoring of the spread of BA.4 and BA.5, and by the time of its retirement, the system was responsible for typing c. 400,000 SARS-CoV-2 samples. When combined with a population-scale testing program, genotyping assays, can offer a rapid and cost-effective method of determining variants and horizon-scanning for changes in the pool of circulating mutations. Strategies to prepare diagnostics infrastructure for Pathogen X should consider the development of flexible systems with interchangeable components that can be rapidly re-configured to meet uncertain and changing requirements.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Siu Yi Lee", - "author_inst": "Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University" - }, - { - "author_name": "Stefan Grujic", - "author_inst": "Omix, Limited" - }, - { - "author_name": "Sam Modern", - "author_inst": "The New Zealand Institute for Plant and Food Research Ltd" - }, - { - "author_name": "Angela Wann", - "author_inst": "Biomatics, Limited" - }, - { - "author_name": "Donald Peter Fraser", - "author_inst": "Omix, Limited" - }, - { - "author_name": "Benita Clare Percival", - "author_inst": "De Montfort University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.31.23290618", "rel_title": "Social genomics, cognition, and well-being during the COVID-19 pandemic", @@ -92563,6 +93801,457 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.05.30.23290732", + "rel_title": "Challenges of COVID-19 Case Forecasting in the US, 2020-2021", + "rel_date": "2023-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.30.23290732", + "rel_abs": "During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naive baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.\n\nAuthor SummaryAs SARS-CoV-2 began to spread throughout the world in early 2020, modelers played a critical role in predicting how the epidemic could take shape. Short-term forecasts of epidemic outcomes (for example, infections, cases, hospitalizations, or deaths) provided useful information to support pandemic planning, resource allocation, and intervention. Yet, infectious disease forecasting is still a nascent science, and the reliability of different types of forecasts is unclear. We retrospectively evaluated COVID-19 case forecasts, which were often unreliable. For example, forecasts did not anticipate the speed of increase in cases in early winter 2020. This analysis provides insights on specific problems that could be addressed in future research to improve forecasts and their use. Identifying the strengths and weaknesses of forecasts is critical to improving forecasting for current and future public health responses.", + "rel_num_authors": 109, + "rel_authors": [ + { + "author_name": "Velma Lopez", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Estee Y Cramer", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Robert Pagano", + "author_inst": "Unafilliated" + }, + { + "author_name": "John M Drake", + "author_inst": "University of Georgia" + }, + { + "author_name": "Eamon B O'Dea", + "author_inst": "University of Georgia" + }, + { + "author_name": "Benjamin P Linas", + "author_inst": "Boston University" + }, + { + "author_name": "Turgay Ayer", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Jade Xiao", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Madeline Adee", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jagpreet Chhatwal", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Mary A Ladd", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Peter P Mueller", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Ozden O Dalgic", + "author_inst": "Value Analytics Lab" + }, + { + "author_name": "Johannes Bracher", + "author_inst": "Karlsruher Institut fur Technologie" + }, + { + "author_name": "Tilmann Gneiting", + "author_inst": "Heidelberg Institute for Theoretical Studies" + }, + { + "author_name": "Anja M\u00fchlemann", + "author_inst": "University of Bern: Universitat Bern" + }, + { + "author_name": "Jarad Niemi", + "author_inst": "Iowa State University" + }, + { + "author_name": "Ray L Evan", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Martha Zorn", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Yuxin Huang", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Yijin Wang", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Aaron Gerding", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Ariane Stark", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Dasuni Jayawardena", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Khoa Le", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Nutcha Wattanachit", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Abdul H Kanji", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Alvaro J Castro Rivadeneira", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Sen Pei", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Teresa K Yamana", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Xinyi Li", + "author_inst": "Clemson University" + }, + { + "author_name": "Guannan Wang", + "author_inst": "William & Mary" + }, + { + "author_name": "Lei Gao", + "author_inst": "George Mason University" + }, + { + "author_name": "Zhiling Gu", + "author_inst": "Iowa State University" + }, + { + "author_name": "Myungjin Kim", + "author_inst": "Kyungpook National University" + }, + { + "author_name": "Lily Wang", + "author_inst": "George Mason University" + }, + { + "author_name": "Yueying Wang", + "author_inst": "Amazon" + }, + { + "author_name": "Shan Yu", + "author_inst": "University of Virginia" + }, + { + "author_name": "Daniel J Wilson", + "author_inst": "Federal Reserve Bank San Francisco" + }, + { + "author_name": "Samuel R Tarasewicz", + "author_inst": "Federal Reserve Bank San Francisco" + }, + { + "author_name": "Brad Suchoski", + "author_inst": "IEM" + }, + { + "author_name": "Steve Stage", + "author_inst": "IEM" + }, + { + "author_name": "Heidi Gurung", + "author_inst": "IEM" + }, + { + "author_name": "Sid Baccam", + "author_inst": "IEM" + }, + { + "author_name": "Maximilian Marshall", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Lauren Gardner", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Sonia Jindal", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Kristen Nixon", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Joseph C Lemaitre", + "author_inst": "Ecole Polytechnique Federale de Lausanne" + }, + { + "author_name": "Juan Dent", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Alison L Hill", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Joshua Kaminsky", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Justin Lessler", + "author_inst": "UNC-Chapel Hill: The University of North Carolina at Chapel Hill" + }, + { + "author_name": "Claire P Smith", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Shaun Truelove", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Matt Kinsey", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Katharine Tallaksen", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Shelby Wilson", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Luke C Mullany", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Lauren Shin", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Kaitlin Rainwater-Lovett", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Dean Karlen", + "author_inst": "University of Victoria" + }, + { + "author_name": "Lauren Castro", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Geoffrey Fairchild", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Isaac Michaud", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dave Osthus", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jessica T Davis", + "author_inst": "Northeastern University" + }, + { + "author_name": "Kunpeng Mu", + "author_inst": "Northeastern University" + }, + { + "author_name": "Xinyue Xiong", + "author_inst": "Northeastern University" + }, + { + "author_name": "Ana Pastore y Piontti", + "author_inst": "Northeastern University" + }, + { + "author_name": "Shun Zheng", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Zhifeng Gao", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Wei Cao", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Jiang Bian", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Chaozhuo Li", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Xing Xie", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Tie-Yan Liu", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Juan Lavista Ferres", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Shun Zhang", + "author_inst": "Microsoft Corp" + }, + { + "author_name": "Robert Walraven", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Jinghui Chen", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Quanquan Gu", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Lingxiao Wang", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Pan Xu", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Weitong Zhang", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Difan Zou", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Graham Casey Gibson", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Daniel Sheldon", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Ajitesh Srivastava", + "author_inst": "University of Southern California" + }, + { + "author_name": "Aniruddha Adiga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin Hurt", + "author_inst": "University of Virginia" + }, + { + "author_name": "Gursharn Kaur", + "author_inst": "University of Virginia" + }, + { + "author_name": "Bryan Lewis", + "author_inst": "University of Virginia" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "University of Virginia" + }, + { + "author_name": "Akhil S Peddireddy", + "author_inst": "Discreet Labs" + }, + { + "author_name": "Przemyslaw Porebski", + "author_inst": "University of Virginia" + }, + { + "author_name": "Srinivasan Venkatramanan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Lijing Wang", + "author_inst": "University of Virginia" + }, + { + "author_name": "Pragati V Prasad", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Alexander E Webber", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jo W Walker", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Rachel B Slayton", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Matthew Biggerstaff", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Michael A Johansson", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.05.31.23290613", "rel_title": "A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches", @@ -93244,77 +94933,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.05.31.543159", - "rel_title": "Combinatorial Regimens Augment Drug Monotherapy for SARS-CoV-2 Clearance in Mice", - "rel_date": "2023-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.31.543159", - "rel_abs": "Direct acting antivirals (DAAs) represent critical tools for combating SARS-CoV-2 variants of concern (VOCs) that evolve to escape spike-based immunity and future coronaviruses with pandemic potential. Here, we used bioluminescence imaging to evaluate therapeutic efficacy of DAAs that target SARS-CoV-2 RNA-dependent RNA polymerase (favipiravir, molnupiravir) or Main protease (nirmatrelvir) against Delta or Omicron VOCs in K18-hACE2 mice. Nirmatrelvir displayed the best efficacy followed by molnupiravir and favipiravir in suppressing viral loads in the lung. Unlike neutralizing antibody treatment, DAA monotherapy did not eliminate SARS-CoV-2 in mice. However, targeting two viral enzymes by combining molnupiravir with nirmatrelvir resulted in superior efficacy and virus clearance. Furthermore, combining molnupiravir with Caspase-1/4 inhibitor mitigated inflammation and lung pathology whereas combining molnupiravir with COVID-19 convalescent plasma yielded rapid virus clearance and 100% survival. Thus, our study provides insights into treatment efficacies of DAAs and other effective combinations to bolster COVID-19 therapeutic arsenal.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Irfan Ullah", - "author_inst": "Yale University" - }, - { - "author_name": "Fanny Escudie", - "author_inst": "Drugs for Neglected Diseases initiative (DNDi)" - }, - { - "author_name": "Ivan Scandale", - "author_inst": "Drugs for Neglected Diseases initiative (DNDi)" - }, - { - "author_name": "Zoela Gilani", - "author_inst": "Yale University" - }, - { - "author_name": "Gabrielle Gendron-Lepage", - "author_inst": "CHUM" - }, - { - "author_name": "Fluer Gaudette", - "author_inst": "CHUM" - }, - { - "author_name": "Charles Mowbray", - "author_inst": "Drugs for Neglected Diseases initiative (DNDi)" - }, - { - "author_name": "Laurent Fraisse", - "author_inst": "Drugs for Neglected Diseases initiative (DNDi)" - }, - { - "author_name": "Renee Bazin", - "author_inst": "Hema-Quebec" - }, - { - "author_name": "Andres Finzi", - "author_inst": "University of Montreal" - }, - { - "author_name": "Walther Mothes", - "author_inst": "Yale University" - }, - { - "author_name": "Priti Kumar", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Eric Chatelain", - "author_inst": "Drugs for Neglected Diseases initiative (DNDi)" - }, - { - "author_name": "Pradeep D Uchil", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.06.01.543234", "rel_title": "Prenatal SARS-CoV-2 infection alters postpartum human milk-derived extracellular vesicles", @@ -94329,6 +95947,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.05.22.23290323", + "rel_title": "Analysing the psychosocial and health impacts of Long COVID in Pakistan: A cross sectional study", + "rel_date": "2023-05-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.22.23290323", + "rel_abs": "Long COVID corresponds to the occurrence of symptoms beyond twelve weeks after the onset of acute COVID-19 illness. The study aimed to analyze impacts of long COVID on the general health and psychosocial well-being of the Pakistani population. This cross-sectional study aimed to analyse the impacts of long COVID on general health and psychosocial well-being. For this study, the participants were interviewed, and their responses were recorded on a questionnaire capturing information on demographics, COVID-19 status, duration of symptoms and long COVID symptoms. The psychological impacts of the pandemic were assessed using scales like Short Mood and feeling questionnaire (sMFQ), Warwick-Edinburgh Mental Well-being Scale (WEMWBS), Generalized Anxiety Disorder Assessment (GAD-7) and Perceived Stress Scale (PSS). Regression analysis was conducted to analyse the predictors of long COVID. A total of 300 participants were interviewed, of which 155 (52%) had COVID-19 illness. Of these 54 (35%) had persistent symptoms for a period of more than 12 weeks classified as long COVID. Muscle problems and fatigue were the most frequent (14.7%) symptoms encountered, followed by breathing problems (12.6%) and cognitive issues (12.6%). Symptoms such as decrease in appetite and confusion or disorientation during the initial phase of the infection were associated with long COVID. Majority of the participants (83.3%) had moderate level of perceived stress while moderate to severe levels of stress was observed in 17.3% of the individuals. Moreover, a high level positive mental wellbeing was also observed.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Madeeha Khan", + "author_inst": "Directorate of Research, Shifa Tameer-e-Millat University, Islamabad, Pakistan" + }, + { + "author_name": "Sadaf Majeed", + "author_inst": "Department of Physiology, Shifa College of Medicine, Shifa Tameer e Millat University, Islamabad, Pakistan" + }, + { + "author_name": "Quratul Ain", + "author_inst": "Directorate of Research, Shifa Tameer-e-Millat University, Islamabad, Pakistan" + }, + { + "author_name": "Amjad Nawaz", + "author_inst": "Directorate of Research, Shifa Tameer-e-Millat University, Islamabad, Pakistan" + }, + { + "author_name": "Khadija Awais Sumra", + "author_inst": "Agha Khan University, Karachi, Pakistan" + }, + { + "author_name": "Vilma Lammi", + "author_inst": "Institute for Molecular Medicine, Helsinki Institute of Life Science, University of Helsinki, Finland" + }, + { + "author_name": "Faizan Nihal", + "author_inst": "Department of Vascular Surgery, Shifa International Hospital, Islamabad, Pakistan" + }, + { + "author_name": "Aleena Afrah", + "author_inst": "Department of Psychology, University of Wah, Wah Cantt, Pakistan" + }, + { + "author_name": "Ejaz Ahmed Khan", + "author_inst": "Department of Infectious Diseases, Shifa International Hospital, Islamabad, Pakistan" + }, + { + "author_name": "Mohammad Iqbal Khan", + "author_inst": "Shifa Tameer-e-Millat University, Islamabad, Pakistan" + }, + { + "author_name": "Fouzia Sadiq", + "author_inst": "Shifa Tameer-e-Millat University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.24.23290470", "rel_title": "Missing data and missed infections: Investigating racial and ethnic disparities in SARS-CoV-2 testing and infection rates in Holyoke, Massachusetts", @@ -95702,45 +97379,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.05.26.542392", - "rel_title": "Modifications to the SR-Rich Region of the SARS-CoV-2 Nucleocapsid Regulate Self-Association and Attenuate RNA Interactions", - "rel_date": "2023-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.26.542392", - "rel_abs": "The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, and maturation. N is comprised of two folded domains that are separated by a highly conserved, disordered, Ser/Arg-rich linker, and flanked by disordered tails. Using NMR spectroscopy and analytical ultracentrifugation we identify an alpha-helical region in the linker that undergoes concentration dependent self-association. NMR and gel shift assays show that the linker binds viral RNA but this binding is dampened by both phosphorylation and a naturally occurring mutation, whereas in contrast, RNA binding to the full-length protein is not affected. Interestingly, phase separation with RNA is significantly reduced upon phosphorylation but enhanced with the mutation. We attribute these differences to changes in the linker helix self-association which dissociates upon phosphorylation but forms more stable higher order oligomers in the variant. These data provide a structural mechanism for how the linker region contributes to protein-protein interactions, RNA-protein interactions, liquid-liquid phase separation and N protein regulation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Patrick N Reardon", - "author_inst": "Oregon State University" - }, - { - "author_name": "Hannah Stuwe", - "author_inst": "Oregon State University" - }, - { - "author_name": "Sahana Shah", - "author_inst": "Oregon State University" - }, - { - "author_name": "Zhen Yu", - "author_inst": "Oregon State University" - }, - { - "author_name": "Kaitlyn Hughes", - "author_inst": "Oregon State University" - }, - { - "author_name": "Elisar Barbar", - "author_inst": "Oregon State University" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.05.19.23290192", "rel_title": "The secretory IgA (sIgA) response in human milk against the SARS-CoV-2 Spike is highly durable and neutralizing for at least 1 year of lactation post-infection", @@ -97011,6 +98649,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.05.22.23290332", + "rel_title": "Wastewater-based reproduction numbers and projections of COVID-19 cases in multiple cities in Japan, 2022", + "rel_date": "2023-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.22.23290332", + "rel_abs": "BackgroundWastewater surveillance has expanded globally to monitor the spread of infectious diseases. An inherent challenge is substantial noise and bias in wastewater data due to their sampling and quantification process, leading to the limited applicability of wastewater surveillance as a monitoring tool and the difficulty.\n\nAimIn this study, we present an analytical framework for capturing the growth trend of circulating infections from wastewater data and conducting scenario analyses to guide policy decisions.\n\nMethodsWe developed a mathematical model for translating the observed SARS-CoV-2 viral load in wastewater into effective reproduction numbers. We used an extended Kalman filter to infer underlying transmissions by smoothing out observational noise. We also illustrated the impact of different countermeasures such as expanded vaccinations and non-pharmaceutical interventions on the projected number of cases using three study areas in Japan as an example.\n\nResultsOur analyses showed an adequate fit to the data, regardless of study area and virus quantification method, and the estimated reproduction numbers derived from wastewater data were consistent with notification-based reproduction numbers. Our projections showed that a 10-20% increase in vaccination coverage or a 10% reduction in contact rate may suffice to initiate a declining trend in study areas.\n\nConclusionOur study demonstrates how wastewater data can be used to track reproduction numbers and perform scenario modelling to inform policy decisions. The proposed framework complements conventional clinical surveillance, especially when reliable and timely epidemiological data are not available.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shogo Miyazawa", + "author_inst": "Data Science Department, Shionogi & Co, Ltd, Osaka, Japan" + }, + { + "author_name": "TingSam Wong", + "author_inst": "AdvanSentinel Inc., Osaka, Japan" + }, + { + "author_name": "Genta Ito", + "author_inst": "Data Science Department, Shionogi & Co, Ltd, Osaka, Japan" + }, + { + "author_name": "Ryo Iwamoto", + "author_inst": "AdvanSentinel Inc., Osaka, Japan" + }, + { + "author_name": "Kozo Watanabe", + "author_inst": "Center for Marine Environmental Studies (CMES), Ehime University, Ehime, Japan" + }, + { + "author_name": "Michiel van Boven", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Fuminari Miura", + "author_inst": "Center for Marine Environmental Studies (CMES), Ehime University, Ehime, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.16.23290059", "rel_title": "Distinct T cell functional profiles in SARS-CoV-2 seropositive and seronegative children associated with endemic human coronavirus cross-reactivity", @@ -97584,33 +99269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2023.05.19.23290239", - "rel_title": "Drug Overdose Mortality Rates by Educational Attainment and Sex for Adults Aged 25 to 64 in the United States Before and During the COVID-19 Pandemic, 2015 to 2021", - "rel_date": "2023-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.19.23290239", - "rel_abs": "IntroductionDramatic increases in U.S. drug overdose deaths involving synthetic opioids, especially fentanyl, beginning around 2014 have driven a marked progression in overall drug overdose deaths in the U.S., sharply rising after the onset of the COVID-19 pandemic. Disparities in drug overdose deaths by educational attainment (EA) during the fentanyl era of the drug overdose epidemic and its intersection with the COVID-19 pandemic have not been widely scrutinized.\n\nMethodsUtilizing restricted-use mortality data from the National Vital Statistics System and population estimates from the American Community Survey, we estimated annual national age-adjusted mortality rates (AAMRs) from drug overdoses jointly stratified by EA and sex for adults aged 25-64 from 2015 to 2021. State-level AAMRs in 2015 and 2021 were also estimated to examine the geographic variation in the cumulative evolution of EA-related disparities over the course of the analysis period.\n\nResultsNationally, AAMRs rose fastest among persons with at most a high school-level education, whereas little to no change was observed for bachelors degree holders, widening pre-existing disparities. During the analysis period, the difference in national AAMRs between persons with at most a high school-level education and bachelors degree holders increased from less than 8-fold (2015) to approximately 13-fold (2021). The national widening of EA-related disparities accelerated amid the COVID-19 pandemic, and they widened in nearly every state. Among non-bachelors degree holders, national AAMRs increased markedly faster for males.\n\nConclusionsThe widening disparities in drug overdose deaths by EA are a likely indicator of a rapidly increasing socioeconomic divide in drug overdose mortality more broadly. Policy strategies should address upstream socioeconomic drivers of drug use and overdose, particularly among males.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jay J Xu", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Marissa J Seamans", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Joseph R Friedman", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.05.15.23289993", "rel_title": "Impact of the COVID-19 pandemic on low back pain management in commercially insured and Medicare Advantage cohorts. A retrospective cohort study", @@ -98829,6 +100487,101 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.05.12.23289890", + "rel_title": "Heterogeneous changes in mobility in response to the SARS-CoV-2 Omicron BA.2 outbreak in Shanghai", + "rel_date": "2023-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.12.23289890", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic and the measures taken by authorities to control its spread had altered human behavior and mobility patterns in an unprecedented way. However, it remains unclear whether the population response to a COVID-19 outbreak varies within a city or among demographic groups. Here we utilized passively recorded cellular signaling data at a spatial resolution of 1km x 1km for over 5 million users and epidemiological surveillance data collected during the SARS-CoV-2 Omicron BA.2 outbreak from February to June 2022 in Shanghai, China, to investigate the heterogeneous response of different segments of the population at the within-city level and examine its relationship with the actual risk of infection. Changes in behavior were spatially heterogenous within the city and population groups, and associated with both the infection incidence and adopted interventions. We also found that males and individuals aged 30-59 years old traveled more frequently, traveled longer distances, and their communities were more connected; the same groups were also associated with the highest SARS-CoV-2 incidence. Our results highlight the heterogeneous behavioral change of the Shanghai population to the SARS-CoV-2 Omicron BA.2 outbreak and the its effect on the heterogenous spread of COVID-19, both spatially and demographically. These findings could be instrumental for the design of targeted interventions for the control and mitigation of future outbreaks of COVID-19 and, more broadly, of respiratory pathogens.\n\nSignificance StatementOur study utilized passively recorded cellular signaling data and epidemiological surveillance data to investigate the changes human mobility to a COVID-19 outbreak at an unprecedented within-city level and examine its relationship with the actual risk of infection. Our findings highlight the heterogeneous behavioral change of the Shanghai population to the 2022 SARS-CoV-2 Omicron BA.2 outbreak and its heterogenous effect on the SARS-CoV-2 spread, both spatially and demographically. The implications of our findings could be instrumental to inform spatially targeted interventions at the within-city scale to mitigate possible new surges of COVID-19 cases as well as fostering preparedness for future respiratory infections disease outbreaks.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Juanjuan Zhang", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Suoyi Tan", + "author_inst": "College of Systems Engineering, National University of Defense Technology" + }, + { + "author_name": "Cheng Peng", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Xiangyanyu Xu", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Mengning Wang", + "author_inst": "College of Systems Engineering, National University of Defense Technology" + }, + { + "author_name": "Wanying Lu", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Yanpeng Wu", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Bin Sai", + "author_inst": "College of Systems Engineering, National University of Defense Technology" + }, + { + "author_name": "Mengsi Cai", + "author_inst": "College of Systems Engineering, National University of Defense Technology" + }, + { + "author_name": "Allisandra G. Kummer", + "author_inst": "Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health" + }, + { + "author_name": "Zhiyuan Chen", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Junyi Zou", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Wenxin Li", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Wen Zheng", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Yuxia Liang", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Yuchen Zhao", + "author_inst": "School of Public Health, Fudan University" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health" + }, + { + "author_name": "Xin Lu", + "author_inst": "College of Systems Engineering, National University of Defense Technology; Department of Public Health Sciences, Karolinska Institutet" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.05.11.23289882", "rel_title": "Understanding COVID-19 Vaccine Uptake and Hesitancy Among People With HIV in Freetown, Sierra Leone: A Cross-sectional Study", @@ -99334,45 +101087,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.10.23289764", - "rel_title": "Ability to detect fake news predicts sub-national variation in COVID-19 vaccine uptake across the UK", - "rel_date": "2023-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.10.23289764", - "rel_abs": "Susceptibility to believing false or misleading information is associated with a range of adverse outcomes. However, it is notoriously difficult to study the link between susceptibility to misinformation and consequential real-world behaviors such as vaccine uptake. In this preregistered study, we devise a large-scale socio-spatial model that combines the rigor of a psychometrically validated test of misinformation susceptibility administered to a nationally representative sample of 16,477 individuals with COVID-19 vaccine uptake data of 129 sub-national regions published by the United Kingdom (UK) government, to show that the general ability to detect misinformation strongly and positively predicts regional vaccine uptake in the UK. We put this practically significant correlational effect size into perspective by noting how psychological interventions that reduce individuals misinformation susceptibility could be associated with additional vaccine uptake.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sahil Loomba", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rakoen Maertens", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jon Roozenbeek", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Friedrich M. G\u00f6tz", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Sander van der Linden", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Alexandre de Figueiredo", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.05.12.23288889", "rel_title": "Immune response to SARS CoV2 infection by TLR3, TLR4 and TLR7 expression", @@ -100455,6 +102169,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.05.10.540124", + "rel_title": "PandoGen: Generating complete instances of future SARS-CoV2 sequences using Deep Learning", + "rel_date": "2023-05-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.10.540124", + "rel_abs": "One of the challenges in a viral pandemic is the emergence of novel variants with different phenotypical characteristics. An ability to forecast future viral individuals at the sequence level enables advance preparation by characterizing the sequences and closing vulnerabilities in current preventative and therapeutic methods. In this article, we explore, in the context of a viral pandemic, the problem of generating complete instances of undiscovered viral protein sequences, which have a high likelihood of being discovered in the future using protein language models. Current approaches to training these models fit model parameters to a known sequence set, which does not suit pandemic forecasting as future sequences differ from known sequences in some respects. To address this, we develop a novel method, called PandoGen, to train protein language models towards the pandemic protein forecasting task. PandoGen combines techniques such as synthetic data generation, conditional sequence generation, and reward-based learning, enabling the model to forecast future sequences, with a high propensity to spread. Applying our method to modeling the SARS-CoV-2 Spike protein sequence, we find empirically that our model forecasts twice as many novel sequences with five times the case counts compared to a model that is thirty times larger. Our method forecasts unseen lineages months in advance, whereas models 4x and 30x larger forecast almost no new lineages. When trained on data available up to a month before the onset of important Variants of Concern, our method consistently forecasts sequences belonging to those variants within tight sequence budgets.\n\nPandoGen is available at: https://github.com/UIUC-ChenLab/PandoGen", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Anand Ramachandran", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Steven S Lumetta", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Deming Chen", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.05.10.23289557", "rel_title": "Healthcare resource utilisation and costs of hospitalisation and primary care among adults with COVID-19 in England: a population-based cohort study", @@ -101080,77 +102821,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2023.05.05.539661", - "rel_title": "Host inducible-HSP70A1A is an irresistible drug target to combat SARS-CoV-2 infection and pathogenesis", - "rel_date": "2023-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.05.539661", - "rel_abs": "One of the fundamental mechanisms developed by the host to contain the highly infectious and rapidly proliferating SARS coronavirus is elevation of body temperature, a natural fallout of which is Heat Shock Protein (HSP) over-expression. Here, for the first time, we demonstrate that the SARS-CoV-2 virus exploits the host Hsp70 chaperone for its entry and propagation and blocking it can combat the infection. SARS-CoV-2 infection as well as febrile temperature enhanced Hsp70 overexpression in host Vero E6 cells. In turn, Hsp70 overexpression elevated the host cell autophagic response that is a prerequisite for viral propagation. Suppressive and prophylactic treatment of Vero E6 cells with HSP70 inhibitor PES-Cl, a small molecule derivative of Pifithrin , abrogated viral infection more potently than the currently used drug Remdesivir by suppressing host HSP70 and autophagic response. In conclusion, our study not only provides a fundamental insight into the role of host Hsp70 in SARS-CoV-2 pathogenesis, it paves the way for the development of potent and irresistible anti-viral therapeutics.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Prerna Joshi", - "author_inst": "Jawaharlal Nehru University, Delhi, India" - }, - { - "author_name": "Swati Garg", - "author_inst": "Jawaharlal Nehru University, Delhi, India" - }, - { - "author_name": "Shailendra Mani", - "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" - }, - { - "author_name": "Kamini Jakhar", - "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" - }, - { - "author_name": "Manisha Marothia", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Rumaisha Shoaib", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Shreeja Biswas", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Jhalak Singhal", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Ankita Behl", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Amandeep Kaur Kahlon", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Maxim Shevtsov", - "author_inst": "Institute of Cytology of the Russian Academy of Sciences (RAS)" - }, - { - "author_name": "Pramod Garg", - "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" - }, - { - "author_name": "Shailja Singh", - "author_inst": "Jawaharlal Nehru University, New Delhi" - }, - { - "author_name": "Anand Ranganathan", - "author_inst": "Jawaharlal Nehru University, New Delhi" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.05.06.539715", "rel_title": "SARS-COV-2 Spike Protein Fragment eases Amyloidogenesis of \u03b1-Synuclein", @@ -102061,6 +103731,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.05.05.23289561", + "rel_title": "COVID-19 vaccination at a hospital in Paris: spatial analyses and inverse equity hypothesis", + "rel_date": "2023-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.05.23289561", + "rel_abs": "BackgroundVaccination against SARS-CoV-2 has been deployed in France since January 2021. Evidence was beginning to show that the most vulnerable populations were the most affected by COVID-19. Without specific action for different population subgroups, the inverse equity hypothesis postulates that people in the least deprived neighbourhoods will be the first to benefit.\n\nMethodsWe performed a spatial analysis using primary data from the vaccination centre of the Avicenne Hospital in Bobigny (Seine-Saint-Denis, France) from January 8th to September 30th, 2021. We used secondary data to calculate the social deprivation index. We performed flow analysis, k-means aggregation, and mapping.\n\nResultsDuring the period, 32,712 people were vaccinated at the study centre. Vaccination flow to the hospital shows that people living in the least disadvantaged areas were the first to be vaccinated. The number of people immunized according to the level of social deprivation then scales out with slightly more access to the vaccination centre for the most advantaged. The furthest have travelled more than 100 kilometres, and more than 1h45 of transport time to get to this vaccination centre. Access times are, on average, 50 minutes in February to 30 minutes in May 2021.\n\nConclusionThe study confirms the inverse equity hypothesis and shows that vaccination preparedness strategies must take equity issues into account. Public health interventions should be implemented according to proportionate universalism and use community health, health mediation, and outreach activities for more equity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Valery Ridde", + "author_inst": "University of Paris: Universite Paris Cite" + }, + { + "author_name": "Gaelle Andre", + "author_inst": "University Paris 1 Pantheon-Sorbonne" + }, + { + "author_name": "Olivier Bouchaud", + "author_inst": "Universite Sorbonne Paris Nord" + }, + { + "author_name": "Emmanuel Bonnet", + "author_inst": "Universite Paris 1 Pantheon-Sorbonne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.05.03.23289488", "rel_title": "COVID-19 Infection Is Associated with Poor Outcomes in Patients with Intracerebral Hemorrhage", @@ -102766,45 +104467,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2023.05.04.23289541", - "rel_title": "THE IMPACT OF THE COVID-19 PANDEMIC ON NON-COVID-19 COMMUNITY-ACQUIRED PNEUMONIA, A RETROSPECTIVE COHORT STUDY", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.04.23289541", - "rel_abs": "BACKGROUNDThe COVID-19 pandemic could impact frequency and mortality of non-COVID-19 community-acquired pneumonia (CAP). Changes in frequency, patient mix, treatment, and organ dysfunction could cascade together to increase mortality of CAP during compared to pre-COVID-19.\n\nMETHODSHospitalized CAP patients at St. Pauls Hospital, Vancouver, Canada pre- (fiscal years 2018/2019 and 2019/2020) and during COVID-19 pandemic (2020/2021 and 2021/2022) were evaluated.\n\nRESULTSIn 5219 CAP patients, there was no significant difference pre-versus during pandemic in mean age, gender and Charlson co-morbidity score. However, hospital mortality increased significantly from pre-versus during COVID-19 (7.5% versus 12.1% respectively, [95% CI for difference: 3.0-6.3%], p<0.001), a 61% relative increase, coincident with increases in ICU admission (18.3% versus 25.5% respectively, [95% CI for difference: 5.0-9.5%] p<0.001, 39% relative increase) and ventilation (12.7% versus 17.5%, respectively, [95% CI for difference: 2.8-6.7%] p<0.001, 38% relative increase). Results remained the same after regression adjustment for confounders. CAP hospital admissions decreased 27% from pre- (n=1349 and 1433, 2018/2019 and 2019/2020 respectively) versus the first COVID-19 pandemic year (n=1047 in 2020/2021) then rose to pre-pandemic number (n=1390 in 2021/2022). During pre-pandemic years, CAP admissions peaked in winter; during COVID-19, the CAP admissions peaked every six months.\n\nCONCLUSIONS AND RELEVANCEThe COVID-19 pandemic was associated with increases in hospital mortality, ICU admission and invasive mechanical ventilation rates of non-COVID-19 CAP and a transient, one year frequency decrease. There was no winter seasonality of CAP during the COVID-19 pandemic era. Future pandemic planning for CAP hospital care is needed.\n\nWhat is already known on this topicThe COVID-19 pandemic could impact frequency and mortality of non-COVID-19 community-acquired pneumonia (CAP). No prior study has examined this hypothesis.\n\nWhat this study addsThe COVID-19 pandemic was associated with increases in hospital mortality, ICU admission and invasive mechanical ventilation rates of non-COVID-19 CAP and a transient, one year frequency decrease. There was no winter seasonality of CAP during the COVID-19 pandemic era.\n\nHow this study might affect research, practice or policyFuture pandemic planning for CAP hospital care is needed.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Terry Lee", - "author_inst": "1.\tCentre for Health Evaluation and Outcome Science" - }, - { - "author_name": "Keith R Walley", - "author_inst": "Centre for Heart Lung Innovation, St. Paul's Hospital" - }, - { - "author_name": "John H Boyd", - "author_inst": "Centre for Heart Lung Innovation, St. Paul's Hospital" - }, - { - "author_name": "Kelly A Cawcutt", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Andre C Kalil", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "James A Russell", - "author_inst": "Centre for Heart Lung Innovation, St. Paul's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.05.01.538506", "rel_title": "Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic", @@ -104063,6 +105725,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.05.02.23289404", + "rel_title": "Sex and age-dependent alterations of drug consumption during the COVID-19 lockdown in Spain: Lessons learned for the future", + "rel_date": "2023-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.02.23289404", + "rel_abs": "In order to reduce the spread of COVID-19, lockdown has been one of the most implemented measures worldwide. Spain had one of the harshest lockdowns in Europe, impacting the social and psychological health of the population. The aim of this paper is to study how the lockdown has affected drug consumption patterns and the extent to which age and sex are influential factors. We have developed an online survey in which people were asked about their consumption of alcohol, marihuana, cocaine, and sedative and tranquilizers before and during the COVID-19 lockdown. Data revealed a general reduction in the consumption of all the drugs surveyed. Interestingly, when data was analysed by sex or age, we detected alterations in the consumption patterns depending on these variables that were of special relevance in the case of alcohol, marihuana and non-prescription sedatives and tranquilizers. Our data revealed a general decrease in the use of these drugs in the case of young adults, revealing that their use is strongly linked to social life, whereas the middle-aged population has experienced alterations in their consumption patterns, whereby their use has increased to daily. In addition, the use of non-prescription sedatives and tranquilizers has increased in specific populations. In conclusion, our data reveals important alterations during the lockdown in the consumption pattern of both legal and illegal drugs (sex and age dependent) in the Spanish population, and these alterations might be considered for future national strategies of preventative actions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jesus David Lorente", + "author_inst": "Department of Pharmacy and Pharmaceutical Technology and Parasitology, University of Valencia, Valencia, Spain" + }, + { + "author_name": "Anabel Forte", + "author_inst": "Department of Statistics and Operations Research. University of Valencia, Valencia, Spain" + }, + { + "author_name": "Javier Cuitavi", + "author_inst": "Department of Pharmacy and Pharmaceutical Technology and Parasitology, University of Valencia, Valencia, Spain" + }, + { + "author_name": "Francesc Verdu", + "author_inst": "Drug Dependence Section of the Department of Universal Health and Public Health, Generalitat Valenciana. Systems Information area of Government Delegation for t" + }, + { + "author_name": "Lucia Hipolito", + "author_inst": "Department of Pharmacy and Pharmaceutical Technology and Parasitology, University of Valencia, Valencia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2023.05.01.23289163", "rel_title": "COVID AMP: An Open Access Database of COVID-19 Response Policies", @@ -105196,65 +106893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.04.26.23289183", - "rel_title": "Temporal Trend in Mortality from COVID-19 Associated with Cardiovascular Disease", - "rel_date": "2023-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.26.23289183", - "rel_abs": "BackgroundThe COVID-19 pandemic has endured for over three years with over twelve variants afflicting humans worldwide. The impact and longevity of the pandemic has driven the medical community and researchers to identify high-risk populations, yet few studies have explored temporal trends during the pandemic. The objective of this study is to investigate trends in all-cause mortality associated with co-morbid cardiovascular disease (CVD) throughout the consecutive waves of the COVID-19 pandemic.\n\nMethodsA retrospective cohort study was conducted on patients with COVID-19 infection who received care at a tertiary care center in Chicago between March 2020 and September 2022.\n\nMultivariable logistic regression was used to investigate associations between co-existing CVD (defined as congestive heart failure, myocardial infarction, cerebrovascular disease, peripheral vascular disease) and mortality, adjusting for age, sex, race, and comorbidities defined in the Charlson comorbidity index.\n\nResultsThe study included 38651 participants (mean age 45 years, 57.6% female, 11.4% with co-existing CVD). All-cause mortality in COVID-19 patients was highest during the Delta wave and remained elevated until the late Omicron wave. Mortality associated with co-existing CVD increased during the early pandemic waves, decreased in the later waves, but remained elevated relative to the overall population. When adjusted for age, sex, and race, all-cause mortality was 2.3-fold higher in patients with co-existing CVD compared to those with non-CVD comorbidities (OR = 2.30, 95% CI 1.95 - 2.62; p < 0.001).\n\nConclusionsWhile overall mortality rates declined toward the later waves of the pandemic, all-cause mortality associated with CVD remained elevated compared to individuals without CVD.\n\nClinical PerspectiveO_ST_ABSWhat is new?C_ST_ABS- This study found that individuals with co-existing CVD have 2.3-fold higher risk of all-cause mortality compared to those with non-CVD comorbidities.\n- Mortality associated with co-existing CVD was highest during the early waves of the pandemic and declined during the later waves, yet remained elevated relative to the overall population.\n\n\nWhat are the clinical implications?- Increased all-cause mortality in COVID-19 patients with co-morbid CVD may be multifactorial from socioeconomic, psychosocial, behavioral, and biological variables.\n- Individuals with co-existing CVD who become infected with COVID-19 should be considered an at-risk population for increased mortality.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alexandra V Sarau", - "author_inst": "Rush University" - }, - { - "author_name": "Shengyuan Luo", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Elaine Yi-Shuan Chen", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Susan Gawel", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Pankaja Desai", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Nagarjuna Tippireddy", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Anil Saldanha", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Tisha M Suboc", - "author_inst": "Rush University" - }, - { - "author_name": "Gavin Cloherty", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Alan L. Landay", - "author_inst": "Rush University Medical Center" - }, - { - "author_name": "Annabelle Santos Volgman", - "author_inst": "Rush University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.27.23289157", "rel_title": "Cohort Profile: A longitudinal Victorian COVID-19 cohort (COVID PROFILE)", @@ -106533,6 +108171,245 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.04.25.538264", + "rel_title": "Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA", + "rel_date": "2023-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.25.538264", + "rel_abs": "Previous studies have documented natural infections of SARS-CoV-2 in various domestic and wild animals. More recently, studies have been published noting the susceptibility of members of the Cervidae family, and infections in both wild and captive cervid populations. In this study, we investigated the presence of SARS-CoV-2 in mammalian wildlife within the state of Vermont. 739 nasal or throat samples were collected from wildlife throughout the state during the 2021 and 2022 harvest season. Data was collected from red and gray foxes (Vulpes vulples and Urocyon cineroargentus, respectively), fishers (Martes pennati), river otters (Lutra canadensis), coyotes (Canis lantrans), bobcats (Lynx rufus rufus), black bears (Ursus americanus), and white-tailed deer (Odocoileus virginianus). Samples were tested for the presence of SARS-CoV-2 via quantitative RT-qPCR using the CDC N1/N2 primer set and/or the WHO-E gene primer set. Our results indicate that no sampled wildlife were positive for SARS-CoV-2. This finding is surprising, given that most published North America studies have found SARS-CoV-2 within their deer populations. The absence of SARS-CoV-2 RNA in populations sampled here may provide insights in to the various environmental and anthropogenic factors that reduce spillover and spread in North Americans wildlife populations.", + "rel_num_authors": 56, + "rel_authors": [ + { + "author_name": "Hannah W. Despres", + "author_inst": "University of Vermont" + }, + { + "author_name": "Margaret G. Mills", + "author_inst": "University of Washington" + }, + { + "author_name": "Madaline M. Schmidt", + "author_inst": "University of Vermont" + }, + { + "author_name": "Jolene Gov", + "author_inst": "University of Washington" + }, + { + "author_name": "Yael Perez", + "author_inst": "University of Washington" + }, + { + "author_name": "Mars Jindrich", + "author_inst": "University of Washington" + }, + { + "author_name": "Allison M. L. Crawford", + "author_inst": "University of Washington" + }, + { + "author_name": "Warren T. Kohl", + "author_inst": "University of Washington" + }, + { + "author_name": "Elias Rosenblatt", + "author_inst": "University of Washington" + }, + { + "author_name": "Hannah C. Kubinski", + "author_inst": "University of Vermont" + }, + { + "author_name": "Benjamin C. Simmons", + "author_inst": "University of Vermont" + }, + { + "author_name": "Miles C. Nippes", + "author_inst": "University of Vermont" + }, + { + "author_name": "Anne J. Goldenberg", + "author_inst": "University of Vermont" + }, + { + "author_name": "Kristina E. Murtha", + "author_inst": "University of Vermont" + }, + { + "author_name": "Samantha Nicoloro", + "author_inst": "University of Vermont" + }, + { + "author_name": "Mia J. Harris", + "author_inst": "University of Vermont" + }, + { + "author_name": "Avery C. Feeley", + "author_inst": "University of Vermont" + }, + { + "author_name": "Taylor K. Gelinas", + "author_inst": "University of Vermont" + }, + { + "author_name": "Maeve K. Cronin", + "author_inst": "University of Vermont" + }, + { + "author_name": "Robert S. Frederick", + "author_inst": "University of Vermont" + }, + { + "author_name": "Matthew Thomas", + "author_inst": "University of Vermont" + }, + { + "author_name": "Meaghan E. Johnson", + "author_inst": "University of Vermont" + }, + { + "author_name": "James Murphy", + "author_inst": "University of Vermont" + }, + { + "author_name": "Elle B. Lenzini", + "author_inst": "University of Vermont" + }, + { + "author_name": "Peter A. Carr Jr.", + "author_inst": "University of Vermont" + }, + { + "author_name": "Danielle H. Berger", + "author_inst": "University of Vermont" + }, + { + "author_name": "Soham P. Mehta", + "author_inst": "University of Vermont" + }, + { + "author_name": "Christopher J. Floreani", + "author_inst": "University of Vermont" + }, + { + "author_name": "Amelia C. Koval", + "author_inst": "University of Vermont" + }, + { + "author_name": "Aleah L. Young", + "author_inst": "University of Vermont" + }, + { + "author_name": "Jess H. Fish", + "author_inst": "University of Vermont" + }, + { + "author_name": "Jack Wallace", + "author_inst": "University of Vermont" + }, + { + "author_name": "Ella Chaney", + "author_inst": "University of Vermont" + }, + { + "author_name": "Grace Ushay", + "author_inst": "University of Vermont" + }, + { + "author_name": "Madeline Waterman", + "author_inst": "University of Vermont" + }, + { + "author_name": "Rebecca S. Ross", + "author_inst": "University of Vermont" + }, + { + "author_name": "Erin M. Vostal", + "author_inst": "University of Vermont" + }, + { + "author_name": "Maya C. Thisner", + "author_inst": "University of Vermont" + }, + { + "author_name": "Kyliegh E. Gonet", + "author_inst": "University of Vermont" + }, + { + "author_name": "Owen C. Deane", + "author_inst": "University of Vermont" + }, + { + "author_name": "Pelletiere R. Kari", + "author_inst": "University of Vermont" + }, + { + "author_name": "Vegas C. Rockafeller", + "author_inst": "University of Vermont" + }, + { + "author_name": "Madeline Waterman", + "author_inst": "University of Vermont" + }, + { + "author_name": "Tyler W. Barry", + "author_inst": "University of Vermont" + }, + { + "author_name": "Catriona C. Goering", + "author_inst": "University of Vermont" + }, + { + "author_name": "Sarah D. Shipman", + "author_inst": "University of Vermont" + }, + { + "author_name": "Allie C. Shiers", + "author_inst": "University of Vermont" + }, + { + "author_name": "Claire E. Reilly", + "author_inst": "University of Vermont" + }, + { + "author_name": "Alanna M. Duff", + "author_inst": "University of Vermont" + }, + { + "author_name": "David J. Shirley", + "author_inst": "Faraday Inc." + }, + { + "author_name": "Keith R. Jerome", + "author_inst": "Univerity of Washington" + }, + { + "author_name": "Ailyn C. P\u00e9rez-Osorio", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Nick Fortin", + "author_inst": "Vermont Agency of Natural Resources" + }, + { + "author_name": "Brittany A. Mosher", + "author_inst": "University of Vermont" + }, + { + "author_name": "Emily A. Bruce", + "author_inst": "University of Vermont" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.04.25.538336", "rel_title": "Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market", @@ -107046,61 +108923,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.04.20.23288813", - "rel_title": "Bivalent COVID-19 mRNA booster vaccination (BA.1 or BA.4/BA.5) increases neutralization of matched Omicron variants", - "rel_date": "2023-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.20.23288813", - "rel_abs": "We report SARS-CoV-2 neutralizing antibody titers in sera of triple-vaccinated individuals who received a booster dose of an original monovalent or a bivalent BA.1- or BA.4/BA.5-adapted vaccine, or had a breakthrough infection with Omicron variants BA.1, BA.2 or BA.4/BA.5. A bivalent BA.4/BA.5 booster or Omicron-breakthrough infection induced increased Omicron-neutralization titers compared with the monovalent booster. The XBB.1.5 variant effectively evaded neutralizing-antibody responses elicited by current vaccines and/or infection with previous variants.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "David Niklas Springer", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Michael Bauer", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Iris Medits", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Jeremy V. Camp", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Stephan W. Aberle", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Clemens Burtscher", - "author_inst": "Health Center Erste Bank, Austria" - }, - { - "author_name": "Eva Hoeltl", - "author_inst": "Health Center Erste Bank, Austria" - }, - { - "author_name": "Lukas Weseslindtner", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Karin Stiasny", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Judith H Aberle", - "author_inst": "Medical University of Vienna" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2023.04.19.23288799", "rel_title": "Using extracted data from Kaplan-Meier curves to compare COVID-19 vaccine efficacy", @@ -108307,6 +110129,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.04.20.537680", + "rel_title": "Establishment of a screening platform based on human coronavirus OC43 for the identification of microbial natural products with antiviral activity", + "rel_date": "2023-04-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.20.537680", + "rel_abs": "Human coronaviruses (HCoVs) cause respiratory tract infections and are of great importance due to the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Human betacoronavirus OC43 (HCoV-OC43) is an adequate surrogate for SARS-CoV-2 because it infects the human respiratory system, presents a comparable biology, and is transmitted in a similar way. Its use is advantageous since it only requires biosafety level (BSL)-2 infrastructure which minimizes costs and biosafety associated limitations. In this report, we describe a high-throughput screening (HTS) platform to identify compounds that inhibit the propagation of HCoV-OC43. Optimization of assays based on inhibition of the cytopathic effect and virus immunodetection with a specific antibody, has provided a robust methodology for the screening of a selection of microbial natural product extracts from the Fundacion MEDINA collection. Using this approach, a subset of 1280 extracts has been explored. Of these, upon hit confirmation and early LC-MS dereplication, 10 extracts were identified that contain potential new compounds. In addition, we report on the novel antiviral activity of some previously described natural products whose presence in bioactive extracts was confirmed by LC/MS analysis.\n\nIMPORTANCEThe COVID-19 pandemic has revealed the lack of effective treatments against betacoronaviruses and the urgent need for new broad-spectrum antivirals. Natural products are a valuable source of bioactive compounds with pharmaceutical potential that may lead to the discovery of new antiviral agents. Specifically, compared to conventional synthetic molecules, microbial natural extracts possess a unique and vast chemical diversity and are amenable to large-scale production. The implementation of a high-throughput screening platform using the betacoronavirus OC43 in a human cell line infection model has provided proof of concept of the approach and has allowed for the rapid and efficient evaluation of 1280 microbial extracts. The identification of several active compounds validates the potential of the platform for the search for new compounds with antiviral capacity.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Blanca Mart\u00ednez-Arribas", + "author_inst": "Consejo Superior de Investigaciones Cientificas" + }, + { + "author_name": "Frederick Boye Annang", + "author_inst": "Fundaci\u00f3n Centro De Excelencia en Investigaci\u00f3n de Medicamentos Innovadores en Andaluc\u00eda, Fundaci\u00f3n MEDINA, Granada" + }, + { + "author_name": "Rosario D\u00edaz-Gonz\u00e1lez", + "author_inst": "Consejo Superior de Investigaciones Cientificas" + }, + { + "author_name": "Guiomar P\u00e9rez-Moreno", + "author_inst": "Consejo Superior de Investigaciones Cient\u00edficas" + }, + { + "author_name": "Jes\u00fas Mart\u00edn", + "author_inst": "Fundaci\u00f3n MEDINA, Centro de Excelencia en Investigaci\u00f3n de Medicamentos Innovadores en Andaluc\u00eda" + }, + { + "author_name": "Thomas A Mackenzie", + "author_inst": "Fundacion Centro de Excelencia en Investigacion de Medicamentos Innovadores en Andalucia" + }, + { + "author_name": "Francisco Castillo", + "author_inst": "Fundacion Centro de Excelencia en Investigacion de Medicamentos Innovadores en Andalucia" + }, + { + "author_name": "Fernando Reyes", + "author_inst": "Fundaci\u00f3n MEDINA, Centro de Excelencia en Investigaci\u00f3n de Medicamentos Innovadores en Andaluc\u00eda" + }, + { + "author_name": "Olga Genilloud", + "author_inst": "Fundaci\u00f3n MEDINA, Spain" + }, + { + "author_name": "Luis Miguel Ru\u00edz-P\u00e9rez", + "author_inst": "Consejo Superior de Investigaciones Cientificas" + }, + { + "author_name": "Francisca Vicente", + "author_inst": "Fundaci\u00f3n MEDINA, Centro de Excelencia en Investigaci\u00f3n de Medicamentos Innovadores en Andaluc\u00eda" + }, + { + "author_name": "Mar\u00eda C Ramos", + "author_inst": "Fundacion Centro de Excelencia en Investigacion de Medicamentos Innovadores en Andalucia" + }, + { + "author_name": "Dolores Gonzalez-Pacanowska", + "author_inst": "Consejo Superior de Investigaciones Cientificas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.04.20.537738", "rel_title": "An in vitro experimental pipeline to characterize the binding specificity of SARS-CoV-2 neutralizing antibodies", @@ -109072,49 +110961,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.04.17.23288661", - "rel_title": "The Effect of COVID-19 Public Health Measures On Mental Health in California", - "rel_date": "2023-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.17.23288661", - "rel_abs": "California was the first state to implement statewide public health measures, including lockdown and curfews, to mitigate transmission of SARS-CoV-2. The implementation of these public health measures may have had unintended consequences related to mental health for persons in California. This study is a retrospective review of electronic health records of patients who sought care in the University of California Health System to examine changes in mental health status during the pandemic. Data were extracted prior to the pandemic (March-October 2019) and during the pandemic (March-October 2020). Weekly values of new mental health disorders were extracted and further classified based on age. Paired t-tests were performed to test for differences in the occurrence of each mental health disorder for each age group. A two-way ANOVA was performed to assess for between group differences. When compared with pre-pandemic diagnoses, persons aged 26-35 had the greatest increase in mental health diagnoses overall during the pandemic, specifically for anxiety, bipolar disorder, depression, mood disturbance, and psychosis. The mental health of persons age 25-35 were more affected than any other age group.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Milad Asgari Mehrabadi", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Erika Nurmi", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Jessica Borelli", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Natalie Lambert", - "author_inst": "Indiana Univeristy" - }, - { - "author_name": "Amir M. Rahmani", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Charles A Downs", - "author_inst": "University Of Miami" - }, - { - "author_name": "Melissa D. Pinto", - "author_inst": "University of Clifornia, Irvine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.04.19.23288791", "rel_title": "Outcomes of non-hospitalized isolation service during COVID-19 pandemic", @@ -110617,6 +112463,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.04.15.537011", + "rel_title": "SARS-CoV-2 shifts transcription of host gene to increase Spike acylation and boost infectivity", + "rel_date": "2023-04-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.15.537011", + "rel_abs": "SARS-CoV-2 infection requires Spike protein mediating fusion between the viral and cellular membranes. The fusogenic activity of Spike requires its post-translational lipid modification by host S-acyltransferases, predominantly ZDHHC20. Previous observations indicate that SARS-CoV-2 infection augments the S-acylation of Spike when compared to transfection. Here, we find that SARS-CoV-2 infection triggers a change in the transcriptional start site of the zddhc20 gene, both in cells and in an in vivo infection model, resulting in a 67-amino-acid-long N-terminally extended protein with 37-times higher Spike acylating activity, leading to enhanced viral infectivity. Furthermore, we observed the same induced transcriptional change in response to other challenges, such as chemically induced colitis, indicating that SARS-CoV-2 hijacks an existing cell damage response pathway to generate more infectious viruses.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Francisco Sarmento Mesquita", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Laurence Abrami", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Lucie Bracq", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Nattawadee Panyain", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Vincent Mercier", + "author_inst": "ACCESS, Department of Biochemistry, University of Geneva, Switzerland" + }, + { + "author_name": "Beatrice Kunz", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Audrey Chuat", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Joana Carlevaro-Fita", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "Didier Trono", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + }, + { + "author_name": "F. Gisou van der Goot", + "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.04.15.536998", "rel_title": "Human airway ex vivo models: new tools to study the airway epithelial cell response to SARS-CoV-2 infection", @@ -111102,73 +113003,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2023.04.15.23288582", - "rel_title": "Symptom persistence and biomarkers in post-COVID-19/chronic fatigue syndrome - results from a prospective observational cohort", - "rel_date": "2023-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.15.23288582", - "rel_abs": "IntroductionPost-COVID-19 syndrome (PCS) is characterized by a wide range of symptoms, predominantly fatigue and exertional intolerance. While disease courses during the first year post infection have been repeatedly described, little is known about long-term health consequences.\n\nMethodsWe assessed symptom severity and various biomarkers at three time points post infection (3-8 months (mo), 9-16mo, 17-20mo) in 106 PCS patients with moderate to severe fatigue and exertional intolerance. A subset of patients fulfilled diagnostic criteria of myalgic encephalomyelitis/chronic fatigue syndrome (PCS-ME/CFS) based on the Canadian Consensus Criteria.\n\nResultsWhile PCS-ME/CFS patients showed persisting symptom severity and disability up to 20mo post infection, PCS patients reported an overall health improvement. Inflammatory biomarkers equally decreased in both groups. Lower hand grip force at onset correlated with symptom persistence especially in PCS-ME/CFS.\n\nDiscussionDebilitating PCS may persist beyond 20mo post infection, particularly in patients fulfilling diagnostic criteria for ME/CFS.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Anna Franziska Legler", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Lil Meyer-Arndt", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Lukas Moedl", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Claudia Kedor", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Helma Freitag", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Elena Steinle", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Uta Hoppmann", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Rebekka Rust", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Frank Konietschke", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Andreas Thiel", - "author_inst": "Si-M Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Friedemann Paul", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Carmen Scheibenbogen", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Judith Bellmann-Strobl", - "author_inst": "Charite - Universitaetsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2023.04.12.23288412", "rel_title": "Severity of Prior COVID-19 Infection is Associated with Postoperative Outcomes Following Major Inpatient Surgery", @@ -112246,6 +114080,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2023.04.11.23288403", + "rel_title": "Effectiveness of mRNA COVID-19 monovalent and bivalent vaccine booster doses against Omicron severe outcomes among adults aged >=50 years in Ontario, Canada", + "rel_date": "2023-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.11.23288403", + "rel_abs": "ObjectiveWe estimated the effectiveness of booster doses of monovalent and bivalent mRNA COVID-19 vaccines against Omicron-associated severe outcomes among adults aged [≥]50 years in Ontario, Canada.\n\nMethodsWe used a test-negative design to estimate vaccine effectiveness (VE), with unvaccinated adults as the comparator, against hospitalization or death among SARS-CoV-2-tested adults aged [≥]50 years between June 19, 2022 and January 28, 2023 stratified by time since vaccination. We explored VE by vaccine product (Moderna Spikevax(R) monovalent; Pfizer-BioNTech Comirnaty(R) monovalent; Moderna Spikevax(R) BA.1 bivalent; Pfizer-BioNTech Comirnaty(R) BA.4/BA.5 bivalent).\n\nResultsWe included 3,755 Omicron cases and 14,338 test-negative controls. For the Moderna and Pfizer-BioNTech monovalent vaccines, VE 7-29 days after vaccination was 85% (95% confidence interval [CI], 72-92%) and 88% (95%CI, 82-92%), respectively, and was 82% (95%CI, 76-87%) and 82% (95%CI, 77-86%) 90-119 days after vaccination. For the Moderna BA.1 bivalent vaccine, VE was 86% (95%CI, 82-90%) 7-29 days after vaccination and was 76% (95%CI, 66-83%) 90-119 days after vaccination. For the Pfizer-BioNTech BA.4/BA.5 bivalent vaccine, VE 7-29 days after vaccination was 83% (95%CI, 77-88%) and was 81% (95%CI 72-87%) 60-89 days after vaccination.\n\nConclusionsBooster doses of monovalent and bivalent mRNA COVID-19 vaccines provided similar, strong initial protection against severe outcomes in community-dwelling adults aged [≥]50 years in Ontario. Nonetheless, uncertainty remains around waning protection of these vaccines.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Ramandip Grewal", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Lena Nguyen", + "author_inst": "ICES" + }, + { + "author_name": "Sharifa Nasreen", + "author_inst": "University of Toronto" + }, + { + "author_name": "Peter C Austin", + "author_inst": "ICES" + }, + { + "author_name": "Kevin A Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Jonathan Gubbay", + "author_inst": "BC Children's Hospital" + }, + { + "author_name": "Nelson Lee", + "author_inst": "University of Toronto" + }, + { + "author_name": "Kevin L Schwartz", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Mina Tadrous", + "author_inst": "Women's College Hospital" + }, + { + "author_name": "Kumanan Wilson", + "author_inst": "Ottawa Hospital Research Institute" + }, + { + "author_name": "Sarah E Wilson", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Jeffrey C Kwong", + "author_inst": "ICES" + }, + { + "author_name": "- on behalf of the CIRN Provincial Collaborative Network investigators", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.04.05.23288177", "rel_title": "The Impact Of COVID-19 on Health Financing in Kenya", @@ -113111,65 +115016,6 @@ "type": "confirmatory results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.04.03.535004", - "rel_title": "The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 Gamma variant", - "rel_date": "2023-04-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.03.535004", - "rel_abs": "The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity towards the viral spike protein, whether acquired from infection or vaccination. Mutations that impact N-glycosylation of spike may be particularly important in influencing antigenicity, but their consequences are difficult to predict. Here, we compare the glycosylation profiles and antigenicity of recombinant viral spike of ancestral Wu-1 and the Gamma strain, which has two additional N-glycosylation sites due to amino acid substitutions in the N-terminal domain (NTD). We found that a mutation at residue 20 from threonine to asparagine within the NTD caused the loss of NTD-specific antibody binding. Glycan site-occupancy analyses revealed that the mutation resulted in N-glycosylation switching to the new sequon at N20 from the native N17 site. Site-specific glycosylation profiles demonstrated distinct glycoform differences between Wu-1, Gamma, and selected NTD variant spike proteins, but these did not affect antibody binding. Finally, we evaluated the specificity of spike proteins against convalescent COVID-19 sera and found reduced cross-reactivity against some mutants, but not Gamma spike compared to Wuhan spike. Our results illustrate the impact of viral divergence on spike glycosylation and SARS-CoV-2 antibody binding profiles.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Cassandra L Pegg", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Naphak Modhiran", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Rhys Parry", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Benjamin Liang", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Alberto A Amarilla", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Alexander Khromykh", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Lucy Burr", - "author_inst": "Mater Health Services" - }, - { - "author_name": "Paul Young", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Keith Chappell", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Benjamin L. Schulz", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Daniel Watterson", - "author_inst": "The University of Queensland" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.04.07.535766", "rel_title": "Silymarin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells", @@ -114236,6 +116082,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.03.23287498", + "rel_title": "Longitudinal Analysis of Humoral and Cellular Immune Response Following SARS-CoV-2 Vaccination Supports Utilizing Point-Of-Care Tests to Enhance COVID-19 Booster Uptake.", + "rel_date": "2023-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.03.23287498", + "rel_abs": "Individuals with weaker neutralizing responses show reduced protection with SARS-CoV-2 variants. Booster vaccines are recommended for vaccinated individuals, but the uptake is low. We present the feasibility of utilizing point-of-care tests (POCT) to support evidence-based decision-making around COVID-19 booster vaccinations. Using infectious virus neutralization, ACE2 blocking, spike binding, and TCR sequencing assays, we investigated the dynamics of changes in the breadth and depth of blood and salivary antibodies as well as T-cell clonal response following mRNA vaccination in a cohort of healthcare providers. We evaluated the accuracy of two POCTs utilizing either blood or saliva to identify those in whom humoral immunity was inadequate. >4 months after two doses of mRNA vaccine, SARS-CoV-2 binding and neutralizing Abs (nAbs) and T-cell clones declined 40-80%, and 2/3rd lacked Omicron nAbs. After the third mRNA booster, binding and neutralizing Abs increased overall in the systemic compartment; notably, individuals with previously weak nAbs gained sharply. The third dose failed to stimulate secretory IgA, but salivary IgG closely tracked systemic IgG levels. Vaccine boosting increased Ab breadth against a divergent bat sarbecovirus, SHC014, although the TCR-beta sequence breadth was unchanged. Post 3rd booster dose, Ab avidity increased for the Wuhan and Delta strains, while avidity against Omicron and SHC014 increased to levels seen for Wuhan after the second dose. Negative results on POCTs strongly correlated with a lack of functional humoral immunity. The third booster dose helps vaccinees gain depth and breadth of systemic Abs against evolving SARS-CoV-2 and related viruses. Our findings show that POCTs are useful and easy-to-access tools to inform inadequate humoral immunity accurately. POCTs designed to match the circulating variants can help individuals with booster vaccine decisions and could serve as a population-level screening platform to preserve herd immunity.\n\nOne Sentence SummarySARS-CoV-2 point-of-care antibody tests are valuable and easy-to-access tools to inform inadequate humoral immunity and to support informed decision-making regarding the current and future booster vaccination.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Michael Mallory", + "author_inst": "Department of Microbiology & Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Jennifer E. Munt", + "author_inst": "Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Tara M. Narowski", + "author_inst": "Department of Microbiology & Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Izabella Castillo", + "author_inst": "Department of Microbiology & Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Edwing Cuadra", + "author_inst": "Department of Microbiology & Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Nora Pisanic", + "author_inst": "Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA" + }, + { + "author_name": "Paul Fields", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA." + }, + { + "author_name": "John M. Powers", + "author_inst": "Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Alexandria Dickson", + "author_inst": "Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA." + }, + { + "author_name": "Rohan Harris", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "Richard Wargowsky", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "Seamus Moran", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "Ahmed Allabban", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "Kristin Raphel", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "Timothy A. McCaffrey", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "James D. Brien", + "author_inst": "Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA." + }, + { + "author_name": "Christopher D. Heaney", + "author_inst": "Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA" + }, + { + "author_name": "John E. Lafleur", + "author_inst": "Department Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA." + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Lakshmanane Premkumar", + "author_inst": "Department of Microbiology & Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.03.23287649", "rel_title": "Early Treatment with Hydroxychloroquine and Azithromycin: A Real-Life Monocentric Retrospective Cohort Study of 30,423 COVID-19 Patients", @@ -114997,45 +116938,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.04.02.23287895", - "rel_title": "Exploratory Study to Characterise the Individual Types of Health Literacy and Beliefs and Their Associations with Infection Prevention Behaviours amid the COVID-19 Pandemic in Japan: A Longitudinal Study", - "rel_date": "2023-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.02.23287895", - "rel_abs": "BackgroundDuring a global infectious disease pandemic such as the coronavirus disease 2019 (COVID-19), individuals infection prevention/risk-taking behaviours are likely to differ depending on their health literacy and beliefs regarding the disease. To effectively promote infection prevention behaviours, it is necessary to enable information dissemination and risk communication that consider individuals health literacy and beliefs. In this study, we exploratorily characterised segments based on individual health literacy and beliefs regarding COVID-19 among the Japanese during the early stage of the COVID-19 pandemic, and investigated whether infection prevention/risk-taking behaviours and fear of COVID-19 differed among these segments.\n\nMethodsIn this study, we conducted two web-based longitudinal surveys in Japan (PHASE 1, 1-30 November 2020, 6,000 participants; PHASE 2, 1-31 December 2020, 3,800 participants). We characterised segments of the target population using cluster analysis on health literacy and beliefs regarding COVID-19 obtained in PHASE 1. We further investigated the associations between the clusters and infection prevention/risk-taking behaviours and fear of COVID-19, obtained from PHASE 2.\n\nResultsFive clusters were identified: Calm/hoax denial, Hoax affinity/threat denial, Minority/indifference, Over vigilance, and Optimism. There were significant differences in infection prevention/risk-taking behaviours and fear of COVID-19 among the five clusters. The belief in susceptibility to infection, rather than affinity for hoaxes and conspiracy theories, was coherently associated with infection prevention/risk-taking behaviours and fear of infection across clusters. This study provides foundational knowledge for creating segment-specific public messages and developing interactive risk communication to encourage infection prevention behaviours.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mao YAGIHASHI", - "author_inst": "Center for Infectious Disase Education, and Research, Osaka University" - }, - { - "author_name": "Michio Murakami", - "author_inst": "Center for Infectious Disease Education, and Research Osaka University" - }, - { - "author_name": "Mai Kato", - "author_inst": "Osaka University Graduate School of Human Sciences" - }, - { - "author_name": "Myo Yamaura", - "author_inst": "Osaka University Graduate School of Human Sciences" - }, - { - "author_name": "Asako Miura", - "author_inst": "Osaka University Graduate School of Human Sciences" - }, - { - "author_name": "Kei Hirai", - "author_inst": "Osaka University Graduate School of Human Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.04.02.535277", "rel_title": "Community structure and temporal dynamics of SARS-CoV-2 epistatic network allows for early detection of emerging variants with altered phenotypes", @@ -116114,6 +118016,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.26.23287673", + "rel_title": "Total-Body Multiparametric PET Quantification of 18F-FDG Delivery and Metabolism in the Study of COVID-19 Recovery", + "rel_date": "2023-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.26.23287673", + "rel_abs": "Conventional whole-body 18F-FDG PET imaging provides a semi-quantitative evaluation of overall glucose metabolism without gaining insight into the specific transport and metabolic steps. Here we demonstrate the ability of total-body multiparametric 18F-FDG PET to quantitatively evaluate glucose metabolism using macroparametric quantification and assess specific glucose delivery and phosphorylation processes using microparametric quantification for studying recovery from coronavirus disease 2019 (COVID-19).\n\nMethodsThe study included thirteen healthy subjects and twelve recovering COVID-19 subjects within eight weeks of confirmed diagnosis. Each subject had a dynamic 18F-FDG scan on the uEXPLORER total-body PET/CT system for one hour. Semiquantitative standardized uptake value (SUV) and SUV ratio relative to blood (SUVR) were calculated for regions of interest (ROIs) in different organs to measure glucose utilization. Tracer kinetic modeling was performed to quantify microparametric rate constants K1 and k3 that characterize 18F-FDG blood-to-tissue delivery and intracellular phosphorylation, respectively, and a macroparameter Ki that represents 18F-FDG net influx rate. Statistical tests were performed to examine differences between the healthy controls and recovering COVID-19 subjects. Impact of COVID-19 vaccination was investigated. We further generated parametric images to confirm the ROI-based analysis.\n\nResultsWe detected no significant difference in lung SUV but significantly higher lung SUVR and Ki in the recovering COVID-19 subjects, indicating an improved sensitivity of kinetic quantification for detecting the difference in glucose metabolism. A significant difference was also observed in the lungs with the phosphorylation rate k3, but not with the delivery rate K1, which suggests it is glucose phosphorylation, not glucose delivery, that drives the observed difference of glucose metabolism in the lungs. Meanwhile, there was no or little difference in bone marrow metabolism measured with SUV, SUVR and Ki, but a significant increase in bone-marrow 18F-FDG delivery rate K1 in the COVID-19 group (p < 0.05), revealing a difference of glucose delivery in this immune-related organ. The observed differences were lower or similar in vaccinated COVID-19 subjects as compared to unvaccinated ones. The organ ROI-based findings were further supported by parametric images.\n\nConclusionsHigher lung glucose metabolism and bone-marrow glucose delivery were observed with total-body multiparametric 18F-FDG PET in recovering COVID-19 subjects as compared to healthy subjects, which suggests continued inflammation due to COVID-19 during the early stages of recovery. Total-body multiparametric PET of 18F-FDG delivery and metabolism can provide a more sensitive tool and more insights than conventional static whole-body 18F-FDG imaging to evaluate metabolic changes in systemic diseases such as COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yiran Wang", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Lorenzo Nardo", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Benjamin A. Spencer", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Yasser G. Abdelhafez", + "author_inst": "University of California, Davis, and Assiut University" + }, + { + "author_name": "Elizabeth J. Li", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Negar Omidvari", + "author_inst": "University of California Davis" + }, + { + "author_name": "Abhijit J. Chaudhari", + "author_inst": "University of California Davis" + }, + { + "author_name": "Ramsey D. Badawi", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Terry Jones", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Simon R. Cherry", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Guobao Wang", + "author_inst": "University of California - Davis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2023.03.29.23287924", "rel_title": "Younger and Rural Children are More Likely to be Hospitalized for SARS-CoV-2 Infections.", @@ -116718,25 +118679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.25.23287550", - "rel_title": "ACEI or not to ACEI: Review on using ACEI and ARBs on COVID-19 patients", - "rel_date": "2023-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.25.23287550", - "rel_abs": "Purpose and motivation of this studyAngiotensin-converting enzyme inhibitors (ACEI) and Aldosterone receptor blockers (ARBs) are one most commonly used drugs for the treatment of cardiovascular disease among other comorbidities. As multiple studies have shown that covid virus binds to the ACE2 receptor for entry into the cell. ACEI and ARBs are shown to modulate the ACE2 receptor hence, it is important to see if there are any correlations between the use of medicine and the infectivity of COVID-19. The purpose of this study is to find if the use of ACEI /ARBs can in fact increase or decrease the spread of COVID-19.\n\nMethodThis is a systemic review study during which all studies which helped us answer the question, of how the use of ACEI and ARBs can affect the transmission of the COVID-19 virus, were analyzed and reviewed to draw a conclusion about clinical safety and requirements of ACEI and ARBs in COVID-19 patients.\n\nResultAfter a complete review of all the available data very conflicting results were found. Many studies showed an increase in the transmission of COVID-19 while others showed a decreased risk of COVID-19 transmission with ACEI and ARBs use. Both results were statistically significant.\n\nConclusionWith these conflicting results the question we started with comes up again. Should we or should we not use ACEI & ARBs with covid patients? What should be the best clinical response with the use of ACEI & ARBs if it modulates transmission? To answer these, one must look not only at the statistically significant results of studies but also at the disease progression without ACEI & ARBs treatment regimes. Due to the small amount of data, there is currently no clear conclusive evidence to suggest that ACE inhibitors either increase or decrease the risk of COVID-19 transmission or the severity of the disease. Thus, more and larger studies should be developed to find a concrete answer. Until that these medicines should not be discontinued as the morbidities of cardiovascular diseases are high, and the use of ACEI and ARBs is central to the treatment.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ribhav Walia", - "author_inst": "Tianjin Medical University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.28.534602", "rel_title": "Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple epitopes", @@ -117611,6 +119553,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.03.27.23287800", + "rel_title": "Lower vaccination coverage against COVID-19 in school-aged children is associated with low socioeconomic status in the Metropolitan Area of Santiago, Chile.", + "rel_date": "2023-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.27.23287800", + "rel_abs": "BackgroundThe burden of COVID-19 has been heterogeneous, indicating that the effects of this disease are synergistic with both other non-communicable diseases and socioeconomic status (SES), high-lighting its syndemic character. While the appearance of vaccines has moderated the pandemic effects, their coverage has also been heterogeneous, both when comparing different countries, and when comparing different populations within countries. Of note, once again SES appears to be a correlated factor.\n\nMethodsTo examine the relationship between SES and vaccination coverage, we analyzed publicly available data detailing the percentage of school-aged vaccinated children in different municipalities belonging to the Metropolitan Area (MA) of Santiago, Chile, one of the most largely vaccinated countries in the world. Vaccination data was compiled per school type, either public, state-subsidized and private, at three different dates along the COVID-19 pandemic so to cover the dispersion of Delta, and Omicron, including Omicron subvariants BA.4 and BA.5. We computed the median vaccination ratio for each municipality and school type and calculated their Spearmans rank correlation coefficient with each one of nine SES indices.\n\nFindingsIn the MA of Santiago, Chile, the percentage of school-age children who have received vaccinations against COVID-19 correlates with SES. Vulnerable municipalities with low SES exhibit low levels of vaccination coverage. Of note, this strong correlation is observed in both public and state-subsidized schools, but to a meaningless extent in private schools. Although inequity in vaccination coverage decreases over time, it remains higher among students enrolled either in public and state-subsidized schools compared to those of private schools.\n\nInterpretationAvailable data is insufficient to explore plausible causes behind lower vaccination coverage in vulnerable municipalities in the MA of Santiago, Chile. However, considering the available literature, it is likely that a combination of factors including the lack of proper information about the importance of vaccination, the lack of incentives for childrens vaccination, low trust in the government, and/or limited access to vaccines for lower-income people, may all have contributed to this low vaccination coverage. Importantly, unless corrected, the inequity in vaccination coverage will exacerbate the syndemic nature of COVID-19.\n\nFundingThis material is based upon work supported by the U.S. Air Force Office of Scientific Research under award number FA9550-20-1-0196. Financial support is also acknowledged to Centro Ciencia & Vida, FB210008, Financiamiento Basal para Centros Cientificos y Tecnologicos de Excelencia de ANID.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Enzo Guerrero-Araya", + "author_inst": "Fundacion Ciencia & Vida" + }, + { + "author_name": "Cesar R Ravello", + "author_inst": "Universidad San Sebastian" + }, + { + "author_name": "Mario Rosemblatt", + "author_inst": "Fundacion Ciencia & Vida, Universidad San Sebastian" + }, + { + "author_name": "Tomas Perez-Acle", + "author_inst": "Fundacion Ciencia y Vida, Universidad San Sebastian" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.22.23287571", "rel_title": "Trends in STI testing, diagnoses, and use of online chlamydia self-sampling services among young people during the first year of the COVID-19 pandemic in England", @@ -118448,65 +120421,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.24.23287677", - "rel_title": "SARS-CoV-2 convalescence and hybrid immunity elicits mucosal immune responses", - "rel_date": "2023-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287677", - "rel_abs": "Mucosal antibodies play a key role in the protection against SARS-CoV-2 infection in the upper respiratory tract, and potentially in limiting virus replication and therefore onward transmission. While systemic immunity to SARS-CoV-2 is well understood, little is known about the antibodies present on the nasal mucosal surfaces.\n\nIn this study, we evaluated SARS-CoV-2 mucosal antibodies in response to infection, vaccination, or a combination of both. Paired nasal fluid and serum samples were collected from 136 individuals, which include convalescent, vaccinated, or breakthrough infections.\n\nWe detected a high correlation between IgG responses in serum and nasal fluids, which were higher in both compartments in vaccinated compared to convalescent participants. Contrary, nasal and systemic SARS-CoV-2 IgA responses were weakly correlated, indicating a compartmentalization between the local and systemic IgA responses. SARS-CoV-2 secretory component IgA (s-IgA) antibodies, present exclusively on mucosal surfaces, were detected in the nasal fluid only in a minority of vaccinated subjects and were significantly higher in previously infected individuals. s-IgA binding antibodies showed significant correlation with neutralizing activity of nasal fluids against SARS-CoV-2 ancestral B.1 and Omicron-BA.5 variant, indicating that s-IgA is the crucial contributor to neutralization in the nasal mucosa. Neutralization against both SARS-CoV-2 strains was higher in the mucosa of subjects with previous SARS-CoV-2 infections compared to vaccinated participants.\n\nIn summary, we demonstrate that currently available vaccines elicit strong systemic antibody responses, but SARS-CoV-2 infection generates more potent binding and neutralizing mucosal antibodies. Our results support the importance to develop SARS-CoV-2 vaccines that elicit mucosal antibodies.\n\nOne Sentence SummarySARS-CoV-2 infection or combination of infection and vaccination (hybrid immunity) elicit binding and functional mucosal antibody responses superior of those after systemic vaccination.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Olha Puhach", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Mathilde Bellon", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Kenneth Adea", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Meriem Bekliz", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Krisztina Hosszu-Fellous", - "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Genev" - }, - { - "author_name": "Pascale Sattonnet", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Sophie Coudurier-Boeuf", - "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Genev" - }, - { - "author_name": "Isabelle Arm-Vernez", - "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Genev" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Genev" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Geneva Centre for Emerging Viral Diseases, Ge" - }, - { - "author_name": "Benjamin Meyer", - "author_inst": "Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.23.23287633", "rel_title": "Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 antigen testing as a case study", @@ -119393,6 +121307,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.03.21.23287546", + "rel_title": "How influenza vaccination changed over the COVID-19 pandemic?", + "rel_date": "2023-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.21.23287546", + "rel_abs": "BackgroundVaccination for seasonal influenzas is particularly important during the COVID-19 pandemic, but the influenza vaccination coverage in the U.S. was far lower than the targeted rate.\n\nObjectiveTo examine how peoples actual uptake of the influenza vaccine and the disparity of the vaccination changed during the pandemic.\n\nMethodsA survey was conducted online in November 2022. Respondents were asked for influenza vaccination during each of the three latest seasons, prior influenza vaccination history, and COVID-19 vaccination. A linear regression model was used to estimate how the respondents change in influenza vaccination was associated with their demographics, COVID-19 vaccination status, and other related variables.\n\nResultsNearly 70% of US adults had influenza vaccine each season during past the three seasons of the COVID-19 pandemic. The prevalence of influenza vaccination varied markedly across demographics. Non-Hispanic Black, Hispanic, and people with low educational attainment were more likely to see relatively negative changes in their level of influenza vaccination. Respondents who uptook their COVID-19 vaccine in 2022 increased their level of influenza vaccine more than those who uptook the vaccine in 2021.\n\nConclusionsOur study indicated that influenza vaccination increased during the pandemic compared with before the pandemic. The disparity of influenza vaccination by race/ethnicity and socioeconomic status may enlarge during the pandemic. Tailored interventions were needed to target some groups to promote their vaccination uptake.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Yong Yang", + "author_inst": "University of Memphis" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.22.23287566", "rel_title": "COVID-19 Genome Surveillance: A Geographical Landscape and Mutational Mapping of SARS-CoV-2 Variants in Central India over Two Years", @@ -119982,65 +121915,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.17.23287390", - "rel_title": "Single-cell transcriptomics identifies different immune signatures between macrophage activation-like syndrome and immune paralysis in sepsis", - "rel_date": "2023-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.17.23287390", - "rel_abs": "Different immune phenotypes characterize sepsis patients, including hyperinflammation and/or immunosuppression, but the biological mechanisms driving this heterogeneity remain largely unknown. We used single-cell RNA sequencing to profile circulating leukocytes of healthy controls and sepsis patients classified as either hyperinflammatory (macrophage activation-like syndrome [MALS]), immune paralysis, or unclassified (when criteria for neither of these two immune subgroups were applicable). Pronounced differences were detected in the transcriptional signature of monocytes from sepsis patients, with clear distinction between MALS and immune paralysis patients. Unsupervised clustering analysis revealed the existence of MALS-specific monocyte clusters, as well as one sepsis-specific monocyte cluster that was linked to disease severity. In separate cohorts, urosepsis was characterized by heterogeneous MALS and immunosuppression monocyte signatures, while MALS-specific monocyte clusters showed overlapping transcriptional signatures with severe COVID-19. In conclusion, our findings shed light on the heterogeneous immune landscape underlying sepsis, and provide opportunities for patient stratification for future therapeutic development.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Inge Grondman", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Valerie Koeken", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Athanasios Karageorgos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Wenchao LI", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Nikolaos Antonakos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Bowen Zhang", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Georgia Damoraki", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Cheng-Jian Xu", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Evangelos Giamarellos-Bourboulis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Yang Li", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Mihai Netea", - "author_inst": "Radboud University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.17.23287140", "rel_title": "Reconstructing the first COVID-19 pandemic wave with minimal data", @@ -121410,6 +123284,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.17.23287411", + "rel_title": "Protection against symptomatic SARS-CoV-2 BA.5 infection conferred by the Pfizer-BioNTech Original/BA.4-5 bivalent vaccine compared to the mRNA Original (ancestral) monovalent vaccines - a matched cohort study in France", + "rel_date": "2023-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.17.23287411", + "rel_abs": "This cohort study aimed to evaluate the protection against symptomatic SARS-CoV-2 infection conferred by the Pfizer-BioNTech Original/BA.4-5 bivalent vaccine compared to mRNA Original (ancestral) monovalent vaccines. Individuals of [≥]60 years old who received a booster dose between 03/10/2022 and 06/11/2022, when both the bivalent and monovalent vaccines were used in France, were included. Individuals who received a booster dose with (1) a monovalent Original mRNA vaccine (Pfizer- BioNTech or Moderna) or (2) the bivalent Pfizer-BioNTech Original/BA.4-5 vaccine were matched. The outcome of interest was a positive SARS-CoV-2 RT-PCR or antigenic test associated to self-reported symptoms, at least seven days after receiving the booster dose. Data were analysed with a Cox Proportional-Hazards model adjusted for the presence of previous infection, age, sex, and the presence of medium risk comorbidities. A total of 136,852 individuals were included and followed for a median period of 77 days. The bivalent vaccine conferred an additional protection of 8% [95% CI: 0% - 16%, p=0.045] against symptomatic SARS-CoV-2 infection compared to the monovalent vaccines.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Vincent Auvigne", + "author_inst": "Public Health France" + }, + { + "author_name": "Cynthia Tamandjou", + "author_inst": "Public Health France" + }, + { + "author_name": "Justine Schaeffer", + "author_inst": "Public Health France" + }, + { + "author_name": "Sophie Vaux", + "author_inst": "Public Health France" + }, + { + "author_name": "Isabelle Parent du Chatelet", + "author_inst": "Public Health France" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.17.23287413", "rel_title": "Trends in Pediatric Firearm-Related Encounters during the COVID-19 Pandemic by Age Group, Race/Ethnicity, and Schooling Mode in Tennessee", @@ -122099,49 +124008,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.16.532924", - "rel_title": "A general computational design strategy for stabilizing viral class I fusion proteins", - "rel_date": "2023-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.16.532924", - "rel_abs": "Many pathogenic viruses, including influenza virus, Ebola virus, coronaviruses, and Pneumoviruses, rely on class I fusion proteins to fuse viral and cellular membranes. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more favorable and stable postfusion state. An increasing amount of evidence exists highlighting that antibodies targeting the prefusion conformation are the most potent. However, many mutations have to be evaluated before identifying prefusion-stabilizing substitutions. We therefore established a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. As a proof of concept, we applied this principle to the fusion protein of the RSV, hMPV, and SARS-CoV-2 viruses. For each protein, we tested less than a handful of designs to identify stable versions. Solved structures of designed proteins from the three different viruses evidenced the atomic accuracy of our approach. Furthermore, the immunological response of the RSV F design compared to a current clinical candidate in a mouse model. While the parallel design of two conformations allows identifying and selectively modifying energetically less optimized positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. We recaptured many approaches previously introduced manually for the stabilization of viral surface proteins, such as cavity-filling, optimization of polar interactions, as well as postfusion-disruptive strategies. Using our approach, it is possible to focus on the most impacting mutations and potentially preserve the immunogen as closely as possible to its native version. The latter is important as sequence re-design can cause perturbations to B and T cell epitopes. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Karen J Gonzalez", - "author_inst": "University of Georgia" - }, - { - "author_name": "Jiachen Huang", - "author_inst": "University of Georgia" - }, - { - "author_name": "Miria F Criado", - "author_inst": "University of Auburn" - }, - { - "author_name": "Avik Banerjee", - "author_inst": "University of Georgia" - }, - { - "author_name": "Stephen Mark Tompkins", - "author_inst": "University of Georgia" - }, - { - "author_name": "Jarrod J Mousa", - "author_inst": "University of Georgia" - }, - { - "author_name": "Eva Maria Strauch", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.03.17.23287405", "rel_title": "Molecular Neuropathology and Cerebrospinal Fluid Diagnostic Biomarkers of SARS-Cov2 Infection in Central Nervous System: A Scoping Review Protocol", @@ -123228,6 +125094,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2023.03.15.23287292", + "rel_title": "Living alone and mental health: parallel analyses in longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic", + "rel_date": "2023-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.15.23287292", + "rel_abs": "ObjectivesTo describe the mental health gap between those who live alone and those who live with others, and to examine whether the COVID-19 pandemic had an impact on this gap.\n\nDesignTen population based prospective cohort studies, and a retrospective descriptive cohort study based on electronic health records (EHRs).\n\nSettingUK Longitudinal population-based surveys (LPS), and primary and secondary care records within the OpenSAFELY-TPP database.\n\nParticipantsParticipants from the LPS were included if they had information on living status in early 2020, valid data on mental ill-health at the closest pre-pandemic assessment and at least once during the pandemic, and valid data on a key minimum set of covariates. The EHR dataset included 16 million adults registered with primary care practices in England using TPP SystmOne software on 1st February 2020, with at least three months of registration, valid address data, and living in households of <16 people.\n\nMain outcome measuresIn the LPS, self-reported survey measures of psychological distress and life satisfaction were assessed in the nearest pre-pandemic sweep and three periods during the pandemic: April-June 2020, July-October 2020, and November 2020-March 2021. In the EHR analyses, outcomes were morbidity codes recorded in primary or secondary care between March 2018 and January 2022 reflecting the diagnoses of depression, self-harm, anxiety, obsessive compulsive disorder, eating disorders, and severe mental illnesses.\n\nResultsThe LPS consisted of 37,544 participants (15.2% living alone) and we found greater psychological distress (SMD: 0.09 (95% CI: 0.04, 0.14) and lower life satisfaction (SMD: -0.22 (95% CI: -0.30, -0.15) in those living alone pre-pandemic, and the gap between the two groups stayed similar after the onset of the pandemic. In the EHR analysis of almost 16 million records (21.4% living alone), codes indicating mental health conditions were more common in those who lived alone compared to those who lived with others (e.g., depression 26 and severe mental illness 58 cases more per 100,000). Recording of mental health conditions fell during the pandemic for common mental health disorders and the gap between the two groups narrowed.\n\nConclusionsMultiple sources of data indicate that those who live alone experience greater levels of common and severe mental illnesses, and lower life satisfaction. During the pandemic this gap in need remained, however, there was a narrowing of the gap in service use, suggesting greater barriers to healthcare access for those who live alone.\n\nSummary BoxO_ST_ABSWhat is already known on the topic?C_ST_ABSHouseholds with one individual are an increasing demographic, comprising over a quarter of all households in the UK in 2021. However, the mental health gap between those who live alone compared to those who live with others is not well described and even less is known about the relative gaps in need and healthcare-seeking and access. The pandemic and associated restrictive measures further increased the likelihood of isolation for this group, which may have impacted mental health.\n\nWhat this study adds?We present comprehensive evidence from both population-based surveys and electronic health records regarding the greater levels of mental health symptoms and in recorded diagnoses for common (anxiety, depression) and less common (OCD, eating disorders, SMIs) mental health conditions for people living alone compared to those living with others.\n\nOur analyses indicate that mental health conditions are more common among those who live alone compared to those who live with others. Although levels of reported distress increased for both groups during the pandemic, healthcare-seeking dropped in both groups, and the rates of healthcare-seeking among those who live alone converged with those who live with others for common mental health conditions. This suggests greater barriers for treatment access among those that live alone.\n\nThe findings have implications for mental health service planning and efforts to reduce barriers to treatment access, especially for individuals who live on their own.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Eoin McElroy", + "author_inst": "School of Psychology, Ulster University, Coleraine, UK" + }, + { + "author_name": "Emily Herrett", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Kishan Patel", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London, London, UK" + }, + { + "author_name": "Dominik M Piehlmaier", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford; University of Sussex Business Sch" + }, + { + "author_name": "Giorgio Di Gessa", + "author_inst": "Department of Epidemiology & Public Health, University College London, London, UK" + }, + { + "author_name": "Charlotte Huggins", + "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Michael J Green", + "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Alex SF Kwong", + "author_inst": "MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK; Division of Psychiatry, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London" + }, + { + "author_name": "Jingmin Zhu", + "author_inst": "Department of Epidemiology & Public Health, University College London, London, UK" + }, + { + "author_name": "Kathryn E Mansfield", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Richard J Silverwood", + "author_inst": "Centre for Longitudinal Studies, University College London, London, UK" + }, + { + "author_name": "Rosie Mansfield", + "author_inst": "Centre for Longitudinal Studies, University College London, London, UK" + }, + { + "author_name": "Jane Maddock", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London, London, UK" + }, + { + "author_name": "Rohini Mathur", + "author_inst": "Centre for Primary Care, Wolfson Insitute of Population Health, Queen Mary, University of London, London" + }, + { + "author_name": "Ruth E Costello", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Anthony A Matthews", + "author_inst": "Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "John Tazare", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Alasdair Henderson", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Kevin Wing", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Lucy Bridges", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford" + }, + { + "author_name": "Sebastian Bacon", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford" + }, + { + "author_name": "- OpenSafely Collaborative", + "author_inst": "" + }, + { + "author_name": "Richard John Shaw", + "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Jacques Wels", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London, London, UK" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Nishi Chaturvedi", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London, London, UK" + }, + { + "author_name": "Laurie Tomlinson", + "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" + }, + { + "author_name": "Praveetha Patalay", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Longitudinal Studies, University College London, London, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.03.15.23287298", "rel_title": "Post-COVID-19 syndrome and related dysautonomia affect patients life and work productivity", @@ -123849,37 +125850,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.03.14.532590", - "rel_title": "Persistence of SARS-CoV-2 and its surrogate, bacteriophage Phi6, on surfaces and in water", - "rel_date": "2023-03-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.14.532590", - "rel_abs": "The COVID-19 pandemic has motivated research on the persistence of infectious SARS-CoV-2 in environmental reservoirs such as surfaces and water. Viral persistence data has been collected for SARS-CoV-2 and its surrogates, including bacteriophage Phi6. Despite its wide use, no side-by-side comparisons between Phi6 and SARS-CoV-2 exist. Here, we quantified the persistence of SARS-CoV-2 and Phi6 on surfaces (plastic and metal) and in water and evaluated the influence that the deposition solution has on viral persistence by using four commonly used deposition solutions: two culture media (DMEM and Tryptone Soya Broth (TSB)), Phosphate Buffered Saline (PBS), and human saliva. Phi6 remained infectious in water significantly longer than SARS-CoV-2, having a half-life of 27 hours as compared with 15 hours for SARS-CoV-2. The persistence of viruses on surfaces was significantly influenced by the virus used and the deposition solution, but not by the surface material. Phi6 remained infectious significantly longer than SARS-CoV-2 when the inoculation solution was culture media (DMEM, TSB) and saliva. Using culture media and saliva led to half-lives between 9 hours and 2 weeks for Phi6, as compared to 0.5 to 2 hours for SARS-CoV-2. Using PBS as a deposition solution led to half-lives shorter than 4 hours for both viruses on all surfaces. Our results showed that, although it has been frequently used as a surrogate for coronaviruses, bacteriophage Phi6 is not an adequate surrogate for studies quantifying SARS-CoV-2 persistence, as it over-estimates infectiousness. Additionally, our findings reveal the need of using adequate deposition solutions when evaluating viral persistence on surfaces.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ana K Pitol", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Samiksha Venkatesan", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Michael Hoptroff", - "author_inst": "Unilever Research and Development" - }, - { - "author_name": "Grant L Hughes", - "author_inst": "Liverpool School of Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.03.14.532528", "rel_title": "Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants", @@ -124742,6 +126712,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.09.23286855", + "rel_title": "Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types", + "rel_date": "2023-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23286855", + "rel_abs": "ImportanceAt-home rapid COVID-19 tests utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater exposure and transmission to contacts.\n\nObjectiveWe assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity but longer turnaround times, and/or that utilize non-nasal specimen types).\n\nDesignIn this observational cohort study, members of households with a recent COVID-19 case were screened for infection at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. Participants reported demographic/medical information (including COVID-19 testing), symptom and exposure information, and household infection-control practices. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case).\n\nSettingSouthern California, September 2020--June 2021 and November 2021--March 2022.\n\nParticipantsCohort of 370 individuals from 85 households.\n\nMain Outcome(s) and Measure(s)Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR).\n\nResultsAn aSAR of 53.6% (95% CI 38.8-68.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% 95% CI 19.5- 35.0%, P=0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95% CI 1.65-14.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types.\n\nConclusions and RelevanceUse of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may not limit transmission as well as other test types.\n\nKey Points1. QuestionDoes identification of index cases by rapid nasal-swab tests limit household transmission of SARS-CoV-2 as well as other test types?\n\n2. FindingSignificantly higher adjusted secondary attack rates and adjusted odds ratios for transmission were observed in households where the index case used a nasal rapid COVID-19 test for initial detection versus other test types.\n\n3. MeaningThe use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may not limit transmission as well as other test types.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jenny Ji", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Alexander Viloria Winnett", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Natasha Shelby", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jessica A. Reyes", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Noah W. Schlenker", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Hannah Davich", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Saharai Caldera", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Colten Tognazzini", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Ying-Ying Goh", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Matthew Feaster", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Rustem F. Ismagilov", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.09.23286797", "rel_title": "Molecular pathology of acute respiratory distress syndrome, mechanical ventilation and abnormal coagulation in severe COVID-19", @@ -125367,45 +127396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.08.23286582", - "rel_title": "Assessing the utility of COVID-19 case reports as a leading indicator for hospitalization forecasting in the United States", - "rel_date": "2023-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.08.23286582", - "rel_abs": "Identifying data streams that can consistently improve the accuracy of epidemiological forecasting models is challenging. Using models designed to predict daily state-level hospital admissions due to COVID-19 in California and Massachusetts, we investigated whether incorporating COVID-19 case data systematically improved forecast accuracy. Additionally, we considered whether using case data aggregated by date of test or by date of report from a surveillance system made a difference to the forecast accuracy. Evaluating forecast accuracy in a test period, after first having selected the best-performing methods in a validation period, we found that overall the difference in accuracy between approaches was small, especially at forecast horizons of less than two weeks. However, forecasts from models using cases aggregated by test date showed lower accuracy at longer horizons and at key moments in the pandemic, such as the peak of the Omicron wave in January 2022. Overall, these results highlight the challenge of finding a modeling approach that can generate accurate forecasts of outbreak trends both during periods of relative stability and during periods that show rapid growth or decay of transmission rates. While COVID-19 case counts seem to be a natural choice to help predict COVID-19 hospitalizations, in practice any benefits we observed were small and inconsistent.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nicholas G Reich", - "author_inst": "University of Massachusetts - Amherst" - }, - { - "author_name": "Yijin Wang", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Meagan Burns", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Rosa Ergas", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Estee Y. Cramer", - "author_inst": "University of Massachusetts - Amherst" - }, - { - "author_name": "Evan Lowell Ray", - "author_inst": "University of Massachusetts, Amherst" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.10.23287107", "rel_title": "Sociodemographic inequity in COVID-19 vaccine uptake among youth in Zimbabwe", @@ -126568,6 +128558,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.06.23286853", + "rel_title": "Oral SARS-CoV-2 host responses predict the early COVID-19 disease course", + "rel_date": "2023-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286853", + "rel_abs": "ObjectivesOral fluids provide ready detection of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host responses. This study sought to determine relationships between oral virus, oral anti-SARS-CoV-2-specific antibodies, and symptoms.\n\nMethodsSaliva/throat wash (saliva/TW) were collected from asymptomatic and symptomatic, nasopharyngeal (NP) SARS-CoV-2 RT-qPCR+, subjects (n=47). SARS-CoV-2 RT-qPCR, N-antigen detection by immunoblot and lateral flow assay (LFA) were performed. RT-qPCR targeting viral subgenomic RNA (sgRNA) was sequence confirmed. SARS-CoV-2-anti-S protein RBD LFA assessed IgM and IgG responses. Structural analysis identified host salivary molecules analogous to SARS-CoV-2-N-antigen. Statistical analyses were performed.\n\nResultsAt baseline, LFA-detected N-antigen was immunoblot-confirmed in 82% of TW. However, only 3/17 were saliva/TW qPCR+. Sixty percent of saliva and 83% of TW demonstrated persistent N-antigen at 4 weeks. N-antigen LFA signal in three negative subjects suggested potential cross-detection of 4 structurally analogous salivary RNA binding proteins (alignment 19-29aa, RMSD 1-1.5 Angstroms). At entry, symptomatic subjects demonstrated replication-associated sgRNA junctions, were IgG+ (94%/100% in saliva/TW), and IgM+ (75%/63%). At 4 weeks, SARS-CoV-2 IgG (100%/83%) and IgM (80%/67%) persisted. Oral IgG correlated 100% with NP+PCR status. Cough and fatigue severity (p=0.0008 and 0.016), and presence of nausea, weakness, and composite upper respiratory symptoms (p=0.005, 0.037 and 0.017) were negatively associated with oral IgM. Female oral IgM levels were higher than male (p=0.056).\n\nConclusionImportant to transmission and disease course, oral viral replication and persistence showed clear relationships with select symptoms, early Ig responses, and gender during early infection. N-antigen cross-reactivity may reflect mimicry of structurally analogous host proteins.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "William T Seaman", + "author_inst": "National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "Olive Keener", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Wenwen Me", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Katie R Mollan", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Corbin D Jones", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Audrey Pettifor", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Natalie M Bowman", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "- UNC OBSc Working Group", + "author_inst": "-" + }, + { + "author_name": "Frank Wang", + "author_inst": "Biomedomics Inc, Morrisville, NC" + }, + { + "author_name": "Jennifer Webster-Cyriaque", + "author_inst": "National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.03.23286284", "rel_title": "Trends in Antibody Titers after SARS-CoV-2 Vaccination - Insights from a Self-Paid Tests at a General Internal Medicine Clinic", @@ -127161,45 +129206,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2023.03.07.23286911", - "rel_title": "The impact of COVID-19-related disruptions to HPV vaccination - a modelled analysis", - "rel_date": "2023-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286911", - "rel_abs": "COVID-19 disrupted school attendance in many countries, delaying routine adolescent vaccination against human papillomavirus (HPV) in some settings. We used the Policy1-Cervix HPV model (natural history/vaccination/screening/HPV-related cancers), to estimate the impact on HPV-related cancers from disruptions to HPV vaccination in a high-income setting. Compared to no disruption (nonavalent vaccine uptake, age 12 [females:82.4%; males:75.5%] as in Australia), additional lifetime HPV-related cancer cases were calculated for three disruption scenarios affecting one birth cohort (2008): i) 1-year delay (no doses missed); ii) 1 to 7-year delay (slow catch-up); iii) no catch-up (herd effects only). A fourth scenario assumed no catch-up for two cohorts (2008,2009). We found a 1-year delay could result in [≤]0.3% more HPV-related cancers (n=4) but the increase would be greater if catch-up was slower (5%; n=70), and especially if there was no catch-up (49%; n=750). Additional cancers for a single missed cohort were most commonly cervical (23%), oropharyngeal (males:20%) or anal (females:16%). In the worst-case scenario of two cohorts missing vaccination, [≤]62% more HPV-related cancers would be diagnosed (n=1,892). In conclusion, providing catch-up of missed HPV vaccines is conducted, short-term delays in vaccinating adolescents are unlikely to have substantial long-term effects on cancer.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Louiza S Velentzis", - "author_inst": "Daffodil Center" - }, - { - "author_name": "Megan A. Smith", - "author_inst": "Daffodil Center" - }, - { - "author_name": "James Killen", - "author_inst": "Daffodil Center" - }, - { - "author_name": "Julia ML Brotherton", - "author_inst": "Australian Centre for the Prevention of Cervical Cancer" - }, - { - "author_name": "Rebecca Guy", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Karen Canfell", - "author_inst": "Daffodil Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.03.07.23286894", "rel_title": "Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance", @@ -128314,6 +130320,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.05.531213", + "rel_title": "The significant yet short-term influence of research covidization on journal citation metrics", + "rel_date": "2023-03-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.05.531213", + "rel_abs": "COVID-19 has emerged as a significant research hotspot in recent years, leading to a surge in production and citations received by COVID-19 papers. While concerns have been raised about the potential citation boost on journals associated with publishing COVID-19 papers, the extent and mechanisms of such gain remain unclear. This study uses a generalized difference-in-differences approach to examine the impact of publishing COVID-19 papers on journal citations and related metrics in four highly covidized fields. Our results demonstrate that journals starting publishing COVID-19 papers in health sciences fields in 2020 experienced a significant increase in citations compared with other journals. This trend continued in 2021, although to a lesser extent. However, such citation premiums became insignificant for journals starting to publish COVID-19 papers in 2021. In some fields, we also observed that COVID-19 papers increased the citations of non-COVID-19 papers in the same journals, but only for journals starting to publish COVID-19 papers in 2020. Our heterogeneity test indicates that COVID-19 papers published in prestigious journals brought more significant citation premiums to the journals and non-COVID-19 papers in most fields. We finally show that these citation premiums can affect various citation-based journal metrics. Our findings reveal a \"gold rush\" pattern in which early entrants are more likely to establish their citation advantage in research hotspots and caution against using such metrics to evaluate journal quality.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Xiang Zheng", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Chaoqun Ni", + "author_inst": "University of Wisconsin-Madison" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2023.03.03.23286122", "rel_title": "Phenome-wide association study to explore the long-term symptoms after infection with novel coronavirus in the UK Biobank", @@ -128983,93 +131012,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.01.23286420", - "rel_title": "MANAGEMENT OF RISK FACTORS FOR HEALTH CARE WORKERS AFTER INITIAL CONTACT WITH PATIENTS INFECTED WITH SARS-CoV-2 IN NIAMEY, THE CENTER OF THE EPIDEMIC IN NIGER", - "rel_date": "2023-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.01.23286420", - "rel_abs": "BackgroundThe covid-19 pandemic is caused by a new corona virus called SARS Cov-2. Health care workers are particularly exposed target.\n\nAimthis study aims to analyze the risk factors of SARS-Cov-2 infection in health workers who have been in contact with positive patient.\n\nMethodsThis is a prospective cohort conducted among health workers from March 2022 to January 2021 in health care facilities in Niamey. A questionnaire was administrated at inclusion. rRT-PCR was performed if clinical signs were present. ELISA testing was performed at baseline, day15 and day 30. The chi-square or Fisher test, Kaplan-Meir survival model, Cow regression and logistic regression were used as statistical test.\n\nResults259 health workers were included. More than half of the respondents were female. 45.95% of the participants were nurses and 36.68% were physicians. The prevalence of Covid-19 was 28.8%. 56.4% of the participants had positive serology at day 30. The risk factors associated with Covid-19 were professional category (p=0.024). Membership structure (p<0.001) and the chronic liver disease (p=0.034). Hand hygiene (p=0.019) and alcohol-based hand cleaning (p<0.001) protects against the occurrence of SARS-Cov-2 infection. According to the characterization of the preventive measures those who practiced them rarely were associated with a positive rRT-PCR and those who practice them occasionally or most of the time were associated with negative serology and rRT-PCR.\n\nConclusionComorbidities, function and affiliation are the main risk factors for Covid-19 and hand hygiene is a protective factor.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "HAMIDOU LAZOUMAR Ramatoulaye", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Aliou Sanda Abdal-Kader", - "author_inst": "Facult\u00e9 des Sciences et Technique de l'Universit\u00e9 Abdou Moumouni de Niamey" - }, - { - "author_name": "Adamou Lagare", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Mahamadou Maiga", - "author_inst": "EPICENTRE" - }, - { - "author_name": "Fakani Aboutalib Aliane", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Fran\u00e7ois Comlan Aida Sylviane", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Idi Issa", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Bibata Abdou Sidikou", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Garda Id\u00e9 Oumarou", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Zeinabou Abdou Aouta", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Amina Moussa", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Zeinabou Dioffo Alassan", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Ibrahim Karidjo", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - }, - { - "author_name": "Goni Alhassane Maman Bachir", - "author_inst": "Facult\u00e9 des Sciences de la Sant\u00e9 de l'Universit\u00e9 Andr\u00e9 Salifou de Zinder" - }, - { - "author_name": "Issifou Djibo", - "author_inst": "Direction de la Surveillance et de la Riposte aux Epid\u00e9mies (DSRE)" - }, - { - "author_name": "Salia Moussa", - "author_inst": "Hopital G\u00e9n\u00e9ral de R\u00e9f\u00e9rence" - }, - { - "author_name": "ibrahim Maman Laminou", - "author_inst": "CERMES: Centre de Recherche Medecine Sciences Sante Sante Mentale Societe" - }, - { - "author_name": "Ronan Jambou", - "author_inst": "Centre de Recherche M\u00e9dicale et Sanitaire (CERMES)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.01.23286624", "rel_title": "Risk of cardiovascular events following COVID-19 in people with and without pre-existing chronic respiratory disease", @@ -129984,6 +131926,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.27.23286501", + "rel_title": "Combining models to generate a consensus effective reproduction number R for the COVID-19 epidemic status in England", + "rel_date": "2023-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.27.23286501", + "rel_abs": "The effective reproduction number R was widely accepted as a key indicator during the early stages of the COVID-19 pandemic. In the UK, the R value published on the UK Government Dashboard has been generated as a combined value from an ensemble of epidemiological models via a collaborative initiative between academia and government. In this paper we outline this collaborative modelling approach and illustrate how, by using an established combination method, a combined R estimate can be generated from an ensemble of epidemiological models. We analyse the R values calculated for the period between April 2021 and December 2021, to show that this R is robust to different model weighting methods and ensemble size, and that using heterogeneous data sources for validation increases its robustness and reduces the biases and limitations associated with a single source of data. We discuss how R can be generated from different data sources and is therefore a good summary indicator of the current dynamics in an epidemic.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Harrison Manley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Josie Park", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Luke Bevan", + "author_inst": "University College London" + }, + { + "author_name": "Alberto Sanchez-Marroquin", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Gabriel Danelian", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Thomas Bayley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Veronica Bowman", + "author_inst": "Defence Science and Technology Laboratory" + }, + { + "author_name": "Thomas Maishman", + "author_inst": "Defence Science and Technology Laboratory" + }, + { + "author_name": "Thomas Finnie", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Andre Charlett", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "- Nowcasts Models Contribution Group", + "author_inst": "-" + }, + { + "author_name": "Nicholas A Watkins", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Johanna Hutchinson", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Steven Riley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.27.23286454", "rel_title": "Mixed methods approach to examining the implementation experience of a phone-based health research survey investigating risk factors for SARS-CoV-2 infection in California", @@ -130729,177 +132746,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.27.530277", - "rel_title": "Engineered Immunogens to Expose Conserved Epitopes Targeted by Broad Coronavirus Antibodies", - "rel_date": "2023-02-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.27.530277", - "rel_abs": "Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employed computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant RBD. These engineered proteins bound with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interacted with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicited sera with broad betacoronavirus reactivity and protected as \"boosts\" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Brenda Kapingidza", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Daniel J Marston", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Caitlin Harris", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Daniel Wrapp", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Kaitlyn Winters", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Duke University, Durham, NC" - }, - { - "author_name": "Dieter Mielke", - "author_inst": "Department of Surgery, Duke University, Durham, NC. Center for Human Systems Immunology, Duke University, Durham, NC, USA" - }, - { - "author_name": "Lu Xiaozhi", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Qi Yin", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Andrew Foulger", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Rob Parks", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Maggie Barr", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Amanda Newman", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Alexandra Schaefer", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Amanda Eaton", - "author_inst": "Department of Surgery, Duke University, Durham, NC" - }, - { - "author_name": "Justine Mae Flores", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Austin Hamer", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Nicholas J Cantazaro Jr.", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Michael L Mallory", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Melissa D Mattocks", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Christopher Berverly", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Brianna Rhodes", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Katayoun Mansouri", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC" - }, - { - "author_name": "Elizabeth Van Itallie", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Pranay Vure", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Duke University, Durham, NC" - }, - { - "author_name": "Brooke Manness", - "author_inst": "Department of Surgery, Duke University, Durham, NC" - }, - { - "author_name": "Taylor Keyes", - "author_inst": "Department of Surgery, Duke University, Durham, NC" - }, - { - "author_name": "Sherry Stanfield-Oakley", - "author_inst": "Department of Surgery, Duke University, Durham, NC" - }, - { - "author_name": "Christopher W Woods", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC; Center for Infectious Diseases and Diagnostic In" - }, - { - "author_name": "Elizabeth A Petzold", - "author_inst": "Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC" - }, - { - "author_name": "Emmanuel B Walter", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Pediatrics, Duke University, Durham, NC" - }, - { - "author_name": "Kevin Wiehe", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Robert J Edwards", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC. Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "David Montefiori", - "author_inst": "Department of Surgery, Duke University, Durham, NC" - }, - { - "author_name": "Guido Ferrari", - "author_inst": "Duke Human Vaccine Institute; Department of Surgery; Center for Human Systems Immunology; Department of Molecular Genetics and Microbiology, Duke University, Du" - }, - { - "author_name": "Ralph Baric", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Derek W Cain", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - }, - { - "author_name": "Kevin O Saunders", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Immunology, Duke University, Durham, NC; Department of Surgery, Duke University, Durham" - }, - { - "author_name": "Barton F Haynes", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC; Department of Immunology, Duke University, Durha" - }, - { - "author_name": "Mihai L Azoitei", - "author_inst": "Duke Human Vaccine Institute, Duke University, Durham, NC; Department of Medicine, Duke University, Durham, NC" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.02.27.530294", "rel_title": "Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor", @@ -131782,6 +133628,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.23.23286390", + "rel_title": "Was access and quality of healthcare affected during COVID-19 pandemic? A qualitative enquiry into healthcare access for non-communicable diseases in Central India", + "rel_date": "2023-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.23.23286390", + "rel_abs": "ObjectiveCOVID-19 pandemic has had significant impacts on healthcare systems across the world. However, its impact on healthcare systems in Low- and Middle-Income Countries (LMICs) has been especially devastating, resulting in restricted access to healthcare. The present study was conducted to assess healthcare access for non-communicable diseases (NCDs) in Central India.\n\nDesignInductive and deductive thematic analysis of in-depth semi-structured interviews.\n\nSettingStudy was conducted in communities of two urban and rural districts of central India.\n\nParticipantsInterviewed participants included PLNCDs, their caregivers, community dwellers, CHWs such as, Accredited Social Health Activists (ASHAs) and Anganwadi Workers (AWWs), Medical Officers, and Community Leaders. Recruitment of the participants was done via purposive and convenience sampling.\n\nResultA total of fifty Key Informant Interviews were (KIIs) conducted. All participants reported facing considerable difficulties while trying to access care from both public as well as private healthcare facilities. Absence of staff, equipment and medicines, restricted commute, misconceptions regarding the spread of COVID-19, and the stigma attached to COVID-19 infection acted as major barriers to accessing care, while door-to-door visits by community health workers, community support, and presence of privately owned healthcare facilities in the vicinity acted as facilitators.\n\nConclusionIn our study, we found that continued functioning of primary healthcare centres, ensuring uninterrupted supply of medicine and effective dissemination of information regarding COVID-19 could have acted to ease access to healthcare. Going ahead, capacity building to offset the impact of future emergencies and pandemics should be a crucial consideration while developing resilient healthcare systems.\n\nStrengths and limitations of this studyO_LIOur study is the first study to explore the barriers faced by PLNCDs of low socio-economic status during the pandemic.\nC_LIO_LIWe explored the perspectives of both patients and healthcare workers before triangulating the data findings.\nC_LIO_LIThe study was conducted in the PLNCDs of lower socio-economic group and hence the perspectives and experiences of other socio-economic groups are yet to be explored.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Raunaq Singh Nagi", + "author_inst": "All India Institute of Medical Sciences, Bhopal" + }, + { + "author_name": "Anirban Chatterjee", + "author_inst": "All India Institute of Medical Sciences-Bhopal" + }, + { + "author_name": "Kritika Singhal", + "author_inst": "All India Institute of Medical Sciences-Bhopal" + }, + { + "author_name": "Arun Mahadeo Kokane", + "author_inst": "All India Institute of Medical Sciences-Bhopal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2023.02.21.23286239", "rel_title": "Performance of Rapid Antigen Tests Based on Symptom Onset and Close Contact Exposure: A secondary analysis from the Test Us At Home prospective cohort study", @@ -132587,121 +134464,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.15.23285923", - "rel_title": "Rapid emergence of transmissible SARS-CoV-2 variants in mild community cases", - "rel_date": "2023-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285923", - "rel_abs": "SARS-CoV-2 immune-escape variants have only been observed to arise in immunosuppressed COVID-19 cases, during prolonged viral shedding. Through daily longitudinal RT-qPCR, quantitative viral culture and sequencing, we observe for the first time the evolution of transmissible variants harbouring mutations consistent with immune-escape in mild community cases within 2 weeks of infection.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Michael Andrew Crone", - "author_inst": "Imperial College London" - }, - { - "author_name": "Seran Hakki", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Imperial College London" - }, - { - "author_name": "Carolina Rosadas de Oliveira", - "author_inst": "Imperial College London" - }, - { - "author_name": "Kieran J Madon", - "author_inst": "Imperial College London" - }, - { - "author_name": "Aleksandra V Koycheva", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anjna Badhan", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jakob Jonnerby", - "author_inst": "Imperial College London" - }, - { - "author_name": "Joe Fenn", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rhia Kundu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jack L Barnett", - "author_inst": "Imperial College London" - }, - { - "author_name": "Sean Nevin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Emily Conibear", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nieves Derqui-Fernandez", - "author_inst": "Imperial College London" - }, - { - "author_name": "Timesh D Pillay", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert Varro", - "author_inst": "Imperial College London" - }, - { - "author_name": "Constanta Luca", - "author_inst": "Imperial College London" - }, - { - "author_name": "Valerie Quinn", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ahmad Shazaad", - "author_inst": "Manchester University NHS Foundation Trust" - }, - { - "author_name": "Maria Zambon", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Wendy Barclay", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jake Dunning", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul S Freemont", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graham P Taylor", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ajit Lalvani", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.22.23286293", "rel_title": "SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues", @@ -133576,6 +135338,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.02.17.23286049", + "rel_title": "Evidence of Leaky Protection Following COVID-19 Vaccination and SARS-CoV-2 Infection in a US Correctional Facility Population", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286049", + "rel_abs": "Whether SARS-CoV-2 infection and COVID-19 vaccines confer exposure-dependent (\"leaky\") protection against infection remains unknown. We examined the effect of prior infection, vaccination, and hybrid immunity on infection risk among residents of Connecticut correctional facilities during periods of predominant Omicron and Delta transmission. Residents with cell, cellblock, and no documented exposure to SARS-CoV-2 infected residents were matched by facility and date. During the Omicron period, prior infection, vaccination, and hybrid immunity reduced the infection risk of residents without a documented exposure (HR: 0.36 [0.25-0.54]; 0.57 [0.42-0.78]; 0.24 [0.15-0.39]; respectively) and with cellblock exposures (0.61 [0.49-0.75]; 0.69 [0.58-0.83]; 0.41 [0.31-0.55]; respectively) but not with cell exposures (0.89 [0.58-1.35]; 0.96 [0.64-1.46]; 0.80 [0.46-1.39]; respectively). Associations were similar during the Delta period and when analyses were restricted to tested residents. Although associations may not have been thoroughly adjusted due to dataset limitations, the findings suggest that prior infection and vaccination may be leaky, highlighting the potential benefits of pairing vaccination with non-pharmaceutical interventions in crowded settings.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Margaret L Lind", + "author_inst": "Yale University" + }, + { + "author_name": "Murilo Dorion", + "author_inst": "Yale University" + }, + { + "author_name": "Amy J Houde", + "author_inst": "Connecticut Department of Correction" + }, + { + "author_name": "Mary Lansing", + "author_inst": "Connecticut Department of Correction" + }, + { + "author_name": "Sarah Lapidus", + "author_inst": "Yale University" + }, + { + "author_name": "Russell Thomas", + "author_inst": "Yale University" + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Yale University" + }, + { + "author_name": "Saad B Omer", + "author_inst": "Yale University" + }, + { + "author_name": "Wade L Schulz", + "author_inst": "Yale University" + }, + { + "author_name": "Jason R Andrews", + "author_inst": "Stanford University" + }, + { + "author_name": "Matt DT Hitchings", + "author_inst": "University of Florida" + }, + { + "author_name": "Byron S Kennedy", + "author_inst": "Connecticut Department of Correction" + }, + { + "author_name": "Robert P Richeson", + "author_inst": "Connecticut Department of Correction" + }, + { + "author_name": "Derek AT Cummings", + "author_inst": "University of Florida" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.17.23286059", "rel_title": "A unique cytotoxic CD4+ T cells signature defines critical COVID-19", @@ -134309,25 +136146,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.02.17.23286115", - "rel_title": "An SEIDR Model for the Early Spread of COVID-19", - "rel_date": "2023-02-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286115", - "rel_abs": "In this article, we conduct a literature review on the history and mathematical modeling of infectious diseases and COVID-19. Next, some simple epidemic dynamic models and the basic reproductive number theory are introduced. We propose a SEIDR model for COVID-19 and provide the solution methods for the basic reproduction number, parameters, and dynamic model. Finally, we simulate the early stages of the COVID-19 epidemic in Argentina, Indonesia, Mexico, and South Africa with the SEIDR model.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Tingrui Cao", - "author_inst": "HarrowSchool HongKong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.13.23285851", "rel_title": "Athlete deaths during the COVID-19 vaccination campaign: contextualisation of online information", @@ -135350,6 +137168,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.17.528968", + "rel_title": "Speedy-PASEF: Analytical flow rate chromatography and trapped ion mobility for deep high-throughput proteomics", + "rel_date": "2023-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.17.528968", + "rel_abs": "Increased throughput in proteomic experiments can improve accessibility of proteomic platforms, reduce costs and facilitate new approaches in systems biology and biomedical research. Here we propose Speedy-PASEF, a combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition and data analysis with the DIA-NN software suite, for conducting fast, high-quality proteomic experiments that require only moderate sample amounts. For instance, using a 500-l/min flow rate and a 3-minute chromatographic gradient, Speedy-PASEF quantified 5,211 proteins from 2 g of a mammalian cell-line standard at high quantitative accuracy and precision. We further used Speedy-PASEF to analyze blood plasma samples from a cohort of COVID-19 inpatients, using a 3-minute chromatographic gradient and alternating column regeneration on a dual pump system, for processing 398 samples per day. Speedy-PASEF delivered a comprehensive view of the COVID-19 plasma proteome, allowing classification of the patients according to disease severity and revealing plasma biomarker candidates. Speedy-PASEF thus facilitates acquisition of high-quality proteomes in large numbers.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lukasz Szyrwiel", + "author_inst": "Department of Biochemistry, Charite, Universitaetsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Christoph Gille", + "author_inst": "Department of Biochemistry, Charite, Universitaetsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Michael Muelleder", + "author_inst": "Core Facility High-Throughput Mass Spectrometry, Charite Universitaetsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Vadim Demichev", + "author_inst": "Department of Biochemistry, Charite Universitaetsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Markus Ralser", + "author_inst": "Department of Biochemistry, Charite Universitaetsmedizin Berlin, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.02.18.23286126", "rel_title": "Mental health symptoms in Latin America during the first year of COVID-19 pandemic: a meta-analysis of prevalence and potential moderator variables", @@ -135863,41 +137716,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.02.16.23286041", - "rel_title": "Effectiveness of SARS-CoV-2 Vaccines against Omicron Infection and Severe Events: A Systematic Review and Meta-Analysis of Test-Negative Design Studies", - "rel_date": "2023-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.16.23286041", - "rel_abs": "BackgroundEvaluating vaccine effectiveness (VE) of a full vaccine series and booster doses against COVID-19 is important for health decision-making.\n\nMethodsWe systematically searched papers that evaluated VE of SARS-CoV-2 vaccines on PubMed, Web of Science, Cochrane Library, Google Scholar, Embase, Scopus, and preprint servers (bioRxiv and medRxiv) published from November 26th, 2021 to June 27th, 2022 (for full doses and first booster), and to January 8th, 2023 (for the second booster). The pooled VE against Omicron-associated symptomatic or any infection as well as severe events are estimated in a meta-analysis framework.\n\nResultsFrom 2,552 citations identified, a total of 42 were included. The vaccination of the first booster provided stronger protection against Omicron than the full doses alone, shown by the VE estimates of 53.1% (95% CI: 48.0-57.8) vs. 28.6% (95% CI: 18.5-37.4) against infection and 82.5% (95% CI: 77.8-86.2) vs. 57.3% (95% CI: 48.5-64.7) against severe disease. The second booster offered strong protection among adults within 60 days of vaccination against infection (VE=53.1%, 95% CI: 48.0-57.8) and severe disease (VE=87.3% (95% CI: 75.5-93.4), comparable to the first booster with corresponding VE estimates of 59.9% against infection and 84.8% against severe disease. The VEs of the booster doses against severe disease among adults sustained beyond 60 days, 77.6% (95% CI: 69.4-83.6) for the first and 85.9% (95% CI: 80.3-89.9) for the second booster. The VE against infection was less sustainable regardless of dose type. Pure mRNA vaccines provided comparable protection to partial mRNA vaccines, but both provided higher protection than non-mRNA vaccination.\n\nConclusionOne or two booster doses of current SARS-CoV-2 vaccines provide considerable protection against Omicron infection and substantial and sustainable protection against Omicron-induced severe clinical outcomes.\n\nFundingUS CDC U01 CK000670", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shangchen Song", - "author_inst": "University of Florida" - }, - { - "author_name": "Zachary J. Madewell", - "author_inst": "University of Florida" - }, - { - "author_name": "Mingjin Liu", - "author_inst": "University of Florida" - }, - { - "author_name": "Ira M. Longini Jr.", - "author_inst": "University of Florida" - }, - { - "author_name": "Yang Yang", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.17.528914", "rel_title": "A burns and COVID-19 shared stress responding gene network deciphers CD1C-CD141- DCs as the key cellular components in septic prognosis", @@ -137048,6 +138866,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.16.23285816", + "rel_title": "Estimates of protection against SARS-CoV-2 infection and severe COVID-19 in Germany before the 2022/2023 winter season - the IMMUNEBRIDGE project", + "rel_date": "2023-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.16.23285816", + "rel_abs": "Despite the need to generate valid and reliable estimates of protection against SARS-CoV-2 infection and severe course of COVID-19 for the German population in summer 2022, there was a lack of systematically collected population-based data allowing for the assessment of the protection level in real-time.\n\nIn the IMMUNEBRIDGE project, we harmonised data and biosamples for nine population-/hospital-based studies (total number of participants n=33,637) to provide estimates for protection levels against SARS-CoV-2 infection and severe COVID-19 between June and November 2022. Based on evidence synthesis, we formed a combined endpoint of protection levels based on the number of self-reported infections/vaccinations in combination with nucleocapsid/spike antibody responses (\"confirmed exposures\"). Four confirmed exposures represented the highest protection level, and no exposure represented the lowest.\n\nMost participants were seropositive against the spike antigen; 37% of the participants [≥]79 years had less than four confirmed exposures (highest level of protection) and 5% less than three. In the subgroup of participants with comorbidities, 46-56% had less than four confirmed exposures. We found major heterogeneity across federal states, with 4%-28% of participants having less than three confirmed exposures.\n\nUsing serological analyses, literature synthesis and infection dynamics during the survey period, we observed moderate to high levels of protection against severe COVID-19, whereas the protection against SARS-CoV-2 infection was low across all age groups. We found relevant protection gaps in the oldest age group and amongst individuals with comorbidities, indicating a need for additional protective measures in these groups.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Berit Lange", + "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany; German Center for Infection Research (DZIF), TI BBD, Braunschw" + }, + { + "author_name": "Veronika K Jaeger", + "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" + }, + { + "author_name": "Manuela Harries", + "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany" + }, + { + "author_name": "Viktoria Ruecker", + "author_inst": "Institute of Clinical Epidemiology and Biometry, University Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Hendrik Streeck", + "author_inst": "Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Braunschweig," + }, + { + "author_name": "Sabine Blaschke", + "author_inst": "Emergency Department, University Medical Center Goettingen, Goettingen, Germany" + }, + { + "author_name": "Astrid Petersmann", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Oldenburg, Oldenburg, Germany; Institute of Clinical Chemistry and Laboratory Medic" + }, + { + "author_name": "Nicole Toepfner", + "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" + }, + { + "author_name": "Matthias Nauck", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), " + }, + { + "author_name": "Max J Hassenstein", + "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany" + }, + { + "author_name": "Marein Dreier", + "author_inst": "Institute for Epidemiology, Social Medicine and Health Systems Research, Hannover Medical School, Hannover, Germany" + }, + { + "author_name": "Isabell von Holt", + "author_inst": "Institute for Epidemiology, Social Medicine and Health Systems Research, Hannover Medical School, Hannover, Germany" + }, + { + "author_name": "Axel Budde", + "author_inst": "Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Braunschweig," + }, + { + "author_name": "Antonia Bartz", + "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" + }, + { + "author_name": "Julia Ortmann", + "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany" + }, + { + "author_name": "Marc-Andre Kurosinski", + "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" + }, + { + "author_name": "Reinhard Berner", + "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" + }, + { + "author_name": "Max Borsche", + "author_inst": "Institute of Neurogenetics, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Gunnar Brandhorst", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Oldenburg, Oldenburg, Germany" + }, + { + "author_name": "Melanie Brinkmann", + "author_inst": "Institute for Epidemiology, Social Medicine and Health Systems Research, Hannover Medical School, Hannover, Germany" + }, + { + "author_name": "Kathrin Budde", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany" + }, + { + "author_name": "Marek Deckena", + "author_inst": "Labor Krone, Bad Salzuflen, Germany" + }, + { + "author_name": "Geraldine Engels", + "author_inst": "University Hospital Wuerzburg, Department of Pediatrics, Pediatric Infectiology, Wuerzburg, Germany" + }, + { + "author_name": "Marc Fenzlaff", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany" + }, + { + "author_name": "Christoph Haertel", + "author_inst": "University Hospital Wuerzburg, Department of Pediatrics, Pediatric Infectiology, Wuerzburg, Germany" + }, + { + "author_name": "Olga Hovardovska", + "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany" + }, + { + "author_name": "Alexander Katalinic", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Katja Kehl", + "author_inst": "Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Braunschweig," + }, + { + "author_name": "Mirjam Kohls", + "author_inst": "Institute of Clinical Epidemiology and Biometry, University Wuerzburg; Clinical Trial Center, University Hospital Wuerzburg; Institute for Medical Data Science," + }, + { + "author_name": "Stefan Krueger", + "author_inst": "dimap, das Institut fuer Markt- und Politikforschung GmbH, Germany" + }, + { + "author_name": "Wolfgang Lieb", + "author_inst": "Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany" + }, + { + "author_name": "Kristin M Meyer-Schlinkmann", + "author_inst": "Labor Krone, Bad Salzuflen, Germany" + }, + { + "author_name": "Tobias Pischon", + "author_inst": "Molecular Epidemiology Research Group, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, Berlin; Biobank Technology Platform, Max Delbru" + }, + { + "author_name": "Daniel Rosenkranz", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Oldenburg, Oldenburg, Germany" + }, + { + "author_name": "Nicole Ruebsamen", + "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" + }, + { + "author_name": "Jan Rupp", + "author_inst": "Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, German Center for Infection Research (DZIF), Partner Site Hamburg-Lu" + }, + { + "author_name": "Christian Schaefer", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany" + }, + { + "author_name": "Mario Schattschneider", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany" + }, + { + "author_name": "Anne Schlegtendal", + "author_inst": "University Children's Hospital, Ruhr University Bochum, Bochum, Germany" + }, + { + "author_name": "Simon Schlinkert", + "author_inst": "dimap, das Institut fuer Markt- und Politikforschung GmbH, Germany" + }, + { + "author_name": "Lena Schmidbauer", + "author_inst": "Institute of Clinical Epidemiology and Biometry, University Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Kai Schulze-Wundling", + "author_inst": "Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Braunschweig," + }, + { + "author_name": "Stefan Stoerk", + "author_inst": "Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center (CHFC), and Department of Internal Medicine I, University Hospital Wuerzburg," + }, + { + "author_name": "Carsten Tiemann", + "author_inst": "Labor Krone, Bad Salzuflen, Germany" + }, + { + "author_name": "Henry Voelzke", + "author_inst": "Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany" + }, + { + "author_name": "Theresa Winter", + "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany" + }, + { + "author_name": "Christine Klein", + "author_inst": "Institute of Neurogenetics, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Johannes Liese", + "author_inst": "University Hospital Wuerzburg, Department of Pediatrics, Pediatric Infectiology, Wuerzburg, Germany" + }, + { + "author_name": "Folke Brinkmann", + "author_inst": "University Children's Hospital, Ruhr University Bochum, Bochum, Germany" + }, + { + "author_name": "Patrick F Ottensmeyer", + "author_inst": "Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Braunschweig," + }, + { + "author_name": "Jens-Peter Reese", + "author_inst": "Institute of Clinical Epidemiology and Biometry, University Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Peter Heuschmann", + "author_inst": "Institute of Clinical Epidemiology and Biometry, University Wuerzburg; Clinical Trial Center, University Hospital Wuerzburg; Institute for Medical Data Science," + }, + { + "author_name": "Andre Karch", + "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.15.23285994", "rel_title": "Characteristics and outcomes of 7620 Multiple Sclerosis patients admitted with COVID-19 in the United States", @@ -137841,25 +139886,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.09.23285743", - "rel_title": "Long term vaccination strategies to mitigate the impact of SARS-CoV-2 transmission: a modelling study", - "rel_date": "2023-02-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.09.23285743", - "rel_abs": "BackgroundVaccines have reduced severe disease and death from COVID-19. However, with evidence of waning efficacy coupled with continued evolution of the virus, health programmes need to evaluate the requirement for regular booster doses, considering their impact and cost-effectiveness in the face of ongoing transmission and substantial infection-induced immunity.\n\nMethods and findingsWe developed a combined immunological-transmission model parameterised with data on transmissibility, severity, and vaccine effectiveness. We simulated SARS-CoV-2 transmission and vaccine rollout in characteristic global settings with different population age-structures, contact patterns, health system capacities, prior transmission, and vaccine uptake. We quantified the impact of future vaccine booster dose strategies with both original and variant-adapted vaccine products, in the presence of both continuing transmission of Omicron subvariants and considering the potential future emergence of new variants with modified transmission, immune escape, and severity properties. We found that regular boosting of the oldest age group (75+) is the most efficient strategy, although large numbers of hospitalisations and deaths can be averted by extending vaccination to younger age groups. In countries with low vaccine coverage and high infection-derived immunity, boosting older at-risk groups is more effective than continuing primary vaccination into younger ages. These findings hold if even if virus drift results in a gradual reduction in vaccine effectiveness over time due to immune escape. In a worst-case scenario where a new variant emerges that is 10% more transmissible, as severe as Delta, and exhibits substantial further immune escape, demand on health services could be similar to that experienced during 2020.\n\nConclusionsRegular boosting of the high-risk population remains an important tool to reduce morbidity and mortality from current and future SARS-CoV-2 variants. The cost-effectiveness of boosting is difficult to assess given the ongoing uncertainty in the likelihood of future variants and their properties but focusing vaccination in the highest-risk cohorts remains the most efficient strategy to reduce morbidity and mortality.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Azra C Ghani", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.10.23285717", "rel_title": "The long COVID evidence gap: comparing self-reporting and clinical coding of long COVID using longitudinal study data linked to healthcare records.", @@ -138854,6 +140880,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.10.23285516", + "rel_title": "Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England", + "rel_date": "2023-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.10.23285516", + "rel_abs": "As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantified the impact of non-pharmaceutical interventions (NPIs), therapeutics, and vaccination on virus transmission and severity. Each successive variant had a higher intrinsic transmissibility. Omicron (BA.1) had the highest basic reproduction number at 8.3 (95% credible interval (CrI) 7.7-8.8). Varying levels of NPIs were crucial in controlling virus transmission until population immunity accumulated. Immune escape properties of Omicron decreased effective levels of immunity in the population by a third. Furthermore, in contrast to previous studies, we found Alpha had the highest basic infection fatality ratio (2.9%, 95% CrI 2.7-3.2), followed by Delta (2.2%, 95% CrI 2.0-2.4), Wildtype (1.2%, 95% CrI 1.1-1.2), and Omicron (0.7%, 95% CrI 0.6-0.8). Our findings highlight the importance of continued surveillance. Long-term strategies for monitoring and maintaining effective immunity against SARS-CoV-2 are critical to inform the role of NPIs to effectively manage future variants with potentially higher intrinsic transmissibility and severe outcomes.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Pablo N Perez-Guzman", + "author_inst": "Imperial College London" + }, + { + "author_name": "Edward S Knock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Natsuko Imai", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas Rawson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Yasin A Elmaci", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joana Alcada", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lilith K Whittles", + "author_inst": "Imperial College London" + }, + { + "author_name": "Divya Thekke Kanapram", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Raphael Sonabend", + "author_inst": "Imperial College London" + }, + { + "author_name": "Katy A M Gaythorpe", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wes R Hinsley", + "author_inst": "Imperial College London" + }, + { + "author_name": "Richard G FitzJohn", + "author_inst": "Imperial College London" + }, + { + "author_name": "Erik Volz", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robert Verity", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Anne Cori", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.07.23285380", "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemic in Mainland China During December 31 2021-December 6 2022", @@ -139347,53 +141456,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.08.23285654", - "rel_title": "Characteristics and Outcomes of COVID-19 Patients Presumed to be Treated with Sotrovimab in NHS Hospitals in England", - "rel_date": "2023-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285654", - "rel_abs": "IntroductionThere is limited real-world evidence describing the effectiveness of early treatments for Coronavirus disease 2019 (COVID-19) during the period where Omicron was the dominant variant. Here we describe characteristics and acute clinical outcomes in patients with COVID-19 treated with a monoclonal antibody (mAb; presumed to be sotrovimab) across six distinct periods covering the emergence and subsequent dominance of Omicron subvariants (BA.1, BA.2 and BA.5) in England.\n\nMethodsRetrospective cohort study using data from Hospital Episode Statistics database between 1st January - 31st July 2022. Included patients were aged [≥]12 years and received a mAb delivered by a National Health Service (NHS) hospital as a day-case, for which the primary diagnosis was COVID-19. Patients were presumed to have received sotrovimab on the basis of available NHS data showing that 99.98% of individuals who received COVID-19 treatment during the period covered by the study were actually treated with sotrovimab. COVID-19-attributable hospitalisations were reported overall and across six distinct periods of Omicron sub-variant prevalence. A multivariate Poisson regression model was used to estimate incidence rate ratios for each period. Subgroup analyses were conducted in patients with severe renal disease and active cancer.\n\nResultsIn total, 10,096 patients were included. The most common high-risk comorbidities were Immune-Mediated Inflammatory Disorders (43.0%; n = 4,337), severe renal disease (14.1%; n = 1,422), rare neurological conditions (10.4%; n = 1,053) and active cancer (9.0%; n = 910). The proportions of patients with a COVID-19-attributable hospitalisation was 1.0% (n = 96), or with a hospital visit due to any cause was 4.6% (n = 465) during the acute period. The percentage of patients who died due to any cause during the acute study period was 0.3% (n = 27). COVID-19-attributable hospitalisation rates were consistent among subgroups and no significant differences (p-values ranged from 0.13 to 0.64) were observed across periods of Omicron subvariants.\n\nConclusionLow levels of COVID-19-attributable hospitalisations and deaths were recorded in mAb-treated patients. Results were consistent for patients with severe renal disease and active cancer. No evidence of differences in hospitalisation rates were observed whilst Omicron BA.1, and BA.2 or BA.5 subvariants were predominant, despite reported reductions in in vitro neutralisation activity of sotrovimab against BA.2 and BA.5.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vishal Patel", - "author_inst": "GSK, Middlesex, UK" - }, - { - "author_name": "Bethany Levick", - "author_inst": "Open Health Evidence & Access, Marlow, UK" - }, - { - "author_name": "Stephen Boult", - "author_inst": "Harvey Walsh, OPEN Health, Cheshire, UK" - }, - { - "author_name": "Daniel C. Gibbons", - "author_inst": "GSK, Middlesex, UK" - }, - { - "author_name": "Myriam Drysdale", - "author_inst": "GSK, Middlesex, UK" - }, - { - "author_name": "Emily J. Lloyd", - "author_inst": "GSK, Middlesex, UK" - }, - { - "author_name": "Moushmi Singh", - "author_inst": "GSK, Middlesex, UK" - }, - { - "author_name": "Helen J. Birch", - "author_inst": "GSK, Middlesex, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.09.23285583", "rel_title": "Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants", @@ -140512,6 +142574,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.02.06.23285411", + "rel_title": "Time series analysis of routine immunisation coverage during the COVID-19 pandemic in 2021 shows continued global decline and increases in Zero Dose children", + "rel_date": "2023-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.06.23285411", + "rel_abs": "Whilst it is now widely recognised that routine immunisation (RI) was disrupted by the COVID-19 pandemic in 2020 compared to previous immunisation performance, the extent of continued interruptions in 2021 and/or rebounds to previous trends remains unclear, with sporadic surveys reporting signs of immunisation system recovery at the end of 2020.\n\nWe modelled country-specific RI trends using validated estimates of national coverage from the World Health Organisation and United Nation Childrens Fund for over 160 countries, to project expected diphtheria, tetanus, and pertussis-containing vaccine first-dose (DTP1), third-dose (DTP3) and measles-containing vaccine first-dose (MCV1) coverage for 2021 based on pre-pandemic trends (from 2000-2019).\n\nWe estimated a 3{middle dot}6% (95%CI: [2{middle dot}6%; 4{middle dot}6%]) decline in global DTP3 coverage in 2021 compared to 2000-2019 trends, from an expected 90{middle dot}1% to a reported 86{middle dot}5% across 164 reporting countries, and similar results for DTP1 (2{middle dot}8% decline; 95%CI: [2{middle dot}0%; 3{middle dot}6%]), and for MCV1 (3{middle dot}8% decline; 95%CI: [4{middle dot}8%; 2{middle dot}7%]). 86{middle dot}5% global coverage in 2021 represents a further decrease from that reported in 2020 and 2019, and translates to a 16-year setback in RI coverage, i.e., 2005 levels. Hypothesised and early signals of rebounds to pre-pandemic coverage were not seen in most countries. The Americas, Africa, and Asia were the most impacted regions, with low- and middle-income countries the most affected income groups.\n\nThe number of Zero Dose children also continued to increase in 2021. DTP1 coverage declined worldwide from an expected 93{middle dot}7% to a reported 90{middle dot}9% (2{middle dot}8% decline; 95%CI: [2{middle dot}0%; 3{middle dot}6%]) which translates into an additional 3.4 million Zero Dose children on top of an expected 11.0 million (30.9% increase) at the global level.\n\nWe hope this work will provide an objective baseline to inform future interventions and prioritisation aiming to facilitate rebounds in coverage to previous levels and catch-up of growing populations of under- and un-immunised children.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Beth Evans", + "author_inst": "University of Geneva" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "University of Geneva" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Thibaut Jombart", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.07.23285570", "rel_title": "Who Wears the Face Mask? Preventive Measures Against COVID-19 in Latin America Before Vaccination", @@ -141161,109 +143254,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.02.23285205", - "rel_title": "Heterologous inactivated virus/mRNA vaccination response to BF.7, BQ.1.1, and XBB.1", - "rel_date": "2023-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.02.23285205", - "rel_abs": "The emergence of highly immune-escape Omicron variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as BQ and XBB, has led to concerns about the efficacy of vaccines. Using lentivirus-based pseudovirus neutralizing assay, we showed that heterologous vaccination involving parental mRNA vaccine as a booster or second booster in individuals that received two or three doses of inactivated vaccines strongly augments the neutralizing activity against emerging Omicron subvariants, including BF.7, BQ.1.1, and XBB.1, by 4.3-to 219-folds. Therefore, a heterologous boosting strategy with mRNA-based vaccines should be considered in populations where inactivated vaccines were primarily used.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Fanglei Zuo", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Rui Sun", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Hassan Abolhassani", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Likun Du", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Yating Wang", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Stelios Vlachiotis", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Federico Bertoglio", - "author_inst": "Technische Universitat Braunschweig" - }, - { - "author_name": "Maren Schubert", - "author_inst": "Technische Universitat Braunschweig" - }, - { - "author_name": "Nima Rezaei", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Zahra Chavoshzadeh", - "author_inst": "Shahid Beheshti University of Medical Sciences" - }, - { - "author_name": "Concetta Guerra", - "author_inst": "Universita della Svizzera italiana" - }, - { - "author_name": "Andrea Cavalli", - "author_inst": "Universita della Svizzera italiana" - }, - { - "author_name": "Juni Andrell", - "author_inst": "Stockholm University" - }, - { - "author_name": "Makiko Kumagai-Braesch", - "author_inst": "Karolinska Institutet at Karolinska University Hospital" - }, - { - "author_name": "Yintong Xue", - "author_inst": "Peking University Health Science Center" - }, - { - "author_name": "Yunlong Cao", - "author_inst": "Peking University" - }, - { - "author_name": "Michael Hust", - "author_inst": "Technische Universitat Braunschweig" - }, - { - "author_name": "Davide F. Robbiani", - "author_inst": "Universita della Svizzera italiana" - }, - { - "author_name": "Xiaoliang Xie", - "author_inst": "Peking University" - }, - { - "author_name": "Lennart Hammarstrom", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Harold Marcotte", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Qiang Pan-Hammarstrom", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2023.02.06.527376", "rel_title": "A SARS-CoV-2 vaccine designed for manufacturability results in unexpected potency and non-waning humoral response", @@ -142178,6 +144168,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.02.06.23285513", + "rel_title": "A Rapid review on the COVID-19 Pandemic's Global Impact on Breast Cancer Screening Participation Rates and Volumes from January-December 2020", + "rel_date": "2023-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.06.23285513", + "rel_abs": "BackgroundCOVID-19 has strained population breast mammography screening programs that aim to diagnose and treat breast cancers earlier. As the pandemic has affected countries differently, we aimed to quantify changes in breast screening volume and uptake during the first year of the COVID-19 pandemic.\n\nMethodsWe systematically searched Medline, the WHO (World Health Organization) COVID-19 database, and governmental databases. Studies covering January 2020 to March 2022 were included. We extracted and analyzed data regarding study methodology, screening volume and uptake. To assess for risk-of-bias, we used the Joanna Briggs Institute Critical Appraisal tool.\n\nResultsTwenty-six cross-sectional descriptive studies were included out of 935 independent records. Reductions in screening volume and uptake rates were observed among eight countries. Changes in screening participation volume in five countries with national population-based screening ranged from -13% to -31%. Among two countries with limited population-based programs the decline ranged from -61% to -41%. Within the USA, population participation volumes varied ranging from +18% to -39% with suggestion of differences by insurance status (HMO, Medicare, and low-income programs). Almost all studies had high risk-of-bias due to insufficient statistical analysis and confounding factors.\n\nDiscussion and ConclusionExtent of COVID-19-induced reduction in breast screening participation volume differed by region and data suggested potential differences by healthcare setting (e.g., national health insurance vs private health care). Recovery efforts should monitor access to screening and early diagnosis to determine if prevention services need strengthening to increase coverage of marginalized groups and reduce disparities.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Reagan Lee", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "- UNCOVER", + "author_inst": "-" + }, + { + "author_name": "Wei Xu", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "- International Partnership for Resilience in Cancer Systems (I-PaRCS), Breast Cancer Working Group 2", + "author_inst": "-" + }, + { + "author_name": "Marshall Dozier", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Ruth McQuillan", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Evropi Theodoratou", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Jonine Figueroa", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.02.23285377", "rel_title": "Disease severity of unvaccinated SARS-CoV-2 positive adults less than 65 years old without comorbidity, in the Omicron period and pre-Omicron periods", @@ -142831,45 +144868,6 @@ "type": "confirmatory results", "category": "genomics" }, - { - "rel_doi": "10.1101/2023.02.02.526761", - "rel_title": "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques", - "rel_date": "2023-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.02.526761", - "rel_abs": "The molecular mechanisms underlying the recognition of epitopes by T cell receptors (TCRs) are critical for activating T cell immune responses and rationally designing TCR-based therapeutics. Single-cell sequencing techniques vastly boost the accumulation of TCR sequences, while the limitation of available TCR-pMHC structures hampers further investigations. In this study, we proposed a comprehensive strategy that incorporates structural information and single-cell sequencing data to investigate the epitope-recognition mechanisms of TCRs. By antigen specificity clustering, we mapped the epitope sequences between epitope-known and epitope-unknown TCRs from COVID-19 patients. One reported SARS-CoV-2 epitope, NQKLIANQF (S919-927), was identified for a TCR expressed by 614 T cells (TCR-614). Epitope screening also identified a potential cross-reactive epitope, KLKTLVATA (NSP31790-1798), for a TCR expressed by 204 T cells (TCR-204). According to the molecular dynamics (MD) simulations, we revealed the detailed epitope-recognition mechanisms for both TCRs. The structural motifs responsible for epitope recognition revealed by the MD simulations are consistent with the sequential features recognized by the sequence-based clustering method. This strategy will facilitate the discovery and optimization of TCR-based therapeutics. In addition, the comprehensive strategy can also promote the development of cancer vaccines in virtue of the ability to discover neoepitopes and epitope-recognition mechanisms.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kaiyuan Song", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Honglin Xu", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yi Shi", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jie Hao", - "author_inst": "Fudan University" - }, - { - "author_name": "Lintai Da", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Xin Zou", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.31.23285300", "rel_title": "Global generalisability of AI-driven COVID-19 vaccination policies: a cross-sectional observational study", @@ -144020,6 +146018,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.31.23285232", + "rel_title": "Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour", + "rel_date": "2023-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285232", + "rel_abs": "Key FeaturesO_LIVirus Watch is a national community cohort study of COVID-19 in households in England and Wales, established in June 2020. The study aims to provide evidence on which public health approaches are most effective in reducing transmission, and investigate community incidence, symptoms, and transmission of COVID-19 in relation to population movement and behaviours.\nC_LIO_LI28,527 households and 58,628 participants of age (0-98 years, mean age 48), were recruited between June 2020 - July 2022\nC_LIO_LIData collected include demographics, details on occupation, co-morbidities, medications, and infection-prevention behaviours. Households are followed up weekly with illness surveys capturing symptoms and their severity, activities in the week prior to symptom onset and any COVID-19 test results. Monthly surveys capture household finance, employment, mental health, access to healthcare, vaccination uptake, activities and contacts. Data have been linked to Hospital Episode Statistics (HES), inpatient and critical care episodes, outpatient visits, emergency care contacts, mortality, virology testing and vaccination data held by NHS Digital.\nC_LIO_LINested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555).\nC_LIO_LIStudy data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS.\nC_LI", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Thomas Edward Byrne", + "author_inst": "University College London" + }, + { + "author_name": "Jana Kovar", + "author_inst": "University College London" + }, + { + "author_name": "Sarah Beale", + "author_inst": "University College London" + }, + { + "author_name": "Isobel Braithwaite", + "author_inst": "University College London" + }, + { + "author_name": "Ellen Fragaszy", + "author_inst": "UCL" + }, + { + "author_name": "Wing Lam Erica Fong", + "author_inst": "University College London" + }, + { + "author_name": "Cyril Geismar", + "author_inst": "University College London" + }, + { + "author_name": "Susan J Hoskins", + "author_inst": "Univerity College London" + }, + { + "author_name": "Annalan Mathew Dwight Navaratnam", + "author_inst": "University College London" + }, + { + "author_name": "Vincent Nguyen", + "author_inst": "University College London" + }, + { + "author_name": "Parth Patel", + "author_inst": "University College London" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "University College London" + }, + { + "author_name": "Alexei Yavlinsky", + "author_inst": "University College London" + }, + { + "author_name": "Pia Hardelid", + "author_inst": "University College London" + }, + { + "author_name": "Linda Wijlaars", + "author_inst": "University College London" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCLH" + }, + { + "author_name": "Moira Spyer", + "author_inst": "University College London" + }, + { + "author_name": "Anna Ayree", + "author_inst": "University College London" + }, + { + "author_name": "Ingemar Cox", + "author_inst": "University College London" + }, + { + "author_name": "Vasileios Lampos", + "author_inst": "University College London" + }, + { + "author_name": "Rachel A McKendry", + "author_inst": "University College London" + }, + { + "author_name": "Tao Cheng", + "author_inst": "University College London" + }, + { + "author_name": "Anne M Johnson", + "author_inst": "University College London" + }, + { + "author_name": "Susan Fiona Michie", + "author_inst": "University College London" + }, + { + "author_name": "Jo Gibbs", + "author_inst": "University College London" + }, + { + "author_name": "Richard Gilson", + "author_inst": "University College London" + }, + { + "author_name": "Alison Rodger", + "author_inst": "University College London" + }, + { + "author_name": "Ibrahim Abubakar", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Hayward", + "author_inst": "University College London" + }, + { + "author_name": "Robert W Aldridge", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.31.23285233", "rel_title": "Sociodemographic and socioeconomic disparities in COVID-19 vaccine uptake - A nationwide record linkage study", @@ -144725,61 +146858,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.01.30.23285219", - "rel_title": "Coinfection with Strongyloides and SARS-CoV-2: protocol for a systematic review", - "rel_date": "2023-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.30.23285219", - "rel_abs": "Rationale for the reviewCOVID-19 treatment can worsen parasitic disease in patients with coinfection. Consequently, there is a need to investigate the infection with SARS-CoV-2 and Strongyloides. We aim to systematically review clinical and laboratory features of COVID-19 and Strongyloides coinfection, to investigate possible interventions and outcomes in this pathology. Also, we aim to identify difficulties in managing the parasitic disease manifestations in this context and to emphasize research gaps requiring further attention.\n\nMethodsWe will search two electronic databases - LitCOVID, and WHO COVID-19 and will include studies on SARS-CoV-2 and Strongyloides coinfection. We will adapt the WHO-UMC system for standardized case causality assessment to evaluate if using corticosteroids or other immunosuppressive drugs in COVID-19 patients determined acute strongyloidiasis manifestations.\n\nExpected resultsWe will present the evidence in three distinct packages: study description, methodological quality assessment and data extracted. We will summarize the evidence and will draw conclusions as to the quality of the evidence.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elena Cecilia Rosca", - "author_inst": "Victor Babes University of Medicine and Pharmacy of Timisoara" - }, - { - "author_name": "Carl Heneghan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth A Spencer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Annette Pluddemann", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susanna Maltoni", - "author_inst": "IRCCS Azienda Ospedaliero-Universitaria di Bologna" - }, - { - "author_name": "Sara Gandini", - "author_inst": "European Institute of oncology" - }, - { - "author_name": "IGHO ONAKPOYA", - "author_inst": "UNIVERSITY OF OXFORD" - }, - { - "author_name": "David Evans", - "author_inst": "University of Alberta" - }, - { - "author_name": "John M Conly", - "author_inst": "Synder Institute for Chronic Diseases, O Brien Institute for Public Health, Cumming School of Medicine, University of Calgary, Alberta Health Services, Calgary," - }, - { - "author_name": "Tom Jefferson", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.30.23285173", "rel_title": "Current Status and Emerging Trends of COVID-19-related Studies in Seven ''Tropical Medicine''-entitled Journals", @@ -145938,6 +148016,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.24.23284947", + "rel_title": "What interventions or best practice are there to support people with Long COVID, or similar post-viral conditions or conditions characterised by fatigue, to return to normal activities: a rapid review", + "rel_date": "2023-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.24.23284947", + "rel_abs": "Previous research has categorised symptoms of COVID-19 / Long COVID into 12 thematic areas including: fever, myalgia, fatigue, impaired cognitive function, and that COVID-19 survivors had reduced levels of physical function, activities of daily living, and health-related quality of life. Our aim was to review the evidence for interventions or best practice to support people with Long COVID, or similar post-viral conditions characterised by fatigue, to return to normal activities.\n\nEvidence was included from guidelines, systematic reviews (SR), and primary studies. The primary studies focussed on Long COVID (LC) indicated that there should be a needs-based focus to care for those with LC. Consideration should be given to individuals living with LC in the same way as people with disabilities are accommodated in terms of workplace adjustment. Two SRs indicated that non-pharmaceutical interventions (NPIs) for patients with LC or chronic fatigue syndrome could help improve function for activities of daily life. However, the third, most recent SR, concluded that there is a lack of robust evidence for NPIs. LC fatigue management methods may be beneficial under certain conditions. One SR reported work capability as an outcome however they did not find any studies which evaluated the impact of interventions on return to work/ normal life. One primary study, on individuals with CFS, described a written self-management programme. Following this intervention there was an 18% increase in the number of patients in employment.\n\nPolicy and practice implications: Long COVID is still being established as a post-viral condition with many symptoms. Patient-centred treatment options such as occupational therapy, self-management therapy and talking therapy may be considered in the same way as for other debilitating conditions. Return-to-work accommodations are needed for all workers unable to return to full-time employment. Due to the nature of the studies included, there was little reported evidence of effectiveness of getting individuals back into their normal activities.\n\nFunding statementThe Bangor Institute for Health and Medical Research was funded for this work by the Wales COVID-19 Evidence Centre, itself funded by Health & Care Research Wales on behalf of Welsh Government.\n\nRapid Review DetailsO_ST_ABSReview conducted byC_ST_ABSBangor Institute for Health and Medical Research (BIHMR), Bangor University.\n\nReview Team{blacksquare} Dr Llinos Haf Spencer, l.spencer@bangor.ac.uk\n{blacksquare}Dr Annie Hendry, a.hendry@bangor.ac.uk\n{blacksquare}Mr Abraham Makanjuola, a.makanjuola@bangor.ac.uk\n{blacksquare}Ms Bethany Fern Anthony, b.anthony@bangor.ac.uk\n{blacksquare}Mr Jacob Davies, jacob.davies@bangor.ac.uk\n{blacksquare}Ms Kalpa Pisavadia, kalpa.pisavadia@bangor.ac.uk\n{blacksquare}Professor Dyfrig Hughes, d.a.hughes@bangor.ac.uk\n{blacksquare}Professor Deb Fitzsimmons, d.fitzsimmons@bangor.ac.uk\n{blacksquare}Professor Clare Wilkinson, c.wilkinson@bangor.ac.uk\n{blacksquare}Professor Rhiannon Tudor Edwards, r.t.edwards@bangor.ac.uk\n\n\nReview submitted to the WCEC on11 January 2023\n\nStakeholder consultation meeting8th November 2022\n\nRapid Review report issued by the WCEC inJanuary 2022\n\nWCEC TeamAdrian Edwards, Ruth Lewis, Alison Cooper and Micaela Gal involved in drafting the Topline Summary and editing.\n\nThis review should be cited asRR00042_ Wales COVID-19 Evidence Centre\n\nDisclaimerThe views expressed in this publication are those of the authors, not necessarily Health and Care Research Wales. The WCEC and authors of this work declare that they have no conflict of interest.\n\nTOPLINE SUMMARYO_ST_ABSWhat is a Rapid Review?C_ST_ABSOur rapid reviews (RR) use a variation of the systematic review (SR) approach, abbreviating or omitting some components to generate the evidence to inform stakeholders promptly whilst maintaining attention to bias. They follow the methodological recommendations and minimum standards for conducting and reporting RR, including a structured protocol, systematic search, screening, data extraction, critical appraisal, and evidence synthesis to answer a specific question and identify key research gaps. They take 1 to 2 months, depending on the breadth and complexity of the research topic/question(s), extent of the evidence base, and type of analysis required for synthesis.\n\nWho is this summary for?Policymakers in Welsh Government to plan and deliver services for individuals with Long COVID as they re-enter training, education, employment, and informal caring responsibilities.\n\nBackground / Aim of Rapid ReviewPrevious research has categorised symptoms of COVID-19/Long COVID into 12 thematic areas including: fever, myalgia, fatigue, impaired cognitive function, and that COVID-19 survivors had reduced levels of physical function, activities of daily living, and health-related quality of life (Amdal et al., 2021; de Oliveira Almeida et al., 2022). NICE guidelines highlight the impact of the condition on quality of life and the challenge of determining best practice based on the current evidence (National Institute for Health and Care Excellence et al., 2022). Treatments for other post-viral syndromes may also apply to people living with Long COVID (Wong and Weitzer, 2021). Our aim was to review the evidence for interventions or best practice to support people with Long COVID, or similar post-viral conditions characterised by fatigue, to return to normal activities (including return to the workforce, education, childcare, or housework).\n\nKey FindingsEvidence was included from guidelines (n=3), systematic reviews (SRs) (n=3), and primary studies (n=4).\n\nExtent of the evidence base{blacksquare} Two SRs included non-pharmacological interventions for Long COVID or post-viral syndromes, including Long COVID (Chandan et al., 2022; Fowler-Davis et al., 2021). The remaining SR focused on interventions for Chronic Fatigue Syndrome (CFS).\n{blacksquare}The four primary studies were conducted in the UK, USA, Norway, and Turkey. The SRs included studies from across Europe, Asia, Africa, and Australasia.\n{blacksquare}Included SRs and primary studies evaluated non-pharmaceutical interventions, including fatigue management, exercise therapy, Cognitive Behavioural Therapy (CBT), workplace support, self-management, sleep therapy, music therapy, and counselling.\n{blacksquare}Two relevant guidelines were identified for Long COVID and one for ME/CFS. The Long COVID guideline was aimed at employers, and the ME/CFS guideline was aimed at service providers and users.\n\n\nRecency of the evidence base{blacksquare} Included papers were from 2014 to 2022.\n\n\nEvidence of effectiveness{blacksquare} The primary studies focussed on Long COVID indicated that there should be a needs-based focus to care for those with Long COVID (Lunt et al., 2022; Skilbeck, 2022; Wong et al., 2022). Consideration should be given to individuals living with Long COVID in the same way as people with disabilities are accommodated in terms of workplace adjustment (e.g. part-time hours, working from home, or hybrid working).\n{blacksquare}Two SRs indicated that non-pharmaceutical interventions for patients with Long COVID or CFS could help improve function for activities of daily life (Fowler-Davis et al., 2021; Larun et al., 2019). However, the third and most recent SR concluded that there is a lack of robust evidence for non-pharmaceutical interventions (Chandan et al., 2022).\n{blacksquare}Long COVID fatigue management by exercise therapy, electrical nerve stimulation, sleep and touch therapy, and behavioural self-management may be beneficial when: physical and psychological support is delivered in groups, people can plan their functional response to fatigue, strengthening rather than endurance is used to prevent deconditioning, fatigue is regarded in the context of an individuals lifestyle and home-based activities are used (Fowler-Davis et al 2021).\n{blacksquare}One SR (Chandan et al 2022) reported work capability as an outcome however they did not find any studies which evaluated the impact of interventions on return to work/ normal life.\n{blacksquare}One primary study concentrated on individuals with CFS (Nyland et al., 2014). Nyland et al. (2014) described a written self-management programme featuring active coping (with CFS) strategies for daily life. Following this intervention, there was an 18% increase in the number of patients in employment (from baseline to follow-up) (Nyland et al., 2014).\n\n\nBest quality evidence{blacksquare} The three SRs (Chandan et al., 2022; Fowler-Davis et al., 2021; Larun et al., 2019) were of high quality, as was one of the cohort studies (Lunt et al., 2022).\n\n\nPolicy Implications{blacksquare} Long COVID is still being established as a post-viral condition with many symptoms. The Welsh Government may seek to consider patient-centred treatment options such as occupational therapy, self-management therapy and talking therapy (such as Cognitive Behavioural Therapy) in the same way as for other debilitating conditions including ME/CFS.\n{blacksquare}Return-to-work accommodations are needed for all workers unable to return to full-time employment.\n{blacksquare}Due to the nature of the studies included, there was little reported evidence of effectiveness of getting individuals back into their normal activities.\n\n\nStrength of EvidenceConfidence in the findings is low. Only four primary studies reported outcomes relating to work capacity and return to normal activities such as childcare and housework.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Llinos Haf Spencer", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Annie Hendry", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Abraham Makanjuola", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Bethany F Anthony", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Jacob Davies", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Kalpa Pisavadia", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Dyfrig Hughes", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Deb Fitzsimmons", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Clare Wilkinson", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Rhiannon Tudor Edwards", + "author_inst": "Bangor Institute for Health and Medical Research, Bangor University, Wales, UK" + }, + { + "author_name": "Ruth Lewis", + "author_inst": "Wales COVID-19 Evidence Centre, Wales, UK" + }, + { + "author_name": "Alison Cooper", + "author_inst": "Wales COVID-19 Evidence Centre, Wales, UK" + }, + { + "author_name": "Adrian G Edwards", + "author_inst": "Wales COVID-19 Evidence Centre, Wales, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.01.24.23284959", "rel_title": "Effectiveness of a chatbot in improving the mental wellbeing of health workers in Malawi during the COVID-19 pandemic: A randomized, controlled trial", @@ -146543,65 +148688,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.27.23285111", - "rel_title": "Examining the impact of the COVID-19 pandemic on cervical cancer screening practices among clinicians practicing in Federally Qualified Health Centers: A mixed methods study", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.27.23285111", - "rel_abs": "BackgroundThe COVID-19 pandemic led to reductions in cervical cancer screening and colposcopy. Therefore, in this mixed method study we explored perceived pandemic-related practice changes to cervical cancer screenings in federally qualified health centers.\n\nMethodsBetween October 2021 and June 2022, a national sample of 148 clinicians completed surveys; a subset (n=13) clinicians completed qualitative interviews. Most (86%) reported reduced cervical cancer screening early in the pandemic, and 28% reported continued reduction in services at the time of survey completion (October 2021-July 2022). Nearly half (45%) reported staff shortages impacting their ability to screen or track patients.\n\nResultsCompared to clinicians in OBGYN/Womens health, those in family medicine and other specialties were less likely to report maintaining or increasing screening compared to pre-pandemic. Advanced practice providers (compared to MDs/DOs,) and Hispanic/Latinx/other clinicians (compared to white non-Hispanic) were more likely to report maintaining or increasing screening vs. pre-pandemic. Most (91%) felt that screening using HPV self-sampling would be helpful to address screening backlogs. Qualitative interviews highlighted the impacts of staff shortages and strategies for improvement.\n\nConclusionsIdentifying barriers to screening and instituting solutions in federally qualified health centers is critical to preventing cervical cancers among patients at highest risk.\n\nFundingThis study was funded by the American Cancer Society, who had no role in the studys design, conduct, or reporting.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lindsay Fuzzell", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Paige W Lake", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Naomi C Brownstein", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Holly B Fontenot", - "author_inst": "University of Hawaii at Manoa" - }, - { - "author_name": "Ashley Whitmer", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Alexandra Michel", - "author_inst": "University of Hawaii at Manoa" - }, - { - "author_name": "McKenzie McIntyre", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Sarah L Rossi", - "author_inst": "Boston University" - }, - { - "author_name": "Sidika Kajtezovich", - "author_inst": "Boston University" - }, - { - "author_name": "Susan T Vadaparampil", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Rebecca B Perkins", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2023.01.27.23285105", "rel_title": "Waves in time, but not in space - An analysis of pandemic severity of COVID-19 in Germany based on spatio-temporal clustering", @@ -147788,6 +149874,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.22.23284881", + "rel_title": "Second monovalent SARS-CoV-2 mRNA booster restores Omicron-specific neutralizing activity in both nursing home residents and health care workers", + "rel_date": "2023-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.22.23284881", + "rel_abs": "We examined whether the second monovalent SARS-CoV-2 mRNA booster increased antibody levels and their neutralizing activity to Omicron variants in nursing home residents (NH) residents and healthcare workers (HCW). We sampled 367 NH residents and 60 HCW after primary mRNA vaccination, first and second boosters, for antibody response and pseudovirus neutralization assay against SARS-CoV-2 wild-type (WT) (Wuhan-Hu-1) strain and Omicron BA1 variant. Antibody levels and neutralizing activity progressively increased with each booster but subsequently waned over weeks. NH residents, both those without and with prior infection, had a robust geometric mean fold rise (GMFR) of 10.2 (95% CI 5.1, 20.3) and 6.5 (95% CI 4.5, 9.3) respectively in Omicron-BA.1 subvariant specific neutralizing antibody levels following the second booster vaccination (p<0.001). These results support the ongoing efforts to ensure that both NH residents and HCW are up to date on recommended SARS-CoV-2 vaccine booster doses.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Clare Nugent", + "author_inst": "Brown University Alpert Medical School, Division of Geriatric and Palliative Care Medicine" + }, + { + "author_name": "Yasin Abul", + "author_inst": "Brown Alpert Medical School Division of Geriatric and Palliative Care Medicine" + }, + { + "author_name": "Elizabeth White", + "author_inst": "Department of Health Services, Policy, and Practice, Brown University School of Public Health, Providence, RI" + }, + { + "author_name": "Fadi Shehadeh", + "author_inst": "Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "Matthew Kaczynski", + "author_inst": "Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "Lewis Oscar Felix", + "author_inst": "Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "Narchonai Ganesan", + "author_inst": "Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "Oladayo A. Oyebanji", + "author_inst": "Case Western Reserve University School of Medicine, Cleveland, OH" + }, + { + "author_name": "Igor Vishnepolskiy", + "author_inst": "Brown University Alpert Medical School, Division of Geriatric and Palliative Care Medicine" + }, + { + "author_name": "Elise M. Didion", + "author_inst": "Geriatric Research, Education and Clinical Center, VA Northeast Ohio Healthcare System, Cleveland VA" + }, + { + "author_name": "Alexandra Paxitzis", + "author_inst": "Case Western Reserve University School of Medicine, Cleveland, OH" + }, + { + "author_name": "Maegan L. Sheehan", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA" + }, + { + "author_name": "Eleftherios Mylonakis", + "author_inst": "Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "Brigid M. Wilson", + "author_inst": "Case Western Reserve University School of Medicine, Cleveland, OH , Geriatric Research, Education and Clinical Center, VA Northeast Ohio Healthcare System, Cle" + }, + { + "author_name": "Alejandro Benjamin Balazs", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Philip A. Chan", + "author_inst": "Department of Behavioral and Social Sciences, Brown University School of Public Health, Providence, RI, USA" + }, + { + "author_name": "Christopher L King", + "author_inst": "Case Western Reserve University School of Medicine, Cleveland, OH" + }, + { + "author_name": "Walther M. Pfeifer", + "author_inst": "East Side Clinical Laboratory, East Providence, RI" + }, + { + "author_name": "Evan Dickerson", + "author_inst": "Division of Geriatrics and Palliative Medicine, Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "David H. Canaday", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Stefan Gravenstein", + "author_inst": "Brown University Alpert Medical School, Division of Geriatric and Palliative Care Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.24.525413", "rel_title": "RAMEN identifies effective indicators for severe COVID and Long COVID patients", @@ -148517,113 +150702,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.01.20.524748", - "rel_title": "A Novel Monoclonal Antibody Targeting a Large Surface of the Receptor Binding Motif Shows Pan-neutralizing SARS-CoV-2 Activity Including BQ.1.1 Variant", - "rel_date": "2023-01-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.20.524748", - "rel_abs": "In the present study we report the functional and structural characterization of 17T2, a new highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody (mAb) isolated from a convalescent COVID-19 individual infected during the first wave of the COVID-19 pandemic. 17T2 is a class 1 VH1-58/{kappa}3-20 antibody, derived from a receptor binding domain (RBD)-specific IgA memory B cell and developed as a human recombinant IgG1. Functional characterization revealed that 17T2 mAb has a high and exceptionally broad neutralizing activity against all SARS-CoV-2 spike variants tested, including BQ.1.1. Moreover, 17T2 mAb has in vivo prophylactic activity against Omicron BA.1.1 infection in K18-hACE2 transgenic mice. 3D reconstruction from cryogenic-electron microscopy (cryo-EM) showed that 17T2 binds the Omicron BA.1 spike protein with the RBD domains in \"up\" position and recognizes an epitope overlapping with the receptor binding motif, as it is the case for other structurally similar neutralizing mAbs, including S2E12. Yet, unlike S2E12, 17T2 retained its high neutralizing activity against all Omicron sublineages tested, probably due to a larger contact area with the RBD, which could confer a higher resilience to spike mutations. These results highlight the impact of small structural antibody changes on neutralizing performance and identify 17T2 mAb as a potential candidate for future therapeutic and prophylactic interventions.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Leire de Campos-Mata", - "author_inst": "Translational Clinical Research Program, Institut Hospital del Mar de Investigacions M\u00e8diques (IMIM), Barcelona, Spain" - }, - { - "author_name": "Benjamin Trinit\u00e9", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Andrea Modrego", - "author_inst": "Centro Nacional de Biotecnolog\u00eda (CNB-CSIC), Madrid, Spain" - }, - { - "author_name": "Sonia Tejedor Vaquero", - "author_inst": "Translational Clinical Research Program, Institut Hospital del Mar de Investigacions M\u00e8diques (IMIM), Barcelona, Spain" - }, - { - "author_name": "Edwards Pradenas", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Natalia Rodrigo Melero", - "author_inst": "Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain" - }, - { - "author_name": "Diego Carlero", - "author_inst": "Centro Nacional de Biotecnolog\u00eda (CNB-CSIC), Madrid, Spain" - }, - { - "author_name": "Silvia Marfil", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Anna Pons-Grifols", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Maria Teresa Bueno-Carrasco", - "author_inst": "Centro Nacional de Biotecnolog\u00eda (CNB-CSIC), Madrid, Spain" - }, - { - "author_name": "C\u00e9sar Santiago", - "author_inst": "Centro Nacional de Biotecnolog\u00eda (CNB-CSIC), Madrid, Spain" - }, - { - "author_name": "Ferran Tarr\u00e9s-Freixas", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Victor Urrea", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Nuria Izquierdo", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Eva Riveira-Mu\u00f1oz", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "Ester Ballana", - "author_inst": "IrsiCaixa AIDS Research Institute, Hospital Germans Trias I Pujol, Campus Can Ruti, Badalona, Spain" - }, - { - "author_name": "M\u00f3nica P\u00e9rez", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "J\u00falia Vergara-Alert", - "author_inst": "IRTA-CRESA" - }, - { - "author_name": "Joaquim Segal\u00e9s", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "Carlo Carolis", - "author_inst": "CRG: Centre de Regulacio Genomica" - }, - { - "author_name": "Roc\u00edo Arranz", - "author_inst": "Centro Nacional de Biotecnolog\u00eda (CNB-CSIC), Madrid, Spain" - }, - { - "author_name": "Juli\u00e0 Blanco", - "author_inst": "Institut de Recerca de la SIDA irsiCaixa - HIVACAT" - }, - { - "author_name": "Giuliana Magri", - "author_inst": "Translational Clinical Research Program, Institut Hospital del Mar de Investigacions M\u00e8diques (IMIM), Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.21.524927", "rel_title": "CompCorona: A Web Portal for Comparative Analysis of the Host Transcriptome of PBMC and Lung SARS-CoV-2, SARS-CoV, and MERS-CoV", @@ -149554,6 +151632,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2023.01.21.23284855", + "rel_title": "Safety of bivalent omicron-containing mRNA-booster vaccines: a nationwide cohort study", + "rel_date": "2023-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.21.23284855", + "rel_abs": "BackgroundSafety data to support bivalent omicron-containing mRNA-booster vaccination are lacking.\n\nMethodsIn a Danish nationwide cohort study from 1 January 2021 to 10 December 2022, we examined the association between bivalent omicron-containing mRNA-booster vaccination as a fourth Covid-19 vaccine dose and risk of adverse events in individuals aged [≥]50 years. Using incidence rate ratios estimated with Poisson regression, we compared the rates of hospital visits for 27 different adverse events in a 28-day main risk period following vaccination with a bivalent omicron-containing mRNA-booster vaccine as a fourth dose to reference period rates from day 29 after the third or fourth vaccine dose and onward. Secondary analyses included stratifying by sex, age, and vaccine type and assessing the associations using self-controlled case series and observed vs. expected cohort analyses.\n\nResults1,740,417 individuals (mean age 67.8 years, standard deviation 10.7) received a bivalent omicron-containing mRNA-booster vaccine as a fourth dose. Fourth dose vaccination with a bivalent omicron-containing booster did not statistically significantly increase the rate of any of the 27 adverse outcomes within 28 days, nor when analyzed according to age, sex, vaccine type, or using alternative analytical approaches. However, post-hoc analysis detected signals for myocarditis (statistically significantly so in females), although the outcome was very rare and findings were based on few cases. No risk of cerebrovascular infarction was found.\n\nConclusionsBivalent omicron-containing mRNA-booster vaccination as a fourth dose was not associated with an increased risk of 27 different adverse events in 50+-year-olds.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Niklas Worm Andersson", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Emilia Myrup Thiesson", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Joergen Vinsloev Hansen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Anders Hviid", + "author_inst": "Statens Serum Institut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.20.524893", "rel_title": "Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature", @@ -150207,89 +152316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.19.524684", - "rel_title": "Immunogenicity and safety in pigs of PHH-1V, a SARS-CoV-2 RBD fusion heterodimer vaccine candidate", - "rel_date": "2023-01-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.19.524684", - "rel_abs": "The continuing high global incidence of COVID-19 and the undervaccinated status of billions of persons strongly motivate the development of a new generation of efficacious vaccines. We have developed an adjuvanted vaccine candidate, PHH-1V, based on a protein comprising the receptor binding domain (RBD) of the Beta variant of SARS-CoV-2 fused in tandem with the equivalent domain of the Alpha variant, with its immunogenicity, safety and efficacy previously demonstrated in mouse models. In the present study, we immunized pigs with different doses of PHH-1V in a prime-and-boost scheme showing PHH-1V to exhibit an excellent safety profile in pigs and to produce a solid RBD-specific humoral response with neutralising antibodies to 7 distinct SARS-CoV-2 variants of concern, with the induction of a significant IFN{gamma}+ T-cell response. We conclude that PHH-1V is safe and elicits a robust immune response to SARS-CoV-2 in pigs, a large animal preclinical model.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Alexandra Moros", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Antoni Prefaneta", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Antonio Barreiro", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Eva Perozo", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Alex Fernandez", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Manuel Canete", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Luis Gonzalez", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Carme Garriga", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain." - }, - { - "author_name": "Edwards Pradenas", - "author_inst": "IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain." - }, - { - "author_name": "Silvia Marfil", - "author_inst": "IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain." - }, - { - "author_name": "Julia Blanco", - "author_inst": "Institut de Recerca de la SIDA irsiCaixa - HIVACAT" - }, - { - "author_name": "Paula Cebollada-Rica", - "author_inst": "Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain." - }, - { - "author_name": "Marta Sistere-Oro", - "author_inst": "Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain." - }, - { - "author_name": "Andreas Meyerhans", - "author_inst": "Universitat Pompeu Fabra" - }, - { - "author_name": "Teresa Prat Cabanas", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain" - }, - { - "author_name": "Ricard March", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain" - }, - { - "author_name": "Laura Ferrer", - "author_inst": "HIPRA. Avda. La Selva, 135, 17170 Amer (Girona), Spain" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.18.524571", "rel_title": "Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature: a retrospective study", @@ -151424,6 +153450,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.14.23284558", + "rel_title": "Determinants of protection against SARS-CoV-2 Omicron BA.1 and Delta infections in fully vaccinated outpatients", + "rel_date": "2023-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.14.23284558", + "rel_abs": "ObjectivesWe aimed to evaluate the association between the humoral and cellular immune responses and symptomatic SARS-CoV-2 infection with Delta or Omicron BA.1 variants in fully vaccinated outpatients.\n\nMethodsAnti-RBD IgG levels and IFN-{gamma} release were evaluated at PCR-diagnosis of SARS-CoV-2 in 636 samples from negative and positive patients during Delta and Omicron BA.1 periods.\n\nResultsMedian levels of anti-RBD IgG in positive patients were significantly lower than in negative patients for both variants (p < 0.05). The risk of Delta infection was inversely correlated with anti-RBD IgG titres (aOR = 0.63, 95% CI [0.41; 0.95], p = 0.03) and it was lower in the hybrid immunity group compared to the homologous vaccination group (aOR = 0.22, 95% CI [0.05; 0.62], p = 0.01). In contrast, neither the vaccination scheme nor anti-RBD IgG titers were associated with the risk of BA.1 infection in multivariable analysis. IFN-{gamma} release post-SARS-CoV-2 peptide stimulation was not different between samples from patients infected (either with Delta or Omicron BA.1 variant) or not (p = 0.77).\n\nConclusionsOur results show that high circulating levels of anti-RBD IgG and hybrid immunity were independently associated with a lower risk of symptomatic SARS-CoV-2 infection in outpatients with differences according to the infecting variant.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Alvaro Roy", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Carla Saade", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Universite Claude Bernard Lyon 1, CNRS, Lyon 69364, France" + }, + { + "author_name": "Laurence Josset", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Benedicte Clement", + "author_inst": "Services des urgences, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Lyon 69004, France" + }, + { + "author_name": "Florence Morfin", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Gregory Destras", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Martine Valette", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Vinca Icard", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Antoine Oblette", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Marion Debombourg", + "author_inst": "Joint Research Unit Civils Hospices of Lyon-bioMerieux, Hopital Lyon Sud, Hospices Civils de Lyon, Pierre-Benite 69310, France" + }, + { + "author_name": "Christine Garrigou", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Karen Brengel-Pesce", + "author_inst": "Joint Research Unit Civils Hospices of Lyon-bioMerieux, Hopital Lyon Sud, Hospices Civils de Lyon, Pierre-Benite 69310, France" + }, + { + "author_name": "Laurence Generenaz", + "author_inst": "Joint Research Unit Civils Hospices of Lyon-bioMerieux, Hopital Lyon Sud, Hospices Civils de Lyon, Pierre-Benite 69310, France" + }, + { + "author_name": "Kahina Saker", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Romain Hernu", + "author_inst": "Services des urgences, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Lyon 69004, France" + }, + { + "author_name": "Bruno Pozzetto", + "author_inst": "Laboratoire des Agents Infectieux, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne 42270, France" + }, + { + "author_name": "Bruno Lina", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Mary Anne Trabaud", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Sophie Trouillet-Assant", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + }, + { + "author_name": "Antonin Bal", + "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associe au Centre National de Reference des virus des infections respiratoires, Hospices C" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.16.23284633", "rel_title": "Differences Between Reported COVID-19 Deaths and Estimated Excess Deaths in Counties Across the United States, March 2020 to February 2022", @@ -152009,77 +154130,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.01.18.23284713", - "rel_title": "Development of a Novel Medium Throughput Flow-Cytometry Based Micro-Neutralisation Test for SARS-CoV-2 with Applications in Clinical Vaccine Trials and Antibody Screening", - "rel_date": "2023-01-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.18.23284713", - "rel_abs": "Quantifying neutralising capacity of circulating SARS-COV-2 antibodies is critical in evaluating protective humoral immune responses generated post-infection/post-vaccination. Here we describe a novel medium-throughput flow cytometry-based micro-neutralisation test to evaluate Neutralising Antibody (NAb) responses against live SARS-CoV-2 Wild Type and Variants of Concern (VOC) in convalescent/vaccinated populations. Flow Cytometry-Based Micro-Neutralisation Test (Micro-NT) was performed in 96-well plates using clinical isolates WT-B, WT-B.177.18 and/or VOCs Beta and Omicron. Plasma samples (All Ireland Infectious Diseases (AIID) Cohort) were serially diluted (8 points, half-log) from 1/20 and pre-incubated with SARS-CoV-2 (1h, 37{degrees}C). Virus-plasma mixture were added onto VERO E6/VERO E6 TMPRSS2 cells for 18h. Percentage infected cells was analysed by automated flow cytometry following trypsinisation, fixation and SARS-CoV-2 Nucleoprotein intracellular staining. Half-maximal Neutralisation Titres (NT50) were determined using four-parameter logistic regression. Our assay was compared to Plaque Reduction Neutralisation Test (PRNT) and validated against WHO anti-SARS-CoV-2 Immunoglobulin Standards. Using WHO Standards with low, medium or high anti-SARS-CoV-2 IgG, both Micro-NT and PRNT achieved comparable NT50 values. Micro-NT was found to be highly reproducible (inter-assay CV of 11.64%). Screening 190 convalescent samples and 11 COVID-19 naive controls (AIID cohort) we demonstrated that Micro-NT has broad dynamic range differentiating NT50s <1/20 to >1/5000. We could also characterise immune-escape VOC observing up to 10-fold reduction in NT50 against SARS-CoV-2 Beta variant. Our flow cytometry-based Micro-NT is a robust and reliable assay to quantify NAb titres, and has been selected as an endpoint in clinical trials. It has higher throughput (96 well format versus 12 well) and reduced infection time (18h vs 48-96h) compared to the gold standard PRNT.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Sophie Rose O'Reilly", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Grace Kenny", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin; Department of Infectious Diseases, St V" - }, - { - "author_name": "Tamara Alrawahneh", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Nathan Francois", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Matthew Angeliadis", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Valentin de Masson d'Autume", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Alejandro Garcia Leon", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Eoin R. Feeney", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin; Department of Infectious Diseases, St V" - }, - { - "author_name": "Obada Yousif", - "author_inst": "Endocrinology Department, Wexford General Hospital, Carricklawn, Wexford, Ireland" - }, - { - "author_name": "Aoife Cotter", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin; Department of Infectious Diseases, Mate" - }, - { - "author_name": "Eoghan de Barra", - "author_inst": "Department of Infectious Diseases, Beaumont Hospital, Beaumont, Dublin 9, Ireland; Department of International Health and Tropical Medicine, Royal College of Su" - }, - { - "author_name": "Mary Horgan", - "author_inst": "Department of Infectious Diseases, Cork University Hospital, Wilton, Co Cork, Ireland" - }, - { - "author_name": "Patrick WG Mallon", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin; Department of Infectious Diseases, St V" - }, - { - "author_name": "Virginie Gautier", - "author_inst": "Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2023.01.18.23284602", "rel_title": "Assessment of Retrospective Collection of EQ-5D-5L in US Patients with COVID-19", @@ -153330,6 +155380,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.12.23284489", + "rel_title": "Cross-sectional Ct distributions from qPCR tests can provide an early warning signal for the spread of COVID-19 in communities", + "rel_date": "2023-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.12.23284489", + "rel_abs": "BackgroundSARS-CoV-2 PCR testing data has been widely used for COVID-19 surveillance. Existing COVID-19 forecasting models mainly rely on case counts, even though the binary PCR results provide a limited picture of the pandemic trajectory. Most forecasting models have failed to accurately predict the COVID-19 waves before they occur. Recently a model utilizing cross-sectional population cycle threshold (Ct) values obtained from PCR tests (Ct-based model) was developed to overcome the limitations of using only binary PCR results. In this study, we aimed to improve on COVID-19 forecasting models using features derived from the Ct-based model, to detect epidemic waves earlier than case-based trajectories.\n\nMethodsPCR data was collected weekly at Northeastern University (NU) between August 2020 and January 2022. The NU campus epidemic trajectories were generated from the campus incidence rates. In addition, epidemic trajectories were generated for Suffolk County, where NU is located, based on publicly available case-counts. A novel forecasting approach was developed by enhancing a recent deep learning model with Ct-based features, along with the models default features. For this, cross-sectional Ct values from PCR data were used to generate Ct-based epidemic trajectories, including effective reproductive rate (Rt) and incidence. The improvement in forecasting performance was compared using absolute errors and residual squared errors with respect to actual observed cases at the 7-day and 14-day forecasting horizons. The model was also tested prospectively over the period January 2022 to April 2022.\n\nResultsRt estimates from the Ct-based model preceded NU campus and Suffolk County cases by 12 and 14 days respectively, with a three-way synched Spearman correlation of 0.57. Enhancing the forecasting models with Ct-based information significantly decreased absolute error and residual squared error compared to the original model without Ct features (p-value <0.001 for both 7 and 14-days forecasting horizons).\n\nConclusionCt-based epidemic trajectories can herald an earlier signal for impending epidemic waves in the community and forecast transmission peaks. Moreover, COVID-19 forecasting models can be enhanced using these Ct features to improve their forecasting accuracy.\n\nPolicy implicationsWe make the case that public health agencies should publish Ct values along with the binary positive/negative PCR results. Early and accurate forecasting of epidemic waves can inform public health policies and countermeasures which can mitigate spread.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Mahfuza Sharmin", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Mani Manivannan", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "David Woo", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Oceane Sorel", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Jared Auclair", + "author_inst": "Northeastern University" + }, + { + "author_name": "Manoj Gandhi", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Imran Mujawar", + "author_inst": "Thermo Fisher Scientific" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.13.23284507", "rel_title": "SARS-CoV-2 VARIANT PREVALENCE ESTIMATION USING WASTEWATER SAMPLES", @@ -153835,65 +155928,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.01.13.23284518", - "rel_title": "Diagnostic performance of lateral flow immunoassays for COVID-19 antibodies in Peruvian population", - "rel_date": "2023-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284518", - "rel_abs": "BackgroundSerological assays have been used in seroprevalence studies to inform the dynamics of COVID-19. Lateral flow immunoassay (LFIA) tests are a very practical technology to use for this objective; however, one of their challenges may be variable diagnostic performance. Given the numerous available LFIA tests, evaluation of their accuracy is critical before real-world implementation.\n\nMethodsWe performed a retrospective diagnostic evaluation study to independently determine the diagnostic accuracy of 4 different antibody-detection LFIA tests. The sample panel was comprised of specimens collected and stored in biobanks; specifically, specimens that were RT-PCR positive for SARS-CoV-2 collected at various times throughout the COVID-19 disease course and those that were collected before the pandemic, during 2018 or earlier, from individuals with upper respiratory symptoms but were negative for tuberculosis. Clinical performance (sensitivity and specificity) was analyzed overall, and subset across individual antibody isotypes, and days from symptoms onset.\n\nResultsA very high specificity (98% - 100%) was found for all four tests. Overall sensitivity was variable, ranging from 29% [95% CI: 21%-39%] to 64% [95% CI: 54%-73%]. When considering detection of IgM only, the highest sensitivity was 42% [95% CI: 32%-52%], compared to 57% [95% CI: 47%-66%] for IgG only. When the analysis was restricted to at least 15 days since symptom onset, across any isotype, the sensitivity reached 90% for all four brands.\n\nConclusionAll four LFIA tests proved effective for identifying COVID-19 antibodies when two conditions were met: 1) at least 15 days have elapsed since symptom onset and 2) a sample is considered positive when either IgM or IgG is present. With these considerations, the use of this assays could help in seroprevalence studies or further exploration of its potential uses.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rodrigo Alonso Calderon-Flores", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Guillermo Caceres-Cardenas", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Karla Al\u00ed", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Margaretha De Vos", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Devy Emperador", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Tatiana C\u00e1ceres", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Anika Eca", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Luz Villa", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Audrey Albertini", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Jilian A. Sacks", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Cesar Ugarte-Gil", - "author_inst": "Universidad Peruana Cayetano Heredia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.13.23284506", "rel_title": "Effectiveness of Paxlovid - a review", @@ -155004,6 +157038,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.10.23284410", + "rel_title": "Addressing spatial misalignment in population health research: a case study of US congressional district political metrics and county health data", + "rel_date": "2023-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.10.23284410", + "rel_abs": "Areal spatial misalignment, which occurs when data on multiple variables are collected using mismatched boundary definitions, is a ubiquitous obstacle to data analysis in public health and social science research. As one example, the emerging sub-field studying the links between political context and health in the United States faces significant spatial misalignment-related challenges, as the congressional districts (CDs) over which political metrics are measured and administrative units, e.g., counties, for which health data are typically released, have a complex misalignment structure. Standard population-weighted data realignment procedures can induce measurement error and invalidate inference, which has prompted the development of fully model-based approaches for analyzing spatially misaligned data. One such approach, atom-based regression models (ABRM), holds particular promise but has scarcely been used in practice due to the lack of appropriate software or examples of implementation. ABRM use \"atoms\", the areas created by intersecting all sets of units on which variables of interest are measured, as the units of analysis and build models for the atom-level data, treating the atom-level variables (generally unmeasured) as latent variables. In this paper, we demonstrate the feasibility and strengths of the ABRM in a case study of the association between political representatives voting behavior (CD-level) and COVID-19 mortality rates (county-level) in a post-vaccine period. The adjusted ABRM results suggest that more conservative voting record is associated with an increase in COVID-19 mortality rates, with estimated associations smaller in magnitude but consistent in direction with those of standard realignment methods. The results also indicate that ABRM may enable more robust confounding adjustment and more realistic uncertainty estimates, properly representing the uncertainties arising from all analytic procedures. We also implement the ABRM in modern optimized Bayesian computing programs and make our code publicly available, which may enable these methods to be more widely adopted.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rachel C. Nethery", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Christian Testa", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Loni P. Tabb", + "author_inst": "Drexel Dornsife School of Public Health" + }, + { + "author_name": "William P. Hanage", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Jarvis T. Chen", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Nancy Krieger", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.10.23284397", "rel_title": "Prior SARS-CoV-2 Infection and COVID-19 Vaccine Effectiveness against Outpatient Illness during Widespread Circulation of SARS-CoV-2 Omicron Variant, US Flu VE Network", @@ -155673,61 +157746,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.01.10.23284400", - "rel_title": "ADAPTIVE TIME LOCATION SAMPLING FOR COMPASS, A SARS-COV-2 PREVALENCE STUDY IN FIFTEEN DIVERSE COMMUNITIES IN THE UNITED STATES", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.10.23284400", - "rel_abs": "The COVPN 5002 (COMPASS) study aimed to estimate the prevalence of SARS-CoV-2 (active SARS-CoV-2 or prior SARS-CoV-2 infection) in children and adults attending public venues in 15 socio-demographically diverse communities in the United States. To protect against potential challenges in implementing traditional sampling strategies, time-location sampling (TLS) using complex sampling involving stratification, clustering of units, and unequal probabilities of selection was used to recruit individuals from neighborhoods in selected communities. The innovative design adapted to constraints such as closure of venues; changing infection hotspots; and uncertain policies. Recruitment of children and the elderly raised additional challenges in sample selection and implementation. To address these challenges, the TLS design adaptively updated both the sampling frame and the selection probabilities over time using information acquired from prior weeks. Although the study itself was specific to COVID-19, the strategies presented in this paper could serve as a case study that can be adapted for performing rigorous population-level inferences in similar settings and could help inform rapid and effective responses to future global public health challenges.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sahar Z Zangeneh", - "author_inst": "RTI International" - }, - { - "author_name": "Timothy Skalland", - "author_inst": "Fred Hutch Cancer Center" - }, - { - "author_name": "Krista Yuhas", - "author_inst": "Fred Hutch Cancer Center" - }, - { - "author_name": "Lynda Emel", - "author_inst": "Fred Hutch Cancer Center" - }, - { - "author_name": "Jean De Dieu Tapsoba", - "author_inst": "Fred Hutch Cancer Center" - }, - { - "author_name": "Domonique Reed", - "author_inst": "Columbia University" - }, - { - "author_name": "Christopher Amos", - "author_inst": "Baylor University" - }, - { - "author_name": "Deborah Donnell", - "author_inst": "Fred Hutch Cancer Center" - }, - { - "author_name": "Ayana Moore", - "author_inst": "FHI 360" - }, - { - "author_name": "Jessica Justman", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.10.23284300", "rel_title": "The Smoldering Pandemic: Self-Reported Prevalence Assessment of Prolonged Grief Disorder. A cross sectional study of bereaving adults during the Covid Pandemic in Pakistan.", @@ -156610,6 +158628,153 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.01.08.523127", + "rel_title": "Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants", + "rel_date": "2023-01-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.08.523127", + "rel_abs": "The early Omicron lineage variants evolved and gave rise to diverging lineages that fueled the COVID-19 pandemic in 2022. Bivalent mRNA vaccines, designed to broaden protection against circulating and future variants, were authorized by the U.S. Food and Drug Administration (FDA) in August 2022 and recommended by the U.S. Centers for Disease Control and Prevention (CDC) in September 2022. The impact of bivalent vaccination on eliciting neutralizing antibodies against homologous BA.4/BA.5 viruses as well as emerging heterologous viruses needs to be analyzed. In this study, we analyze the neutralizing activity of sera collected after a third dose of vaccination (2-6 weeks post monovalent booster) or a fourth dose of vaccination (2-7 weeks post bivalent booster) against 10 predominant/recent Omicron lineage viruses including BA.1, BA.2, BA.5, BA.2.75, BA.2.75.2, BN.1, BQ.1, BQ.1.1, XBB, and XBB.1. The bivalent booster vaccination enhanced neutralizing antibody titers against all Omicron lineage viruses tested, including a 10-fold increase in neutralization of BQ.1 and BQ.1.1 viruses that predominated in the U.S. during the last two months of 2022. Overall, the data indicate the bivalent vaccine booster strengthens protection against Omicron lineage variants that evolved from BA.5 and BA.2 progenitors.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Nannan Jiang", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Li Wang", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Masato Hatta", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Chenchen Feng", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Michael Currier", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Xudong Lin", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Jaber Hossain", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Dan Cui", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Brian R. Mann", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Nicolas A. Kovacs", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Wei Wang", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Ginger Atteberry", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Malania Wilson", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Reina Chau", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Kristine A. Lacek", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Clinton R. Paden", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Norman Hassell", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Benjamin Rambo-Martin", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "John R. Barnes", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Rebecca J. Kondor", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Wesley H. Self", + "author_inst": "Vanderbilt University Medical Center, Nashville, TN, USA" + }, + { + "author_name": "Jillian P. Rhoads", + "author_inst": "Vanderbilt University Medical Center, Nashville, TN, USA" + }, + { + "author_name": "Adrienne Baughman", + "author_inst": "Vanderbilt University Medical Center, Nashville, TN, USA" + }, + { + "author_name": "James D. Chappell", + "author_inst": "Vanderbilt University Medical Center, Nashville, TN, USA" + }, + { + "author_name": "Nathan I. Shapiro", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard University, Cambridge, MA, USA" + }, + { + "author_name": "Kevin W. Gibbs", + "author_inst": "Wake Forest Baptist Medical Center, Winston-Salem, NC, USA" + }, + { + "author_name": "David N. Hager", + "author_inst": "Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Adam S. Lauring", + "author_inst": "University of Michigan, Ann Arbor, MI, USA" + }, + { + "author_name": "Diya Surie", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Meredith L. McMorrow", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "David E. Wentworth", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.01.07.523115", "rel_title": "The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2", @@ -157267,65 +159432,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.06.23284260", - "rel_title": "SARS-CoV-2 wastewater concentration and linked longitudinal seroprevalence: a spatial analysis of strain mutation, post-COVID-19 vaccination effect, and hospitalization burden forecasting", - "rel_date": "2023-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.06.23284260", - "rel_abs": "Despite wide scale assessments, it remains unclear how large-scale SARS-CoV-2 vaccination affected the wastewater concentration of the virus or the overall disease burden as measured by hospitalization rates. We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021-August 2021 in Jefferson County, Kentucky (USA). Our susceptible (S), vaccinated (V), variant-specific infected (I1 and I2), recovered (R), and seropositive (T) model (SVI2 RT) tracked prevalence longitudinally. This was related to wastewater concentration. The 64% county vaccination rate translated into about 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence was a 24-fold increase of infection counts, which corresponded to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration had the strongest correlation (r = 0.95) at 1 week lag. Our study underscores the importance of continued environmental surveillance post-vaccine and provides a proof-of-concept for environmental epidemiology monitoring of infectious disease for future pandemic preparedness.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rochelle H Holm", - "author_inst": "University of Louisville" - }, - { - "author_name": "Grzegorz Rempala", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Boseung Choi", - "author_inst": "Korea University" - }, - { - "author_name": "J Michael Brick", - "author_inst": "Westat, Inc" - }, - { - "author_name": "Alok Amraotkar", - "author_inst": "University of Louisville" - }, - { - "author_name": "Rachel Keith", - "author_inst": "University of Louisville" - }, - { - "author_name": "Eric Christian Rouchka", - "author_inst": "University of Louisville" - }, - { - "author_name": "Julia H. Chariker", - "author_inst": "University of Louisville" - }, - { - "author_name": "Kenneth Palmer", - "author_inst": "University of Louisville" - }, - { - "author_name": "Ted R Smith", - "author_inst": "University of Louisville" - }, - { - "author_name": "Aruni Bhatnagar", - "author_inst": "University of Louisville" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.06.23284199", "rel_title": "Who Gets Long COVID and Suffers its Mental Health and Socioeconomic Consequences in the United States? Preliminary Findings from a Large Nationwide Study", @@ -158772,6 +160878,77 @@ "type": "new results", "category": "animal behavior and cognition" }, + { + "rel_doi": "10.1101/2023.01.04.522794", + "rel_title": "Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses", + "rel_date": "2023-01-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.04.522794", + "rel_abs": "The Coronavirus (CoV) family includes a variety of viruses able to infect humans. Endemic CoVs that can cause common cold belong to the alphaCoV and betaCoV genera, with the betaCoV genus also containing subgenera with zoonotic and pandemic concern, including sarbecoCoV (SARS-CoV and SARS-CoV-2) and merbecoCoV (MERS-CoV). It is therefore warranted to explore pan-CoV vaccine concepts, to provide adaptive immune protection against new potential CoV outbreaks, particularly in the context of betaCoV sub lineages. To explore the feasibility of eliciting CD4+ T cell responses widely cross-recognizing different CoVs, we utilized samples collected pre-pandemic to systematically analyze T cell reactivity against representative alpha (NL63) and beta (OC43) common cold CoVs (CCC). Similar to previous findings on SARS-CoV-2, the S, N, M, and nsp3 antigens were immunodominant for both viruses while nsp2 and nsp12 were immunodominant for NL63 and OC43, respectively. We next performed a comprehensive T cell epitope screen, identifying 78 OC43 and 87 NL63-specific epitopes. For a selected subset of 18 epitopes, we experimentally assessed the T cell capability to cross-recognize sequences from representative viruses belonging to alphaCoV, sarbecoCoV, and beta-non-sarbecoCoV groups. We found general conservation within the alpha and beta groups, with cross-reactivity experimentally detected in 89% of the instances associated with sequence conservation of >67%. However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. Overall, these results provided critical insights in the development of future pan-CoV vaccines.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Alison Tarke", + "author_inst": "La Jolla Institute for immunology" + }, + { + "author_name": "Yun Zhang", + "author_inst": "J. Craig Venter Institute" + }, + { + "author_name": "Nils Methot", + "author_inst": "La Jolla Institute for immunology" + }, + { + "author_name": "Tara N Narowski", + "author_inst": "University of North Carolina School of Medicine" + }, + { + "author_name": "Elizabeth Phillips", + "author_inst": "VUMC: Vanderbilt University Medical Center" + }, + { + "author_name": "Simon Mallal", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "April Frazier", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Gilberto Filaci", + "author_inst": "University of Genoa" + }, + { + "author_name": "Daniela Weiskopf", + "author_inst": "La Jolla Institute For Immunology" + }, + { + "author_name": "Jennifer M Dan", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Prem Lakshmanane", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Richard H. Scheuermann", + "author_inst": "J. Craig Venter Institute" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "La Jolla Institute for immunology" + }, + { + "author_name": "Alba Grifoni", + "author_inst": "La Jolla Institute for Immunology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.01.05.522845", "rel_title": "Poor neutralizing antibody responses against SARS-CoV-2 Omicron BQ.1.1 and XBB in Norway in October 2022", @@ -159589,33 +161766,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.31.22284091", - "rel_title": "Machine Learning Algorithms to Fight the COVID-19 Pandemic", - "rel_date": "2023-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.31.22284091", - "rel_abs": "The ongoing novel COVID-19 global pandemic is one of the health emergencies in 21st century after hundred years of Spanish flu that affected almost all the countries in the world. The objective of this study is to generate STM and LTM real-time out of sample forecasts of the future COVID-19 confirmed and death cases respectively for the top five mostly affected countries in the world namely USA, India, Brazil, Russia and UK. As of January 17, 2021, it has caused a pandemic outbreak with more than 94.5 million confirmed cases and more than 2 million reported deaths worldwide. Due to extreme robust behaviour in the univariate time series data, forecasting of both COVID-19 confirmed and death cases has become the exigent task for the government officials, healthcare workers, economists, corporate leaders, government, decision makers, public-policy makers, and scientific experts to allocate health resources. To solve this problem different hybrid approaches are applied which eliminate both linear and non-linear errors of the time series datasets and the predictions of for these countries will be practical to act as forewarning for all.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "MONALISHA PATTNAIK", - "author_inst": "SAMBALPUR UNIVERSITY" - }, - { - "author_name": "ARYAN PATTNAIK", - "author_inst": "KIIT UNIVERSITY" - }, - { - "author_name": "ALIPSA PATTNAIK", - "author_inst": "BIRLA GLOBAL UNIVERSITY" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.03.23284131", "rel_title": "Estimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach", @@ -160790,6 +162940,61 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.01.02.522505", + "rel_title": "Nanoparticle-Conjugated TLR9 Agonists Improve the Potency, Durability, and Breadth of COVID-19 Vaccines", + "rel_date": "2023-01-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.02.522505", + "rel_abs": "Development of effective vaccines for infectious diseases has been one of the most successful global health interventions in history. Though, while ideal subunit vaccines strongly rely on antigen and adjuvant(s) selection, the mode and timescale of exposure to the immune system has often been overlooked. Unfortunately, poor control over the delivery of many adjuvants, which play a key role in enhancing the quality and potency of immune responses, can limit their efficacy and cause off-target toxicities. There is critical need for new adjuvant delivery technologies to enhance their efficacy and boost vaccine performance. Nanoparticles have been shown to be ideal carriers for improving antigen delivery due to their shape and size, which mimic viral structures, but have been generally less explored for adjuvant delivery. Here, we describe the design of self-assembled poly(ethylene glycol)-b-poly(lactic acid) nanoparticles decorated with CpG, a potent TLR9 agonist, to increase adjuvanticity in COVID-19 vaccines. By controlling the surface density of CpG, we show that intermediate valency is a key factor for TLR9 activation of immune cells. When delivered with the SARS-CoV-2 spike protein, CpG nanoparticle (CpG-NP) adjuvant greatly improve the magnitude and duration of antibody responses when compared to soluble CpG, and result in overall greater breadth of immunity against variants of concern. Moreover, encapsulation of CpG-NP into injectable polymeric-nanoparticle (PNP) hydrogels enhance the spatiotemporal control over co-delivery of CpG-NP adjuvant and spike protein antigen such that a single immunization of hydrogel-based vaccines generates comparable humoral responses as a typical prime-boost regimen of soluble vaccines. These delivery technologies can potentially reduce the costs and burden of clinical vaccination, both of which are key elements in fighting a pandemic.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ben S. Ou", + "author_inst": "Stanford University" + }, + { + "author_name": "Julie Baillet", + "author_inst": "Stanford University, University of Bordeaux" + }, + { + "author_name": "Vittoria C.T.M. Picece", + "author_inst": "Stanford University, ETH Zurich" + }, + { + "author_name": "Emily C. Gale", + "author_inst": "Stanford University" + }, + { + "author_name": "Abigail E. Powell", + "author_inst": "Stanford University" + }, + { + "author_name": "Olivia M. Saouaf", + "author_inst": "Stanford University" + }, + { + "author_name": "Jerry Yan", + "author_inst": "Stanford University" + }, + { + "author_name": "Anahita Nejatfard", + "author_inst": "Stanford University" + }, + { + "author_name": "Hector Lopez Hernandez", + "author_inst": "Stanford University" + }, + { + "author_name": "Eric Appel", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.01.03.522427", "rel_title": "Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion", @@ -161443,45 +163648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.28.22284012", - "rel_title": "Association between recent COVID-19 diagnosis on depression and anxiety symptoms among slum residents in Kampala, Uganda", - "rel_date": "2022-12-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.28.22284012", - "rel_abs": "BackgroundAn increase in mental health problems has been reported since the beginning of the COVID-19 pandemic. However, little is known about the prevalence of depressive and anxiety disorders, and how recent COVID-19 diagnosis may influence risk of these conditions especially in low-income settings. In this study, we assessed the association between recent COVID-19 diagnosis and depressive and anxiety symptoms among residents in an urban slum setting in Uganda.\n\nMethodsA cross-sectional study was conducted among 284 individuals in a slum settlement in Kampala, Uganda between April and May 2022. We assessed generalized anxiety and depression symptoms using two validated questionnaires. We collected data on sociodemographic characteristics, and self-reported recent COVID-19 diagnosis (in the previous 30 days). Using a modified Poisson regression, adjusted for age, sex, gender and household income, we separately provided prevalence ratios and 95% confidence intervals for the associations between recent COVID-19 diagnosis and depressive and anxiety symptoms.\n\nResultsOverall, 33.8% and 13.4% of the participants met the depression and generalized anxiety screening criteria respectively. People with recent COVID-19 diagnosis were more likely to be depressed (53.1%) than those with no recent diagnosis (31.4%). Participants who were recently diagnosed with COVID-19 reported higher prevalence of anxiety (34.4%) compared to those with no recent diagnosis of COVID-19 (10.7%). After adjusting for confounding, recent diagnosis with COVID-19 was associated with depression (PR= 1.60, 95% CI 1.09 - 2.34) and anxiety (PR = 2.83, 95% CI 1.50 - 5.31).\n\nConclusionThis study suggests an increased risk of depressive symptoms and GAD in adults following a COVID-19 diagnosis. We recommend additional mental health support for recently diagnosed persons. The long-term of COVID-19 on mental health effects also need to be investigated.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Solomon Tsebeni Wafula", - "author_inst": "Makerere University School of Public Health" - }, - { - "author_name": "Lesley R Ninsiima", - "author_inst": "Makerere University College of Health Sciences" - }, - { - "author_name": "Hilbert Mendoza", - "author_inst": "University of Antwerp Drie Eiken Campus: Universiteit Antwerpen Campus Drie Eiken" - }, - { - "author_name": "John C Ssempebwa", - "author_inst": "Makerere University College of Health Sciences" - }, - { - "author_name": "Florian Walter", - "author_inst": "The University of Manchester Faculty of Biology Medicine and Health" - }, - { - "author_name": "David Musoke", - "author_inst": "Makerere University College of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.12.28.22284008", "rel_title": "The kinetics of humoral and cellular responses after the booster dose of COVID-19 vaccine in inflammatory arthritis patients", @@ -162392,6 +164558,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.12.21.22283740", + "rel_title": "Prior infection- and/or vaccine-induced protection against Omicron BA.1, BA.2 and BA.4/BA.5-related hospitalisations in older adults: a test-negative case-control study in Quebec, Canada", + "rel_date": "2022-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.21.22283740", + "rel_abs": "BackgroundDue to severe outcomes, elderly adults 60 years or older are prioritized for COVID-19 vaccination but accumulated SARS-CoV-2 infection and vaccination likely modifies their risk. We estimated vaccine effectiveness against omicron-associated hospitalisation among elderly adults, by number of doses, prior infection history and time since last immunological event.\n\nMethodsWe conducted a test-negative case-control study among symptomatic elderly adults tested for SARS-CoV-2 in Quebec, Canada during BA.1-, BA.2- and BA.4/5-dominant periods. Relative to unvaccinated, infection-naive participants, we compared COVID-19 hospitalisation risk by mRNA vaccine dose and/or prior infection (pre-omicron or omicron) history.\n\nFindingsDuring BA.1, BA.2 and BA.4/5 periods, two- vs. four-dose vaccine effectiveness alone against hospitalisation was: 78% (95%CI:75-80) vs. 96% (95%CI:93-98); 60% (95%CI:50-97) vs. 84% (95%CI:81-87); and 40% (95%CI:30-49) vs. 68% (95%CI:63-72), respectively, consistent with longer median time since second vs fourth dose. By respective period, effectiveness of pre-omicron vs. omicron infection alone against hospitalisation was: 93% (95%CI:80-97) vs. [not estimable]; 88% (95%CI:50-97) vs. 96% (95%CI:68-99); and 69% (95%CI:30-85) vs. 90% (95%CI:79-95). Regardless of doses (2-5) or prior infection type, hybrid protection was [≥]90%, lasting at least 6-8 months during the BA.4/5 period. Prior omicron infection alone reduced BA.4/5 hospitalisation risk by >80% for at least 6-8 months.\n\nInterpretationElderly adults with history of both prior SARS-CoV-2 infection and [≥]2 vaccine doses appear well-protected for a prolonged period against omicron hospitalisation, including BA.4/5. Ensuring infection-naive older adults remain up-to-date with vaccination may further reduce COVID-19 hospitalisations most efficiently.\n\nFundingMinistere de la Sante et des Services sociaux du Quebec.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sara Carazo", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Danuta M Skowronski", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Marc Brisson", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec-Universit\u00e9 Laval Research Center" + }, + { + "author_name": "Chantal Sauvageau", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Nicholas Brousseau", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Judith M Fafard", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec, Institut national de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Rodica Gilca", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Denis Talbot", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec-Universit\u00e9 Laval Research Center" + }, + { + "author_name": "Manale Ouakki", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Yossi Febriani", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec-Universit\u00e9 Laval Research Center" + }, + { + "author_name": "Genevi\u00e8ve Deceuninck", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec-Universit\u00e9 Laval Research Center" + }, + { + "author_name": "Philippe De Wals", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Gaston De Serres", + "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.26.521940", "rel_title": "ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses", @@ -163157,57 +165390,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.12.27.522023", - "rel_title": "Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs.", - "rel_date": "2022-12-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.27.522023", - "rel_abs": "RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs (svRNAs) generated by SARS-CoV-1 and SARS-CoV-2 remained largely unexplored, mainly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing. By analyzing publicly available small RNA-seq datasets, we observed that human cells infected by SARS-CoV-1 or SARS-CoV-2 produce multiple short viral RNAs (svRNAs), ranging in size from 15 to 26 nt and deriving predominantly from (+) RNA strands. In addition, we verified the presence of the five most abundant SARS-CoV-2 svRNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by qPCR. Interestingly, the copy number of the observed SARS-CoV-2 svRNAs dramatically exceeded the expression of previously reported viral miRNAs in the same cells. We hypothesize that the reported SARS-CoV-2 svRNAs could serve as biomarkers for early infection stages due to their high abundance. Finally, we found that both SARS-CoV-1 and SARS-CoV-2 infection induced up- and down-regulation of multiple endogenous human short RNAs that align predominantly to protein-coding and lncRNA transcripts. Interestingly, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various hg38 sequences, suggesting opportunities to investigate regulatory roles of svRNAs during infection. Further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tom Driedonks", - "author_inst": "Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA." - }, - { - "author_name": "Lyle Nyberg", - "author_inst": "Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA." - }, - { - "author_name": "Abigail Conte", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA." - }, - { - "author_name": "Zexu Ma", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA." - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA." - }, - { - "author_name": "Eduard Duban", - "author_inst": "SciBerg e.Kfm, Mannheim, Germany." - }, - { - "author_name": "Holger S\u00fcltmann", - "author_inst": "Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany" - }, - { - "author_name": "Andrey Turchinovich", - "author_inst": "Heidelberg Biolabs GmbH, Heidelberg, Germany." - }, - { - "author_name": "Kenneth Witwer", - "author_inst": "Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.12.23.22283896", "rel_title": "No patient is the same; lessons learned from antibody repertoire profiling in hospitalized severe COVID-19 patients", @@ -164518,6 +166700,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.22.521696", + "rel_title": "Omicron BA.5 infects human brain organoids and is neuroinvasive and lethal in K18-hACE2 mice", + "rel_date": "2022-12-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.22.521696", + "rel_abs": "The reduced pathogenicity of the omicron BA.1 sub-lineage compared to earlier variants is well described, although whether such attenuation is retained for later variants like BA.5 and XBB remains controversial. We show that BA.5 and XBB isolates were significantly more pathogenic in K18-hACE2 mice than a BA.1 isolate, showing increased neuroinvasiveness, resulting in fulminant brain infection and mortality, similar to that seen for original ancestral isolates. BA.5 also infected human cortical brain organoids to a greater extent than the BA.1 and original ancestral isolates. In the brains of mice, neurons were the main target of infection, and in human organoids neuronal progenitor cells and immature neurons were infected. Although fulminant brain infection is not a feature of COVID-19, evidence for brain infection and brain damage in some COVID-19 patients with severe disease is becoming compelling, with the results herein suggesting that evolving omicron variants may have increasing intrinsic neuropathogenic potential.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Romal Stewart", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Kexin Yan", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Sevannah A Ellis", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Cameron R Bishop", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Troy Dumenil", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Bing Tang", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Wilson Nguyen", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Thibaut Larcher", + "author_inst": "INRAE, Oniris, PAnTher, APEX, Nantes, France" + }, + { + "author_name": "Rhys Parry", + "author_inst": "University of Queensland" + }, + { + "author_name": "Julian De Jun Sng", + "author_inst": "University of Queensland" + }, + { + "author_name": "Alexander A Khromykh", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland Brisbane QLD Australia." + }, + { + "author_name": "Robert K P Sullivan", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Mary Lor", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Frederic A Meunier", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia." + }, + { + "author_name": "Daniel J Rawle", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Andreas Suhrbier", + "author_inst": "QIMR Berghofer Medical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.12.21.22283753", "rel_title": "Outpatient treatment of Covid-19 with metformin, ivermectin, and fluvoxamine and the development of Long Covid over 10-month follow-up.", @@ -165191,37 +167452,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.21.22283786", - "rel_title": "Is it possible to flatten-the-curve after the initial outbreak of Covid-19? A data-driven modeling analysis for Omicron pandemic in China", - "rel_date": "2022-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.21.22283786", - "rel_abs": "In the current coronavirus disease 2019 (COVID-19) pandemic, the Omicron variant of severe acute respiratory syndrome coronavirus 2 has become the predominant strain circulating worldwide. In China, enormous controversies exist regarding the \"dynamic zero tolerance\" (DZT) and \"totally no inventions\" (TNI) strategies for preventing the spread of the Omicron variant. Currently, China is gradually relaxing the COVID-19 measures from DZT level. In such situations, the \"flatten-the-curve\" (FTC) strategy, which decreases and maintains the low rate of infection to avoid overwhelming the healthcare system by adopting relaxed nonpharmaceutical interventions (NPIs) after the initial outbreak, has been perceived as most appropriate and effective method to prevent the spread of the Omicron variant. Hence, we established a data-driven model of Omicron transmission based on the pandemic data of Macau, Hong Kong, and Singapore in 2022 to deduce the overall prevention effect throughout China. In the current immunity level without any NPI applied, more than 12.7 billion (including asymptomatic individuals) were infected with the Omicron variant within 90 days, but the daily new infections sharply declined; moreover, Omicron outbreak would result to 1.49 million deaths within 180 days. The application of FTC could decrease the deaths by 36.91% within 360 days. Age-stratified analyses showed that the NPI application among individuals aged >60 years would also result in 0.81 million deaths within 360 days, and the application of FTC strategy through treatment with anti-COVID drugs can reduce the number of deaths to 0.40 million. In a model of completed vaccination, the application of TNI strategy would also result in 0.56 million deaths and slightly decrease the infection numbers. The strict implementation of FTC policy combined with completed vaccination and drug use, which only resulted in 0.19 million deaths in an age-stratified model, will help end the pandemic within about 240 days. The pandemic would be terminated within a shorter period of time without resulting in a high fatality rate; therefore, the FTC policy could be strictly implemented through enhancement of immunity and drug use.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jiaqi Sun", - "author_inst": "Department of Mathematics, Faculty of Science and Technology, University of Macau" - }, - { - "author_name": "Yusi Li", - "author_inst": "Department of Mathematics, Faculty of Science and Technology, University of Macau, Taipa, Macau" - }, - { - "author_name": "Ning-Yi Shao", - "author_inst": "Department of Biomedical Sciences, Faculty of Health Sciences, MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR" - }, - { - "author_name": "Miao Liu", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.21.22283811", "rel_title": "Antiviral treatments lead to the rapid accrual of hundreds of SARS-CoV-2 mutations in immunocompromised patients", @@ -166176,6 +168406,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.12.20.521221", + "rel_title": "Structure adaptation in Omicron SARS-CoV-2/hACE2:Biophysical origins of evolutionary driving forces", + "rel_date": "2022-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.20.521221", + "rel_abs": "Since its emergence, the Covid19 pandemic has been sustained by a series of transmission waves initiated by new variants of the SARS-CoV-2 virus. Some of these arise with higher transmissivity and/or increased disease severity. Here we use molecular dynamics simulations to examine the modulation of the fundamental interactions between the receptor binding domain (RBD) of the spike glycoprotein and the host cell receptor (human angiotensin-converting enzyme 2: hACE2) arising from Omicron variant mutations (BA.1 and BA.2) relative to the original wild type strain. We find significant structural differences in the complexes which overall bring the spike protein and its receptor into closer proximity. These are consistent with and attributed to the higher positive charge on the RBD conferred by BA.1 and BA.2 mutations relative to the wild type. However, further differences between sub-variants BA.1 and BA.2 (which have equivalent RBD charges) are also evident: Mutations affect interdomain interactions between the up-chain and its clockwise neighbor chain, resulting in enhanced flexibility for BA.2. Consequently, additional close contacts arise in BA.2 which include binding to hACE2 by a second spike protein monomer, in addition to the up-chain - a motif not found in BA.1. Finally, the mechanism by which the glycans stabilize the up state of the Spike protein differs for the wild type and the Omicrons. We also found the glycan on N90 of hACE2 turns from inhibiting, to facilitating the binding to Omicron spike protein. These structural and electrostatic differences offer further insight into the mechanisms by which viral mutations modulate host cell binding and provide a biophysical basis for evolutionary driving forces.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ya-Wen Hsiao", + "author_inst": "The Hartree Centre, Daresbury Laboratory, STFC" + }, + { + "author_name": "Tseden Taddese", + "author_inst": "The Hartree Centre, Daresbury Lab, STFC" + }, + { + "author_name": "Guadalupe Jimenez-Serratos", + "author_inst": "The Hartree Centre, Daresbury Lab, STFC" + }, + { + "author_name": "David J Bray", + "author_inst": "The Hartree Centre, Daresbury Lab, STFC" + }, + { + "author_name": "Jason Crain", + "author_inst": "IBM Research Europe; University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.12.20.521247", "rel_title": "Identification of new drugs to counteract anti-spike IgG-induced hyperinflammation in severe COVID-19", @@ -166825,113 +169090,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.19.22283645", - "rel_title": "SARS-CoV-2 mRNA vaccination exposes progressive adaptive immune dysfunction in patients with chronic lymphocytic leukemia", - "rel_date": "2022-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283645", - "rel_abs": "Chronic lymphocytic leukemia (CLL) patients have lower seroconversion rates and antibody titers following SARS-CoV-2 vaccination, but the reasons for this diminished response are poorly understood. Here, we studied humoral and cellular responses in 95 CLL patients and 30 healthy controls after two BNT162b2 or mRNA-2173 mRNA immunizations. We found that 42% of CLL vaccinees developed SARS-CoV-2-specific binding and neutralizing antibodies (NAbs), while 32% had no response. Interestingly, 26% were seropositive, but had no detectable NAbs, suggesting the maintenance of pre-existing endemic human coronavirus-specific antibodies that cross-react with the S2 domain of the SARS-CoV-2 spike. These individuals had more advanced disease. In treatment-naive CLL patients, mRNA-2173 induced 12-fold higher NAb titers and 1.7-fold higher response rates than BNT162b2. These data reveal a graded loss of immune function, with pre-existing memory being preserved longer than the capacity to respond to new antigens, and identify mRNA-2173 as a superior vaccine for CLL patients.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Kai Qin", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Kazuhito Honjo", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Scott Sherrill-Mix", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Weimin Liu", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Regina M Stoltz", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Allisa K Oman", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Lucinda A Hall", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Ran Li", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Sarah Sterrett", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Ellen R Frederick", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Jeffrey R Lancaster", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Mayur Narkhede", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Amitkumar Mehta", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Foluso J Ogunsile", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Rima B Patel", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Thomas J Ketas", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Victor M Cruz Portillo", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Albert Cupo", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Benjamin M Larimer", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Anju Bansal", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Paul A Goepfert", - "author_inst": "UAB School of Medicine: The University of Alabama at Birmingham Heersink School of Medicine" - }, - { - "author_name": "Beatrice H Hahn", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Randall S. Davis", - "author_inst": "University of Alabama at Birmingham" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.12.20.22283717", "rel_title": "Impact of guidance on trends of steroid prescriptions for COVID-19 inpatients: an analysis of the nation-wide administrative database in Japan", @@ -168026,6 +170184,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.12.15.22283474", + "rel_title": "Bacillus Calmette-Guerin vaccine to reduce COVID-19 infections and hospitalisations in healthcare workers: a living systematic review and prospective ALL-IN meta-analysis of individual participant data from randomised controlled trials", + "rel_date": "2022-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.15.22283474", + "rel_abs": "BACKGROUNDThe objective is to determine the impact of the Bacillus Calmette-Guerin (BCG) vaccine compared to placebo or no vaccine on COVID-19 infections and hospitalisations in healthcare workers. We are using a living and prospective approach to Individual-Participant-Data (IPD) meta-analysis of ongoing studies based on the Anytime Live and Leading Interim (ALL-IN) meta-analysis statistical methodology.\n\nMETHODSPlanned and ongoing randomised controlled trials were identified from trial registries and by snowballing (final elicitation: Oct 3 2022). The methodology was specified prospectively - with no trial results available - for trial inclusion as well as statistical analysis. Inclusion decisions were made collaboratively based on a risk-of-bias assessment by an external protocol review committee (Cochrane risk-of-bias tool adjusted for use on protocols), expected homogeneity in treatment effect, and agreement with the predetermined event definitions. The co-primary endpoints were incidence of COVID-19 infection and COVID-19-related hospital admission. Accumulating IPD from included trials was analysed sequentially using the exact e-value logrank test (at level = 0.5% for infections and level = 4.5% for hospitalisations) and anytime-valid 95%-confidence intervals (CIs) for the hazard ratio (HR) for a predetermined fixed-effects approach to meta-analysis (no measures of statistical heterogeneity). Infections were included if demonstrated by PCR tests, antigen tests or suggestive lung CTs. Participants were censored at date of first COVID-19-specific vaccination and two-stage analyses were performed in calendar time, with a stratification factor per trial.\n\nRESULTSSix trials were included in the primary analysis with 4 433 participants in total. The e-values showed no evidence of a favourable effect of minimal clinically relevance (HR < 0.8) in comparison to the null (HR = 1) for COVID-19 infections, nor for COVID-19 hospitalisations (HR < 0.7 vs HR = 1). COVID-19 infection was observed in 251 participants receiving BCG and 244 participants not receiving BCG, HR 1.02 (anytime-valid 95%-CI 0.78-1.35). COVID-19 hospitalisations were observed in 13 participants receiving BCG and 7 not receiving BCG, resulting in an uninformative estimate (HR 1.88; anytime-valid 95%-CI 0.26-13.40).\n\nDISCUSSIONIt is highly unlikely that BCG has a clinically relevant effect on COVID-19 infections in healthcare workers. With only limited observations, no conclusion could be drawn for COVID-19 related hospitalisation. Due to the nature of ALL-IN meta-analysis, emerging data from new trials can be included without violating type-I error rates or interval coverage. We intend to keep this meta-analysis alive and up-to-date, as more trials report. For COVID-19 related hospitalisations, we do not expect enough future observations for a meaningful analysis. For BCG-mediated protection against COVID-19 infections, on the other hand, more observations could lead to a more precise estimate that concludes the meta-analysis for futility, meaning that the current interval excludes the HR of 0.8 predetermined as effect size of minimal clinical relevance.\n\nOTHERNo external funding. Preregistered at PROSPERO: CRD42021213069.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Judith ter Schure", + "author_inst": "Amsterdam UMC/CWI, Amsterdam, the Netherlands" + }, + { + "author_name": "Alexander Ly", + "author_inst": "University of Amsterdam/CWI, Amsterdam, the Netherlands" + }, + { + "author_name": "Lisa Belin", + "author_inst": "Sorbonne Universite, INSERM, Institut Pierre Louis dEpidemiologie et de Santee Publique, AP-HP, Hoopital Pitiee Salpetriere, Deepartement de Santee Publique, Un" + }, + { + "author_name": "Christine S. Benn", + "author_inst": "Bandim Health Project, Open Patient Data Explorative Network, Department of Clinical Research and Danish Institute for Advanced Study, University of Southern De" + }, + { + "author_name": "Marc J.M. Bonten", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Jeffrey D. Cirillo", + "author_inst": "Center for Airborne Pathogen Research and Imaging, Texas A and M School of Medicine, Bryan, TX 77807" + }, + { + "author_name": "Johanna A.A. Damen", + "author_inst": "Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Ines Fronteira", + "author_inst": "Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Universidade NOVA de Lisboa" + }, + { + "author_name": "Kelly D. Hendriks", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Anna Paula Junqueira-Kipnis", + "author_inst": "Federal University of Goias, Institute of Tropical Medicine and Public Health, Goiania, Brazil" + }, + { + "author_name": "Andre Kipnis", + "author_inst": "Federal University of Goias, Institute of Tropical Medicine and Public Health, Goiania, Brazil" + }, + { + "author_name": "Odile Launay", + "author_inst": "AP-HP" + }, + { + "author_name": "Jose Euberto Mendez-Reyes", + "author_inst": "Global and Immigrant Health, Baylor College of Medicine, Houston, TX" + }, + { + "author_name": "Judit Moldvay", + "author_inst": "National Koranyi Institute of Pulmonology, Budapest, Hungary" + }, + { + "author_name": "Mihai G. Netea", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands" + }, + { + "author_name": "Sebastian Nielsen", + "author_inst": "Bandim Health Project, Open Patient Data Explorative Network, Department of Clinical Research, University of Southern Denmark, Denmark" + }, + { + "author_name": "Caryn M. Upton", + "author_inst": "TASK, Parow, Cape Town, South Africa" + }, + { + "author_name": "Gerben van den Hoogen", + "author_inst": "TASK, Parow, Cape Town, South Africa" + }, + { + "author_name": "Jesper M. Weehuizen", + "author_inst": "Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Peter D. Grunwald", + "author_inst": "CWI, Amsterdam, the Netherlands" + }, + { + "author_name": "Henri van Werkhoven", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.18.22283593", "rel_title": "Evaluation of bivalent Omicron BA.1 booster vaccination after different priming regimens in healthcare workers (SWITCH ON): a randomized controlled trial", @@ -168931,57 +171188,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.18.22283627", - "rel_title": "Quantifying the rebound of influenza epidemics after relaxing nonpharmaceutical interventions during the coronavirus disease 2019 pandemic in China", - "rel_date": "2022-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.18.22283627", - "rel_abs": "The co-existence of coronavirus disease 2019 (COVID-19) and seasonal influenza epidemics has become a potential threat to human health, particularly in China in the oncoming season. However, with the relaxation of nonpharmaceutical interventions (NPIs) during the COVID-19 pandemic, the rebound extent of the influenza activities is still poorly understood. In this study, we constructed a susceptible-vaccinated-infectious-recovered-susceptible (SVIRS) model to simulate influenza transmission and calibrated it using influenza surveillance data from 2018 to 2022. We projected the influenza transmission over the next 3 years using the SVIRS model. We observed that, in epidemiological year 2021-2022, the reproduction numbers of influenza in southern and northern China were reduced by 64.0% and 34.5%, respectively, compared with those before the pandemic. The percentage of people susceptible to influenza virus increased by 138.6% and 57.3% in southern and northern China by October 1, 2022, respectively. After relaxing NPIs, the potential accumulation of susceptibility to influenza infection may lead to a large-scale influenza outbreak in the year 2022-2023, the scale of which may be affected by the intensity of the NPIs. And later relaxation of NPIs in the year 2023 would not lead to much larger rebound of influenza activities in the year 2023-2024. To control the influenza epidemic to the pre-pandemic level after relaxing NPIs, the influenza vaccination rates in southern and northern China should increase to 53.8% and 33.8%, respectively. Vaccination for influenza should be advocated to reduce the potential reemergence of the influenza epidemic in the next few years.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hao Lei", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Lei Yang", - "author_inst": "Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Mengya Yang", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Jing Tang", - "author_inst": "Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Jiaying Yang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Minju Tan", - "author_inst": "Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Shigui Yang", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Dayan Wang", - "author_inst": "Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Yuelong Shu", - "author_inst": "Sun Yat-sen University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.15.22283495", "rel_title": "Impact of COVID-19 on access to healthcare by persons with disabilities", @@ -169976,6 +172182,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.15.22283522", + "rel_title": "Estimating the transmission dynamics of Omicron in Beijing, November to December 2022", + "rel_date": "2022-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.15.22283522", + "rel_abs": "We tracked the effective reproduction number Rt of SARS-CoV-2 Omicron BF.7 in Beijing in November - December 2022 by fitting a transmission dynamic model parameterized with real-time mobility data to (i) the daily number of new symptomatic cases on November 1-11 (when the zero-covid interventions were still strictly enforced) and (ii) the proportion of individuals who participated in online polls on December 10-22 and self-reported to have been previously test-positive since November 1. After the announcement of \"20 measures\", we estimated that Rt increased to 3.44 (95% CrI: 2.82 - 4.14) on November 18 and the infection incidence peaked on December 11. The cumulative infection attack rate (i.e. the proportion of population who have been infected since November 1) was 43.1% (95% CrI: 25.6 - 60.9) on December 14 and 75.7% (95% CrI: 60.7 - 84.4) on December 22. Surveillance programmes should be rapidly set up to monitor the evolving epidemiology and evolution of SARS-CoV-2 across China.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kathy Leung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Eric Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Carlos Wong", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Gabriel M Leung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Joseph Wu", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.14.22283419", "rel_title": "Using Social Media to Help Understand Long COVID Patient-Reported Health Outcomes: A Natural Language Processing Approach", @@ -170585,53 +172826,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.12.14.520483", - "rel_title": "Crowdsourcing Temporal Transcriptomic Coronavirus Host Infection Data: resources, guide, and novel insights.", - "rel_date": "2022-12-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.14.520483", - "rel_abs": "The emergence of SARS-CoV-2 reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of COVID-19 during the pandemic. This study coupled existing transcriptomic data from SARS-CoV-1 lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g., CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA Damage Response and Repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients that died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens. The data from this study is available in an interactive portal (http://18.222.95.219:8047).", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "James Flynn", - "author_inst": "Illumina, Inc" - }, - { - "author_name": "Mehdi M Ahmadi", - "author_inst": "Bioinfo Solutions LLC, Parker, CO" - }, - { - "author_name": "Chase T McFarland", - "author_inst": "Bioinfo Solutions LLC, Parker, CO" - }, - { - "author_name": "Michael D Kubal", - "author_inst": "Illumina, Inc" - }, - { - "author_name": "Mark A Taylor", - "author_inst": "Bioinfo Solutions LLC, Parker, CO" - }, - { - "author_name": "Zhang Cheng", - "author_inst": "Illumina, Inc" - }, - { - "author_name": "Enrique C Torchia", - "author_inst": "Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO" - }, - { - "author_name": "Michael G Edwards", - "author_inst": "Bioinfo Solutions LLC, Parker, CO" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.12.15.520569", "rel_title": "Progressive loss of conserved spike protein neutralizing antibody sites in Omicron sublineages is balanced by preserved T-cell recognition epitopes", @@ -172010,6 +174204,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.12.22283388", + "rel_title": "The Impact of COVID-19 Pandemic on Mental Health: A Scoping Review", + "rel_date": "2022-12-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283388", + "rel_abs": "BackgroundThis scoping review assessed the COVID-19 impacts on mental health and associated risk factors.\n\nMethodsA systematic literature search for relevant articles published in the period March 2020 to July 2022, was conducted in the APA PsychInfo, JBI Evidence Synthesis, Epistemonikos, PubMed, and Cochrane databases.\n\nResultsA total of 72 studies met the inclusion criteria. Results showed that the commonly used mental health assessment tools were the Patient Health Questionnaire (41.7%), Generalized Anxiety Disorder Scale (36%), 21-item Depression, Anxiety, and Stress (13.9%), Impact of Event Scale (12.5%), Pittsburgh Sleep Quality Index (9.7%), Symptom Checklist and the General Health Questionnaire (6.9% each). The prevalence rate of depression ranged from 5-76.5%, 5.6-80.5% for anxiety, 9.1-65% for Post-Traumatic Stress Disorder, 8.3-61.7% for sleep disorders, 4.9-70.1% for stress, 7-71.5% for psychological distress, and 21.4-69.3% for general mental health conditions. The major risks included female gender, healthcare-related/frontline jobs, isolation/quarantine, poverty, lower education, COVID-19 risk, age, commodities, mental illness history, negative psychology, and higher social media exposure. The incidence of mental disorders increased along with the increasing cases of COVID-19 and the corresponding government restrictions.\n\nConclusionStandard assessment tools were used for mental health assessment by the reviewed studies which were conducted during COVID-19. Mental health disorders like depression, anxiety, and stress increased during the COVID-19 pandemic and lockdowns. Various factors impacted the prevalence of mental health disorders. Policymakers need to provide social protective measures to improve coping capacities during critical health events to avoid negative impacts on the population. Further studies should investigate the effectiveness of interventions for reducing the prevalence and risk factors for mental health conditions during a public health challenge.\n\nBackground", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Blessing O. Josiah", + "author_inst": "Turks and Caicos Islands Community College" + }, + { + "author_name": "France Ncube", + "author_inst": "UNICAF University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.12.12.22283336", "rel_title": "Heat wave, COVID-19, and mortality excess in the 2022 summer: a cohort study on data from Italian surveillances.", @@ -172622,41 +174839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.09.22283296", - "rel_title": "Healthcare Facility Water, Sanitation and Hygiene Service Status and Barriers in Ethiopia: Its Implication for COVID-19 pandemic and Healthcare Acquired Infection Prevention.", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.09.22283296", - "rel_abs": "BackgroundDespite the public health significance of healthcare Water, Sanitation, and Hygiene (WASH) service in reduction of nosocomial infection and improving quality of care is paramount little is known on the status of WASH service in a health care facility at the time of pandemic and the barriers that hinder the service in the health care setting in Ethiopia.\n\nObjectiveThe aim of this study was to assess status of basic water, sanitation, hand hygiene, healthcare waste management, and environmental cleanliness service and its barriers at public health care facilities in the city of Addis Ababa, Ethiopia 2022.\n\nMethodsConvergent parallel mixed design was conducted among 86 public health care facilities located in Addis Ababa city. Stratified sampling technique was used to select health care facilities. A semi-structured observational checklist tool was used to measure the availability of services. For the qualitative study, semi-structured interview was conducted among 16 key informants and thematic data analysis was done to identify the barriers.\n\nFindingThis study found that no one healthcare facility had basic access to overall WASH services. The independent WASH domain analysis showed that, about 86% healthcare facilities had basic water access, 100% had limited sanitation access, 88.4% had limited hand hygiene service, 69.8% had limited healthcare waste management service, and 97.7% had limited environmental cleaning service. Built environments of WASH infrastructure; Resource availability and allocation; leadership and stakeholder participation; inadequate training and poor behaviour; and legal issues were identified barriers to provision of basic healthcare WASH services.\n\nConclusion and recommendationThe availability of healthcare WASH services in Addis Ababa city remains far from the pace to achieve the sustainable goal target by 2025. The limited access to WASH services makes worsening the prevention and control of COVID-19 pandemics, healthcare acquired infection in the facility. The country need to act now on more financial investment, capacity building, facilitating committed leadership, and participation of stakeholders to ensuring basic WASH services at healthcare setting.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Atimen Derso", - "author_inst": "Addis Ababa University" - }, - { - "author_name": "Taffere Addis", - "author_inst": "EIWR: Ethiopian Institute of Water Resources" - }, - { - "author_name": "Bezatu Mengistie", - "author_inst": "EIWR: Ethiopian Institute of Water Resources" - }, - { - "author_name": "Awoke Keleb", - "author_inst": "Wollo University" - }, - { - "author_name": "Ayechew Adedmas", - "author_inst": "Wollo University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.13.22283409", "rel_title": "Stress, Genetics and Mood: Impact of COVID-19 on a College Freshman Sample", @@ -173811,6 +175993,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.12.11.520008", + "rel_title": "Using machine learning to detect coronaviruses potentially infectious to humans", + "rel_date": "2022-12-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.11.520008", + "rel_abs": "Establishing the host range for novel viruses remains a challenge. Here, we address the challenge of identifying non-human animal coronaviruses that may infect humans by creating an artificial neural network model that learns from the binding of the spike protein of alpha and beta coronaviruses to their host receptor. The proposed method produces a human-Binding Potential (h-BiP) score that distinguishes, with high accuracy, the binding potential among human coronaviruses. Two viruses, previously unknown to bind human receptors, were identified: Bat coronavirus BtCoV/133/2005 (a MERS related virus) and Rhinolophus affinis coronavirus isolate LYRa3 a SARS related virus. We further analyze the binding properties of these viruses using molecular dynamics. To test whether this model can be used for surveillance of novel coronaviruses, we re-trained the model on a set that excludes SARS-COV-2 viral sequences. The results predict the binding of SARS-CoV-2 with a human receptor, indicating that machine learning methods are an excellent tool for the prediction of host expansion events.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Georgina Gonzalez-Isunza", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Muhammad- Zaki Jawaid", + "author_inst": "University of California Davis" + }, + { + "author_name": "Pengyu Liu", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Daniel L Cox", + "author_inst": "UC Davis" + }, + { + "author_name": "Mariel Vazquez", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Javier Arsuaga", + "author_inst": "University of California, Davis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.12.10.518819", "rel_title": "Identification of genomic signatures and multiple lineage markers from the second and third wave samples of COVID-19 in Western Rajasthan, India", @@ -174300,77 +176521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.09.519765", - "rel_title": "TMPRSS2 is essential for SARS-CoV-2 Beta and Omicron infection", - "rel_date": "2022-12-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.09.519765", - "rel_abs": "The COVID-19 pandemic remains a global health threat and novel antiviral strategies are urgently needed. SARS-CoV-2 employs the cellular serine protease TMPRSS2 for entry into lung cells and TMPRSS2 inhibitors are being developed for COVID-19 therapy. However, the SARS-CoV-2 Omicron variant, which currently dominates the pandemic, prefers the endo/lysosomal cysteine protease cathepsin L over TMPRSS2 for cell entry, raising doubts whether TMPRSS2 inhibitors would be suitable for treatment of patients infected with the Omicron variant. Nevertheless, the contribution of TMPRSS2 to spread of SARS-CoV-2 in the infected host is largely unclear. Here, we show that loss of TMPRSS2 strongly reduced the replication of the Beta variant in nose, trachea and lung of C57BL mice and protected the animals from weight loss and disease. Infection of mice with the Omicron variant did not cause disease, as expected, but again TMPRSS2 was essential for efficient viral spread in the upper and lower respiratory tract. These results identify a key role of TMPRSS2 in SARS-CoV-2 Beta and Omicron infection and highlight TMPRSS2 as an attractive target for antiviral intervention.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kristin Metzdorf", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Henning Jacobsen", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Marina C Greweling-Pils", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Markus Hoffmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Tatjana Lueddecke", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Felicitas Miller", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Lars Melcher", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Amy M Kempf", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Inga Nehlmeier", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fuer Primatenforschung" - }, - { - "author_name": "Dunja Bruder", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Marek Widera", - "author_inst": "University Hospital, Goethe University Frankfurt am Main" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "University Hospital, Goethe University Frankfurt am Main" - }, - { - "author_name": "Stefan Poehlmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Luka Cicin-Sain", - "author_inst": "Helmholtz Centre for Infection Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.12.08.519593", "rel_title": "Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants", @@ -175665,6 +177815,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.07.519460", + "rel_title": "Reduced SARS-CoV-2 mRNA vaccine immunogenicity and protection in mice with diet-induced obesity and insulin resistance.", + "rel_date": "2022-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.07.519460", + "rel_abs": "BackgroundObesity and Type 2 Diabetes Mellitus (T2DM) are associated with an increased risk of severe outcomes from infectious diseases, including COVID-19. These conditions are also associated with distinct responses to immunization, including an impaired response to widely used SARS-CoV-2 mRNA vaccines.\n\nObjectiveTo establish a connection between reduced immunization efficacy via modeling the effects of metabolic diseases on vaccine immunogenicity that is essential for the development of more effective vaccines for this distinct vulnerable population.\n\nMethodsWe utilized a murine model of diet-induced obesity and insulin resistance to model the effects of comorbid T2DM and obesity on vaccine immunogenicity and protection.\n\nResultsMice fed a high-fat diet (HFD) developed obesity, hyperinsulinemia, and glucose intolerance. Relative to mice fed a normal diet (ND), HFD mice vaccinated with a SARS-CoV-2 mRNA vaccine exhibited significantly lower anti-spike IgG titers, predominantly in the IgG2c subclass, associated with a lower type 1 response, along with a 3.83-fold decrease in neutralizing titers. Furthermore, enhanced vaccine-induced spike-specific CD8+ T cell activation and protection from lung infection against SARS-CoV-2 challenge were seen only in ND mice but not in HFD mice.\n\nConclusionWe demonstrate impaired immunity following SARS-CoV-2 mRNA immunization in a murine model of comorbid T2DM and obesity, supporting the need for further research into the basis for impaired anti-SARS-CoV-2 immunity in T2DM and investigation of novel approaches to enhance vaccine immunogenicity among those with metabolic diseases.\n\nCapsule summaryObesity and type 2 diabetes impair SARS-CoV-2 mRNA vaccine efficacy in a murine model.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Marisa E. McGrath", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Carly Dillen", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Hyuk-Soo Seo", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Sirano Dhe-Paganon", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Robert K. Ernst", + "author_inst": "University of Maryland School of Dentistry" + }, + { + "author_name": "Matthew B. Frieman", + "author_inst": "University of Maryland School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.06.519378", "rel_title": "The Australian academic STEMM workplace post-COVID: a picture of disarray", @@ -176158,85 +178347,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2022.12.05.519032", - "rel_title": "Superiority of intranasal over systemic administration of bioengineered soluble ACE2 for survival and brain protection against SARS-CoV-2 infection", - "rel_date": "2022-12-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.05.519032", - "rel_abs": "The present study was designed to investigate the effects of a soluble ACE2 protein termed ACE2 618-DDC-ABD, bioengineered to have long duration of action and high binding affinity to SARS-CoV-2, when administered either intranasally (IN) or intraperitoneally (IP) and before or after SARS-CoV-2 inoculation.\n\nK18hACE2 mice permissive for SARS-CoV-2 infection were inoculated with 2x104 PFU wildtype SARS-CoV-2. In one protocol, ACE2 618-DDC-ABD was given either IN or IP, pre- and post-viral inoculation. In a second protocol, ACE2 618-DDC-ABD was given either IN, IP or IN+IP but only post-viral inoculation. In addition, A549 and Vero E6 cells were used to test neutralization of SARS-CoV-2 variants by ACE2 618-DDC-ABD at different concentrations.\n\nSurvival by day 5 was 0% in infected untreated mice, and 40% in mice from the ACE2 618-DDC-ABD IP-pre treated group. By contrast, in the IN-pre group survival was 90%, histopathology of brain and kidney was essentially normal and markedly improved in the lungs. When ACE2 618-DDC-ABD was administered only post viral inoculation, survival was 30% in the IN+IP group, 20% in the IN and 0% in the IP group. Brain SARS-CoV-2 titers were high in all groups except for the IN-pre group where titers were undetectable in all mice. In cells permissive for SARS-CoV-2 infection, ACE2 618-DDC-ABD neutralized wildtype SARS-CoV-2 at high concentrations, whereas much lower concentrations neutralized omicron BA. 1.\n\nWe conclude that ACE2 618-DDC-ABD provides much better survival and organ protection when administered intranasally than when given systemically or after viral inoculation and that lowering brain titers is a critical determinant of survival and organ protection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Luise Hassler", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois and Charite Universitaetsme" - }, - { - "author_name": "Jan Wysocki", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Jared T. Ahrendsen", - "author_inst": "Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Minghao Ye", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Ian Gelarden", - "author_inst": "Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Vlad Nicolaescu", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Anastasia Tomatsidou", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Haley Gula", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Cosimo Cianfarini", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Nigar Khurram", - "author_inst": "Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Yashpal Kanwar", - "author_inst": "Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Benjamin David Singer", - "author_inst": "Divison of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Glenn Randall", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Dominique M Missiakas", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Jack Henkin", - "author_inst": "Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois" - }, - { - "author_name": "Daniel Batlle", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2022.12.04.519037", "rel_title": "Genome charaterization based on the Spike-614 and NS8-84 loci of SARS-CoV-2 reveals two major onsets of the COVID-19 pandemic", @@ -177339,6 +179449,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.12.02.518937", + "rel_title": "Deep mutational scanning to predict antibody escape in SARS-CoV-2 Omicron subvariants", + "rel_date": "2022-12-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.02.518937", + "rel_abs": "The major concern of COVID-19 therapeutic monoclonal antibodies is the loss of efficacy to continuously emerging SARS-CoV-2 variants. To predict the antibodies efficacy to the future Omicron subvariants, we conducted deep mutational scanning (DMS) encompassing all single mutations in the receptor binding domain of BA.2 strain. In case of bebtelovimab that preserves neutralization activity against BA.2 and BA.5, broad range of amino acid substitutions at K444, V445 and G446 and some substitutions at P499 and T500 were indicated to achieve the antibody escape. Among currently increasing subvariants, BA2.75 carrying G446S partly and XBB with V445P and BQ.1 with K444T completely evade the neutralization of bebtelovimab, consistent with the DMS results. DMS can comprehensively characterize the antibody escape for efficient and effective management of future variants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mellissa C Alcantara", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Yusuke Higuchi", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Yuhei Kirita", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Satoaki Matoba", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Atsushi Hoshino", + "author_inst": "KPUM" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.12.03.518963", "rel_title": "Enhanced Protection from SARS-CoV-2 Variants by MVA-Based Vaccines Expressing Matched or Mismatched S Proteins Administered Intranasally to hACE2 Mice", @@ -177988,33 +180133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.12.02.22283039", - "rel_title": "Death, Inequality, and the Pandemic in the Nation's Capital", - "rel_date": "2022-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283039", - "rel_abs": "Abrupt changes in mortality rates and life expectancy allow us to understand how shocks like COVID-19 can exacerbate health inequalities across groups. We look at Washington, D.C., a major city with a diverse population and long-standing socio-economic divisions, to describe the all-cause mortality trends from 2015 to 2021 by age, sex, race, and ward of residence. We report differences in cause-specific mortality pre- and post-COVID-19 outbreak and estimate the Years of Life Lost (YLL) attributable to COVID-19. We compute death rates using information from death certificates and the Census, and we calculate YLL using the life table approach, comparing the life expectancy of people with and without COVID-19. We find that in 2020 and 2021, there were respectively 1,128 and 629 excess deaths (158 per 100K and 94 per 100K) compared to the annual average over the previous five years, and 689 and 363 deaths in 2020 and 2021, respectively (97 per 100K and 54 per 100K) listing COVID-19 as a cause of death. Death rates in 2020 and 2021, compared to the five previous years, were higher for men than women by about 12pp and 5pp and occurred almost entirely among residents 45 and older. Excess deaths between 2020 and 2021 were higher for Black and Hispanic residents by about 286 and 97 per 100K, respectively--with the highest proportional increase (almost twofold) for Hispanics in 2020. YLL was highest for Hispanic males and lowest for White females.\n\nSignificance StatementThe leading causes of death in DC were historically heart disease and cancer. In 2020, the leading cause of death was COVID. Accidental and violent deaths increased dramatically and disproportionately by race. Racial disparities in COVID and non-COVID deaths indicate that these correlate with socioeconomic conditions.\n\nLife expectancy in the United States decreased for the first time in 2020 due to COVID-19. In the nations capital, the decline in life expectancy was more significant for Hispanic and non-Hispanic Black than White people, widening the already large difference in life expectancy among these groups.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maria Alva", - "author_inst": "Georgetown University" - }, - { - "author_name": "Sai Srujana Illa", - "author_inst": "Georgetown University" - }, - { - "author_name": "Jaren R Haber", - "author_inst": "Dartmouth College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.02.22283046", "rel_title": "The Societal Value of Vaccines: Expert-Based Conceptual Framework and Methods Using COVID-19 Vaccines as A Case Study", @@ -179417,6 +181535,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.01.518149", + "rel_title": "SARS-CoV-2 mRNA vaccine is re-adenylated in vivo, enhancing antigen production and immune response", + "rel_date": "2022-12-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.01.518149", + "rel_abs": "Though mRNA vaccines against COVID-19 have revolutionized vaccinology and have been administered in billions of doses, we know incredibly little about how mRNA vaccines are metabolized in vivo. Here we implemented enhanced nanopore Direct RNA sequencing (eDRS), to enable the analysis of single Modernas mRNA-1273 molecules, giving in vivo information about the sequence and poly(A) tails.\n\nWe show that mRNA-1273, with all uridines replaced by N1-methylpseudouridine (m{Psi}), is terminated by a long poly(A) tail (~100 nucleotides) followed by an m{Psi}Cm{Psi}AG sequence. In model cell lines, mRNA-1273 is swiftly degraded in a process initiated by the removal of m{Psi}Cm{Psi}AG, followed by CCR4-NOT-mediated deadenylation. In contrast, intramuscularly inoculated mRNA-1273 undergoes more complex modifications. Notably, mRNA-1273 molecules are re-adenylated after m{Psi}Cm{Psi}AG removal. Detailed analysis of immune cells involved in antigen production revealed that in macrophages, after m{Psi}Cm{Psi}AG removal, vaccine mRNA is very efficiently re-adenylated, and poly(A) tails can reach up to 200A. In contrast, in dendritic cells, vaccine mRNA undergoes slow deadenylation-dependent decay. We further demonstrate that enhancement of mRNA stability in macrophages is mediated by TENT5 poly(A) polymerases, whose expression is induced by the vaccine itself. Lack of TENT5-mediated re-adenylation results in lower antigen production and severely compromises specific immunoglobulin production following vaccination.\n\nTogether, our findings provide an unexpected principle for the high efficacy of mRNA vaccines and open new possibilities for their improvement. They also emphasize that, in addition to targeting a protein of interest, the design of mRNA therapeutics should be customized to its cellular destination.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Pawel S Krawczyk", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland" + }, + { + "author_name": "Olga Gewartowska", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland" + }, + { + "author_name": "Michal Mazur", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland" + }, + { + "author_name": "Wiktoria Orzel", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland; Faculty of Biology, University of Warsaw, 5a Pawinskiego, 02-106," + }, + { + "author_name": "Katarzyna Matylla-Kulinska", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland; Faculty of Biology, University of Warsaw, 5a Pawinskiego, 02-106," + }, + { + "author_name": "Sebastian Jelen", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland; Faculty of Biology, University of Warsaw, 5a Pawinskiego, 02-106," + }, + { + "author_name": "Pawel Turowski", + "author_inst": "ExploRNA Therapeutics, 101 Zwirki i Wigury, 02-089, Warsaw, Poland" + }, + { + "author_name": "Tomasz Spiewla", + "author_inst": "Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland" + }, + { + "author_name": "Bartosz Tarkowski", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland" + }, + { + "author_name": "Agnieszka Tudek", + "author_inst": "Institute of Biochemistry and Biophysics, 5A Pawinskiego, 02-106 Warsaw, Poland" + }, + { + "author_name": "Aleksandra Brouze", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland; Faculty of Biology, University of Warsaw, 5a Pawinskiego, 02-106," + }, + { + "author_name": "Aleksandra Wesolowska", + "author_inst": "Laboratory of Human Milk and Lactation Research at Regional Human Milk Bank in Holy Family Hospital, Department of Medical Biology, Medical University of Warsaw" + }, + { + "author_name": "Dominika Nowis", + "author_inst": "Laboratory of Experimental Medicine, Medical University of Warsaw, 5 Nielubowicza St., 02-097 Warsaw, Poland" + }, + { + "author_name": "Jakub Golab", + "author_inst": "Department of Immunology, Medical University of Warsaw, 5 Nielubowicza Str., 02-097, Warsaw, Poland" + }, + { + "author_name": "Joanna Kowalska", + "author_inst": "Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland" + }, + { + "author_name": "Jacek Jemielity", + "author_inst": "Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland" + }, + { + "author_name": "Andrzej Dziembowski", + "author_inst": "International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 Warsaw, Poland; Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, W" + }, + { + "author_name": "Seweryn Mroczek", + "author_inst": "Faculty of Biology, University of Warsaw, 5a Pawinskiego, 02-106, Warsaw, Poland; International Institute of Molecular and Cell Biology, 4 Ks. Trojdena, 02-106 " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.11.30.22282831", "rel_title": "Severe acute infection and chronic pulmonary disease are risk factors for developing post-COVID-19 conditions", @@ -179910,97 +182115,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2022.11.29.22282916", - "rel_title": "Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population", - "rel_date": "2022-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282916", - "rel_abs": "Following primary SARS-CoV-2 vaccination, understanding the relative extent of protection against SARS-CoV-2 infection from boosters or from breakthrough infections (i.e. infection in the context of previous vaccination) has important implications for vaccine policy. In this study, we investigated correlates of protection against Omicron BA.4/5 infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults [≥]18y from the United Kingdom general population. We found that higher anti-spike IgG antibody levels were associated with increased protection against Omicron BA.4/5 infection and that breakthrough infections were associated with higher levels of protection at any given antibody level than booster vaccinations. Breakthrough infections generated similar antibody levels to third/booster vaccinations, and the subsequent declines in antibody levels were similar to or slightly slower than those after third/booster vaccinations. Taken together our findings show that breakthrough infection provides longer lasting protection against further infections than booster vaccinations. For example, considering antibody levels associated with 67% protection against infection, a third/booster vaccination did not provide long-lasting protection, while a Delta/Omicron BA.1 breakthrough infection could provide 5-10 months of protection against Omicron BA.4/5 reinfection. 50-60% of the vaccinated UK population with a breakthrough infection would still be protected by the end of 2022, compared to <15% of the triple-vaccinated UK population without previous infection. Although there are societal impacts and risks to some individuals associated with ongoing transmission, breakthrough infection could be an efficient immune-boosting mechanism for subgroups of the population, including younger healthy adults, who have low risks of adverse consequences from infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Jia Wei", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philippa C Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole Stoesser", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Newton", - "author_inst": "Public Health England" - }, - { - "author_name": "Ian Diamond", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ruth Studley", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Nick Taylor", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "John Bell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jeremy Farrar", - "author_inst": "Wellcome Trust" - }, - { - "author_name": "Brian Marsden", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jaison Kolenchery", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Hoosdally", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yvonne Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Stuart", - "author_inst": "University of Oxford" - }, - { - "author_name": "Derrick Crook", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tim E Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ann Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Koen Pouwels", - "author_inst": "University of Oxford" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.29.22282903", "rel_title": "Effect of COVID-19 during pregnancy: Studying the maternal and neonatal outcomes and assessing the placental changes related to SARS-CoV-2", @@ -181059,6 +183173,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.29.22282856", + "rel_title": "The Detection of COVID-19 in Chest X-Rays Using Ensemble CNN Techniques", + "rel_date": "2022-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282856", + "rel_abs": "Advances in the field of image classification using convolutional neural networks (CNNs) have greatly improved the accuracy of medical image diagnosis by radiologists. Numerous research groups have applied CNN methods to diagnose respiratory illnesses from chest x-rays, and have extended this work to prove the feasibility of rapidly diagnosing COVID-19 to high degrees of accuracy. One issue in previous research has been the use of datasets containing only a few hundred images of chest x-rays containing COVID-19, causing CNNs to overfit the image data. This leads to a lower accuracy when the model attempts to classify new images, as would be clinically expected of it. In this work, we present a model trained on the COVID-QU-Ex dataset, overall containing 33,920 chest x-ray images, with an equal share of COVID-19, Non-COVID pneumonia, and Normal images. The model itself is an ensemble of pre-trained CNNs (ResNet50, VGG19, VGG16) and GLCM textural features. It achieved a 98.34% binary classification accuracy (COVID-19/no COVID-19) on a balanced test dataset of 6581 chest x-rays, and 94.68% for distinguishing between COVID-19, Non-COVID pneumonia and normal chest x-rays. Also, we herein discuss the effects of dataset size, demonstrating that a 98.82% 3-class accuracy can be achieved using the model if the training dataset only contains a few thousand images, but that generalisability of the model suffers with such small datasets.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Domantas Kuzinkovas", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Sandhya Clement", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2022.11.26.22282782", "rel_title": "Rethinking Transfer Learning for Medical Image Classification", @@ -181568,65 +183705,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.22.22282199", - "rel_title": "Monoclonal antibody levels and protection from COVID-19", - "rel_date": "2022-11-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.22.22282199", - "rel_abs": "Multiple monoclonal antibodies have been shown to be effective for both prophylaxis and therapy for SARS-CoV-2 infection. Here we aggregate data from randomized controlled trials assessing the use of monoclonal antibodies in preventing symptomatic SARS-CoV-2 infection. We use data on changes in the in vivo concentration of monoclonal antibodies, and the associated protection from COVID-19, over time to model the dose-response relationship of monoclonal antibodies for prophylaxis. We estimate that 50% protection from COVID-19 is achieved with a monoclonal antibody concentration of 54-fold of the in vitro IC50 (95% CI: 16 - 183). This relationship provides a quantitative tool allowing prediction of the prophylactic efficacy and duration of protection for new monoclonal antibodies administered at different doses and against different SARS-CoV-2 variants.\n\nFinally, we compare the relationship between neutralization titer and protection from COVID-19 after either monoclonal antibody treatment or vaccination. We find no evidence for a difference between the 50% protective titer for monoclonal antibodies and vaccination.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Eva Stadler", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Martin T Burgess", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Timothy E Schlub", - "author_inst": "University of Sydney" - }, - { - "author_name": "Khai Li Chai", - "author_inst": "Monash University, Melbourne" - }, - { - "author_name": "Zoe K McQuilten", - "author_inst": "Monash University, Melbourne" - }, - { - "author_name": "Erica M Wood", - "author_inst": "Monash University, Melbourne" - }, - { - "author_name": "Mark N Polizzotto", - "author_inst": "The Australian National University" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Deborah Cromer", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Miles P Davenport", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "David S Khoury", - "author_inst": "Kirby Institute, UNSW Sydney" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.23.22282280", "rel_title": "The impacts of social restrictions during the COVID-19 pandemic on the physical activity levels of over 50-year olds: the CHARIOT COVID-19 Rapid Response (CCRR) cohort study", @@ -183057,6 +185135,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2022.11.23.22282463", + "rel_title": "Heterogeneity of treatment effect of higher dose dexamethasone by geographic region in patients with COVID-19 and severe hypoxemia - A post hoc evaluation of the COVID STEROID 2 trial", + "rel_date": "2022-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282463", + "rel_abs": "BackgroundThe COVID-STEROID 2 trial found high probability of benefit with dexamethasone 12 mg vs. 6 mg daily among patients with COVID-19 and severe hypoxemia. There was suggestion of heterogeneity of treatment effects (HTE)between patients enrolled from Europe vs. India on the primary outcome. Whether there was HTE by geographical region for the remaining prespecified patient-important outcomes is unclear.\n\nMethodsWe evaluated HTE by geographical region (Europe vs. India) for all secondary outcomes assessed in the trial with analyses adjusted for stratification variables. The results are presented as risk differences (RDs) or mean differences (MDs) with 99% confidence intervals (CIs) and P-values from interaction tests.\n\nResultsWe found HTE for mortality at day 28 (RD for Europe -8.3% (99 % CI: -17.7 to 1.0) vs. RD for India 0.1% (99% CI: -10.0 to 10.0)), mortality at day 90 (RD for Europe -7.4% (99% CI: -17.1 to 2.0) vs. RD for India -1.4% (99% CI:-12.8 to 9.8)), mortality at day 180 (RD for Europe -6.7% (99%CI:-16.4 to 2.9) vs. RD for India -1.0% (99%CI:-12.3 to 10.3)), and number of days alive without life support at day 90 (MD for Europe 6.1 days (99% CI:-1.3 to 13.4) vs. MD for India 1.7 days (99% CI:-8.4 to11.8)). For serious adverse reactions, the direction was reversed (RD for Europe -1.0% (99% CI:-7.1 to 5.2) vs. RD for India -5.3% (99% CI: -16.2 to 5.0). For HRQoL outcomes, MD in EQ-5D-5L index values was 0.08(99%CI: -0.01 to 0.16) for Europe and 0.02(99%CI:-0.10 to 0.14) for India. For EQ VAS, MD was 4.4(95%CI:-3.1 to 11.9) for Europe and 2.6(99%CI:-9.0 to 14.2) for India. P values for all tests of interaction were [≥]0.12.\n\nConclusionsIn this post hoc exploratory analysis, we found that higher dose dexamethasone may have lower beneficial effects for patients in India as compared with those in Europe without an increase in serious adverse reactions.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Bharath Kumar Tirupakuzhi Vijayaraghavan", + "author_inst": "Apollo Hospitals Chennai" + }, + { + "author_name": "Anders Granholm", + "author_inst": "Copenhagen University Hospital: Rigshospitalet" + }, + { + "author_name": "Sheila N Myatra", + "author_inst": "TMH: Tata Memorial Hospital" + }, + { + "author_name": "Vivekanand Jha", + "author_inst": "The George Institute for Global Health India" + }, + { + "author_name": "Naomi Hammond", + "author_inst": "The George Institute for Global Health" + }, + { + "author_name": "Sharon Micallef", + "author_inst": "The George Institute for Global Health" + }, + { + "author_name": "Marie Warrer Munch", + "author_inst": "Copenhagen University Hospital: Rigshospitalet" + }, + { + "author_name": "Maj-Brit N Kj\u00e6r", + "author_inst": "Copenhagen University Hospital: Rigshospitalet" + }, + { + "author_name": "Morten Hylander M\u00f8ller", + "author_inst": "Copenhagen University Hospital: Rigshospitalet" + }, + { + "author_name": "Theis Lange", + "author_inst": "University of Copenhagen Department of Public Health: Kobenhavns Universitet Institut for Folkesundhedsvidenskab" + }, + { + "author_name": "Anders Perner", + "author_inst": "Copenhagen University Hospital: Rigshospitalet" + }, + { + "author_name": "Balasubramanian Venkatesh", + "author_inst": "The George Institute for Global Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.11.24.22282735", "rel_title": "Immunogenicity and durability against Omicron BA.1, BA.2 and BA.4/5 variants at 3 to 4 months after a heterologous COVID-19 booster vaccine in healthy adults with a two-doses CoronaVac vaccination", @@ -183698,65 +185839,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2022.11.22.517574", - "rel_title": "Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 Spike protein", - "rel_date": "2022-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.22.517574", - "rel_abs": "SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic. Its high pathogenicity is due to SARS-CoV-2 spike protein (S protein) contacting host-cell receptors. A critical hallmark of COVID-19 is the occurrence of coagulopathies. Here, we report the direct observation of the interactions between S protein and platelets. Live imaging showed that the S protein triggers platelets to deform dynamically, in some cases, leading to their irreversible activation. Strikingly, cellular cryo-electron tomography revealed dense decorations of S protein on the platelet surface, inducing filopodia formation. Hypothesizing that S protein binds to filopodia-inducing integrin receptors, we tested the binding to RGD motif-recognizing platelet integrins and found that S protein recognizes integrin v{beta}3. Our results infer that the stochastic activation of platelets is due to weak interactions of S protein with integrin, which can attribute to the pathogenesis of COVID-19 and the occurrence of rare but severe coagulopathies.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christopher Cyrus Kuhn", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Nirakar Basnet", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Satish Bodakuntla", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Pelayo Alvarez- Brecht", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Scott Nichols", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Antonio Martinez-Sanchez", - "author_inst": "Department of Computer Sciences, Faculty of Sciences - Campus Llamaquique, University of Oviedo, Oviedo 33007, Spain" - }, - { - "author_name": "Lorenzo Agostini", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Young-Min Soh", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Junichi Takagi", - "author_inst": "Osaka University Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan" - }, - { - "author_name": "Christian Biertumpfel", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - }, - { - "author_name": "Naoko Mizuno", - "author_inst": "Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Dr., Bethesda, MD, 20892, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2022.11.23.517609", "rel_title": "Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses", @@ -184927,6 +187009,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.11.21.517390", + "rel_title": "Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England", + "rel_date": "2022-11-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.21.517390", + "rel_abs": "Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is expected to substantially impact disease epidemiology and evolution. However, we dont yet have an understanding of how genetic drift changes over time or across locations. Furthermore, noise that results from data collection can potentially confound estimates of genetic drift. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. Our method is highly scalable to increasingly large genomic datasets, which overcomes a limitation in commonly used phylogenetic methods. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium and separately infer the strength of genetic drift for pre-B.1.177, B.1.177, Alpha, and Delta. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude, which cannot be explained by literature values of superspreading. Our estimates of genetic drift will be informative for parameterizing evolutionary models and studying potential mechanisms for increased drift.\n\nAuthor SummaryThe transmission of pathogens like SARS-CoV-2 is strongly affected by chance effects in the contact process between infected and susceptible individuals, collectively referred to as random genetic drift. We have an incomplete understanding of how genetic drift changes across time and locations. To address this gap, we developed a computational method that infers the strength of genetic drift from time series genomic data that corrects for non-biological noise and is computationally scalable to the large numbers of sequences available for SARS-CoV-2, overcoming a major challenge of existing methods. Using this method, we quantified the strength of genetic drift for SARS-CoV-2 transmission in England throughout time and across locations. These estimates constrain potential mechanisms and help parameterize models of SARS-CoV-2 evolution. More generally, the computational scalability of our method will become more important as increasingly large genomic datasets become more common.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "QinQin Yu", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Joao A Ascensao", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Takashi Okada", + "author_inst": "University of California Berkeley, Kyoto University, RIKEN" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", + "author_inst": "-" + }, + { + "author_name": "Olivia Boyd", + "author_inst": "Imperial College London" + }, + { + "author_name": "Erik Volz", + "author_inst": "Imperial College London; The COVID-19 Genomics UK Consortium" + }, + { + "author_name": "Oskar Hallatschek", + "author_inst": "University of California Berkeley; Leipzig University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.11.19.22282451", "rel_title": "Catch-up Routine Immunization to Restore Childhood Immunization Coverage following COVID-induced Declines in Zamboanga Peninsula, Philippines", @@ -185456,41 +187581,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.19.22281995", - "rel_title": "Excess mortality associated with the COVID-19 pandemic (2020-2021) in an urban community of Bangladesh: Evidence from cemetery-based death registration", - "rel_date": "2022-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.19.22281995", - "rel_abs": "Measurement of COVID-19-attributed mortality is vital for public health policy decisions. Unlike high-income countries, the magnitude of COVID-19-related mortality is largely unknown in many low- and middle-income countries due to inadequate COVID-19 testing capacity and a lack of robust civil registration and vital statistics systems. COVID-19-associated excess mortality was investigated in an urban setting in Bangladesh using a cemetery-based death registration dataset. A total of 6,271 deaths (3,790 male and 2,481 female) recorded between January 2015 and December 2021 were analyzed by using the Bayesian structural time series model (BSTS). During the pre-COVID-19 period, the average monthly number of deaths was 69, whereas, during the COVID-19 period, this number significantly increased to 92. Overall, according to model-based results, during COVID-19 period, the number of deaths increased on average by 17% (95% CrI: -18%, 57%): males 29% (95 % CrI: -15%, 75%) and 2.9% for females (95% CrI: -61%, 70%). This first-of-its-kind study in Bangladesh has revealed the excess mortality due to the COVID-19 pandemic (2020-2021) in an urban community. It appears that cemetery-based death registration could help track various crises (e.g., COVID-19), especially when collecting data on the ground is challenging for resource-limited countries.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mohammad Sorowar Hossain", - "author_inst": "Biomedical Research Foundation, Bangladesh" - }, - { - "author_name": "Jahidur Rahman Khan", - "author_inst": "Biomedical Research Foundation, Bangladesh" - }, - { - "author_name": "SM Abdullah Al Mamun", - "author_inst": "Biomedical Research Foundation, Bangladesh" - }, - { - "author_name": "Mohammad Tariqul Islam", - "author_inst": "Jamalpur General Hospital, Jamalpur, Bangladesh" - }, - { - "author_name": "Enayetur Raheem", - "author_inst": "Biomedical Research Foundation, Bangladesh" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.18.22282414", "rel_title": "Immunogenicity and safety of a 4th homologous booster dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): a phase 2, randomized, placebo-controlled trial", @@ -186625,6 +188715,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.11.17.22282452", + "rel_title": "Association between long COVID symptoms and employment status", + "rel_date": "2022-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.17.22282452", + "rel_abs": "BackgroundSymptoms of Coronavirus-19 (COVID-19) infection persist beyond 2 months in a subset of individuals, a phenomenon referred to as long COVID, but little is known about its functional correlates and in particular the relevance of neurocognitive symptoms.\n\nMethodWe analyzed a previously-reported cohort derived from 8 waves of a nonprobability-sample internet survey called the COVID States Project, conducted every 4-8 weeks between February 2021 and July 2022. Primary analyses examined associations between long COVID and lack of full employment or unemployment, adjusted for age, sex, race and ethnicity, education, urbanicity, and region, using multiple logistic regression with interlocking survey weights.\n\nResultsThe cohort included 15,307 survey respondents ages 18-69 with test-confirmed COVID-19 at least 2 months prior, of whom 2,236 (14.6%) reported long COVID symptoms, including 1,027/2,236 (45.9%) reporting either brain fog or impaired memory. Overall, 1,418/15,307 (9.3%) reported being unemployed, including 276/2,236 (12.3%) of those with long COVID and 1,142/13,071 (8.7%) of those without; 8,228 (53.8%) worked full-time, including 1,017 (45.5%) of those with long COVID and 7,211 (55.2%) without. In survey-weighted regression models, presence of long COVID was associated with being unemployed (crude OR 1.44, 95% CI 1.20-1.72; adjusted OR 1.23, 95% CI 1.02-1.48), and with lower likelihood of working full-time (crude OR 0.73, 95% CI 0.64-0.82; adjusted OR 0.79, 95% CI 0.70 -0.90). Among individuals with long COVID, the presence of cognitive symptoms - either brain fog or impaired memory - was associated with lower likelihood of working full time (crude OR 0.71, 95% CI 0.57-0.89, adjusted OR 0.77, 95% CI 0.61-0.97).\n\nConclusionLong COVID was associated with a greater likelihood of unemployment and lesser likelihood of working full time in adjusted models. Presence of cognitive symptoms was associated with diminished likelihood of working full time. These results underscore the importance of developing strategies to respond to long COVID, and particularly the associated neurocognitive symptoms.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kristin Lunz Trujillo", + "author_inst": "Harvard Kennedy School of Government" + }, + { + "author_name": "Roy H Perlis", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Alauna Safarpour", + "author_inst": "Harvard Kennedy School of Government" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Northeastern University" + }, + { + "author_name": "Katherine Ognyanova", + "author_inst": "Rutgers University" + }, + { + "author_name": "James Druckman", + "author_inst": "Northwestern University" + }, + { + "author_name": "David Lazer", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.18.517046", "rel_title": "Rising SARS-CoV-2 Seroprevalence and Patterns of Cross-Variant Antibody Neutralization in UK Domestic Cats", @@ -187242,49 +189375,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.09.22282065", - "rel_title": "Observational methods for COVID-19 vaccine effectiveness research: a trial emulation and empirical evaluation", - "rel_date": "2022-11-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.09.22282065", - "rel_abs": "Despite much research on the topic, little work has been done comparing the use of methods to control for confounding in the estimation of COVID-19 vaccine effectiveness in routinely collected medical record data. We conducted a trial emulation study to replicate the ChAdOx1 (Oxford/AstraZeneca) and BNT162b2 (BioNTech/Pfizer) COVID-19 phase 3 efficacy studies. We conducted a cohort study including individuals aged 75+ from UK CPRD AURUM (N = 916,128) in early 2021. Three different methods were assessed: Overlap weighting, inverse probability treatment weighting, and propensity score matching. All three methods successfully replicated the findings from both phase 3 trials, and overlap weighting performed best in terms of confounding, systematic error, and precision. Despite lack of trial data beyond 3 weeks, we found that even 1 dose of BNT162b2 was effective against SARS-CoV-2 infection for up to 12 weeks before a second dose was administered. These results support the UK Joint Committee on Vaccination and Immunisation modelling and related UK vaccination strategies implemented in early 2021.\n\nKey messagesO_LIReal world evidence generated using weighting (overlapping weights and inverse probability of treatment weights) and propensity score matching: all methods successfully replicate the findings of Phase 3 trials for COVID-19 vaccine effectiveness.\nC_LIO_LIOverlap weighting provides the least biased estimates in our study and should be considered amongst the most suitable methods for future COVID-19 vaccine effectiveness research.\nC_LIO_LIDespite a lack of trial data, our findings suggest that first-dose BNT162b2 provides effective protection against SARS-COV-2 infection for up to 12 weeks, in line with UKs Joint Committee on Vaccination and Immunisation modelling and subsequent vaccination strategies.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Marti Catala", - "author_inst": "Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK" - }, - { - "author_name": "Edward Burn", - "author_inst": "Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK" - }, - { - "author_name": "Trishna Rathod-Mistry", - "author_inst": "Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK" - }, - { - "author_name": "Junqing Xie", - "author_inst": "Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK" - }, - { - "author_name": "Antonella Delmestri", - "author_inst": "Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK" - }, - { - "author_name": "Daniel Prieto-Alhambra", - "author_inst": "1.Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK 2.Department of Me" - }, - { - "author_name": "Annika M Jodicke", - "author_inst": "Center for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.16.22282121", "rel_title": "A single-centre, observational study to evaluate immune response to Covid-19 vaccines in immunocompromised patients with haematological disorders (COVAC-IC)", @@ -188399,6 +190489,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.11.14.22282297", + "rel_title": "Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values", + "rel_date": "2022-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.14.22282297", + "rel_abs": "The continuing emergence of SARS-CoV-2 variants of concern (VOCs) presents a serious public health threat, exacerbating the effects of the COVID19 pandemic. Although millions of genomes have been deposited in public archives since the start of the pandemic, predicting SARS-CoV-2 clinical characteristics from the genome sequence remains challenging. In this study, we used a collection of over 29,000 high quality SARS-CoV-2 genomes to build machine learning models for predicting clinical detection cycle threshold (Ct) values, which correspond with viral load. After evaluating several machine learning methods and parameters, our best model was a random forest regressor that used 10-mer oligonucleotides as features and achieved an R2 score of 0.521 {+/-} 0.010 (95% confidence interval over 5 folds) and an RMSE of 5.7 {+/-} 0.034, demonstrating the ability of the models to detect the presence of a signal in the genomic data. In an attempt to predict Ct values for newly emerging variants, we predicted Ct values for Omicron variants using models trained on previous variants. We found that approximately 5% of the data in the model needed to be from the new variant in order to learn its Ct values. Finally, to understand how the model is working, we evaluated the top features and found that the model is using a multitude of k-mers from across the genome to make the predictions. However, when we looked at the top k-mers that occurred most frequently across the set of genomes, we observed a clustering of k-mers that span spike protein regions corresponding with key variations that are hallmarks of the VOCs including G339, K417, L452, N501, and P681, indicating that these sites are informative in the model and may impact the Ct values that are observed in clinical samples.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Lea Duesterwald", + "author_inst": "Horace Greeley High School, Chappaqua, NY, USA" + }, + { + "author_name": "Marcus Nguyen", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Paul Christensen", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Scott Wesley Long", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Randall J. Olsen", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "James M. Musser", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "James J. Davis", + "author_inst": "Argonne National Laboratory" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.14.22282295", "rel_title": "Detection of infectious SARS-CoV-2 in frozen aerosol samples collected from hospital rooms of patients with COVID-19", @@ -189076,97 +191209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.11.11.516125", - "rel_title": "Bispecific antibodies combine breadth, potency, and avidity of parental antibodies to neutralize sarbecoviruses", - "rel_date": "2022-11-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516125", - "rel_abs": "SARS-CoV-2 mutational variants evade humoral immune responses elicited by vaccines and current monoclonal antibody (mAb) therapies. Novel antibody-based treatments will thus need to exhibit broad neutralization against different variants. Bispecific antibodies (bsAbs) combine the specificities of two distinct antibodies into one antibody taking advantage of the avidity, synergy and cooperativity provided by targeting two different epitopes. Here we used controlled Fab-arm exchange (cFAE), a versatile and straightforward method, to produce bsAbs that neutralize SARS-CoV and SARS-CoV-2 variants, including Omicron and its subvariants, by combining potent SARS-CoV-2-specific neutralizing antibodies with broader but less potent antibodies that also neutralize SARS-CoV. We demonstrate that the parental IgGs rely on avidity for their neutralizing activity by comparing their potency to bsAbs containing one irrelevant \"dead\" Fab arm. We used single particle mass photometry to measure formation of antibody:spike complexes, and determined that bsAbs increase binding stoichiometry compared to corresponding cocktails, without a loss of binding affinity. The heterogeneous binding pattern of bsAbs to spike (S), observed by negative-stain electron microscopy and mass photometry provided evidence for both intra- and inter-spike crosslinking. This study highlights the utility of cross-neutralizing antibodies for designing bivalent or multivalent agents to provide a robust activity against circulating variants, as well as future SARS-like coronaviruses.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Laura Radi\u0107", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Kwinten Sliepen", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Victor Yin", - "author_inst": "Utrecht University" - }, - { - "author_name": "Mitch Brinkkemper", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Joan Capella-Pujol", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Angela I. Schriek", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Jonathan L. Torres", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Sandhya Bangaru", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Judith A. Burger", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Meliawati Poniman", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Ilja Bontjer", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Joey H. Bouhuijs", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "David Gideonse", - "author_inst": "National Institute for Public Health and The Environment (RIVM)" - }, - { - "author_name": "Dirk Eggink", - "author_inst": "National Institute for Public Health and The Environment (RIVM)" - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Albert J.R. Heck", - "author_inst": "Utrecht University" - }, - { - "author_name": "Marit J. van Gils", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Rogier W. Sanders", - "author_inst": "Amsterdam UMC location AMC" - }, - { - "author_name": "Janke Schinkel", - "author_inst": "Amsterdam UMC location AMC" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.11.11.516206", "rel_title": "SARS-CoV-2 vaccination of laboratory rhesus monkeys (Macaca mulatta): Monitoring and efficacy", @@ -190325,6 +192367,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.11.11.516114", + "rel_title": "A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein", + "rel_date": "2022-11-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516114", + "rel_abs": "The ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used mRNA display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor binding domain, N-terminal domain and S2 region, distal to the ACE2 receptor-interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target.\n\nSignificance statementThis study reports on the discovery of a macrocyclic peptide that is able to inhibit SARS-CoV-2 infection by exploiting a new vulnerable site in the spike glycoprotein. This region is highly conserved across SARS-CoV-2 variants and the subgenus sarbecovirus. Due to the inaccessability and mutational contraint of this site, it is anticipated to be resistant to the development of resistance through antibody selective pressure. In addition to the discovery of a new molecule for development of potential new peptide or biomolecule therapeutics, the discovery of this broadly active conserved site can also stimulate a new direction of drug development, which together may prevent future outbreaks of related viruses.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Vito Thijssen", + "author_inst": "Utrecht University, Vrije Universiteit Amsterdam" + }, + { + "author_name": "Daniel L. Hurdiss", + "author_inst": "Utrecht University" + }, + { + "author_name": "Oliver J Debski-Antoniak", + "author_inst": "Utrecht University" + }, + { + "author_name": "Matthew A Spence", + "author_inst": "Australian National University" + }, + { + "author_name": "Charlotte Franck", + "author_inst": "University of Sydney" + }, + { + "author_name": "Alexander Norman", + "author_inst": "University of Sydney" + }, + { + "author_name": "Anupriya Aggarwal", + "author_inst": "Kirby Institute" + }, + { + "author_name": "Nadia J Mokiem", + "author_inst": "Utrecht University" + }, + { + "author_name": "David A A van Dongen", + "author_inst": "Utrecht University, Vrije Universiteit Amsterdam" + }, + { + "author_name": "Stein W Vermeir", + "author_inst": "Universiteit Utrecht, Vrije Universiteit Amsterdam" + }, + { + "author_name": "Minglong Liu", + "author_inst": "Utrecht University, Vrije Universiteit Amsterdam" + }, + { + "author_name": "Wentao Li", + "author_inst": "Utrecht University" + }, + { + "author_name": "Marianthi Chatziandreou", + "author_inst": "Utrecht University" + }, + { + "author_name": "Tim Donselaar", + "author_inst": "Utrecht University" + }, + { + "author_name": "Wenjuan Du", + "author_inst": "Utrecht University" + }, + { + "author_name": "Ieva Drulyte", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Berend Jan Bosch", + "author_inst": "Utrecht University" + }, + { + "author_name": "Joost Snijder", + "author_inst": "Utrecht University" + }, + { + "author_name": "Stuart Grant Turville", + "author_inst": "Kirby Institute" + }, + { + "author_name": "Richard J Payne", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Colin J Jackson", + "author_inst": "Australian National University" + }, + { + "author_name": "Frank J.M. van Kuppeveld", + "author_inst": "Utrecht University" + }, + { + "author_name": "Seino A K Jongkees", + "author_inst": "Vrije Universiteit Amsterdam" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.11.10.22282181", "rel_title": "WHAT IS THE RISK OF DEVELOPING A SEVERE FORM OF COVID-19 INFECTION AMONG ADULTS WHO CURRENTLY SMOKE COMPARED TO EX-SMOKERS? A protocol for systematic review and meta-analysis", @@ -190962,37 +193111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.08.22282050", - "rel_title": "Characterizing responsiveness to the COVID-19 pandemic in the United States and Canada using mobility data", - "rel_date": "2022-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.08.22282050", - "rel_abs": "BackgroundMobile phone-derived human mobility data are a proxy for disease transmission risk and have proven useful during the COVID-19 pandemic for forecasting cases and evaluating interventions. We propose a novel metric using mobility data to characterize responsiveness to rising case rates.\n\nMethodsWe examined weekly reported COVID-19 incidence and retail and recreation mobility from Google Community Mobility Reports for 50 U.S. states and nine Canadian provinces from December 2020 to November 2021. For each jurisdiction, we calculated the responsiveness of mobility to COVID-19 incidence when cases were rising. Responsiveness across countries was summarized using subgroup meta-analysis. We also calculated the correlation between the responsiveness metric and the reported COVID-19 death rate during the study period.\n\nFindingsResponsiveness in Canadian provinces ({beta} = -1{middle dot}45; 95% CI: -2{middle dot}45, -0{middle dot}44) was approximately five times greater than in U.S. states ({beta} = -0{middle dot}30; 95% CI: -0{middle dot}38, -0{middle dot}21). Greater responsiveness was moderately correlated with a lower reported COVID-19 death rate during the study period (Spearmans{rho} = 0{middle dot}51), whereas average mobility was only weakly correlated the COVID-19 death rate (Spearmans{rho} = 0{middle dot}20).\n\nInterpretationOur study used a novel mobility-derived metric to reveal a near-universal phenomenon of reductions in mobility subsequent to rising COVID-19 incidence across 59 states and provinces of the U.S. and Canada, while also highlighting the different public health approaches taken by the two countries.\n\nFundingThis study received no funding.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSThere exists a wide body of literature establishing the usefulness of mobile phone-derived human mobility data for forecasting cases and other metrics during the COVID-19 pandemic. We performed a literature search to identify studies examining the opposite relationship, attempting to quantify the responsiveness of human mobility to changes in COVID-19 incidence. We searched PubMed on October 21, 2022 using the keywords \"COVID-19\", \"2019-nCoV\", or \"SARS-CoV-2\" in combination with \"responsiveness\" and one or more of \"mobility\", \"distancing\", \"lockdown\", and \"non-pharmaceutical interventions\". We scanned 46 published studies and found one that used a mobile phone data-derived index to measure the intensity of social distancing in U.S. counties from January 2020 to January 2021. The authors of this study found that an increase in cases in the last 7 days was associated with an increase in the intensity of social distancing, and that this effect was larger during periods of lockdown/shop closures.\n\nAdded value of the studyOur study developed a metric of the responsiveness of mobility to rising case rates for COVID-19 and calculated it for 59 subnational jurisdictions in the United States and Canada. While nearly all jurisdictions displayed some degree of responsiveness, average responsiveness in Canada was nearly five times greater than in the United States. Responsiveness was moderately associated with the reported COVID-19 death rate during the study period, such that jurisdictions with greater responsiveness had lower death rates, and was more strongly associated with death rates than average mobility in a jurisdiction.\n\nImplications of all the available evidenceMobile phone-derived human mobility data has proven useful in the context of infectious disease surveillance during the COVID-19 pandemic, such as for forecasting cases and evaluating non-pharmaceutical interventions. In our study, we derived a metric of responsiveness to show that mobility data may be used to track the efficiency of public health responses as the pandemic evolves. This responsiveness metric was also correlated with reported COVID-19 death rates during the study period. Together, these results demonstrate the usefulness of mobility data for making broad characterizations of public health responses across jurisdictions during the COVID-19 pandemic and reinforce the value of mobility data as an infectious disease surveillance tool for answering present and future threats.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jean-Paul R. Soucy", - "author_inst": "University of Toronto" - }, - { - "author_name": "David N. Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Derek R. MacFadden", - "author_inst": "Ottawa Hospital Research Institute" - }, - { - "author_name": "Kevin A. Brown", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.08.22282086", "rel_title": "Assessing the accuracy of California county level COVID-19 hospitalization forecasts to inform public policy decision making", @@ -191931,6 +194049,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.08.515436", + "rel_title": "Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.", + "rel_date": "2022-11-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.08.515436", + "rel_abs": "We analyzed the dynamics of the earliest T cell response to SARS-COV-2. A wave of TCRs strongly but transiently expand during infection, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Most epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains, but not with circulating human coronaviruses. Many expanding CDR3s were also present at high precursor frequency in pre-pandemic TCR repertoires. A similar set of early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the pre-infection naive repertoire. High frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection.\n\nOne-Sentence SummaryHigh frequency naive precursors underly the rapid T cell response during the crucial early phases of acute viral infection.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Martina Milighetti", + "author_inst": "University College London" + }, + { + "author_name": "Yanchun Peng", + "author_inst": "University of Oxford" + }, + { + "author_name": "Cedric C.S. Tan", + "author_inst": "University College London" + }, + { + "author_name": "Michal Mark", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Gayathri Nageswaran", + "author_inst": "University College London" + }, + { + "author_name": "Suzanne Byrne", + "author_inst": "University College London" + }, + { + "author_name": "Tahel Ronel", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Peacock", + "author_inst": "University College London" + }, + { + "author_name": "Andreas Mayer", + "author_inst": "University College London" + }, + { + "author_name": "Aneesh Chandran", + "author_inst": "University College London" + }, + { + "author_name": "Joshua Rosenheim", + "author_inst": "University College London" + }, + { + "author_name": "Matthew Wheelan", + "author_inst": "University College London" + }, + { + "author_name": "Xuan Yao", + "author_inst": "University of Oxford" + }, + { + "author_name": "Guihai Liu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Suet Ling Felce", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tao Dong", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alexander J Mentzer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julian Charles Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Francois Balloux", + "author_inst": "Imperial College Faculty of Medicine" + }, + { + "author_name": "Erez Greenstein", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Shlomit Reich-Zeliger", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Corinna Pade", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Joseph M Gibbons", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Amanda Semper", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Tim Brooks", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Ashley Otter", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Daniel M Altmann", + "author_inst": "Imperial College London" + }, + { + "author_name": "Rosemary J Boyton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mala K Maini", + "author_inst": "University College London" + }, + { + "author_name": "Aine McKnight", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Charlotte Manisty", + "author_inst": "University College London" + }, + { + "author_name": "Thomas A Treibel", + "author_inst": "University College London" + }, + { + "author_name": "James C Moon", + "author_inst": "University College London" + }, + { + "author_name": "- COVIDsortium Investigators", + "author_inst": "-" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "University College London" + }, + { + "author_name": "Benny Chain", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.11.08.515567", "rel_title": "Enhanced stability of the SARS CoV-2 spike glycoprotein trimer following modification of an alanine cavity in the protein core.", @@ -192464,53 +194741,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2022.11.05.515197", - "rel_title": "Pharmacological modulators of epithelial immunity uncovered by synthetic genetic tracing of SARS-CoV-2 infection responses", - "rel_date": "2022-11-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.05.515197", - "rel_abs": "Epithelial immune responses govern tissue homeostasis and offer drug targets against maladaptation. Here, we report a framework to generate drug discovery-ready reporters of cellular responses to viral infection. We reverse engineered epithelial cell responses to SARS-CoV-2, the viral agent fueling the ongoing COVID-19 pandemic and designed synthetic transcriptional reporters whose molecular logic comprises interferon-/{beta}/{gamma}-, and NF-{kappa}B pathways. Such regulatory potential reflected single-cell data from experimental models to severe COVID-19 patient epithelial cells infected by SARS-CoV-2. SARS-CoV-2, type-I interferons, and RIG-I drive reporter activation. Live-cell-image-based phenotypic drug screens identified JAK inhibitors and DNA damage inducers as antagonistic modulators of epithelial cell response to interferons, RIG-I stimulation, and SARS-CoV-2. Synergistic or antagonistic modulation of the reporter by drugs underscored their similar mechanism of action. Thus, this study describes a tool for dissecting antiviral responses to infection and sterile cues, and a rapid approach to other emerging viruses of public health concern in order to discover rational drug combinations.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ben Jiang", - "author_inst": "Max-Delbruck-Center for Molecular Medicine (MDC)" - }, - { - "author_name": "Matthias Jurgen Schmitt", - "author_inst": "Max-Delbruck-Center for Molecular Medicine (MDC)" - }, - { - "author_name": "Ulfert Rand", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Carlos Company", - "author_inst": "Max-Delbruck-Center for Molecular Medicine (MDC)" - }, - { - "author_name": "Melanie Grossmann", - "author_inst": "Max-Delbruck-Center for Molecular Medicine (MDC)" - }, - { - "author_name": "Michela Serresi", - "author_inst": "Max-Delbruck-Center for Molecular Medicine (MDC)" - }, - { - "author_name": "Luka Cicin-Sain", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Gaetano Gargiulo", - "author_inst": "Max-Delbruck-Center for Molecular Medicine (MDC)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.11.05.515305", "rel_title": "Novel inhibitors against COVID-19 main protease suppressed viral infection", @@ -193477,6 +195707,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.04.22281910", + "rel_title": "Surveillance of COVID-19 vaccine safety among elderly persons aged 65 years and older", + "rel_date": "2022-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281910", + "rel_abs": "BackgroundMonitoring safety outcomes following COVID-19 vaccination is critical for understanding vaccine safety especially when used in key populations such as elderly persons age 65 years and older who can benefit greatly from vaccination. We present new findings from a nationally representative early warning system that may expand the safety knowledge base to further public trust and inform decision making on vaccine safety by government agencies, healthcare providers, interested stakeholders, and the public.\n\nMethodsWe evaluated 14 outcomes of interest following COVID-19 vaccination using the US Centers for Medicare & Medicaid Services (CMS) data covering 30,712,101 elderly persons. The CMS data from December 11, 2020 through Jan 15, 2022 included 17,411,342 COVID-19 vaccinees who received a total of 34,639,937 doses. We conducted weekly sequential testing and generated rate ratios (RR) of observed outcome rates compared to historical (or expected) rates prior to COVID-19 vaccination.\n\nFindingsFour outcomes met the threshold for a statistical signal following Pfizer-BioNTech vaccination including pulmonary embolism (PE; RR=1.54), acute myocardial infarction (AMI; RR=1.42), disseminated intravascular coagulation (DIC; RR=1.91), and immune thrombocytopenia (ITP; RR=1.44). After further evaluation, only the RR for PE still met the statistical threshold for a signal; however, the RRs for AMI, DIC, and ITP no longer did. No statistical signals were identified following vaccination with either the Moderna or Janssen vaccines.\n\nInterpretationThis early warning system is the first to identify temporal associations for PE, AMI, DIC, and ITP following Pfizer-BioNTech vaccination in the elderly. Because an early warning system does not prove that the vaccines cause these outcomes, more robust epidemiologic studies with adjustment for confounding factors, including age and nursing home residency, are underway to further evaluate these signals. FDA strongly believes the potential benefits of COVID-19 vaccination outweigh the potential risks of COVID-19 infection.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Hui-Lee Wong", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Ellen Tworkoski", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Cindy Zhou", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Mao Hu", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Deborah Thompson", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Bradley Lufkin", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Rose Do", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Laurie Feinberg", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Rositsa Dimova", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Patricia Lloyd", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Thomas MaCurdy", + "author_inst": "Acumen, LLC" + }, + { + "author_name": "Richard Forshee", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Jeffrey Kelman", + "author_inst": "Centers for Medicare & Medicaid Services" + }, + { + "author_name": "Azadeh Shoaibi", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Steven Anderson", + "author_inst": "U.S. Food and Drug Administration" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.30.22281737", "rel_title": "Spatial Optimization to Improve COVID-19 Vaccine Allocation", @@ -194098,33 +196403,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.11.02.514944", - "rel_title": "The Longitudinal Analysis of Convergent Antibody VDJ Regions in SARS-CoV-2 Positive Patients Using RNA-seq", - "rel_date": "2022-11-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.02.514944", - "rel_abs": "The severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has infected over 600 million individuals and caused over 6.5 million deaths. To understand the immune response individuals have from the SARS-CoV-2 infection, we studied the immunoglobulins against the viruss antigens. The diversified complementarity determining region 3 (CDR3) can be used to characterize an antibody. We downloaded four public RNA-seq data sets that were collected be-tween March 2020 and March 2022 from the Gene Expression Omnibus (GEO) in our longitudinal analysis. In total, there were 269 SARS-CoV-2 positive patients and 26 negative patients who served as a control group. Samples were grouped based on their SARS-CoV-2 variant type and/or the time they were collected. Among 629,137 immunoglobulin V(D)J sequences identified by reconstructing the V(D)J sequences, we found 1011 common V(D)Js (same V gene, J gene and CDR3 sequences in each SARS-CoV-2 positive group) shared by more than one patient in each group and no common V(D)Js were from the negative control group. In our clustering analysis, we identified 129 convergent clusters from the SARS-CoV-2 positive groups. One of these convergent clusters matched the protein sequence of crystal 3D structures of the antibodies against SARS-CoV-2 in the Protein Data Bank (PDB). In our longitudinal analysis between the Alpha and Omicron variant, we found 2.7% of common CDR3s were shared although the longitudinal profiling of common V(D)Js was variant specific. Although diverse immunoglobulin profiles were observed, the convergence of common V(D)Js suggests that there exists antibodies with similar antigenic specificities across patients in different groups over various stages of the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kate J Liu", - "author_inst": "University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Monika A Zelazowska", - "author_inst": "University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kevin M McBride", - "author_inst": "University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.11.01.22281794", "rel_title": "COVID-19 and non-Hodgkins lymphoma: a common susceptibility pattern?", @@ -195358,33 +197636,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.27.22281612", - "rel_title": "The Impact of COVID-19 on Life Expectancy among Asian American Subgroups", - "rel_date": "2022-10-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.27.22281612", - "rel_abs": "Despite recognition of the diversity of the Asian American population, the mortality impact of the COVID-19 pandemic has been limited to estimates for non-Hispanic Asian Americans in aggregate. This study provides estimates of life expectancy at birth before (2019) and during the pandemic, along with a broad set of demographic, health-related, and socioeconomic risk factors for COVID-19, for the six largest Asian American subgroups: Asian Indians, Chinese, Filipino, Japanese, Korean, and Vietnamese. Our study places these estimates in the context of the broader U.S. population by including the corresponding estimates for non-Hispanic Whites, non-Hispanic Blacks, Hispanics, and non-Hispanic Native Americans. We use data on age-specific all-cause mortality from CDC WONDER and population estimates from the 2015-2019 American Community Survey to construct life tables for each Asian subgroup by year. While losses in life expectancy during the second year of the pandemic diminished significantly among all racial/ethnic and Asian subgroups, these improvements do not compensate for the large increases in death rates in 2020. All major Asian subgroups except Japanese experienced greater losses of life in 2019-2020 as well as cumulatively (2019-2021) than Whites, with Vietnamese, Filipinos, and other South/Southeast Asians having suffered the largest declines in life expectancy among non-Hispanic Asians. Vietnamese and other Southeast Asians experienced the greatest cumulative losses across all racial/ethnic groups except Native Americans. Our findings underscore the heterogeneity of loss in life expectancy within the Asian American population while identifying some of the risk factors that likely underlie this large variation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sung S Park", - "author_inst": "Princeton University" - }, - { - "author_name": "Noreen Goldman", - "author_inst": "Princeton University" - }, - { - "author_name": "Theresa Andrasfay", - "author_inst": "University of Southern California" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.28.22281636", "rel_title": "Long-term humoral response following simultaneous Delta and Omicron BA.1 co-infection", @@ -196464,6 +198715,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.27.22281632", + "rel_title": "Application of a Multiplicative Cascade Model to Detect the Early Signs of SARS-CoV-2 Infection Using Heart Rate Data", + "rel_date": "2022-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.27.22281632", + "rel_abs": "BackgroundWrist-worn devices can keep track of a persons daily health status, including those likely to become infected with the SARS-CoV-2 virus. Technological solutions using mobile devices are being developed to predict the time course of COVID-19.\n\nObjectiveIn this proof-of-concept study, we use heart rate data to detect the first sign of infection in people who have been diagnosed with COVID-19 and to monitor the time-course of the illness.\n\nMethodsThe heart-rate data were analysed using a multiplicative cascade driven by a Gaussian process. This provides two parameters, mean and standard deviation, which when combined with similar parameters estimated from control series, provide a Health Index.\n\nResultsFor 90% of 31 cases, the Health Index tracked COVID-19 infection with the virus and subsequent recovery. The first-sign of COVID-19 was detected on average nine days before symptoms were reported.\n\nConclusionsEarly detection of COVID-19 may lead to a reduction in the spread of the virus. The Heath Indexs potential use for the early detection of complications arising from Long COVID would be an important innovation.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Rachel Ann Heath", + "author_inst": "School of Psychological Sciences, University of Newcastle, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.27.514012", "rel_title": "Vitamin D deficiency and SARS-CoV-2 infection: Big-data analysis from March 2020 to March 2021. D-COVID study", @@ -197540,41 +199810,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.10.25.22281504", - "rel_title": "On the frontlines in Shanghai: Stress, burnout and perceived benefit among COVID-19 testers and other personnel during the Omicron wave lockdown", - "rel_date": "2022-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.25.22281504", - "rel_abs": "BackgroundCOVID-19 control measure stringency including testing has been among the highest globally in China. Psychosocial impact on pandemic workers in Shanghai, and their pandemic-related attitudes were investigated.\n\nMethodsParticipants in this cross-sectional study were healthcare providers (HCP) and other support workers. A Mandarin self-report survey was administered via Wenjuanxing between April-June 2022 during the omicron-wave lockdown. The Perceived Stress Scale (PSS) and Maslach Burnout Inventory were administered, as well as pandemic-specific questions.\n\nResults887 workers participated, of which 691 (77.9%) were HCPs. They were working a mean of 6.25{+/-}1.24 days/week for 9.77{+/-}4.28 hours/day. Most participants were burnt-out, with 143(16.1%) moderately and 98(11.0%) seriously. Total PSS was 26.85{+/-}9.92/56, with 353(39.8%) participants having elevated stress. Workers perceived their families primarily as fully supportive (n=610, 68.8%), or also extremely concerned (n=203, 22.9%). Most wanted counselling and stress relief, but half(n=430) reported no time for it; indeed, 2/3rds wanted a few days off to rest (n=601).Many workers perceived benefits: that they fostered more cohesive relationships (n=581, 65.5%), they will be more resilient (n=693, 78.1%), and were honored to serve (n=747, 84.2%).Negative impacts were greater in HCPs, those with economic insecurity, and that did not perceive benefit (all p<.05).In adjusted analyses, those perceiving benefits showed significantly less burnout (OR=0.573, 95% CI=0.411 - 0.799), among other correlates.\n\nConclusionsPandemic work, including among non-HCP, is stressful, but some can derive benefits.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zhimin Xu", - "author_inst": "Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Xia Liu", - "author_inst": "Chengdu Wanda UPMC Hospital, Chengdu, China" - }, - { - "author_name": "Gabriela L M Ghisi", - "author_inst": "University Health Network" - }, - { - "author_name": "Lixian Cui", - "author_inst": "Division of Arts and Sciences, NYU Shanghai, Shanghai, China" - }, - { - "author_name": "Sherry L Grace", - "author_inst": "Faculty of Health, York University, Toronto M3J 1P3, Canada; and KITE-Toronto Rehabilitation Institute & Peter Munk Cardiac Centre, University Health Network, U" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.27.514054", "rel_title": "Intranasal virus-particle mimicking vaccine enhances SARS-CoV-2 clearance in the Syrian hamster model", @@ -198850,6 +201085,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.10.25.22281247", + "rel_title": "Occupational risk of SARS-CoV-2 infection: a nationwide register-based study of the Danish workforce during the Covid-19 pandemic 2020-21", + "rel_date": "2022-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.25.22281247", + "rel_abs": "ObjectivesMost earlier studies on occupational risk of Covid-19 covering the entire workforce are based on relatively rare outcomes such as hospital admission and mortality. This study examines the incidence of SARS-CoV-2 infection by occupational group based upon real-time polymerase chain reaction tests (RT-PCR).\n\nMethodsThe cohort includes 2.4 million Danish employees, 20-69 years of age. All data were retrieved from public registries. The sex-specific incidence rate ratios (IRR) of first-occurring positive RT-PCR test from week 8 of 2020 through week 50 of 2021 were computed by Poisson regression for each 4-digit DISCO-08 job code with more than 100 employees (337 in men; 297 in women). Occupational groups with low risk of workplace infection according to a job exposure matrix constituted the reference group. Risk estimates were adjusted by demographic, social and health characteristics including household size, completed Covid-19 vaccination, pandemic wave and occupation-specific frequency of testing.\n\nResultsIRRs of SARS-CoV-2 infection were elevated in 34 occupations comprising 12 % of male employees and 45 occupations comprising 41 % of female employees. All IRR estimates were below 2.0. Decreased IRRs were observed in 85 occupations in men but none in women.\n\nDiscussionWe observed a modestly increased risk of SARS-CoV-2 infection among employees in numerous occupations indicating a large potential for preventive actions, especially in the female workforce. Cautious interpretation of observed risk in specific occupations is needed because of methodological issues inherent in analyses of RT-PCR-test results and because of multiple statistical tests.\n\nWHAT IS ALREADY KNOW ABOUT THIS TOPIC?O_LIEpidemiological studies suggest that the workplace contribute to the Covid-19 pandemic\nC_LIO_LIResults are mostly based upon studies of less frequent outcomes as Covid-19 morbidity or mortality which limits inference about risk in specific occupations\nC_LI\n\nWHAT THIS STUDY ADDSO_LIThe risk of Covid-19 infection was increased in 34 of 337 occupations in men and in 45 of 297 occupations in women\nC_LIO_LISome 12% of the Danish male workforce and 41% of the female workforce are at increased risk of Covid-19 infection\nC_LI\n\nHOW THIS RESEARCH MIGHT AFFECT RESEARCH, PRACTICE OR POLICY?O_LIPreventive actions targeting the workplace may contribute substantially to alleviate disease occurrence in the ongoing Covid-19 and similar future pandemics.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jens Peter Ellekilde Bonde", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Luise Moelenberg Begtrup", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Johan Hoej Jensen", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Esben Meulengracht Flachs", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Vivi Schlunssen", + "author_inst": "Department of Public Health, Research Unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark" + }, + { + "author_name": "Henrik Albert Kolstad", + "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, Denmark" + }, + { + "author_name": "Kristina Jakobsson", + "author_inst": "School of Public Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden" + }, + { + "author_name": "Christel Nielsen", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Kerstin Nielsson", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Lars Rylander", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Andreas Vilhelmsson", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Kajsa Kirstine Ugelvig Petersen", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Sandra Soegaard Toettenborg", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.10.24.22281104", "rel_title": "Which curve are we flattening? The disproportionate impact of COVID-19 among economically marginalized communities in Ontario, Canada, was unchanged from wild-type to omicron", @@ -199942,173 +202244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.21.512606", - "rel_title": "Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques", - "rel_date": "2022-10-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.21.512606", - "rel_abs": "Type-I interferons (IFN-I) are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, and for the first time, IFN-I signaling was modulated in rhesus macaques (RMs) prior to and during acute SARS-CoV-2 infection using a mutated IFN2 (IFN-modulator; IFNmod), which has previously been shown to reduce the binding and signaling of endogenous IFN-I. In SARS-CoV-2-infected RMs, IFNmod reduced both antiviral and inflammatory ISGs. Notably, IFNmod treatment resulted in a potent reduction in (i) SARS-CoV-2 viral load in Bronchoalveolar lavage (BAL), upper airways, lung, and hilar lymph nodes; (ii) inflammatory cytokines, chemokines, and CD163+MRC1-inflammatory macrophages in BAL; and (iii) expression of Siglec-1, which enhances SARS-CoV-2 infection and predicts disease severity, on circulating monocytes. In the lung, IFNmod also reduced pathogenesis and attenuated pathways of inflammasome activation and stress response during acute SARS-CoV-2 infection. This study, using an intervention targeting both IFN- and IFN-{beta} pathways, shows that excessive inflammation driven by type 1 IFN critically contributes to SARS-CoV-2 pathogenesis in RMs, and demonstrates the potential of IFNmod to limit viral replication, SARS-CoV-2 induced inflammation, and COVID-19 severity.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Timothy N. Hoang", - "author_inst": "Emory University" - }, - { - "author_name": "Elise G. Viox", - "author_inst": "Emory University" - }, - { - "author_name": "Amit A. Upadhyay", - "author_inst": "Emory University" - }, - { - "author_name": "Zachary Strongin", - "author_inst": "Emory University" - }, - { - "author_name": "Gregory K. Tharp", - "author_inst": "Emory University" - }, - { - "author_name": "Maria Pino", - "author_inst": "Emory University" - }, - { - "author_name": "Rayhane Nchioua", - "author_inst": "Ulm University" - }, - { - "author_name": "Maximilian Hirschenberger", - "author_inst": "Ulm University" - }, - { - "author_name": "Matthew Gagne", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Kevin Nguyen", - "author_inst": "Emory University" - }, - { - "author_name": "Justin L. Harper", - "author_inst": "Emory University" - }, - { - "author_name": "Shir Marciano", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Arun K. Boddapati", - "author_inst": "Emory University" - }, - { - "author_name": "Kathryn L. Pellegrini", - "author_inst": "Emory University" - }, - { - "author_name": "Jennifer Tisoncik-Go", - "author_inst": "University of Washington" - }, - { - "author_name": "Leanne S. Whitmore", - "author_inst": "University of Washington" - }, - { - "author_name": "Kirti A. Karunakaran", - "author_inst": "Emory University" - }, - { - "author_name": "Melissa Roy", - "author_inst": "Emory University" - }, - { - "author_name": "Shannon Kirejczyk", - "author_inst": "Emory University" - }, - { - "author_name": "Elizabeth H. Curran", - "author_inst": "Emory University" - }, - { - "author_name": "Chelsea Wallace", - "author_inst": "Emory University" - }, - { - "author_name": "Jennifer S. Wood", - "author_inst": "Emory University" - }, - { - "author_name": "Fawn Connor-Stroud", - "author_inst": "Emory University" - }, - { - "author_name": "Sudhir P. Kasturi", - "author_inst": "Emory University" - }, - { - "author_name": "Rebecca D. Levit", - "author_inst": "Emory University" - }, - { - "author_name": "Michael Gale Jr.", - "author_inst": "University of Washington" - }, - { - "author_name": "Thomas H. Vanderford", - "author_inst": "Emory University" - }, - { - "author_name": "Guido Silvestri", - "author_inst": "Emory University" - }, - { - "author_name": "Kathleen Busman-Sahay", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Jacob D. Estes", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Monica Vaccari", - "author_inst": "Tulane University" - }, - { - "author_name": "Daniel C. Douek", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Konstantin M.J. Sparrer", - "author_inst": "Ulm University" - }, - { - "author_name": "Frank Kirchhoff", - "author_inst": "Ulm University" - }, - { - "author_name": "R. Paul Johnson", - "author_inst": "Emory University" - }, - { - "author_name": "Gideon Schreiber", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Steven E. Bosinger", - "author_inst": "Emory University" - }, - { - "author_name": "Mirko Paiardini", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.10.22.513349", "rel_title": "Antibody responses to Omicron BA.4/BA.5 bivalent mRNA vaccine booster shot", @@ -201128,6 +203263,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.21.22281171", + "rel_title": "Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID-19 cases treated with Sotrovimab in the community in England", + "rel_date": "2022-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.21.22281171", + "rel_abs": "ObjectivesSotrovimab is one of several therapeutic agents that have been licensed to treat people at risk of severe outcomes following COVID-19 infection. However, there are concerns that it has reduced efficacy to treat people with the BA.2 sub-lineage of the Omicron (B.1.1.529) SARS-CoV-2 variant. We compared individuals with the BA.1 or BA.2 sub-lineage of the Omicron variant treated Sotrovimab in the community to assess their risk of hospital admission.\n\nMethodsWe performed a retrospective cohort study of individuals treated with Sotrovimab in the community and either had BA.1 or BA.2 variant classification.\n\nResultsUsing a Stratified Cox regression model it was estimated that the hazard ratios (HR) of hospital admission with a length of stay of two or more days was 1.17 for BA.2 compared to BA.1 (95% CI 0.74-1.86) and for such admissions where COVID-19 ICD-10 codes was recorded the HR was 0.98 (95% CI 0.58-1.65).\n\nConclusionThese results suggest that the risk of hospital admission is similar between BA.1 and BA.2 cases treated with Sotrovimab in the community.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Katie Harman", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Sophie G Nash", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Harriet H Webster", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Natalie Groves", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jo Hardstaff", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jessica Bridgen", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Paula B Blomquist", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Russell Hope", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Efejiro Ashano", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Richard Myers", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Sakib Rokadiya", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Colin S Brown", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Meera Chand", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Gavin Dabrera", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Simon Thelwall", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.19.22281256", "rel_title": "Changes in Treatment and Severity of Multisystem Inflammatory Syndrome in Children: An EHR-based cohort study from the RECOVER program", @@ -201772,33 +203986,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2022.10.19.22281255", - "rel_title": "Encoding generation time changes within reproduction numbers", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.19.22281255", - "rel_abs": "We introduce the angular reproduction number {Omega}, which measures time-varying changes in epidemic transmissibility resulting from variations in both the effective reproduction number R, and generation time distribution w. Predominant approaches for tracking pathogen spread either infer R or the epidemic growth rate r. However, R is biased by mismatches between the assumed and true w, while r is difficult to interpret in terms of the individual-level branching process underpinning transmission. R and r may also disagree on the relative transmissibility of epidemics or variants (i.e., rA>rB does not imply RA>RB for variants A and B). We find that {Omega} responds meaningfully to mismatches and time-variations in w while mostly maintaining the interpretability of R. We prove that {Omega}>1 implies R>1 and that {Omega} agrees with r on the relative transmissibility of pathogens. Estimating {Omega} is no more difficult than inferring R, uses existing software, and requires no generation time measurements. These advantages come at the expense of selecting one free parameter. We propose {Omega} as complementary statistic to R and r that improves transmissibility estimates when w is misspecified or time-varying and better reflects the impact of interventions, when those interventions concurrently change R and w or alter the relative risk of co-circulating pathogens.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kris V Parag", - "author_inst": "Imperial College London" - }, - { - "author_name": "Benjamin Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ben C Lambert", - "author_inst": "University of Exeter" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.20.22281300", "rel_title": "Uptake of COVID-19 vaccines among healthcare workers within primary healthcare facilities, Entebbe municipality Uganda", @@ -203170,6 +205357,117 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.20.512999", + "rel_title": "Altered infective competence of the human gut microbiome in COVID-19", + "rel_date": "2022-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.20.512999", + "rel_abs": "ObjectivesInfections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19.\n\nDesignWe used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.\n\nResultsWe found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19 positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19 positive individuals compared to healthy controls.\n\nConclusionOur analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Laura de Nies", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Valentina Galata", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Camille Martin-Gallausiaux", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Milena Despotovic", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Susheel Bhanu Busi", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Chantal J. Snoeck", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Lea Delacour", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Deepthi Poornima Budagavi", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Cedric Christian Laczny", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Janine Habier", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Paula-Cristina Lupu", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Rashi Halder", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Joelle V. Fritz", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Taina Marques", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Estelle Sandt", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Soumyabrata Ghosh", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Venkata Satagopam", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "- CON-VINCE Consortium", + "author_inst": "-" + }, + { + "author_name": "Rejko Kruger", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Guy Fagherazzi", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Markus Ollert", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Feng Q. Hefeng", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Patrick May", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Paul Wilmes", + "author_inst": "University of Luxembourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.19.512957", "rel_title": "SARS-CoV-2 infected cells sprout actin-rich filopodia that facilitate viral invasion", @@ -203962,49 +206260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.10.18.22281050", - "rel_title": "Interim Analysis of a Phase I Randomized Clinical Trial on the Safety and Immunogenicity of the mRNA-1283 SARS-CoV-2 Vaccine in Adults", - "rel_date": "2022-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281050", - "rel_abs": "BackgroundThis interim analysis of an ongoing phase I randomized clinical trial evaluated the safety, reactogenicity, and immunogenicity of mRNA-1283, a next-generation SARS-CoV-2 messenger RNA (mRNA)-based vaccine encoding 2 segments of the spike protein (ie, receptor binding and N-terminal domains).\n\nMethodsHealthy aged adults 18-55 years (n = 104) were randomized (1:1:1:1:1) to receive 2 doses of mRNA-1283 (10, 30, or 100 g) or mRNA-1273 (100 g) administered 28 days apart, or a single dose of mRNA-1283 (100 g). Safety was assessed and immunogenicity was measured by serum neutralizing antibody (nAb) or binding antibody (bAb) responses.\n\nResultsAt the interim analysis, no safety concerns were identified and no serious adverse events, adverse events of special interest, or deaths were reported. Solicited systemic adverse reactions were more frequent with higher dose levels of mRNA-1283 than with mRNA-1273. At day 57, all dose levels of the 2-dose mRNA-1283 regimen (including the lowest dose level [10 g]) induced robust nAb and bAb responses that were comparable to those of mRNA-1273 (100 g).\n\nConclusionsmRNA-1283 was generally safe in adults, with all dose levels of the 2-dose regimen (10, 30, and 100 g) eliciting similar immunogenicity as the 2-dose mRNA-1273 regimen (100 g).\n\nClinical Trials RegistrationClinicaltrials.gov, NCT04813796", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Patrick Yassini", - "author_inst": "University of California, San Diego, California; Optimal Research, San Diego, California" - }, - { - "author_name": "Mark Hutchens", - "author_inst": "Optimal Research, Austin, Texas" - }, - { - "author_name": "Yamuna D. Paila", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Lorraine Schoch", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Anne Aunins", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Uma Siangphoe", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Robert Paris", - "author_inst": "Moderna, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.19.512816", "rel_title": "A collaborative approach to improving representation in viral genomic surveillance", @@ -205216,6 +207471,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.17.22281168", + "rel_title": "A systematic review on outbreaks of COVID-19 among children within households in the European region", + "rel_date": "2022-10-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.17.22281168", + "rel_abs": "ObjectivesThis systematic review aims to identify the secondary attack rates (SAR) to adults and other children when children are the index cases within household settings.\n\nMethodsThis literature review assessed European-based studies published in Medline and Embase between January 2020 and January 2022 that assessed the secondary transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within household settings. The inclusion criteria were based on the PEO framework (P-Population, E-Exposure, O-Outcome) for systematic reviews. Thus, the study population was restricted to humans within the household setting in Europe (population), in contact with pediatric index cases 1-17 years old (exposure) that led to the transmission of SARS-CoV-2 reported as either a SAR or the probability of onward infection (outcome).\n\nResultsOf 1,819 studies originally identified, 25 met the inclusion criteria. Overall, the SAR ranged from 13% to 75% in 23 studies, while there was no evidence of secondary transmission from children to other household members in two studies. Evidence indicated that asymptomatic SARS-CoV-2 index cases also have a lower SAR than those with symptoms and that younger children may have a lower SAR than adolescents (>12 years old) within household settings.\n\nConclusionsSARS-CoV-2 secondary transmission from paediatric index cases ranged from 0% to 75%, within household settings between January 2020 and January 2022, with differences noted by age and by symptomatic/asymptomatic status of the index case. Given the anticipated endemic circulation of SARS-CoV-2, continued monitoring and assessment of household transmission is necessary.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Constantine Vardavas", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Aslanoglou", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Apostolos Kamekis", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Nithya Ramesh", + "author_inst": "Department of Oral Health Policy and Epidemiology, Harvard School of Dental Medicine, Harvard University, Boston, MA, USA" + }, + { + "author_name": "Emmanouil Symvoulakis", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Israel Agaku", + "author_inst": "Department of Oral Health Policy and Epidemiology, Harvard School of Dental Medicine, Harvard University, Boston, MA, USA" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Jo Leonardi-Bee", + "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Esteve Fernandez", + "author_inst": "Catalan Institute of Oncology, Barcelona, Spain" + }, + { + "author_name": "Orla Condell", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + }, + { + "author_name": "Favelle Lamb", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + }, + { + "author_name": "Charlotte Deogan", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + }, + { + "author_name": "Jonathan E Suk", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.17.22281175", "rel_title": "Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data", @@ -205944,29 +208270,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.15.512351", - "rel_title": "Investigating the role of binding free energy, binding affinity and antibody escape in the evolution of SARS-CoV-2 spike protein.", - "rel_date": "2022-10-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.15.512351", - "rel_abs": "SARS-CoV-2 is considered a pandemic virus and presents a major strain on public health globally. SARS-CoV-2 infects mammalian cells by binding to its receptor, ACE2 which is mediated by the viral spike glycoprotein, specifically the receptor binding domain (RBD) within the spike protein. Recent development of vaccines against SARS-CoV-2 spike protein are currently the best strategy to reduce morbidity and mortality from infection. Like all viruses, SARS-CoV-2 evolves which may result in mutations which are benign or alter its viral fitness. The evolution of SARS-CoV-2 may increase the virulence, possibly by increasing the infectivity of the virus through strengthening the binding of the RBD to ACE2 or enabling the virus to evade naturally or vaccine induced immune responses. To address the need to characterise the evolution of SARS-CoV-2, this study has compared SARS-CoV2 sequences globally to the Wuhan reference strain at different time points. Additionally, by assigning scores to sequence data, which quantify each sequences binding strength to ACE2 and ability to evade patient derived antibodies, we have demonstrated that over time SARS-CoV-2 has evolved in less than one year to increase its ability to evade antibodies and increase the binding free energy between the RBD and ACE2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Matthew Young", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Samantha J Lycett", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.10.15.512346", "rel_title": "Comparative Mutagenesis of SARS-CoV-2 Nonstructural Proteins (NSPs) Across Variants: The Case for RdRp as a Therapeutic Target", @@ -207098,6 +209401,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.11.22280868", + "rel_title": "High titers of infectious SARS-CoV-2 in COVID-19 corpses", + "rel_date": "2022-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.11.22280868", + "rel_abs": "BackgroundThe prolonged presence of infectious severe acute respiratory syndrome coronavirus (SARS-CoV-2) in deceased coronavirus disease 2019 (COVID-19) patients has been reported. However, infectious virus titers have not been determined. Such information is important for public health, death investigation, and handling corpses.\n\nAimThe aim of this study was to assess the level of SARS-CoV-2 infectivity in COVID-19 corpses.\n\nMethodsWe collected 11 nasopharyngeal swabs and 19 lung tissue specimens from 11 autopsy cases with COVID-19 in 2021. We then investigated the viral genomic copy number by real-time reverse transcription-polymerase chain reaction and infectious titers by cell culture and virus isolation.\n\nResultsInfectious virus was present in 6 of 11 (55%) cases, 4 of 11 (36%) nasopharyngeal swabs, and 9 of 19 (47%) lung specimens. The virus titers ranged from 6.00E + 01 plaque-forming units (PFU)/mL to 2.09E + 06 PFU/g. In all cases in which an infectious virus was found, the time from death to discovery was within 1 day and the longest postmortem interval was 13 days.\n\nConclusionCOVID-19 corpses may have high titers of infectious virus after a long postmortem interval (up to 13 days). Therefore, appropriate infection control measures must be taken when handling corpses.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Hisako Saitoh", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Yuko Tagawa Sakai", + "author_inst": "Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Sayaka Nagasawa", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Suguru Torimitsu", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Kazumi Kubota", + "author_inst": "Department of Healthcare Information Management, The University of Tokyo Hospital" + }, + { + "author_name": "Yuichiro Hirata", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Kiyoko Horimoto Iwatsuki", + "author_inst": "Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Ayumi Motomura", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Namiko Ishii", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Keisuke Okaba", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Kie Horioka", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Hiroyuki Abe", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Masako Ikemura", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Hirofumi Rokutan", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Munetoshi Hinata", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Yoichi Yasunaga", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Makoto Nakajima", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Rutsuko Yamaguchi", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Shigeki Tsuneya", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Kei Kira", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Susumu Kobayashi", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Go Inokuchi", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Fumiko Chiba", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Yumi Hoshioka", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Aika Mori", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Isao Yamamoto", + "author_inst": "Department of Forensic Medicine, Kanagawa Dental University" + }, + { + "author_name": "Kimiko Nakagawa", + "author_inst": "Department of Forensic Medicine, Kanagawa Dental University" + }, + { + "author_name": "Harutaka Katano", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Shun Iida", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Tadaki Suzuki", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Shinji Akitomi", + "author_inst": "Japan Medical Association Research Institute" + }, + { + "author_name": "Iwao Hasegawa", + "author_inst": "Department of Forensic Medicine, Kanagawa Dental University" + }, + { + "author_name": "Tetsuo Ushiku", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Daisuke Yajima", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Hirotaro Iwase", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Yohsuke Makino", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Yoshihiro Kawaoka", + "author_inst": "University of Wisconsin-Madison" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.10.22280850", "rel_title": "Anti-SARS-CoV-2 antibody containing plasma improves outcome in patients with hematologic or solid cancer and severe COVID-19 via increased neutralizing antibody activity. A randomized clinical trial", @@ -207834,57 +210304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2022.10.13.22281055", - "rel_title": "Increased levels of inflammatory molecules in blood of Long COVID patients point to thrombotic endotheliitis", - "rel_date": "2022-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.13.22281055", - "rel_abs": "The prevailing hypotheses for the persistent symptoms of Long COVID have been narrowed down to immune dysregulation and autoantibodies, widespread organ damage, viral persistence, and fibrinaloid microclots (entrapping numerous inflammatory molecules) together with platelet hyperactivation. Here we demonstrate significantly increased concentrations of Von Willebrand Factor, platelet factor 4,serum amyloid A, -2antiplasmin E-selectin, and platelet endothelial cell adhesion molecule-1, in the soluble part of the blood. It was noteworthy that the mean level of -2-antiplasmin exceeded the upper limit of the laboratory reference range in Long COVID patients, and the other 5 were significantly elevated in Long COVID patients as compared to the controls. This is alarming if we take into consideration that a significant amount of the total burden of these inflammatory molecules has previously been shown to be entrapped inside fibrinolysis-resistant microclots (thus decreasing the apparent level of the soluble molecules). We also determined that by individually adding E-selectin and PECAM-1 to healthy blood, these molecules may indeed be involved in protein-protein interactions with plasma proteins (contributing to microclot formation) and platelet hyperactivation. This investigation was performed as a laboratory model investigation and the final exposure concentration of these molecules was chosen to mimic concentrations found in Long COVID. We conclude that presence of microclotting, together with relatively high levels of six inflammatory molecules known to be key drivers of endothelial and clotting pathology, points to thrombotic endotheliitis as a key pathological process in Long COVID. This has implications for the choice of appropriate therapeutic options in Long COVID.\n\nSENTENCE SUMMARYThe presence of fibrinaloid microclots and multiple inflammatory molecules in the soluble part of blood points to thrombotic endotheliitis as a key pathological process in Long COVID.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Simone Turner", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Caitlin Naidoo", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Thomas Usher", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Arneaux Kruger", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Chantelle Venter", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Gert J Laubscher", - "author_inst": "Mediclinic Stellenbosch" - }, - { - "author_name": "M Asad Khan", - "author_inst": "Directorate of Respiratory Medicine, Manchester University Hospitals" - }, - { - "author_name": "Douglas B Kell", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Etheresia Pretorius", - "author_inst": "Stellenbosch University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.11.22280860", "rel_title": "Risk of Myocarditis and Pericarditis Following Coronavirus Disease 2019 Messenger RNA Vaccination - A Nationwide Study", @@ -209044,6 +211463,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.10.22280915", + "rel_title": "Infection-induced immunity is associated with protection against SARS-CoV-2 infection, but not decreased infectivity during household transmission", + "rel_date": "2022-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280915", + "rel_abs": "BackgroundUnderstanding the impact of infection-induced immunity on SARS-CoV-2 transmission will provide insight into the transition of SARS-CoV-2 to endemicity. Here we estimate the effects of prior infection induced immunity and children on SARS-CoV-2 transmission in households.\n\nMethodsWe conducted a household cohort study between March 2020-June 2022 in Managua, Nicaragua where when one household member tests positive for SARS-CoV-2, household members are closely monitored for SARS-CoV-2 infection. Using a pairwise survival model, we estimate the association of infection period, age, symptoms, and infection-induced immunity with secondary attack risk.\n\nResultsOverall transmission occurred in 72.4% of households, 42% of household contacts were infected and the secondary attack risk was 13.0% (95% CI: 11.7, 14.6). Prior immunity did not impact the probability of transmitting SARS-CoV-2. However, participants with pre-existing infection-induced immunity were half as likely to be infected compared to naive individuals (RR 0.53, 95% CI: 0.39, 0.72), but this reduction was not observed in children. Likewise, symptomatic infected individuals were more likely to transmit (RR 24.4, 95% CI: 7.8, 76.1); however, symptom presentation was not associated with infectivity of young children. Young children were less likely to transmit SARS-CoV-2 than adults. During the omicron era, infection-induced immunity remained protective against infection.\n\nConclusionsInfection-induced immunity is associated with protection against infection for adults and adolescents. While young children are less infectious, prior infection and asymptomatic presentation did not reduce their infectivity as was seen in adults. As SARS-CoV-2 transitions to endemicity, children may become more important in transmission dynamics.\n\nArticle summaryInfection-induced immunity protects against SARS-CoV-2 infection for adolescents and adults; however, there was no protection in children. Prior immunity in an infected individual did not impact the probability they will spread SARS-CoV-2 in a household setting.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Aaron M Frutos", + "author_inst": "University of Michigan" + }, + { + "author_name": "Guillermina Kuan", + "author_inst": "Health Center Socrates Flores Vivas, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Roger Lopez", + "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua," + }, + { + "author_name": "Sergio Ojeda", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Abigail Shotwell", + "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" + }, + { + "author_name": "Nery Sanchez", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Saira Saborio", + "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua," + }, + { + "author_name": "Miguel Plazaola", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Carlos Barilla", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Eben Kenah", + "author_inst": "Biostatistics Division, College of Public Health, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Angel Balmaseda", + "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua," + }, + { + "author_name": "Aubree Gordon", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.11.22280942", "rel_title": "Impact of the COVID-19 pandemic on exercise habits and overweight in Japan: a nation-wide panel survey", @@ -209824,81 +212306,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2022.10.07.22280822", - "rel_title": "Impact of the COVID-19 Vaccination Program on Case Incidence, Emergency Department Visits, and Hospital Admissions among Children Aged 5-17 Years during the Delta and Omicron Periods --United States, December 2020 to April 2022", - "rel_date": "2022-10-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.07.22280822", - "rel_abs": "BackgroundIn the United States, national ecological studies suggest a positive impact of COVID-19 vaccination coverage on outcomes in adults. However, the national impact of the vaccination program on COVID-19 in children remains unknown. To determine the association of COVID-19 vaccination with U.S. case incidence, emergency department visits, and hospital admissions for pediatric populations during the Delta and Omicron periods.\n\nMethodsWe conducted an ecological analysis among children aged 5-17 and compared incidence rate ratios (RRs) of COVID-19 cases, emergency department visits, and hospital admissions by pediatric vaccine coverage, with jurisdictions in the highest vaccine coverage quartile as the reference.\n\nResultsRRs comparing states with lowest pediatric vaccination coverage to the highest pediatric vaccination coverage were 2.00 and 0.64 for cases, 2.96 and 1.11 for emergency department visits, and 2.76 and 1.01 for hospital admissions among all children during the Delta and Omicron periods, respectively. During the 3-week peak period of the Omicron wave, only children aged 12-15 and 16-17 years in the states with the lowest versus highest coverage, had a significantly higher rate of emergency department visits (RR=1.39 and RR=1.34, respectively).\n\nConclusionsCOVID-19 vaccines were associated with lower case incidence, emergency department visits and hospital admissions among children during the Delta period but the association was weaker during the Omicron period. Pediatric COVID-19 vaccination should be promoted as part of a program to decrease COVID-19 impact among children; however, vaccine effectiveness may be limited when available vaccines do not match circulating viral variants.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Katherine Topf", - "author_inst": "Booz Allen Hamilton" - }, - { - "author_name": "Michael Sheppard", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Grace Marx", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ryan Wiegand", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ruth Link-Gelles", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Alison Binder", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Andrea Cool", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "B. Casey Lyons", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sohyun Park", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Hannah Fast", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Arthur Presnetsov", - "author_inst": "Booz Allen Hamilton" - }, - { - "author_name": "G Roseric Azondekon", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Karl Soetebier", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jennifer Adjemian", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Kamil Elie Barbour", - "author_inst": "CDC" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.10.22280762", "rel_title": "Immune response after SARS-CoV-2 infection with residual post COVID symptoms", @@ -210898,6 +213305,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.10.06.22280798", + "rel_title": "Impact of vaccination on post-acute sequelae of SARS CoV-2 infection in patients with rheumatic diseases", + "rel_date": "2022-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.06.22280798", + "rel_abs": "ObjectiveVaccination decreases the risk of severe COVID-19 but its impact on post-acute sequelae of COVID-19 (PASC) is unclear among patients with systemic autoimmune rheumatic diseases (SARDs) who may have blunted vaccine immunogenicity and be vulnerable to PASC.\n\nMethodsWe prospectively enrolled SARD patients from a large healthcare system who survived acute infection to complete surveys. The symptom-free duration and the odds of PASC (any symptom lasting [≥] 28 or 90 days) were evaluated using restricted mean survival time and multivariable logistic regression, respectively, among those with and without breakthrough infection ([≥] 14 days after initial vaccine series).\n\nResultsAmong 280 patients, the mean age was 53 years, 80% were female, and 82% were white. The most common SARDs were inflammatory arthritis (59%) and connective tissue disease (24%). Those with breakthrough infection had more upper respiratory symptoms, and those with non-breakthrough infection had more anosmia, dysgeusia, and joint pain. Compared to those with non-breakthrough COVID-19 infection (n=164), those with breakthrough infection (n=116) had significantly more symptom-free days over the follow-up period (+28.9 days, 95% CI: 8.83, 48.89; p=0.005) and lower odds of PASC at 28 and 90 days (aOR 0.49, 95% CI: 0.29, 0.83 and aOR 0.10, 95% CI: 0.04, 0.22, respectively).\n\nConclusionVaccinated patients with SARDs were less likely to experience PASC compared to those not fully vaccinated. These findings support the benefits of vaccination for patients with SARDs and suggest that the immune response to acute infection is important in the pathogenesis of PASC in SARD patients.\n\nKey MessagesO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIPost-acute sequelae of COVID-19 (PASC) affects 20-50% of COVID-19 survivors, though the impact of vaccination on the risk and severity of PASC is unclear, especially among those with systemic autoimmune rheumatic diseases (SARDs) who may have impaired responses to vaccines and be particularly vulnerable to PASC.\nC_LI\n\nWhat this study adds?O_LIIn this prospective cohort of SARD patients recovering from COVID-19, we found that those with breakthrough vs non-breakthrough infection had more symptom-free days over the follow-up period (adjusted difference +28.9 days, 95% CI: 8.38, 48.89; p=0.005) and a lower odds of PASC at 28 days (aOR 0.49, 95% CI: 0.29, 0.83) and at 90 days (aOR 0.10, 95% CI: 0.04, 0.22).\nC_LIO_LIPatient-reported pain and fatigue scores were lower, reflecting less severe pain and fatigue, in those with breakthrough infection compared to those with non-breakthrough infection.\nC_LI\n\nHow this study might affect research, practice, or policy?O_LIThis study extends our understanding of the benefits of vaccination against COVID-19 in patients living with SARDs and reinforces the importance of vaccinating this vulnerable population.\nC_LIO_LIOur findings suggest that the initial immune response to acute SARS-CoV-2, as influenced by vaccination, affects PASC risk but this requires further study.\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Naomi J Patel", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Claire Cook", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Kathleen MM Vanni", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Xiaoqing Fu", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Xiaosong Wang", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Yumeko Kawano", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Grace Qian", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Buuthien Hang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Shruthi Srivatsan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Emily Banasiak", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Emily Kowalski", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Katarina Bade", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Yuqing Zhang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey A. Sparks", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Zachary S Wallace", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2022.10.06.22280795", "rel_title": "Long COVID Risk and Pre-COVID Vaccination: An EHR-Based Cohort Study from the RECOVER Program", @@ -211658,125 +214140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.10.04.22280704", - "rel_title": "Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose", - "rel_date": "2022-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.04.22280704", - "rel_abs": "The emergence of the SARS-CoV-2 Omicron sublineages resulted in drastically increased transmission rates and reduced protection from vaccine-induced immunity. To counteract these effects, multiple booster strategies were used in different countries, although data comparing their efficiency in improving protective immunity remains sparse, especially among vulnerable populations, including older adults. The inactivated CoronaVac vaccine was among the most widely distributed worldwide, particularly in China, and South America. However, whether homologous versus heterologous booster doses in those fully vaccinated with CoronaVac induce distinct humoral responses and whether these responses vary across age groups remain unknown. We analyzed plasma antibody responses from CoronaVac-vaccinated younger or older individuals in central and south America that received a homologous CoronaVac or heterologous BNT162b2 or ChAdOx1 booster vaccines. We found that both IgG levels against SARS-CoV-2 spike or RBD, as well as neutralization titers against Omicron sublineages, were substantially reduced in participants that received homologous CoronaVac when compared to heterologous BNT162b2 or ChAdOx1 booster. This effect was specifically prominent in recipients older than 50 years of age. In this group, CoronaVac booster induced low virus-specific IgG levels and failed to elevate their neutralization titers against any omicron sublineage. Our results point to significant inefficiency in mounting protective anti-viral humoral immunity in those who were primed with CoronaVac followed by CoronaVac booster, particularly among older adults, urging a heterologous regimen in high-risk populations fully vaccinated with CoronaVac.\n\nOne Sentence SummaryHomologous CoronaVac boosters do not improve neutralization responses against current VOCs in older adults in contrast to heterologous regimens.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Bruno Andraus Filardi", - "author_inst": "Instituto do Cancer Brasil" - }, - { - "author_name": "Valter Silva Monteiro", - "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA" - }, - { - "author_name": "Pedro Vellosa Schwartzmann", - "author_inst": "Intensive Cardiac Unit, Unimed Hospital, Ribeirao Preto, SP" - }, - { - "author_name": "Vivian do Prado Martins", - "author_inst": "Instituto do Cancer Brasil - Unidade de Ribeirao Preto, SP, Brazil" - }, - { - "author_name": "Luis Eduardo Rosa Zucca", - "author_inst": "Instituto do Cancer Brasil - Unidade de Ribeirao Preto, SP, Brazil" - }, - { - "author_name": "Gabriela Crispim Baiocchi", - "author_inst": "UNIVERSITY OF SAO PAULO" - }, - { - "author_name": "Anne M. Hahn", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA" - }, - { - "author_name": "Nicholas Chen", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA" - }, - { - "author_name": "Kien Pham", - "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA" - }, - { - "author_name": "Eddy Perez-Then", - "author_inst": "Two Oceans in Health, Santo Domingo, Dominican Republic" - }, - { - "author_name": "Marija Miric", - "author_inst": "Two Oceans In Health" - }, - { - "author_name": "Vivian Brache", - "author_inst": "Profamilia, Biomedical Research Department, Santo Domingo, Dominican Republic" - }, - { - "author_name": "Leila Cochon", - "author_inst": "Profamilia, Biomedical Research Department, Santo Domingo, Dominican Republic" - }, - { - "author_name": "Rafael Larocca", - "author_inst": "Center of Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston MA." - }, - { - "author_name": "- Yale SARS-CoV-2 Genomic Surveillance Initiative,", - "author_inst": "" - }, - { - "author_name": "Roberto Della Rosa Mendez", - "author_inst": "Federal University of Mato Grosso do Sul, Tres Lagoas, MS, Brazil" - }, - { - "author_name": "Douglas Bardini Silveira", - "author_inst": "Laboratorio de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianopolis, SC, Brazil" - }, - { - "author_name": "Aguinaldo Roberto Pinto", - "author_inst": "Laboratorio de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianopolis, SC, Brazil" - }, - { - "author_name": "Julio Croda", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Inci Yildirim", - "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." - }, - { - "author_name": "Saad B. Omer", - "author_inst": "Yale Institute for Global Health, Yale University, New Haven, CT, USA." - }, - { - "author_name": "Albert Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Sten Vermund", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Nathan D Grubaugh", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Carolina Lucas", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.04.22280696", "rel_title": "Vaccines alone cannot slow the evolution of SARS-CoV-2", @@ -212740,6 +215103,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.05.22280716", + "rel_title": "Kinetics of naturally induced binding and neutralizing anti-SARS-CoV-2 antibody levels and potencies among Kenyan patients with diverse grades of COVID-19 severity", + "rel_date": "2022-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.05.22280716", + "rel_abs": "BackgroundGiven the low levels of COVID-19 vaccine coverage in Sub-Saharan Africa, despite high levels of natural SARS-CoV-2 exposures, strategies for extending the breadth and longevity of naturally acquired immunity are warranted. Designing such strategies will require a good understanding of natural immunity.\n\nMethodsWe used ELISA to measure whole-spike IgG and spike-receptor binding domain (RBD) total immunoglobulins (Igs) on 585 plasma samples collected longitudinally over five successive time points within six months of COVID-19 diagnosis in 309 COVID-19 patients. We measured antibody neutralizing potency against the wild-type (Wuhan) SARS-CoV-2 pseudo-virus in a subset of 51 patients over three successive time points. Binding and neutralizing antibody levels and potencies were then tested for correlations with COVID-19 severities, graded according to the National Institute of Health (NIH), USA criteria.\n\nResultsRates of sero-conversion increased from Day 0 (day of PCR testing) to Day 180 (six months) (63.6% to 100 %) and (69.3 % to 97%) for anti-spike IgG and anti-spike-RBD binding Igs, respectively. Levels of these binding antibodies peaked at Day 28 (P<0.0001) and were subsequently maintained for six months without significant decay (p>0.99). Similarly, antibody neutralizing potencies peaked at Day 28 (p<0.0001) but had decreased by three-folds, six months after COVID-19 diagnosis (p<0.0001). Binding antibodies levels were highly correlated with neutralizing antibody potencies at all the time points analyzed (r>0.6, P<0.0001). Levels and potencies of binding and neutralizing antibodies increased with disease severity.\n\nConclusionMost COVID-19 patients from Sub-Saharan Africa generate SARS-CoV-2 specific binding antibodies that remain stable during the first six months of infection. Although antibody binding levels and neutralizing potencies were directly correlated, the respective neutralizing antibodies decayed three-fold by the sixth month of COVID-19 diagnosis suggesting that they are short-lived, consistent with what has been observed elsewhere. Thus, just like for other populations, regular vaccination boosters will be required to broaden and sustain the high levels of predominantly naturally acquired anti-SARS-CoV-2 neutralizing antibodies.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "John Kimotho", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Yiakon Sein", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Shahin M Sayed", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Reena Shah", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Kennedy Mwai", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Mansoor Saleh", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Perpetual Wanjiku", + "author_inst": "KEMRI Wellcome" + }, + { + "author_name": "Jedida Mwacharo", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "James Nyangwange", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Henry Karanja", + "author_inst": "KEMRI Wellcome" + }, + { + "author_name": "Bernadette Kutima", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "John Gitonga", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Daisy Mugo", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Ann Karanu", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Linda Moranga", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Viviane Oluoch", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Jasmit Shah", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Julius Mutiso", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Afred G Mburu", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Zaitun Nneka", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Peter Betti", + "author_inst": "Agha Khan University-Kenya" + }, + { + "author_name": "Wanzila U Mutinda", + "author_inst": "Pwani University-Kenya" + }, + { + "author_name": "Abdirahman I Abdi", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Philip Bejon", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Isabella L Ochola", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "George M Warimwe", + "author_inst": "KEMRI-Wellcome Trust Research Programme - Kenya" + }, + { + "author_name": "Eunice Nduati", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Francis M Ndungu", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.04.22280459", "rel_title": "Association between COVID-19 mRNA vaccination and COVID-19 illness and severity during Omicron BA.4 and BA.5 sublineage periods", @@ -213688,77 +216178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.04.22280642", - "rel_title": "A scoping review of regulatory T cell dynamics in convalescent COVID-19 patients - Implications for Long COVID?", - "rel_date": "2022-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.04.22280642", - "rel_abs": "BackgroundRecovery from coronavirus disease 2019 (COVID-19) can be impaired by the persistence of symptoms or new-onset health complications, commonly referred to as Long COVID. In a subset of patients, Long COVID is associated with immune system perturbations of unknown etiology, which could be related to compromised immunoregulatory mechanisms.\n\nObjectiveThe aim of this scoping review was to investigate if regulatory T cell (Treg) dysregulation is observable beyond the acute illness and if it might be involved in Long COVID immunopathology.\n\nDesignA systematic search of studies investigating Tregs during COVID-19 convalescence was conducted on MEDLINE (via Pubmed) and Web of Science.\n\nResultsThe literature search yielded 17 relevant studies, of which three included a distinct cohort of patients with Long COVID. The reviewed studies suggest that the Treg population of COVID-19 patients can reconstitute quantitatively and functionally during recovery. However, the comparison between recovered and seronegative controls revealed that an infection-induced dysregulation of the Treg compartment can be sustained for at least several months. The small number of studies investigating Tregs in Long COVID allowed no firm conclusions to be drawn about their involvement in the syndromes etiology. Yet, even almost one year post-infection Long COVID patients exhibit significantly altered proportions of Tregs within the CD4+ T cell population.\n\nConclusionsPersistent alterations in cell frequency in Long COVID patients indicate that Treg dysregulation might be linked to immune system-associated sequelae. Future studies should aim to address the association of Treg adaptations with different symptom clusters and blood parameters beyond the sole quantification of cell frequencies while adhering to consensualized phenotyping strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Simon Haunhorst", - "author_inst": "Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany" - }, - { - "author_name": "Wilhelm Bloch", - "author_inst": "Department for Molecular and Cellular Sports Medicine, Institute for Cardiovascular Research and Sports Medicine, German Sport University Cologne, Cologne, Germ" - }, - { - "author_name": "Florian Javelle", - "author_inst": "Department for Molecular and Cellular Sports Medicine, Institute for Cardiovascular Research and Sports Medicine, German Sport University Cologne, Cologne, Germ" - }, - { - "author_name": "Karsten Krueger", - "author_inst": "Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Giessen, Giessen, Germany" - }, - { - "author_name": "Sabine Baumgart", - "author_inst": "Institute for Immunology, Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Sebastian Drube", - "author_inst": "Institute for Immunology, Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Christina Lemhoefer", - "author_inst": "Institute of Physiotherapy, Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Philipp Reuken", - "author_inst": "Clinic for Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Andreas Stallmach", - "author_inst": "Clinic for Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Michael Mueller", - "author_inst": "Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Immunology, Hans Knoell Institute, Jena, Germany" - }, - { - "author_name": "Christina E. Zielinski", - "author_inst": "Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Immunology, Hans Knoell Institute, Jena, Germany" - }, - { - "author_name": "Mathias W. Pletz", - "author_inst": "Institute for Immunology, Jena University Hospital, Jena, Germany; Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germ" - }, - { - "author_name": "Holger H.W. Gabriel", - "author_inst": "Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany" - }, - { - "author_name": "Christian Puta", - "author_inst": "Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.04.22280689", "rel_title": "Population-level relative effectiveness of the COVID-19 vaccines and the contribution of naturally acquired immunity", @@ -214990,6 +217409,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.30.22280586", + "rel_title": "COVID treatment and in-hospital length of stay inequalities between race in the US over time", + "rel_date": "2022-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.30.22280586", + "rel_abs": "IntroductionDemonstrated health inequalities persist in the United States. SARS-CoV-2 (COVID) has been no exception, with access to treatment and hospitalization differing across race or ethnic group. Here we aim to assess differences in treatment with remdesivir and hospital length of stay across four waves of the pandemic.\n\nMethodsUsing a subset of the Truveta data we examine odds ratios (OR) of in-hospital remdesivir treatment and risk ratios (RR) of in-hospital length of stay between Black or African American (Black) to white patients. We adjusted for confounding factors such as age, sex, and comorbidity status.\n\nResultsThere were statically significant lower rates of remdesivir treatment and longer in-hospital lengths of stay comparing Black patients to white patients early in the pandemic (OR for treatment: 0.88, 95% confidence interval [CI]: 0.80, 0.96; RR for length of stay: 1.17, CI: 1.06, 1.21). Rates became close to parity between groups as the pandemic progressed.\n\nConclusionsWhile inpatient remdesivir treatment rates increased and length of stay decreased over the beginning course of the pandemic, there are still inequalities in patient care.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Benjamin Muir Althouse", + "author_inst": "Truveta" + }, + { + "author_name": "Charlotte Baker", + "author_inst": "Truveta" + }, + { + "author_name": "Peter D Smits", + "author_inst": "Truveta" + }, + { + "author_name": "Samuel Gratzl", + "author_inst": "Truveta" + }, + { + "author_name": "Ryan H Lee", + "author_inst": "Truveta" + }, + { + "author_name": "Brianna M Goodwin Cartwright", + "author_inst": "Truveta" + }, + { + "author_name": "Michael Siminov", + "author_inst": "Truveta" + }, + { + "author_name": "Michael D Wang", + "author_inst": "Truveta" + }, + { + "author_name": "Nicholas Stucky", + "author_inst": "Truveta" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.29.22280522", "rel_title": "A simple non-invasive C reactive protein-based score can predict outcome in patients with COVID-19", @@ -215690,89 +218160,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2022.09.28.22280449", - "rel_title": "Populational analysis of the immunoglobulin G response to different COVID-19 vaccines in Brazil", - "rel_date": "2022-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.28.22280449", - "rel_abs": "Vaccination is a strategy that confers protection against symptomatic infections and/or development of severe COVID-19. In Brazil, COVID-19 vaccination began in January 2021 and has been performed using vaccines from different manufactures including CoronaVac (Sinovac), ChAdOx1 (Oxford/AstraZeneca) and BNT162b2 (Pfizer/BioNTech). One of the main protective mechanisms triggered by vaccination involves the production of IgG antibodies reactive to the Spike antigen of SARS-CoV-2, the levels of which correlates with vaccine efficacy. Although phase III clinical studies confirmed the efficacy of the vaccines used in Brazil, there are just few studies comparing vaccine immunogenicity in a real-world scenario. This study aimed to depict the IgG response to natural infections and to vaccination using different types of vaccines at population scale in Matinhos, a city located in south of Brazil. Nucleocapsid seroconversion rates indicated that more than a quarter of the cohort has been subjected to natural infections by SARS-CoV-2 by the first trimester of 2022. Spike seroconversion rates achieved >95% by February 2022 and maintained stable as far as June 2022 confirming the effectiveness of the vaccination program. Immunogenicity concerning IgG reactive to Spike was higher using the BNT162b2 vaccine, followed by ChAdOx1 and CoronaVac. Natural infections boosted IgG levels reactive to Spike in those individuals that completed primary vaccination with ChAdOx1 and CoronaVac but not with BNT162b2. The levels of IgG reactive to Spike increased with the number of vaccine doses administered. The application of BNT162b2 as booster dose resulted in high levels of IgG reactive to Spike which were similar despite the type of the vaccine used during primary vaccination.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nigella M Paula Sr.", - "author_inst": "UFPR" - }, - { - "author_name": "Marcelo dos Santos Conzentino", - "author_inst": "UFPR" - }, - { - "author_name": "Ana C Goncalves Sr.", - "author_inst": "UFPR" - }, - { - "author_name": "Renata Silva", - "author_inst": "UFPR" - }, - { - "author_name": "Karin V Weissheimer", - "author_inst": "UFPR" - }, - { - "author_name": "Carlos H Kluge", - "author_inst": "ufpr" - }, - { - "author_name": "Paulo H Marins", - "author_inst": "UFPR" - }, - { - "author_name": "Haxely S Camargo", - "author_inst": "UFPR" - }, - { - "author_name": "Lucas R Farias", - "author_inst": "ufpr" - }, - { - "author_name": "Thamyres P Santana", - "author_inst": "UFPR" - }, - { - "author_name": "Leticia R Vargas", - "author_inst": "UFPR" - }, - { - "author_name": "Juliane D Aldrighi", - "author_inst": "UFPR" - }, - { - "author_name": "Enio S Lima", - "author_inst": "UFPR" - }, - { - "author_name": "Guiomar T Jacotenski", - "author_inst": "ufpr" - }, - { - "author_name": "Alan G Goncalves", - "author_inst": "ufpr" - }, - { - "author_name": "Emerson Joucoski", - "author_inst": "ufpr" - }, - { - "author_name": "Luciano Huergo Sr.", - "author_inst": "Universidade Federal do Parana" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.28.22280465", "rel_title": "Differences in COVID-19 cyclicity and predictability among U.S. counties and states reflect the effectiveness of protective measures", @@ -216804,6 +219191,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.26.22280387", + "rel_title": "Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study", + "rel_date": "2022-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280387", + "rel_abs": "BackgroundGuidelines for SARS-CoV-2 have relied on limited data on duration of viral infectiousness and correlation with COVID-19 symptoms and diagnostic testing.\n\nMethodsWe enrolled ambulatory adults with acute SARS-CoV-2 infection and performed serial measurements of COVID-19 symptoms, nasal swab viral RNA, nucleocapsid (N) and spike (S) antigens, and replication-competent SARS-CoV-2 by culture. We determined average time from symptom onset to a first negative test result and estimated risk of infectiousness, as defined by a positive viral culture.\n\nResultsAmong 95 adults, median [interquartile range] time from symptom onset to first negative test result was 9 [5] days, 13 [6] days, 11 [4] days, and >19 days for S antigen, N antigen, viral culture growth, and viral RNA by RT-PCR, respectively. Beyond two weeks, viral cultures and N antigen titers were rarely positive, while viral RNA remained detectable among half (26/51) of participants tested 21-30 days after symptom onset. Between 6-10 days from symptom onset, N antigen was strongly associated with viral culture positivity (relative risk=7.61, 95% CI: 3.01-19.2), whereas neither viral RNA nor symptoms were associated with culture positivity. During the 14 days following symptom onset, presence of N antigen (adjusted relative risk=7.66, 95% CI: 3.96-14.82), remained strongly associated with viral culture positivity, regardless of COVID-19 symptoms.\n\nConclusionsMost adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset, and N antigen testing is a strong predictor of viral infectiousness. Within two weeks from symptom onset, N antigen testing, rather than absence of symptoms or viral RNA, should be used to safely discontinue isolation.\n\nFundingBill and Melinda Gates Foundation", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Paul K Drain", + "author_inst": "University of Washington" + }, + { + "author_name": "Ronit R Dalmat", + "author_inst": "University of Washington" + }, + { + "author_name": "LINHUI HAO", + "author_inst": "University of Washington" + }, + { + "author_name": "Meagan J Bemer", + "author_inst": "University of Washington" + }, + { + "author_name": "Elvira Budiawan", + "author_inst": "University of Washington" + }, + { + "author_name": "Jennifer F Morton", + "author_inst": "University of Washington" + }, + { + "author_name": "Renee C Ireton", + "author_inst": "University of Washington" + }, + { + "author_name": "Tien-Ying Hsiang", + "author_inst": "University of Washington" + }, + { + "author_name": "Zarna Marfatia", + "author_inst": "University of Washington" + }, + { + "author_name": "Roshni Prabhu", + "author_inst": "University of Washington" + }, + { + "author_name": "Claire Woosley", + "author_inst": "University of Washington" + }, + { + "author_name": "Adenech Gichamo", + "author_inst": "University of Washington" + }, + { + "author_name": "Elena Rechkina", + "author_inst": "University of Washington" + }, + { + "author_name": "Daphne Hamilton", + "author_inst": "University of Washington" + }, + { + "author_name": "Michalina Montano", + "author_inst": "University of Washington" + }, + { + "author_name": "Jason L Cantera", + "author_inst": "Global Health Labs" + }, + { + "author_name": "Alexey Ball", + "author_inst": "Global Health Labs" + }, + { + "author_name": "Inah Golez", + "author_inst": "University of Washington" + }, + { + "author_name": "Elise Smith", + "author_inst": "University of Washington" + }, + { + "author_name": "Alex Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "M Juliana McElrath", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Matthew Thompson", + "author_inst": "University of Washington" + }, + { + "author_name": "Benjamin D Grant", + "author_inst": "Global Health Labs" + }, + { + "author_name": "Allison Meisner", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Geoffrey S Gottlieb", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael J Gale Jr.", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.26.22280362", "rel_title": "Household transmission of SARS-CoV-2 during the Omicron wave in Shanghai, China: a case-ascertained study", @@ -217528,45 +220034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.26.22280377", - "rel_title": "Impact of Differential Vaccine Effectiveness on COVID-19 Hospitalization Cases: Projections for 10 Developed Countries where Booster Vaccines were Recommended", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280377", - "rel_abs": "Background & ObjectivesIn a previous analysis, a decision-analytic model was used to analyze the clinical and economic impact of the differences in effectiveness between the two licensed mRNA COVID-19 booster vaccines, mRNA-1273 and BNT162b2, in 2022 for adults aged 18 years and older in the United States (US). In this analysis, the same model was used to estimate the impact that administering first booster doses with mRNA-1273 could have had on COVID-related hospitalizations and costs over a 6-month period in 10 developed countries (Australia, Canada, France, Germany, Italy, Japan, South Korea, Spain, United Kingdom [UK], and US), considering updated effectiveness data.\n\nMethodsThe model was used to estimate number of hospitalizations and related costs using the actual vaccine distribution for the first COVID-19 booster from each country. These estimates were compared to a scenario where 100% of doses for that 6-month period was assumed to be mRNA-1273. The effectiveness of mRNA-1273 compared to BNT162b2 was estimated from real world data from the UK.\n\nResultsThe total number of doses switched to the mRNA-1273 booster would range from 4.3 million in Spain to 39.4 million in Japan. The number of hospitalizations and associated hospitalization costs would be expected to fall in all countries, with the proportional decrease ranging from 1.1% (16,800 fewer) in Germany to 8.8% (25,100 fewer) in Australia.\n\nConclusionsReal-world effectiveness data suggest that a booster dose of the mRNA-1273 vaccine may be more effective compared to other vaccines used for booster doses. Given this difference in effectiveness, results of this analysis demonstrate that switching to 100% mRNA-1273 boosters would have reduced the number of hospitalizations and associated costs in each country during the first 6 months of the omicron period.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Michael Maschio", - "author_inst": "Quadrant Health Economics, Inc." - }, - { - "author_name": "Kelly Fust", - "author_inst": "Quadrant Health Economics, Inc." - }, - { - "author_name": "Amy Lee", - "author_inst": "Quadrant Health Economics, Inc." - }, - { - "author_name": "Nicolas Van de Velde", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Philip O. Buck", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Michele Kohli", - "author_inst": "Quadrant Health Economics Inc." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2022.09.27.22280403", "rel_title": "Comparative adverse effects, perceptions and attitudes related to BNT162b2, mRNA1273, or JNJ-78436735 SARS-CoV-2 vaccines: A population-based longitudinal cohort", @@ -218690,6 +221157,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.26.509459", + "rel_title": "Nanobodies for the treatment of SARS-CoV-2 in animals: a meta-analysis", + "rel_date": "2022-09-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.26.509459", + "rel_abs": "This meta-analysis aimed to find the effect of variable domain of heavy-chain antibodies (VHHs) for the treatment of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in animals. The databases of the PubMed, China National Knowledge Infrastructure (CNKI), Wan fang data, Cochrane Library, and Embase were searched for articles published before August 2022 on the protective effects of VHHs in animals. The articles retrieved were screened using inclusion and exclusion criteria. The data were analyzed using Review Manager 5.4. Six articles were selected from 667 articles based on the inclusion and exclusion criteria in VHHs. A forest plot showed that VHHs could offer protection against SARS-CoV-2 infection in animals [Mantel-Haenszel (MH) = 172.94, 95% confidence interval (CI) = (43.96, 678.42), P < 0.00001]. There was almost no heterogeneity in this study (I2 = 0). A funnel plot showed that the bias of the data analysis was small. This is a special meta-analysis proved that VHHs could treat and prevent SARS-CoV-2 in animals.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "jiao jiao", + "author_inst": "shihezi university" + }, + { + "author_name": "shu lan lin", + "author_inst": "shihezi university" + }, + { + "author_name": "zhen qi liang", + "author_inst": "shihezi university" + }, + { + "author_name": "Peng Wu", + "author_inst": "Shehezi University" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.25.509344", "rel_title": "Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against Omicron", @@ -220190,25 +222688,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.09.25.22280326", - "rel_title": "Healthcare system overstretch and in-hospital mortality of intubated COVID-19 patients in Greece: an updated analysis, September 2020 to April 2022", - "rel_date": "2022-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.25.22280326", - "rel_abs": "BackgroundOur previous analysis showed how in-hospital mortality of intubated COVID-19 patients in Greece is adversely affected by patient load and regional disparities. We aimed to update this analysis to include the large \"delta\" and \"omicron\" waves that affected Greece during 2021-2022, while also considering the effect of vaccination.\n\nMethodsAnonymized surveillance data were analyzed from all COVID-19 patients in Greece intubated between 1 September 2020 and 4 April 2022, and followed up until 17 May 2022. Poisson regression was used to estimate the hazard of dying as a function of fixed and time-varying covariates.\n\nResultsMortality was significantly higher above 400 patients, with an adjusted Hazard Ratio of 1.22, 95% CI: 1.09-1.38), rising progressively up to 1.48 (95% CI: 1.31-1.69) for 800+ patients. Hospitalization away from Attica region was also independently associated with increased mortality, as was hospitalization after 1 September 2021 (HR=1.21, 95% CI: 1.09-1.36). Vaccination did not affect the mortality of these already severely ill patients.\n\nConclusionOur results confirm that in-hospital mortality of severely ill COVID-19 patients is adversely affected by high patient load and regional disparities, and point to a further significant deterioration after 1 September especially away from Attica and Thessaloniki. This highlights the need for urgent strengthening of healthcare services in Greece, ensuring equitable and high-quality care for all.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Theodore Lytras", - "author_inst": "School of Medicine, European University Cyprus, Nicosia, Cyprus" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.09.23.22280281", "rel_title": "The impact of COVID-19 vaccination in the US: averted burden of SARS-COV-2-related cases, hospitalizations and deaths", @@ -221420,6 +223899,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.09.22.22280222", + "rel_title": "Effects of SARS-CoV-2 Infection on Attention, Memory, and Sensorimotor Performance", + "rel_date": "2022-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.22.22280222", + "rel_abs": "BackgroundRecovery after SARS-CoV-2 infection is extremely variable, with some individuals recovering quickly, and others experiencing persistent long-term symptoms or developing new symptoms after the acute phase of infection, including fatigue, poor concentration, impaired attention, or memory deficits. Many existing studies reporting cognitive deficits associated with SARS-CoV-2 infection are limited by the exclusive use of self-reported measures or a lack of adequate comparison groups.\n\nMethodsForty-five participants, ages 18-70, (11 Long-COVID, 14 COVID, and 20 No-COVID) underwent behavioral testing with the NIH Toolbox Neuro-Quality of Life survey and selected psychometric tests, including a flanker interference task and the d2 Test of Attention.\n\nResultsWe found greater self-reported anxiety, apathy, fatigue, emotional dyscontrol, sleep disturbance and cognitive dysfunction in COVID compared No-COVID groups. After categorizing COVID patients according to self-reported concentration problems, we observed declining performance patterns in multiple attention measures across No-COVID controls, COVID and Long-COVID groups. COVID participants, compared to No-COVID controls, exhibited worse performance on NIH Toolbox assessments, including the Eriksen Flanker, Nine-Hole Pegboard and Auditory Verbal Learning tests.\n\nConclusionThis study provides convergent evidence that previous SARS-CoV-2 infection is associated with impairments in sustained attention, processing speed, self-reported fatigue and concentration. The finding that some patients have cognitive and visuomotor dysfunction in the absence of self-reported problems suggests that SARS-CoV-2 infection can have unexpected and persistent subclinical consequences.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Erin O'Connor", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Nikita Rednam", + "author_inst": "univrsity of Marylnd School of Medicine" + }, + { + "author_name": "Rory OBrien", + "author_inst": "Lantern Laboratory" + }, + { + "author_name": "Shea OBrien", + "author_inst": "Lantern Laboratory" + }, + { + "author_name": "Peter Rock", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Andrea Levine", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Thomas A Zeffiro", + "author_inst": "University of Maryland School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.21.22280219", "rel_title": "Excess death estimates from multiverse analysis in 2009-2021", @@ -222112,77 +224634,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2022.09.20.22280094", - "rel_title": "Food Insecurity During the First Year of COVID-19: An Analysis of Employment and Sociodemographic Factors Among a Longitudinal Cohort (CHASING COVID)", - "rel_date": "2022-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.20.22280094", - "rel_abs": "ObjectivesWhile much has been reported about the impact of COVID-19 on U.S. food insecurity, longitudinal data and the variability experienced by people working in different industries are limited. This study aims to further characterize individuals experiencing food insecurity during the pandemic in terms of employment and sociodemographic characteristics and degree of food insecurity.\n\nMethodsThe study sample consisted of people enrolled in a U.S. prospective cohort study (CHASING COVID) who completed all food insecurity questionnaires from Visit 1 (April-July 2020) through Visit 7 (May-June 2021). Descriptive statistics and logistic regression models were used to determine employment and sociodemographic correlates of food insecurity (using a screening question from the USDA HFSS). Patterns of food insecurity and utilization of food benefit programs were also examined.\n\nResultsThirty-one percent (1251/4019) of the sample were food insecure. Black and Hispanic respondents, households with children, and those with lower income and education levels had a higher odds of food insecurity. People employed in construction, leisure/hospitality and trade/transportation industries had the highest burden of both food insecurity and income loss. Among those reporting food insecurity, 40% were persistently food insecure ([≥]4 consecutive visits), and 46% did not utilize any food benefit programs.\n\nConclusionsThe pandemic resulted in widespread food insecurity in our cohort, much of which was persistent. In addition to addressing sociodemographic disparities, future policies should focus on the needs of those working in vulnerable industries and ensure those experiencing food insecurity can easily participate in food benefit programs for which they are eligible.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Yvette Ng", - "author_inst": "Graduate School of Public Health and Health Policy, Urban Food Policy Institute, City University of New York, New York, NY" - }, - { - "author_name": "Mindy Chang", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY," - }, - { - "author_name": "McKaylee Robertson", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY" - }, - { - "author_name": "Christian Grov", - "author_inst": "Institute for Implementation Science in Population Health (ISPH) and Department of Community Health and Social Sciences, Graduate School of Public Health and He" - }, - { - "author_name": "Andrew Maroko", - "author_inst": "Institute for Implementation Science in Population Health (ISPH) and Department of Environmental, Occupational, and Geospatial Health Sciences, Graduate School " - }, - { - "author_name": "Rebecca Zimba", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY" - }, - { - "author_name": "Drew Westmoreland", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY" - }, - { - "author_name": "Madhura Rane", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY" - }, - { - "author_name": "Chloe Mirzayi", - "author_inst": "Institute for Implementation Science in Population Health (ISPH) and Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health P" - }, - { - "author_name": "Angela M. Parcesepe", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY and Gillings School of Public Health, University of " - }, - { - "author_name": "Sarah Kulkarni", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY" - }, - { - "author_name": "William Salgado-You", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York, New York, NY" - }, - { - "author_name": "Nevin Cohen", - "author_inst": "Graduate School of Public Health and Health Policy, Urban Food Policy Institute, City University of New York, New York, NY" - }, - { - "author_name": "Denis Nash", - "author_inst": "Institute for Implementation Science in Population Health (ISPH) and Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health P" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.09.21.22280193", "rel_title": "Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity", @@ -223354,6 +225805,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.09.20.22280135", + "rel_title": "Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments", + "rel_date": "2022-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.20.22280135", + "rel_abs": "The role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored. Here, we show that patients treated with various anti-SARS-CoV-2 mAb regimens develop evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Mutations develop more frequently in immunocompromised patients and strongly correlate not only with the neutralizing capacity of the therapeutic mAbs, but also with an anti-inflammatory and healing-promoting host milieu. Machine-learning models based on soluble host-derived biomarkers identified patients at high risk of developing escape mutations against therapeutic mAbs with high accuracy. While our data demonstrate that host-driven immune and non-immune responses are essential for development of mutant SARS-CoV-2, these data could also support point-of-care decision making in reducing the risk of mAb treatment failure and improving mitigation strategies for possible dissemination of escape SARS-CoV-2 mutants.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Akshita Gupta", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Angelina Konnova", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Mathias Smet", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Matilda Berkell", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Alessia Savoldi", + "author_inst": "University of Verona" + }, + { + "author_name": "Matteo Morra", + "author_inst": "University of Verona" + }, + { + "author_name": "Vincent Van averbeke", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Fien De Winter", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Denise Peserico", + "author_inst": "University of Verona" + }, + { + "author_name": "Elisa Danese", + "author_inst": "University of Verona" + }, + { + "author_name": "An Hotterbeekx", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Elda Righi", + "author_inst": "University of Verona" + }, + { + "author_name": "- mAb ORCHESTRA working group", + "author_inst": "-" + }, + { + "author_name": "Pasquale De Nardo", + "author_inst": "University of Verona" + }, + { + "author_name": "Evelina Tacconelli", + "author_inst": "University of Verona" + }, + { + "author_name": "Surbhi Malhotra-Kumar", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Samir Kumar-Singh", + "author_inst": "University of Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.20.22280138", "rel_title": "Prevalence of SARS-CoV-2 and co-occurrence/co-infection with malaria during the first wave of the pandemic (the Burkina Faso case)", @@ -224078,77 +226612,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.09.15.22280000", - "rel_title": "SARS-CoV-2 mRNA vaccination elicits broad and potent Fc effector functions to VOCs in vulnerable populations", - "rel_date": "2022-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.15.22280000", - "rel_abs": "SARS-CoV-2 variants have continuously emerged even as highly effective vaccines have been widely deployed. Reduced neutralization observed against variants of concern (VOC) raises the question as to whether other antiviral antibody activities are similarly compromised, or if they might compensate for lost neutralization activity. In this study, the breadth and potency of antibody recognition and effector function was surveyed in both healthy individuals as well as immunologically vulnerable subjects following either natural infection or receipt of an mRNA vaccine. Considering pregnant women as a model cohort with higher risk of severe illness and death, we observed similar binding and functional breadth for healthy and immunologically vulnerable populations. In contrast, considerably greater functional antibody breadth and potency across VOC was associated with vaccination than prior infection. However, greater antibody functional activity targeting the endemic coronavirus OC43 was noted among convalescent individuals, illustrating a dichotomy in recognition between close and distant human coronavirus strains that was associated with exposure history. Probing the full-length spike and receptor binding domain (RBD) revealed that antibody-mediated Fc effector functions were better maintained against full-length spike as compared to RBD. This analysis of antibody functions in healthy and vulnerable populations across a panel of SARS-CoV-2 VOC and extending through endemic alphacoronavirus strains suggests the differential potential for antibody effector functions to contribute to protecting vaccinated and convalescent subjects as the pandemic progresses and novel variants continue to evolve.\n\nOne Sentence SummaryAs compared to natural infection with SARS-CoV-2, vaccination drives superior functional antibody breadth raising hopes for candidate universal CoV vaccines.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Andrew P Hederman", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Harini Natarajan", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Joshua A Wiener", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Peter F Wright", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Evan M Bloch", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Aaron AR Tobian", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Andrew D Redd", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Joel N. Blankson", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Amihai Rottenstreich", - "author_inst": "Hadassah-Hebrew University Medical Center" - }, - { - "author_name": "Gila Zarbiv", - "author_inst": "Hadassah-Hebrew University Medical Center" - }, - { - "author_name": "Dana Wolf", - "author_inst": "Hadassah-Hebrew University Medical Center" - }, - { - "author_name": "Tessa Goetghebuer", - "author_inst": "Universit\u00e9 libre de Bruxelles" - }, - { - "author_name": "Arnaud Marchant", - "author_inst": "Universit\u00e9 libre de Bruxelles" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Dartmouth College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.13.22279702", "rel_title": "Accounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S.", @@ -225104,6 +227567,125 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2022.09.15.507787", + "rel_title": "Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution", + "rel_date": "2022-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.15.507787", + "rel_abs": "Continuous evolution of Omicron has led to a rapid and simultaneous emergence of numerous variants that display growth advantages over BA. 5. Despite their divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots. The driving force and destination of such convergent evolution and its impact on humoral immunity remain unclear. Here, we demonstrate that these convergent mutations can cause striking evasion of neutralizing antibody (NAb) drugs and convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2 binding capability. BQ.1.1.10, BA.4.6.3, XBB, and CH. 1.1 are the most antibody-evasive strain tested, even exceeding SARS-CoV-1 level. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies (mAbs) isolated from BA.2 and BA.5 breakthrough-infection convalescents. Importantly, due to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection caused significant reductions in the epitope diversity of NAbs and increased proportion of non-neutralizing mAbs, which in turn concentrated humoral immune pressure and promoted convergent evolution. Moreover, we showed that the convergent RBD mutations could be accurately inferred by integrated deep mutational scanning (DMS) profiles, and the evolution trends of BA.2.75/BA.5 subvariants could be well-simulated through constructed convergent pseudovirus mutants. Together, our results suggest current herd immunity and BA.5 vaccine boosters may not provide good protection against infection. Broad-spectrum SARS-CoV-2 vaccines and NAb drugs development should be highly prioritized, and the constructed mutants could help to examine their effectiveness in advance.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Yunlong Cao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University; Changping Laboratory" + }, + { + "author_name": "Fanchong Jian", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Jing Wang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Yuanling Yu", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Weiliang Song", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Ayijiang Yisimayi", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Jing Wang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Ran An", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Xiaosu Chen", + "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University" + }, + { + "author_name": "Na Zhang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Yao Wang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Peng Wang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Lijuan Zhao", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Haiyan Sun", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Lingling Yu", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Sijie Yang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Xiao Niu", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Tianhe Xiao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Qingqing Gu", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Fei Shao", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Xiaohua Hao", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Yanli Xu", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Zhongyang Shen", + "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University" + }, + { + "author_name": "Youchun Wang", + "author_inst": "Changping Laboratory; Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug C" + }, + { + "author_name": "Xiaoliang Sunney Xie", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University; Changping Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.15.508120", "rel_title": "SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF", @@ -225912,129 +228494,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2022.09.12.22279810", - "rel_title": "Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types", - "rel_date": "2022-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.12.22279810", - "rel_abs": "The relationship between N-antigen concentration and viral load within a specimen and across different specimens is essential for interpretation of rapid diagnostic tests (RDT) clinical performance in different use cases. A prospective study was conducted in Porto Velho, Brazil, to investigate RDT performance in different specimen types as a function of the correlation between antigen concentration and viral load. The study included 214 close contacts with recent exposures to confirmed cases, aged 12 years and older and with various levels of vaccination. Antigen concentration was measured in nasopharyngeal swab (NPS), anterior nares swab (ANS), and saliva specimens. Reverse transcriptase (RT)-PCR was conducted on the NPS and saliva specimens, and two RDTs were conducted on ANS and one on saliva. Antigen concentration correlated with viral load when measured in the same specimen type but not across specimen types. Antigen levels were higher in symptomatic cases compared to asymptomatic/oligosymptomatic cases and lower in saliva compared to NPS and ANS samples. Discordant results between the RDTs conducted on ANS and the RT-PCR on NPS were resolved by antigen concentration values. The analytical limit-of-detection of RDTs can be used to predict the performance of the tests in populations for which the antigen concentration is known. The antigen dynamics across different sample types observed in SARS-CoV-2 disease progression support use of RDTs in nasal samples. Given lower antigen concentrations in saliva, tests using saliva is expected to require improved analytical sensitivity to achieve clinical sensitivity similar to testing of nasal samples.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Allison Golden", - "author_inst": "PATH" - }, - { - "author_name": "Michelle Oliveira-Silva", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Hannah Slater", - "author_inst": "PATH" - }, - { - "author_name": "Alexia Martines Vieira", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Pooja Bansil", - "author_inst": "PATH" - }, - { - "author_name": "Emily Gerth-Guyette", - "author_inst": "PATH" - }, - { - "author_name": "Brandon T Leader", - "author_inst": "PATH" - }, - { - "author_name": "Stephanie Zobrist", - "author_inst": "PATH" - }, - { - "author_name": "Alan Kennedy Braga Ferreira", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Erika Crhistina Santos de Araujo", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Catherine Duran de Lucena Cruz", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Eduardo Garbin", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Greg T Bizilj", - "author_inst": "PATH" - }, - { - "author_name": "Sean J Carlson", - "author_inst": "PATH" - }, - { - "author_name": "Mariana Sagalovsky", - "author_inst": "PATH" - }, - { - "author_name": "Sampa Pal", - "author_inst": "PATH" - }, - { - "author_name": "Vin Gupta", - "author_inst": "Amazon.com" - }, - { - "author_name": "Leo Wolansky", - "author_inst": "The Rockefeller Foundation" - }, - { - "author_name": "David S Boyle", - "author_inst": "PATH" - }, - { - "author_name": "Deusilene Souza Vieira Dall'Aqua", - "author_inst": "Fundacao Oswaldo Cruz (FIOCRUZ) (FIOCRUZ)," - }, - { - "author_name": "Felipe Gomes Naveca", - "author_inst": "Instituto Leonidas e Maria Deane (ILMD), Fundacao Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Valdinete Alves do Nascimento", - "author_inst": "Instituto Leonidas e Maria Deane (ILMD), Fundacao Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Juan Miguel Villalobos Salcedo", - "author_inst": "Fundacao Oswaldo Cruz (FIOCRUZ) (FIOCRUZ)," - }, - { - "author_name": "Paul K Drain", - "author_inst": "University of Washington" - }, - { - "author_name": "Alexandre Dias Tavares Costa", - "author_inst": "Instituto Carlos Chagas (ICC), Fundacaoo Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Dhelio Pereira", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Gonzalo J Domingo", - "author_inst": "PATH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.14.22279931", "rel_title": "Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar", @@ -227110,6 +229569,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.14.507948", + "rel_title": "HLA variants and TCR diversity against SARS-CoV-2 in the pre-COVID-19 era", + "rel_date": "2022-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.14.507948", + "rel_abs": "HLA antigen presentation and T-cell immunity are critical to control viral infection such as SARS-CoV-2. This study performed on samples collected in the pre-COVID-19 era demonstrates that individuals are fully equiped at the genetic level in terms of TCR repertoire and HLA variants to recognize and kill SARS-CoV-2 infected cells. HLA diversity, heterologous immunity and random somatic TCR recombination could explain these observations.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Stephane Buhler", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Zuleika Calderin Sollet", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Florence Bettens", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Antonia Schaefer", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Marc Ansari", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Sylvie Ferrari-Lacraz", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Jean Villard", + "author_inst": "Geneva University Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.14.507904", "rel_title": "The SARS-CoV-2 spike N-terminal domain engages 9-O-acetylated \u03b12-8-linked sialic acids", @@ -227782,29 +230284,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.12.22278744", - "rel_title": "A general theory for infectious disease dynamics.", - "rel_date": "2022-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.12.22278744", - "rel_abs": "We present a general theory of infection spreading, which directly follows from conservation laws and takes as inputs the probability density functions of latent times. The derivation of the theory substantially differs from Kermack and McKendrick (1927) argument, which instead was based on the concept of removal rates. We demonstrate the formal equivalence of the two approaches, but our theory provides a clear interpretation of the kernels of the integro-differential equations governing the infection spreading in terms of survival function of the latent times distributions. This aspect was never captured before. Real distributions of latent times can be, then, employed, thus overcoming the limitations of standard SIR, SEIR and other similar models, which implicitly make use of exponential or exponential-related distributions. SIR and SEIR-type models are, in fact, a subclass of the theory here presented. We show that beside the infection rate{nu} , the joint probability density function pEI ({tau}, {tau}1) of latent times in the exposed and infectious compartments governs the infection spreading. Assuming that the number of infected individuals is negligible compare to the entire population, we were able to study the stability of the dynamical system and provide the general solution of equations in terms characteristic functions of the probability distribution of latent times. We present asymptotic solutions for the case R0 = 1 and demonstrate that the moments of the latent times distribution govern the rate of disease spreading in this case. The present theory is employed to simulate the diffusion of COVID-19 infection in Italy during the first 120 days. The estimated value of the basic reproduction number is R0 {approx} 3.5, in very good agreement with existing data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Giuseppe Carbone", - "author_inst": "Department of Mechanics Mathematics and Management, Polytechnic University of Bari, via Orabona 4, 70125, Bari - Italy" - }, - { - "author_name": "Ilario De Vincenzo", - "author_inst": "Department of Mechanics Mathematics and Management, Polytechnic University of Bari, via Orabona 4, 70125, Bari - Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.12.507671", "rel_title": "Evaluation of endogenous and therapeutic 25-hydroxycholesterols in murine models of pulmonary SARS-CoV-2 infection", @@ -228876,6 +231355,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.09.507303", + "rel_title": "Expression profiling of immune-response-genes common in SARS-CoV-1 and influenza A virus disease, viz-a-viz neutropenia disorder, using integrated bioinformatics tools", + "rel_date": "2022-09-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.09.507303", + "rel_abs": "Viral diseases have proven to be an existential threat to man due to its fatality and its consistent emergence and re-emergence, so the need for novel ideas in combating this menace. Advances in genetic studies has proven to be indispensable in this fight as knowledge of organismal genetic variability has been useful in therapy development, as well as in mounting defense against the treacherous infectious agents. However, there are still fallow grounds needing to be explored in this war which informed this study, with focus on expression profiling of similar immune-responsegenes in SARS-COV-1 and influenza A virus (AIV) in respect to neutropenia (NP), using integrated bioinformatics techniques such as extraction of microarray dataset in the gene expression omnibus (GEO) database, generation of DEGs using GEO2R tool, construction of protein-protein interaction (PPI) network using string and Cytoscape software, Venn diagram analysis and then gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) for enrichment and pathway analysis respectively. Ten genes which includes ELANE, ITGA2B, CXCR1, CSF3R, SPI1, MS4A3, MMP8, CEACAM8, RNASE3, and DEFA4 were identified, with ELANE gene moreover identified as a key gene, which might be responsible in the regulation of immune response during viral infection, based on its characteristic feature in the PPI network.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ayinde Charles Olaniyi", + "author_inst": "Ladoke Akintola University of Technology" + }, + { + "author_name": "Obasanmi Dorcas Oluwadamilola", + "author_inst": "university of Lagos" + }, + { + "author_name": "Alabi Temitope Oluwabunmi", + "author_inst": "Ladoke Akintola University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.09.09.22279725", "rel_title": "Effectiveness of incentivized peer referral to increase enrollment in a community-based chlamydia screening and treatment study among young Black men", @@ -229988,69 +232494,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.06.22279637", - "rel_title": "Head-to head comparison of anterior nares and nasopharyngeal swabs for SARS-CoV-2 antigen detection in a community drive-through test centre in the UK", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279637", - "rel_abs": "ObjectiveTo conduct a head-to-head diagnostic accuracy evaluation of professionally taken anterior nares (AN) and nasopharyngeal (NP) swabs for SARS-CoV-2 antigen detection using rapid diagnostic tests (Ag-RDT).\n\nMethodsNP swabs for SARS-CoV-2 reverse transcription quantitative polymerase chain reaction (RT-qPCR) testing and paired AN and NP swabs for the antigen detection were collected from symptomatic participants enrolled at a community drive-through COVID-19 test centre in Liverpool. Two Ag-RDT brands were evaluated: Sure-Status (PMC, India) and Biocredit (RapiGEN, South Korea). The visual read out of the Ag-RDT test band was quantitative scored and the 50% and 95% limit of detection (LoD) of both Ag-RDT brands using AN and NP swabs was calculated using a probabilistic logistic regression model.\n\nResultsA total of 604 participants were recruited of which 241 (40.3%) were SARS-CoV-2 positive by RT-qPCR. Sensitivity and specificity of AN swabs was equivalent to the obtained with NP swabs: 83.2% (75.2-89.4%) and 98.8% (96.5-99.6%) utilising NP swabs and 84.0% (76.2-90.1%) and 99.2% (97.0-99.8%) with AN swabs for Sure-Status and; 81.2% (73.1-87.7%) and 99.0% (94.7-86.5%) with NP swabs and 79.5% (71.3-86.3%) and 100% (96.5-100%) with AN swabs for Biocredit. The agreement of the AN and NP swabs was high for both brands with an inter-rater relatability ({kappa}) of 0.918 and 0.833 for Sure-Status and Biocredit, respectively. The overall 50% LoD and 95% LoD was 0.9-2.4 x 104 and 3.0-3.2 x 108 RNA copies/mL for NP swabs and 0.3-1.1 x 105 and 0.7-7.9 x 107 RNA copies/mL and for AN swabs with no significant difference on LoD for any of the swabs types or test brands. Quantitative read-out of test line intensity was more often higher when using NP swabs with significantly higher scores for both Ag-RDT brands.\n\nConclusionsthe diagnostic accuracy of the two SARS-CoV-2 Ag-RDTs brands evaluated in this study was equivalent using AN swabs than NP swabs. However, test line intensity was lower when using AN swabs which could influence negatively the interpretation of the Ag-RDT results for lay users. Studies on Ag-RDT self-interpretation using AN and NP swabs are needed to ensure accurate test use in the wider community.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Rachel Louise Byrne", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Ghaith Aljayyoussi", - "author_inst": "Liverpool school of Tropical Medicine" - }, - { - "author_name": "Konstantina Kontogianni", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Karina Clerkin", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Matthew McIntyre", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Jahanara Wardale", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Christopher T Willams", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Richard Body", - "author_inst": "Manchester Hospital University Trust" - }, - { - "author_name": "Emily R Adams", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Camille Escadafal", - "author_inst": "FIND" - }, - { - "author_name": "Ana I Cubas Atienzar", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Margaretha de Vos", - "author_inst": "Foundation for Innovative New Diagnostics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.06.22279649", "rel_title": "Portable Breath-Based Volatile Organic Compound Monitoring for the Detection of COVID-19: Challenges of Emerging Variants", @@ -231170,6 +233613,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.05.22279623", + "rel_title": "Modeling vaccine allocation and equity implications of COVID-19 containment strategies", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.05.22279623", + "rel_abs": "Given the shortage of global COVID-19 vaccines, a critical public concern is whether the strategy of allocation exerts a heterogeneous effect on settings that have imbalanced accessibility. Exacerbated by the mutational characteristics of the pathogen, traits of immunity protection of vaccines, and diversification of human behaviors, the pathway to the full eradication of the COVID-19 pandemic is becoming increasingly complicated and indeterminate. Population-wide evaluation of public interventions remains crucial to evaluate the performance of epidemiology policies. This study employs a mathematical compartmental model combined with the observational data of the United States to examine the potential effect of vaccine allocation on the trajectory of COVID-19 transmission and the elicited equity implications. The outcomes imply that allocation strategies substantially impact the cumulative equilibrium size of a pandemic controlling for confounding factors. Under a framework of a two-dose primary vaccination strategy aiming to curb the total infections for high-accessibility settings (HAS) and low-accessibility settings(LAS), the traits of vaccination, pathogen, and human effort integrally affect the equilibrium of the COVID-19 pandemic in the medium perspective (i.e., up to 5 years). Vaccine allocation increases the healthcare and cost burden for HAS temporarily, in contrast, it reduces the risk of COVID-19 transmission for the LAS. The effects are consistent across a variety of profiles. By enhancing the administration rates of primary doses (i.e., mainly through dose 1 and dose 2), the magnitude of the COVID-19 pandemic decreases contingent on confounding factors. To minimize the magnitude of infection, it is of importance to dynamically monitor the immunity protection of vaccines, the dynamics of virus transmission, and the gap in the human effort.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ichiro Nakamoto", + "author_inst": "Fujian University of Technology, School of Internet Economics and Business" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.09.22279760", "rel_title": "Parental experiences of the impacts of COVID-19 on the care of young children; qualitative interview findings from the Nairobi Early Childcare in Slums (NECS) Project", @@ -231902,29 +234364,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.09.09.507307", - "rel_title": "A new and highly effective method for predicting T-cell response targets implemented on SARS-CoV-2 data", - "rel_date": "2022-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.09.507307", - "rel_abs": "Computational T-cell epitope prediction is essential in many immunological projects, including the development of vaccines. T-cells of immunocompetent vertebrate hosts can recognize as non-self only peptides which are present in the parasites proteins and absent in the hosts proteins. This basic principle allows us to predict which peptides can elicit T-cells response. We built on the fact that the specificity of T-cells reacting to SARS-CoV-2 antigens has been recently mapped in detail. Using Monte Carlo tests, we found that empirically confirmed peptides that stimulate T-cells contain an increased fraction of pentapeptides, hexapeptides, and heptapeptides which are not found in the human proteome (p < 0.0001). Similarly, hexapeptides absent in human proteins were overrepresented in peptides that elicited T-cell response in a published empirical study (p = 0.027). The new theory-based method predicted T-cell immunogenicity of SARS-CoV-2 peptides four times more effectively than current empirically based methods.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jaroslav Flegr", - "author_inst": "Fac. Science, Charles University" - }, - { - "author_name": "Daniel Zahradnik", - "author_inst": "Department of Biological Risks, The Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Pruhonice, Czech Republic" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.09.07.506919", "rel_title": "A clinical stage LMW-DS drug inhibits cell infection by coronaviruses and modulates reactive cytokine release from microglia", @@ -233008,6 +235447,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.05.506626", + "rel_title": "Immune dynamics at single cell protein level after delta/omicron infection in COVID-19 vaccinated convalescent individuals", + "rel_date": "2022-09-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.05.506626", + "rel_abs": "Both COVID-19 mRNA or recombinant Adenovirus vector (rAdVV) based vaccines have shown a great efficacy in generating humoral and cellular immune responses. Two doses of the COVID-19 vaccines generate enough antibodies and generate spike-specific T cell responses. However, after 6-8 months there is a decline in antibody production and T cell responses. Due to the rise of new SARS-CoV-2 variants of concern, a third or even fourth dose of vaccine was recommended for the elderly, immune comprised and frontline medical health care workers. However, despite additional booster doses given, those who were infected with either delta or omicron (during December 2021 - March 2022) had symptoms of illness. By what means these COVID-19 vaccines provide immunity against the SARS-CoV-2 virus at the molecular level is not explored extensively yet and, it is an emerging research field as to how the SARS-CoV-2 virus is able to evade the host immunity. Most of the infected people had mild symptoms whilst some were asymptomatic. Many of the people had developed nucleocapsid antibodies against the SARS-CoV-2 delta/omicron variants confirming a humoral immune response against viral infection. Furthermore, cellular analysis shows that post-vaccinated recovered COVID-19 individuals have significantly reduced NK cells and increased T naive CD4+, TEM CD8+ and B cells. This decrease in cellular immunity corresponds to individuals who recovered from alpha variants infection and had mild symptoms. Our results highlight that booster doses clearly reduce the severity of infection against delta/omicron infection. Furthermore, our cellular and humoral immune system is trained by vaccines and ready to deal with breakthrough infections in the future.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rimpi Bajaj", + "author_inst": "Tuebingen University" + }, + { + "author_name": "Zhiqi Yang", + "author_inst": "FK, Tuebingen University, Tuebingen" + }, + { + "author_name": "Vincent Hammer", + "author_inst": "IMGAG Tuebingen University" + }, + { + "author_name": "Simone Poeschel", + "author_inst": "Tuebingen University Hospital" + }, + { + "author_name": "Kristin Beiber", + "author_inst": "Tuebingen University Hospital" + }, + { + "author_name": "Madhuri S Salker", + "author_inst": "FK Tuebingen University" + }, + { + "author_name": "Nicolas Casadei", + "author_inst": "Tuebingen University" + }, + { + "author_name": "Stephan Ossowski", + "author_inst": "University of Tuebingen" + }, + { + "author_name": "Olaf Riess", + "author_inst": "Tuebingen University" + }, + { + "author_name": "Yogesh Singh", + "author_inst": "Tuebingen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.06.506714", "rel_title": "Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine", @@ -234076,73 +236570,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.02.22279455", - "rel_title": "Epidemiological pattern of births from the largest surveillance database of live births in Brazil \"SINASC\" before and during the COVID-19 pandemic in the Brazilian Amazon", - "rel_date": "2022-09-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.02.22279455", - "rel_abs": "The surveillance of live births in Brazil has been carried out since 1990 by the Information System on Live Births (SINASC), which was implemented by the Ministry of Health aiming at standardized registration on a national level. The state of Para is part of the Brazilian Amazon, northern Brazil, which has several unique characteristics. Thus, the purpose of this study was to identify the epidemiological pattern of live births before and during the pandemic of COVID-19 in the state of Para, 2016 to 2020. This is an ecological epidemiological time-series study, using epidemiological surveillance data from DATASUS, referring to the Live Births Information System (SINASC). These are data that have been treated by surveillance and are in aggregate format. The study population is the live births residing in the state of Para, in the period from 2016 to 2020. The data collection instrument was the Declaration of Live Births (DLB). There were 689,454 live births, and the highest rates of births were and continued to remain in the Marajo II, Baixo Amazonas, Xingu, and Tapajos regions. The Metropolitan I and Araguaia regions were and continue to be the lowest rates in the state. Age of the mother 15 to 19 years old 22.29%, 20 to 24 years old 30.05% and 25 to 29 years old 22.58%, most of the single pregnancy type 98.32%, prenatal consultations, performed 7 or more 48.10%, followed by 4 to 6 consultations 33.98%, most presented 7 or more years of the study 48.10%, followed by 3 to 6 years 33.98%. Represented 51.21% male and 48.77% female. The occurrence of congenital anomalies represented 0.52% of live births. Another congenital malformation and deformity were the most prevalent at 25.53%, followed by Congenital deformities of the feet 14.90%, Other congenital malformations of the nervous system 14.84%, and Other congenital malformations 10.77%, Cleft lip, and cleft palate 8.88%, Other congenital malformations digestive tract 8.10%. The demographic transition has already occurred for several decades, including the reduction of fertility and birth rate, so our study showed that the reduction in the number of live births was already a reality in the country, but we emphasize that this reduction was enhanced by the pandemic. We observed greater adherence to prenatal care and a lower prevalence of low birth weight compared to other studies, but the limitation was the absence of studies in the same place of the research. Regarding data incompleteness, we emphasize the ignored fields that reflect the fragility in the surveillance of live births, which was reinforced by the literature.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Daniele Melo Sardinha", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Andrea Maria da Silva Luz", - "author_inst": "FSCMPA" - }, - { - "author_name": "Katia Raquel Almeida Carneiro", - "author_inst": "FSCMPA" - }, - { - "author_name": "Mauro Daniele Rodrigues Paixao", - "author_inst": "Universidade da Amazonia UNAMA" - }, - { - "author_name": "Sebastiao Kaua de Sousa Bispo", - "author_inst": "Universidade da Amazonia UNAMA" - }, - { - "author_name": "Natasha Cristina Oliveira Andrade", - "author_inst": "Universidade da Amazonia UNAMA" - }, - { - "author_name": "Juliane Lima Alencar", - "author_inst": "PPGEVS/IEC" - }, - { - "author_name": "Tamires de Nazare Soares", - "author_inst": "PPGENF/UEPA" - }, - { - "author_name": "Joyce dos Santos Freitas", - "author_inst": "ICS/FAENF/UFPA" - }, - { - "author_name": "Rubenilson Caldas Valois", - "author_inst": "PPGENF/UEPA" - }, - { - "author_name": "Ana Lucia da Silva Ferreira", - "author_inst": "PPGBPA/IEC/UEPA" - }, - { - "author_name": "Karla Valeria Batista Lima", - "author_inst": "PPGBPA/IEC/UEPA" - }, - { - "author_name": "Luana Nepomuceno Gondim Costa Lima", - "author_inst": "Programa de Pos-Graduacao em Biologia Parasitaria na Amazonia PPGBPA/IEC/UEPA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.09.04.22279366", "rel_title": "Frequency and Risk Factors of Resident Burnout Before and During the COVID19 Pandemic", @@ -235058,6 +237485,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.02.506305", + "rel_title": "Novel monoclonal antibodies showing broad neutralizing activity for SARS-CoV-2 variants including Omicrons BA.5 and BA.2.75", + "rel_date": "2022-09-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.02.506305", + "rel_abs": "We identified novel neutralizing monoclonal antibodies against SARS-CoV-2 variants (including Omicron) from individuals received two doses of mRNA vaccination after they had been infected with wildtype. We named them MO1, MO2 and MO3. MO1 shows high neutralizing activity against authentic variants: D614G, Delta, BA.1, BA.1.1, BA.2, and BA.2.75 and BA.5. Our findings confirm that the wildtype-derived vaccination can induce neutralizing antibodies that recognize the epitopes conserved among the SARS-CoV-2 variants (including BA.5 and BA.2.75). The monoclonal antibodies obtained herein could serve as novel prophylaxis and therapeutics against not only current SARS-CoV-2 viruses but also future variants that may arise.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hanako Ishimaru", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Mitsuhiro Nishimura", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Lidya Handayani Tjan", + "author_inst": "Kobe university Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Silvia Sutandhio", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Maria Istiqomah Marini", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Gema Barlian Effendi", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Hideki Shigematsu", + "author_inst": "Japan Synchrotron Radiation Research Institute SPring-8" + }, + { + "author_name": "Koji Kato", + "author_inst": "Japan Synchrotron Radiation Research Institute SPring-8" + }, + { + "author_name": "Natsumi Hasegawa", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Kaito Aoki", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Yukiya Kurahashi", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Koichi Furukawa", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Mai Shinohara", + "author_inst": "Kobe university Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Tomoka Nakamura", + "author_inst": "kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Jun Arii", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Tatsuya Nagno", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Sachiko Nakamura", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Shigeru Sano", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Sachiyo Iwata", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.09.01.506266", "rel_title": "Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA", @@ -235666,169 +238188,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.30.22279372", - "rel_title": "Implementation of a Non-Invasive Helmet Ventilation Solution for the Management of Severe COVID-19 Respiratory Disease in Nigeria: The CircumVent Project", - "rel_date": "2022-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.30.22279372", - "rel_abs": "Affordable novel strategies are needed to treat COVID-19 cases complicated by respiratory compromise in resource limited settings. We report a mixed-methods pre-post assessment of 1) the useability of CPAP/O2 helmet non-invasive ventilation (NIV) to treat COVID-19, at [~] 1% the cost of mechanical ventilation; 2) the effectiveness of a train-the-trainer practice facilitation intervention; and 3) whether use of CPAP/O2 helmet NIV was associated with increased COVID-19 infection among healthcare workers. At baseline, eight COVID-19 treatment centers in Nigeria (CircumVent network) received CPAP/O2 helmet systems, and were instructed on its use. After five months, clinicians within the CircumVent netwok participated in a 2-day train-the-trainers educational intervention. The physicians completed i) standardized forms on patient demographics, clinical course, and outcomes for patients seen in the treatment centers; ii) standardized surveys of feasibility and acceptability of use of CPAP/O2 helmet systems; and iii) in-depth-interviews to explore facilitators and barriers to implementation of CPAP/O2 helmet NIV. Physicians described the CPAP/O2 helmet ventilator as easy to use and they felt comfortable training their staff on its use. They rated CPAP/O2 helmet NIV as feasible, acceptable, and appropriate (mean score of 4.0, 3.8, and 3.9 out of 5, respectively, on standardized scales). Case report forms for 546 patients with suspected and/or confirmed COVID-19 infection were obtained between May 2020 and November 2021. Of these, 69% (n=376) were treated before the training; and 29.7% (n=162) were treated with CPAP/O2 helmet ventilation. CPAP/O2 helmet NIV was well-tolerated by patients, with 12% reporting claustrophobia, and 2% reporting loose- or tight-fitting helmets. Although patient outcomes improved among CPAP/O2 helmet users overall, this was not associated with training (P=0.2). This finding persisted after adjustment for disease severity at presentation. Serosurvey of 282 health workers across treatment centers revealed that 40% (n=112) were seropositive for SARS-CoV-2. Seropositivity was significantly associated with direct contact with COVID-19 patients and limited access to PPE and hand hygiene during aerosol generating procedures (P = 0.02), but not use of CPAP/O2 helmet (Ps [≥] 0.2). In conclusion, physicians effectively used CPAP/O2 helmet NIV systems to treat COVID-19 patients in Nigeria without need for practice facilliation of their training and without increased risk of infection among healthcare workers. The use of CPAP/O2 helmet NIV could be an important strategy for treating individuals with COVID-19 infection and other disease conditions complicated by respiratory distress, particularly in settings were resources such mechanical ventilation are limited.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Aima A. Ahonkhai", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Aliyu Abdu", - "author_inst": "Department of Medicine, Bayero University Kano, Kano, Nigeria; Africa Center of Excellence in Population Health and Policy, Aminu Kano Teaching Hospital, Kano, " - }, - { - "author_name": "Olukemi Adekanmbi", - "author_inst": "University College Hospital, Ibadan; University of Nigeria Teaching, Oyo, Nigeria" - }, - { - "author_name": "Nnennaya A. Ajayi", - "author_inst": "Department of Internal Medicine, College of Health Sciences, Ebonyi State University, Abakaliki/ Alex Ekwueme Federal University Teaching Hospital, Abakaliki, E" - }, - { - "author_name": "Samuel Ajayi", - "author_inst": "University College Hospital, Ibadan; University of Nigeria Teaching, Oyo, Nigeria" - }, - { - "author_name": "Happy Akpobi", - "author_inst": "Delta State University Teaching Hospital, Oghara, Nigeria" - }, - { - "author_name": "Ejiro Benjamin Akpochafo", - "author_inst": "Delta State University Teaching Hospital, Oghara, Nigeria" - }, - { - "author_name": "Muktar H. Aliyu", - "author_inst": "Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, " - }, - { - "author_name": "Adaeze C. Ayuk", - "author_inst": "College of Medicine, University of Nigeria / University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu, Enugu State, Nigeria" - }, - { - "author_name": "Adedamola A. Dada", - "author_inst": "Federal Medical Centre, Ebute Metta, Lagos, Nigeria" - }, - { - "author_name": "Oliver C. Ezechi", - "author_inst": "Nigerian Institute of Medical Research, Lagos, Nigeria" - }, - { - "author_name": "Catherine O. Falade", - "author_inst": "University College Hospital, Ibadan; University of Nigeria Teaching, Oyo, Nigeria" - }, - { - "author_name": "Alex Horstein", - "author_inst": "Inventilator LLC, Providence, RI, USA" - }, - { - "author_name": "Idowu Olusola", - "author_inst": "University College Hospital, Ibadan; University of Nigeria Teaching, Oyo, Nigeria" - }, - { - "author_name": "Ifeoma Idigbe", - "author_inst": "Nigerian Institute of Medical Research, Lagos, Nigeria" - }, - { - "author_name": "Sunday Mogaj", - "author_inst": "Federal Medical Centre, Ebute Metta, Lagos, Nigeria" - }, - { - "author_name": "Aleem A. Morenikeji", - "author_inst": "Federal Medical Centre, Abeokuta; Ogun, Nigeria" - }, - { - "author_name": "Baba M. Musa", - "author_inst": "Department of Medicine, Bayero University Kano, Kano, Nigeria; Africa Center of Excellence in Population Health and Policy, Aminu Kano Teaching Hospital, Kano, " - }, - { - "author_name": "Nnamdi I. Nwosu", - "author_inst": "College of Medicine, University of Nigeria / University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu, Enugu State, Nigeria" - }, - { - "author_name": "Adenike A. Odewabi", - "author_inst": "Federal Medical Centre, Abeokuta; Ogun, Nigeria" - }, - { - "author_name": "Igho Ofokotun", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, USA" - }, - { - "author_name": "Gbenga Ogedegbe", - "author_inst": "Institute for Excellence in Health Equity, NYU Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Onome Ogueh", - "author_inst": "Delta State University Teaching Hospital, Oghara, Nigeria" - }, - { - "author_name": "Temitope O Oyewole", - "author_inst": "Federal Medical Centre, Abeokuta; Ogun, Nigeria" - }, - { - "author_name": "Adeshola I. Sotannde", - "author_inst": "Federal Medical Centre, Abeokuta; Ogun, Nigeria" - }, - { - "author_name": "Alan B. Steinbach", - "author_inst": "Joint Medical Program, UCB/UCSF, Berkeley, CA" - }, - { - "author_name": "Ifeoma I. Ulasi", - "author_inst": "College of Medicine, University of Nigeria / University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu, Enugu State, Nigeria" - }, - { - "author_name": "Kingsley N. Ukwaj", - "author_inst": "Department of Internal Medicine, College of Health Sciences, Ebonyi State University, Abakaliki/ Alex Ekwueme Federal University Teaching Hospital, Abakaliki, E" - }, - { - "author_name": "Uchechukwu S. Unigwe", - "author_inst": "Delta State University Teaching Hospital, Oghara, Nigeria" - }, - { - "author_name": "Olagoke A. Usman", - "author_inst": "College of Medicine, University of Nigeria / University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu, Enugu State, Nigeria" - }, - { - "author_name": "Cyril Uzoke", - "author_inst": "Delta State University Teaching Hospital, Oghara, Nigeria" - }, - { - "author_name": "Adesola Z. Musa", - "author_inst": "Federal Medical Centre, Ebute Metta, Lagos, Nigeria" - }, - { - "author_name": "Muyiwa K. Rotimi", - "author_inst": "Lagos University Teaching Hospital; Lagos, Nigeria" - }, - { - "author_name": "Iorhen E. Akase", - "author_inst": "Lagos University Teaching Hospital; Lagos, Nigeria" - }, - { - "author_name": "Wasiu L. Adeyemo", - "author_inst": "Lagos University Teaching Hospital; Lagos, Nigeria" - }, - { - "author_name": "Andre A. Fenton", - "author_inst": "Neurobiology of Cognition Laboratory, Center for Neural Science, New York University, New York, USA; Neuroscience Institute, NYU Langone Medical Center, New Yor" - }, - { - "author_name": "Babatunde L. Salako", - "author_inst": "Nigerian Institute of Medical Research, Lagos, Nigeria" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.31.22279450", "rel_title": "Risk averse reproduction numbers improve resurgence detection", @@ -236780,6 +239139,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.29.22279354", + "rel_title": "Coverage and correlates of COVID-19 vaccination among children aged 5-11 years in Alberta, Canada", + "rel_date": "2022-08-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279354", + "rel_abs": "Background and ObjectivesIn Alberta, Canada, the COVID-19 vaccination program for children aged 5-11 years opened on November 26, 2021. Our objectives were to determine the cumulative vaccine coverage, stratified by age, during the first seven months of vaccine availability, and investigate factors associated with vaccine uptake.\n\nMethodsThis retrospective cohort study used population-based administrative health data to assess COVID-19 vaccination coverage among children aged 5-11 years in Alberta, Canada. We determined cumulative vaccine coverage since the time of vaccine availability and used a modified Poisson regression to evaluate factors associated with vaccine uptake.\n\nResultsOf 377,753 eligible children, 43.8 % (n=165,429) received one or more doses of COVID-19 vaccine during the study period (11.2% received only one dose, while 32.5 % received 2 doses). Almost 90% of initial doses were received within the first two months of vaccine availability. Of those eligible for a second dose, only 75.1% (n=122,973) received it during the study time period. We found a step-wise relationship between increasing child age and higher vaccine coverage. Other factors associated with higher vaccine coverage included living in a neighborhood with higher income, in a more densely populated area, and in certain geographic health zones. Registration in a private school was associated with lower vaccine coverage.\n\nConclusionsMessaging around COVID-19 vaccine safety and need should be tailored to child age, rather than uniform across the 5-11 year age range. Opportunities for targeted vaccination interventions should be considered.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shannon E MacDonald", + "author_inst": "University of Alberta" + }, + { + "author_name": "Laura Reifferscheid", + "author_inst": "University of Alberta" + }, + { + "author_name": "Yuba Raj Paudel", + "author_inst": "University of Alberta" + }, + { + "author_name": "JOAN ROBINSON", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.26.22279283", "rel_title": "An effective volunteer community-based COVID-19 response program: the Vashon, WA Medical Reserve Corp experience", @@ -237464,69 +239854,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.08.29.505713", - "rel_title": "Receptor binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2", - "rel_date": "2022-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.29.505713", - "rel_abs": "Neutralization assays are experimental surrogates for the effectiveness of infection- or vaccine-elicited polyclonal antibodies and therapeutic monoclonal antibodies targeting SARS-CoV-2. However, the measured neutralization can depend on details of the experimental assay. Here we systematically assess how ACE2 expression in target cells affects neutralization by antibodies to different spike epitopes in lentivirus pseudovirus neutralization assays. For high ACE2-expressing target cells, receptor binding domain (RBD) antibodies account for nearly all neutralizing activity in polyclonal human sera. But for lower ACE2-expressing target cells, antibodies targeting regions outside the RBD make a larger (although still modest) contribution to serum neutralization. These serum-level results are mirrored for monoclonal antibodies: N-terminal domain (NTD) antibodies and RBD antibodies that do not compete for ACE2 binding incompletely neutralize on high ACE2-expressing target cells, but completely neutralize on cells with lower ACE2 expression. Our results show that ACE2 expression level in the target cells is an important experimental variable, and that high ACE2 expression emphasizes the role of a subset of RBD-directed antibodies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ariana Ghez Farrell", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Bernadeta Dadonaite", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Allison J Greaney", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Rachel Eguia", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Andrea N Loes", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Nicholas M Francko", - "author_inst": "University of Washington" - }, - { - "author_name": "Jennifer Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Juan Manuel Carreno", - "author_inst": "Mount Sinai School of Medicine" - }, - { - "author_name": "Anass Abbad", - "author_inst": "Mount Sinai School of Medicine" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Kenneth A Matreyek", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.08.30.505897", "rel_title": "BindingSiteAugmentedDTA: Enabling A Next-Generation Pipeline for Interpretable Prediction Models in Drug-Repurposing", @@ -238678,6 +241005,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.26.22279242", + "rel_title": "A survey of patient and public perceptions and awareness of SARS-CoV-2-related risks among participants in India and South Africa", + "rel_date": "2022-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.26.22279242", + "rel_abs": "A cross-sectional survey was performed among the adult population of participating countries, India and South Africa. The purpose of this study was to explore perceptions and awareness of SARS-CoV-2-related risks in the relevant countries. The main outcome measures were the proportion of participants aware of SARS-CoV-2, and their perception of infection risks.\n\nSelf-administered questionnaires were used to collect data via a web- and paper-based survey over three months. For data capturing, Microsoft Excel was employed, and descriptive statistics used for presenting data. Pearsons Chi-squared test was used to assess relationships between variables, and a p-value less than 0.05 was considered significant.\n\nThere were 844 respondents (India: n=660, South Africa: n=184; response rate 87.6%), with a 61.1% vs 38.3% female to male ratio. Post-high-school or university education was the lowest qualification reported by most respondents in India (77.3%) and South Africa (79.3%). Sources of information about the pandemic were usually media and journal publications (73.2%), social media (64.6%), family and friends (47.7%) and government websites (46.2%). Most respondents correctly identified infection prevention measures (such as physical distancing, mask use), with 90.0% reporting improved hand hygiene practices since the pandemic. Hesitancy or refusal to accept the SARS-CoV-2 vaccine was reported among 17.9% and 50.9% of respondents in India and South Africa, respectively. Reasons cited included rushed vaccine development and the futility of vaccines for what respondents considered a self-limiting flu-like illness.\n\nRespondents identified public health promotion measures for SARS-CoV-2. Reported hesitancy to the up-take of SARS-CoV-2 vaccines was much higher in South Africa. Vaccination campaigns should consider robust public engagement and contextually fit communication strategies with multimodal, participatory online and offline initiatives to address public concerns, specifically towards vaccines developed for this pandemic and general vaccine hesitancy.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Oluchi N Mbamalu", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Surya Surendran", + "author_inst": "The George Institute for Global Health India" + }, + { + "author_name": "Vrinda Nampoothiri", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Candice Bonaconsa", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Fabia Edathadathil", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Nina Zhu", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Vanessa Carter", + "author_inst": "Health Communication and Social Media" + }, + { + "author_name": "Helen Lambert", + "author_inst": "University of Bristol Medical School" + }, + { + "author_name": "Carolyn Tarrant", + "author_inst": "University of Leicester Department of Health Sciences" + }, + { + "author_name": "Raheelah Ahmad", + "author_inst": "City University of London" + }, + { + "author_name": "Adrian Brink", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Ebrahim Steenkamp", + "author_inst": "University of Cape Town Department of Statistical Sciences" + }, + { + "author_name": "Alison Holmes", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Sanjeev Singh", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Esmita Charani", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Marc Mendelson", + "author_inst": "University of Cape Town Faculty of Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.25.22279238", "rel_title": "Evaluation of Secondary Chemistry due to Disinfection of Indoor Air with Germicidal Ultraviolet Lamps", @@ -239478,73 +241884,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.08.22.22278930", - "rel_title": "Correlation of patient serum IgG, IgA and IgM antigen binding with COVID-19 disease severity using multiplexed SARS-CoV-2 antigen microarray and maintained relative IgA and IgM antigen binding over time", - "rel_date": "2022-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22278930", - "rel_abs": "Zoonotic spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans in December 2019 caused the coronavirus disease 2019 (COVID-19) pandemic. Serological monitoring is critical for detailed understanding of individual immune responses to infection and protection to guide clinical therapeutic and vaccine strategies. We developed a high throughput multiplexed SARS-CoV-2 antigen microarray incorporating spike (S) and nucleocapsid protein (NP) and fragments expressed in various hosts which allowed simultaneous assessment of serum IgG, IgA, and IgM responses. Antigen glycosylation influenced antibody binding, with S glycosylation generally increasing and NP glycosylation decreasing binding. Purified antibody isotypes demonstrated a binding pattern and intensity that differed from the same isotype in the presence of other isotypes in whole serum, probably due to competition. Using purified antibody isotypes from naive Irish COVID-19 patients, we correlated antibody isotype binding to different panels of antigens with disease severity, with significance for binding to the S region S1 expressed in insect cells (S1 Sf21) for all three antibody isotypes. Assessing longitudinal response for constant concentrations of antibody isotypes for a subset of patients demonstrated that while the relative proportion of antigen-specific IgGs decreased over time for severe disease, the relative proportion of antigen-specific IgA binding remained at the same magnitude at 5 and 9 months post-first symptom onset. Further, the relative proportion of IgM binding decreased for S antigens but remained the same for NP antigens. This may support antigen specific serum IgA and IgM playing a role in maintaining longer-term protection, of importance for developing and assessing vaccine strategies. Overall, these data demonstrate the multiplexed platform as a sensitive and useful platform for expanded humoral immunity studies, allowing detailed elucidation of antibody isotypes response against multiple antigens. This approach will be useful for monoclonal antibody therapeutic studies and screening of donor polyclonal antibodies for patient infusions.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Marie Le Berre", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Terezia Paulovcakova", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Carolina De Marco Verissimo", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Sean Doyle", - "author_inst": "Maynooth University" - }, - { - "author_name": "John P. Dalton", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Claire Masterson", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Eduardo Ribes Martinez", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Laura Walsh", - "author_inst": "University College Dublin" - }, - { - "author_name": "Conor Gormley", - "author_inst": "Royal College of Surgeons in Ireland" - }, - { - "author_name": "John G Laffey", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Bairbre McNicholas", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Andrew J Simpkin", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "Michelle Kilcoyne", - "author_inst": "National University of Ireland Galway" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.23.22278585", "rel_title": "Nirmatrelvir/ritonavir and molnuipiravir in the treatment of mild/moderate COVID-19: results of a real-life study", @@ -240412,6 +242751,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.23.505031", + "rel_title": "New Insights into How JUUL Electronic Cigarette Aerosols and Aerosol Constituents Affect SARS-CoV-2 Infection of Human Bronchial Epithelial Cells", + "rel_date": "2022-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.23.505031", + "rel_abs": "BackgroundThe relationship between the use of tobacco products and SARS-CoV-2 infection is poorly understood and controversial. Most studies have been done with tobacco cigarettes, while few have examined the effect of electronic cigarettes (ECs) on SARS-CoV-2 infection. We tested the hypothesis that EC fluids and aerosols with high concentrations of nicotine promote SARS-COV-2 infection by increasing viral entry into human respiratory epithelial cells.\n\nMethodsResponses of BEAS-2B cells to authentic JUUL aerosols or their individual constituents (propylene glycol (PG)/vegetable glycerin (VG) and nicotine) were compared using three exposure platforms: submerged culture, air-liquid-interface (ALI) exposure in a cloud chamber, and ALI exposure in a Cultex(R) system, which produces authentic heated EC aerosols. SARS-CoV-2 infection machinery was assessed using immunohistochemistry and Western blotting. Specifically, the levels of the SARS-CoV-2 receptor ACE2 (angiotensin converting enzyme 2) and a spike modifying enzyme, TMPRSS2 (transmembrane serine protease 2), were evaluated. Following each exposure, lentivirus pseudoparticles with spike protein and a green-fluorescent reporter were used to test viral penetration and the susceptibility of BEAS-2B cells to infection.\n\nResultsNicotine, EC fluids, and authentic JUUL aerosols increased both ACE2 levels and TMPRSS2 activity, which in turn increased viral particle entry into cells. While most data were in good agreement across the three exposure platforms, cells were more responsive to treatments when exposed at the ALI in the Cultex system, even though the exposures were brief and intermittent. In the Cultex system, PG/VG, PG/VG/nicotine, and JUUL aerosols significantly increased infection above clean air controls. However, both the PG/VG and JUUL treatments were significantly lower than nicotine/PG/VG. PG/VG increased infection only in the Cultex(R) system, which produces heated aerosol.\n\nConclusionOur data are consistent with the conclusion that authentic JUUL aerosols or their individual constituents (nicotine or PG/VG) increase SARS-CoV-2 infection. The strong effect produced by nicotine was modulated in authentic JUUL aerosols, demonstrating the importance of studying mixtures and aerosols from actual EC products. These data support the idea that vaping increases the likelihood of contracting COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rattapol Phandthong", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Man Wong", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Ann Song", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Teresa Martinez", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Prue Talbot", + "author_inst": "University of California, Riverside" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.08.24.22279160", "rel_title": "Comparing the Safety and Immunogenicity of homologous (Sputnik V) and heterologous (BNT162B2) COVID-19 prime-boost vaccination", @@ -241344,45 +243718,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.18.22278786", - "rel_title": "Nation-wide participation in FIT-based colorectal cancer screening in Denmark during the COVID-19 pandemic: An observational study", - "rel_date": "2022-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.18.22278786", - "rel_abs": "BackgroundWorldwide, most colorectal cancer screening programmes were paused at the start of the COVID-19 pandemic, whilst the Danish faecal immunochemical test (FIT)-based programme continued without pausing. We examined colorectal cancer screening participation and compliance with subsequent colonoscopy in Denmark throughout the pandemic.\n\nMethodsWe used data from the Danish Colorectal Cancer Screening Database among individuals aged 50-74 years old invited to participate in colorectal cancer screening from 2018-2021 combined with population-wide registries. Using a generalised linear model, we estimated prevalence ratios (PR) and 95% confidence intervals (CI) of colorectal cancer screening participation within 90 days since invitation and compliance with colonoscopy within 60 days since a positive FIT test during the pandemic in comparison with the previous years adjusting for age, month and year of invitation.\n\nResultsAltogether, 3,133,947 invitations were sent out to 1,928,725 individuals and there were 94,373 positive FIT tests (in 92,848 individuals) during the study period. Before the pandemic, 60.7% participated in screening within 90 days. A minor reduction in participation was observed at the start of the pandemic (PR=0.95; 95% CI: 0.94-0.96 in pre-lockdown and PR=0.85; 95% CI: 0.85-0.86 in 1st lockdown) corresponding to a participation rate of 54.9% during pre-lockdown and 53.0% during 1st lockdown. This was followed by a 5-10% increased participation in screening corresponding to a participation rate of up to 64.9%. The largest increase in participation was observed among 55-59 year olds, individuals living alone or cohabiting and immigrants. The compliance with colonoscopy within 60 days was 89.9% before the pandemic. A slight reduction was observed during 1st lockdown (PR=0.96; 95% CI: 0.93-0.98), where after it resumed to normal levels.\n\nConclusionsParticipation in the Danish FIT-based colorectal cancer screening programme and subsequent compliance to colonoscopy after a positive FIT result was only slightly affected by the COVID-19 pandemic.\n\nFundingThe study was funded by the Danish Cancer Society Scientific Committee (grant number R321-A17417) and the Danish regions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tina Bech Olesen", - "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" - }, - { - "author_name": "Henry Jensen", - "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" - }, - { - "author_name": "Henrik M\u00f8ller", - "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" - }, - { - "author_name": "Jens Winther Jensen", - "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" - }, - { - "author_name": "Berit Andersen", - "author_inst": "University Research Clinic for Cancer Screening, Department of Public Health Programmes, Randers Regional Hospital, Aarhus, Denmark and Department of Clinical " - }, - { - "author_name": "Morten Rasmussen", - "author_inst": "The Colorectal Cancer Screening Programme, the Capital Region and Abdominal Center, Bispebjerg Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.22.22278955", "rel_title": "Rates of COVID-19-Associated Hospitalization in Immunocompromised Individuals in Omicron-era: A Population-Based Observational Study Using Surveillance Data in British Columbia, Canada", @@ -242294,6 +244629,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.21.22279044", + "rel_title": "SARS-CoV-2 IgM and IgG serology and clinical outcomes in COVID-19 patients", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279044", + "rel_abs": "BackgroundThe SARS-CoV-2 virus has become pandemic for the last 2 years. Inflammatory response to the virus leads to organ dysfunction and death. Predicting the severity of inflammatory response helps in managing critical patients using serology tests IgG and IgM. We conducted a longitudinal study to correlate serum SARS-CoV-2 IgM and IgG serology with clinical outcomes in COVID-19 patients.\n\nMethodsWe analyzed patient data from March to December of 2020 for those who were admitted at AIIMS Rishikesh. Clinical and laboratory data of these patients were collected from the e-hospital portal and analysed. Correlation was seen with clinical outcomes and was assessed using MS Excel 2010 and SPSS software.\n\nResultsOut of 494 patients, the mean age of patients was 48.95 {+/-} 16.40 years and there were more male patients in the study (66.0%). The patients were classified into 4 groups; mild-moderate 328 (67.1%), severe 131 (26.8%) and critical 30 (6.1%). The mean duration from symptom onset to serology testing was 19.87 {+/-} 30.53 days. In-hospital mortality was observed in 25.1% patients. The seropositivity rate (i.e., either IgG or IgM >10 AU) was 50%. There was a significant difference between the 2 groups in terms of IgM Levels (AU/mL) (W = 33428.000, p = <0.001) and IgG Levels (AU/mL) (W = 39256.500, p = <0.001), with the median IgM/ IgG Levels (AU/mL) being highest in the RT-PCR-Positive group. There was no significant difference between the groups in terms of IgM Levels and IgG levels with all other clinical outcomes (disease severity, septic shock, Intensive care admission, mechanical ventilation and mortality).\n\nConclusionSerology (IgM and IgG) levels are high in RTPCR positive group compared to clinical COVID-19. However, serology cannot be useful for the prediction of disease outcomes except few situations. The study also highlights the importance of doing serology at a particular time as antibody titres vary with the duration of the disease.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mohan S", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Pratap Kumar", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Vikram Jain", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Rohit Raina", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Sarama Saha", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Vivekandan S", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Balram J Omar", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.19.22278986", "rel_title": "Increased adverse events following third dose of BNT162b2/Pfizer vaccine in those with previous COVID-19, but not with concurrent influenza vaccine.", @@ -243006,61 +245388,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.18.22278764", - "rel_title": "Impact of vaccination with SCB-2019 COVID-19 vaccine on transmission of SARS-CoV-2 infection: a household contact study in the Philippines", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.18.22278764", - "rel_abs": "BackgroundAn exploratory household transmission study was nested in SPECTRA, the phase 2/3 efficacy study of the adjuvanted recombinant protein-based COVID-19 vaccine SCB-2019. We compared occurrence of confirmed COVID-19 infections between households and household contacts of infected SPECTRA participants who were either placebo or SCB-2019 recipients.\n\nMethodsSPECTRA trial participants at eight study sites in the Philippines who developed rRT-PCR-confirmed COVID-19 were contacted by a study team blinded to assignment of index cases to vaccine or placebo groups to enroll in this household transmission study. Enrolled households and household contacts were monitored for three weeks using rRT-PCR and rapid antigen testing to detect new COVID-19 infections.\n\nResultsObservation of the households of 154 eligible COVID-19 index cases, 130 symptomatic and 24 asymptomatic at diagnosis, revealed household secondary attack rates for any COVID-19 infection of SCB-2019 index cases of 0.76% (90% CI: 0.15-3.90) compared with 5.88% (90% CI: 3.20-10.8) in placebo index case households, a relative risk reduction of 79% (90% CI: -28-97). The relative risk reduction of symptomatic COVID-19 was 84% (90% CI: 28-97) for household contacts of all COVID-19 infected index cases, and 80% (90% CI: 7-96) for household contacts of index cases with symptomatic COVID-19.\n\nConclusionsIn this prospective household contact study vaccination with SCB-2019 reduced SARS-CoV-2 transmission in households, so decreasing infections of household contacts, compared with placebo.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Birkneh Tilahun Tadesse", - "author_inst": "International Vaccine Institute, Seoul, Republic of Korea" - }, - { - "author_name": "Lulu Bravo", - "author_inst": "University of the Philippines Manila, Ermita, Manila, The Philippines" - }, - { - "author_name": "Florian Marks", - "author_inst": "International Vaccine Institute, Seoul, Republic of Korea" - }, - { - "author_name": "Asma Binte Aziz", - "author_inst": "International Vaccine Institute, Seoul, Republic of Korea" - }, - { - "author_name": "Young AE You", - "author_inst": "International Vaccine Institute, Seoul, Republic of Korea" - }, - { - "author_name": "Jonathan D Sugimoto", - "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutchinson Research Institute, Seattle, WA, USA" - }, - { - "author_name": "Ping Li", - "author_inst": "Clover Biopharmaceuticals, Cambridge, MA, USA" - }, - { - "author_name": "Joyce Garcia", - "author_inst": "Clover Biopharmaceuticals, Cambridge, MA, USA" - }, - { - "author_name": "Frank Rockhold", - "author_inst": "Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA" - }, - { - "author_name": "Ralf Clemens", - "author_inst": "International Vaccine Institute, Seoul, Republic of Korea" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.19.22278987", "rel_title": "Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England", @@ -244076,6 +246403,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.08.17.504362", + "rel_title": "Ancestral lineage of SARS-CoV-2 is more stable in human biological fluids than Alpha, Beta and Omicron variants of concern", + "rel_date": "2022-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.17.504362", + "rel_abs": "SARS-CoV-2 is a zoonotic virus which was first identified in 2019, and has quickly spread worldwide. The virus is primarily transmitted through respiratory droplets from infected persons; however, the virus-laden excretions can contaminate surfaces which can serve as a potential source of infection. Since the beginning of the pandemic, SARS-CoV-2 has continued to evolve and accumulate mutations throughout its genome leading to the emergence of variants of concern (VOCs) which exhibit increased fitness, transmissibility, and/or virulence. However, the stability of SARS-CoV-2 VOCs in biological fluids has not been thoroughly investigated so far. The aim of this study was to determine and compare the stability of different SARS-CoV-2 strains in human biological fluids. Here, we demonstrate that the ancestral strain of Wuhan-like lineage A was more stable than the Alpha VOC B.1.1.7, and the Beta VOC B.1.351 strains in human liquid nasal mucus and sputum. In contrast, there was no difference in stability among the three strains in dried biological fluids. Furthermore, we also show that the Omicron VOC B.1.1.529 strain was less stable than the ancestral Wuhan-like strain in liquid nasal mucus. These studies provide insight into the effect of the molecular evolution of SARS-CoV-2 on environmental virus stability, which is important information for the development of countermeasures against SARS-CoV-2.\n\nImportanceGenetic evolution of SARS-CoV-2 leads to the continuous emergence of novel variants, posing a significant concern to global public health. Five of these variants have been classified so far into variants of concern (VOCs); Alpha, Beta, Gamma, Delta, and Omicron. Previous studies investigated the stability of SARS-CoV-2 under various conditions, but there is a gap of knowledge on the survival of SARS-CoV-2 VOCs in human biological fluids which are clinically relevant. Here, we present evidence that Alpha, Beta, and Omicron VOCs were less stable than the ancestral Wuhan-like strain in human biological fluids. Our findings highlight the potential risk of contaminated human biological fluids in SARS-CoV-2 transmission and contribute to the development of countermeasures against SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Taeyong Kwon", + "author_inst": "Kansas State University" + }, + { + "author_name": "Natasha N Gaudreault", + "author_inst": "Kansas State University" + }, + { + "author_name": "David Meekins", + "author_inst": "Kansas State University" + }, + { + "author_name": "Chester McDowell", + "author_inst": "Kansas State Univeristy" + }, + { + "author_name": "Konner Cool", + "author_inst": "Kansas State University" + }, + { + "author_name": "Juergen A Richt", + "author_inst": "Kansas State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.17.504313", "rel_title": "Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape", @@ -244768,57 +247134,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.15.22278798", - "rel_title": "Development and use of a method based on the anti-N reactivity of longitudinal samples to better estimate SARS-CoV-2 seroprevalence in a vaccinated population", - "rel_date": "2022-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.15.22278798", - "rel_abs": "BackgroundEmerging evidence suggests that COVID-19 vaccination decreases the sensitivity of anti-nucleocapsid (N) serologies, making them less reliable to assess recently-acquired infections. We therefore developed and tested a new approach based on the ratio of the anti-N absorbance of longitudinal samples to overcome this limitation.\n\nMethodsPreviously vaccinated repeat plasma donors provided at least one pre-infection (reference) and one post-infection (test) sample. All samples were tested using an in-house anti-N ELISA. Seropositivity was determined based on the ratio between the anti-N absorbance of the test and reference samples. The ratio approach was tested in a real-world setting during three cross-sectional serosurveys carried out among plasma donors in Quebec, Canada.\n\nResultsUsing a cut-off ratio of 1.5, the approach had a sensitivity of 95.2% among the 248 previously vaccinated and infected donors compared with 63.3% for the conventional approach. When tested in a real-world setting, the ratio-based approach yielded an adjusted seroprevalence of 27.4% (95% confidence interval [CI]=23.8%-30.9%) at the latest time point considered, compared to 15.1% (95% CI=12.2%-18.0%) for the conventional approach.\n\nConclusionsThis article describes a new and highly-sensitive approach that captures a significantly greater proportion of vaccinated individuals with a recent history of SARS-CoV-2 infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ren\u00e9e Bazin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Samuel Rochette", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Jos\u00e9e Perreault", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Marie-Jos\u00e9e Fournier", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Yves Gr\u00e9goire", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Am\u00e9lie Boivin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Antoine Lewin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Marc Germain", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Christian Renaud", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.12.22278203", "rel_title": "Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington: A Test-Negative Design Study of the Greater Seattle Coronavirus Assessment Network", @@ -245754,6 +248069,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.13.22278740", + "rel_title": "Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations", + "rel_date": "2022-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.13.22278740", + "rel_abs": "A multitude of demographic, health, and genetic factors are associated with the risk of developing severe COVID-19 following infection by the SARS-CoV-2. There is a need to perform studies across human societies and to investigate the full spectrum of genetic variation of the virus. Using data from 869 COVID-19 patients in Bahrain between March 2020 and March 2021, we analyzed paired viral sequencing and non-genetic host data to understand host and viral determinants of severe COVID-19. We estimated the effects of demographic variables specific to the Bahrain population and found that the impact of health factors are largely consistent with other populations. To extend beyond the common variants of concern in the Spike protein analyzed by previous studies, we used a viral burden approach and detected a protective effect of low-frequency missense viral mutations in the RNA-dependent RNA polymerase (Pol) gene on disease severity. Our results contribute to the survey of severe COVID-19 in diverse populations and highlight the benefits of studying rare viral mutations.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Evan M Koch", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Justin Du", + "author_inst": "Yale University" + }, + { + "author_name": "Michelle Dressner", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Hashmeya Erahim Alwasti", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Zahra Al Taif", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Fatima Shehab", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Afaf Merza Mohamed", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Amani Alhajeri", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Amna Alawadhi", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Nabeel Almoamen", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Khulood Ashoor", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Sara Hasan", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Amjad Ghanem", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Alireza Haghighi", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Shamil Sunyaev", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Maha Farhat", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.12.22278726", "rel_title": "BNT162b2 induced neutralizing and non-neutralizing antibody functions against SARS-CoV-2 diminish with age", @@ -246366,73 +248760,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.12.503154", - "rel_title": "CD98 is critical for a conserved inflammatory response to diverse injury stimuli relevant to IPF exacerbations and COVID pneumonitis", - "rel_date": "2022-08-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.12.503154", - "rel_abs": "Progressive fibrosing interstitial lung diseases (PFILDs) cause substantial morbidity and mortality. Antifibrotic agents slow progression, but most of the clinical need remains unmet. The archetypal PFILD is idiopathic pulmonary fibrosis (IPF). Chronic progression is driven by transforming growth factor (TGF-){beta}1 signalling. It is punctuated by inflammatory flares known as acute exacerbations (AE-IPF), which are associated with accelerated decline and high mortality. We hypothesized that acute injury responses underlying exacerbations and the mechanisms of chronic fibrosis overlap at the molecular level, via a cell surface assembly nucleated by galectin-3 that we term the gal-3-fibrosome. We focused upon a putative pro-inflammatory galectin-3 ligand, the CD98:integrin complex. Our data indicate CD98 and {beta}1-integrin co-localise with galectin-3 within epithelial cells in IPF lung tissue, and within 40 nm in human lung tissue treated with TGF-{beta}1 compared to controls. CD98 is required for interleukin (IL-)6 and IL-8 responses to biochemical and biophysical conditions mimicking stimuli of AE-IPF in vivo, ex vivo and in cells, and for an interstitial neutrophilic response in a mouse model. We demonstrate this pathway progresses via intracellular influx of Ca2+ mediated by TRPV4, and NF-{kappa}B activation, operating in positive feedback. Lastly we show the CD98- and galectin-3-dependence of IL-6 and IL-8 responses to the SARS-CoV-2 spike protein receptor binding domain and the conservation of this response pattern between lung epithelial cells and monocyte-derived macrophages. Taken together our findings identify CD98 as a key mediator of both pro-fibrotic and acute inflammatory responses in the lung with relevance to AE- and chronic progression of IPF, and the priming of fibrotic lungs for acute inflammatory responses. They similarly implicate CD98 and galectin-3 as mediators of COVID pneumonitis and worse outcomes in ILD patients with COVID.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Panayiota Stylianou", - "author_inst": "University of Leicester" - }, - { - "author_name": "Mohammed Azim Miah", - "author_inst": "University of Leicester" - }, - { - "author_name": "Omeed Darweesh", - "author_inst": "University of Leicester" - }, - { - "author_name": "Alison Mackinnon", - "author_inst": "Galecto, Inc" - }, - { - "author_name": "Katy M Roach", - "author_inst": "University of Leicester" - }, - { - "author_name": "Charles J Hitchman", - "author_inst": "University of Leicester" - }, - { - "author_name": "Oksana Gonchar", - "author_inst": "University of Leicester" - }, - { - "author_name": "Stephen Thorpe", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Richard Haigh", - "author_inst": "University of Leicester" - }, - { - "author_name": "Jessica Beasley", - "author_inst": "University of Leicester" - }, - { - "author_name": "Michael R Barer", - "author_inst": "University of Leicester" - }, - { - "author_name": "Peter H Bradding", - "author_inst": "University of Leicester" - }, - { - "author_name": "Martin M Knight", - "author_inst": "Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2022.08.13.503846", "rel_title": "Monkeypox virus shows potential to infect a diverse range of native animal species across Europe, indicating high risk of becoming endemic in the region", @@ -247600,6 +249927,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.08.08.22278550", + "rel_title": "Cohort Study Protocol of the Brazilian Collaborative Research Network on COVID-19: strengthening WHO global data", + "rel_date": "2022-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278550", + "rel_abs": "IntroductionWith the COVID-19 pandemic, hospitals in low-income countries were faced with a triple challenge. First, a large number of patients required hospitalization because of the infections more severe symptoms. Second, there was a lack of systematic and broad testing policies for early identification of cases. Third, there were weaknesses in the integration of information systems, which led to the need to search for available information from the hospital information systems. Accordingly, it is also important to state that relevant aspects of COVID-19s natural history had not yet been fully clarified. The aim of this research protocol is to present the strategies of a Brazilian network of hospitals to perform systematized data collection on COVID-19 through the World Health Organization (WHO) Platform.\n\nMethods and AnalysisThis is a multicenter project among Brazilian hospitals to provide data on COVID-19 through the WHO global platform, which integrates patient care information from different countries. From October 2020 to March 2021, a committee worked on defining a flowchart for this platform, specifying the variables of interest, data extraction standardization and analysis.\n\nEthics and DisseminationThis protocol was approved by the Research Ethics Committee (CEP) of the Research Coordinating Center of Brazil (CEP of the Hospital Nossa Senhora da Conceicao), on January 29, 2021, under approval No. 4.515.519 and by the National Research Ethics Commission (CONEP), on February 5, 2021, under approval No. 4.526.456. The project results will be explained in WHO reports and published in international peer-reviewed journals, and summaries will be provided to the funders of the study.\n\nStrengths and limitations of this studyAs the study involves a convenience and non-probabilistic sample of patients hospitalized in health units, it may not represent the population of patients with COVID-19 hospitalized in the country. However, the information generated by this research can serve as a basis for the development of maps of the evolution of SARS-CoV-2 infection and public policies to face pandemics. It is a study that uses secondary data, and therefore, information bias may occur, but on the other hand, it has a low cost and facilitates a population-based study with national coverage.\n\nArticle SummaryThis is a multicenter project among Brazilian hospitals to provide data on COVID-19 through the WHO global platform.\n\nIt is expected to deepen knowledge about the pandemic scenario and help hospital institutions to develop preventive measures, health service protocols and strengthen the training of teams in the existing complications.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Fernando Anschau", + "author_inst": "Conceicao Hospitalar Group" + }, + { + "author_name": "Natalia Del' Angelo Aredes", + "author_inst": "Universidade Federal de Goias, Nursing School Goiania, Goias, BR" + }, + { + "author_name": "Ludovic Reveiz", + "author_inst": "Pan American Health Organization, DC, USA" + }, + { + "author_name": "Monica Padilla", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Rosane de Mendonca Gomes", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Wellington Mendes Carvalho", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Fernando Antonio Gomes Leles", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Fernanda Baeumle Reese", + "author_inst": "Complexo Hospitalar do Trabalhador Curitiba, PR, BR" + }, + { + "author_name": "Andre Hostilio Hubert", + "author_inst": "Complexo Hospitalar do Trabalhador Curitiba, Parana, BR" + }, + { + "author_name": "Elisandrea Sguario Kemper", + "author_inst": "Hospital da Crianca de Brasilia Distrito Federal, BR" + }, + { + "author_name": "Renilson Rehem de Souza", + "author_inst": "Hospital da Crianca de Brasilia, Distrito Federal, BR" + }, + { + "author_name": "Cristiane Feitosa Salviano", + "author_inst": "Hospital da Crianca de Brasilia, DF, BR" + }, + { + "author_name": "Hevelin Silveira e Silva", + "author_inst": "Hospital da Crianca de Brasilia, DF, BR" + }, + { + "author_name": "Eduardo Barbosa Coelho", + "author_inst": "Brazilian Company of Hospital Services Belo Horizonte, Minas Gerais, BR" + }, + { + "author_name": "Giuseppe Cesare Gatto", + "author_inst": "Brazilian Company of Hospital Services Belo Horizonte, Minas Gerais, BR" + }, + { + "author_name": "Rafael Freitas de Morais", + "author_inst": "Brazilian Company of Hospital Services Brasilia, Distrito Federal, BR" + }, + { + "author_name": "Leonardo Nunes Alegre", + "author_inst": "Brazilian Company of Hospital Services Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Rodrigo Citton Padilha dos Reis", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Joaquim Francisco dos Santos Neto", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Cesar Perdomo Purper", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Veridian Baldon dos Santos", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Andressa Fontoura Garbini", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Rafaela dos Santos Charao de Almeida,", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Bruna Donida", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Rogerio Farias Bitencourt", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Luciane Kopittke", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Fernanda Costa dos Santos", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Raquel Lutkmeier", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Daniela dos Reis Carazai", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Virginia Angelica Silveira Reis", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Flavio Clemente Deulefeu,", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Fernanda Gadelha Severino", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Jose Gustavo da Costa Neto", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Nirvania do Vale Carvalho", + "author_inst": "Health Department of the State of Piaui, Hospital Getulio Vargas Teresina, Piaui, BR" + }, + { + "author_name": "Andre Jamson Rocha de Andrade", + "author_inst": "Health Department of the State of Piaui, Hospital Getulio Vargas Teresina, Piaui, BR" + }, + { + "author_name": "Adriana Melo Teixeira", + "author_inst": "Brazilian Ministry of Health, Department of Hospital, Home, and Emergency Care (DAHU) of the Specialized Health Care Office (SAES) Brasilia, Distrito Federal, B" + }, + { + "author_name": "Olavo Braga Neto", + "author_inst": "Brazilian Ministry of Health, Department of Hospital, Home, and Emergency Care (DAHU) of the Specialized Health Care Office (SAES) Brasilia, Distrito Federal, B" + }, + { + "author_name": "Gabriel Cardozo Muller", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Ricardo de Souza Kuchenbecker", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.05.22278487", "rel_title": "Excess mortality in Cyprus during the COVID-19 pandemic and its lack of association with vaccination rates", @@ -248480,113 +250978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.08.22278494", - "rel_title": "Brief Report: Impact of age and SARS-CoV-2 breakthrough infection on humoral immune responses after three doses of COVID-19 mRNA vaccine", - "rel_date": "2022-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278494", - "rel_abs": "BackgroundLonger-term immune response data after three doses of COVID-19 mRNA vaccine remain limited, particularly among older adults and following Omicron breakthrough infection.\n\nMethodsWe quantified wild-type- and Omicron-specific serum IgG levels, ACE2 displacement activities and live virus neutralization up to six months post-third dose in 116 adults aged 24-98 years who remained COVID-19-naive or experienced their first SARS-CoV-2 infection during this time.\n\nResultsAmong 78 participants who remained COVID-19-naive throughout follow-up, wild-type- and Omicron BA.1-specific IgG concentrations were comparable between younger and older adults, though BA.1-specific responses were consistently significantly lower than wild-type-specific responses in both groups. Wild-type- and BA.1-specific IgG concentrations declined at similar rates among COVID-19-naive younger and older adults, with median half-lives ranging from 69-78 days. Antiviral antibody function declined substantially over time in COVID-19-naive individuals, particularly older adults: by six months, BA.1-specific neutralization was undetectable in 96% of older adults, versus 56% of younger adults. SARS-CoV-2 infection, experienced by 38 participants, boosted IgG levels and neutralization above those induced by vaccination alone. Nevertheless, BA.1-specific neutralization remained significantly lower than wild-type, with BA.5-specific neutralization lower still.\n\nConclusionsOur findings underscore the immune benefits of third COVID-19 mRNA vaccine doses in adults of all ages, but rapid decline of Omicron-specific neutralization activity in COVID-19-naive individuals, particularly among older adults, demonstrates the need for fourth doses within 3-6 months to maintain systemic responses. Individuals who experienced SARS-CoV-2 breakthrough infection post-third vaccine dose however can likely delay a fourth dose beyond this timeframe.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Francis M Mwimanzi", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Hope R Lapointe", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Canada" - }, - { - "author_name": "Peter K. Cheung", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada; British Columbia Centre for Excellence in HIV/AIDS, Canada" - }, - { - "author_name": "Yurou Sang", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Fatima Yaseen", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Rebecca Kalikawe", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Sneha Datwani", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Laura Burns", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada" - }, - { - "author_name": "Landon Young", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada" - }, - { - "author_name": "Victor Leung", - "author_inst": "Department of Medicine, University of British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Canada" - }, - { - "author_name": "Siobhan Ennis", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Chanson J Brumme", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Canada; Department of Medicine, University of British Columbia, Canada" - }, - { - "author_name": "Julio S.G. Montaner", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Canada; Department of Medicine, University of British Columbia, Canada" - }, - { - "author_name": "Winnie Dong", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "Department of Pathology and Laboratory Medicine, University of British Columbia, Canada; British Columbia Centre for Disease Control Public Health Laboratory, V" - }, - { - "author_name": "Christopher Fong Jen Lowe", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Cana" - }, - { - "author_name": "Mari L. DeMarco", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Cana" - }, - { - "author_name": "Daniel T. Holmes", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Cana" - }, - { - "author_name": "Janet Simons", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Cana" - }, - { - "author_name": "Masahiro Niikura", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada" - }, - { - "author_name": "Marc G. Romney", - "author_inst": "Division of Medical Microbiology and Virology, St. Pauls Hospital, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Cana" - }, - { - "author_name": "Zabrina L. Brumme", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada; British Columbia Centre for Excellence in HIV/AIDS, Canada" - }, - { - "author_name": "Mark A Brockman", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Canada; British Columbia Centre for Excellence in HIV/AIDS, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.09.22278329", "rel_title": "Efficacy and safety of convalescent plasma to treat hospitalised COVID-19 patients with or without underlying immunodeficiency: a randomized clinical trial", @@ -249990,6 +252381,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.08.503231", + "rel_title": "Vitamin B12 attenuates leukocyte inflammatory signature in COVID-19 via methyl-dependent changes in epigenetic marks", + "rel_date": "2022-08-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.08.503231", + "rel_abs": "COVID-19 induces chromatin remodeling in host immune cells, and it had previously been shown that vitamin B12 downregulates some inflammatory genes via methyl-dependent epigenetic mechanisms. In this work, whole blood cultures from moderate or severe COVID-19 patients were used to assess the potential of B12 as adjuvant drug. The vitamin normalized the expression of a panel of inflammatory genes still dysregulated in the leukocytes despite glucocorticoid therapy during hospitalization. B12 also increased the flux of the sulfur amino acid pathway, raising the bioavailability of methyl. Accordingly, B12-induced downregulation of CCL3 strongly and negatively correlated with the hypermethylation of CpGs in its regulatory regions. Transcriptome analysis revealed that B12 attenuates the effects of COVID-19 on most inflammation-related pathways affected by the disease. As far as we are aware, this is the first study to demonstrate that pharmacological modulation of epigenetic marks in leukocytes favorably regulates central components of COVID-19 physiopathology.\n\nTeaserB12 has great potential as an adjuvant drug for alleviating inflammation in COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Vanessa C Silva", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Marina S Oliveira", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Barbara V O Prado", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" + }, + { + "author_name": "Cristianne G Cardoso", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" + }, + { + "author_name": "Anna C M Salim", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Gloria R Franco", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Saionara C Francisco", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" + }, + { + "author_name": "Roney S Coimbra", + "author_inst": "FIOCRUZ" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.08.09.503270", "rel_title": "Acetylsalicylic acid and Salicylic acid inhibit SARS-CoV-2 replication in precision-cut lung slices", @@ -250650,65 +253088,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.07.22278512", - "rel_title": "Understanding the impact of COVID-19 risk perceptions on mitigation behaviors: A mixed methods approach using survey instruments and serious games", - "rel_date": "2022-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278512", - "rel_abs": "COVID-19 risk mitigation behavior, including social distancing and mask wearing, was a principal factor influencing the spread of COVID-19. Yet this behavior, and its association with COVID-19 perceptions and beliefs, is poorly understood. Here we used a mixed methods approach combining serious game data with survey instruments to describe relationships between perceptions and behavior. Using a series of survey questions, participants were described along a spectrum denoting their perception of their susceptibility to COVID-19 associated with a list of activities. Afterwards, participants engaged with a serious game to examine behavioral responses to scenarios involving shopping at a grocery store and going to a park during simulated pandemic conditions. Messages describing the simulated infection risk were shown to drive many behavioral decisions. Another significant correlate, derived from survey results, was the participants perception of susceptibility associated with various activities for acquiring the COVID-19 infection. Individuals that perceived every day activities, such as grocery shopping, as unlikely to lead to a COVID-19 infection spent more time near others in the game-simulated grocery store environment compared to those that consider such activities as risky. Additionally, we found that participant behavior became increasingly risky as time progresses if they were lucky enough not to experience an infection. This reflects behavior observed in the United States and more broadly, possibly explains how people update their perception of the risk of activities. Overall, results show a link between perception and action with regards to COVID-19 and support the use of targeted risk messaging to influence behavior. Moreover, the link between reported real-world perceptions and game behavior suggest that serious games can be used as valuable tools to test policies, risk messaging and communication, with the goal of nudging individuals with varied and nuanced perceptions and belief sets towards behaviors that will reduce the impact of COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Scott C. Merrill", - "author_inst": "University of Vermont" - }, - { - "author_name": "Sarah A. Nowak", - "author_inst": "University of Vermont" - }, - { - "author_name": "Trisha R. Shrum", - "author_inst": "University of Vermont College of Agriculture and Life Sciences" - }, - { - "author_name": "John P. Hanley", - "author_inst": "University of Vermont" - }, - { - "author_name": "Eric M. Clark", - "author_inst": "University of Vermont" - }, - { - "author_name": "Luke Fredrickson", - "author_inst": "University of Vermont" - }, - { - "author_name": "Tung-Lin Liu", - "author_inst": "University of Vermont" - }, - { - "author_name": "Robert M. Beattie", - "author_inst": "University of Vermont" - }, - { - "author_name": "Aislinn O\u2019Keefe", - "author_inst": "University of Vermont" - }, - { - "author_name": "Asim Zia", - "author_inst": "University of Vermont" - }, - { - "author_name": "Christopher J. Koliba", - "author_inst": "University of Vermont" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.08.22278493", "rel_title": "Inequalities in colorectal cancer screening uptake in Wales: examination of the impact of the temporary suspension of the screening programme during the COVID-19 pandemic", @@ -251956,6 +254335,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, + { + "rel_doi": "10.1101/2022.08.06.22278449", + "rel_title": "Severity Predictors of COVID-19 in SARS-CoV-2 Variant, Delta and Omicron Period; Single Center Study", + "rel_date": "2022-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.06.22278449", + "rel_abs": "BackgroundThe outcomes of coronavirus disease 2019 (COVID-19) treatment have improved due to vaccination and the establishment of better treatment regimens. However, the emergence of variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, and the corresponding changes in the characteristics of the disease present new challenges in patient management. This study aimed to analyze predictors of COVID-19 severity caused by the delta and omicron variants of SARS-CoV-2.\n\nMethodsWe retrospectively analyzed the data of patients who were admitted for COVID-19 at Yokohama City University Hospital from August 2021 to March 2022.\n\nResultsA total of 141 patients were included in this study. Of these, 91 had moderate COVID-19, whereas 50 had severe COVID-19. There were significant differences in sex, vaccination status, dyspnea, sore throat symptoms, and body mass index (BMI) (p <0.0001, p <0.001, p <0.001, p=0.02, p< 0.0001, respectively) between the moderate and severe COVID-19 groups. Regarding comorbidities, smoking habit and renal dysfunction were significantly different between the two groups (p=0.007 and p=0.01, respectively). Regarding laboratory data, only LDH level on the first day of hospitalization was significantly different between the two groups (p<0.001). Multiple logistic regression analysis revealed that time from the onset of COVID-19 to hospitalization, BMI, smoking habit, and LDH level were significantly different between the two groups (p<0.03, p=0.039, p=0.008, p<0.001, respectively). The cut-off value for the time from onset of COVID-19 to hospitalization was four days (sensitivity, 0.73; specificity, 0.70).\n\nConclusionsTime from the onset of COVID-19 to hospitalization is the most important factor in the prevention of the aggravation of COVID-19 caused by the delta and omicron SARS-CoV-2 variants. Appropriate medical management within four days after the onset of COVID-19 is essential for preventing the progression of COVID-19, especially in patients with smoking habits.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Fumihiro Ogawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Yasufumi Oi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Hiroshi Honzawa", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Naho Misawa", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Tomoaki Takeda", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Yushi Kikuchi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Ryosuke Fukui", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Katsushi Tanaka", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Daiki Kano", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University Hospital, Infection prevention and control department" + }, + { + "author_name": "Takeru Abe", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Ichiro Takeuchi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.07.499047", "rel_title": "Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir", @@ -252676,141 +255118,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.04.22278445", - "rel_title": "Intra-pulmonary and intra-cardiac shunts in adult COVID-19 versus non-COVID ARDS ICU patients using echocardiography and contrast bubble studies (COVID-Shunt Study): a prospective, observational cohort study", - "rel_date": "2022-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278445", - "rel_abs": "ImportanceStudies have suggested intra-pulmonary shunts may contribute to hypoxemia in COVID-19 ARDS and may be associated with worse outcomes.\n\nObjectiveTo evaluate the presence of right-to-left (R-L) shunts in COVID-19 and non-COVID ARDS patients using a comprehensive hypoxemia work-up for shunt etiology and associations with mortality.\n\nDesign, Setting, ParticipantsWe conducted a multi-centre (4 Canadian hospitals), prospective, observational cohort study of adult critically ill, mechanically ventilated, ICU patients admitted for ARDS from both COVID-19 or non-COVID (November 16, 2020-September 1, 2021).\n\nInterventionContrast-enhanced agitated-saline bubble studies with transthoracic echocardiography/transcranial Doppler (TTE/TCD) {+/-} transesophageal echocardiography (TEE) assessed for the presence of R-L shunts.\n\nMain Outcomes and MeasuresPrimary outcomes were shunt incidence and association with hospital mortality. Logistic regression analysis was used to determine association of shunt presence/absence with covariables.\n\nResultsThe study enrolled 226 patients (182 COVID-19 vs. 42 non-COVID). Median age was 58 years (interquartile range [IQR]: 47-67) and APACHE II scores of 30 (IQR: 21-36). In COVID-19 patients, the incidence of R-L shunt was 31/182 patients (17.0%; intra-pulmonary: 61.3%; intra-cardiac: 38.7%) versus 10/44 (22.7%) non-COVID patients. No evidence of difference was detected between the COVID-19 and non-COVID-19 shunt rates (risk difference [RD]: -5.7%, 95% CI: -18.4-7.0, p=0.38). In the COVID-19 group, hospital mortality was higher for those with R-L shunt compared to those without (54.8% vs 35.8%, RD: 19.0%, 95% CI 0.1-37.9, p=0.05). But this did not persist at 90-day mortality, nor after regression adjustments for age and illness severity.\n\nConclusionsThere was no evidence of increased R-L shunt rates in COVID-19 compared to non-COVID controls. Right-to-left shunt was associated with increased in-hospital mortality for COVID-19 patients, but this did not persist at 90-day mortality or after adjusting using logistic regression.\n\nKey Points\n\nQuestionDoes right-to-left shunt incidence increase with COVID-19 ARDS compared to non-COVID, and is there association with shunt incidence and mortality?\n\nFindingsIn this prospective, observational cohort study, we showed no statistically significant difference in shunt prevalence between COVID-19 ARDS patients (17.0%) and non-COVID patients (22.7%). However, in COVID-19 patients, there was a difference in hospital mortality for those with shunt (54.8%) compared to those without shunt (35.8%), but this difference did not persist at 90-day mortality, nor after regression adjustments for age and illness severity.\n\nMeaningThere was no evidence of increased R-L shunt rates in COVID-19 compared to non-COVID or historical controls. Right-to-left shunt presence was associated with increased hospital mortality for COVID-19 patients, but this did not persist for 90-day mortality or after adjustment using logistic regression.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Vincent Issac Lau", - "author_inst": "University of Alberta" - }, - { - "author_name": "Graham Mah", - "author_inst": "University of Alberta" - }, - { - "author_name": "Xiao Ming Wang", - "author_inst": "University of Alberta" - }, - { - "author_name": "Leon Byker", - "author_inst": "University of Alberta" - }, - { - "author_name": "Andrea Robinson", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lazar Milovanovic", - "author_inst": "University of Alberta" - }, - { - "author_name": "Aws Alherbish", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jeff Odenbach", - "author_inst": "University of Calgary" - }, - { - "author_name": "Cristian Vadeanu", - "author_inst": "University of Alberta" - }, - { - "author_name": "David Lu", - "author_inst": "University of Alberta" - }, - { - "author_name": "Leo Smyth", - "author_inst": "University of Alberta" - }, - { - "author_name": "Mitchell Rohatensky", - "author_inst": "University of Calgary" - }, - { - "author_name": "Brian Whiteside", - "author_inst": "University of Alberta" - }, - { - "author_name": "Phillip Gregoire", - "author_inst": "University of Alberta" - }, - { - "author_name": "Warren Luksun", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sean Van Diepen", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dustin Anderson", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sanam Verma", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jocelyn Slemko", - "author_inst": "University of Alberta" - }, - { - "author_name": "Peter Brindley", - "author_inst": "University of Alberta" - }, - { - "author_name": "Demetrios Jim Kutsogiannis", - "author_inst": "University of Alberta" - }, - { - "author_name": "Michael Jacka", - "author_inst": "University of Alberta" - }, - { - "author_name": "Andrew Shaw", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Matt Wheatley", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jonathan Windram", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dawn Opgenorth", - "author_inst": "University of Alberta" - }, - { - "author_name": "Nadia Baig", - "author_inst": "University of Alberta" - }, - { - "author_name": "Oleksa G Rewa", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sean M Bagshaw", - "author_inst": "University of Alberta" - }, - { - "author_name": "Brian M Buchanan", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.08.04.22278391", "rel_title": "Forecasting COVID-19 activity in Australia to support pandemic response: May to October 2020", @@ -254202,6 +256509,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2022.08.03.22278363", + "rel_title": "Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic.", + "rel_date": "2022-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278363", + "rel_abs": "BackgroundThe global prevalence of PASC is estimated to be present in 0{middle dot}43 and based on the WHO estimation of 470 million worldwide COVID-19 infections, corresponds to around 200 million people experiencing long COVID symptoms. Despite this, its clinical features are not well defined.\n\nMethodsWe collected retrospective data from 140 patients with PASC in a post-COVID-19 clinic on demographics, risk factors, illness severity (graded as one-mild to five-severe), functional status, and 29 symptoms and principal component symptoms cluster analysis. The Institute of Medicine (IOM) 2015 criteria were used to determine the ME/CFS phenotype.\n\nFindingsThe median age was 47 years, 59{middle dot}0% were female; 49{middle dot}3% White, 17{middle dot}2% Hispanic, 14{middle dot}9% Asian, and 6{middle dot}7% Black. Only 12{middle dot}7% required hospitalization. Seventy-two (53{middle dot}5%) patients had no known comorbid conditions. Forty-five (33{middle dot}9%) were significantly debilitated. The median duration of symptoms was 285{middle dot}5 days, and the number of symptoms was 12. The most common symptoms were fatigue (86{middle dot}5%), post-exertional malaise (82{middle dot}8%), brain fog (81{middle dot}2%), unrefreshing sleep (76{middle dot}7%), and lethargy (74{middle dot}6%). Forty-three percent fit the criteria for ME/CFS.\n\nInterpretationsMost PASC patients evaluated at our clinic had no comorbid condition and were not hospitalized for acute COVID-19. One-third of patients experienced a severe decline in their functional status. About 43% had the ME/CFS subtype.\n\nFundingThe study did not received funding.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Hector Bonilla", + "author_inst": "Stanford University" + }, + { + "author_name": "Tom Quach", + "author_inst": "Stanford University" + }, + { + "author_name": "Anushri Tiwari", + "author_inst": "Stanford University" + }, + { + "author_name": "Andres Bonilla", + "author_inst": "University of Michigan" + }, + { + "author_name": "Mitchell G Miglis", + "author_inst": "Stanford University" + }, + { + "author_name": "Phillip Yang", + "author_inst": "Stanford University" + }, + { + "author_name": "Lauren Eggert", + "author_inst": "Stanford University" + }, + { + "author_name": "Husham Sharifi", + "author_inst": "Stanford University" + }, + { + "author_name": "Audra Horomanski", + "author_inst": "Stanford University" + }, + { + "author_name": "Aruna K Subramanian", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Liza Smirnoff", + "author_inst": "Stanford University" + }, + { + "author_name": "Norah Simpson", + "author_inst": "Stanford University" + }, + { + "author_name": "Houssam Halawi", + "author_inst": "Stanford University" + }, + { + "author_name": "Oliver Sum-Ping", + "author_inst": "Stanford University" + }, + { + "author_name": "Agnieszka Kalinowski", + "author_inst": "Stanford University" + }, + { + "author_name": "Zara Patel", + "author_inst": "Stanford University" + }, + { + "author_name": "Robert William Shafer", + "author_inst": "Stanford University" + }, + { + "author_name": "Linda Geng", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.03.22278386", "rel_title": "SARS-CoV-2 BA.4/5 Spike recognition and neutralization elicited after the third dose of mRNA vaccine", @@ -254898,65 +257292,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.02.22278300", - "rel_title": "Real-world uptake of COVID-19 vaccination among individuals expressing vaccine hesitancy: a registry-linkage study", - "rel_date": "2022-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.02.22278300", - "rel_abs": "BackgroundUptake of COVID-19 vaccination remains suboptimal in the United States and other settings. Though early reports indicated that a strong majority of people were interested in receiving the COVID-19 vaccine, the association between vaccine intention and uptake is not yet fully understood.\n\nMethodsDuring 24 February-5 December 2021, we enrolled California residents receiving molecular tests for SARS-CoV-2 infection who had not yet received any COVID-19 vaccine doses. Unvaccinated participants provided information on their intentions to receive COVID-19 vaccination in a telephone-administered survey. We matched study participants with a state-wide immunization registry and fit a Cox proportional hazards model comparing time to vaccination among those unvaccinated at study enrollment by vaccination intention (willing, unsure, or unwilling).\n\nFindingsAmong 864 participants who were unvaccinated at the time of interview, 272 (31%) had documentation of receipt of COVID-19 vaccination later; including 194/423 (45.9%) who had initially reported being willing to receive vaccination, 41/185 (22.2%) who reported being unsure about vaccination, and 37/278 (13.3%) who reported unwillingness to receive vaccination. Adjusted hazard ratios (aHRs) for registry-confirmed COVID-19 vaccination were 0.49 (95% confidence interval: 0.32-0.76) and 0.21 (0.12-0.36) for participants expressing uncertainty and unwillingness to receive vaccination, respectively, as compared with participants who reported being willing to receive vaccination. Time to vaccination was shorter among participants from higher-income households (aHR 3.30 [2.02-5.39]) and who reported co-morbidities or immunocompromising conditions (aHR 1.54 [1.01-2.36]); time to vaccination was longer among participants who tested positive for SARS-CoV-2 infection (aHR 0.60 [0.43-0.84]). Sensitivity of self-reported COVID-19 vaccination status was 82% (80-85%) overall, and 98% (97-99%) among those referencing vaccination records; specificity was 87% (86-89%).\n\nInterpretationParticipants stated willingness to receive COVID-19 vaccination was an imperfect predictor of real-world vaccine receipt. Improving messaging about the importance of COVID-19 vaccination, regardless of previous SARS-CoV-2 infection status, may improve vaccine uptake among populations who express hesitancy to initiate vaccination.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and medR{chi}iv for variations and combinations of the terms \"vaccine hesitancy\", \"vaccine confidence\", \"vaccine uptake\", \"COVID-19\", and \"SARS-CoV-2\" to identify original research articles published by March 8, 2022. The majority of screened articles were cross-sectional surveys conducted prior to or after implementation of COVID-19 vaccines to assess trends or predictors of participant-reported COVID-19 vaccine hesitancy. While some studies included random population-based samples, many were conducted within subgroups like health care professionals, parents of school aged children, or college students. Evidence about the association between COVID-19 vaccine intentions and subsequent vaccine uptake remains scarce. Three observational studies quantified associations between willingness to receive COVID-19 vaccination and subsequent initiation of vaccination; however, in these studies, follow-up time was limited to the period prior to widespread availability of COVID-19 vaccination or initiation of vaccine mandates in workplaces, schools, and other public places. Therefore, it was unclear whether remaining unvaccinated at follow-up in these studies was a choice or a consequence of the lack of universal access to COVID-19 vaccines. Additionally, most efforts to identify subsequent vaccine uptake relied on self-reported vaccination status, which may be subject to reporting or interviewer bias. We also searched PubMed and medR{chi}iv with variations and combinations of the terms \"self-reported\", \"vaccination\", \"accuracy\", and \"COVID-19\" and did not discover any articles validating self-reported COVID-19 vaccination status against immunization registry data; whereas, such studies were available for other vaccine-preventable pathogens including influenza, Streptococcus pneumoniae, and human papillomavirus.\n\nAdded value of this studyWe linked data collected through an ongoing case-control study and a comprehensive state-wide immunization registry to evaluate the association between COVID-19 vaccination intention and subsequent uptake. We also assessed the reliability of self-reported COVID-19 vaccination status by linking participant records with a state-wide immunization registry. We are not aware of another published study assessing predictors of COVID-19 vaccine uptake spanning over 7 months of age-eligible follow-up time and adjudicating the use of self-reported COVID-19 vaccination status. We found that expressing hesitancy to receive COVID-19 vaccination was associated with lower adjusted hazards of subsequent vaccine uptake as compared with expressing willingness to receive vaccination (aHR: 0.49; 95% CI: 0.32-0.76), although uptake was also suboptimal among individuals who expressed willingness (45%). Participants from lower income households or who had recently tested positive for SARS-CoV-2 were slower to initiate vaccination than from higher income households or who had recently tested negative. People who were pregnant and initially deferred vaccination were faster to receive vaccination than participants who did not cite pregnancy as a reason for refusal. Upon assessing the accuracy of self-reported vaccination status, we found referencing a vaccination card or another calendar reference source improved sensitivity of self-reported vaccination status.\n\nImplications of all available evidenceWe provide an evaluation of predictors of COVID-19 vaccine uptake and assess the validity of self-reported COVID-19 vaccination status in comparison with a state-wide immunization registry. We identified that self-reported vaccination intent was a strong but imperfect predictor of subsequent vaccine initiation. However, no single reason for participants to express vaccine hesitancy predicted their likelihood of eventual vaccine receipt. As such, public health campaigns addressing multiple factors underlying vaccine hesitancy including those correcting sources of misinformation, and allaying concerns about short- or long-term side effects and vaccine safety remain important tools to improve acceptance in hesitant populations. Future studies reliant on the use of self-reported COVID-19 vaccination status should strive to utilize additional reference sources like COVID-19 vaccination cards or vaccination registries to reduce misclassification of vaccination status.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kristin L Andrejko", - "author_inst": "School of Public Health, University of California, Berkeley" - }, - { - "author_name": "Jennifer F Myers", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "Nozomi Fukui", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "Lauren Nelson", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "Rui Zhao", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "John Openshaw", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "James P Watt", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "Seema Jain", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "Joseph A Lewnard", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Jake M Pry", - "author_inst": "California Department of Public Health, Richmond, California" - }, - { - "author_name": "- California COVID-19 Case-Control Study Team", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.01.22278286", "rel_title": "Nano assembly of plasmonic probe-virus particles enabled rapid and ultrasensitive point-of-care SARS-CoV-2 detection", @@ -255884,6 +258219,125 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.08.02.502439", + "rel_title": "Serological surveillance for wild rodent infection with SARS-CoV-2 in Europe", + "rel_date": "2022-08-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.02.502439", + "rel_abs": "We report serological surveillance for exposure to SARS-CoV-2 in 1,237 wild rodents and other small mammals across Europe. All samples were negative with the possible exception of one. Given the ongoing circulation of this virus in humans and potential host jumps, we suggest such surveillance be continued.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Vincent Bourret", + "author_inst": "University of Helsinki, INRAE" + }, + { + "author_name": "Lara Dutra", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Hussein Alburkat", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Sanna Maki", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Ella Lintunen", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Marine Wasniewski", + "author_inst": "ANSES" + }, + { + "author_name": "Ravi Kant", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Maciej Grzybek", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Vinaya Venkat", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Hayder Asad", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Julien Pradel", + "author_inst": "INRAE" + }, + { + "author_name": "Marie Bouilloud", + "author_inst": "IRD" + }, + { + "author_name": "Herwig Leirs", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Valeria Carolina Colombo", + "author_inst": "University of Antwerp, CONICET" + }, + { + "author_name": "Vincent Sluydts", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Peter Stuart", + "author_inst": "Munster Technological University" + }, + { + "author_name": "Andrew McManus", + "author_inst": "Munster Technological University" + }, + { + "author_name": "Jana A. Eccard", + "author_inst": "University of Potsdam" + }, + { + "author_name": "Jasmin Firozpoor", + "author_inst": "University of Potsdam" + }, + { + "author_name": "Christian Imholt", + "author_inst": "Julius Kuhn Institute" + }, + { + "author_name": "Joanna Nowicka", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Aleksander Goll", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Nathan Ranc", + "author_inst": "INRAE" + }, + { + "author_name": "Guillaume Castel", + "author_inst": "INRAE" + }, + { + "author_name": "Nathalie Charbonnel", + "author_inst": "INRAE" + }, + { + "author_name": "Tarja Sironen", + "author_inst": "University of Helsinki" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.02.502100", "rel_title": "NF-\u03baB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids", @@ -256612,77 +259066,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.30.501940", - "rel_title": "Recombinant Human ACE2-Fc : A promising therapy for SARS-CoV2 infection", - "rel_date": "2022-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.30.501940", - "rel_abs": "SARS-CoV2 entry is mediated by binding of viral spike-protein(S) to the transmembrane Angiotensin-Converting Enzyme-2 (ACE2) of the host cell. Thus, to prevent transmission of disease, strategies to abrogate the interaction are important. However, ACE2 cannot be blocked since its normal function is to convert the Angiotensin II peptide to Angiotensin(1-7) to reduce hypertension. This work reports a recombinant cell line secreting soluble ACE2-ectopic domain (MFcS2), modified to increase binding and production efficacy and fused to human immunoglobulin-Fc. While maintaining its enzymatic activity, the molecule trapped and neutralized SARS CoV2 virus in vitro with an IC50 of 64 nM. In vivo, with no pathology in the vital organs, it inhibited the viral load in lungs in SARS-CoV2 infected Golden-Syrian-hamster. The Intravenous pharmacokinetic profiling of MFcS2 in hamster at a dose of 5 mg/Kg presented a maximum serum concentration of 23.45 {micro}g/mL with a half-life of 29.5 hrs. These results suggest that MFcS2 could be used as an effective decoy based therapeutic strategy to treat COVID19. This work also reports usage of a novel oral-cancer cell line as in vitro model of SARS-Cov2 infection, validated by over expressing viral-defence pathways upon RNA-seq analysis and over-expression of ACE2 and TMPRSS upon growth in hyperglycaemic condition.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Smitha P.K", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Radha Krishan Shandil", - "author_inst": "Foundation for Neglected Disease Research" - }, - { - "author_name": "Pushkarni Suresh", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Kunal Biswas", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Gudepalya Renukaiah Rudramurthy", - "author_inst": "Foundation for Neglected Disease Research" - }, - { - "author_name": "Naveenkumar Chakenahalli Nanjegowda", - "author_inst": "Foundation for Neglected Disease Research" - }, - { - "author_name": "Bharathkumar Kumaraswamy", - "author_inst": "Foundation for Neglected Disease Research" - }, - { - "author_name": "Naga Puspha Battula", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Suprabuddha Datta Chowdhury", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Sakshi Sinha", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Sarmistha Dutta", - "author_inst": "Dr. Reddys Laboratories" - }, - { - "author_name": "Sujan K. Dhar", - "author_inst": "Mazumdar Shaw Medical Foundation" - }, - { - "author_name": "Shridhar Narayanan", - "author_inst": "Foundation for Neglected Disease Research" - }, - { - "author_name": "Manjula Das", - "author_inst": "Mazumdar Shaw Medical Foundation" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.07.31.501809", "rel_title": "InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires", @@ -257698,6 +260081,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.30.22278213", + "rel_title": "Higher Perceived Stress during the COVID-19 pandemic increased Menstrual Dysregulation and Menopause Symptoms", + "rel_date": "2022-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.30.22278213", + "rel_abs": "ObjectiveThe increased stress the globe has experienced with the COVID-19 pandemic has affected mental health, disproportionately affecting women. However, how perceived stress in the first year affected menstrual and menopausal symptoms has not yet been investigated.\n\nMethodsResidents in British Columbia, Canada, were surveyed online as part of the COVID-19 Rapid Evidence Study of a Provincial Population-Based Cohort for Gender and Sex (RESPPONSE). A subgroup (n=4171) who were assigned female sex at birth (age 25-69) and were surveyed within the first 6-12 months of the pandemic (August 2020-February 2021), prior to the widespread rollout of vaccines, were retrospectively asked if they noticed changes in their menstrual or menopausal symptoms, as well as completing validated measures of stress, depression, and anxiety.\n\nResultsWe found that 27.8% reported menstrual cycle disturbances and 6.7% reported increased menopause symptoms. Those who scored higher on perceived stress, depression, and anxiety scales were more likely to have reproductive cycle disturbances. Free text responses revealed that reasons for disturbances were perceived to be related to the pandemic.\n\nConclusionsThe COVID-19 pandemic has highlighted the need to research womens health issues, such as menstruation. Our data indicates that in the first year of the pandemic, almost a third of the menstruating population reported disturbances in their cycle, which is approximately two times higher than in non-pandemic situations and four times higher than any reported changes in menopausal symptoms across that first year of the pandemic.\n\nSummary SentencesWomen+ with higher anxiety, depression or perceived stress scores during the first year of the pandemic were more likely to have experienced menstrual cycle phase disturbance or menopausal status disruption. Younger women were particularly prone to disturbances in their reproductive cycles.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Romina Garcia de Leon", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Alexandra Baaske", + "author_inst": "Women's Health Research Institute" + }, + { + "author_name": "Arianne Albert", + "author_inst": "Women's Health Research Institute" + }, + { + "author_name": "Amy Booth", + "author_inst": "University of British Columbia" + }, + { + "author_name": "C. Sarai Racey", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Shanlea Gordon", + "author_inst": "Womens Health Research Institute" + }, + { + "author_name": "Laurie Smith", + "author_inst": "BC Cancer" + }, + { + "author_name": "Anna Gottschlich", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Angela Kaida", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Gina Ogilvie", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Lori Brotto", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Liisa A.M Galea", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2022.07.29.22278186", "rel_title": "Comparative effectiveness of BNT162b2 versus mRNA-1273 boosting in England: a cohort study in OpenSAFELY-TPP", @@ -258378,57 +260828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.27.22278003", - "rel_title": "Early Detection of SARS-CoV-2 Omicron BA.4/5 in German wastewater", - "rel_date": "2022-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.27.22278003", - "rel_abs": "Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. Omicron sub-variants BA.4/5 have spread globally displacing the predeceasing variants. Due to the severe transmissibility and immune escape potential of BA.4/5, early monitoring was required to asses and implement countermeasures in time.\n\nIn this study, we monitored the prevalence of SARS-CoV-2 BA.4/5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North-Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability to detect BA.4/5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022 and the presence of BA.4/5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V. Finally, the mutant fractions were quantitatively monitored by digital PCR confirming BA.4/5 as the majority variant by 5th June 2022.\n\nIn conclusions, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variant spreading independent of individual test capacities.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alexander Wilhelm", - "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany" - }, - { - "author_name": "Jens Schoth", - "author_inst": "Emschergenossenschaft/Lippeverband, Kronprinzenstrasse 24, D-45128 Essen, Germany" - }, - { - "author_name": "Christina Meinert-Berning", - "author_inst": "Ruhrverband, Kronprinzenstrasse 37, D-45128 Essen, Germany" - }, - { - "author_name": "Daniel Bastian", - "author_inst": "FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University , Kackertstrasse 15-17, D-52056 Aachen, Germany" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany" - }, - { - "author_name": "Burkhard Teichgraeber", - "author_inst": "Emschergenossenschaft/Lippeverband, Kronprinzenstrasse 24, D-45128 Essen, Germany" - }, - { - "author_name": "Thomas Wintgens", - "author_inst": "Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074, Aachen, Germany" - }, - { - "author_name": "Frank-Andreas Weber", - "author_inst": "FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University , Kackertstrasse 15-17, D-52056 Aachen, Germany" - }, - { - "author_name": "Marek Widera", - "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.27.22278129", "rel_title": "Immune Heterogeneity and Epistasis Explain Punctuated Evolution of SARS-CoV-2", @@ -259544,6 +261943,109 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.07.27.501719", + "rel_title": "Development of Equine Polyclonal Antibodies as a Broad-Spectrum Therapy Against SARS-CoV-2 Variants", + "rel_date": "2022-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.27.501719", + "rel_abs": "The Coronavirus disease 19 (COVID-19) pandemic has accumulated over 550 million confirmed cases and more than 6.34 million deaths worldwide. Although vaccinations has largely protected the population through the last two years, the effect of vaccination has been increasingly challenged by the emerging SARS-CoV-2 variants. Although several therapeutics including both monoclonal antibodies and small molecule drugs have been used clinically, high cost, viral escape mutations, and potential side effects have reduced their efficacy. There is an urgent need to develop a low cost treatment with wide-spectrum effect against the novel variants of SARS-CoV-2.\n\nHere we report a product of equine polyclonal antibodies that showed potential broad spectrum neutralization effect against the major variants of SARS-CoV-2. The equine polyclonal antibodies were generated by horse immunization with the receptor binding domain (RBD) of SARS-CoV-2 spike protein and purified from equine serum. A high binding affinity between the generated equine antibodies and the RBD was observed. Although designed against the RBD of the early wild type strain sequenced in 2020, the equine antibodies also showed a highly efficient neutralization capacity against the major variants of SARS-CoV-2, including the recent BA.2 Omicron variant (IC50 =1.867g/ml) in viral neutralization assay in Vero E6 cells using live virus cultured. The broad-spectrum neutralization capacity of the equine antibodies was further confirmed using pseudovirus neutralization assay covering the major SARS-CoV-2 variants including wild type, alpha, beta, delta, and omicron, showing effective neutralization against all the tested strains. Ex vivo reconstructed human respiratory organoids representing nasal, bronchial, and lung epitheliums were employed to test the treatment efficacy of the equine antibodies. Antibody treatment protected the human nasal, bronchial, and lung epithelial organoids against infection of the novel SARS-CoV-2 variants challenging public health, the Delta and Omicron BA.2 isolates, by reducing >95% of the viral load. The equine antibodies were further tested for potential side effects in a mouse model by inhalation and no significant pathological feature was observed.\n\nEquine antibodies, as a mature medical product, have been widely applied in the treatment of infectious diseases for more than a century, which limits the potential side effects and are capable of large scale production at a low cost. A cost-effective, wide-spectrum equine antibody therapy effective against the major SARS-CoV-2 variants can contribute as an affordable therapy to cover a large portion of the world population, and thus potentially reduce the transmission and mutation of SARS-CoV-2.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Shumin Liao", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China; The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Yunjiao He", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Jing Qu", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Yue Shi", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Yingzi Liu", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China; School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Keli Zhao", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China" + }, + { + "author_name": "Junhui Chen", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China" + }, + { + "author_name": "Yue Jing", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Clifton Kwang-Fu Shen", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd.Jiangxi; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen; Hainan Institute of P" + }, + { + "author_name": "Chong Ji", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Guxun Luo", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Xusheng Zhao", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Shuo Li", + "author_inst": "Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; The Sixth Affiliated Hospital of Shenzhen University Health Science Cent" + }, + { + "author_name": "Yunping Fan", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Ziquan Lv", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Shisong Fang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Yaqing He", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Chunli Wu", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Renli Zhang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Xuan Zou", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Peng Wang", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Liang Li", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China; Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced T" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.07.27.501708", "rel_title": "Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain", @@ -260324,65 +262826,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.26.501505", - "rel_title": "The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity", - "rel_date": "2022-07-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.26.501505", - "rel_abs": "The binding of SARS-CoV-2 nucleocapsid (N) protein to both the 5'- and 3'-ends of genomic RNA has different implications arising from its binding to the central region during virion assembly. However, the mechanism underlying selective binding remains unknown. Herein, we performed the high-throughput RNA-SELEX (HTR-SELEX) to determine the RNA-binding specificity of the N proteins of various SARS-CoV-2 variants as well as other {beta}-coronaviruses and showed that N proteins could bind two unrelated sequences, both of which were highly conserved across all variants and species. Interestingly, both these sequence motifs are virtually absent from the human transcriptome; however, they exhibit a highly enriched, mutually complementary distribution in the coronavirus genome, highlighting their varied functions in genome packaging. Our results provide mechanistic insights into viral genome packaging, thereby increasing the feasibility of developing drugs with broad-spectrum anti-coronavirus activity by targeting RNA binding by N proteins.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Shaorong Fan", - "author_inst": "Northwest University" - }, - { - "author_name": "Wenju Sun", - "author_inst": "Northwest University" - }, - { - "author_name": "Ligang Fan", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Nan Wu", - "author_inst": "Northwest University" - }, - { - "author_name": "Wei Sun", - "author_inst": "Northwest University" - }, - { - "author_name": "Haiqian Ma", - "author_inst": "Northwest University" - }, - { - "author_name": "Siyuan Chen", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Zitong Li", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Yu Li", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Jilin Zhang", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Jian Yan", - "author_inst": "City University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.07.26.22278084", "rel_title": "Visual Transformer and Deep CNN Prediction of High-risk COVID-19 Infected Patients using Fusion of CT Images and Clinical Data", @@ -261274,6 +263717,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.24.22277968", + "rel_title": "Effects of wearing FFP2 masks on SARS-CoV-2 infection rates in classrooms", + "rel_date": "2022-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.24.22277968", + "rel_abs": "ImportanceDifferent mitigation measures are mandated in schools worldwide to control the spread of SARS-CoV-2. The efficacy of most measures, however, has not been investigated thus far.\n\nObjectiveTo investigate the usefulness of FFP-2 masks in classrooms to prevent the spread of SARS-CoV-2.\n\nDesignA retrospective comparative cohort study of infection rates (evaluated by PCR screening in school) in students wearing FFP-2 masks continuously and students in sports classes with limited face mask use.\n\nSettingA single-center evaluation comparing classes (middle school: age 10-16 years, 4-year high school: age 14-20 years) with a high sports focus (SF), with regular classes during the Delta and Omicron waves (September 2021-April 2022).\n\nParticipantsIn total, 616 children/families were invited to participate in the comparative evaluation, and 614 (99.7%) followed this invitation by providing relevant information concerning their SARS-CoV-2 infection status. A total of 213 legal guardians (for children < 14 years) and 401 adolescents ([≥]14 years) reported SARS-CoV-2 infections during the 2021/22 school year.\n\nMain Outcomes and MeasuresA comparative analysis of cumulative SARS-CoV-2 infection rates in sports and non-sports classes (the 7-day classroom incidence of SARS-CoV-2 infections, and potential secondary infections among school classmates).\n\nResultsCumulative SARS-CoV-2 infection rates were clearly higher in sports classes (with limited mask use) than in non-sports classes (continuous mask use). After the relaxation of the mitigation measures, students in non-sports classes, however, showed a clear \"catch-up\" of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (April 30, 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p=0.037, {varphi}=0.09) was detected between classes with a sports focus and those without a sports focus.\n\nConclusions and RelevanceWearing FFP2 face masks reduces the risk of SARS-CoV-2 infection if strict mitigation measures are applied. Following the relaxation of strict measures, previously \"protected\" students show a significant \"catch-up\" infection rate. Thus, continuous face mask use postpones rather than avoids SARS-CoV-2 infection in many cases. Therefore, the advantage of reduced transmission must be carefully balanced against the disadvantages associated with mask wearing throughout schools.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gerald Jarnig", + "author_inst": "Institute of Human Movement Science, Sport and Health, University of Graz, Graz, Austria" + }, + { + "author_name": "Reinhold Kerbl", + "author_inst": "Department of Pediatrics and Adolescent Medicine, LKH Hochsteiermark/Leoben, Austria" + }, + { + "author_name": "Mireille van Poppel", + "author_inst": "Institute of Human Movement Science, Sport and Health, University of Graz, Graz, Austria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.07.20.22277718", "rel_title": "Biomarkers and Outcomes in Hospitalized Covid-19 Patients: A Prospective Registry", @@ -262110,33 +264580,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.19.22277821", - "rel_title": "Characterizing spatiotemporal trends in self-reported mask-wearing behavior in the United States", - "rel_date": "2022-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.19.22277821", - "rel_abs": "BackgroundFace mask-wearing has been identified as an effective strategy to prevent transmission of SARS-CoV-2, yet mask mandates were never imposed nationally in the United States. This decision resulted in a patchwork of local policies and varying compliance potentially generating heterogeneities in the local trajectories of COVID-19 in the U.S. While numerous studies have investigated patterns and predictors of masking behavior nationally, most suffer from survey biases and none have been able to characterize mask-wearing at fine spatial scales across the U.S. through different phases of the pandemic.\n\nObjectiveUrgently needed is a debiased spatiotemporal characterization of mask-wearing behavior in the U.S. This information is critical to further assess the effectiveness of masking, evaluate drivers of transmission at different time points during the pandemic, and guide future public health decisions through, for example, forecasting disease surges.\n\nMethodsWe analyze spatiotemporal masking patterns in over eight million behavioral survey responses from across the United States starting in September 2020 through May 2021. We adjust for sample size and representation using binomial regression models and survey raking, respectively, to produce county-level monthly estimates of masking behavior. We additionally debias self-reported masking estimates using bias measures derived by comparing vaccination data from the same survey to official records at the county-level. Lastly, we evaluate whether individuals perceptions of their social environment can serve as a less biased form of behavioral surveillance than self-reported data.\n\nResultsWe find that county-level masking behavior is spatially heterogeneous along an urban-rural gradient, with mask-wearing peaking in winter 2021 and declining sharply through May 2021. Our results identify regions where targeted public health efforts could have been most effective and suggest that individuals frequency of mask-wearing may be influenced by national guidance and disease prevalence. We validate our bias-correction approach by comparing debiased self-reported mask-wearing estimates with community-reported estimates, after addressing issues of small sample size and representation. Self-reported behavior estimates are especially prone to social desirability and non-response biases and our findings demonstrate that these biases can be reduced if individuals are asked to report on community rather than self behaviors.\n\nConclusionsOur work highlights the importance of characterizing public health behaviors at fine spatiotemporal scales to capture heterogeneities that may drive outbreak trajectories. Our findings also emphasize the need for a standardized approach to incorporating behavioral big data into public health response efforts. Even large surveys are prone to bias; thus, we advocate for a social sensing approach to behavioral surveillance to enable more accurate estimates of health behaviors. Finally, we invite the public health and behavioral research communities to use our publicly available estimates to consider how bias-corrected behavioral estimates may improve our understanding of protective behaviors during crises and their impact on disease dynamics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Juliana C. Taube", - "author_inst": "Georgetown University" - }, - { - "author_name": "Zachary Susswein", - "author_inst": "Georgetown University" - }, - { - "author_name": "Shweta Bansal", - "author_inst": "Georgetown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.21.22277907", "rel_title": "The Effect of SARS-COV-2 Variant on Respiratory Features and Mortality Among Vaccinated and Non-Fully Vaccinated Patients", @@ -262992,6 +265435,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.07.21.501010", + "rel_title": "Durability of the Neutralizing Antibody Response to mRNA Booster Vaccination Against SARS-CoV-2 BA.2.12.1 and BA.4/5 Variants", + "rel_date": "2022-07-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.501010", + "rel_abs": "The recent emergence of the SARS-CoV-2 BA.4/5 and BA.2.12.1 variants has led to rising COVID-19 case numbers and concerns over the continued efficacy of mRNA booster vaccination. Here we examine the durability of neutralizing antibody (nAb) responses against these SARS-CoV-2 Omicron subvariants in a cohort of health care workers 1-40 weeks after mRNA booster dose administration. Neutralizing antibody titers fell by [~]1.5-fold 4-6 months and by [~]2.5-fold 7-9 months after booster dose, with average nAb titers falling by 11-15% every 30 days, far more stable than two dose induced immunity. Notably, nAb titers from booster recipients against SARS-CoV-2 BA.1, BA.2.12.1, and BA.4/5 variants were [~]4.7-, 7.6-, and 13.4-fold lower than against the ancestral D614G spike. However, the rate of waning of booster dose immunity was comparable across variants. Importantly, individuals reporting prior infection with SARS-CoV-2 exhibited significantly higher nAb titers compared to those without breakthrough infection. Collectively, these results highlight the broad and stable neutralizing antibody response induced by mRNA booster dose administration, implicating a significant role of virus evolution to evade nAb specificity, versus waning humoral immunity, in increasing rates of breakthrough infection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "PANKE QU", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Julia N. Faraone", + "author_inst": "The Ohio State University" + }, + { + "author_name": "John P. Evans", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Yi-Min Zheng", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Claire Carlin", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Gerard Lozanski", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Linda J. Saif", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Eugene M. Oltz", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Richard J. Gumina", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.07.21.501023", "rel_title": "Learning from pre-pandemic data to forecast viral antibody escape", @@ -263744,49 +266242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.21.500987", - "rel_title": "Temporal profiling of CD4 T-cell activation and differentiation upon SARS-CoV-2 spike protein immunisation", - "rel_date": "2022-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.500987", - "rel_abs": "CD4 T-cells require T-cell receptor (TCR) signalling for their activation and differentiation. Foxp3+ regulatory T-cells (Treg) are dependent on TCR signals for their differentiation and suppressive function. However, it is not fully known how TCR signalling controls the differentiation of polyclonal CD4 T-cells upon antigen recognition at the single-cell level in vivo. In this study, using Nr4a3-Tocky (Timer-of-cell-kinetics-and-activity), which analyses temporal changes of antigen-reactive T-cells following TCR signalling, we investigated T-cell response to Spike protein fragments (S1a, S1b, S2a, and S2b) upon immunisation. We show that S1a and S2a induced the differentiation of PD1hiCXCR5+ T follicular helper (Tfh) cells, which is related to CD4 T-cell immunogenicity. In contrast, S1b induced CD25hiGITRhiPD-1int Treg, which intermittently received TCR signalling. Using Foxp3-Tocky, which analyses Foxp3 transcriptional dynamics, the S1b-reactive Treg sustained Foxp3 transcription over time, which is a hallmark of activated Treg. Foxp3 fate-mapping showed that the S1b-reactive Treg were derived not from pre-existing thymic Treg, suggesting Foxp3 induction in non-Treg cells. Thus, the current study reveals temporally dynamic differentiation of CD4 T-cells and Treg upon immunisation in the polyclonal TCR repertoire.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jos\u00e9 Almeida-Santos", - "author_inst": "Department of Life Sciences, Imperial College London" - }, - { - "author_name": "Rita Berkachy", - "author_inst": "Department of Life Sciences, Imperial College London" - }, - { - "author_name": "Chanidapa Adele Tye", - "author_inst": "Department of Life Sciences, Imperial College London" - }, - { - "author_name": "Jehanne Hassan", - "author_inst": "Department of Life Sciences, Imperial College London; Institute of Cancer Research" - }, - { - "author_name": "Bahire Kalfaoglu", - "author_inst": "Department of Life Sciences, Imperial College London" - }, - { - "author_name": "Murray E Selkirk", - "author_inst": "Department of Life Sciences, Imperial College London" - }, - { - "author_name": "Masahiro Ono", - "author_inst": "Department of Life Sciences, Imperial College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.21.500897", "rel_title": "Buying time: detecting VOCs in SARS-CoV-2 via co-evolutionary signals", @@ -264794,6 +267249,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.07.18.22277694", + "rel_title": "Determinants of healthcare employee preference to continue teleworking after the COVID-19 pandemic: a cross-sectional study using hierarchical regression", + "rel_date": "2022-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277694", + "rel_abs": "Employees post-pandemic telework preference is an important consideration for navigating post-pandemic work arrangements and can inform organizational planning and workforce management. A cross-sectional survey of employees (n=400, participation rate =36.4%) of a regional health authority who teleworked during the COVID-19 pandemic was conducted. The most common post-pandemic telework preference was all the time (52%) followed by over half but not all the time (32%) and less than half the time or not at all (16%). Using hierarchical multinomial logistic regression models and less than half the time or not at all as the reference outcome, being a provider of direct patient care and productivity while teleworking were strong determinants of post-pandemic telework preference while two or more weekly teleconference hours, work-life balance and having one or more people over five years of age in the home while teleworking were moderate determinants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrea Marie Jones", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jonathan Fan", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Leah Thomas-Olson", + "author_inst": "Fraser Health Authority" + }, + { + "author_name": "Wei Zhang", + "author_inst": "University of British Columbia/ Centre for Health Evaluation and Outcome Sciences" + }, + { + "author_name": "Christopher B McLeod", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.07.19.22277747", "rel_title": "Cumulative incidence of SARS-CoV-2 infection in the general population of the Valencian Community (Spain) after the surge of the Omicron BA.1 variant", @@ -265502,117 +267992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.15.22277639", - "rel_title": "Ad26.COV2.S priming provides a solid immunological base for mRNA-based COVID-19 booster vaccination", - "rel_date": "2022-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277639", - "rel_abs": "A large proportion of the global population received a single dose of the Ad26.COV2.S coronavirus disease-2019 (COVID-19) vaccine as priming vaccination, which was shown to provide protection against moderate to severe COVID-19. However, the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants that harbor immune-evasive mutations in the spike protein led to the recommendation of booster vaccinations after Ad26.COV2.S priming. Recent studies showed that heterologous booster vaccination with an mRNA-based vaccine following Ad26.COV2.S priming leads to high antibody levels. However, how heterologous booster vaccination affects other functional aspects of the immune response remains unknown. Here, we performed immunological profiling on samples obtained from Ad26.COV2.S-vaccinated individuals before and after a homologous (Ad26.COV2.S) or heterologous (mRNA-1273 or BNT162b2) booster vaccination. Both homologous and heterologous booster vaccination increased antibodies with multiple functionalities towards ancestral SARS-CoV-2, the Delta and Omicron BA.1 variants. Especially, mRNA-based booster vaccination induced high levels of neutralizing antibodies and antibodies with various Fc-mediated effector functions such as antibody-dependent cellular cytotoxicity and phagocytosis. In contrast, T cell responses were similar in magnitude following homologous or heterologous booster vaccination, and retained functionality towards Delta and Omicron BA.1. However, only heterologous booster vaccination with an mRNA-based vaccine led to the expansion of SARS-CoV-2-specific T cell clones, without an increase in the breadth of the T cell repertoire as assessed by T cell receptor sequencing. In conclusion, we show that Ad26.COV2.S priming vaccination provides a solid immunological base for heterologous boosting with an mRNA-based COVID-19 vaccine, increasing humoral and cellular responses targeting newly emerging variants of concern.\n\nOne sentence summaryAd26.COV2.S priming provides a solid immunological base for extension of cellular and humoral immune responses following an mRNA-based booster.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Daryl Geers", - "author_inst": "Erasmus Medical Centre: Erasmus MC" - }, - { - "author_name": "Roos Sablerolles", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Debbie van Baarle", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Neeltje Kootstra", - "author_inst": "Amsterdam University Medical Center (location AMC)" - }, - { - "author_name": "Wim Rietdijk", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Katharina Schmitz", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Susanne Bogers", - "author_inst": "Erasmus Medical Centre: Erasmus MC" - }, - { - "author_name": "Lennert Gommers", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Nella Nieuwkoop", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Laura van Dijk", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Eva van Haren", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Melvin Lafeber", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Virgil A.S.H. Dalm", - "author_inst": "Erasmus Medical Centre: Erasmus MC" - }, - { - "author_name": "Bram Goorhuis", - "author_inst": "Amsterdam University Medical Center (location AMC)" - }, - { - "author_name": "Douwe Postma", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Leo Visser", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Anke Huckriede", - "author_inst": "University Medical Center and University of Groningen" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Rik de Swart", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Marion Koopmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Hugo van der Kuy", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Corine GeurtsvanKessel", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Rory D. de Vries", - "author_inst": "Erasmus MC" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.17.22277721", "rel_title": "A simple SEIR-V model to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission using wastewater-based surveillance data", @@ -266620,6 +268999,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.15.22277497", + "rel_title": "Global patterns and drivers of influenza decline during the COVID-19 pandemic", + "rel_date": "2022-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277497", + "rel_abs": "Influenza circulation declined during the COVID-19 pandemic. The timing and extent of decline and its association with interventions against COVID-19 were described for some regions. Here, we provide a global analysis of the influenza decline between March 2020 and September 2021 and investigate its potential drivers. We computed influenza change by country and trimester relative to the 2014-2019 period using the number of samples in the FluNet database. We used random forests to determine important predictors in a list of 20 covariates including demography, weather, pandemic preparedness, COVID-19 incidence, and COVID-19 pandemic response. With a regression tree we then classified observations according to these predictors. We found that influenza circulation decreased globally, with COVID-19 incidence and pandemic preparedness being the two most important predictors of this decrease. The regression tree showed interpretable groups of observations by country and trimester: Europe and North America clustered together in spring 2020, with limited influenza decline despite strong COVID-19 restrictions; in the period afterwards countries of temperate regions, with high pandemic preparedness, high COVID-19 incidence and stringent social restrictions grouped together having strong influenza decline. Conversely, countries in the tropics, with altogether low pandemic preparedness, low reported COVID-19 incidence and low strength of COVID-19 response showed low influenza decline overall. A final group singled out four \"zero-Covid\" countries, with the lowest residual influenza levels. The spatiotemporal decline of influenza during the COVID-19 pandemic was global, yet heterogeneous. The sociodemographic context and stage of the COVID-19 pandemic showed non-linear associations with this decline. Zero-Covid countries maintained the lowest levels of reduction with strict border controls and despite close-to-normal social activity. These results suggest that the resurgence of influenza could take equally diverse paths. It also emphasises the importance of influenza reseeding in driving countries seasonal influenza epidemics.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Francesco Bonacina", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Pierre-Yves Bo\u00eblle", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" + }, + { + "author_name": "Olivier Lopez", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Maud Thomas", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Chiara Poletto", + "author_inst": "INSERM and Sorbonne Universit\u00e9" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.16.22277705", "rel_title": "Attitudes toward COVID-19 pandemic among fully vaccinated individuals: evidence from Greece two years after the pandemic", @@ -267712,29 +270130,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.12.22277534", - "rel_title": "BA.4/BA.5 early surge report Austria", - "rel_date": "2022-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277534", - "rel_abs": "More than two years into the COVID-19 pandemic, the emergence of the Omicron subvariants BA.4 and BA.5 initiated the fifth wave. BA.4/BA.5 share identical spike proteins and are thus difficult to differentiate using standard diagnostic tests. The true frequency and diversity of the two variants in Austria is therefore largely unknown. Aim of this report is to take stock about the frequency and diversity of BA.4 & BA.5 and their subvariants based on whole genome sequencing (WGS) data as deposited at GISAID database. Results show that most sequenced cases belong to BA.5 (c. 86 %) rather than BA.4 (c. 14 %) and that most of the global diversity (24 out of 32 subvariants) of BA.4 and BA.5 in terms of subvariants described is already present in Austria. However, most cases can be attributed to a few subvariants (e.g. BA.5.1, BE.1.1, BA.5.3, BA.5.2.1) with high estimated growth advantage over BA.2 (ranging 103 to 159 %) and may be worth monitoring as the immediate wave unfolds.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alexander Gamisch", - "author_inst": "Dr. Mustafa, Dr. Richter Labor fuer medizinisch-chemische und mikrobiologische Diagnostik GmbH, Abteilung Molekularbiologie, Strubergasse 20, 5020 Salzburg" - }, - { - "author_name": "Maria Elisabeth Mustafa", - "author_inst": "Dr. Mustafa, Dr. Richter Labor fuer medizinisch-chemische und mikrobiologische Diagnostik GmbH, Abteilung Molekularbiologie, Strubergasse 20, 5020 Salzburg" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.14.22277643", "rel_title": "Bubble-PAPR: Phase I clinical evaluation of an in-house developed prototype powered air-purifying respirator for use by healthcare workers", @@ -268854,6 +271249,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.13.22277575", + "rel_title": "SARS-CoV-2 infections during Omicron (BA.1) dominant wave and subsequent population immunity in Gauteng, South Africa", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.13.22277575", + "rel_abs": "BackgroundThe B.1.1.529 (Omicron BA.1) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global resurgence of coronavirus disease 2019 (Covid-19). The contribution of BA.1 infection to population immunity and its effect on subsequent resurgence of B.1.1.529 sub-lineages warrant investigation.\n\nMethodsWe conducted an epidemiologic survey to determine the sero-prevalence of SARS-CoV-2 IgG from March 1 to April 11, 2022, after the BA.1-dominant wave had subsided in Gauteng (South Africa), and prior to a resurgence of Covid-19 dominated by the BA.4 and BA.5 (BA.4/BA.5) sub-lineages. Population-based sampling included households in an earlier survey from October 22 to December 9, 2021 preceding the BA.1 dominant wave. Dried-blood-spot samples were quantitatively tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein. Epidemiologic trends in Gauteng for cases, hospitalizations, recorded deaths, and excess deaths were evaluated from the inception of the pandemic to the onset of the BA.1 dominant wave (pre-BA.1), during the BA.1 dominant wave, and for the BA.4/BA.5 dominant wave through June 6, 2022.\n\nResultsThe 7510 participants included 2420 with paired samples from the earlier survey. Despite only 26.7% (1995/7470) of individuals having received a Covid-19 vaccine, the overall sero-prevalence was 90.9% (95% confidence interval [CI], 90.2 to 91.5), including 89.5% in Covid-19 unvaccinated individuals. Sixty-four percent (95%CI, 61.8-65.9) of individuals with paired samples had serological evidence of SARS-CoV-2 infection during the BA.1 dominant wave. Of all cumulative recorded hospitalisations and deaths, 14.1% and 5.9% were contributed by the BA.1 dominant wave, and 5.1% and 1.6% by the BA.4/BA.5 dominant wave. The SARS-CoV-2 infection fatality risk was lower in the BA.1 compared with pre-BA.1 waves for recorded deaths (0.02% vs. 0.33%) and Covid-19 attributable deaths based on excess mortality estimates (0.03% vs. 0.67%).\n\nConclusionsGauteng province experienced high levels of infections in the BA.1 -dominant wave against a backdrop of high (73%) sero-prevalence. Covid-19 hospitalizations and deaths were further decoupled from infections during BA.4/BA.5 dominant wave than that observed during the BA.1 dominant wave.\n\n(Funded by the Bill and Melinda Gates Foundation.)", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shabir Madhi", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Gaurav Kwatra", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Jonathan E. Myers", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Waasila Jassat", + "author_inst": "National institute for communicable diseases of South Africa" + }, + { + "author_name": "Nisha Dhar", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Christian K. Mukendi", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Lucille Blumberg", + "author_inst": "National institute for communicable diseases of South Africa" + }, + { + "author_name": "Richard Welch", + "author_inst": "National institute for communicable diseases of South Africa" + }, + { + "author_name": "Alane Izu", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Portia C. Mutevedzi", + "author_inst": "University of the Witwatersrand" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.14.22277647", "rel_title": "Estimating waning vaccine effectiveness from population-level surveillance data in multi-variant epidemics", @@ -269462,53 +271912,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.14.500041", - "rel_title": "Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies", - "rel_date": "2022-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.14.500041", - "rel_abs": "Since the end of 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant outcompeted other variants and took over the world. After the emergence of original Omicron BA.1, Omicron BA.2 subvariant emerged and outcompeted BA.1. As of July 2022, some BA.2 subvariants, including BA.2.12.1, BA.4 and BA.5, emerged in multiple countries and begun outcompeting original BA.2. Moreover, a novel BA.2 subvariant, BA.2.75, was detected in eight countries including India at the end of June 2022, and preliminary investigations suggest that BA.2.75 is more transmissible over the other BA.2 subvariants. On July 7, 2022, the WHO classified BA.2.75 as a variant-of-concern lineage under monitoring. We have recently demonstrated that BA.4/5 is highly resistant to a therapeutic monoclonal antibody, cilgavimab, than BA.2. The resistance of SARS-CoV-2 variants to therapeutic antibodies can be attributed to the mutations in the viral spike protein. Compared to the BA.2 spike, BA.2.12.1 and BA.4/5 respectively bear two and four mutations in their spike proteins. On the other hand, the majority of BA.2.75 spike bears nine substitutions. The fact that the mutation number in the BA.2.75 spike is larger than those in the BA.4/5 spike raises the possibility that the BA.2.75 spike significantly reduces sensitivity towards therapeutic monoclonal antibodies than BA.2 and BA.4/5. In this study, we generated pseudoviruses harboring the spike proteins of BA.2.75, BA.4/5 and BA.2 and evaluated the efficacy of ten therapeutic monoclonal antibodies and three antibody cocktails against BA.2.75.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Daichi Yamasoba", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Izumi Kimura", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Yusuke Kosugi", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Keiya Uriu", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Shigeru Fujita", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Jumpei Ito", - "author_inst": "The Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "Kei Sato", - "author_inst": "Institute of Medical Science, The University of Tokyo" - }, - { - "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.07.14.500063", "rel_title": "Genome-first detection of emerging resistance to novel therapeutic agents for SARS-CoV-2", @@ -270536,6 +272939,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.10.22277467", + "rel_title": "Development of an Accurate and Rapid Antigen Assay for COVID-19 Diagnostics Using Saliva", + "rel_date": "2022-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.10.22277467", + "rel_abs": "The global outbreak of COVID-19 highlighted the need for rapid and accurate diagnostic testing to control the spread of this highly contagious disease (1-5). Here, we describe the nCoVega COVID-19 antigen rapid test ([~] 15min) that can detect the presence of the SARS-COV-2 virus particles from saliva sample on a portable device. The portable reader instrument, the Vega-200, has a small footprint and is designed for use at point of care settings. The test detects the fluorescence signal using wide-field illumination from antigen-antibody complexes captured on a special filter matrix (6). Results of this clinical evaluation of 183 subjects demonstrates that the nCoVega COVID-19 test performs at par with qRT-PCR tests (7) (gold standard) for both symptomatic and asymptomatic patients, with a strong inverse correlation between RFU (relative fluorescence units) and Ct counts (from RT-PCR) maintaining detection accuracy even at very low viral loads. The test has an analytical performance of 15.3 TCID50/mL, and 100% specificity for COVID-19 as compared to other human respiratory viruses, including other human coronaviruses. The working principle of this assay and test system can be used for developing other rapid, inexpensive antigen assays and it can offer an end-to-end, point-of-care solution to meet the continuous demand in tackling existing and emerging infectious diseases across the globe.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Camille Troup", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Debnath Mukhopadhyay", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Tania Chakrabarty", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Anup Madan", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Sri Satyanarayana", + "author_inst": "Kaya17, inc" + }, + { + "author_name": "Shreefal Mehta", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Sulatha Dwarakanath", + "author_inst": "Kaya17 Inc" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.11.22277511", "rel_title": "Effect of Stay-at-Home Orders and Other COVID-Related Policies on Trauma Hospitalization Rates and Disparities in the United States: A Statewide Time-Series Analysis", @@ -271244,85 +273690,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.07.12.499603", - "rel_title": "Enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants BA.4 and BA.5", - "rel_date": "2022-07-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.12.499603", - "rel_abs": "SARS-CoV-2 adaptation to humans is evidenced by the emergence of variants of concern (VOCs) with distinct genotypes and phenotypes that facilitate immune escape and enhance transmission frequency. Most recently Omicron subvariants have emerged with heavily mutated spike proteins which facilitate re-infection of immune populations through extensive antibody escape driving replacement of previously-dominant VOCs Alpha and Delta. Interestingly, Omicron is the first VOC to produce distinct subvariants. Here, we demonstrate that later Omicron subvariants, particularly BA.4 and BA.5, have evolved an enhanced capacity to suppress human innate immunity when compared to earliest subvariants BA.1 and BA.2. We find that, like previously dominant VOCs, later Omicron subvariants tend to increase expression of viral innate immune antagonists Orf6 and nucleocapsid. We show Orf6 to be a key contributor to enhanced innate immune suppression during epithelial replication by BA.5 and Alpha, reducing innate immune signaling through IRF3 and STAT1. Convergent VOC evolution of enhanced innate immune antagonist expression suggests common pathways of adaptation to humans and links VOC, and in particular Omicron subvariant, dominance to improved innate immune evasion.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ann-Kathrin Reuschl", - "author_inst": "University College London" - }, - { - "author_name": "Lucy G Thorne", - "author_inst": "University College London" - }, - { - "author_name": "Matthew X.V. Whelan", - "author_inst": "University College London" - }, - { - "author_name": "Roberta Ragazzini", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Wilhelm Furnon", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Vanessa M Cowton", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Giuditta de Lorenzo", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Dejan Mesner", - "author_inst": "University College London" - }, - { - "author_name": "Jane E Turner", - "author_inst": "University College London" - }, - { - "author_name": "Giulia Dowgier", - "author_inst": "University College London" - }, - { - "author_name": "Nathasha Bogoda", - "author_inst": "University College London" - }, - { - "author_name": "Paola Bonfanti", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Massimo Palmarini", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Arvind H Patel", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Clare Jolly", - "author_inst": "University College London" - }, - { - "author_name": "Greg J Towers", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.07.11.499644", "rel_title": "Insights from Incorporating Quantum Computing into Drug Design Workflows", @@ -272598,6 +274965,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.05.22277189", + "rel_title": "Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination", + "rel_date": "2022-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.05.22277189", + "rel_abs": "Repeated mRNA vaccinations are an efficient tool to combat the SARS-CoV-2 pandemic. High levels of neutralizing SARS-CoV-2-antibodies are an important component of vaccine-induced immunity. Shortly after the first or second mRNA vaccine dose, the IgG response mainly consists of the pro-inflammatory isotypes IgG1 and IgG3 and is driven by T helper (Th) 1 cells. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG2 and particularly IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. While IgG antibodies were affinity matured and of high neutralization capacity, the switch in constant domains caused changes in fragment crystallizable (Fc)-receptor mediated effector functions, including a decreased capacity to facilitate phagocytosis. IgG4 induction was neither induced by Th2 cells nor observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. In addition, IgG2- and IgG4-producing memory B cells were phenotypically indistinguishable from IgG1- or IgG3-producing cells. Since Fc-mediated effector functions are critical for antiviral immunity, the described class switch towards non-inflammatory IgG isotypes, which otherwise rarely occurs after vaccination or viral infection, may have consequences for the choice and timing of vaccination regimens using mRNA vaccines.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Pascal Irrgang", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Juliane Gerling", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Katharina Kocher", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Dennis Lapuente", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Philipp Steininger", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Monika Wytopil", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Simon Sch\u00e4fer", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Katharina Habenicht", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Jahn Zhong", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "George Ssebyatika", + "author_inst": "Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Thomas Krey", + "author_inst": "Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Valeria Falcone", + "author_inst": "Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" + }, + { + "author_name": "Christine Sch\u00fclein", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Antonia Sophia Peter", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Krystelle Nganou-Makamdop", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Hartmut Hengel", + "author_inst": "Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" + }, + { + "author_name": "J\u00fcrgen Held", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Christian Bogdan", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Klaus \u00dcberla", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Kilian Schober", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Thomas H Winkler", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Matthias Tenbusch", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.07.22277364", "rel_title": "Altered affinity to ACE2 and reduced Fc functional antibodies to SARS-CoV-2 RBD variants", @@ -273494,81 +275964,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2022.07.08.22277420", - "rel_title": "Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection", - "rel_date": "2022-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.08.22277420", - "rel_abs": "As SARS-CoV-2 infections have been shown to affect the central nervous system, the investigation of associated alterations of brain structure and neuropsychological sequelae is crucial to help address future health care needs. Therefore, we performed a comprehensive neuroimaging and neuropsychological assessment of 223 non-vaccinated individuals recovered from a mild to moderate SARS-CoV-2 infection (100 female/123 male, age [years], mean {+/-} SD, 55.54 {+/-} 7.07; median 9.7 months after infection) in comparison with 223 matched controls (93 female/130 male, 55.74 {+/-} 6.60) within the framework of the Hamburg City Health Study. Primary study outcomes were advanced diffusion magnetic resonance imaging (MRI) measures of white matter microstructure, cortical thickness, white matter hyperintensity load and neuropsychological test scores. Among all 11 MRI markers tested, significant differences were found in global measures of mean diffusivity and extracellular free-water which were elevated in the white matter of post-SARS-CoV-2 individuals comparing to matched controls (free-water: 0.148 {+/-} 0.018 vs. 0.142 {+/-} 0.017, P<.001; mean diffusivity [10-3 mm2/s]: 0.747 {+/-} 0.021 vs. 0.740 {+/-} 0.020, P<.001). Group classification accuracy based on diffusion imaging markers was up to 80%. Neuropsychological test scores did not significantly differ between groups. Collectively, our findings suggest that subtle changes in white matter extracellular water content last beyond the acute infection with SARS-CoV-2. However, in our sample, a mild to moderate SARS-CoV-2 infection was not associated with neuropsychological deficits, significant changes in cortical structure or vascular lesions several months after recovery. External validation of our findings and longitudinal follow-up investigations are needed.\n\nSignificance statementIn this case-control study, we demonstrate that non-vaccinated individuals recovered from a mild to moderate SARS-CoV-2 infection show significant alterations of the cerebral white matter identified by diffusion weighted imaging, such as global increases in extracellular free-water and mean diffusivity. Despite the observed brain white matter alterations in this sample, a mild to moderate SARS-CoV-2 infection was not associated with worse cognitive functions within the first year after recovery. Collectively, our findings indicate the presence of a prolonged neuroinflammatory response to the initial viral infection. Further longitudinal research is necessary to elucidate the link between brain alterations and clinical features of post-SARS-CoV-2 individuals.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Marvin Petersen", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Felix L. Naegele", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Carola Mayer", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Maximilian Schell", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Elina Petersen", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Simone Kuehn", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Juergen Gallinat", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jens Fiehler", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Ofer Pasternak", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jakob Matschke", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Markus Glatzel", - "author_inst": "University of Hamburg-Eppendorf" - }, - { - "author_name": "Raphael Twerenbold", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Christian Gerloff", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Goetz Thomalla", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Bastian Cheng", - "author_inst": "University Medical Center Hamburg-Eppendorf" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.07.22277394", "rel_title": "A Case-Crossover Phenome-wide Association Study (PheWAS) for Understanding Post-COVID-19 Diagnosis Patterns", @@ -274768,6 +277163,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.06.22277303", + "rel_title": "Quantifying the impact of vaccines and booster doses on COVID-19 in the U.S.", + "rel_date": "2022-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277303", + "rel_abs": "The COVID-19 pandemic continues to have a devastating impact on health systems and economies across the globe. Implementing public health measures in tandem with effective vaccination strategies have been instrumental in curtailing the burden of the pandemic. With the three vaccines authorized for use in the U.S. having varying efficacies and waning effects against major COVID-19 strains, understanding the impact of these vaccines on COVID-19 incidence and fatalities is critical. Here, we formulate and use mathematical models to assess the impact of vaccine type, vaccination and booster uptake, and waning of natural and vaccine-induced immunity on the incidence and fatalities of COVID-19 and to predict future trends of the disease in the U.S. when existing control measures are reinforced or relaxed. Results of the study show a 5, 1.8, and 2 times reduction in the reproduction number during the period in which vaccination, first booster, and second booster uptake started, respectively, compared to the previous period. Due to waning of vaccine-induced immunity, vaccinating up to 96% of the U.S. population might be required to attain herd immunity, if booster uptake is low. Additionally, vaccinating and boosting more people from the onset of vaccination and booster uptake, especially with mRNA vaccines (which confer superior protection than the Johnson & Johnson vaccine) would have led to a significant reduction in COVID-19 cases and deaths in the U.S. Furthermore, adopting natural immunity-boosting measures is important in fighting COVID-19 and transmission rate reduction measures such as mask-use are critical in combating COVID-19. The emergence of a more transmissible COVID-19 variant, or early relaxation of existing control measures can lead to a more devastating wave, especially if transmission rate reduction measures and vaccination are relaxed simultaneously, while chances of containing the pandemic are enhanced if both vaccination and transmission rate reduction measures are reinforced simultaneously. We conclude that maintaining or improving existing control measures and boosting with mRNA vaccines are critical in curtailing the burden of the pandemic in the U.S.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Calistus N. Ngonghala", + "author_inst": "Department of Mathematics, University of Florida, Gainesville, FL 32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA." + }, + { + "author_name": "Michael Asare-Baah", + "author_inst": "Department of Epidemiology, University of Florida, 2004 Mowry Road, Gainesville, FL 32610, USA; Emerging Pathogens Institute, University of Florida, Gainesville" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.02.22277181", "rel_title": "Integrative analysis of viral entry networks and clinical outcomes identifies a protective role for spironolactone in severe COVID-19", @@ -275564,77 +277982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.07.04.22277207", - "rel_title": "Efficacy of Anakinra in the Management of Patients with COVID-19 Infection: A Randomized Clinical Trial", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277207", - "rel_abs": "BackgroundThe global pandemic of COVID-19 infections continues to grow worldwide, with rising number of deaths day by day. The hyperinflammation state contributes to the multiorgan failure associated with COVID-19 infections. This study aims to explore the efficacy and safety of anakinra in COVID-19 patients with both respiratory distress and cytokine release syndromes.\n\nMethodsThis was an open-label, multicenter, randomized clinical trial. Patients were randomized in 1:1 ratio to receive standard of care (SOC) alone, or anakinra plus SOC. Adults with confirmed COVID-19 infection with evidence of both respiratory distress and cytokine release syndrome were included. The primary outcome was treatment success at day 14, defined as WHO clinical progression score of [≤]3. The primary analysis was based on intention-to-treat population, with p-value of <0.05.\n\nResultsA total of 80 patients were enrolled in the study. The mean age was 49.9 years (SD=11.7), with 82.5% (n=66) male patients. The primary outcome was not statistically different (87.5% (n=35) in anakinra group vs. 92.5% (n=37) in SOC group, p=0.712). The majority of reported adverse events were mild in severity and not related to the study treatment. Increased aspartate aminotransferase was the only significant adverse event (35% (n=14) in anakinra group vs. 15% (n=6) in SOC group, p=0.039); yet, was not associated with treatment discontinuation.\n\nConclusionIn patients with severe COVID-19 infection, the addition of anakinra to SOC treatment was not associated with significant improvement in the WHO clinical progression scale. Further studies investigating patients subgroups that might benefit from anakinra are warranted. The trial was registered at ClinicalTrials.gov (NCT04643678).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Eman Zeyad I. Elmekaty", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Aya Maklad", - "author_inst": "Qatar University College of Pharmacy" - }, - { - "author_name": "Rawan Abouelhassan", - "author_inst": "Qatar University College of Pharmacy" - }, - { - "author_name": "Waqar Munir", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohamed Izham Mohamed Ibrahim", - "author_inst": "Qatar University College of Pharmacy" - }, - { - "author_name": "Arun Nair", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Rim Alibrahim", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Fatima Iqbal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ahmad Al Bishawi", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Alaaeldin Abdelmajid", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohamed Aboukamar", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohammed Abu Khattab", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hussam Al Soub", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Muna Al Maslamani", - "author_inst": "Hamad Medical Corporation" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.04.22277103", "rel_title": "Design and Performance Characteristics of the Elecsys Anti-SARS-CoV-2 S assay", @@ -277730,6 +280077,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.03.22277196", + "rel_title": "Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of COVID-19 in Africa", + "rel_date": "2022-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.03.22277196", + "rel_abs": "BackgroundThe COVID-19 pandemic has had a devastating impact on global health, the magnitude of which appears to differ intercontinentally: for example, reports suggest 271,900 per million people have been infected in Europe versus 8,800 per million people in Africa. While Africa is the second largest continent by population, its reported COVID-19 cases comprise <3% of global cases. Although social, environmental, and environmental explanations have been proposed to clarify this discrepancy, systematic infection underascertainment may be equally responsible.\n\nMethodsWe seek to quantify magnitude of underascertainment in COVID-19s cumulative incidence in Africa. Using serosurveillance and postmortem surveillance, we constructed multiplicative factors estimating ratios of true infections to reported cases in African nations since March 2020.\n\nResultsMultiplicative factors derived from serology data - in a subset of 12 nations - suggested a range of COVID-19 reporting rates, from 1 in 630 infections reported in Kenya (May 2020) to 1 in 15 infections reported in South Africa (November 2021). The largest multiplicative factor, 3,795, corresponded to Malawi (June 2020), suggesting <0.05% of infections captured. A similar set of multiplicative factors for all nations derived from postmortem data points toward the same conclusion: reported COVID-19 cases are unrepresentative of true infections, suggesting a key reason for low case burden in many African nations is significant underdetection and underreporting.\n\nConclusionsWhile estimating COVID-19s exact burden is challenging, the multiplicative factors we present provide incidence curves reflecting likely-to-worst-case ranges of infection. Our results stress the need for expansive surveillance to allocate resources in areas experiencing severe discrepancies between reported cases, projected infections, and deaths.\n\nSummaryHere we present a range of estimates quantifying the extent of underascertainment of COVID-19 cumulative incidence in Africa. These estimates, constructed from serology and mortality data, suggest that systematic underdetection and underreporting may be contributing to the seemingly low burden of COVID-19 reported in Africa.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicole Kogan", + "author_inst": "Harvard T. H. Chan School of Public Health | Northeastern University" + }, + { + "author_name": "Shae Gantt", + "author_inst": "Harvard T. H. Chan School of Public Health" + }, + { + "author_name": "David Swerdlow", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Muhammed Semakula", + "author_inst": "Rwanda Biomedical Centre" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T. H. Chan School of Public Health | CDC" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Northeastern University | Harvard T. H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.29.498117", "rel_title": "COVID-19 Neuropathology: evidence for SARS-CoV-2 invasion of Human Brainstem Nuclei", @@ -278814,45 +281204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2022.06.30.22277101", - "rel_title": "Online grocery shopping during the COVID-19 pandemic - perspectives of adolescents and young adults", - "rel_date": "2022-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277101", - "rel_abs": "ObjectiveTo assess perspectives of online grocery shopping during the COVID-19 pandemic among youth, rural residents, and Supplemental Nutrition Assistance Program (SNAP) participants.\n\nDesignOpen-ended text message survey data. Survey questions assessed rates of use and perspectives of online grocery shopping among youth and their families during the COVID-19 pandemic. Qualitative analysis of survey data from 875 participants (response rate=76.4%) to identify themes in experience with multivariable logistic regression to test associations between online grocery shopping (pickup, delivery, or either) with rurality and SNAP participation.\n\nSettingUnited States\n\nParticipantsNationwide text-messaging poll of youth (14-24 years-old) recruited to meet benchmarks based on the American Community Survey.\n\nResultsDuring the pandemic online grocery shopping was used frequently (46.7%). Safety and convenience were the primary reasons for preferring a shopping mode (in-person or online). Most online shoppers had positive experiences (59.4%), primarily due to convenience; negative experiences (28.3%) were from inaccuracies, inconveniences of the process, and delivery costs. Rural and suburban residence was associated with higher pickup (OR 2.02 and 1.51, respectively, p=.03) and lower delivery use (OR 0.33 and 0.72, respectively, p=.003) compared to urban residence. SNAP participation was not associated with any type of online grocery shopping.\n\nConclusionsOnline grocery shopping is common among youth and their families regardless of rurality or SNAP participation, but there are several youth-identified areas for improvement.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/22277101v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1deebb7org.highwire.dtl.DTLVardef@456b86org.highwire.dtl.DTLVardef@19656a9org.highwire.dtl.DTLVardef@113a660_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Eric J Brandt", - "author_inst": "University of Michigan Hospital" - }, - { - "author_name": "Nicole Hadler", - "author_inst": "University of Michigan Medical School" - }, - { - "author_name": "Ione Locher", - "author_inst": "University of Michigan Medical School" - }, - { - "author_name": "Charlie T Hoffs", - "author_inst": "Stanford University" - }, - { - "author_name": "Marika E Waselewski", - "author_inst": "University of Michigan Department of Family Medicine" - }, - { - "author_name": "Tammy Chang", - "author_inst": "University of Michigan Department of Family Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.30.22277080", "rel_title": "MENTAL STATUS OVERVIEW IN THE ELDERLY DURING THE COVID-19 PANDEMIC: A PHYLOSOPHICAL PERSPECTIVE", @@ -279768,6 +282119,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.07.01.22277163", + "rel_title": "Phase 2 randomised placebo-controlled trial of spironolactone and dexamethasone versus dexamethasone in COVID-19 hospitalised patients in Delhi", + "rel_date": "2022-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.01.22277163", + "rel_abs": "BackgroundIn this phase 2 randomised placebo-controlled clinical trial, we hypothesised that blocking mineralocorticoid receptors with spironolactone in patients with COVID-19 is safe and may reduce illness severity.\n\nMethodsHospitalised patients with confirmed COVID-19 were randomly allocated to low dose oral spironolactone (50mg day 1, then 25mg once daily for 21 days) or standard care in a 2:1 ratio. Both groups received dexamethasone 6mg for 10 days. Group allocation was blinded to the patient and research team. Primary outcomes were time to recovery, defined as the number of days until patients achieved WHO Ordinal Scale (OS) category [≤] 3, and the effect of spironolactone on aldosterone, D-dimer, angiotensin II and Von Willebrand Factor (VWF).\n\nResults120 patients were recruited in Delhi from 01 February to 30 April 2021. 74 were randomly assigned to spironolactone and dexamethasone (SpiroDex), and 46 to dexamethasone alone (Dex). There was no significant difference in the time to recovery between SpiroDex and Dex groups (SpiroDex median 4.5 days, Dex median 5.5 days, p = 0.055). SpiroDex patients had lower aldosterone levels on day 7 and lower D-dimer levels on days 4 and 7 (day 7 D-dimer mean SpiroDex 1.15{micro}g/mL, Dex 3.15 {micro}g/mL, p = 0.0004). There was no increase in adverse events in patients receiving SpiroDex. Post hoc analysis demonstrated reduced clinical deterioration (pre specified as escalating to WHO OS category >4) in the SpiroDex group vs Dex group (5.4% vs 19.6%).\n\nConclusionLow dose oral spironolactone in addition to dexamethasone was safe and reduced D-Dimer and aldosterone. Although time to recovery was not significantly reduced, fewer patients progressed to severe disease. Phase 3 randomised controlled trials with spironolactone should be considered.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Bharti Wadhwa", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Vikas Malhotra", + "author_inst": "Department of ENT & Head and Neck Surgery, Maulana Azad Medical College & Associated Hospitals, New Delhi, India" + }, + { + "author_name": "Sukhyanti Kerai", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Farah Husain", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Nalini Bala Pandey", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Kirti N Saxena", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Vinay Singh", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Tom Michael Quinn", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Feng Li", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Erin Gaughan", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Manu Shankar-Hari", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Bethany Mills", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Jean Antonelli", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Annya Bruce", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Keith Finlayson", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Anne Moore", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Christopher Edwards", + "author_inst": "Imperial College, Hammersmith Campus, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.06.30.498338", "rel_title": "Transcriptional Profiles Analysis of COVID-19 and Malaria Patients Reveals Potential Biomarkers in Children", @@ -280424,41 +282862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.29.22277056", - "rel_title": "Chronic fatigue, depression and anxiety symptoms in Long COVID are strongly predicted by neuroimmune and neuro-oxidative pathways which are caused by the inflammation during acute infection.", - "rel_date": "2022-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277056", - "rel_abs": "BackgroundLong-term coronavirus disease 2019 (Long COVID) is associated with physio-somatic (chronic fatigue syndrome and somatic symptoms) and affective (depression and anxiety) symptoms. The severity of the Long COVID physio-affective phenome is largely predicted by peak body temperature (BT) and lowered oxygen saturation (SpO2) during the acute infectious phase. This study aims to delineate whether the association of BT and SpO2 during the acute phase and the Long COVID physio-affective phenome is mediated by neurotoxicity (NT) resulting from activated immune-inflammatory and oxidative stress pathways.\n\nMethodsWe recruited 86 patients with Long COVID (3-4 months after the acute phase) and 39 healthy controls and assessed serum C-reactive protein (CRP), caspase-1, interleukin (IL)-1{beta}, IL-18, IL-10, myeloperoxidase (MPO), advanced oxidation protein products (AOPP), total antioxidant capacity (TAC), and calcium (Ca), as well as peak BT and SpO2 during the acute phase.\n\nResultsCluster analysis revealed that a significant part (34.9%) of Long COVID patients (n=30) show a highly elevated NT index computed based on IL-1{beta}, IL-18, Caspase-1, CRP, MPO and AOPP. Partial Least Squares analysis showed that 61.6% of the variance in the physio-affective phenome of Long COVID is explained by the NT index, lowered Ca, peak BT/SpO2 in the acute phase, and prior vaccinations with Astra-Zeneca or Pfizer. The most important predictors of the physio-affective phenome are Ca, CRP, IL-1{beta}, AOPP and MPO.\n\nConclusionThe infectious-immune-inflammatory core of acute COVID-19 strongly predicts the development of physio-affective symptoms 3-4 months later, and these effects are partly mediated by neuro-immune and neuro-oxidative pathways.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hussein Kadhem Al-Hakeim", - "author_inst": "kufa university" - }, - { - "author_name": "Haneen Tahseen Al-Rubaye", - "author_inst": "College of Medical laboratory Techniques, Imam Ja'afar Al-Sadiq University, Najaf, Iraq" - }, - { - "author_name": "Abbas F. Almulla", - "author_inst": "Chulalongkorn university" - }, - { - "author_name": "Dhurgham Shihab Al-Hadrawi", - "author_inst": "Al-Najaf Center for Cardiac Surgery and Transcatheter Therapy, Najaf, Iraq" - }, - { - "author_name": "Michael F. Maes", - "author_inst": "Chulalongkorn University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.30.22277084", "rel_title": "The Citation of Retracted COVID-19 Papers is Common and Rarely Critical", @@ -281442,6 +283845,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.29.22277010", + "rel_title": "Exploring the Role of Superspreading Events in SARS-CoV-2 Outbreaks", + "rel_date": "2022-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277010", + "rel_abs": "The novel coronavirus SARS-CoV-2 emerged in 2019 and subsequently spread throughout the world, causing over 529 million cases and 6 million deaths thus far. In this study, we formulate a continuous-time Markov chain model to investigate the influence of superspreading events (SSEs), defined here as public or social events that result in multiple infections over a short time span, on SARS-CoV-2 outbreak dynamics. Using Gillespies direct algorithm, we simulate a continuous-time Markov chain model for SARS-CoV-2 spread under multiple scenarios: first, with neither hospitalisation nor quarantine; second, with hospitalisation, quarantine, premature hospital discharge, and quarantine violation; and third, with hospitalisation and quarantine but neither premature hospital discharge nor quarantine violation. We also vary quarantine violation rates. Results indicate that, in most cases, SSE-dominated outbreaks are more variable but less severe than non-SSE-dominated outbreaks, though the most severe SSE-dominated outbreaks are more severe than the most severe non-SSE-dominated outbreaks. SSE-dominated outbreaks are outbreaks with relatively higher SSE rates. In all cases, SSE-dominated outbreaks are more sensitive to control measures, with premature hospital discharge and quarantine violation substantially reducing control measure effectiveness.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jordan Bramble", + "author_inst": "University of Kansas" + }, + { + "author_name": "Alexander Fulk", + "author_inst": "University of Kansas" + }, + { + "author_name": "Raul Saenz", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Folashade Agusto", + "author_inst": "University of Kansas" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.27.497749", "rel_title": "The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients", @@ -282386,49 +284820,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.06.27.497248", - "rel_title": "Pre-existing immunity modulates responses to mRNA boosters", - "rel_date": "2022-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.27.497248", - "rel_abs": "mRNA vaccines have shown high efficacy in preventing severe COVID-19, but breakthrough infections, emerging variants and waning antibody levels have warranted the use of boosters. Although mRNA boosters have been widely implemented, the extent to which pre-existing immunity influences the efficacy of boosters remains unclear. In a cohort of individuals primed with the mRNA-1273 or BNT162b2 vaccines, we observed that lower antibody levels before boost were associated with higher fold-increase in antibody levels after boost, suggesting that pre-existing antibody modulates the boosting capacity of mRNA vaccines. Mechanistic studies in mice show that pre-existing antibodies significantly limit antigen expression and priming of B cell responses after mRNA vaccination. Furthermore, we demonstrate that the relative superiority of an updated Omicron vaccine over the original vaccine is critically dependent on the serostatus of the host. These data demonstrate that pre-existing immunity dictates responses to mRNA vaccination, elucidating specific circumstances when updated SARS-CoV-2 vaccines confer superior protection to original vaccines.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tanushree Dangi", - "author_inst": "Northwestern University" - }, - { - "author_name": "Sarah Sanchez", - "author_inst": "Northwestern University" - }, - { - "author_name": "Min Han Lew", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lavanya Visvabharathy", - "author_inst": "Northwestern University" - }, - { - "author_name": "Justin M Richner", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Igor Koralnik", - "author_inst": "Northwestern University" - }, - { - "author_name": "Pablo Penaloza-MacMaster", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.27.497875", "rel_title": "Combination therapy with nirmatrelvir and molnupiravir improves the survival of SARS-CoV-2 infected mice", @@ -283272,6 +285663,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.24.22276852", + "rel_title": "Compliant citizens, defiant rebels or neither? Exploring changing COVID-19 vaccine attitudes and decisions in Bradford, UK: Findings from a follow-up qualitative study", + "rel_date": "2022-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276852", + "rel_abs": "BackgroundCOVID-19 vaccines have been the central pillar of the public health response to the pandemic, intended to enable us to live with Covid. It is important to understand COVID-19 vaccines attitudes and decisions in order to maximise uptake through an empathetic lens.\n\nObjectiveTo explore the factors that influenced peoples COVID-19 vaccines decisions and how attitudes towards the vaccines had changed in an eventful year.\n\nDesign and participantsThis is a follow up study that took place in Bradford, UK one year after the original study, between October 2021 and January 2022. In-depth phone interviews were conducted with 12 (of the 20 originally interviewed) people from different ethnic groups and areas of Bradford. Reflexive thematic analysis was conducted.\n\nResults11 of the 12 participants interviewed had received both doses of the COVID-19 vaccine and most intended to have a booster dose. Participants described a variety of reasons why they had decided to have the vaccines, including: feeling at increased risk at work; protecting family and others in their communities, unrestricted travel and being influenced by the vaccine decisions of family, friends and colleagues. All participants discussed ongoing interaction with COVID-19 misinformation and for some this meant they were uneasy about their decision to have the vaccine. They described feeling overloaded by and disengaged from COVID-19 information, which they often found contradictory and some felt mistrustful of the UK governments motives and decisions during the pandemic.\n\nConclusionsThe majority of participants had managed to navigate an overwhelming amount of circulating COVID-19 misinformation and chosen to have two or more COVID-19 vaccines, even if they had been previously said they were unsure. However, these decisions were complicated, and demonstrate the continuum of vaccine hesitancy and acceptance. This follow up study underlines that vaccine attitudes are changeable and contextual.\n\nPatient or Public ContributionThe original study was developed through a rapid community and stakeholder engagement process in 2020. Discussion with the Bradford Council Public Health team and the public through the Bradford COVID-19 Community Insights Group was undertaken in 2021 to identify important priorities for this follow up study.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Bridget Lockyer", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Rachael H Moss", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Charlotte Endacott", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Shahid Islam", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Laura Sheard", + "author_inst": "Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "- Bradford Institute for Health Research Covid-19 Scientific Advisory Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.22.22276744", "rel_title": "Vaccination saves lives: How do patients with chronic diseases and severe COVID-19 fare? Analysis from Indias National Clinical registry for COVID-19", @@ -283892,53 +286322,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.06.26.22276912", - "rel_title": "Coupling Wastewater-Based Epidemiological Surveillance and Modelling of SARS-COV-2/COVID-19: Practical Applications at the Public Health Agency of Canada", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.26.22276912", - "rel_abs": "Wastewater-based surveillance (WBS) of SARS-CoV-2 offers a complementary tool for clinical surveillance to detect and monitor Coronavirus Disease 2019 (COVID-19). Since both symptomatic and asymptomatic individuals infected with SARS-CoV-2 can shed the virus through the fecal route, WBS has the potential to measure community prevalence of COVID-19 without restrictions from healthcare-seeking behaviors and clinical testing capacity. During the Omicron wave, the limited capacity of clinical testing to identify COVID-19 cases in many jurisdictions highlighted the utility of WBS to estimate disease prevalence and inform public health strategies. However, there is a plethora of in-sewage, environmental and laboratory factors that can influence WBS outputs. The implementation of WBS therefore requires a comprehensive framework to outline an analysis pipeline that accounts for these complex and nuanced factors. This article reviews the framework of the national WBS conducted at the Public Health Agency of Canada to present WBS methods used in Canada to track and monitor SARS-CoV-2. In particular, we focus on five Canadian cities - Vancouver, Edmonton, Toronto, Montreal and Halifax - whose wastewater signals are analyzed by a mathematical model to provide case forecasts and reproduction number estimates. This work provides insights on approaches to implement WBS at the national scale in an accurate and efficient manner. Importantly, the national WBS system has implications beyond COVID-19, as a similar framework can be applied to monitor other infectious disease pathogens or antimicrobial resistance in the community.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Meong Jin Joung", - "author_inst": "Dalla Lana School of Public Health, University of Toronto. Public Health Agency of Canada, National Microbiology Laboratory" - }, - { - "author_name": "Chand S Mangat", - "author_inst": "Public Health Agency of Canada, National Microbiology Laboratory" - }, - { - "author_name": "Edgard Mejia", - "author_inst": "Public Health Agency of Canada, National Microbiology Laboratory" - }, - { - "author_name": "Audra Nagasawa", - "author_inst": "Statistics Canada" - }, - { - "author_name": "Anil Nichani", - "author_inst": "Public Health Agency of Canada, National Microbiology Laboratory" - }, - { - "author_name": "Carol Perez-Iratxeta", - "author_inst": "Statistics Canada" - }, - { - "author_name": "Shelley W Peterson", - "author_inst": "Public Health Agency of Canada, National Microbiology Laboratory" - }, - { - "author_name": "David Champredon", - "author_inst": "Public Health Agency of Canada" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.26.22276913", "rel_title": "Analysis of 16S rRNA gene sequence of nasopharyngeal exudate from healthy donors reveals changes in key microbial communities associated with aging", @@ -284946,6 +287329,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.23.497376", + "rel_title": "Monitoring SARS-CoV-2 infection using a double reporter-expressing virus", + "rel_date": "2022-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.23.497376", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the highly contagious agent responsible for the coronavirus disease 2019 (COVID-19) pandemic. An essential requirement for understanding SARS-CoV-2 fundamental biology and the impact of anti-viral therapeutics are robust methods to detect for the presence of the virus in infected cells or animal models. Despite the development and successful generation of recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter genes, knowledge acquired from their use in in vitro assays and/or in live animals are limited to the properties of the fluorescent or luciferase reporter genes. Herein, for the first time, we engineered a replication-competent rSARS-CoV-2 that expresses both fluorescent (mCherry) and luciferase (Nluc) reporter genes (rSARS-CoV-2/mCherry-Nluc) to overcome limitations associated with the use of a single reporter gene. In cultured cells, rSARS-CoV-2/mCherry-Nluc displayed similar viral fitness as rSARS-CoV-2 expressing single reporter fluorescent and luciferase genes (rSARS-CoV-2/mCherry and rSARS-CoV-2/Nluc, respectively), or wild-type (WT) rSARS-CoV-2, while maintaining comparable expression levels of both reporter genes. In vivo, rSARS-CoV-2/mCherry-Nluc has similar pathogenicity in K18 human angiotensin converting enzyme 2 (hACE2) transgenic mice than rSARS-CoV-2 expressing individual reporter genes, or WT rSARS-CoV-2. Importantly, rSARS-CoV-2/mCherry-Nluc facilitates the assessment of viral infection and transmission in golden Syrian hamsters using in vivo imaging systems (IVIS). Altogether, this study demonstrates the feasibility of using this novel bireporter-expressing rSARS-CoV-2 for the study SARS-CoV-2 in vitro and in vivo.\n\nIMPORTANCEDespite the availability of vaccines and antivirals, the coronavirus disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to ravage health care institutions worldwide. Previously, we have generated replication-competent recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter proteins to track viral infection in vitro and/or in vivo. However, these rSARS-CoV-2 are restricted to express only a single fluorescent or a luciferase reporter gene, limiting or preventing their use to specific in vitro assays and/or in vivo studies. To overcome this limitation, we have engineered a rSARS-CoV-2 expressing both fluorescent (mCherry) and luciferase (Nluc) genes and demonstrated its feasibility to study the biology of SARS-CoV-2 in vitro and/or in vivo, including the identification and characterization of neutralizing antibodies and/or antivirals. Using rodent models, we visualize SARS-CoV-2 infection and transmission through in vivo imaging systems (IVIS).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Richard K. Plemper", + "author_inst": "Georgia State University" + }, + { + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.23.497404", "rel_title": "The Functional Landscape of SARS-CoV-2 3CL Protease", @@ -285722,97 +288156,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.22.22276787", - "rel_title": "Improved SARS-CoV-2 neutralization of Delta and Omicron variants of concern after fourth vaccination in hemodialysis patients", - "rel_date": "2022-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276787", - "rel_abs": "BackgroundHemodialysis patients are exposed to a markedly increased risk when infected with SARS-CoV-2. To date it is unclear if hemodialysis patients benefit from a fourth vaccination.\n\nMethodsA total of 142 hemodialysis patients (median age 72.6 years, 33.8% female) received four COVID-19 vaccinations between December 2020 and March 2022. RDB binding antibody titers were determined in a competitive surrogate neutralization assay. Vero-E6 cells were infected with SARS-CoV-2 variants of concern (VoC) Delta (B.1.617.2) or Omicron (B.1.1.529, sub lineage BA.1) in a biosafety level 3 laboratory to determine serum infection neutralization capacity before and after vaccination.\n\nResultsAfter the fourth vaccination serum infection neutralization capacity significantly increased from a 50% inhibitory concentration (IC50, serum dilution factor 1:x) of 247.0 (46.3-1560.8) to 2560.0 (1174.0-2560.0) for the Delta VoC, and from 37.5 (20.0-198.8) to 668.5 (182.2-2560.0) for the Omicron VoC (each p<0.001). A significant increase of the neutralization capacity was even observed for patients who had high antibody titers after three vaccinations (p<0.001). Univariate regression analysis indicated immunosuppressive medication (p=0.001) and hepatitis B vaccination non-response (p=0.046), and multivariate analysis immunosuppressive medication as the only factor associated with a reduced effect against Delta (p<0.001). Ten patients with SARS-CoV-2 breakthrough infection before the fourth vaccination had by trend lower prior neutralization capacity for Omicron (p=0.051).\n\nConclusionsOur findings suggest that hemodialysis patients benefit from a fourth vaccination in particular in the light of the highly infectious SARS-CoV-2 Omicron variant. A routinely applied four-time vaccination seems to broaden immunity against variants and would be recommended in hemodialysis patients.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Cho-Chin Cheng", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology,, Klinikum rechts der Isar, Munich Germany" - }, - { - "author_name": "Louise Platen", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Catharina Christa", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, Helmholtz Center Munich, Klinikum rechts der Isar, Munich Germany" - }, - { - "author_name": "Myriam Tellenbach", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Verena Kappler", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Romina Bester", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, Helmholtz Center Munich, Klinikum rechts der Isar, Munich Germany" - }, - { - "author_name": "Bo-Hung Liao", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, Helmholtz Center Munich, Klinikum rechts der Isar, Munich Germany" - }, - { - "author_name": "Christopher Holzmannn-Littig", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany TUM Medical Education Center, Technica" - }, - { - "author_name": "Maia Werz", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Emely Schoenhals", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Eva Platen", - "author_inst": "Kidney Center Eifel Dialyse" - }, - { - "author_name": "Peter Eggerer", - "author_inst": "KfH Kidney Center Harlaching" - }, - { - "author_name": "Laetitia Treguer", - "author_inst": "KfH Kidney Center" - }, - { - "author_name": "Claudius Kuechle", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Christoph Schmaderer", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Uwe Heemann", - "author_inst": "Technical University of Munich, Germany; School of Medicine, Department of Nephrology, Klinikum rechts der Isar" - }, - { - "author_name": "Lutz Renders", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - }, - { - "author_name": "Ulrike Protzer", - "author_inst": "Technical University of Munich / Helmholtz Zentrum Muenchen" - }, - { - "author_name": "Matthias Christoph Braunisch", - "author_inst": "Technical University of Munich, School of Medicine, Department of Nephrology, Klinikum rechts der Isar, Munich, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2022.06.22.22276782", "rel_title": "Receipt of anti-SARS-CoV-2 pharmacotherapies among U.S. Veterans with mild to moderate COVID-19, January-February 2022", @@ -286720,6 +289063,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.21.22276724", + "rel_title": "COVID-19 rebound after Paxlovid and Molnupiravir during January-June 2022", + "rel_date": "2022-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.21.22276724", + "rel_abs": "ImportanceRecent case reports document that some patients who were treated with Paxlovid experienced rebound COVID-19 infections and symptoms 2 to 8 days after completing a 5-day course of Paxlovid. The Centers for Disease Control and Prevention (CDC) has recently issued a Health Alert Network Health Advisory to update the public on the potential for COVID-19 rebound after Paxlovid treatments. However, the rates of COVID-19 rebound in a real-world population or whether rebound is unique to Paxlovid remains unknown.\n\nObjectivesTo examine the rates and relative risks of COVID-19 rebound in patients treated with Paxlovid or with Molnupiravir and to compare characteristics of patients who experienced COVID-19 rebound to those who did not.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of electronic health records (EHRs) of 92 million patients from a multicenter and nationwide database in the US. The study population comprised 13,644 patients age [≥] 18 years who contracted COVID-19 between 1/1/2022-6/8/2022 and were treated with Paxlovid (n =11,270) or with Molnupiravir (n =2,374) within 5 days of their COVID-19 infection.\n\nExposuresPaxlovid or Molnupiravir.\n\nMain Outcomes and MeasuresThree types of COVID-19 rebound outcomes (COVID-19 infections, COVID-19 related symptoms, and hospitalizations) were examined. Hazard ratios and 95% confidence interval (CI) of 7-day and 30-day risk for COVID-19 rebound between patients treated with Paxlovid and patients treated with Molnupiravir were calculated before and after propensity-score matching.\n\nResultsThe 7-day and 30-day COVID-19 rebound rates after Paxlovid treatment were 3.53% and 5.40% for COVID-19 infection, 2.31% and 5.87% for COVID-19 symptoms, and 0.44% and 0.77% for hospitalizations. The 7-day and 30-day COVID-19 rebound rates after Molnupiravir treatment were 5.86% and 8.59% for COVID-19 infection, 3.75% and 8.21% for COVID-19 symptoms, and 0.84% and 1.39% for hospitalizations. After propensity-score matching, there were no significant differences in COVID-19 rebound risks between Paxlovid and Molnupiravir: infection (HR 0.90, 95% CI: 0.73-1.11), COVID-19 symptoms (HR: 1.03, 95% CI: 0.83-1.27), or hospitalizations (HR: 0.92, 95% CI: 0.56-1.55). Patients with COVID-19 rebound had significantly higher prevalence of underlying medical conditions than those without.\n\nConclusions and RelevanceCOVID-19 rebound occurred both after Paxlovid and Molnupiravir, especially in patients with underlying medical conditions. This indicates that COVID-19 rebound is not unique to Paxlovid and the risks were similar for Paxlovid and Molnupiravir. For both drugs the rates of COVID-19 rebound increased with time after treatments. Our results call for continuous surveillance of COVID-19 rebound after Paxlovid and Molnupiravir treatments. Studies are necessary to determine the mechanisms underlying COVID-19 rebounds and to test dosing and duration regimes that might prevent such rebounds in vulnerable patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lindsey Wang", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Nathan A Berger", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Pamela B Davis", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "David C Kaelber", + "author_inst": "MetroHealth" + }, + { + "author_name": "Nora Volkow", + "author_inst": "NIH/NIDA" + }, + { + "author_name": "Rong Xu", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.21.22276660", "rel_title": "Evidence of recent Epstein-Barr virus reactivation in individuals experiencing Long COVID", @@ -287628,209 +290010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.22.22276764", - "rel_title": "An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients", - "rel_date": "2022-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276764", - "rel_abs": "BackgroundWhilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.\n\nMethodsHere, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.\n\nResultsOur analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61 - 0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.\n\nConclusionsAlthough clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Bronner P Gon\u00e7alves", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "- ISARIC Clinical Characterisation Group", - "author_inst": "-" - }, - { - "author_name": "Matthew D Hall", - "author_inst": "University of Oxford" - }, - { - "author_name": "Waasila Jassat", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Valeria Balan", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Srinivas Murthy", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Christiana Kartsonaki", - "author_inst": "University of Oxford" - }, - { - "author_name": "Calum Semple", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Amanda Rojek", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Joaqu\u00edn Baruch", - "author_inst": "University of Oxford" - }, - { - "author_name": "Luis Felipe Reyes", - "author_inst": "Universidad de La Sabana" - }, - { - "author_name": "Abhishek Dasgupta", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Jake Dunning", - "author_inst": "University of Oxford" - }, - { - "author_name": "Barbara Wanjiru Citarella", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark Pritchard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alejandro Mart\u00edn-Quiros", - "author_inst": "Hospital Universitario La Paz" - }, - { - "author_name": "Uluhan Sili", - "author_inst": "Marmara University Pendik Training and Research Hospital" - }, - { - "author_name": "John Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh" - }, - { - "author_name": "Diptesh Aryal", - "author_inst": "Nepal Mediciti Hospital" - }, - { - "author_name": "Yaseen Arabi", - "author_inst": "King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences" - }, - { - "author_name": "Aasiyah Rashan", - "author_inst": "Critical Care Asia" - }, - { - "author_name": "Andrea Angheben", - "author_inst": "IRCCS Sacro Cuore Don Calabria Hospital" - }, - { - "author_name": "Janice Caoili", - "author_inst": "Makati Medical Center" - }, - { - "author_name": "Fran\u00e7ois Martin Carrier", - "author_inst": "Centre hospitalier de l'Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Ewen M Harrison", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Joan G\u00f3mez-Junyent", - "author_inst": "Universitat Aut\u00f2noma de Barcelona" - }, - { - "author_name": "Claudia Figueiredo-Mello", - "author_inst": "Instituto de Infectologia Em\u00eclio Ribas" - }, - { - "author_name": "James Joshua Douglas", - "author_inst": "Lions Gate Hospital" - }, - { - "author_name": "Mohd Basri Mat Nor", - "author_inst": "International Islamic University Malaysia" - }, - { - "author_name": "Yock Ping Chow", - "author_inst": "Clinical Research Centre, Sunway Medical Centre" - }, - { - "author_name": "Xin Ci Wong", - "author_inst": "Digital Health Research and Innovation Unit, Institute for Clinical Research, National Institutes of Health (NIH)" - }, - { - "author_name": "Silvia Bertagnolio", - "author_inst": "World Health Organization" - }, - { - "author_name": "Soe Soe Thwin", - "author_inst": "World Health Organization" - }, - { - "author_name": "Anca Streinu-Cercel", - "author_inst": "Carol Davila University of Medicine and Pharmacy" - }, - { - "author_name": "Leonardo Salazar", - "author_inst": "Fundaci\u00f3n Cardiovascular de Colombia" - }, - { - "author_name": "Asgar Rishu", - "author_inst": "Critical Care Research Unit, Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Rajavardhan Rangappa", - "author_inst": "Department of Critical Care Medicine, Manipal Hospital Whitefield," - }, - { - "author_name": "David S.Y. Ong", - "author_inst": "Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland" - }, - { - "author_name": "Madiha Hashmi", - "author_inst": "Critical Care Asia and Ziauddin University" - }, - { - "author_name": "Gail Carson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Janet Diaz", - "author_inst": "World Health Organization" - }, - { - "author_name": "Rob Fowler", - "author_inst": "Department of Critical Care Medicine, Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Moritz U G Kraemer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Evert-Jan Wils", - "author_inst": "Department of Intensive Care, Franciscus Gasthuis & Vlietland" - }, - { - "author_name": "Peter W Horby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laura Merson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Piero Luigi Olliaro", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.22.22276766", "rel_title": "Acceleration of regional, racial and gender disparities in drug overdoses across the United States driven by COVID-19 and fentanyl use", @@ -288670,6 +290849,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.06.20.22276596", + "rel_title": "Kinetics of neutralising antibodies against Omicron variant in Vietnamese healthcare workers after primary immunisation with ChAdOx1-S and booster with BNT162b2", + "rel_date": "2022-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276596", + "rel_abs": "We studied the development and persistence of neutralising antibodies against SARS-CoV-2 ancestral strain, and Delta and Omicron (BA.1 and BA.2) variants in Vietnamese healthcare workers (HCWs) up to 15 weeks after booster vaccination. We included 47 HCWs with different pre-existing immune statuses (group 1 (G1): n=21, and group 2 (G2): n=26 without and with prior breakthrough Delta variant infection, respectively). The study participants had completed primary immunisation with ChAdOx1-S and booster vaccination with BNT162b2. Neutralising antibodies were measured using a surrogate virus neutralisation assay. Of the 21 study participants in G1, neutralising antibodies against ancestral strain, Delta variant, BA.1 and BA.2 were (almost) abolished at month 8 after the second dose, but all had detectable neutralising antibodies to the study viruses at week two post booster dose. Of the 26 study participants in G2, neutralising antibody levels to BA.1 and BA.2 were significantly higher than those to the corresponding viruses measured at week 2 post breakthrough infection and before the booster dose. At week 15 post booster vaccination, neutralising antibodies to BA.1 and BA.2 dropped significantly, with more profound changes observed in those without breakthrough Delta variant infection. Booster vaccination enhanced neutralising activities against ancestral strain and Delta variant, as compared to those induced by primary vaccination. These responses were maintained at high levels for at least 15 weeks. Our findings emphasise the importance of the first booster dose in producing cross-neutralising antibodies against Omicron variant. A second booster dose might be needed to maintain long-term protection against Omicron variant.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nguyen Van Vinh Chau", + "author_inst": "Department of Health, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Lam Anh Nguyet", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Dung", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Vo Minh Quang", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Truong", + "author_inst": "Tan Phu Hospital, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Mau Toan", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Manh Hung", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dinh Nguyen Huy Man", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dao Bach Khoa", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Phong", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nghiem My Ngoc", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Huynh Phuong Thao", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dinh Thi Bich Ty", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Pham Ba Thanh", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thi Han Ny", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Kim Thanh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Cao Thu Thuy", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen To Anh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thi Thu Hong", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Nguyen Truc Nhu", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Lam Minh Yen", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Tran Tan Thanh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Van Tan", + "author_inst": "OUCRU-VN" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.14.22276397", "rel_title": "Association between Bisphosphonate use and COVID-19 related outcomes: a retrospective cohort study", @@ -289446,41 +291736,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2022.06.17.22276570", - "rel_title": "Is COVID-19 seasonal? A time series modeling approach", - "rel_date": "2022-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.17.22276570", - "rel_abs": "BackgroundDetermining whether SARS-CoV-2 is or will be seasonal like other respiratory viruses is critical for public health planning, including informing vaccine policy regarding the optimal timing for deploying booster doses. To help answer this urgent public health question, we evaluated whether COVID-19 case rates in the United States and Europe followed a seasonal pattern using time series models.\n\nMethodsWe analyzed COVID-19 data from Our World in Data from Mar 2020 through Apr 2022 for the United States (and Census Region) and five European countries (Italy, France, Germany, Spain, and the United Kingdom). For each, anomalies were identified using Twitters decomposition method and Generalized Extreme Studentized Deviate tests. We performed sensitivity analyses to determine the impact of data source (i.e., using US Centers for Disease Control and Prevention [CDC] data instead of OWID) and whether findings were similar after adjusting for multiple covariates. Finally, we determined whether our time series models accurately predicted seasonal influenza trends using US CDC FluView data.\n\nResultsAnomaly plots detected COVID-19 rates that were higher than expected between November and March each year in the United States and Europe. In the US Southern Census Region, in addition to seasonal peaks in the fall/winter, a second peak in Aug/Sep 2021 was identified as anomalous. Results were robust to sensitivity analyses.\n\nConclusionsOur results support employing annual protective measures against SARS-CoV-2 such as administration of seasonal booster vaccines or other non-pharmaceutical interventions in a similar timeframe as those already in place for influenza prevention.\n\nSummary of the Main PointAlthough SARS-CoV-2 continues to cause morbidity and mortality year-round due to its high transmissibility and rapid viral evolution, our results suggest that COVID-19 activity in the United States and Europe peaks during the traditional winter viral respiratory season.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Timothy Lee Wiemken", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Farid Khan", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Jennifer L Nguyen", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Luis Jodar", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "John M McLaughlin", - "author_inst": "Pfizer Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.18.22276591", "rel_title": "Estimating RSV seasonality from pandemic disruptions: a modelling study", @@ -290612,6 +292867,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.16.22276392", + "rel_title": "COVID-19 redux: clinical, virologic, and immunologic evaluation of clinical rebound after nirmatrelvir/ritonavir", + "rel_date": "2022-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276392", + "rel_abs": "Clinical rebound of COVID-19 after nirmatrelvir/ritonavir treatment has been reported. We performed clinical, virologic, and immune measurements in seven patients with symptomatic rebound, six after nirmatrelvir/ritonavir treatment and one without previous treatment. There was no evidence of severe disease or impaired antibody and T-cell responses in people with rebound symptoms.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Brian P Epling", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Joseph M Rocco", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Kristin L Boswell", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Elizabeth Laidlaw", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Frances Galindo", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Anela Kellogg", + "author_inst": "Leidos Biomedical Research" + }, + { + "author_name": "Sanchita Das", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Allison Roder", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Elodie Ghedin", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Allie Kreitman", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Robin L Dewar", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Sophie E. M. Kelly", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering" + }, + { + "author_name": "Heather Kalish", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering" + }, + { + "author_name": "Tauseef Rehman", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Jeroen Highbarger", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Adam Rupert", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Gregory Kocher", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Michael R Holbrook", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Andrea Lisco", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Maura Manion", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Richard A Koup", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Irini Sereti", + "author_inst": "National Institute of Allergy and Infectious Diseases" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.17.22276478", "rel_title": "The prevalence, incidence and longevity of antibodies against SARS-CoV-2 among primary healthcare providers in Belgium: a prospective cohort study with 12 months of follow-up", @@ -291300,29 +293658,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.13.22276321", - "rel_title": "Cycle threshold values in symptomatic COVID-19 cases in England", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276321", - "rel_abs": "IntroductionSince the start of the pandemic SARS-CoV-2 infection has most commonly been confirmed using reverse transcriptase polymerase chain reaction (RT-PCR), with results translated into a binary positive/negative outcomes. Previous studies have found that there is additional useful information in the level of the Cycle threshold (Ct value) of positive cases. Here we characterise variation in Ct values as a proxy for viral loads in more than 3 million test-positive COVID-19 cases in England with the aim of better quantifying the utility of such data.\n\nMethodsWe used individual N gene Ct values from symptomatic PCR positive (with Ct value less than 30) Pillar 2 cases in England who self-reported the date of symptom onset, and for whom age, reinfection status, variant status, and the number of vaccines received was available. Those with a positive test result more than 6 days after their reported symptom onset were excluded to mitigate the potential impact of recall bias. We used a generalised additive model, to estimate Ct values empirical mean Ct values for each strata of interest independently as well as to predict Ct values using a model that adjusted for a range of demographic and epidemiological covariates jointly. We present empirical Ct values and compare them to predicted mean Ct values.\n\nResultsWe found that mean Ct values varied by vaccine status, and reinfection status with the number of vaccine doses having little apparent effect. Modelling Ct values as a smooth function of time since onset and other variables struggled to reproduce the individual variation in the data but did match the population-level variation over time relatively well with this being apparently dominated by large differences between variants. Other variation over time was also captured to some degree though their remained several periods where the model could not capture the empirical means with a potential explanation being epidemic phase bias.\n\nConclusionsAnalysing a large dataset of routine Ct values from symptomatic COVID-19 cases in England we found variation based on time since symptom onset, vaccine status, age, and variant. Ct values were highest 1-3 days after symptom onset and differed most due to variant status. We found no clear correlation between previously estimated differences in intrinsic transmissibility and Ct values indicating that this is potentially mediated at least partly by factors other than viral load as estimated using Ct values. We found evidence that a model adjusting for a range of covariates could explain some of the population-level variation over time but systematically underestimated Ct values when incidence was increasing, and overestimated them when incidence was decreasing. This indicates the utility of Ct values from this data source as a tool for surveillance, potentially avoiding some of the biases of aggregated positive counts.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.15.22276467", "rel_title": "The influence of place on COVID-19 vaccine coverage in Alberta: A multilevel analysis", @@ -292442,6 +294777,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.06.13.22276339", + "rel_title": "Effects of hydrometeorological and other factors on SARS-CoV-2 reproduction number in three contiguous countries of Tropical Andean South America: a spatiotemporally disaggregated time series analysis.", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276339", + "rel_abs": "BackgroundThe COVID-19 pandemic has caused societal disruption globally and South America has been hit harder than other lower-income regions. This study modeled effects of 6 weather variables on district-level SARS-CoV-2 reproduction numbers (Rt) in three contiguous countries of Tropical Andean South America (Colombia, Ecuador, and Peru), adjusting for environmental, policy, healthcare infrastructural and other factors.\n\nMethodsDaily time-series data on SARS-CoV-2 infections were sourced from health authorities of the three countries at the smallest available administrative level. Rt values were calculated and merged by date and unit ID with variables from a Unified COVID-19 dataset and other publicly available sources for May - December 2020. Generalized additive mixed effects models were fitted.\n\nFindingsRelative humidity and solar radiation were inversely associated with SARS-CoV-2 Rt. Days with radiation above 1,000 KJ/m2 saw a 1.3%, and those with humidity above 50%, a 1.0% reduction in Rt. Transmission was highest in densely populated districts, and lowest in districts with poor healthcare access and on days with least population mobility. Temperature, region, aggregate government policy response and population age structure had little impact. The fully adjusted model explained 3.9% of Rt variance.\n\nInterpretationDry atmospheric conditions of low humidity increase, and higher solar radiation decrease district-level SARS-CoV-2 reproduction numbers, effects that are comparable in magnitude to population factors like lockdown compliance. Weather monitoring could be incorporated into disease surveillance and early warning systems in conjunction with more established risk indicators and surveillance measures.\n\nFundingNASAs Group on Earth Observations Work Programme (16-GEO16-0047).", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Josh M Colston", + "author_inst": "University of Virginia School of Medicine" + }, + { + "author_name": "Patrick Hinson", + "author_inst": "University of Virginia" + }, + { + "author_name": "Nhat-Lan H Nguyen", + "author_inst": "University of Virginia" + }, + { + "author_name": "Yen Ting Chen", + "author_inst": "Chi-Mei Medical Center" + }, + { + "author_name": "Hamada S. Badr", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Gaige H Kerr", + "author_inst": "George Washington University" + }, + { + "author_name": "Lauren Marie Gardner", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "David N Martin", + "author_inst": "University of Virginia School of Medicine" + }, + { + "author_name": "Antonio M Quispe", + "author_inst": "Universidad Continental" + }, + { + "author_name": "Francesca Schiaffino", + "author_inst": "Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Margaret N Kosek", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin F Zaitchik", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.15.22276436", "rel_title": "Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron", @@ -293682,49 +296080,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.06.15.496006", - "rel_title": "A single-component luminescent biosensor for the SARS-CoV-2 spike protein", - "rel_date": "2022-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.15.496006", - "rel_abs": "Many existing protein detection strategies depend on highly functionalized antibody reagents. A simpler and easier to produce class of detection reagent is highly desirable. We designed a single-component, recombinant, luminescent biosensor that can be expressed in laboratory strains of E. coli and S. cerevisiae. This biosensor is deployed in multiple homogenous and immobilized assay formats to detect recombinant SARS-CoV-2 spike antigen and cultured virus. The chemiluminescent signal generated facilitates detection by an un-augmented cell phone camera. Binding Activated Tandem split-enzyme (BAT) biosensors may serve as a useful template for diagnostics and reagents that detect SARS-CoV-2 antigens and other proteins of interest.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Matthew Ravalin", - "author_inst": "Stanford University" - }, - { - "author_name": "Heegwang Roh", - "author_inst": "Stanford University" - }, - { - "author_name": "Rahul Suryawanshi", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "G. Renuka Kumar", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "John E. Pak", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Melanie Ott", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Alice Y Ting", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.06.14.496214", "rel_title": "Oxysterols drive inflammation via GPR183 during influenza virus and SARS-CoV-2 infection", @@ -294636,6 +296991,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.09.22276030", + "rel_title": "Immunogenicity and safety of coadministration of COVID-19 and influenza vaccination among healthcare workers", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276030", + "rel_abs": "BackgroundA third dose of COVID-19 vaccination ( COVID booster vaccination) has become established as an important measure to strengthen the immune response against SARS-CoV-2. In contrast, seasonal influenza vaccination has been an important infection prevention measure for years, especially among highly exposed healthcare workers (HCWs). Coadministration of vaccines against COVID-19 and seasonal influenza could be an efficient strategy to protect HCWs from two major viral respiratory infections. Yet, the immunogenicity and safety of coadministration remains to be evaluated.\n\nMethodsThis study examines the differences in Anti-SARS-CoV-2-Spike IgG antibody formation as well as side effects based on a digital questionnaire after a third COVID-19 vaccination with or without coadministration of a seasonal quadrivalent influenza vaccine (Influvac Tetra vaccine 2021/2022). 1,231 HCWs were recruited who received a mRNA-based booster COVID-19 vaccination (mRNA-1273 or BNT162b2mRNA) after basic immunisation with BNT162b2mRNA twice. Anti-SARS-CoV-2-Spike IgG levels were determined at least 14 days after vaccination by SERION ELISA agile SARS-CoV-2 IgG.\n\nFindingsAnti-SARS-CoV-2-Spike IgG concentrations were by 25{middle dot}4% lower in individuals with coadministration of the seasonal quadrivalent influenza vaccination than without (p<0{middle dot}01). There was no statistically significant difference in the reported side effects. The concentration of Anti-SARS-CoV-2-Spike IgG was higher in HCWs who had received the influenza vaccine concomitantly with mRNA-1273 than with BNT162b2mRNA as third COVID-19 vaccine (p<0{middle dot}0001).\n\nInterpretationCoadministration of the seasonal quadrivalent influenza vaccine significantly limits the levels in Anti-SARS-CoV-2-Spike IgG levels, with a more restricted elevation in case of a BNT162b2mRNA booster vaccination compared with mRNA-1273 vaccine. The reduced humoral immune response in case of coadministration needs to be considered in seasonal vaccination recommendations, although the consequences of lower Anti-SARS-CoV-2-Spike IgG levels for the protection against SARS-CoV-2 infection and severe COVID-19 disease course are currently unknown. An augmented mRNA-based COVID-19 vaccine dosage may compensate for the restricted immunogenicity in case of coadministration.\n\nFundingThis study was funded by the Federal Ministry for Education and Science (BMBF) through a grant provided to the University Hospital of Wuerzburg by the Network University Medicine on COVID-19 (B-FAST, grant-No 01KX2021) as well as by the Free State of Bavaria with COVID-research funds provided to the University of Wuerzburg, Germany. Nils Petri is supported by the German Research Foundation (DFG) funded scholarship UNION CVD.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFor evaluation of the previously published evidence, PubMed and medRxiv were searched for the terms \"influenza vaccination\", \"influenza vaccine\", \"influenza\", \"flu\", \"seasonality\", combined with \"coadministration\", \"concomitant\", \"COVID-19 vaccination\", \"COVID-19 vaccine\", \"SARS-CoV-2\", in title or abstract, published between 1st of January 2020 and 18th of May 2022.\n\nTo date, it is unclear if coadministration of COVID-19 and influenza vaccine is effective and safe, particularly in the cohort of healthcare workers (HCWs) as key public health stakeholders. For the subunit COVID-19 vaccine NVX-CoV2373, an impairment of Anti-SARS-CoV-2-Spike IgG levels has been shown in individuals coadministered with a seasonal influenza vaccine. The two previously published studies on coadministration of a mRNA-based COVID-19 and a seasonal quadrivalent influenza vaccine have reported a restriction of humoral Anti-SARS-CoV-2-Spike immune response in the coadministration group. These examinations were conducted with limited correspondence to real-life conditions and in smaller cohorts. Additionally, these former studies do not consider the important aspect of side effects as a possible direct effect of the prevention measure on the availability of public health care in combination with Anti-SARS-CoV-2-Spike IgG levels. In summary, the humoral immunogenicity and side effects of a coadministered third COVID-19 and a seasonal influenza vaccine are still unclear and the limited available data is not transferable to the general public.\n\nAdded value of this studyWe performed the first large-scale real-life evaluation of humoral immunogenicity and side effects of COVID-19 and influenza vaccine coadministration in HCWs. Anti-SARS-CoV-2-Spike IgG levels were significantly lower in the coadministered cohort compared to the not coadministered control group, stratified by third COVID-19 vaccine (BNT162b2mRNA or mRNA-1273). Anti-SARS-CoV-2-Spike IgG post-vaccine elevation was lower among BNT162b2mRNA vaccinated HCWs than in those vaccinated with mRNA-1273 as a third COVID-19 vaccination. The influence of the seasonal quadrivalent influenza vaccine is evaluated in a cohort including 1,231 HCWs in total, covering a broad age range. Coadministration did not lead to an increase in side effects, which is a central requirement for considering the option of coadministration, given the role of HCWs as key personnel in maintaining health care capacities.\n\nImplications of all the available evidenceOur data suggest, that coadministration of third mRNA-based COVID-19 and quadrivalent seasonal influenza vaccine is safe and immunogenic, although it leads to a slightly reduced Anti-SARS-CoV-2-Spike antibody formation. While the clinical impact of the observed reduction in humoral Anti-SARS-CoV-2-Spike immune response for protection against SARS-CoV-2 infection and severe COVID-19 disease is still unclear, influenza vaccination remains an important infection prevention measure, especially among highly exposed HCWs. The coadministration does not increase side effects but may improve vaccination rate. A higher-dosed mRNA-based COVID-19 vaccine may compensate for the restricted immunogenicity in case of seasonal influenza vaccine coadministration. Our results will support the development of public health recommendations for coadministration of COVID-19 and influence vaccines in anticipation of the imminent infection waves in the coming winter season.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Isabell Wagenh\u00e4user", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Julia Reusch", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Alexander Gabel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Anna H\u00f6hn", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Thi\u00ean-Tr\u00ed L\u00e2m", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Giovanni Almanzar", + "author_inst": "Paediatric Rheumatology/Special Immunology, Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Martina Prelog", + "author_inst": "Paediatric Rheumatology/Special Immunology, Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Lukas B. Krone", + "author_inst": "Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; University Hospital of Psychiatry and Psychotherapy, University of Bern, Bern," + }, + { + "author_name": "Anna Frey", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Alexandra Schubert-Unkmeir", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Lars D\u00f6lken", + "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Stefan Frantz", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Oliver Kurzai", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg; Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-I" + }, + { + "author_name": "Ulrich Vogel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg," + }, + { + "author_name": "Nils Petri", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Manuel Krone", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg," + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.09.22276150", "rel_title": "Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2", @@ -295436,257 +297870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.09.22276228", - "rel_title": "Vaccine Effectiveness of Primary Series and Booster Doses against Omicron Variant COVID-19-Associated Hospitalization in the United States", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276228", - "rel_abs": "Objectives: To compare the effectiveness of a primary COVID-19 vaccine series plus a booster dose with a primary series alone for the prevention of Omicron variant COVID-19 hospitalization.\n\nDesign: Multicenter observational case-control study using the test-negative design to evaluate vaccine effectiveness (VE).\n\nSetting: Twenty-one hospitals in the United States (US).\n\nParticipants: 3,181 adults hospitalized with an acute respiratory illness between December 26, 2021 and April 30, 2022, a period of SARS-CoV-2 Omicron variant (BA.1, BA.2) predominance. Participants included 1,572 (49%) case-patients with laboratory confirmed COVID-19 and 1,609 (51%) control patients who tested negative for SARS-CoV-2. Median age was 64 years, 48% were female, and 21% were immunocompromised; 798 (25%) were vaccinated with a primary series plus booster, 1,326 (42%) were vaccinated with a primary series alone, and 1,057 (33%) were unvaccinated.\n\nMain Outcome Measures: VE against COVID-19 hospitalization was calculated for a primary series plus a booster and a primary series alone by comparing the odds of being vaccinated with each of these regimens versus being unvaccinated among cases versus controls. VE analyses were stratified by immune status (immunocompetent; immunocompromised) because the recommended vaccine schedules are different for these groups. The primary analysis evaluated all COVID-19 vaccine types combined and secondary analyses evaluated specific vaccine products.\n\nResults: Among immunocompetent patients, VE against Omicron COVID-19 hospitalization for a primary series plus one booster of any vaccine product dose was 77% (95% CI: 71-82%), and for a primary series alone was 44% (95% CI: 31-54%) (p<0.001). VE was higher for a boosted regimen than a primary series alone for both mRNA vaccines used in the US (BNT162b2: primary series plus booster VE 80% (95% CI: 73-85%), primary series alone VE 46% (95% CI: 30-58%) [p<0.001]; mRNA-1273: primary series plus booster VE 77% (95% CI: 67-83%), primary series alone VE 47% (95% CI: 30-60%) [p<0.001]). Among immunocompromised patients, VE for a primary series of any vaccine product against Omicron COVID-19 hospitalization was 60% (95% CI: 41-73%). Insufficient sample size has accumulated to calculate effectiveness of boosted regimens for immunocompromised patients.\n\nConclusions: Among immunocompetent people, a booster dose of COVID-19 vaccine provided additional benefit beyond a primary vaccine series alone for preventing COVID-19 hospitalization due to the Omicron variant.", - "rel_num_authors": 59, - "rel_authors": [ - { - "author_name": "Katherine Adams", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Jillian P. Rhoads", - "author_inst": "Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Diya Surie", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Manjusha Gaglani", - "author_inst": "Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas" - }, - { - "author_name": "Adit A. Ginde", - "author_inst": "Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado" - }, - { - "author_name": "Tresa McNeal", - "author_inst": "Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas" - }, - { - "author_name": "Shekhar Ghamande", - "author_inst": "Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas" - }, - { - "author_name": "David Huynh", - "author_inst": "Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado" - }, - { - "author_name": "H. Keipp Talbot", - "author_inst": "Departments of Medicine and Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Jonathan D. Casey", - "author_inst": "Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Nicholas M. Mohr", - "author_inst": "Department of Emergency Medicine, University of Iowa, Iowa City, Iowa" - }, - { - "author_name": "Anne Zepeski", - "author_inst": "Department of Emergency Medicine, University of Iowa, Iowa City, Iowa" - }, - { - "author_name": "Nathan I. Shapiro", - "author_inst": "Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts" - }, - { - "author_name": "Kevin W. Gibbs", - "author_inst": "Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina" - }, - { - "author_name": "D. Clark Files", - "author_inst": "Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina" - }, - { - "author_name": "Madeline Hicks", - "author_inst": "Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina" - }, - { - "author_name": "David N. Hager", - "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Harith Ali", - "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Matthew E. Prekker", - "author_inst": "Department of Emergency Medicine and Medicine, Hennepin County Medical Center, Minneapolis, Minnesota" - }, - { - "author_name": "Anne E. Frosch", - "author_inst": "Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota" - }, - { - "author_name": "Matthew C. Exline", - "author_inst": "Department of Medicine, The Ohio State University, Columbus, Ohio" - }, - { - "author_name": "Michelle N. Gong", - "author_inst": "Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York" - }, - { - "author_name": "Amira Mohamed", - "author_inst": "Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York" - }, - { - "author_name": "Nicholas J. Johnson", - "author_inst": "Department of Emergency Medicine and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington" - }, - { - "author_name": "Vasisht Srinivasan", - "author_inst": "Department of Emergency Medicine, University of Washington, Seattle, Washington" - }, - { - "author_name": "Jay S. Steingrub", - "author_inst": "Department of Medicine, Baystate Medical Center, Springfield, Massachusetts" - }, - { - "author_name": "Ithan D. Peltan", - "author_inst": "Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City, Utah" - }, - { - "author_name": "Samuel M. Brown", - "author_inst": "Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City, Utah" - }, - { - "author_name": "Emily T. Martin", - "author_inst": "School of Public Health, University of Michigan, Ann Arbor, Michigan" - }, - { - "author_name": "Arnold S. Monto", - "author_inst": "School of Public Health, University of Michigan, Ann Arbor, Michigan" - }, - { - "author_name": "Adam S. Lauring", - "author_inst": "Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan" - }, - { - "author_name": "Akram Khan", - "author_inst": "Department of Medicine, Oregon Health and Sciences University, Portland, Oregon" - }, - { - "author_name": "Catherine L. Hough", - "author_inst": "Department of Medicine, Oregon Health and Sciences University, Portland, Oregon" - }, - { - "author_name": "Laurence W. Busse", - "author_inst": "Department of Medicine, Emory University, Atlanta, Georgia" - }, - { - "author_name": "Caitlin C. ten Lohuis", - "author_inst": "Emory Critical Care Center, Emory Healthcare, Atlanta, Georgia" - }, - { - "author_name": "Abhijit Duggal", - "author_inst": "Department of Medicine, Cleveland Clinic, Cleveland, Ohio" - }, - { - "author_name": "Jennifer G. Wilson", - "author_inst": "Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California" - }, - { - "author_name": "Alexandra June Gordon", - "author_inst": "Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California" - }, - { - "author_name": "Nida Qadir", - "author_inst": "Department of Medicine, University of California-Los Angeles, Los Angeles, California" - }, - { - "author_name": "Steven Y. Chang", - "author_inst": "Department of Medicine, University of California-Los Angeles, Los Angeles, California" - }, - { - "author_name": "Christopher Mallow", - "author_inst": "Department of Medicine, University of Miami, Miami, Florida" - }, - { - "author_name": "Carolina Rivas", - "author_inst": "Department of Medicine, University of Miami, Miami, Florida" - }, - { - "author_name": "Hilary M. Babcock", - "author_inst": "Department of Medicine, Washington University, St. Louis, Missouri" - }, - { - "author_name": "Jennie H. Kwon", - "author_inst": "Department of Medicine, Washington University, St. Louis, Missouri" - }, - { - "author_name": "James D. Chappell", - "author_inst": "Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Natasha Halasa", - "author_inst": "Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Carlos G. Grijalva", - "author_inst": "Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Todd W. Rice", - "author_inst": "Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "William B. Stubblefield", - "author_inst": "Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Adrienne Baughman", - "author_inst": "Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Christopher J. Lindsell", - "author_inst": "Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Kimberly W. Hart", - "author_inst": "Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee" - }, - { - "author_name": "Sandra N. Lester", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Natalie J. Thornburg", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "SoHee Park", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Meredith L. McMorrow", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Manish M. Patel", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Mark W. Tenforde", - "author_inst": "CDC COVID-19 Response Team, Atlanta, Georgia" - }, - { - "author_name": "Wesley H. Self", - "author_inst": "Department of Emergency Medicine and Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.08.22276125", "rel_title": "Pediatric ARDS phenotypes in critical COVID-19: implications for therapies and outcomes.", @@ -296542,6 +298725,109 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.06.12.495779", + "rel_title": "An attenuated vaccinia vaccine encoding the SARS-CoV-2 spike protein elicits broad and durable immune responses, and protects cynomolgus macaques and human ACE2 transgenic mice from SARS-CoV-2 and its variants", + "rel_date": "2022-06-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.12.495779", + "rel_abs": "As long as the coronavirus disease 2019 (COVID-19) pandemic continues, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with altered antigenicity will emerge. The development of vaccines that elicit robust, broad, and durable protection against SARS-CoV-2 variants is urgently needed. We have developed a vaccine (rDIs-S) consisting of the attenuated vaccinia virus DIs strain platform carrying the SARS-CoV-2 S gene. rDIs-S induced neutralizing antibody and T-lymphocyte responses in cynomolgus macaques and human angiotensin converting enzyme 2 (hACE2) transgenic mice, and showed broad protection against SARS-CoV-2 isolates ranging from the early-pandemic strain (WK-521) to the recent Omicron BA. 1 variant (TY38-839). Using a tandem mass tag (TMT) -based quantitative proteomic analysis of lung homogenates from hACE2 transgenic mice, we found that, among mice subjected to challenge infection with WK-521, vaccination with rDIs-S prevented protein expression related to the severe pathogenic effects of SARS-CoV-2 infection (tissue destruction, inflammation, coagulation, fibrosis, and angiogenesis) and restored protein expression related to immune responses (antigen presentation and cellular response to stress). Furthermore, long-term studies in mice showed that rDIs-S maintains S protein-specific antibody titers for at least 6 months after a 1st vaccination. Thus, rDIs-S appears to provide broad and durable protective immunity against SARS-CoV-2, including current and possibly future variants.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Hirohito Ishigaki", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Fumihiko Yasui", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Misako Nakayama", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Akinori Endo", + "author_inst": "Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Naoki Yamamoto", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Kenzaburo Yamaji", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Cong Thanh Nguyen", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Yoshinori Kitagawa", + "author_inst": "Division of Microbiology and Infectious Diseases, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Takahiro Sanada", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Tomoko Honda", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Tsubasa Munakata", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Masahiko Higa", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Sakiko Toyama", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Risa Kono", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Asako Takagi", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Yusuke Matsumoto", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Kaori Hayashi", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Masanori Shiohara", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Koji Ishii", + "author_inst": "Department of Quality Assurance and Radiological Protection, National Institute of Infectious Diseases" + }, + { + "author_name": "Yasushi Saeki", + "author_inst": "Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Yasushi Itoh", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Michinori Kohara", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.13.495912", "rel_title": "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation", @@ -297098,69 +299384,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.06.10.495727", - "rel_title": "Hybrid immunity shifts the Fc-effector quality of SARS-CoV-2 mRNA vaccine-induced immunity", - "rel_date": "2022-06-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.10.495727", - "rel_abs": "Despite the robust immunogenicity of SARS-CoV-2 mRNA vaccines, emerging data reveal enhanced neutralizing antibody and T cell cross-reactivity among individuals that previously experienced COVID-19, pointing to a hybrid immune advantage with infection-associated immune priming. Beyond neutralizing antibodies and T cell immunity, mounting data point to a potential role for additional antibody effector functions, including opsinophagocytic activity, in the resolution of symptomatic COVID-19. Whether hybrid immunity modifies the Fc-effector profile of the mRNA vaccine-induced immune response remains incompletely understood. Thus, here we profiled the SARS-CoV-2 specific humoral immune response in a group of individuals with and without prior COVID-19. As expected, hybrid Spike-specific antibody titers were enhanced following the primary dose of the mRNA vaccine, but were similar to those achieved by naive vaccinees after the second mRNA vaccine dose. Conversely, Spike-specific vaccine-induced Fc-receptor binding antibody levels were higher after the primary immunization in individuals with prior COVID-19, and remained higher following the second dose compared to naive individuals, suggestive of a selective improvement in the quality, rather than the quantity, of the hybrid humoral immune response. Thus, while the magnitude of antibody titers alone may suggest that any two antigen exposures - either hybrid immunity or two doses of vaccine alone - represent a comparable prime/boost immunologic education, we find that hybrid immunity offers a qualitatively improved antibody response able to better leverage Fc effector functions against conserved regions of the virus.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Kathryn A Bowman", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Daniel Stein", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Sally Shin", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Kathie G. Ferbas", - "author_inst": "David Geffen School of Medicine, University of California Los Angeles" - }, - { - "author_name": "Nicole Tobin", - "author_inst": "UCLA" - }, - { - "author_name": "Colin Mann", - "author_inst": "Jonathan and Karin Fielding School of Public Health, University of California Los Angeles" - }, - { - "author_name": "Stephanie Fischinger", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Erica Ollmann Saphire", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Douglas Lauffenberger", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Anne Rimoin", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Grace Aldrovandi", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.10.495670", "rel_title": "SARS-CoV-2 minor variant genomes at the start of the pandemic contained markers of VoCs", @@ -298120,6 +300343,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.06.07.495170", + "rel_title": "Single-cell Multi-omics Integration for Unpaired Data by a Siamese Network with Graph-based Contrastive Loss", + "rel_date": "2022-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.495170", + "rel_abs": "Single-cell omics technology is being rapidly developed to measure the epigenome, genome, and transcriptome across a range of cell types. However, integrating omics data from different modalities is still challenging. Here, we propose a variation of the Siamese neural network framework called MinNet, which is trained to integrate multi-omics data on the single-cell resolution by utilizing graph-based contrastive loss. By training the model and testing it on several benchmark datasets, we showed its accuracy and generalizability in integrating scRNA-seq with scATAC-seq, and scRNA-seq with epitopes data. Further evaluation demonstrated our models unique capacity in removing the batch effect, which is a common problem in actual practice. To show how the integration impacts downstream analysis, we established model-based smoothing and cis-regulatory element inferring method and validated it with external pcHi-C evidence. Finally, the framework was applied to a COVID-19 dataset to compensate the original work with integration-based analysis, showing its necessity in single-cell multi-omics research.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chaozhong Liu", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Linhua Wang", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.06.07.495149", "rel_title": "SARS-CoV-2 spike protein induces long-term TLR4-mediated synapse and cognitive loss recapitulating Post-COVID syndrome", @@ -298840,77 +301086,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.05.494889", - "rel_title": "Neutralization of Omicron sublineages and Deltacron SARS-CoV-2 by 3 doses of BNT162b2 vaccine or BA.1 infection", - "rel_date": "2022-06-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494889", - "rel_abs": "Distinct SARS-CoV-2 Omicron sublineages have evolved showing increased fitness and immune evasion than the original Omicron variant BA.1. Here we report the neutralization activity of sera from BNT162b2 vaccinated individuals or unimmunized Omicron BA.1-infected individuals against Omicron sublineages and \"Deltacron\" variant (XD). BNT162b2 post-dose 3 immune sera neutralized USA-WA1/2020, Omicron BA.1-, BA.2-, BA.2.12.1-, BA.3-, BA.4/5-, and XD-spike SARS-CoV-2s with geometric mean titers (GMTs) of 1335, 393, 298, 315, 216, 103, and 301, respectively; thus, BA.4/5 SARS-CoV-2 spike variant showed the highest propensity to evade vaccine neutralization compared to the original Omicron variants BA.1. BA.1-convalescent sera neutralized USA-WA1/2020, BA.1-, BA.2-, BA.2.12.1-, BA.3-, BA.4/5-, and Deltacron-spike SARS-CoV-2s with GMTs of 15, 430, 110, 109, 102, 25, and 284, respectively. The low neutralization titers of vaccinated sera or convalescent sera from BA. 1 infected individuals against the emerging and rapidly spreading Omicron BA.4/5 variants provide important results for consideration in the selection of an updated vaccine in the current Omicron wave.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Chaitanya Kurhade", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Hongjie Xia", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Mingru Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Qi Yang", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Mark Cutler", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "David Cooper", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Alexander Muik", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ugur Sahin", - "author_inst": "BioNTech" - }, - { - "author_name": "Kathrin U. Jansen", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Ping Ren", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kena A. Swanson", - "author_inst": "Pfizer Vaccines Research & Development" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.07.495101", "rel_title": "Predicting clinical outcomes of SARS-CoV-2 drug treatments with a high throughput human airway on chip platform", @@ -300234,6 +302409,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.06.05.494856", + "rel_title": "A uniquely stable trimeric model of SARS-CoV-2 spike transmembrane domain", + "rel_date": "2022-06-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494856", + "rel_abs": "The spike (S) protein of SARS-CoV-2 effectuates membrane fusion and virus entry into target cells. Its transmembrane domain (TMD) represents a homotrimer of -helices anchoring the spike in the viral envelope. Although S-protein models available to date include the TMD, its precise configuration was given brief consideration. Understanding viral fusion entails realistic TMD models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD (S-TMD) based solely on its primary structure. First, we performed amino acid sequence pattern matching and compared molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and thus selected the TMD of the tumour necrosis factor receptor 1 (TNFR-1) for subsequent template-based modelling. We then iteratively built an all-atom homotrimer model of S-TMD based on \"dynamic MHP portraits\" and residue variability motifs. In this model each helix possessed two overlapping interfaces interacting with either of the remaining helices, which include conservative residues I1216, F1220, I1227, M1229, and M1233. Finally, the stability of this and several alternative models (including a recent NMR structure) and a set of mutant forms was tested in all-atom molecular dynamics (MD) simulations in a POPC bilayer mimicking the viral envelope membrane. Unlike other configurations, our model trimer remained extraordinarily tightly packed over a microsecond-range MD and retained its stability when palmitoylated in accordance with experimental data. Palmitoylation had no significant impact on the TMD conformation nor the way in which the lipid bilayer was perturbed in the presence of the trimer. Overall, the resulting model of S-TMD conforms to known basic principles of TM helix packing and will be further used to explore the complex machinery of membrane fusion from a broader perspective beyond the TMD.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Elena T. Aliper", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + }, + { + "author_name": "Nikolay A. Krylov", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + }, + { + "author_name": "Dmitry E. Nolde", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + }, + { + "author_name": "Anton A. Polyansky", + "author_inst": "Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria" + }, + { + "author_name": "Roman G. Efremov", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.06.05.493249", "rel_title": "Pathogen-Host Adhesion between SARS-CoV-2 S Proteins from Different Variants and Human ACE2 Probed at Single-Molecule and Single-Cell Levels", @@ -300890,37 +303100,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.06.06.491344", - "rel_title": "The T cell epitope landscape of SARS-CoV-2 variants of concern", - "rel_date": "2022-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.06.491344", - "rel_abs": "During the COVID-19 pandemic, several SARS-CoV-2 variants of concern (VOC) emerged, bringing with them varying degrees of health and socioeconomic burdens. In particular, the Omicron VOC displayed distinct features of increased transmissibility accompanied by anti-genic drift in the spike protein that partially circumvented the ability of pre-existing anti-body responses in the global population to neutralize the virus. However, T cell immunity has remained robust throughout all the different VOC transmission waves and has emerged as a critically important correlate of protection against SARS-CoV-2 and its VOCs, in both vaccinated and infected individuals. Therefore, as SARS-CoV-2 VOCs continue to evolve, it is crucial that we characterize the correlates of protection and the potential for immune escape for both B cell and T cell human immunity in the population. Generating the insights necessary to understand T cell immunity, experimentally, for the global human population is at present critical but a time consuming, expensive, and laborious process. Further, it is not feasible to generate global or universal insights into T cell immunity in an actionable time frame for potential future emerging VOCs. However, using computational means we can expedite and provide early insights into the correlates of T cell protection. In this study, we generated and reveal insights on the T cell epitope landscape for the five main SARS-CoV-2 VOCs observed to date. We demonstrated here using a unique AI prediction platform, a strong concordance in global T cell protection across all mutated peptides for each VOC. This was modeled using the most frequent HLA alleles in the human population and covers the most common HLA haplotypes in the human population. The AI resource generated through this computational study and associated insights may guide the development of T cell vaccines and diagnostics that are even more robust against current and future VOCs, and their emerging subvariants.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Simen Tennoe", - "author_inst": "NEC OncoImmunity AS" - }, - { - "author_name": "Marius Gheorghe", - "author_inst": "NEC OncoImmunity AS" - }, - { - "author_name": "Richard Stratford", - "author_inst": "NEC OncoImmunity AS" - }, - { - "author_name": "Trevor Clancy", - "author_inst": "NEC OncoImmunity AS" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.06.494969", "rel_title": "The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells and induces a hyper-inflammatory cytokine storm", @@ -302004,6 +304183,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.03.22275964", + "rel_title": "Indian Female Migrants Face Greater Barriers to Post-Covid Recovery than Males: Evidence from a Panel Study", + "rel_date": "2022-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.03.22275964", + "rel_abs": "BackgroundIndias abrupt nationwide Covid-19 lockdown internally displaced millions of urban migrants, who made arduous journeys to distant rural homes. Documenting their labor market reintegration is a critical aspect of understanding the economic costs of the pandemic for Indias poor. In a country marked by low and declining female labor force participation, identifying gender gaps in labor market reintegration - as a marker of both womens vulnerability at times of crisis and setbacks in womens agency - is especially important. Yet most studies of pandemic-displaced Indian migrants are small, rely on highly selected convenience samples, and lack a gender focus.\n\nMethodsBeginning in April 2020 we enrolled roughly 4,600 displaced migrants who had returned to two of Indias poorest states into a panel survey, which tracked enrollees through July 2021. Survey respondents were randomly selected from the states official databases of return migrants, with sampling stratified by state and gender. 85 percent of enrollees (3,950) were working in urban areas prior to the pandemic. Our analysis focuses on a balanced panel of 1,780 workers who were interviewed three times through July 2021, considering labor market re-entry, earnings, and measures of vulnerability by gender.\n\nFindingsBoth men and women struggle to remigrate - by July 2021 (over a year after the nationwide lockdown ended), no more than 63 percent (95% CI [60,66]) of men and 55 percent [51,59] of women had left their home villages since returning. Initially, returning migrants transition from non-agricultural urban employment into agriculture and unemployment in rural areas. Alongside, incomes plummet, with both genders earning roughly 17 percent of their pre-lockdown incomes in July 2020. Remigration is critical to regaining income - male re-migrants report earnings on par with their pre-lockdown incomes by January 2021, while men remaining in rural areas earn only 23 percent [19,27] of their pre-pandemic income. Remigration benefits women to a lesser extent - female remigrants regain no more than 65 percent [57,73] of their pre-pandemic income at any point. This contrast reflects significantly higher rates of unemployment among women, both among those remaining in rural areas (9 percentage points [6,13] higher than men across waves) and among those who remigrate (13 percentage points [9,17] higher than men across waves). As a result, we observe gender gaps in well-being: female migrants were 7 percentage points [4,10] more likely to report reduced consumption of essential goods and fare 6 percentage points [4,7] worse on a food security index.\n\nInterpretationReturn migrants of both genders experienced persistent hardships for over a year after the initial pandemic lockdown. Female migrants fare worse, driven by both lower rates of remigration and lower rates of labor market re-entry both inside and outside home villages. Some women drop out of the labor force entirely, but most unemployed report seeking or being available to work. In short, pandemic-induced labor market displacement has far-reaching, long-term consequences for migrant workers, especially women.\n\nFundingSurvey costs were funded by research grants from IZA/FCDO Gender, Growth, and Labour Markets in Low Income Countries Programme, J-PAL Jobs and Opportunity Initiative, and the Evidence-based Measures of Empowerment for Research on Gender Equality (EMERGE) program at University of California San Diego. Funders had no role in study design, study implementation, data analysis, or manuscript preparation.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSMost research documenting the experience of displaced domestic migrants during the pandemic is focused on difficulties faced in returning to their home villages and the immediate consequences of this displacement. Existing evidence has found high levels of short-run economic and psychological distress, especially among women and children, and under-coverage of government programs designed to ease the lockdowns sudden economic shock.\n\nAdded value of this studyThis study contributes to existing literature by surveying a large sample of male and female workers, designed to be broadly representative of returned migrants in two of Indias poorest states. Our work takes a longer-term view, tracking study participants efforts to remigrate and reintegrate into the labor force over 15 months. We document sustained difficulties attaining pre-pandemic levels of income and consumption insecurity, especially among women, who struggle even after remigrating.\n\nImplications of all the available evidenceTaken as a whole, the evidence underscores that displaced Indian migrants are a vulnerable and underserved social group, who have faced (and will likely continue to face) lasting negative effects of the Covid-19 pandemic. Displaced migrants - and especially women - would likely benefit from programs designed to facilitate re-entry into urban labor markets; wrap around services that address other effects of the pandemic (e.g. psychological distress) may be particularly valuable.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jenna Allard", + "author_inst": "MacMillan Center, Yale University" + }, + { + "author_name": "Maulik Jagnani", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Yusuf Neggers", + "author_inst": "University of Michigan" + }, + { + "author_name": "Rohini Pande", + "author_inst": "Economic Growth Center, Yale University" + }, + { + "author_name": "Simone Schaner", + "author_inst": "Center for Economic and Social Research, University of Southern California" + }, + { + "author_name": "Charity Troyer Moore", + "author_inst": "MacMillan Center, Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.02.22275918", "rel_title": "Delays in COVID-19 Diagnosis and Hospitalization and Outcomes -- New York City, New York, USA, October 2020-November 2021", @@ -302816,77 +305034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2022.06.02.494502", - "rel_title": "The Nucleocapsid Protein Of SARS-CoV-2, Combined With ODN-39M, Is A Potential Component For An Intranasal Bivalent Pancorona Vaccine", - "rel_date": "2022-06-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.02.494502", - "rel_abs": "Despite the rapid development of vaccines and their reported efficacy for controlling the COVID-19 waves, two key challenges remain: the scope of the immunity against upcoming variants and zoonosis events, and the induction of mucosal immunity able to clear the virus in the upper respiratory tract for halting the transmission. The present study is aiming at assessing a potential component for a new generation of vaccines so as to overcome such limitations. The recombinant nucleocapsid (N) protein from SARS-CoV-2 Delta variant was combined with a phosphodiester backbone CpG ODN (ODN-39M), forming high molecular weight aggregates. The evaluation of its immunogenicity in Balb/C mice revealed that only administration by intranasal route induced a systemic cross-reactive Cell-Mediated-Immunity (CMI). In turn, this combination was able to induce anti-N IgA in lungs, which along with the specific IgG in sera and CMI in spleen, resulted cross-reactive against the nucleocapsid protein of SARS-CoV-1. Furthermore, the nasal administration of the N+ODN-39M preparation combined with the RBD Delta protein, as inductor of neutralizing Abs, enhanced the local and systemic immune response against RBD with a modulation toward a Th1 pattern. Taken together, these results make the N+ODN-39M preparation a suitable component for a future intranasal pancorona vaccine against Sarbecoviruses. Particularly, the bivalent vaccine formulation N+ODN-39M+RBD could be used as an effective nasal booster in previously vaccinated population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Yadira Lobaina", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB) and China-Cuba Biotechnology Joint Innovation Center (CCBJIC)" - }, - { - "author_name": "Rong Chen", - "author_inst": "CCBJIC: China-Cuba Biotechnology Joint Innovation Center (CCBJIC) and Yongzhou Zhong Gu Biotechnology Co., Ltd" - }, - { - "author_name": "Edith Suzarte", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB)" - }, - { - "author_name": "Panchao Ai", - "author_inst": "China-Cuba Biotechnology Joint Innovation Center (CCBJIC) and Yongzhou Zhong Gu Biotechnology Co., Ltd" - }, - { - "author_name": "Vivian Huerta", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB) and China-Cuba Biotechnology Joint Innovation Center (CCBJIC)" - }, - { - "author_name": "Alexis Musacchio", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB) and China-Cuba Biotechnology Joint Innovation Center (CCBJIC)" - }, - { - "author_name": "Ricardo Silva", - "author_inst": "Representative Office BCF in China and China-Cuba Biotechnology Joint Innovation Center (CCBJIC)" - }, - { - "author_name": "Changyuan Tan", - "author_inst": "China-Cuba Biotechnology Joint Innovation Center (CCBJIC) and Yongzhou Zhong Gu Biotechnology Co., Ltd" - }, - { - "author_name": "Alejandro Martin", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB)" - }, - { - "author_name": "Laura Lazo", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB)" - }, - { - "author_name": "Gerardo Guillen", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB)" - }, - { - "author_name": "Ke Yang", - "author_inst": "China-Cuba Biotechnology Joint Innovation Center (CCBJIC) and Yongzhou Zhong Gu Biotechnology Co., Ltd" - }, - { - "author_name": "Yasser Perera", - "author_inst": "Center for Genetic Engineering and Biotechnology (CIGB) and China-Cuba Biotechnology Joint Innovation Center (CCBJIC)" - }, - { - "author_name": "Lisset Hermida", - "author_inst": "Representative Office BCF in China and China-Cuba Biotechnology Joint Innovation Center (CCBJIC)" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.01.494385", "rel_title": "Characterization of entry pathways, species-specific ACE2 residues determining entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants", @@ -303854,6 +306001,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.31.22274501", + "rel_title": "Severe acute respiratory syndrome coronavirus 2 breakthrough infections in healthcare workers vaccinees with BNT162b2 (Pfizer-BioNtech) in Bogota, Colombia", + "rel_date": "2022-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22274501", + "rel_abs": "The healthcare workers are considered as a high-risk group for infection with SARS-CoV-2, so they were included in the first stage of the National Plan for Vaccination against COVID-19 in Colombia.\n\nAn ongoing prospective cohort study to evaluate immune response to vaccination included 490 workers from health institutions in Bogota, Colombia, vaccinated between March and June 2021 with BNT162b2 (Pfizer-BioNtech). Multiple samples were collected during a follow-up period of 6 months after immunization. We report cases of asymptomatic and symptomatic SARS-CoV-2 infections detected in this cohort. For each participant demographic data, vaccination dates, results for SARS-CoV-2 RT-PCR, and detection of antibody (IgG) tests during the follow-up period were collected.\n\nSARS-CoV-2 infection was detected in 38 (7.7 %) volunteers. Of these, 81.6% had a positive RT-PCR for SARS-CoV-2, and 18.4% were confirmed by detection of IgG anti-SARS-CoV-2 nucleoprotein; 76.3% of infections occurred after 7 days of second dose. A total of 57.9% of the cases were asymptomatic. No hospitalizations or deaths were registered. When infection occurred, 81.6% of infected participants had presence of IgG anti-S antibodies. In 12 samples in which genomic characterization was achieved, 83.4% corresponded to the variant Mu, 8.3% Gamma, and 8.3% Delta.\n\nAll findings agree with other reports in different studies that show the benefit of COVID-19 vaccines, protecting specially against severe disease but not against infection or re-infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pilar Tavera-Rodriguez", + "author_inst": "Instituto Nacional de Salud Colombia" + }, + { + "author_name": "Juliana Barbosa-Ramirez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Andrea Bermudez-Forero", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diego Prada-Cardozo", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Jhonnatan Reales-Gonzalez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Dioselina Pelaez-Carvajal", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Malo-Sanchez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Maria-Ximena Meneses-Gil", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Marcela Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.31.22275746", "rel_title": "Symptom variation, correlations, and relationship to physical activity in Long Covid: intensive longitudinal study", @@ -304490,57 +306688,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.31.22275827", - "rel_title": "Descriptive Epidemiology of SARS-CoV-2 Gamma (P.1/501Y.V3) variant cases in England, August 2021", - "rel_date": "2022-05-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275827", - "rel_abs": "PurposeThe Gamma variant of SARS-CoV-2, first detected in travellers from Brazil, was found to have high transmissibility and virulence; following this finding, this paper aims to describe the epidemiology of Gamma cases in England from its first detection on 12 February 2021 to 31 August 2021.\n\nMethodsThe demographic analysis of Gamma cases was stratified by travel exposure. Travel-associated cases were further analysed by countries travelled from, stratified by categories set in place by the Red (highest risk countries), Amber, Green (lowest risk countries) travel policy, which was implemented from May to October 2021.\n\nResultsThere were 251 confirmed Gamma cases detected in England in the study period. 35.1% were imported, 5.6% were secondary, and 29.5% were not travel associated. Early cases were predominantly travel-associated, with later cases likely obtained through community transmission. 51.0% of travel-related cases were travellers from Amber countries, and 40.2% had at least one Red country in their journey.\n\nConclusionThe Gamma variant has not seen the same expansion as other variants such as Delta, most likely due to Delta out-competing community transmission of Gamma. Findings indicate the travel policy requiring quarantine for Red and Amber list travellers may have also contributed to preventing onward transmission of Gamma.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nurin Iwani Binti Abdul Aziz", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Katherine A Twohig", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Mary Sinnathamby", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Asad Zaidi", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Shirin Aliabadi", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Natalie Groves", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Sophie Nash", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Simon Thelwall", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Gavin Dabrera", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.30.22275787", "rel_title": "SARS-COV-2 Delta and Omicron community transmission networks", @@ -305476,6 +307623,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.29.22275277", + "rel_title": "Investigation of a SARS-CoV-2 outbreak in a Texas summer camp resulting from a single introduction", + "rel_date": "2022-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.29.22275277", + "rel_abs": "SARS-CoV-2 is the etiological agent responsible for the COVID-19 pandemic. It is estimated that only 10 aerosol-borne virus particles are sufficient to establish a secondary infection with SARS-CoV-2. However, the dispersal pattern of SARS-CoV-2 is highly variable and only 10- 20% of cases are responsible for up 80% of secondary infections. The heterogeneous nature of SARS-CoV-2 transmission suggests that super-spreader events play an important role in viral transmission. Super-spreader events occur when a single person is responsible for an unusually high number of secondary infections due to a combination of biological, environmental, and/or behavioral factors. While super-spreader events have been identified as a significant factor driving SARS-CoV-2 transmission, epidemiologic studies have consistently shown that education settings do not play a major role in community transmission. However, an outbreak of SARS-CoV-2 was recently reported among 186 children (aged 10-17) and adults (aged 18 +) after attending an overnight summer camp in Texas in June 2021. To understand the transmission dynamics of the outbreak, RNA was isolated from 36 nasopharyngeal swabs collected from patients that attended the camp and 19 control patients with no known connection to the outbreak. Genome sequencing on the Oxford Nanopore platform was performed using the ARTIC approaches for library preparation and bioinformatic analysis. SARS-CoV-2 amplicons were produced from all RNA samples and >70% of the viral genome was successfully reconstructed with >10X coverage for 46 samples. Phylogenetic methods were used to estimate the transmission history and suggested that the outbreak was the result of a single introduction. We also found evidence for secondary transmission from campers to the community. Together, these findings demonstrate that super-spreader events may occur during large gatherings of children.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Daniele Michele Swetnam", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Rojelio Elias Alvarado", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Stephanea Sotcheff", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Brooke M Mitchell", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Allan McConnell", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Rafael R.G. Machado", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Nehad Saada", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Florence P Haseltine", + "author_inst": "University of Texas at Arlington" + }, + { + "author_name": "Sara Maknojia", + "author_inst": "Galveston County Health District" + }, + { + "author_name": "Anajane Smith", + "author_inst": "University of Texas at Arlington" + }, + { + "author_name": "Ping Ren", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Philip Keiser", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Scott Weaver", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Andrew L Routh", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.29.22275262", "rel_title": "Incidence of Post-Covid Syndrome and Associated Symptoms in Outpatient Care in Bavaria, Germany", @@ -306080,61 +308298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.28.22275716", - "rel_title": "Tixagevimab/Cilgavimab for Prevention of COVID-19 during the Omicron Surge: Retrospective Analysis of National VA Electronic Data", - "rel_date": "2022-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.28.22275716", - "rel_abs": "BackgroundLittle is known regarding the effectiveness of tixagevimab/cilgavimab in preventing SARS-CoV-2 infection in this population, particularly after the emergence of the Omicron variant.\n\nObjectiveTo determine the effectiveness of tixagevimab/cilgavimab for prevention of SARS-CoV-2 infection and severe disease among immunocompromised patients.\n\nDesignRetrospective cohort study with propensity matching and difference-in-difference analyses.\n\nSettingU.S. Department of Veterans Affairs (VA) healthcare system.\n\nParticipantsVeterans age [≥]18 years as of January 1, 2022, receiving VA healthcare. We compared a cohort of 1,848 patients treated with at least one dose of intramuscular tixagevimab/cilgavimab to matched controls selected from 251,756 patients who were on immunocompromised or otherwise at high risk for COVID-19. Patients were followed through April 30, 2022, or until death, whichever occurred earlier.\n\nMain OutcomesComposite of SARS-CoV-2 infection, COVID-19-related hospitalization, and all-cause mortality. We used cox proportional hazards modelling to estimate the hazard ratios (HR) and 95% CI for the association between receipt of tixagevimab/cilgavimab and outcomes.\n\nResultsMost (69%) tixagevimab/cilgavimab recipients were [≥]65 years old, 92% were identified as immunocompromised in electronic data, and 73% had [≥]3 mRNA vaccine doses or two doses of Ad26.COV2. Compared to propensity-matched controls, tixagevimab/cilgavimab-treated patients had a lower incidence of the composite COVID-19 outcome (17/1733 [1.0%] vs 206/6354 [3.2%]; HR 0.31; 95%CI, 0.18-0.53), and individually SARS-CoV-2 infection (HR 0.34; 95%CI, 0.13-0.87), COVID-19 hospitalization (HR 0.13; 95%CI, 0.02-0.99), and all-cause mortality (HR 0.36; 95%CI, 0.18-0.73).\n\nLimitationsConfounding by indication and immortal time bias.\n\nConclusionsUsing national real-world data from predominantly vaccinated, immunocompromised Veterans, administration of tixagevimab/cilgavimab was associated with lower rates of SARS-CoV-2 infection, COVID-19 hospitalization, and all-cause mortality during the Omicron surge.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yinong Young-Xu", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, Vermont; Geisel School of Medicine at Dartmouth, Hanover, New Hampshire" - }, - { - "author_name": "Lauren Epstein", - "author_inst": "Atlanta Veterans Affairs Medical Center, Decatur, GA, USA" - }, - { - "author_name": "Vincent C Marconi", - "author_inst": "Atlanta Veterans Affairs Medical Center, Decatur, GA; Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA" - }, - { - "author_name": "Victoria Davey", - "author_inst": "US Department of Veterans Affairs, Office of Research and Development, Washington DC" - }, - { - "author_name": "Gabrielle Zwain", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Jeremy Smith", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Caroline Korves", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Fran Cunningham", - "author_inst": "US Department of Veterans Affairs, PBM, Center for Medication Safety, Hines, IL" - }, - { - "author_name": "Robert Bonomo", - "author_inst": "US Department of Veterans Affairs, VA SHIELD, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA" - }, - { - "author_name": "Adit A Ginde", - "author_inst": "University of Colorado School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.29.22275732", "rel_title": "Uncertainty Quantification in COVID-19 Detection Using Evidential Deep Learning", @@ -307186,6 +309349,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.27.493682", + "rel_title": "Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages", + "rel_date": "2022-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.27.493682", + "rel_abs": "SARS-CoV-2 variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding working mechanisms and developing therapeutic agents. In this study, we characterized previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-EM structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Xiaoman Li", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Yongbing Pan", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Qiangling Yin", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Zejun Wang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Sisi Shan", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Laixing Zhang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Jinfang Yu", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Yuanyuan Qu", + "author_inst": "Institution of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518107, China" + }, + { + "author_name": "Lina Sun", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Fang Gui", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Jia Lu", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Zhaofei Jing", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Wei Wu", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Tao Huang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Xuanling Shi", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Jiandong Li", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Xinguo Li", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Dexin Li", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Shiwen Wang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Maojun Yang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Linqi Zhang", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Kai Duan", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Mifang Liang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Xiaoming Yang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Xinquan Wang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.05.27.493400", "rel_title": "The Glycan-Specificity of the Pineapple Lectin AcmJRL and its Carbohydrate-Dependent Binding of the SARS-CoV-2 Spike Protein", @@ -308494,81 +310772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.25.22275610", - "rel_title": "A repeat pattern of founder events for SARS-CoV-2 variants in Alaska", - "rel_date": "2022-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22275610", - "rel_abs": "Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found that in Alaska the Omicron sublineage BA.2.3 overtook BA.1.1 by the week of 2022-02-27, reaching 48.5% of sequenced cases. On the contrary in the contiguous United States, BA.1.1 dominated cases for longer, eventually being displaced by BA.2 sublineages other than BA.2.3. BA.2.3 only reached a prevalence of 10.9% in the contiguous United States. Using phylogenetics, we found evidence of potential origins of the two major clades of BA.2.3 in Alaska and with logistic regression estimated how it emerged and spread throughout the state. The combined evidence is suggestive of founder events in Alaska and is reflective of how Alaskas unique dynamics influence the emergence of SARS-CoV-2 variants.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Tracie J. Haan", - "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA" - }, - { - "author_name": "Lisa K. Smith", - "author_inst": "Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA" - }, - { - "author_name": "Stephanie DeRonde", - "author_inst": "Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA" - }, - { - "author_name": "Elva House", - "author_inst": "Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA" - }, - { - "author_name": "Jacob Zidek", - "author_inst": "Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA" - }, - { - "author_name": "Diana Puhak", - "author_inst": "Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA" - }, - { - "author_name": "Logan Mullen", - "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA" - }, - { - "author_name": "Matthew Redlinger", - "author_inst": "Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska, USA" - }, - { - "author_name": "Jayme Parker", - "author_inst": "Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA" - }, - { - "author_name": "Brian M. Barnes", - "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA" - }, - { - "author_name": "Jason L. Burkhead", - "author_inst": "Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska, USA" - }, - { - "author_name": "Cindy Knall", - "author_inst": "WWAMI School of Medical Education, University of Alaska Anchorage, Anchorage, Alaska, USA" - }, - { - "author_name": "Eric Bortz", - "author_inst": "Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska, USA; WWAMI School of Medical Education, University of Alaska Anchorage, An" - }, - { - "author_name": "Jack Chen", - "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA; Alaska Division of Public Health, State of Alaska, Fairbanks, Alaska, USA; " - }, - { - "author_name": "Devin M. Drown", - "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA; Department of Biology and Wildlife, University of Alaska Fairbanks, Fairban" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.05.25.22275590", "rel_title": "Impact of school closures and reopening on COVID-19 caseload in 6 cities of Pakistan: An Interrupted Time Series Analysis", @@ -309556,6 +311759,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.26.493529", + "rel_title": "The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS CoV 2 coronavirus", + "rel_date": "2022-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.26.493529", + "rel_abs": "Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus has accumulated an important amount of genetic and genomic variability through mutation and recombination events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize all this sequence variability by computing the Sequence Compositional Complexity (SCC) in more than 23,000 high-quality coronavirus genome sequences from across the globe, covering the period spanning from the start of the pandemic in December 2019 to March 2022. In early samples, we found no statistical support for any trend in SCC values over time, although the virus as a whole appears to evolve faster than Brownian Motion expectation. However, in samples taken after the first Variant of Concern (VoC) with higher transmissibility (Alpha) emerges, and controlling for phylogenetic and sampling effects, we were able to detect a statistically significant trend for decreased SCC values over time. SARS-CoV-2 evolution towards lower values of genome heterogeneity is further intensified by the emergence of successive, widespread VoCs. Concomitantly to the temporal reduction in SCC, its absolute evolutionary rate kept increasing toward the present, meaning that the SCC decrease itself accelerated over time. As compared to Alpha or Delta variants, the currently dominant VoC, Omicron, shows much stronger trends in both SCC values and rates over time. These results indicate that the increases in fitness of variant genomes associated to a higher transmissibility leads to a reduction of their genome sequence heterogeneity, thus explaining the general slowdown of SCC along with the pandemic course.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jos\u00e9 L. Oliver", + "author_inst": "Professor of Genetics, Facultad de Ciencias, Universidad de Granada, Spain" + }, + { + "author_name": "Pedro Bernaola-Galv\u00e1n", + "author_inst": "Professor of Applied Physics, E.T.S. de Ingenieria de Telecomunicacion, Universidad de Malaga, Spain" + }, + { + "author_name": "Francisco Perfectti", + "author_inst": "Professor of Genetics, Grupo de Genetica Evolutiva, Departamento de Genetica and Research Unit Modeling Nature Evoflor, Unidad Asociada al CSIC, Universidad de" + }, + { + "author_name": "Cristina G\u00f3mez-Mart\u00edn", + "author_inst": "Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands" + }, + { + "author_name": "Pasquale Raia", + "author_inst": "Dip.to DiSTAR, Napoli Universita di Napoli Federico II, Dipartimento di Scienze della Terra, dell Ambiente e delle Risorse, Italy" + }, + { + "author_name": "Miguel Verd\u00fa", + "author_inst": "Centro de Investigaciones sobre Desertificacion, Consejo Superior de Investigaciones Cientificas (CSIC), University of Valencia and Generalitat Valenciana, 4611" + }, + { + "author_name": "Andr\u00e9s Moya", + "author_inst": "Professor of Genetics, University of Valencia Chair, Institutional Professorship FISABIO - University of Valencia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.05.21.22275421", "rel_title": "Analysis of the genetic diversity of SARS-CoV-2 genomes carrying the Omicron B.1.1.529 mutation", @@ -310404,85 +312650,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.25.493397", - "rel_title": "Distinct antigenic properties of the SARS-CoV-2 Omicron lineages BA.4 and BA.5", - "rel_date": "2022-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.25.493397", - "rel_abs": "Over the course of the pandemic variants have arisen at a steady rate. The most recent variants to emerge, BA.4 and BA.5, form part of the Omicron lineage and were first found in Southern Africa where they are driving the current wave of infection.\n\nIn this report, we perform an in-depth characterisation of the antigenicity of the BA.4/BA.5 Spike protein by comparing sera collected post-vaccination, post-BA.1 or BA.2 infection, or post breakthrough infection of vaccinated individuals with the Omicron variant. In addition, we assess sensitivity to neutralisation by commonly used therapeutic monoclonal antibodies.\n\nWe find sera collected post-vaccination have a similar ability to neutralise BA.1, BA.2 and BA.4/BA.5. In contrast, in the absence of vaccination, prior infection with BA.2 or, in particular, BA.1 results in an antibody response that neutralises BA.4/BA.5 poorly. Breakthrough infection with Omicron in vaccinees leads to a broad neutralising response against the new variants. The sensitivity of BA.4/BA.5 to neutralisation by therapeutic monoclonal antibodies was similar to that of BA.2.\n\nThese data suggest BA.4/BA.5 are antigenically distinct from BA.1 and, to a lesser extent, BA.2. The enhanced breadth of neutralisation observed following breakthrough infection with Omicron suggests that vaccination with heterologous or multivalent antigens may represent viable strategies for the development of cross-neutralising antibody responses.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Brian J. Willett", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Nazia Thakur", - "author_inst": "The Pirbright Institute, Woking, Surrey, UK, GU24 0NF" - }, - { - "author_name": "Joseph Newman", - "author_inst": "The Pirbright Institute, Woking, Surrey, UK, GU24 0NF" - }, - { - "author_name": "Maria Manali", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Grace Tyson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Nicola Logan", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Pablo R. Murcia", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Department of Infectious Disease, Imperial College London, UK, W2 1PG" - }, - { - "author_name": "Ksenia Sukhova", - "author_inst": "Department of Infectious Disease, Imperial College London, UK, W2 1PG" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Immunisation and Vaccine Preventable Diseases Division, UKHSA" - }, - { - "author_name": "Kevin Brown", - "author_inst": "Immunisation and Vaccine Preventable Diseases Division, UKHSA" - }, - { - "author_name": "Bryan Charleston", - "author_inst": "The Pirbright Institute, Woking, Surrey, UK, GU24 0NF" - }, - { - "author_name": "Emma C. Thomson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Wendy S. Barclay", - "author_inst": "Department of Infectious Diseases, Imperial College London, UK, W2 1PG" - }, - { - "author_name": "Dalan Bailey", - "author_inst": "The Pirbright Institute, Woking, Surrey, UK, GU24 0NF" - }, - { - "author_name": "Thomas P. Peacock", - "author_inst": "Department of Infectious Disease, Imperial College London, UK, W2 1PG" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.05.23.22275454", "rel_title": "Measuring Community Resilience During the COVID-19 based on Community Wellbeing and Resource Distribution", @@ -311458,6 +313625,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.20.22275407", + "rel_title": "Social divisions and risk perception can drive divergent epidemic dynamics and large second and third waves", + "rel_date": "2022-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.20.22275407", + "rel_abs": "During infectious disease outbreaks, individuals may adopt protective measures like vaccination and physical distancing in response to awareness of disease burden. Prior work showed how feedback between epidemic intensity and awareness-based behavior shapes disease dynamics (e.g., producing plateaus and oscillations). These models often overlook social divisions, where population subgroups may be disproportionately impacted by a disease and more responsive to the effects of disease within their group. We hypothesize that socially divided awareness-based behavior could fundamentally alter epidemic dynamics and shift disease burden between groups.\n\nWe develop a compartmental model of disease transmission in a population split into two groups to explore the impacts of awareness separation (relatively greater in-versus out-group awareness of epidemic severity) and mixing separation (relatively greater in-versus out-group contact rates). Protective measures are adopted based on awareness of recent disease-linked mortality. Using simulations, we show that groups that are more separated in awareness have smaller differences in mortality. Fatigue-driven abandonment of protective behavior can drive additional infection waves that can even exceed the size of the initial wave, particularly if uniform awareness drives early protection in one group, leaving that group largely susceptible to future infection. Finally, vaccine or infection-acquired immunity that is more protective against transmission and mortality may indirectly lead to more infections by reducing perceived risk of infection, and thereby reducing vaccine uptake. The dynamics of awareness-driven protective behavior, including relatively greater awareness of epidemic conditions in ones own group, can dramatically impact protective behavior uptake and the course of epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mallory J Harris", + "author_inst": "Biology Department, Stanford University, Stanford, CA 94301" + }, + { + "author_name": "Erin A. Mordecai", + "author_inst": "Biology Department, Stanford University, Stanford, CA 94301" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.22.22275417", "rel_title": "Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe COVID-19 outcomes in non-hospitalised patients: an observational cohort study using the OpenSAFELY platform", @@ -312286,109 +314476,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.05.21.492923", - "rel_title": "Intranasal pediatric parainfluenza virus-vectored SARS-CoV-2 vaccine candidate is protective in macaques", - "rel_date": "2022-05-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.21.492923", - "rel_abs": "Pediatric SARS-CoV-2 vaccines are needed that elicit immunity directly in the airways, as well as systemically. Building on pediatric parainfluenza virus vaccines in clinical development, we generated a live-attenuated parainfluenza virus-vectored vaccine candidate expressing SARS-CoV-2 prefusion-stabilized spike (S) protein (B/HPIV3/S-6P) and evaluated its immunogenicity and protective efficacy in rhesus macaques. A single intranasal/intratracheal dose of B/HPIV3/S-6P induced strong S-specific airway mucosal IgA and IgG responses. High levels of S-specific antibodies were also induced in serum, which efficiently neutralized SARS-CoV-2 variants of concern. Furthermore, B/HPIV3/S-6P induced robust systemic and pulmonary S-specific CD4+ and CD8+ T-cell responses, including tissue-resident memory cells in lungs. Following challenge, SARS-CoV-2 replication was undetectable in airways and lung tissues of immunized macaques. B/HPIV3/S-6P will be evaluated clinically as pediatric intranasal SARS-CoV-2/parainfluenza virus type 3 vaccine.\n\nOne-Sentence SummaryIntranasal parainfluenza virus-vectored COVID-19 vaccine induces anti-S antibodies, T-cell memory and protection in macaques.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Cyril Le Nouen", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Christine E Nelson", - "author_inst": "T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Xueqiao Liu", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Hong-Su Park", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Yumiko Matsuoka", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Cindy Luongo", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Celia Santos", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Lijuan Yang", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Richard Herbert", - "author_inst": "Experimental Primate Virology Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Ashley Castens", - "author_inst": "Experimental Primate Virology Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Ian N Moore", - "author_inst": "Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Temeri Wilder-Kofie", - "author_inst": "Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Rashida Moore", - "author_inst": "Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "April Walker", - "author_inst": "Tuberculosis Imaging Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Peng Zhang", - "author_inst": "Viral Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Paolo Lusso", - "author_inst": "Viral Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Reed F Johnson", - "author_inst": "SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Nicole L Garza", - "author_inst": "SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Laura E Via", - "author_inst": "Tuberculosis Imaging Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Shirin Munir", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Daniel Barber", - "author_inst": "T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Ursula J Buchholz", - "author_inst": "RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.23.493121", "rel_title": "Anti-chemokine antibodies after SARS-CoV-2 infection correlate with favorable disease course", @@ -313616,6 +315703,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.05.18.22275283", + "rel_title": "BNT162b2 induces robust cross-variant SARS-CoV-2 immunity in children", + "rel_date": "2022-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275283", + "rel_abs": "Currently available mRNA vaccines are extremely safe and effective to prevent severe SARS-CoV-2 infections. However, the emergence of novel variants of concerns has highlighted the importance of high population-based vaccine rates to effectively suppress viral transmission and breakthrough infections. While initially left out from vaccine efforts, children have become one of the most affected age groups and are key targets to stop community and household spread. Antibodies are central for vaccine induced protection and emerging data points to the importance of additional Fc effector functions like opsononophagocytosis or cytotoxicity, particularly in the context of variants of concern that escape neutralizing antibodies. Here, we observed delayed induction and reduced magnitude of vaccine induced antibody titers in children 5-11 years receiving two doses of the age recommended 10 g dose of the Pfizer SARS-CoV-2 BNT162b2 vaccine compared to adolescents (12-15 years) or adults receiving the 30 g dose. Conversely, children mounted equivalent or more robust neutralization and opsonophagocytic functions at peak immunogenicity, pointing to a qualitatively more robust humoral functional response in children. Moreover, broad cross-variants of concern responses were observed across children, with enhanced IgM and parallel IgG cross-reactivity to variants of concern (VOCs) in children compared to adults. Collectively, these data argue that despite the lower magnitude of the BNT162b2 induced antibody response in children, vaccine induced immunity in children target VOCs broadly and exhibit enhanced functionality that may contribute to attenuation of disease.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yannic C Bartsch", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jessica W Chen", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jaewon Kang", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Madeline D Burns", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Kerri J St.Denis", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Maegan L Sheehan", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jameson P Davis", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lael M Yonker", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.18.22275240", "rel_title": "Exploring barriers and facilitators to physical activity during the COVID-19 pandemic: a qualitative study", @@ -314280,77 +316422,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.05.19.492641", - "rel_title": "Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests", - "rel_date": "2022-05-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.19.492641", - "rel_abs": "Widespread and frequent testing is critical to prevent the spread of COVID-19, and rapid antigen tests are the diagnostic tool of choice in many settings. With new viral variants continuously emerging and spreading rapidly, the effect of mutations on antigen test performance is a major concern. In response to the spread of variants the National Institutes of Healths Rapid Acceleration of Diagnostics (RADx(R)) initiative created a Variant Task Force to assess the impact of emerging SARS-CoV-2 variants on in vitro diagnostic testing. To evaluate the impact of mutations on rapid antigen tests we developed a lentivirus-mediated mammalian surface-display platform for the SARS-CoV-2 Nucleocapsid protein, the target of the majority of rapid antigen tests. We employed deep mutational scanning (DMS) to directly measure the effect of all possible Nucleocapsid point mutations on antibody binding by 17 diagnostic antibodies used in 11 commercially available antigen tests with FDA emergency use authorization (EUA). The results provide a complete map of the antibodies epitopes and their susceptibility to mutational escape. This approach identifies linear epitopes, conformational epitopes, as well as allosteric escape mutations in any region of the Nucleocapsid protein. All 17 antibodies tested exhibit distinct escape mutation profiles, even among antibodies recognizing the same folded domain. Our data predict no vulnerabilities of rapid antigen tests for detection of mutations found in currently and previously dominant variants of concern and interest. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutation profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system. Further, our mammalian surface-display platform combined with DMS is a generalizable platform for complete mapping of protein-protein interactions.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Filipp Frank", - "author_inst": "Emory University" - }, - { - "author_name": "Meredith Marie Keen", - "author_inst": "Emory University" - }, - { - "author_name": "Anuradha Rao", - "author_inst": "Emory University" - }, - { - "author_name": "Leda Bassit", - "author_inst": "Emory University" - }, - { - "author_name": "Xu Liu", - "author_inst": "Emory University" - }, - { - "author_name": "Heather Brittany Bowers", - "author_inst": "Emory University" - }, - { - "author_name": "Anamika B Patel", - "author_inst": "Emory University" - }, - { - "author_name": "Michael L Cato", - "author_inst": "Emory University" - }, - { - "author_name": "Julie A Sullivan", - "author_inst": "Emory University" - }, - { - "author_name": "Morgan Greenleaf", - "author_inst": "Emory University" - }, - { - "author_name": "Anne Piantadosi", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Wilbur Lam", - "author_inst": "Emory University" - }, - { - "author_name": "William Hudson", - "author_inst": "Emory University" - }, - { - "author_name": "Eric A. Ortlund", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.20.492832", "rel_title": "The spike-stabilizing D614G mutation interacts with S1/S2 cleavage site mutations to promote the infectious potential of SARS-CoV-2 variants", @@ -315494,6 +317565,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.05.14.22275075", + "rel_title": "Self-medication practices and associated factors among COVID-19 recovered patients to prevent future infections: A web-based survey in Bangladesh", + "rel_date": "2022-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.14.22275075", + "rel_abs": "BackgroundHuman health is largely affected by self-medication in both ways, adversely and favorably, as evidenced by the COVID-19 pandemic. The fear of spreading COVID-19 among health workers and hospital environments has led many Bangladeshi people to practice self-medicate for as a preventive strategy against this disease. Consequently, this practice entails an improper and injudicious use of medicine to cure self-recognized symptoms. To date, the COVID-19 has no effective treatment. The lack of a cure for COVID-19 and the continual progression of the diseases in educational settings induce a substantial population to practice self-medication. Therefore a study of self-medication practices is necessary for the framework of the pandemic. This study aimed to estimate the prevalence and factors associated with self-medication to prevent or manage future COVID-19 infections among recovered COVID-19 patients.\n\nMethodsThis cross-sectional study was conducted from September 2020 to February 2021 using an e-survey along with 360 participants. Data were collected using a pre-tested self-reported questionnaire. Descriptive statistics and correlations analysis were performed in the study.\n\nResultsAmong 360 participants, males were 69.7%, and females 30.3%. The prevalence of self-medication is 11%, and monthly family income, residence, education, occupation, and previous history of SM are the associated factors. Among the participants, 29.7% use antibiotics, and 30% use herbal products or drugs as medication.\n\nConclusionThe present study found SMP is moderately prevalent among COVID-19 recovered patients. To minimize the rate of SMP, adequate health care access systems and public education should be introduced, and media & community should be engaged in rational use of medication.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Md. Safaet Hossain Sujan", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" + }, + { + "author_name": "Atefehsadat Haghighathoseini", + "author_inst": "Department of Health Administration and Policy, George Mason University" + }, + { + "author_name": "Rafia Tasnim", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh; Centre for Advanced Research Excellence in Public Health, " + }, + { + "author_name": "Md. Saiful Islam", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" + }, + { + "author_name": "Sarif Mahammad Salauddin", + "author_inst": "Sir Salimullah Medical College, Dhaka-1212, Bangladesh" + }, + { + "author_name": "Mohammad Mohiuddin Hasan", + "author_inst": "Hospital Services Management, DGHS, Mohakhali, Dhaka-1212, Bangladesh" + }, + { + "author_name": "Muhammad Ramiz Uddin", + "author_inst": "Department of Chemistry and Biochemistry, The university of Oklahoma, Norman, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.17.22275154", "rel_title": "COVID-19 booster dose antibody response in pregnant, lactating, and nonpregnant women", @@ -316146,61 +318260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.18.492546", - "rel_title": "mRNA-based vaccines against SARS-CoV-2 do not stimulate interferon stimulatory gene expression in individuals affected by Aicardi Goutieres Syndrome.", - "rel_date": "2022-05-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.18.492546", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses threats to individuals with rare disease, in part because so little is known about the impact of COVID-19 infection and vaccination safety in rare disease populations. Of particular concern, given the overlap in disease manifestations and interferon dysregulation, are a group of heritable autoinflammatory conditions called type I interferonopathies. The most common of these, Aicardi Goutieres Syndrome (AGS), is caused by altered nucleic acid metabolism and sensing, resulting in additional concerns surrounding the use of mRNA vaccination approaches. To determine whether mRNA vaccines induce an interferon response in AGS, we applied mRNA SARS-CoV-2 vaccines to whole blood samples and assessed internalization and interferon signaling gene expression responses to the mRNA. In all cases (11 AGS and 11 control samples), interferon signatures did not significantly increase from baseline, regardless of baricitinib treatment status in the AGS subjects, and were even decreased, when using codon optimized SARS-CoV-2 di-proline modified spike sequence (S2P). Internalization of S2P in human dendritic cells was verified by Western Blot, and in control and AGS blood cells was verified by Luciferase activity. Although numbers of tested samples in this rare disease are small, based on these findings, we suggest that COVID vaccination is unlikely to directly stimulate the interferon signaling gene expression in AGS patients via response to mRNA internalization. The in vitro nature of this study cannot exclude an exaggerated interferon response to spike protein production at a systemic level in individuals with a primary heritable interferonopathy. In the context of continued SARS-CoV-2 spread in the community, we do not recommend withholding vaccination in this rare disease group. However, we recommend that vaccinations for AGS patients are provided in a controlled setting with appropriate observation and used with caution in individuals with prior vaccine associated adverse events.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohamad-Gabriel Alameh", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Benjamin Davis", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Patrick Winters", - "author_inst": "Aicardi-Goutieres Syndrome Advocacy Association" - }, - { - "author_name": "Devon Cordova", - "author_inst": "Aicardi-Goutieres Syndrome Advocacy Association" - }, - { - "author_name": "Taibeen Khandaker", - "author_inst": "Aicardi-Goutieres Syndrome Advocacy Association" - }, - { - "author_name": "Houping Ni", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Ying Tam", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Paulo Lin", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Drew Weissman", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Justine Shults", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.19.492649", "rel_title": "Programming the lymph node immune response with Amphiphile-CpG induces potent cellular and humoral immunity following COVID-19 subunit vaccination in mice and non-human primates", @@ -317096,6 +319155,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.05.17.22275027", + "rel_title": "A Randomized Phase 2/3 Study of Ensitrelvir, a Novel Oral SARS-CoV-2 3C-like Protease Inhibitor, in Japanese Patients With Mild-to-Moderate COVID-19 or Asymptomatic SARS-CoV-2 Infection: Results of the Phase 2a Part", + "rel_date": "2022-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275027", + "rel_abs": "For the treatment of coronavirus disease 2019 (COVID-19), antiviral agents that can achieve rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reduction are warranted. This double-blind, phase 2a part of a phase 2/3 study assessed the efficacy and safety of ensitrelvir, a novel oral SARS-CoV-2 3C-like protease inhibitor, in Japanese patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection. Sixty-nine patients enrolled from 56 sites were randomized (1:1:1) to orally receive 5-day ensitrelvir fumaric acid (375 mg on day 1 followed by 125 mg daily or 750 mg on day 1 followed by 250 mg daily) or placebo and followed up until day 28. The primary outcome was change from baseline in SARS-CoV-2 viral titer. A total of 16, 14, and 17 patients in the ensitrelvir 125 mg, ensitrelvir 250 mg, and placebo groups, respectively, were included in the intention-to-treat population (mean age: 38.8, 40.4, and 38.0 years, respectively). On day 4, the change from baseline in SARS-CoV-2 viral titer (log10 50% tissue culture infectious dose/mL) in patients with positive viral titer and viral RNA at baseline was greater with ensitrelvir 125 mg (mean [standard deviation], -2.42 [1.42]; P = 0.0712) and 250 mg (-2.81 [1.21]; P = 0.0083) versus placebo (-1.54 [0.74]), and ensitrelvir treatment reduced SARS-CoV-2 RNA by -1.4 to -1.5 log10 copies/mL versus placebo. All adverse events were mild to moderate. Ensitrelvir treatment demonstrated rapid SARS-CoV-2 clearance and was well tolerated in patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection (Japan Registry of Clinical Trials identifier: jRCT2031210350).", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Hiroshi Mukae", + "author_inst": "Nagasaki University Graduate School of Biomedical Sciences" + }, + { + "author_name": "Hiroshi Yotsuyanagi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yohei Doi", + "author_inst": "University of Pittsburgh School of Medicine/Fujita Health University School of Medicine" + }, + { + "author_name": "Takumi Imamura", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takuhiro Sonoyama", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takahiro Fukuhara", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Genki Ichihashi", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takao Sanaki", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Keiko Baba", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Yosuke Takeda", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Yuko Tsuge", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takeki Uehara", + "author_inst": "Shionogi & Co., Ltd." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.16.22275163", "rel_title": "Performance and validation of an adaptable multiplex assay for detection of serologic response to SARS-CoV-2 infection or vaccination.", @@ -317752,41 +319878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.05.11.22274962", - "rel_title": "Performance study of a point-of-care antigen test during the SARS-CoV-2 Delta to Omicron variant transition in the USA", - "rel_date": "2022-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.11.22274962", - "rel_abs": "IntroductionConcerns have been raised regarding the accuracy of diagnostic antigen testing for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant. We compared the performance of the LumiraDx SARS-CoV-2 Antigen Test between symptomatic participants recruited prospectively during the Delta to Omicron variant transition in the USA.\n\nMethodsTwo paired anterior nasal swabs were collected from each participant (adults and children) within 12 days of symptom onset between November 24th, 2021 and February 1st, 2022, during which time Omicron replaced Delta as the dominant variant in the sample population. Swabs were tested by the LumiraDx SARS-CoV-2 Antigen Test and compared using real-time polymerase chain reaction (RT-PCR) reference testing. Reference samples identified as positive were sequenced to identify the SARS-CoV-2 variant. Positive percent agreement (PPA) was calculated, with results stratified by RT-PCR cycle threshold (Ct).\n\nResultsOf the 38 participants for whom LumiraDx SARS-CoV-2 Antigen Test results were available, 36 were confirmed positive by RT-PCR. Overall, PPA of the LumiraDx SARS-CoV-2 Antigen Test was 94.7% (95% confidence interval: 82.3%, 99.4%) and PPA was 100% for samples with a Ct <33. Sufficient viral load for sequencing was present in nine samples (six Delta, three Omicron), all of which returned a positive result using the LumiraDx SARS-CoV-2 Antigen Test. There were no performance differences observed between participants with the Delta and Omicron variants.\n\nConclusionsSARS-CoV-2 differences between Delta and Omicron variant mutations did not affect the performance of the LumiraDx SARS-CoV-2 Antigen Test which detects the nucleocapsid protein antigen. The LumiraDx SARS-CoV-2 Antigen Test can be a useful antigen test to diagnose emerging variants of coronavirus disease 2019.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Paul K Drain", - "author_inst": "University of Washington" - }, - { - "author_name": "Gregory Chiklis", - "author_inst": "Medical Research Network" - }, - { - "author_name": "Poppy Guest", - "author_inst": "LumiraDx" - }, - { - "author_name": "Nigel M Lindner", - "author_inst": "LumiraDx" - }, - { - "author_name": "Jayne E Ellis", - "author_inst": "LumiraDx" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.11.22274966", "rel_title": "Infection prevention and control preparedness among public hospitals and COVID-19 temporary treatment and monitoring facilities in the Philippines", @@ -318798,6 +320889,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2022.05.14.491911", + "rel_title": "SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution", + "rel_date": "2022-05-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.14.491911", + "rel_abs": "SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was responsible for disease in patients without comorbidity(97%), while Omicron BA.2 caused disease primarily in those with comorbidity(77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could possibly be due to evolutionary trade-off and explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Urvashi B Singh", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Sushanta Deb", + "author_inst": "All India institute of medical sciences" + }, + { + "author_name": "Rama Chaudhry", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Kiran Bala", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Lata Rani", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Ritu Gupta", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Lata Kumari", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jawed Ahmed", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Sudesh Gaurav", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Sowjanya Perumalla", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Md. Nizam", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Anwita Mishra", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "J. Stephenraj", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jyoti Shukla", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Deepika Bhardwaj", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jamshed Nayer", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Praveen Aggarwal", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Madhulika Kabra", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Vineet Ahuja", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Subrata Sinha", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Randeep Guleria", + "author_inst": "All India Institute of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.05.13.491763", "rel_title": "AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies", @@ -319338,53 +321528,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.11.22274305", - "rel_title": "Radiological Imaging of Viral Pneumonia Cases Identified Before the COVID-19 Pandemic Period and COVID-19 Pneumonia Cases Comparison of Characteristics", - "rel_date": "2022-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.11.22274305", - "rel_abs": "BackgroundThoracic CT imaging is widely used as a diagnostic method in the diagnosis of COVID-19 pneumonia. Radiological differential diagnosis and isolation of other viral agents causing pneumonia in patients gained importance, especially during the pandemic period.\n\nAimsWe aimed to investigate whether there is a difference between the CT imaging findings characteristically defined in COVID-19 pneumonia and the findings detected in pneumonia due to other viral agents, and which finding may be more effective in the diagnosis.\n\nStudy DesignThe study included 249 adult patients with pneumonia found in thorax CT examination and positive COVID-19 RT-PCR test and 94 patients diagnosed with non-COVID pneumonia (viral PCR positive, no bacterial/fungal agents were detected in other cultures) from the last 5 years before the pandemic. It was retrospectively analyzed using the PACS System. CT findings were evaluated by two radiologists with 5 and 20 years of experience who did not know to which group the patient belonged, and it was decided by consensus.\n\nMethodsDemographic data (age, gender, known chronic disease) and CT imaging findings (percentage of involvement, number of lesions, distribution preference, dominant pattern, ground-glass opacity distribution pattern, nodule, tree in bud sign, interstitial changes, crazy paving sign, reversed halo sign, vacuolar sign, halo sign, vascular enlargement, linear opacities, traction bronchiectasis, peribronchial wall thickness, air trapping, pleural retraction, pleural effusion, pericardial effusion, cavitation, mediastinal/hilar lymphadenopathy, dominant lesion size, consolidation, subpleural curvilinear opacities, air bronchogram, pleural thickening) of the patients were evaluated. CT findings were also evaluated with the RSNA consensus guideline and the CORADS scoring system. Data were divided into two main groups as non-COVID-19 and COVID-19 pneumonia and compared statistically with chi-square tests and multiple regression analysis of independent variables.\n\nResultsTwo main groups; RSNA and CORADS classification, percentage of involvement, number of lesions, distribution preference, dominant pattern, nodule, tree in bud, interstitial changes, crazy paving, reverse halo vascular enlargement, peribronchial wall thickness, air trapping, pleural retraction, pleural/pericardial effusion, cavitation and mediastinal/hilar lymphadenopathy were compared, significant differences were found between the groups (p < 0.01). Multiple linear regression analysis of independent variables found a significant effect of reverse halo sign ({beta} = 0.097, p <0.05) and pleural effusion ({beta} = 10.631, p <0.05) on COVID-19 pneumonia.\n\nConclusionPresence of reverse halo and absence of pleural effusion was found to be efficient in the diagnosis of COVID-19 pneumonia.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rana Gunoz COMERT", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Radiology Department" - }, - { - "author_name": "Eda CINGOZ", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Radiology Department" - }, - { - "author_name": "Sevim MESE", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Department of Medical Microbiology" - }, - { - "author_name": "Gorkem DURAK", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Radiology Department" - }, - { - "author_name": "Atadan TUNACI", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Radiology Department" - }, - { - "author_name": "Ali AGACFIDAN", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Department of Medical Microbiology" - }, - { - "author_name": "Mustafa ONEL", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Department of Medical Microbiology" - }, - { - "author_name": "Sukru Mehmet ERTURK", - "author_inst": "Istanbul University, Istanbul Faculty of Medicine, Radiology Department" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2022.05.10.22274869", "rel_title": "Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA", @@ -320368,6 +322511,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.10.491351", + "rel_title": "The SARS-CoV-2 Spike Protein Activates the Epidermal Growth Factor Receptor-Mediated Signaling", + "rel_date": "2022-05-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.10.491351", + "rel_abs": "ObjectivesThe coronavirus disease-19 (COVID-19) pandemic is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the molecular and cellular levels, the SARS-Cov-2 uses its envelope glycoprotein, the spike S protein, to infect the target cells in the lungs via binding with their transmembrane receptor, the angiotensin-converting enzyme 2 (ACE2). Here, we wanted to invesitgate if other molecular targets and pathways may be used by SARS-Cov-2.\n\nMethodsWe investigated the possibility for the spike 1 S protein and its receptor-binding domain (RBD) to target the epidermal growth factor receptor (EGFR) and its downstream signaling pathway in vitro using the lung cancer cell line (A549 cells). Protein expression and phosphorylation was examined upon cell treatment with the recombinant full spike 1 S protein or RBD.\n\nResultsWe demonstrate for the first time the activation of EGFR by the Spike 1 protein associated with the phosphorylation of the canonical ERK1/2 and AKT kinases and an increase of survivin expression controlling the survival pathway.\n\nConclusionsOur study suggests the putative implication of EGFR and its related signaling pathways in SARS-CoV-2 infectivity and Covid-19 pathology. This may open new perspectives in the treatment of Covid-19 patients by targeting EGFR.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Abdulrasheed Palakkott", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Aysha Alneyadi", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Khalid Muhammad", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Eid H Ali", + "author_inst": "Qatar University" + }, + { + "author_name": "Khaled Amiri", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Mohammed Akli Ayoub", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Rabah Iratni", + "author_inst": "The United Arab Emirates University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.05.12.491597", "rel_title": "Delivery of Circular mRNA via Degradable Lipid Nanoparticles against SARS-COV-2 Delta Variant", @@ -321076,33 +323262,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.07.490748", - "rel_title": "Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection", - "rel_date": "2022-05-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.07.490748", - "rel_abs": "The global effort to sequence millions of SARS-CoV-2 genomes has provided an unprecedented view of viral evolution. Characterizing how selection acts on SARS-CoV-2 is critical to developing effective, long-lasting vaccines and other treatments, but the scale and complexity of genomic surveillance data make rigorous analysis challenging. To meet this challenge, we develop Bayesian Viral Allele Selection (BVAS), a principled and scalable probabilistic method for inferring the genetic determinants of differential viral fitness and the relative growth rates of viral lineages, including newly emergent lineages. After demonstrating the accuracy and efficacy of our method through simulation, we apply BVAS to 6.9 million SARS-CoV-2 genomes. We identify numerous mutations that increase fitness, including previously identified mutations in the SARS-CoV-2 Spike and Nucleocapsid proteins, as well as mutations in non-structural proteins whose contribution to fitness is less well characterized. In addition, we extend our baseline model to identify mutations whose fitness exhibits strong dependence on vaccination status as well as pairwise interaction effects, i.e. epistasis. Strikingly, both these analyses point to the pivotal role played by the N501 residue in the Spike protein. Our method, which couples Bayesian variable selection with a diffusion approximation in allele frequency space, lays a foundation for identifying fitness-associated mutations under the assumption that most alleles are neutral.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Martin Jankowiak", - "author_inst": "Broad Institute" - }, - { - "author_name": "Fritz Heinrich Obermeyer", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Jacob Lemieux", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.05.09.491179", "rel_title": "Adenovirus-Vectored SARS-CoV-2 Vaccine Expressing S1-N Fusion Protein", @@ -322402,6 +324561,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.09.22274714", + "rel_title": "Mental-health before and during the COVID-19 pandemic in adults with neurodevelopmental disorders.", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274714", + "rel_abs": "The COVID-19 pandemic negatively impacted mental health globally. Individuals with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD), are at elevated risk of mental health difficulties. Therefore, we investigated the impact of the pandemic on anxiety, depression and mental wellbeing in adults with NDDs using longitudinal data from the Avon Longitudinal Study of Parents and Children study (n=3,058). Mental health data were collected pre-pandemic (age 21-25) and at three timepoints during the pandemic (ages 27-28) using the Short Mood and Feelings Questionnaire, Generalised Anxiety Disorder Assessment-7, and Warwick Edinburgh Mental Wellbeing Scale. ADHD and ASD were defined using validated cut-points of the Strengths and Difficulties Questionnaire and Autism Spectrum Quotient, self-reported at age 25. We used multi-level mixed-effects models to investigate changes in mental health in those with ADHD and ASD compared to those without. Prevalences of depression, anxiety and poor mental wellbeing were higher at all timepoints (pre-pandemic and during pandemic) in those with ADHD and ASD compared to those without. Anxiety increased to a greater extent in those with ADHD ({beta}=0.8 [0.2,1.4], p=0.01) and ASD ({beta}=1.2 [-0.1,2.5], p=0.07), while depression symptoms decreased, particularly in females with ASD ({beta}=-3.1 [-4.6,-1.5], p=0.0001). On average, mental wellbeing decreased in all, but to a lesser extent in those with ADHD ({beta}=1.3 [0.2,2.5], p=0.03) and females with ASD ({beta}=3.0 [0.2,5.9], p=0.04). To conclude, anxiety disproportionately increased in adults with NDDs during the pandemic, however, the related lockdowns may have provided a protective environment for depressive symptoms in the same individuals.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Amy Shakeshaft", + "author_inst": "Cardiff University" + }, + { + "author_name": "Rachel Blakey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lucy Riglin", + "author_inst": "Cardiff University" + }, + { + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Evie Stergiakouli", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Tilling", + "author_inst": "University of Bristol" + }, + { + "author_name": "Anita Thapar", + "author_inst": "Cardiff University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.05.10.22272976", "rel_title": "Have the COVID-19 Pandemic and Lockdown Affected Children's Mental Health in Long Term? A Repeated Cross-Sectional Study.", @@ -323222,33 +325428,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.09.22274854", - "rel_title": "COVID-19 Vaccine Acceptance and Uptake Among Healthcare Workers in Trinidad & Tobago.", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274854", - "rel_abs": "BackgroundCOVID-19 vaccine acceptance is important in ensuring the widespread vaccination of the population to achieve herd immunity. Establishing the acceptance of vaccines among healthcare workers, who play a vital role immunization program success, is important. The aim of this study was to assess the influence of social trust and demographic factors on COVID-19 vaccine acceptance among healthcare workers.\n\nMethodsA cross-sectional survey utilizing an electronic questionnaire inquiring about COVID-19 vaccine uptake, preferences, and concerns was distributed via email to 1,351 North Central Regional Health Authority (NCRHA) healthcare workers of the following categories: medical practitioners, nursing personnel, veterinary surgeons, medical interns, dental interns, paramedics, and pharmacists. These professions were selected as they were granted power to administer COVID-19 vaccines during this period of public emergency by the President of Trinidad and Tobago and were therefore likely to be NCRHA healthcare workers directly involved in vaccine administration services. 584 participants returned a completed questionnaire. Bivariate analysis using Chi-square analysis of association was used to determine the association between the respondents characteristics and the acceptance of the vaccine and the association between vaccine acceptance among healthcare workers and trust. The association between the acceptance of the COVID-19 vaccines and healthcare workers characteristics and trust was established using multinomial logistic regression.\n\nResultsA total of 584 healthcare workers took part in the study and 1.4% showed unwillingness to receive COVID-19 vaccine. The study indicates that age, profession, and the trust in international organizations and other healthcare providers predict the uptake of COVID-19 vaccines among healthcare workers. However, gender of the healthcare workers does not predict vaccine acceptance.\n\nConclusions and RelevanceEfforts towards enhanced vaccine acceptance among healthcare workers should take into consideration age, profession, and the trust in international organizations and other healthcare providers. Sensitization programs should be age-specific as well as occupation-based.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Chavin D. Gopaul", - "author_inst": "North Central Regional Health Authority" - }, - { - "author_name": "Dale Ventour", - "author_inst": "The University of the West Indies at St Augustine" - }, - { - "author_name": "Davlin Thomas", - "author_inst": "North Central Regional Health Authority" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.10.22274889", "rel_title": "Machine learning uncovers blood test patterns subphenotypes at hospital admission discerning increased 30-day ICU mortality rates in COVID-19 elderly patients", @@ -324184,6 +326363,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.05.06.22274782", + "rel_title": "Post-acute health care burden after SARS-CoV-2 infection: A retrospective cohort study among 530,892 adults", + "rel_date": "2022-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274782", + "rel_abs": "ImportanceThe SARS-CoV-2 pandemic portends a significant increase in health care use related to post-acute COVID sequelae, but the magnitude is not known.\n\nObjectiveTo assess the burden of post-acute health care use after a positive versus negative polymerase chain reaction (PCR) test for SARS-CoV-2.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of community-dwelling adults January 1, 2020 to March 31, 2021 in Ontario, Canada, using linked population-based health data. Follow-up began 56 days after PCR testing.\n\nExposuresIndividuals with a positive SARS-CoV-2 PCR test were matched 1:1 to individuals who tested negative based on hospitalization, test date, public health unit, sex, and a propensity score of socio-demographic and clinical characteristics.\n\nMain Outcomes and MeasuresThe health care utilization rate was the number of outpatient clinical encounters, homecare encounters, emergency department visits, days hospitalized, and days in long-term care per person-year. Mean health care utilization for test-positive versus negative individuals was compared using negative binomial regression, and rates at 95th and 99th percentiles were compared. Outcomes were also stratified by sex.\n\nResultsAmong 530,232 unique, matched individuals, mean age was 44 years (sd 17), 51% were female, and 0.6% had received [≥]1 COVID-19 vaccine dose. The mean rate of health care utilization was 11% higher in test-positive individuals (RR 1.11, 95% confidence interval [CI] 1.10-1.13). At the 95th percentile, test-positive individuals had 2.1 (95% CI 1.5-2.6) more health care encounters per person-year, and at the 99th percentile 71.9 (95% CI 57.6-83.2) more health care encounters per person-year. At the 95th percentile, test-positive women had 3.8 (95% CI 2.8-4.8) more health care encounters per person-year while there was no difference for men. At the 99th percentile, test-positive women had 76.7 (95% CI 56.3-89.6) more encounters per person-year, compared to 37.6 (95% CI 16.7-64.3) per person-year for men.\n\nConclusions and RelevancePost-acute health care utilization after a positive SARS-CoV-2 PCR test is significantly higher compared to matched test-negative individuals. Given the number of infections worldwide, this translates to a tremendous increase in use of health care resources. Stakeholders can use these findings to prepare for health care demand associated with long COVID.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow does the burden of health care use [≥]56 days after a positive SARS-CoV-2 polymerase chain reaction (PCR) test compare to matched individuals who tested negative?\n\nFindingsAfter accounting for multiple factors, the mean burden of post-acute health care use was 11% higher among those who tested positive, with higher rates of outpatient encounters, days hospitalized, and days in long-term care. Rates of homecare use were higher for test-positive women but lower for men.\n\nFor perspective, for every day in January 2022 with 100,000 or more infections, this translates to an estimated 72,000 additional post-acute health care encounters per year for the 1% of people who experienced the most severe complications of SARS-CoV-2; among those in the top 50% of health care use, this translates to 245,000 additional health care encounters per year. This increase will occur in the context of an ongoing pandemic and, in many health care systems, a depleted workforce and backlogs of care. Unless addressed, this increase is likely to exacerbate existing health inequities.\n\nMeaningGiven the large number of people infected, stakeholders can use these findings to plan for health care use associated with long COVID.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Candace D McNaughton", + "author_inst": "ICES, Sunnybrook Research Institute, and University of Toronto" + }, + { + "author_name": "Peter C Augstin", + "author_inst": "ICES, Sunnybrook Research Institute, Institute of Health Policy, Management and Evaluation, University of Toronto" + }, + { + "author_name": "Atul Sivaswamy", + "author_inst": "ICES" + }, + { + "author_name": "Jiming Fang", + "author_inst": "ICES" + }, + { + "author_name": "Husam Abdel-Qadir", + "author_inst": "ICES, Institute of Health Policy, Management and Evaluation, University of Toronto, Peter Munk Cardiac Centre, Toronto General Hospital, Division of Cardiology," + }, + { + "author_name": "Nick Daneman", + "author_inst": "ICES, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto" + }, + { + "author_name": "Jacob Allan Udell", + "author_inst": "Women's College Hospital" + }, + { + "author_name": "Walter Wodchis", + "author_inst": "ICES, Sunnybrook Research Institute" + }, + { + "author_name": "Ivona Mostarac", + "author_inst": "Sunnybrook Research Institute" + }, + { + "author_name": "Clare L Atzema", + "author_inst": "ICES, Sunnybrook Research Institute, Institute of Health Policy, Management and Evaluation, University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.05.22273234", "rel_title": "Changes in English medication safety indicators throughout the COVID-19 pandemic: a federated analysis of 57 million patients' primary care records in situ using OpenSAFELY", @@ -324940,145 +327174,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.05.22274628", - "rel_title": "The I-SPY COVID Adaptive Platform Trial for COVID-19 Acute Respiratory Failure: Rationale, Design and Operations", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.05.22274628", - "rel_abs": "IntroductionThe COVID-19 pandemic brought an urgent need to discover novel effective therapeutics for patients hospitalized with severe COVID-19. The ISPY COVID trial was designed and implemented in early 2020 to evaluate investigational agents rapidly and simultaneously on a phase 2 adaptive platform. This manuscript outlines the design, rationale, implementation, and challenges of the ISPY COVID trial during the first phase of trial activity from April 2020 until December 2021.\n\nMethods and analysisThe ISPY COVID Trial is a multi-center open label phase 2 platform trial in the United States designed to evaluate therapeutics that may have a large effect on improving outcomes from severe COVID-19. The ISPY COVID Trial network includes academic and community hospitals with significant geographic diversity across the country. Enrolled patients are randomized to receive one of up to four investigational agents or a control and are evaluated for a family of two primary outcomes--time to recovery and mortality. The statistical design uses a Bayesian model with \"stopping\" and \"graduation\" criteria designed to efficiently discard ineffective therapies and graduate promising agents for definitive efficacy trials. Each investigational agent arm enrolls to a maximum of 125 patients per arm and is compared to concurrent controls. As of December 2021, 11 investigational agent arms had been activated, and 8 arms were complete. Enrollment and adaptation of the trial design is ongoing.\n\nEthics and disseminationISPY COVID operates under a central institutional review board via Wake Forest School of Medicine IRB00066805. Data generated from this trial will be reported in peer reviewed medical journals.\n\nTrial registration numberClinicaltrials.gov registration number NCT04488081\n\nStrengths and limitations of this studyO_LIThe ISPY COVID Trial was developed in early 2020 to rapidly and simultaneously evaluate therapeutics for severe COVID-19 on an adaptive open label phase 2 platform\nC_LIO_LIThe ISPY COVID Adaptive Platform Trial Network is an academic-industry partnership that includes academic and community hospitals spanning a wide geographic area across the United States\nC_LIO_LIOf December 2021, 11 investigational agent arms have been activated on the ISPY COVID Trial Platform\nC_LIO_LIThe ISPY COVID Trial was designed to identify therapeutic agents with a large clinical effect for further testing in definitive efficacy trials--limitations to this approach include the risk of a type 2 error\nC_LI", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "D. Clark Files", - "author_inst": "Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Michael A. Matthay", - "author_inst": "University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Carolyn S. Calfee", - "author_inst": "University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Neil Aggarwal", - "author_inst": "University of Colorado, School of Medicine, Aurora, CO, USA" - }, - { - "author_name": "Adam L. Asare", - "author_inst": "Quantum Leap Healthcare Collaborative, San Francisco, CA, USA" - }, - { - "author_name": "Jeremy R. Beitler", - "author_inst": "Columbia University, Irving Medical Center, New York, NY, USA" - }, - { - "author_name": "Paul A. Berger", - "author_inst": "Sanford Medical Center, Sioux Falls, SD, USA" - }, - { - "author_name": "Ellen L. Burnham", - "author_inst": "University of Colorado, School of Medicine, Aurora, CO, USA" - }, - { - "author_name": "George Cimino", - "author_inst": "Quantum Leap Healthcare Collaborative, San Francisco, CA, USA" - }, - { - "author_name": "Melissa H. Coleman", - "author_inst": "University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Alessio Crippa", - "author_inst": "Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Andrea Discacciati", - "author_inst": "Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Sheetal Gandotra", - "author_inst": "University of Alabama at Birmingham, Birmingham, AL, USA" - }, - { - "author_name": "Kevin W. Gibbs", - "author_inst": "Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Paul T. Henderson", - "author_inst": "Quantum Leap Healthcare Collaborative, San Francisco, CA, USA" - }, - { - "author_name": "Carolyn A.G. Ittner", - "author_inst": "University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA" - }, - { - "author_name": "Alejandra Jauregui", - "author_inst": "University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Kashif T. Khan", - "author_inst": "University of Southern California, Los Angeles, CA, USA" - }, - { - "author_name": "Jonathan L. Koff", - "author_inst": "Yale School of Medicine, New Haven, CT, USA" - }, - { - "author_name": "Julie Lang", - "author_inst": "University of Southern California, Los Angeles, CA, USA" - }, - { - "author_name": "Mary LaRose", - "author_inst": "Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Joe Levitt", - "author_inst": "Stanford Healthcare, Stanford, CA, USA" - }, - { - "author_name": "Ruixiao Lu", - "author_inst": "Quantum Leap Healthcare Collaborative, San Francisco, CA, USA" - }, - { - "author_name": "Jeffrey D. McKeehan", - "author_inst": "University of Colorado, School of Medicine, Aurora, CO, USA" - }, - { - "author_name": "Nuala J. Meyer", - "author_inst": "University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA" - }, - { - "author_name": "Derek W. Russell", - "author_inst": "University of Alabama at Birmingham, Birmingham, AL, USA" - }, - { - "author_name": "Karl W. Thomas", - "author_inst": "Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Martin Eklund", - "author_inst": "Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Laura J. Esserman", - "author_inst": "University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Kathleen D. Liu", - "author_inst": "University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "- ISPY COVID Adaptive Platform Trial Network", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.05.07.22274792", "rel_title": "Assessing the feasibility of sustaining a 'Zero-COVID' policy in China in the era of highly transmissible variants", @@ -325894,6 +327989,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.02.22274456", + "rel_title": "Change in stroke presentations during COVID-19 pandemic in South-Western Sydney.", + "rel_date": "2022-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.02.22274456", + "rel_abs": "BackgroundAustralia managed relatively well during the global COVID-19 pandemic owing to our swift mandated public health response. During the NSW lockdown restrictions, we noted a decrease in acute stroke presentations at our institution, similar to what was subsequently reported worldwide.\n\nAimsWe aimed to test our hypothesis that (i) the true numbers of ischaemic strokes did not change, however patients were presenting later and (ii) the proportion of TIAs decreased.\n\nMethodsWe conducted a retrospective audit of all stroke and TIA presentations in 2020 and compared these with data from 2019. We collected information about stroke subtype, severity, time from stroke/TIA onset to presentation and acute reperfusion therapies.\n\nResultsBetween January-February and April-March 2020, there was a 15% drop in acute stroke presentations (128 vs. 109). In the same period \"stroke mimic\" presentations dropped by 22%. The proportion of patients attending the emergency department within 4.5hrs was only 36% compared with 48% over the similar period in 2019.\n\nConclusionsAlthough the raw numbers of ischemic stroke presentations remained stable during NSW Covid lockdown, the proportion of patients presenting within time window for acute reperfusion therapies fell. The number of TIAs similarly fell suggesting COVID-19 discouraged patients from presenting to hospital which placed them at higher risk of disabling stroke. The opportunity cost of lockdown restrictions on stroke outcome should be considered in future policy directives.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "James Thomas", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Dennis Cordato", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "David Manser", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Paul M Middleton", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Cecilia Cappelen-Smith", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Alan McDougall", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Peter Thomas", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Nicholas Moore", + "author_inst": "Liverpool Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.05.04.22274657", "rel_title": "Have infection control and prevention measures resulted in any adverse outcomes for care home and domiciliary care residents and staff?", @@ -326766,137 +328908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.30.22274532", - "rel_title": "Comparative analysis of the outcomes of COVID-19 between patients infected with SARS-CoV-2 Omicron and Delta variants: a retrospective cohort study", - "rel_date": "2022-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.30.22274532", - "rel_abs": "BackgroundThe SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. It is responsible for the current increase in the COVID-19 infectivity rate worldwide. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Here, we compared the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants and associated with prognostic factors, including age, sex, comorbidities, and smoking.\n\nMethodsWe involved 352 patients, 139 with the Omicron variant and 213 with the Delta variant. The whole-genome sequences of SARS-CoV-2 were conducted using the Illumina MiSeq next-generation sequencer.\n\nResultsCt value and mean age of COVID-19 patients were not significantly different between both groups (Delta: 20.35 {+/-} 4.07 vs. Omicron: 20.62 {+/-} 3.75; p=0.540; and Delta: 36.52 {+/-} 21.24 vs. Omicron: 39.10 {+/-} 21.24; p=0.266, respectively). Patients infected with Omicron and Delta variants showed similar hospitalization (p=0.433) and mortality rates (p=0.565). Multivariate analysis showed that older age ([≥]65 years) had higher risk for hospitalization (OR=3.67 [95% CI=1.22-10.94]; p=0.019) and fatalities (OR=3.93 [95% CI=1.35-11.42]; p=0.012). In addition, patients with cardiovascular disease had higher risk for hospitalization (OR=5.27 [95% CI=1.07-25.97]; p=0.041), whereas patients with diabetes revealed higher risk for fatalities (OR=9.39 [95% CI=3.30-26.72]; p=<0.001).\n\nConclusionsOur study shows that patients infected with Omicron and Delta variants reveal similar clinical outcomes, including hospitalization and mortality. In addition, our findings further confirm that older age, cardiovascular disease, and diabetes are strong prognostic factors for the outcomes of COVID-19 patients.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Gunadi", - "author_inst": "Universitas Gadjah Mada Faculty of Medicine, Public Health and Nursing" - }, - { - "author_name": "Mohamad Saifudin Hakim", - "author_inst": "UGM" - }, - { - "author_name": "Hendra Wibawa", - "author_inst": "Ministry of Agriculture, Indonesia" - }, - { - "author_name": "Khanza Vujira", - "author_inst": "UGM" - }, - { - "author_name": "Dyah Ayu Puspitarani", - "author_inst": "UGM" - }, - { - "author_name": "Endah Supriyati", - "author_inst": "UGM" - }, - { - "author_name": "Ika Trisnawati", - "author_inst": "UGM" - }, - { - "author_name": "Kristy Iskandar", - "author_inst": "UGM" - }, - { - "author_name": "Riat El Khair", - "author_inst": "UGM" - }, - { - "author_name": "Afiahayati", - "author_inst": "UGM" - }, - { - "author_name": "Siswanto", - "author_inst": "UGM" - }, - { - "author_name": "Yunika Puspadewi", - "author_inst": "Dr Sardjito Hospital" - }, - { - "author_name": "Irene", - "author_inst": "Ministry of Health Indonesia" - }, - { - "author_name": "Sri Handayani Irianingsih", - "author_inst": "Ministry of Agriculture Indonesia" - }, - { - "author_name": "Edwin Widyanto Daniwijaya", - "author_inst": "UGM" - }, - { - "author_name": "Dwi Aris Agung Nugrahaningsih", - "author_inst": "UGM" - }, - { - "author_name": "Gita Christy Gabriela", - "author_inst": "UGM" - }, - { - "author_name": "Esensi Tarian Geometri", - "author_inst": "UGM" - }, - { - "author_name": "Laudria Stella Eryvinka", - "author_inst": "UGM" - }, - { - "author_name": "Fadila Dyah Trie Utami", - "author_inst": "UGM" - }, - { - "author_name": "Edita Mayda Devana", - "author_inst": "UGM" - }, - { - "author_name": "Lanang Aditama", - "author_inst": "UGM" - }, - { - "author_name": "Nathania Christi Putri Kinasih", - "author_inst": "UGM" - }, - { - "author_name": "Verrell Christopher Amadeus", - "author_inst": "UGM" - }, - { - "author_name": "Yekti Hediningsih", - "author_inst": "Ministry of Health Indonesia" - }, - { - "author_name": "Nur Rahmi Ananda", - "author_inst": "UGM" - }, - { - "author_name": "Eggi Arguni", - "author_inst": "UGM" - }, - { - "author_name": "Titik Nuryastuti", - "author_inst": "UGM" - }, - { - "author_name": "Tri Wibawa", - "author_inst": "UGM" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.02.22274575", "rel_title": "SOFA score performs worse than age for predicting mortality in patients with COVID-19", @@ -328064,6 +330075,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.01.490203", + "rel_title": "SARS-CoV-2 Main Protease: a Kinetic Approach", + "rel_date": "2022-05-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.01.490203", + "rel_abs": "In this article, I present a new model of the interaction of the main protease (Mpro) from SARS-CoV-2 virus with its substrate. The reaction scheme used to describe this mechanism is an extension of the well-known Michaelis-Menten model proposed in 1913 by Leonor Michaelis and Maud Menten [1]. The model I present here takes into account that one Mpro enzyme monomer interacts with another Mpro monomer in the presence of the substrate, leading to the formation of an enzyme dimer bound to one substrate molecule. Indeed, this dimer is formed by the sequentially binding of one Mpro enzyme monomer to one molecule of substrate, followed by another Mpro enzyme monomer binding to this Mpro-substrate complex. This reaction mechanism is also known in the literature as substrate-induced dimerization [3]. Starting from this new reaction scheme established for this catalytic mechanism, I derived a mathematical expression describing the catalytic rate of the active Mpro enzyme dimer as a function of the substrate concentration [S]. The plot corresponding to this substrate-induced dimerization reaction shows a function f ([S]) that is not monotonic, i.e. not strictly increasing or decreasing, but with a second derivative initially negative and then becoming positive after having passed the Vmax point. This is typically a type of curve showing a phenomenon like the one of substrate inhibition (for instance, inhibition by excess-substrate [7]). The graphical representation of this process shows an interesting behaviour: from zero M/s, the reaction rate increases progressively, similar to the kind of curve described by the Michaelis-Menten model. However, after having reached its maximum catalytic rate, Vmax, the reaction rate decreases progressively as we continue to increase the substrate concentration. I propose an explanation to this interesting behavior. At the moment where Vcat is maximum, we can assume that, in theory, every single substrate molecule in solution is bound to two enzyme monomers (i.e. to one active dimer). The catalytic rate is thus theoretically maximized. At the time where the reaction rate begins to decrease, we observe a new phenomenon that appears: the enzyme monomers begin to be \"diluted\" in the solution containing the excess substrate. The dimers begin to dissociate and to bind increasingly to the substrate as inactive monomers instead of active dimers. Hence, it is more and more unlikely for the enzyme monomers to sequentially bind twice to the same substrate molecule (here, [E] << [S]). Thus, at this stage, the substrate-induced dimerization occurs less often. At the limit, when the substrate is in high excess, there is virtually no more dimerization which occurs. This is one example of excess-substrate inhibition. Furthermore, after having established this fact, I wanted to see if this catalytic behavior was also observed in vitro. Therefore, I conducted an experiment where I measured the catalytic rate of the Mpro dimer for different substrate concentrations. The properties of my substrate construct were such, that I could determine the catalytic rate of the enzyme dimer by directly measuring the spectrophotometric absorbance of the cleaved substrate at{lambda} = 405 nm. The results show explicitly -- within a margin of error -- that the overall shape of the experimental curve looks like the one of the theoretical curve. I thus conclude that the biochemical behavior of the Mpro in vitro follows a new path when it is in contact with its substrate: an excess substrate concentration decreases the activity of the enzyme by the phenomenon of a type of excess-substrate inhibition. This finding could open a new door in the discovery of drugs directed against the Mpro enzyme of the SARS-CoV-2 virus, acting on the inhibition by excess-substrate of the Mpro enzyme, this protein being a key component in the metabolism of the virus. Furthermore, I have established that the maximum of the fitted curve, Vmax, depends only on [E]T and not on [S]. [Formula] exhibits the same dependence pattern. Therefore, if I keep [E]T close to zero, the catalytic rate of the enzyme will also be greatly reduced, which can be understood intuitively. Finally, if we dilute the enzyme sufficiently in the host cell by injecting a suitably high concentration of the octapeptide substrate AVLQSGFR (an inhibitor of the original substrate), this artificial substrate will bind to the \"intermediate\" dimer from the polypeptide and prevent the precursor Mpro from auto-cleaving and dimerizing due to the \"distorted key\" effect of the octapeptide on the \"intermediate\" dimer. The precursor peptide Mpro will auto-cleave to a lesser extent than in the absence of the artificial octapeptide and thus the concentration of the total enzyme [E]T will be lowered in the cell. It would therefore be possible to control the virulence of the virus by adjusting the concentration of the artificial inhibitory octapeptide. However, this is only speculation and has yet to be verified in practice.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Thierry Rebetez", + "author_inst": "ETHZ" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.04.30.489997", "rel_title": "BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection", @@ -329032,33 +331062,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.30.22274526", - "rel_title": "Pre-morbid use of proton pump inhibitors has no effect on the risk of death or hospitalization in COVID-19 patients: a matched cohort study", - "rel_date": "2022-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.30.22274526", - "rel_abs": "AimTo assess whether exposure to proton pump inhibitors (PPIs) shortly preceding COVID-19 diagnosis affected the risk of subsequent hospitalizations and mortality.\n\nMethodsThis population-based study embraced first COVID-19 episodes in adults diagnosed up to August 15 2021 in Croatia. Patients were classified based on exposure to PPIs and burden of PPI-requiring morbidities as \"non-users\" (no issued prescriptions, no recorded treatment-requiring conditions between January 1 2019 and COVID-19 diagnosis), \"possible users\" (no issued prescriptions, but morbidities present; self-medication possible) and \"users\" (at least one prescription within 3 months prior to the COVID-19 diagnosis; morbidities present). Subsets were mutually exactly matched for pre-COVID-19 characteristics. The contrast between \"users\" and \"possible users\" informed about the effect of PPIs that is separate of the effect of PPI-requiring conditions.\n\nResultsAmong 433609 patients, \"users\" and \"possible users\" were matched 41195 (of 55098) to 17334 (of 18170) in the primary and 33272 to 16434 in the sensitivity analysis. There was no relevant difference between them regarding mortality [primary: RR=0.93 (95%CI 0.85-1.02; RD= - 0.34% (-0.73, 0.03); sensitivity: RR=0.88 (0.78-0.98); RD=-0.45% (-0.80, -0.11)] or hospitalizations [primary: RR=1.04 (0.97-1.13); RD=0.29% (-0.16, 0.73); sensitivity: RR=1.05 (0.97-1.15); RD=0.32% (-0.12, 0.75)]. The risks of both were slightly higher in \"possible users\" or \"users\" than in \"non-users\" (absolutely by [~]0.4%-1.6%) indicating the effect of PPI-requiring morbidities.\n\nConclusionPre-morbid exposure to PPIs does not affect the risk of death or hospitalization in adult COVID-19 patients, but PPI-requiring morbidities seemingly slightly increase the risk of both.\n\nWhat is already known about this subject?O_LIIt appears biologically plausible that pre-morbid exposure to proton pump inhibitors (PPIs) might contribute to unfavorable course of COVID-19 disease\nC_LIO_LITwo population-based studies in the early pandemics stage indicated no effect of PPIs, while one suggested a higher risk of death/severe COVID-19 disease in PPI pre-exposed subjects\nC_LI\n\nWhat this study adds?O_LIExposure to PPIs directly preceding SarsCov-2 infection has no effect on the risk of subsequent hospitalizations and mortality\nC_LIO_LIConditions requiring PPI treatment seem to mildly increase the risk of both\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ivan Kodvanj", - "author_inst": "University Hospital Centre Zagreb" - }, - { - "author_name": "Jan Homolak", - "author_inst": "University of Zagreb School of Medicine" - }, - { - "author_name": "Vladimir Trkulja", - "author_inst": "University of Zagreb School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2022.04.28.22274086", "rel_title": "Quantifying the relationship between sub-population wastewater samples and community-wide SARS-CoV-2 seroprevalence", @@ -330102,6 +332105,105 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.04.28.489942", + "rel_title": "Immediate myeloid depot for SARS-CoV-2 in the human lung", + "rel_date": "2022-04-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489942", + "rel_abs": "In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, considerable focus has been placed on a model of viral entry into host epithelial populations, with a separate focus upon the responding immune system dysfunction that exacerbates or causes disease. We developed a precision-cut lung slice model to investigate very early host-viral pathogenesis and found that SARS-CoV-2 had a rapid and specific tropism for myeloid populations in the human lung. Infection of alveolar macrophages was partially dependent upon their expression of ACE2, and the infections were productive for amplifying virus, both findings which were in contrast with their neutralization of another pandemic virus, Influenza A virus (IAV). Compared to IAV, SARS-CoV-2 was extremely poor at inducing interferon-stimulated genes in infected myeloid cells, providing a window of opportunity for modest titers to amplify within these cells. Endotracheal aspirate samples from humans with the acute respiratory distress syndrome (ARDS) from COVID-19 confirmed the lung slice findings, revealing a persistent myeloid depot. In the early phase of SARS-CoV-2 infection, myeloid cells may provide a safe harbor for the virus with minimal immune stimulatory cues being generated, resulting in effective viral colonization and quenching of the immune system.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Melia Magnen", + "author_inst": "UCSF" + }, + { + "author_name": "Ran You", + "author_inst": "UCSF" + }, + { + "author_name": "Arjun A Rao", + "author_inst": "UCSF" + }, + { + "author_name": "Ryan T Davis", + "author_inst": "UCSF" + }, + { + "author_name": "Lauren Rodriguez", + "author_inst": "UCSF" + }, + { + "author_name": "Camille R Simoneau", + "author_inst": "UCSF" + }, + { + "author_name": "Lisiena Hysenaj", + "author_inst": "UCSF" + }, + { + "author_name": "Kenneth H Hu", + "author_inst": "UCSF" + }, + { + "author_name": "- The UCSF COMET Consortium", + "author_inst": "-" + }, + { + "author_name": "Christina Love", + "author_inst": "UCSF" + }, + { + "author_name": "Prescott G Woodruff", + "author_inst": "UCSF" + }, + { + "author_name": "David J Erle", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn M Hendrickson", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn S Calfee", + "author_inst": "UCSF" + }, + { + "author_name": "Michael A Matthay", + "author_inst": "UCSF" + }, + { + "author_name": "Jeroen P Roose", + "author_inst": "UCSF" + }, + { + "author_name": "Anita Sil", + "author_inst": "UCSF" + }, + { + "author_name": "Melanie Ott", + "author_inst": "UCSF" + }, + { + "author_name": "Charles R Langelier", + "author_inst": "UCSF" + }, + { + "author_name": "Matthew F Krummel", + "author_inst": "UCSF" + }, + { + "author_name": "Mark R Looney", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.26.22274264", "rel_title": "Pilot study on the use of low molecular weight heparins in the prevention of thromboembolic disease during pregnancy and puerperium.", @@ -330742,37 +332844,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2022.04.26.22274316", - "rel_title": "Did Norwegian adolescents suffer more violence and sexual abuse during the Covid-19 pandemic? Violence and sexual abuse rates the year before the pandemic compared to rates one year into the pandemic.", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274316", - "rel_abs": "BackgroundThe Covid-19 pandemic is a public health crisis which may cause unintended additional societal costs such as child maltreatment. Considerable concern is raised as to whether the pandemic has led to an increase in violence and sexual abuse against children.\n\nObjectiveThe present study objective is to provide rates of violence and sexual abuse against adolescents the year before the pandemic compared to one year into the pandemic.\n\nParticipants and settingTwo samples of Norwegian 12-16-year-olds were approached. A representative pre-pandemic sample of 9240 adolescents (M age= 14.11), and a sample recruited one year into the pandemic resulting in 3540 responses (M age (SD) = 14.5).\n\nMethodsAn online survey was administered during school hours including established measures of violence and sexual abuse exposure. Sociodemographic characteristics were assessed.\n\nResultsThere was 1.4 percentage point increase in sexual abuse by an adult, and a 3.9 percentage point decrease in psychological violence by a parent during the pandemic compared to the year before the pandemic. Otherwise, violence and sexual abuse rates remained stable across these two time periods. Risk factors for violence and sexual abuse were amplified during the pandemic.\n\nConclusionNorway, a high-income welfare state, imposed measures to counteract the burden of the pandemic mitigation actions for adolescents. This might partly explain the absence of the feared increase in violence towards adolescents. The disproportionate risk for violence and sexual abuse for some groups of adolescents is however concerning, and should be followed up over time.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Else-Marie Augusti", - "author_inst": "Norwegian Centre for Violence and Traumatic Stress Studies" - }, - { - "author_name": "Mia Cathrine Myhre", - "author_inst": "Norwegian Centre for Violence and Traumatic Stress Studies" - }, - { - "author_name": "Tore Wentzel-Larsen", - "author_inst": "Norwegian Centre for Violence and Traumatic Stress Studies; Centre for Child and Adolescent Mental Health, Eastern and Southern Norway (RBUP)" - }, - { - "author_name": "Gertrud Sofie Hafstad", - "author_inst": "Norwegian Centre for Violence and Traumatic Stress Studies" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.27.22274269", "rel_title": "CRISIS AFAR: An International Collaborative Study of the Impact of the COVID-19 Pandemic on Youth with Autism and Neurodevelopmental Conditions.", @@ -332056,6 +334127,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.28.489850", + "rel_title": "GM-CSF-activated human dendritic cells promote type1 T follicular helper cells (Tfh1) polarization in a CD40-dependent manner", + "rel_date": "2022-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489850", + "rel_abs": "T follicular helper (Tfh) cells are specialized CD4+ T cells that regulate humoral immunity by providing B cell help. Tfh1 sub-population was recently identified and associated with severity in infection and autoimmune diseases. The cellular and molecular requirements to induce human Tfh1 differentiation are unknown. Our work investigated the role of human dendritic cells (DC) in promoting Tfh1 differentiation and their physiopathological implication in mycobacterium tuberculosis and mild COVID-19 infection.\n\nActivated human blood CD1c+ DC were cocultured with allogeneic naive CD4+ T cells. Single-cell RNA sequencing was then used alongside protein validation to define the induced Tfh lineage. DC signature and correlation with Tfh1 cells in infected patients was established through bioinformatic analysis.\n\nOur results show that GM-CSF-activated DC drove the differentiation of Tfh1 cells, displaying typical Tfh molecular features, including 1) high levels of PD-1, CXCR5, and ICOS expression; 2) BCL6 and TBET co-expression; 3) IL-21 and IFN-{gamma} secretion. Mechanistically, GM-CSF triggered the emergence of two distinct DC sub-populations defined by their differential expression of CD40 and ICOS-ligand (ICOS-L), and distinct phenotype, morphology, transcriptomic signature, and function. We showed that Tfh1 differentiation was efficiently and specifically induced by CD40highICOS-Llow DC in a CD40-dependent manner. Tfh1 cells were positively associated with a CD40highICOS-LLow DC signature in patients with latent mycobacterium tuberculosis and mild COVID-19 infection.\n\nOur study uncovers a novel CD40-dependent human Tfh1 axis. Immunotherapy modulation of Tfh1 activity might contribute to control diseases where Tfh1 are known to play a key role, such as infections.\n\nSignificance StatementDendritic cells (DC) play a central role in triggering the adaptive immune response due to their T cell priming functions. Among different T cell subsets, it is still not clear how human type1 T follicular helper cells (Tfh1) differentiate. Tfh1 cells are implicated in several physiopathological conditions, including infections. Here we show that GM-CSF induces diversification of human DC. Only CD40highICOS-LLow DC were able to drive Tfh1 cell differentiation. We found that CD40highICOS-LLow DC signature was associated to Tfh1 cells in mycobacterium tuberculosis and COVID-19 patients. Our data reveal a previously undescribed pathway leading to human Tfh1 cell differentiation and highlight the importance of GM-CSF and CD40 as potential targets for the design of anti-infective therapies.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sarantis Korniotis", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis, F-75010, Paris, France" + }, + { + "author_name": "Melissa Saichi", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Coline Trichot", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Caroline Hoffmann", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" + }, + { + "author_name": "Elise Amblard", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Annick Viguier", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" + }, + { + "author_name": "Sophie Grondin", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" + }, + { + "author_name": "Floriane Noel", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Hamid Mattoo", + "author_inst": "Immunology and Inflammation Therapeutic Area, Sanofi, Cambridge MA, USA" + }, + { + "author_name": "Vassili Soumelis", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.28.489772", "rel_title": "Structural and functional characteristics of SARS-CoV-2 Omicron subvariant BA.2 spike", @@ -332876,41 +335002,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.04.22.22273686", - "rel_title": "Clinical evaluation of an automated, rapid mariPOC(R) antigen test in screening of symptomatics and asymptomatics for SARS-CoV-2 infections", - "rel_date": "2022-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22273686", - "rel_abs": "A novel automated mariPOC(R) SARS-CoV-2 antigen test was evaluated in a Health care center laboratory among symptomatic and asymptomatic individuals seeking SARS-CoV-2 testing. According to the national testing strategy, RT-PCR was used as a reference method. A total of 962 subjects were included in this study, 4.8% (46/962) of their samples were SARS-CoV-2 RT-PCR positive, and 87% (40/46) of these were from symptomatics. Among the symptomatics, the overall sensitivity of the mariPOC(R) SARS-CoV-2 test was 82.5% (33/40), though the sensitivity increased to 97.1% (33/34) in samples with a Ct value <30. The mariPOC(R) SARS-CoV-2 test detected 2/6 PCR positive samples among the asymptomatics, four cases that remained antigen test negative had Ct values between 28 and 36. The specificity of the mariPOC(R) SARS-CoV-2 test was 100% (916/916). The evaluation showed that the mariPOC(R) SARS-CoV-2 rapid antigen test is very sensitive and specific for the detection of individuals who most probably are contagious.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Marianne Gunell", - "author_inst": "Turku University Hospital and University of Turku" - }, - { - "author_name": "Kaisa Rantasarkka", - "author_inst": "Turku University Hospital" - }, - { - "author_name": "Rita Arjonen", - "author_inst": "Kaarina City Health Care Center" - }, - { - "author_name": "Antti Sanden", - "author_inst": "Kaarina City Health Care Center" - }, - { - "author_name": "Tytti Vuorinen", - "author_inst": "Turku University Hospital and University of Turku" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.23.22274186", "rel_title": "Determinants of motivated behavior are linked to fatigue and its perturbation by SARS-CoV-2 vaccination", @@ -333766,6 +335857,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.23.22274192", + "rel_title": "Excess all-cause mortality across counties in the United States, March 2020 to December 2021", + "rel_date": "2022-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.23.22274192", + "rel_abs": "Excess mortality is the difference between expected and observed mortality in a given period and has emerged as a leading measure of the overall impact of the Covid-19 pandemic that is not biased by differences in testing or cause-of-death assignment. Spatially and temporally granular estimates of excess mortality are needed to understand which areas have been most impacted by the pandemic, evaluate exacerbating and mitigating factors, and inform response efforts, including allocating resources to affected communities. We estimated all-cause excess mortality for the United States from March 2020 through February 2022 by county and month using a Bayesian hierarchical model trained on data from 2015 to 2019. An estimated 1,159,580 excess deaths occurred during the first two years of the pandemic (first: 620,872; second: 538,708). Overall, excess mortality decreased in large metropolitan counties, but increased in nonmetro counties, between the first and second years of the pandemic. Despite the initial concentration of mortality in large metropolitan Northeast counties, beginning in February 2021, nonmetro South counties had the highest cumulative relative excess mortality. These results highlight the need for investments in rural health as the pandemics disproportionate impact on rural areas continues to grow.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Eugenio Paglino", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dielle J. Lundberg", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Zhenwei Zhou", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Joe A. Wasserman", + "author_inst": "RTI International" + }, + { + "author_name": "Rafeya Raquib", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Anneliese N. Luck", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Katherine Hempstead", + "author_inst": "The Robert Wood Johnson Foundation" + }, + { + "author_name": "Jacob Bor", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Samuel H. Preston", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Irma T. Elo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Andrew C. Stokes", + "author_inst": "Boston University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.22.22274058", "rel_title": "Coronavirus and incomes: the COVID-19 pandemic dynamics in Africa in February 2022", @@ -334426,49 +336576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.19.22273976", - "rel_title": "Do Some Super-Spreaders Spread Better? Effects of individual heterogeneity in epidemiological traits", - "rel_date": "2022-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22273976", - "rel_abs": "Many high-profile outbreaks are driven by super-spreading, including HIV, MERS, Ebola, and the SARS-Cov-2 pandemic. That super-spreading is a common feature of epidemics is immutable, however, the relative importance of 2super-spreaders to the outcome of an epidemic, and the individual-level traits that lead to super-spreading, is less clear. For example, an individual may contribute disproportionately to transmission by way of an extremely high contact rate or by way of low recovery, but how these two super-spreaders differ in their effect on epidemiological dynamics is unclear. Furthermore, epidemiological traits may often covary with one another in ways that promote or inhibit super-spreading. What patterns of covariation, and between what traits, are most likely to lead to large epidemics driven by super-spreading? Using stochastic individual-based simulations of an SIR epidemiological model, we explore how variation and covariation between transmission-related traits (contact rate and infectiousness) and duration-related traits (virulence and recovery) of infected individuals affects super-spreading and peak epidemic size. We show that covariation matters when contact rate and infectiousness covary: peak epidemic size is largest when they covary positively and smallest when they covary negatively. We did not see that more super-spreading always leads to larger epidemics, rather, we show that the relationship between super-spreading and peak epidemic size is dependent on which traits are covarying. This suggests that there may not necessarily be any general relationship between the frequency of super-spreading and the size of an epidemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alexis S Beagle", - "author_inst": "University of Nebraska - Lincoln" - }, - { - "author_name": "Sarah A Budischak", - "author_inst": "Claremont McKenna, Pitzer, and Scripps Colleges" - }, - { - "author_name": "Meggan E Craft", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Richard Hall", - "author_inst": "University of Georgia" - }, - { - "author_name": "Kristian Forbes", - "author_inst": "University of Arkansas at Fayetteville" - }, - { - "author_name": "David Nguyen", - "author_inst": "University of Nebraska - Lincoln" - }, - { - "author_name": "Clay Cressler", - "author_inst": "University of Nebraska-Lincoln" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.22.22274032", "rel_title": "Antibody Responses In Non-Severe SARS-CoV-2 Infections Are Driven By CD4+ T cells and Age.", @@ -335524,6 +337631,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.21.22274155", + "rel_title": "Usage and awareness of antiviral medications for COVID-19", + "rel_date": "2022-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274155", + "rel_abs": "We surveyed people that recently tested positive for SARS-CoV-2 to assess the frequency and correlates of early treatment seeking behavior. Among high risk respondents, 66.0% were aware of treatment for COVID-19 and 36.3% had sought treatment, however only 1.7% reported use of an antiviral for SARS-CoV-2 infection. More public outreach is needed to raise awareness of the benefits of treatment for COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Noah Kojima", + "author_inst": "UCLA" + }, + { + "author_name": "Jeffrey D Klausner", + "author_inst": "USC" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.21.22274082", "rel_title": "COVID-19 patients share common, corticosteroid-independent features of impaired host immunity to pathogenic molds", @@ -336276,93 +338406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.19.22273872", - "rel_title": "Immune response to 2-dose BNT162b2 vaccination and risk of SARS-CoV-2 breakthrough infection: The Shieldvacc-2 study", - "rel_date": "2022-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22273872", - "rel_abs": "It is uncertain to which extent antibody and T-cell responses after vaccination against SARS-CoV-2 are associated with reduced risk of breakthrough infection and whether their measurement enhances risk prediction. We conducted a phase-4 open-label clinical trial in the pre-omicron era, enrolling 2,760 individuals aged [≥]16 years 35{+/-}8 days after having received the second dose of BNT162b2 (baseline 15-21 May 2021). Over a median 5.9-month of follow-up, we identified incident SARS-CoV-2 breakthrough infections using weekly antigen tests, a confirmatory PCR test, and/or serological evidence for incident infection. We quantified relative risks adjusted for age, sex, and prior SARS-CoV-2 infection for different immunological parameters and assessed improvements in risk discrimination. In contrast to the T-cell response, higher plasma levels of binding antibodies and antibodies in a surrogate neutralization assay were associated with reduced risk of breakthrough infection. Furthermore, assessment of anti-spike IgG levels enhanced prediction of breakthrough infection and may therefore be a suitable measurable correlate of protection in practice.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Lisa Seekircher", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Zoltan Banki", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Janine Kimpel", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Annika Roessler", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Helena Schaefer", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Barbara Falkensammer", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "David Bante", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Lukas Forer", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Sebastian Schoenherr", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Teresa Harthaller", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Magdalena Sacher", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Cornelia Ower", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Lena Tschiderer", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Hanno Ulmer", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Dorothee von Laer", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Wegene Borena", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Peter Willeit", - "author_inst": "Medical University of Innsbruck" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.19.22274050", "rel_title": "The impact of community asymptomatic rapid antigen testing on COVID-19 hospital admissions: a synthetic control study", @@ -338962,6 +341005,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.04.20.488873", + "rel_title": "Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants", + "rel_date": "2022-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.20.488873", + "rel_abs": "The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hiam R. S. Arruda", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Tulio M. Lima", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Renata G. F. Alvim", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Fernanda B. A. Victorio", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Daniel P. B. Abreu", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Federico F. Marsili", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Karen D. Cruz", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Patricia Sosa-Acosta", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Mauricio Quinones-Vega", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Jessica S. Guedes", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "F\u00e1bio C. S. Nogueira", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Jerson L. Silva", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Leda R. Castilho", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Guilherme A. P. de Oliveira", + "author_inst": "Federal University of Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.04.20.22274061", "rel_title": "Vaccine effectiveness against SARS-CoV-2 infection and COVID-19-related hospitalization with the Alpha, Delta and Omicron SARS-CoV-2 variants: a nationwide Danish cohort study", @@ -339658,37 +341772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.14.22273819", - "rel_title": "An optimized flow cytometry protocol for simultaneous detection of T cell activation induced markers and intracellular cytokines: application to SARS-Cov-2 vaccinated individuals", - "rel_date": "2022-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22273819", - "rel_abs": "Antigen (ag)-specific T cell analysis is an important step for investigation of cellular immunity in many settings, such as infectious diseases, cancer and vaccines. Multiparameter flow cytometry has advantages in studying both the rarity and heterogeneity of these cells. In the cellular immunologists toolbox, the expression of activation-induced markers (AIM) following antigen exposure has made possible the study and sorting of ag-specific T cells without using human leukocyte antigen (HLA)-multimers. In parallel, assessing the cytokine profile of responding T cells would support a more comprehensive description of the ongoing immune response. Here, a method and flow cytometry panel were optimized to combine the detection of activated CD4+ and CD8+ T cells in a TCR-dependent manner with the evaluation of cytokine production by intracellular staining, without affecting the positivity of activation markers. In particular, the expression of CD134 (OX40) and CD69 have been tested in conjunction with intracellular (ic) CD137 (4-1BB) to detect SARS-Cov-2 Spike protein-specific activated T cells. In our setting, assessing CD134 provided minimal contribution to detect the pool of AIM+ T cells, whereas a key role was described for ic-CD69, which was co-expressed with ic-CD137 in both CD4+ and CD8+ lymphocytes. Moreover, the analysis of TCR-triggered cytokine-producing T cells (IFN{gamma}, TNF and IL-2 were assessed) further confirmed the capacity of ic-CD69 to identify functionally responsive antigen-specific T cells, which were often largely negative or poorly positive for CD134 expression. In parallel, the use of CD45RA, CCR7 and CXCR5 allowed us to describe the T cell matuarion curve and detect T helper follicular CD4+ cells, including the antigen-specific activated subsets.\n\nIn conclusion, we optimized a method and flow cytometry panel combining assessment of activation induced markers and intracellular cytokines that will be useful for measuring TCR stimulation-dependent activation of CD4+ and CD8+ T cells.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tiziana Altosole", - "author_inst": "University of Genoa" - }, - { - "author_name": "Gianluca Rotta", - "author_inst": "BD Biosciences" - }, - { - "author_name": "Scott Bornheimer", - "author_inst": "BD Biosciences" - }, - { - "author_name": "Daniela Fenoglio", - "author_inst": "University of Genoa" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.04.18.22273992", "rel_title": "An Evaluation of Prospective COVID-19 Modeling: From Data to Science Translation", @@ -340580,6 +342663,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.04.14.22273868", + "rel_title": "Effectiveness of Four Vaccines in Preventing SARS-CoV-2 Infection in Kazakhstan", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22273868", + "rel_abs": "BACKGROUNDIn February 2021 Kazakhstan began offering COVID-19 vaccines to adults. Breakthrough SARS-CoV-2 infections raised concerns about real-world vaccine effectiveness. We aimed to evaluate effectiveness of four vaccines against SARS-CoV-2 infection.\n\nMETHODSWe conducted a retrospective cohort analysis among adults in Almaty using aggregated vaccination data and individual-level breakthrough COVID-19 cases ([≥]14 days from 2nd dose) using national surveillance data. We ran time-adjusted Cox-proportional-hazards model with sensitivity analysis accounting for varying entry into vaccinated cohort to assess vaccine effectiveness for each vaccine (measured as 1-adjusted hazard ratios) using the unvaccinated population as reference (N=565,390). We separately calculated daily cumulative hazards for COVID-19 breakthrough among vaccinated persons by age and vaccine month.\n\nRESULTSFrom February 22 to Sept 1, 2021 in Almaty, 747,558 (57%) adults were fully vaccinated (received 2 doses) and 108,324 COVID-19 cases (11,472 breakthrough) were registered. Vaccine effectiveness against infection was 78% (sensitivity estimates: 74-82%) for QazVac, 77% (72- 81%) for Sputnik V, 71% (69-72%) for Hayat-Vax, and 69% (64-72%) for CoronaVac. Among vaccinated persons, the 90-day follow-up cumulative hazard for breakthrough infection was 2.2%. Cumulative hazard was 2.9% among people aged [≥]60 years versus 1.9% among persons aged 18-39 years (p<0.001), and 1.2% for people vaccinated in February-May versus 3.3% in June-August (p<0.001).\n\nCONCLUSIONOur analysis demonstrates high effectiveness of COVID-19 vaccines against infection in Almaty similar to other observational studies. Higher cumulative hazard of breakthrough among people >60 years of age and during variant surges warrants targeted booster vaccination campaigns.\n\nWhat is already known on this topicO_LIPlenty of data are published on effectiveness of mRNA vaccines; however, these vaccines were not widely available in many low- and middle-income countries in 2021.\nC_LIO_LIThere are no real-world effectiveness studies on several vaccines available in the Central Asia region, including QazVac vaccine, an inactivated vaccine developed by Kazakhstan.\nC_LIO_LIUnderstanding how these vaccines are performing outside of clinical trials is critical for the COVID-19 response and lack of published data can contribute to vaccine hesitancy.\nC_LI\n\nWhat this study addsO_LIOur study demonstrated that at the population-level the four vaccines against COVID-19 used in Kazakhstan were effective at preventing SARS-CoV-2 infection.\nC_LIO_LIVaccination reduced the risk of infection by 76% and prevented over 100,000 cases of SARS-CoV-2 infection in Almaty, the countrys most populous city.\nC_LIO_LIThis is also the first study that demonstrated high vaccine effectiveness in real-world conditions of QazVac, developed in Kazakhstan.\nC_LI\n\nHow this study might affect research, practice or policyO_LIPolicy makers in Kazakhstan and the Central Asia region need data on vaccines provided in the region to update evidence-based vaccine guidelines for different populations.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dilyara NABIROVA", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" + }, + { + "author_name": "Roberta Horth", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" + }, + { + "author_name": "Manar Smagul", + "author_inst": "Scientific and practical center of sanitary-epidemiological examination and monitoring, branch of the National Center for Public Health, Almaty, Kazakhstan" + }, + { + "author_name": "Gaukhar Nukenova", + "author_inst": "Scientific and practical center of sanitary-epidemiological examination and monitoring, branch of the National Center for Public Health, Almaty, Kazakhstan" + }, + { + "author_name": "Aizhan Yesmagambetova", + "author_inst": "Ministry of Healthcare of the Republic of Kazakhstan" + }, + { + "author_name": "Daniel Singer", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" + }, + { + "author_name": "Alden Henderson", + "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, USA" + }, + { + "author_name": "Alexey Tsoy", + "author_inst": "Ministry of Healthcare of the Republic of Kazakhstan" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.13.22273837", "rel_title": "How did the COVID-19 Pandemic impact self-reported cancer screening rates in 12 Midwestern states?", @@ -341200,97 +343330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2022.04.08.22273160", - "rel_title": "Household transmission of SARS-CoV-2 from adult index cases living with and without HIV in South Africa, 2020-2021: a case-ascertained, prospective observational household transmission study", - "rel_date": "2022-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273160", - "rel_abs": "BackgroundIn South Africa 19% of the adult population aged 15-49 years are living with HIV (LWH). Few data on the influence of HIV on SARS-CoV-2 household transmission are available.\n\nMethodsWe performed a case-ascertained, prospective household transmission study of symptomatic index SARS-CoV-2 cases LWH and HIV-uninfected adults and their contacts in South Africa. Households were followed up thrice weekly for 6 weeks to collect nasal swabs for SARS-CoV-2 testing. We estimated household cumulative infection risk (HCIR), duration of SARS-CoV-2 positivity (at cycle threshold value<30 as proxy for high viral load), and assessed associated factors.\n\nResultsWe recruited 131 index cases and 457 household contacts. HCIR was 59% (220/373); not differing by index HIV status (60% [50/83] in cases LWH vs 58% [173/293] in HIV-uninfected cases, OR 1.0, 95%CI 0.4-2.3). HCIR increased with index case age (35-59 years: aOR 3.4 95%CI 1.5-7.8 and [≥]60 years: aOR 3.1, 95%CI 1.0-10.1) compared to 18-34 years, and contacts age, 13-17 years (aOR 7.1, 95%CI 1.5-33.9) and 18-34 years (aOR 4.4, 95%CI 1.0-18.4) compared to <5 years. Mean positivity duration at high viral load was 7 days (range 2-28), with longer positivity in cases LWH (aHR 0.3, 95%CI 0.1-0.7).\n\nConclusionsHIV-infection was not associated with higher HCIR, but cases LWH had longer positivity duration at high viral load. Adults aged >35 years were more likely to transmit, and individuals aged 13-34 to acquire SARS-CoV-2 in the household. Health services must maintain HIV testing with initiation of antiretroviral therapy for those HIV-infected.\n\nSummaryIn this case-ascertained, prospective household transmission study, household cumulative infection risk was 59% from symptomatic SARS-CoV-2 index cases, not differing based on index HIV status. Index cases living with HIV were positive for SARS-CoV-2 for longer at higher viral loads.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Jackie Kleynhans", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Sibongile Walaza", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Neil A. Martinson", - "author_inst": "Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa. Johns Hopkins University Center for TB Research, Baltimore, Mar" - }, - { - "author_name": "Mzimasi Neti", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Jinal N. Bhiman", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Dylan Toi", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Daniel G. Amoako", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Amelia Buys", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Kedibone Ndlangisa", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Nicole Wolter", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Leisha Genade", - "author_inst": "Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa." - }, - { - "author_name": "Lucia Maloma", - "author_inst": "Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa." - }, - { - "author_name": "Juanita Chewparsad", - "author_inst": "Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa." - }, - { - "author_name": "Limakatso Lebina", - "author_inst": "Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa. Africa Health Research Institute, Durban, South Africa. Africa " - }, - { - "author_name": "Linda de Gouveia", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Retshidisitswe Kotane", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Stefano Tempia", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Cheryl Cohen", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.08.22273602", "rel_title": "Three-dose mRNA-1273 vaccination schedule: sufficient antibody response in majority of immunocompromised hematology patients", @@ -342282,6 +344321,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.18.22273970", + "rel_title": "A comparative analysis of pediatric mental health-related emergency department utilization in Montreal, Canada before and during the COVID-19 pandemic", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273970", + "rel_abs": "BackgroundReports on longitudinal trends in mental health-related (MHR) emergency department (ED) utilization spanning the pre- and post-pandemic periods are lacking, along with evidence comparing healthcare services utilization by sociodemographic subgroups. The aim of this study was to evaluate COVID-19-associated changes in MHR ED utilization among youth overall and by age, sex, and socioeconomic status (SES).\n\nMethodsThis retrospective cross-sectional study analyzed MHR ED utilization before and during the COVID-19 pandemic at a large urban pediatric tertiary care hospital in Montreal, Canada. All ED visits for children (5-11 years) and adolescents (12-17 years) between April 1, 2016 and November 30, 2021 were included. The main outcome was the monthly count of MHR ED visits. Pre-pandemic and pandemic periods were compared using an interrupted time series design. The effect of seasonality (in months), age (in years), sex (male or female), and SES (low, average, high) were compared using a generalized additive model.\n\nResultsThere were a total of 437,147 ED visits (204,215 unique patients) during the five-year study period of which 9,748 (5.8%) were MHR visits (7,686 unique patients). We observed an increase of 69% (95% CI, +53% to +85%; p = .001) in the mean monthly count of MHR ED visits during the pandemic period, which remained significant after adjusting for seasonality (44% increase, 95% CI, +38% to +51%; p = .001). The chance of presenting for a MHR ED visit increased non-linearly with age. There were increased odds of presenting for a MHR ED visit among girls between the pre-pandemic and pandemic periods (OR 1.42, 95% CI 1.29-1.56). No difference by SES group during and before the COVID-19 pandemic was found (OR 1.01, 95% CI 0.89-1.15 [low]; OR 1.09, 95% CI 0.96-1.25 [high]).\n\nConclusionsOur study shows important increases in MHR ED utilization among youth, and especially among girls, during the first 20 months of the COVID-19 pandemic, highlighting the need for sustained, targeted and scalable mental health resources to support youth mental health during the current and future crises.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Gabrielle Beaudry", + "author_inst": "Department of Psychiatry, University of Oxford, Oxford (UK)" + }, + { + "author_name": "Olivier Drouin", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + }, + { + "author_name": "Jocelyn Gravel", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + }, + { + "author_name": "Anna Smyrnova", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + }, + { + "author_name": "Andreas Bender", + "author_inst": "Department of Statistics, LMU Munich, Munich (Germany)" + }, + { + "author_name": "Massimiliano Orri", + "author_inst": "McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec (Canada)" + }, + { + "author_name": "Marie-Claude Geoffroy", + "author_inst": "McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec (Canada)" + }, + { + "author_name": "Nicholas Chadi", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.04.15.22273460", "rel_title": "Coronavirus infection in neonates: Neurodevelopmental outcomes at 18 months of age", @@ -343086,49 +345172,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.15.22273915", - "rel_title": "Effectiveness of COVID-19 mRNA vaccine booster dose relative to primary series during a period of Omicron circulation", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273915", - "rel_abs": "During a period of Omicron variant circulation, we estimated relative VE of COVID-19 mRNA booster vaccination versus primary two-dose series in an ongoing community cohort. Relative VE was 66% (95% CI: 46%, 79%) favoring the booster dose compared to primary series vaccination. Our results support current booster recommendations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Joshua G Petrie", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Jennifer P King", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "David L. McClure", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Melissa A Rolfes", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jennifer K Meece", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Edward A Belongia", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Huong Q McLean", - "author_inst": "Marshfield Clinic Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.07.22273549", "rel_title": "Dose-response modelling of endemic coronavirus and SARS-CoV-2: human challenge trials reveal the individual variation in susceptibility", @@ -343924,6 +345967,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.11.22273702", + "rel_title": "Making maternity and neonatal care personalised in the COVID-19 pandemic: results from the Babies Born Better Survey in the UK and the Netherlands", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273702", + "rel_abs": "Structured abstractO_ST_ABSBackgroundC_ST_ABSThe COVID-19 pandemic had a severe impact on womens birth experiences. To date, there are no studies that use both quantitative and qualitative data to compare womens birth experiences before and during the pandemic, across more than one country.\n\nAimTo examine womens birth experiences during the COVID-19 pandemic and to compare the experiences of women who gave birth in the United Kingdom (UK) or the Netherlands (NL) either before or during the pandemic.\n\nMethodThis study is based on analyses of quantitative and qualitative data from the online Babies Born Better survey. Responses recorded by women giving birth in the UK and the NL between June and December 2020 have been used, encompassing women who gave birth between 2017 and 2020. Quantitative data were analysed descriptively, and chi-squared tests were performed to compare women who gave birth pre- versus during pandemic and separately by country. Qualitative data was analysed by inductive thematic analysis.\n\nFindingsRespondents in both the UK and the NL who gave birth during the pandemic were as likely, or, if they had a self-reported above average standard of life, more likely to rate their labour and birth experience positively when compared to women who gave birth pre-pandemic. This was despite the fact that those labouring in the pandemic reported less support and choice. Two potential explanatory themes emerged from the qualitative data: respondents had lower expectations during the pandemic, and they appreciated that care providers tried hard to personalise care.\n\nConclusionOur study implies that many women labouring during the COVID-19 pandemic experienced restrictions, but their experience was mitigated by staff actions. However, personalised care should not be maintained by the good will of care providers, but should be a priority in maternity care policy to benefit all service users equitably.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Lauri M.M. van den Berg", + "author_inst": "Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Naseerah Akooji", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Gill Thomson", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Ank de Jonge", + "author_inst": "Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Marie-Clare Balaam", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Anastasia Topalidou", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Soo Downe", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "the ASPIRE COVID-19 research team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2022.04.15.22273412", "rel_title": "COVID-19 vaccine effectiveness against SARS-CoV-2 infection in the United States prior to the Delta and Omicron-associated surges: a retrospective cohort study of repeat blood donors", @@ -344688,49 +346778,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.13.488221", - "rel_title": "Determinants of Spike Infectivity, Processing and Neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2", - "rel_date": "2022-04-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.13.488221", - "rel_abs": "The SARS-CoV-2 Omicron variant rapidly outcompeted other variants and currently dominates the COVID-19 pandemic. Its enhanced transmission, immune evasion and pathogenicity is thought to be driven by numerous mutations in the Omicron Spike protein. Here, we examined the impact of amino acid changes that are characteristic for the BA.1 and/or BA.2 Omicron lineages on Spike function, processing and susceptibility to neutralization. Individual mutations of S371F/L, S375F and T376A in the ACE2 receptor-binding domain as well as Q954H and N969K in the hinge region 1 impaired infectivity, while changes of G339D, D614G, N764K and L981F moderately enhanced it. Most mutations in the N-terminal region and the receptor binding domain reduced sensitivity of the Spike protein to neutralization by sera from individuals vaccinated with the BNT162b2 vaccine or therapeutic antibodies. Our results represent a systematic functional analysis of Omicron Spike adaptations that allowed this SARS-CoV-2 variant to overtake the current pandemic.\n\nHIGHLIGHTSO_LIS371F/L, S373P and S375F impair Spike function and revert in some BA. 1 isolates\nC_LIO_LIChanges of Q954H and N969K in HR1 reduce while L981F enhances S-mediated infection\nC_LIO_LIOmicron-specific mutations in the NTD and RBD of Spike reduce neutralization\nC_LIO_LIN440K, G446S, E484A and Q493K confer resistance to bamlanivimab or imdevimab\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chiara Pastorio", - "author_inst": "Institute for Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany" - }, - { - "author_name": "Fabian Zech", - "author_inst": "Institute for Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany" - }, - { - "author_name": "Sabrina Noettger", - "author_inst": "Institute for Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany" - }, - { - "author_name": "Christoph Jung", - "author_inst": "Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany" - }, - { - "author_name": "Timo Jacob", - "author_inst": "Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany" - }, - { - "author_name": "Konstantin M.J. Sparrer", - "author_inst": "Institute for Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany" - }, - { - "author_name": "Frank Kirchhoff", - "author_inst": "Institute for Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.07.22273168", "rel_title": "Development of highly specific singleplex and multiplex real-time reverse transcription PCR assays for the identification of SARS-CoV-2 Omicron BA.1, BA.2 and Delta variants", @@ -345546,6 +347593,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.12.22273804", + "rel_title": "Nowcasting and Forecasting COVID-19 Waves: The Recursive and Stochastic Nature of Transmission", + "rel_date": "2022-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273804", + "rel_abs": "We propose a parsimonious, yet effective, susceptible-exposed-infected-removed-type model that incorporates the time change in the transmission and death rates. The model is calibrated by Tikhonov-type regularization from official reports from New York City (NYC), Chicago, the State of Sao Paulo, in Brazil, and British Columbia, in Canada. To forecast, we propose different ways to extend the transmission parameter, considering its estimated values. The forecast accuracy is then evaluated using real data from the above referred places. All the techniques accurately provided forecast scenarios for periods 15 days long. One of the models effectively predicted the magnitude of the four waves of infections in NYC, including the one caused by the Omicron variant for periods of 45 days long using out-of-sample data.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.12.22273761", "rel_title": "Multiplex RT-qPCR assay (N200) to detect and estimate prevalence of multiple SARS-CoV-2 Variants of Concern in wastewater", @@ -346370,189 +348431,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.04.11.487879", - "rel_title": "Broadly neutralizing antibodies target the coronavirus fusion peptide", - "rel_date": "2022-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.11.487879", - "rel_abs": "The potential for future coronavirus outbreaks highlights the need to develop strategies and tools to broadly target this group of pathogens. Here, using an epitope-agnostic approach, we identified six monoclonal antibodies that bound to spike proteins from all seven human-infecting coronaviruses. Epitope mapping revealed that all six antibodies target the conserved fusion peptide region adjacent to the S2 cleavage site. Two antibodies, COV44-62 and COV44-79, broadly neutralize a range of alpha and beta coronaviruses, including SARS-CoV-2 Omicron subvariants BA.1 and BA.2, albeit with lower potency than RBD-specific antibodies. In crystal structures of Fabs COV44-62 and COV44-79 with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine at the S2 cleavage site. Importantly, COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings identify the fusion peptide as the target of the broadest neutralizing antibodies in an epitope-agnostic screen, highlighting this site as a candidate for next-generation coronavirus vaccine development.\n\nOne-Sentence SummaryRare monoclonal antibodies from COVID-19 convalescent individuals broadly neutralize coronaviruses by targeting the fusion peptide.", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Cherrelle Dacon", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Courtney Tucker", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Linghang Peng", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Chang-Chun D. Lee", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Ting-Hui Lin", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Meng Yuan", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Yu Cong", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Lingshu Wang", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Lauren Purser", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Jazmean K. Williams", - "author_inst": "Integral Molecular" - }, - { - "author_name": "Chul-Woo Pyo", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Ivan Kosik", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Zhe Hu", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Ming Zhao", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Divya Mohan", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Andrew Cooper", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Mary Peterson", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Jeff Skinner", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Saurabh Dixit", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Erin Kollins", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Louis Huzella", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Donna Perry", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Russell Byrum", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Sanae Lembirik", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Yi Zhang", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Eun Sung Yang", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Man Chen", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Kwanyee Leung", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Rona S. Weinberg", - "author_inst": "New York Blood Center" - }, - { - "author_name": "Amarendra Pegu", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Dan Geraghty", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Edgar Davidson", - "author_inst": "Integral Molecular" - }, - { - "author_name": "Iyadh Douagi", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Susan Moir", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Jonathan W. Yewdell", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Connie Schmaljohn", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Peter D. Crompton", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Michael R. Holbrook", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "David Nemazee", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "John R. Mascola", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Joshua Tan", - "author_inst": "National Institute of Allergy and Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.12.488042", "rel_title": "The SARS-CoV-2 receptor-binding domain facilitates neutrophil transepithelial migration and nanoparticle uptake in the mice airways", @@ -347329,6 +349207,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.07.22273561", + "rel_title": "The effect of the COVID-19 lockdown on mental health care use in South Africa: an interrupted time series analysis", + "rel_date": "2022-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273561", + "rel_abs": "AimsIn March 2020, South Africa introduced a lockdown in response to the COVID-19 pandemic, entailing the suspension of all non-essential activities and a complete ban of tobacco and alcohol sales. We studied the effect of the lockdown on mental health care utilisation rates in private-sector care in South Africa.\n\nMethodsWe did an interrupted time series analysis using insurance claims from January 1, 2017, to June 1, 2020 of beneficiaries 18 years or older from a large private sector medical aid scheme. We calculated weekly outpatient consultation and hospital admission rates for organic mental disorders, substance use disorders, serious mental disorders, depression, anxiety, other mental disorders, any mental disorder, and alcohol withdrawal syndrome. We calculated adjusted odds ratios (OR) for the effect of the lockdown on weekly outpatient consultation and hospital admission rates and the weekly change in rates during the lockdown until June 1, 2020.\n\nResults710,367 persons were followed up for a median of 153 weeks. Hospital admission rates (OR 0.38; 95% CI 0.33-0.44) and outpatient consultation rates (OR 0.74; 95% CI 0.63-0.87) for any mental disorder decreased substantially after the lockdown and did not recover to pre-lockdown levels until June 1, 2020. Health care utilisation rates for alcohol withdrawal syndrome doubled after the introduction of the lockdown, but the statistical uncertainty around the estimates was large (OR 2.24; 95% CI 0.69-7.24).\n\nConclusionsReduced mental health care contact rates during the COVID-19 lockdown likely reflect a substantial unmet need for mental health services with potential long-term consequences for mental health patients and their families. Steps to ensure access and continuity of mental health services during future lockdowns should be considered.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Anja Elisabeth Wettstein", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland and Graduate School for Health Sciences, University of Bern, Switzerland" + }, + { + "author_name": "Mpho Tlali", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "John A Joska", + "author_inst": "HIV Mental Health Research Unit, Department of Psychiatry and Mental Health, Neuroscience Institute, Cape Town, South Africa" + }, + { + "author_name": "Morna Cornell", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Veronika W Skrivankova", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Soraya Seedat", + "author_inst": "Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" + }, + { + "author_name": "Johannes P Mouton", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa and Division of Clinical Pharmacology, Department of M" + }, + { + "author_name": "Leigh L van den Heuvel", + "author_inst": "Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" + }, + { + "author_name": "Nicola Maxwell", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Mary-Ann Davies", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Gary Maartens", + "author_inst": "Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Matthias Egger", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology and Research, University of Cape " + }, + { + "author_name": "Andreas D Haas", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.07.22273593", "rel_title": "Inequities in COVID-19 vaccine and booster coverage across Massachusetts ZIP codes: large gaps persist after the 2021/22 Omicron wave", @@ -347793,89 +349738,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.07.22273545", - "rel_title": "Both COVID-19 infection and vaccination induce high-affinity cross-clade responses to SARS-CoV-2 variants", - "rel_date": "2022-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273545", - "rel_abs": "The B.1.1.529 (omicron) variant has rapidly supplanted most other SARS-CoV-2 variants. Using microfluidics-based antibody affinity profiling (MAAP), we have recently shown that current therapeutic monoclonal antibodies exhibit a drastic loss of affinity against omicron. Here, we have characterized affinity and IgG concentration in the plasma of 39 individuals with multiple trajectories of SARS-CoV-2 infection and/or vaccination as well as in 2 subjects without vaccination or infection. Antibody affinity in patient plasma samples was similar against the wild-type, delta, and omicron variants (KA ranges: 122{+/-}155, 159{+/-}148, 211{+/-}307 M-1, respectively), indicating a surprisingly broad and mature cross-clade immune response. We then determined the antibody iso- and subtypes against multiple SARS-CoV-2 spike domains and nucleoprotein. Postinfectious and vaccinated subjects showed different profiles, with IgG3 (p = 0.002) but not IgG1, IgG2 or IgG4 subtypes against the spike ectodomain being more prominent in the former group. Lastly, we found that the ELISA titers against the wildtype, delta, and omicron RBD variants correlated linearly with measured IgG concentrations (R=0.72) but not with affinity (R=0.29). These findings suggest that the wild-type and delta spike proteins induce a polyclonal immune response capable of binding the omicron spike with similar affinity. Changes in titers were primarily driven by antibody concentration, suggesting that B-cell expansion, rather than affinity maturation, dominated the response after infection or vaccination.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Marc Emmenegger", - "author_inst": "Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland" - }, - { - "author_name": "Sebastian Fiedler", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Silvio D Brugger", - "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland" - }, - { - "author_name": "Sean R A Devenish", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Alexey S Morgunov", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom and Centre for Misfolding Diseases, Yusuf Hamied " - }, - { - "author_name": "Alison Ilsley", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Francesco Ricci", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Anisa Y Malik", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Thomas Scheier", - "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland" - }, - { - "author_name": "Leyla Batkitar", - "author_inst": "Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland" - }, - { - "author_name": "Lidia Madrigal", - "author_inst": "Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland" - }, - { - "author_name": "Marco Rossi", - "author_inst": "Laboratory Medicine, University Hospital Zurich, Switzerland" - }, - { - "author_name": "Andrew K Lynn", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Lanja Saleh", - "author_inst": "Laboratory Medicine, University Hospital Zurich, Switzerland" - }, - { - "author_name": "Arnold von Eckardstein", - "author_inst": "Laboratory Medicine, University Hospital Zurich, Switzerland" - }, - { - "author_name": "Tuomas P J Knowles", - "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" - }, - { - "author_name": "Adriano Aguzzi", - "author_inst": "Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.08.22273608", "rel_title": "Outpatient and Home Pulmonary Rehabilitation Program Post COVID-19: A study protocol for clinical trial", @@ -348847,6 +350709,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.04.07.487520", + "rel_title": "Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response", + "rel_date": "2022-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487520", + "rel_abs": "SARS-CoV-2, responsible for the COVID-19 pandemic, causes respiratory failure and damage to multiple organ systems. The emergence of viral variants poses a risk of vaccine failures and prolongation of the pandemic. However, our understanding of the molecular basis of SARS-CoV-2 infection and subsequent COVID-19 pathophysiology is limited. In this study, we have uncovered a critical role for the evolutionarily conserved Hippo signaling pathway in COVID-19 pathogenesis. Given the complexity of COVID-19 associated cell injury and immunopathogenesis processes, we investigated Hippo pathway dynamics in SARS-CoV-2 infection by utilizing COVID-19 lung samples, and human cell models based on pluripotent stem cell-derived cardiomyocytes (PSC-CMs) and human primary lung air-liquid interface (ALI) cultures. SARS-CoV-2 infection caused activation of the Hippo signaling pathway in COVID-19 lung and in vitro cultures. Both parental and Delta variant of concern (VOC) strains induced Hippo pathway. The chemical inhibition and gene knockdown of upstream kinases MST1/2 and LATS1 resulted in significantly enhanced SARS-CoV-2 replication, indicating antiviral roles. Verteporfin a pharmacological inhibitor of the Hippo pathway downstream transactivator, YAP, significantly reduced virus replication. These results delineate a direct antiviral role for Hippo signaling in SARS-CoV-2 infection and the potential for this pathway to be pharmacologically targeted to treat COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Gustavo Garcia Jr.", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Yijie Wang", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Joseph Ignatius Irudayam", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arjit Vijey Jeyachandran", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Sebastian Castillo Cario", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chandani Sen", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Shen Li", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Yunfeng Li", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Wayne State University" + }, + { + "author_name": "Karin Nielsen-Saines", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Samuel W. French", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Priya S. Shah", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Kouki Morizono", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Brigitte Gomperts", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arjun Deb", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arunachalam Ramaiah", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Vaithilingaraja Arumugaswami", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.04.07.487528", "rel_title": "Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike", @@ -349727,37 +351672,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2022.04.04.22272833", - "rel_title": "Use of face masks did not impact COVID-19 incidence among 10-12-year-olds in Finland", - "rel_date": "2022-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22272833", - "rel_abs": "In fall 2021 in Finland, the recommendation to use face masks in schools for pupils ages 12 years and above was in place nationwide. Some cities recommended face masks for younger pupils as well. Our aim was to compare COVID-19 incidence among 10-12-year-olds between cities with different recommendations on the use of face masks in schools. COVID-19 case numbers were obtained from the National Infectious Disease Registry (NIDR) of the Finnish Institute for Health and Welfare, where clinical microbiology laboratories report all positive SARS-CoV-2 tests with unique identifiers in a timely manner, including information such as date of birth, gender, and place of residence. The NIDR is linked to the population data registry, enabling calculation of incidences. We compared the differences in trends of 14-day incidences between Helsinki and Turku among 10-12-year-olds, and for comparison, also among ages 7-9 and 30-49 by using joinpoint regression. According to our analysis, no additional effect seemed to be gained from this, based on comparisons between the cities and between the age groups of the unvaccinated children (10-12 years versus 7-9 years).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Aapo Juutinen", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Emmi Sarvikivi", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "P\u00e4ivi Laukkanen-Nevala", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Otto Helve", - "author_inst": "Finnish Institute for Health and Welfare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.06.22273202", "rel_title": "Prediction of deterioration from COVID-19 in patients in skilled nursing facilities using wearable and contact-free devices: a feasibility study", @@ -350829,6 +352743,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.06.22273080", + "rel_title": "Serious underlying medical conditions and COVID-19 vaccine hesitancy.", + "rel_date": "2022-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273080", + "rel_abs": "ObjectiveTo examine vaccine uptake, hesitancy and explanatory factors amongst people with serious and/or chronic health conditions, including the impact of underlying disease on attitudes to vaccination.\n\nDesignCross-sectional survey.\n\nSettingTen Australian health services.\n\nParticipants4683 patients (3560 cancer, 842 diabetes and 281 multiple sclerosis) receiving care at the health services participated in the 42-item survey, between June 30 to October 5, 2021.\n\nMain outcome measuresSociodemographic and disease-related characteristics, COVID-19 vaccine uptake, and the scores of three validated scales which measured vaccine hesitancy and vaccine-related beliefs generally and specific to the participants disease, including the Oxford COVID-19 Vaccine Hesitancy Scale, the Oxford COVID-19 Vaccine Confidence and Complacency Scale and the Disease Influenced Vaccine Acceptance Scale. Multivariable logistic regression was used to determine the associations between scale scores and vaccine uptake.\n\nResultsOf all participants, 81.5% reported having at least one COVID-19 vaccine. Unvaccinated status was associated with younger age, female sex, lower education and income, English as a second language, and residence in regional areas (all p<0.05). Unvaccinated participants were more likely to report greater vaccine hesitancy and more negative perceptions toward vaccines (all p<0.05). Disease-related vaccine concerns were associated with unvaccinated status and hesitancy, including greater complacency about COVID-19 infection, and concerns relating to vaccine efficacy and impact on their disease and/or treatment (all p<0.05).\n\nConclusionsDisease-specific concerns impact COVID-19 vaccine-related behaviours and beliefs in people with serious and/or chronic health conditions. This highlights the need to develop targeted strategies and education about COVID-19 vaccination to support medically vulnerable populations and health professionals.\n\nTrial registrationACTRN12621001467820", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Daphne Day", + "author_inst": "Monash Health" + }, + { + "author_name": "Lisa Grech", + "author_inst": "Monash University" + }, + { + "author_name": "Mike Nguyen", + "author_inst": "Monash Health" + }, + { + "author_name": "Nathan Bain", + "author_inst": "Monash Health" + }, + { + "author_name": "Alastair Kwok", + "author_inst": "Monash Health" + }, + { + "author_name": "Sam Harris", + "author_inst": "Bendigo Health" + }, + { + "author_name": "Hieu Chau", + "author_inst": "Latrobe Regional Hospital" + }, + { + "author_name": "Bryan Chan", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Richard Blennerhassett", + "author_inst": "Central Coast Haematology" + }, + { + "author_name": "Louise Nott", + "author_inst": "Icon Cancer Centre Hobart" + }, + { + "author_name": "Nada Hamad", + "author_inst": "St Vincent's Hospital Sydney" + }, + { + "author_name": "Annette Tognela", + "author_inst": "Campbelltown Hospital" + }, + { + "author_name": "David Hoffman", + "author_inst": "Dr David Hoffman" + }, + { + "author_name": "Amelia McCartney", + "author_inst": "Monash Health" + }, + { + "author_name": "Kate Webber", + "author_inst": "Monash Health" + }, + { + "author_name": "Jennifer Wong", + "author_inst": "Monash Health" + }, + { + "author_name": "Craig Underhill", + "author_inst": "Border Medical Oncology" + }, + { + "author_name": "Brett Sillars", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Antony Winkel", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Mark Savage", + "author_inst": "Bendigo Health" + }, + { + "author_name": "Bao Sheng Loe", + "author_inst": "Cambridge University" + }, + { + "author_name": "Daniel Freeman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eva Segelov", + "author_inst": "Monash Health" + }, + { + "author_name": "- CANVACCS, DIABVACCS, and MSVACCS investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.06.22273512", "rel_title": "Pandemic-EBT and grab-and-go school Meals: Costs, reach, and benefits of two approaches to keep children fed during school closures due to COVID-19", @@ -351417,41 +353442,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.30.22273026", - "rel_title": "A comparative analysis of serial measurements of Soluble Urokinase-type Plasminogen Activator Receptor (suPAR) and C-reactive protein in patients with moderate COVID-19: a single center study from India", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273026", - "rel_abs": "Soluble urokinase plasminogen-activator receptor (suPAR) is a secreted protein associated with inflammation and proven its usefulness in triage/risk stratifications. This prospective study aimed to evaluate the utility of suPAR in comparison to C-reactive protein (CRP) in hospitalized moderate COVID-19 patients.\n\nThis is a prospective comparative study during second pandemic wave. Serum suPAR level and CRP were measured serially in 31 confirmed COVID-19 hospitalized patients (20 males, 11 females) on day-1 (24-hours of admission), day-3 and day-5 using suPARnostic AUTO flex ELISA and Nephelometry (ThermoFischer) respectively. Schapiro Wilk test verified the data distribution; Wilcoxon signed rank test compared CRP and suPAR between deceased/alive subject and identified link between co-morbidity and COVID-19 severity.\n\nIn our study, the mean age was 61.8 ranging from 28-82 with 9.7% (n=3/31) mortality rate. Deceased patients showed significant higher suPAR levels correlating with increasing severity from day 1 to 5 (p<0.016-0.006) than CRP (p=0.717). Patients with pre-existing co-morbidities showed significantly elevated suPAR levels on days 1-5, especially those with hypertension (HTN;p<0.03) and chronic kidney disease (CKD;p<0.001).\n\nIn conclusion, levels of suPAR were higher in deceased patients with severe symptoms of COVID-19 during hospitalization and in patients with pre-existing co-morbid conditions, HTN and CKD. This preliminary study provides evidence suggesting that circulating suPAR can be a potential biomarker to assess the severity of COVID 19 compared to CRP.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Atul Kakar", - "author_inst": "Sir Ganga Ram Hospital" - }, - { - "author_name": "Pooja Rani", - "author_inst": "Sir Ganga Ram Hospital" - }, - { - "author_name": "Tanvi Batra", - "author_inst": "Sir Ganga Ram Hospital" - }, - { - "author_name": "Rizwana Hasan", - "author_inst": "Sir Ganga Ram Hospital" - }, - { - "author_name": "Sangeeta Choudhury", - "author_inst": "Sir Ganga Ram Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.04.22273330", "rel_title": "Effectiveness of a nation-wide COVID-19 vaccination program in Mexico", @@ -352483,6 +354473,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2022.03.29.22273148", + "rel_title": "Modeling behavior change and underreporting in the early phase of COVID-19 pandemic in Metro Manila, Philippines", + "rel_date": "2022-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273148", + "rel_abs": "IntroductionAt the start of the pandemic, the Philippine capital Metro Manila was placed under a strict lockdown termed Enhanced Community Quarantine (ECQ). When ECQ was eased to General Community Quarantine (GCQ) after three months, healthcare systems were soon faced with a surge of COVID-19 cases, putting most facilities at high or critical risk and prompting a return to a stricter policy.\n\nMethodsWe developed a mathematical model considering behavior changes and underreporting to represent the first major epidemic wave in Metro Manila. Key parameters were fitted to the cumulative cases in the capital from March to September 2020. A bi-objective optimization problem was formulated that allows easing of restrictions at an earlier time and minimizes the necessary additional beds to ensure sufficient capacity in healthcare facilities once ECQ was lifted.\n\nResultsIf behavior was changed one to four weeks earlier before GCQ, then the cumulative number of cases can be reduced by up to 55% and the peak delayed by up to four weeks. Increasing the reporting ratio during ECQ threefold may increase the reported cases by 23% but can reduce the total cases, including the unreported, by 61% on June 2020. If GCQ began on May 28, 2020, 48 beds should have been added per day to keep the capacity only at high-risk (75% occupancy). Among the optimal solutions, the peak of cases is lowest if ECQ was lifted on May 20, 2020 and with at least 56 additional beds per day.\n\nConclusionSince infectious diseases are likely to reemerge, the formulated model can be used as a decision support tool to improve existing policies and plan effective strategies that can minimize the socioeconomic impact of strict lockdown measures and ensure adequate healthcare capacity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Victoria May P. Mendoza", + "author_inst": "Institute of Mathematics, University of the Philippines Diliman" + }, + { + "author_name": "Renier Mendoza", + "author_inst": "Institute of Mathematics, University of the Philippines Diliman" + }, + { + "author_name": "Youngsuk Ko", + "author_inst": "Department of Mathematics, Konkuk University" + }, + { + "author_name": "Jongmin Lee", + "author_inst": "Department of Mathematics, Konkuk University" + }, + { + "author_name": "Eunok Jung", + "author_inst": "Department of Mathematics, Konkuk University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.03.22273370", "rel_title": "Automated method to extract and purify RNA from wastewater enables more sensitive detection of SARS-CoV-2 markers in community sewersheds", @@ -353191,33 +355216,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.04.22273384", - "rel_title": "A simple algorithm based on initial Ct values predicts the duration to SARS-CoV-2 negativity and allows more efficient test-to-release and return-to-work schedules", - "rel_date": "2022-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273384", - "rel_abs": "Especially during global pandemics but also in the context of epidemic waves, the capacity for diagnostic qRT-PCRs rapidly becomes a limiting factor. Furthermore, excessive testing incurs high costs and can result in an overstrained work force in diagnostics departments. Obviously, people aim to shorten their isolation periods, hospitals need to discharge convalescent people, and re-employ staff members after infection. The aim of the study was to optimize retesting regimens for test-to-release from isolation and return-to-work applications. For this purpose, we investigated the association between Ct values at the first diagnosis of SARS-CoV-2 infection and the period until test negativity was reached, or at least until the Ct value exceeded 30, which is considered to indicate the transition to a non-infectious state. We included results from the testing of respiratory material samples for the detection of SARS-CoV-2 RNA, tested from 01 March 2020 to 31 January 2022.\n\nLower initial Ct values were associated with longer periods of SARS-CoV-2 RNA positivity. Starting with Ct values of <20, 20-25, 25-30, 30-35, and >35, it took median intervals of 20 (interval: 14-25), 16 (interval: 10-21), 12 (interval: 7-16), 7 (interval: 5-14), and 5 (interval: 2-7) days, respectively, until the person tested negative. Accordingly, a Ct threshold of 30 was surpassed after 13 (interval: 8-19), 9 (interval: 6-14), 7 (interval: 6-11), 6 (interval: 4-10), and 3 (interval: 1-6) days, respectively, in individuals with aforementioned start Ct values. Furthermore, the time to negativity was longer for adults versus children, wild-type SARS-CoV-2 variant versus other variants of concern, and in patients who were treated in the intensive care units.\n\nBased on these data, we propose an adjusted retesting strategy according to the initial Ct value in order to optimize available PCR resources.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Olympia E Anastasiou", - "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen" - }, - { - "author_name": "Vu Thuy Khanh Le-Trilling", - "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen" - }, - { - "author_name": "Mirko Trilling", - "author_inst": "Institute for Virology, University Hospital Essen, University of Duisburg-Essen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.04.22273385", "rel_title": "Significant impacts of the COVID-19 pandemic on race/ethnic differences in USA mortality", @@ -354517,6 +356515,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.04.02.22273333", + "rel_title": "High rate of BA.1, BA.1.1 and BA.2 in triple vaccinated", + "rel_date": "2022-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.02.22273333", + "rel_abs": "BackgroundBooster vaccine doses offer protection against severe COVID-19 caused by omicron but are less effective against infection. Characteristics such as serological correlates of protection, viral abundance, and clearance of omicron infection in triple vaccinated individuals are scarce.\n\nMethodsWe conducted a 4-week twice-weekly SARS-CoV-2 qPCR screening shortly after an mRNA vaccine booster in 368 healthcare workers. Spike-specific IgG levels and neutralization titers were determined at study start. qPCR-positive participants were sampled repeatedly for two weeks and monitored for symptoms.\n\nResultIn total 81 (cumulative incidence 22%) omicron infections were detected, divided between BA.1, BA.1.1 and BA.2. Increasing post-booster antibody titers were protective against infection (p<0.05), linked to reduced viral load (p<0.01) and time to viral clearance (p<0.05). Only 10% of infected participants remained asymptomatic through the course of their infection. Viral load peaked at day 3 and live virus could be detected for up to 9 days after first PCR-positive sample. Presence of symptoms correlated to elevated viral load (p<0.0001), but despite resolution of symptoms most participants showed Ct levels <30 at day 9. No significant differences were observed for viral load and time to viral clearance between BA.1, BA.1.1 and BA.2 infected individuals.\n\nConclusionWe report a high incidence of omicron infection despite recent booster vaccination in triple vaccinated individuals. Increasing levels of vaccine-induced spike-specific WT antibodies entail increased protection against infection and reduce viral load if infected. High viral load and secretion of live virus for up to nine days may facilitate transmission in a triple vaccinated population.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ulrika Marking", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Nina Greilert Norin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Oscar Bladh", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Max Gordon", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Henry Ng", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Kim Blom", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Mia Phillipson", + "author_inst": "Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Sara Mangsbo", + "author_inst": "Department of Pharmacy and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Anna Smed-Sorensen", + "author_inst": "Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden." + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sophia Hober", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Mikael Aberg", + "author_inst": "Department of Medical Sciences, Clinical Chemistry and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.31.22273111", "rel_title": "Predictors of all-cause mortality among patients hospitalized with influenza, respiratory syncytial virus, or SARS-CoV-2", @@ -355137,141 +357214,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.03.30.22273143", - "rel_title": "Safety and immunogenicity of a SARS-CoV-2 recombinant protein nanoparticle vaccine (GBP510) adjuvanted with AS03: a phase 1/2, randomized, placebo-controlled, observer-blinded trial", - "rel_date": "2022-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273143", - "rel_abs": "BackgroundVaccination has helped to mitigate the COVID-19 pandemic. Ten traditional and novel vaccines have been listed by the World Health Organization for emergency use. Additional alternative approaches may better address ongoing vaccination globally, where there remains an inequity in vaccine distribution. GBP510 is a recombinant protein vaccine, which consists of self-assembling, two-component nanoparticles displaying the receptor-binding domain (RBD) in a highly immunogenic array.\n\nMethodsWe conducted a randomized, placebo-controlled, observer-blinded, phase 1/2 trial to evaluate the safety and immunogenicity of GBP510 (2-doses at a 28-day interval) adjuvanted with or without AS03 in adults aged 19-85 years. The main outcomes included solicited and unsolicited adverse events; anti-SARS-CoV-2 RBD IgG antibody and neutralizing antibody responses; T-cell immune responses.\n\nFindingsOf 328 participants who underwent randomization, 327 participants received at least 1 dose of vaccine. Each received either 10 g GBP510 adjuvanted with AS03 (n = 101), 10 g unadjuvanted GBP510 (n = 10), 25 g GBP510 adjuvanted with AS03 (n = 104), 25 g unadjuvanted GBP510 (n = 51), or placebo (n = 61). Most solicited adverse events were mild-to-moderate in severity and transient. Higher reactogenicity was observed in the GBP510 adjuvanted with AS03 groups compared to the non-adjuvanted and placebo groups. Reactogenicity was higher post-dose 2 compared to post-dose 1, particularly for systemic adverse events. The geometric mean concentrations of anti-SARS-CoV-2-RBD IgG antibody reached 2163.6/2599.2 BAU/mL in GBP510 adjuvanted with AS03 recipients (10 g/25 g) by 14 days after the second dose. Two-dose vaccination with 10 g or 25 g GBP510 adjuvanted with AS03 induced high titers of neutralizing antibody via pseudovirus (1369.0/1431.5 IU/mL) and wild-type virus (949.8/861.0 IU/mL) assays.\n\nInterpretationGBP510 adjuvanted with AS03 was well tolerated and highly immunogenic. These results support further development of the vaccine candidate, which is currently being evaluated in Phase 3.\n\nFundingCoalition for Epidemic Preparedness Innovations\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for research articles published by December 31, 2021, using the terms \"COVID-19\" or \"SARS-CoV-2,\" \"vaccine,\" and \"clinical trial.\" In previously reported randomized clinical trials, we found that mRNA vaccines were more immunogenic than adenovirus-vectored vaccines. Solicited adverse events were more frequent and more severe in intensity after the first dose compared to the second dose for adenovirus-vectored vaccines, whereas they increased after the second dose of mRNA or recombinant spike-protein nanoparticle vaccines.\n\nAdded value of this studyThis is the first human study evaluating the immunogenicity and safety of recombinant SARS-CoV-2 protein nanoparticle with and without adjuvant AS03, designed to elicit functional cross-protective responses via receptor-binding domain (RBD). Both 10 and 25 g of GBP510 with AS03 formulations were well tolerated with an acceptable safety profile. Potent humoral immune responses against the SARS-CoV-2 RBD were induced and peaked by day 42 (14 days after the second dose). In addition, GBP510 adjuvanted with AS03 elicited a noticeable Th1 response, with production of IFN-{gamma}, TNF-, and IL-2. IL-4 was inconsistent and IL-5 nearly inexistent response across all groups.\n\nImplications of the available evidenceThe results from this phase 1/2 trial indicate that GBP510 adjuvanted with AS03 has an acceptable safety profile with no vaccine-related serious adverse events. Two-dose immunization with GBP510 adjuvanted with AS03 induced potent humoral and cellular immune responses against SARS-CoV-2.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Joon Young Song", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University Guro Hospital, Korea" - }, - { - "author_name": "Won Suk Choi", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University Ansan Hospital, Korea" - }, - { - "author_name": "Jung Yeon Heo", - "author_inst": "Department of Infectious Diseases, Ajou University, Suwon Hospital, Korea" - }, - { - "author_name": "Jin Soo Lee", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Inha University Hospital, Korea" - }, - { - "author_name": "Dong Sik Jung", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Dong-A University Hospital, Korea" - }, - { - "author_name": "Shin-Woo Kim", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Hospital, Korea" - }, - { - "author_name": "Kyung Hwa Park", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Chonnam National University Hospital, Korea" - }, - { - "author_name": "Joong Sik Eom", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Gil Medical Center, Gachon University, Korea" - }, - { - "author_name": "Su Jin Jeong", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University, Korea" - }, - { - "author_name": "Jacob Lee", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Hallym University Hospital, Chuncheon, Korea" - }, - { - "author_name": "Ki Tae Kwon", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Chilgok Hospital, Korea" - }, - { - "author_name": "Hee Jung Choi", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Ewha Womans University, Mokdong Hospital, Korea" - }, - { - "author_name": "Jang Wook Sohn", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University Anam Hospital, Korea" - }, - { - "author_name": "Young Keun Kim", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Yonsei University Wonju Severance Christian Hospital, Korea" - }, - { - "author_name": "Ji Yun Noh", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University Guro Hospital, Korea" - }, - { - "author_name": "Woo Joo Kim", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University Guro Hospital, Korea" - }, - { - "author_name": "Fran\u00e7ois Roman", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Maria Angeles Ceregido", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Francesca Solmi", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Agathe Philippot", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Alexandra C. Walls", - "author_inst": "Howard Hughes Medical Institute, University of Washington, WA, U.S." - }, - { - "author_name": "Lauren Carter", - "author_inst": "Department of Biochemistry & Institute for Protein Design, University of Washington" - }, - { - "author_name": "David Veesler", - "author_inst": "Department of Biochemistry & Howard Hughes Medical Institute, University of Washington" - }, - { - "author_name": "Neil King", - "author_inst": "Department of Biochemistry & Institute for Protein Design, University of Washington" - }, - { - "author_name": "Hun Kim", - "author_inst": "Department of R&D, SK Bioscience, Korea" - }, - { - "author_name": "Ji Hwa Ryu", - "author_inst": "Department of R&D, SK Bioscience, Korea" - }, - { - "author_name": "Su Jeen Lee", - "author_inst": "Department of R&D, SK Bioscience, Korea" - }, - { - "author_name": "Yong Wook Park", - "author_inst": "Department of R&D, SK Bioscience, Korea" - }, - { - "author_name": "Ho keun Park", - "author_inst": "Department of R&D, SK Bioscience, Korea" - }, - { - "author_name": "Hee Jin Cheong", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Korea University Guro Hospital, Korea" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.29.22272714", "rel_title": "Immunogenicity of Pfizer-BioNTech COVID-19 mRNA Primary Vaccination Series in Recovered Individuals Depends on Symptoms at Initial Infection.", @@ -356163,6 +358105,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.03.31.22273262", + "rel_title": "Emulation of epidemics via Bluetooth-based virtual safe virus spread: experimental setup, software, and data", + "rel_date": "2022-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273262", + "rel_abs": "We describe an experimental setup and a currently running experiment for evaluating how physical interactions over time and between individuals affect the spread of epidemics. Our experiment involves the voluntary use of the Safe Blues Android app by participants at The University of Auckland (UoA) City Campus in New Zealand. The app spreads multiple virtual safe virus strands via Bluetooth depending on the social and physical proximity of the subjects. The evolution of the virtual epidemics is recorded as they spread through the population. The data is presented as a real-time (and historical) dashboard. A simulation model is applied to calibrate strand parameters. Participants locations are not recorded, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. Once the experiment is complete, the data will be made available as an open-source anonymized dataset.\n\nThis paper outlines the experimental setup, software, subject-recruitment practices, ethical considerations, and dataset description. The paper also highlights current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The experiment was initially planned in the New Zealand environment, expected to be free of COVID and lockdowns after 2020. However, a COVID Delta strain lockdown shuffled the cards and the experiment is currently extended into 2022.\n\nAuthor summaryIn this paper, we describe the Safe Blues Android app experimental setup and a currently running experiment at the University of Auckland City Campus. This experiment is designed to evaluate how physical interactions over time and between individuals affect the spread of epidemics.\n\nThe Safe Blues app spreads multiple virtual safe virus strands via Bluetooth based on the subjects unobserved social and physical proximity. The app does not record the participants locations, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. When the experiment is finished, the data will be released as an open-source anonymized dataset.\n\nThe experimental setup, software, subject recruitment practices, ethical considerations, and dataset description are all described in this paper. In addition, we present our current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The information we provide here may be useful to other teams planning similar experiments in the future.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Azam Asanjarani", + "author_inst": "The University of Auckland" + }, + { + "author_name": "Aminath Shausan", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Keng Chew", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Thomas Graham", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Kirsty R. Short", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Yoni Nazarathy", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Shane G. Henderson", + "author_inst": "Cornell University" + }, + { + "author_name": "Hermanus M. Jansen", + "author_inst": "Delft University of Technology" + }, + { + "author_name": "Peter G. Taylor", + "author_inst": "The University of melbourne" + }, + { + "author_name": "Aapeli Vuorinen", + "author_inst": "Columbia University" + }, + { + "author_name": "Yuvraj Yadav", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Ilze Ziedins", + "author_inst": "The University of Auckland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.04.01.22273291", "rel_title": "Metabolic alkalosis and mortality in COVID-19", @@ -356927,69 +358932,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.30.486499", - "rel_title": "Brequinar and Dipyridamole in Combination Exhibits Synergistic Antiviral Activity Against SARS-CoV-2 in vitro: Rationale for a host-acting antiviral treatment strategy for COVID-19", - "rel_date": "2022-03-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.30.486499", - "rel_abs": "The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised the efficacy of currently available vaccines and monoclonal antibody (mAb)-based treatment options for COVID-19. The limited number of authorized small-molecule direct-acting antivirals present challenges with pill burden, the necessity for intravenous administration or potential drug interactions. There remains an unmet medical need for effective and convenient treatment options for SARS-CoV-2 infection. SARS-CoV-2 is an RNA virus that depends on host intracellular ribonucleotide pools for its replication. Dihydroorotate dehydrogenase (DHODH) is a ubiquitous host enzyme that is required for de novo pyrimidine synthesis. The inhibition of DHODH leads to a depletion of intracellular pyrimidines, thereby impacting viral replication in vitro. Brequinar (BRQ) is an orally available, selective, and potent low nanomolar inhibitor of human DHODH that has been shown to exhibit broad spectrum inhibition of RNA virus replication. However, host cell nucleotide salvage pathways can maintain intracellular pyrimidine levels and compensate for BRQ-mediated DHODH inhibition. In this report, we show that the combination of BRQ and the salvage pathway inhibitor dipyridamole (DPY) exhibits strong synergistic antiviral activity in vitro against SARS-CoV-2 by enhanced depletion of the cellular pyrimidine nucleotide pool. The combination of BRQ and DPY showed antiviral activity against the prototype SARS-CoV-2 as well as the Beta (B.1.351) and Delta (B.1.617.2) variants. These data support the continued evaluation of the combination of BRQ and DPY as a broad-spectrum, host-acting antiviral strategy to treat SARS-CoV-2 and potentially other RNA virus infections.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "James F Demarest", - "author_inst": "Clear Creek Bio" - }, - { - "author_name": "Maryline Kienle", - "author_inst": "Clear Creek Bio" - }, - { - "author_name": "RuthMabel Boytz", - "author_inst": "National Emerging Infectious Diseases Laboratories (NEIDL)" - }, - { - "author_name": "Mary Ayres", - "author_inst": "MD Anderson Cancer Center" - }, - { - "author_name": "Eunjung Kim", - "author_inst": "University of Louisville" - }, - { - "author_name": "Donghoon Chung", - "author_inst": "University of Louisville" - }, - { - "author_name": "Varsha Gandhi", - "author_inst": "MD Anderson Cancer Center" - }, - { - "author_name": "Robert A. Davey", - "author_inst": "Boston University" - }, - { - "author_name": "David B. Sykes", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Nadim Shohdy", - "author_inst": "Clear Creek Bio" - }, - { - "author_name": "John C Pottage Jr.", - "author_inst": "Clear Creek Bio" - }, - { - "author_name": "Vikram Sheel Kumar", - "author_inst": "Clear Creek Bio" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.30.486461", "rel_title": "Methylene blue, Mycophenolic acid, Posaconazole, and Niclosamide inhibit SARS-CoV-2Omicron variant BA.1 infection of human airway epithelial explant cultures", @@ -358093,6 +360035,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.31.22273226", + "rel_title": "Cross-talk between red blood cells and plasma influences blood flow and omics phenotypes in severe COVID-19", + "rel_date": "2022-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273226", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can affect multiple organs, among which is the circulatory system. Inflammation and mortality risk markers were previously detected in COVID-19 plasma and red blood cells (RBCs) metabolic and proteomic profiles. Additionally, biophysical properties, such as deformability, were found to be changed during the infection. Based on such data, we aim to better characterize RBC functions in COVID-19. We evaluate the flow properties of RBCs in severe COVID-19 patients admitted to the intensive care unit by using in vitro microfluidic techniques and automated methods, including artificial neural networks, for an unbiased RBC analysis. We find strong flow and RBC shape impairment in COVID-19 samples and demonstrate that such changes are reversible upon suspension of COVID-19 RBCs in healthy plasma. Vice versa, healthy RBCs immediately resemble COVID-19 RBCs when suspended in COVID-19 plasma. Proteomics and metabolomics analyses allow us to detect the effect of plasma exchanges on both plasma and RBCs and demonstrate a new role of RBCs in maintaining plasma equilibria at the expense of their flow properties. Our findings provide a framework for further investigations of clinical relevance for therapies against COVID-19 and possibly other infectious diseases.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Steffen M. Recktenwald", + "author_inst": "Saarland University" + }, + { + "author_name": "Greta Simionato", + "author_inst": "Saarland University" + }, + { + "author_name": "Marcelle G.M. Lopes", + "author_inst": "Cysmic GmbH" + }, + { + "author_name": "Fabia Gamboni", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Monika Dzieciatkowska", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Patrick Meybohm", + "author_inst": "University Hospital Wuerzburg" + }, + { + "author_name": "Kai Zacharowski", + "author_inst": "University Hospital Frankfurt" + }, + { + "author_name": "Andreas von Knethen", + "author_inst": "University Hospital Frankfurt" + }, + { + "author_name": "Christian Wagner", + "author_inst": "saarland University" + }, + { + "author_name": "Lars Kaestner", + "author_inst": "Saarland University" + }, + { + "author_name": "Angelo D'Alessandro", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Stephan Quint", + "author_inst": "Cysmic GmbH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.03.30.22273206", "rel_title": "Remdesivir for the treatment of hospitalised patients with COVID-19: final results from the DisCoVeRy randomised, controlled, open-label trial", @@ -358997,61 +361002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.29.22273044", - "rel_title": "Reduction in risk of death among patients admitted with COVID-19 between first and second epidemic waves in New York City", - "rel_date": "2022-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273044", - "rel_abs": "Many regions have experienced successive epidemic waves of COVID-19 since the emergence of SARS-CoV-2 with heterogeneous differences in mortality. Elucidating factors differentially associated with mortality between epidemic waves may inform clinical and public health strategies. We examined clinical and demographic data among patients admitted with COVID-19 during the first (March-June 2020) and second (December 2020-March 2021) epidemic waves at an academic medical center in New York City. Hospitalized patients (N=4631) had lower mortality during the second wave (14%) than the first (23%). Patients in the second wave had a lower 30-day mortality (Hazard Ratio (HR) 0.52, 95% CI 0.44, 0.61) than those in the first wave. The mortality decrease persisted after adjusting for confounders except for the volume of COVID-19 admissions (HR 0.88, 95% CI 0.70, 1.11), a measure of health system strain. Several demographic and clinical patient factors were associated with an increased risk of mortality independent of wave.\n\nArticle summaryUsing clinical and demographic data from COVID-19 hospitalizations at a tertiary New York City medical center, we show that a reduction in mortality during the second epidemic wave was associated with decreased strain on healthcare resources.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Anthony Bowen", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Jason E. Zucker", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Yanhan Shen", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Simian Huang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Qiheng Yan", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Medini K Annavajhala", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Anne-Catrin Uhlemann", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Louise Kuhn", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Magdalena E Sobieszczyk", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Delivette Castor", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.27.22273000", "rel_title": "Nationwide Effectiveness of First and Second SARS-CoV2 Booster Vaccines during the Delta and Omicron Pandemic Waves in Hungary (HUN-VE 2 Study)", @@ -360703,6 +362653,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2022.03.29.486173", + "rel_title": "A mosaic-type trimeric RBD-based COVID-19 vaccine candidate induces potent neutralization against Omicron and other SARS-CoV-2 variants", + "rel_date": "2022-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.29.486173", + "rel_abs": "Large-scale populations in the world have been vaccinated with COVID-19 vaccines, however, breakthrough infections of SARS-CoV-2 are still growing rapidly due to the emergence of immune-evasive variants, especially Omicron. It is urgent to develop effective broad-spectrum vaccines to better control the pandemic of these variants. Here, we present a mosaic-type trimeric form of spike receptor-binding domain (mos-tri-RBD) as a broad-spectrum vaccine candidate, which carries the key mutations from Omicron and other circulating variants. Tests in rats showed that the designed mos-tri-RBD, whether used alone or as a booster shot, elicited potent cross-neutralizing antibodies against not only Omicron but also other immune-evasive variants. Neutralizing antibody titers induced by mos-tri-RBD were substantially higher than those elicited by homo-tri-RBD (containing homologous RBDs from prototype strain) or the inactivated vaccine BBIBP-CorV. Our study indicates that mos-tri-RBD is highly immunogenic, which may serve as a broad-spectrum vaccine candidate in combating SARS-CoV-2 variants including Omicron.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Jing Zhang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Zi Bo Han", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Yu Liang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xue Feng Zhang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Yu Qin Jin", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Li Fang Du", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Shuai Shao", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Hui Wang", + "author_inst": "Beijing Institute of Biological Products Company Limited" + }, + { + "author_name": "Jun Wei Hou", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Ke Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Ze Hua Lei", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Zhao Ming Liu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Jin Zhang", + "author_inst": "Beijing Institute of Biological Products Company Limited" + }, + { + "author_name": "Ya Nan Hou", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Ning Liu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Fu Jie Shen", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Jin Juan Wu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xiang Zheng", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xin Yu Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xin Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Wei Jin Huang", + "author_inst": "National Institute for Food and Drug Control (NIFDC)" + }, + { + "author_name": "Gui Zhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Ji Guo Su", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Qi Ming Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.29.486253", "rel_title": "Discovery of a druggable copper-signaling pathway that drives cell plasticity and inflammation", @@ -361879,29 +363940,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.25.485826", - "rel_title": "Identification of consensus hairpin loop structure among the negative sense sub-genomic RNAs of SARS-CoV-2", - "rel_date": "2022-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.25.485826", - "rel_abs": "SARS-CoV-2 is the causative agent of worldwide pandemic disease COVID-19. SARS-CoV-2 bears positive sense RNA genome, that have organized and complex pattern of replication/transcription process including the generation of subgenomic RNAs. Transcription regulatory sequences (TRS) have important role in the pausing of replication/transcription and generation of subgenomic RNAs. In the present bioinformatics analysis a consensus secondary structure was identified among negative sense subgenomic RNAs at the adjacent of initiation codon. This study proposed that consensus structured domain could involve in mediating the long pausing of replication/transcription complex and responsible for subgenomic RNA production.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Naveen Prakash Bokolia", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - }, - { - "author_name": "Ravisekhar Gadepalli", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.03.26.485922", "rel_title": "Unique molecular signatures sustained in circulating monocytes and regulatory T cells in Convalescent COVID-19 patients", @@ -363273,6 +365311,145 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.23.485509", + "rel_title": "Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq", + "rel_date": "2022-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.23.485509", + "rel_abs": "Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Sara E Vazquez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sabrina A Mann", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Aaron Bodansky", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrew F Kung", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Zoe Quandt", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Elise M N Ferr\u00e9", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nils Landegren", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Daniel Eriksson", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Paul Bastard", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Shen-Ying Zhang", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Jamin Liu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Anthea Mitchell", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Caleigh Mandel-Brehm", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Brenda Miao", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Gavin Sowa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kelsey Zorn", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alice Y Chan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Chisato Shimizu", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Adriana Tremoulet", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Kara Lynch", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michael R Wilson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Olle K\u00e4mpe", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kerry Dobbs", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ottavia M Delmonte", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Luigi D Notarangelo", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Jane C Burns", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Michail S Lionakis", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Troy R Torgerson", + "author_inst": "Allen Institute for Immunology" + }, + { + "author_name": "Mark S Anderson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Joseph L DeRisi", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.24.485734", "rel_title": "SARS-CoV-2 harnesses host translational shutoff and autophagy to optimize virus yields: The role of the envelope (E) protein", @@ -363765,49 +365942,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.18.22272356", - "rel_title": "Optimized infection control practices augment the robust protective effect of vaccination for ESRD patients during a hemodialysis facility SARS-CoV-2 outbreak", - "rel_date": "2022-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.18.22272356", - "rel_abs": "BackgroundWhile dialysis patients are at greater risk of serious SARS-CoV-2 complications, stringent infection prevention measures can help mitigate the risk of infection and transmission within dialysis facilities. We describe an outbreak of 14 cases diagnosed in a 13-day period in the second quarter of 2021 in a hospital-based ESRD facility, and our coordinated use of epidemiology, viral genome sequencing, and infection control practices to quickly end the cycle of transmission.\n\nMethodsSymptomatic patients and staff members were diagnosed via RT-PCR tests. Facility-wide screening was conducted using rapid SARS-CoV-2 antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic PCR specimens.\n\nResultsOf the 106 patients who received dialysis in the facility, 10 were diagnosed with SARS-CoV-2 infection, as was one patient support person. Of three positive staff members, two were unvaccinated and had provided care for six and four of the affected patients, respectively. Sequencing demonstrated that all the cases in the cluster shared an identical B.1.1.7./Alpha substrain. Attack rates were greatest among unvaccinated patients and staff. Vaccine effectiveness was 88% among patients.\n\nConclusionsPrompt recognition of an infection cluster and rapid intervention efforts successfully ended the outbreak. Alongside consistent adherence to core infection prevention measures, vaccination was highly effective in reducing disease incidence and morbidity in this vulnerable population.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Megan E Meller", - "author_inst": "Gundersen Health System, La Crosse, WI" - }, - { - "author_name": "Bridget L Pfaff", - "author_inst": "Gundersen Health System, La Crosse, WI" - }, - { - "author_name": "Andrew J Borgert", - "author_inst": "Gundersen Medical Foundation, La Crosse, WI" - }, - { - "author_name": "Craig S Richmond", - "author_inst": "Gundersen Medical Foundation, La Crosse, WI" - }, - { - "author_name": "Deena M Athas", - "author_inst": "Gundersen Health System, La Crosse, WI" - }, - { - "author_name": "Paraic A Kenny", - "author_inst": "Gundersen Medical Foundation, La Crosse, WI" - }, - { - "author_name": "Arick P Sabin", - "author_inst": "Gundersen Health System, La Crosse, WI" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.25.22272949", "rel_title": "Risk factors and preventive interventions for post Covid-19 condition: systematic reviews", @@ -364655,6 +366789,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.24.22272835", + "rel_title": "Relative Effectiveness of Four Doses Compared to Three Dose of the BNT162b2 Vaccine in Israel", + "rel_date": "2022-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272835", + "rel_abs": "ObjectivesThe rapid spread of the Omicron variant (B.1.1.529) alongside evidence of a relatively rapid waning of the third dose prompted Israel to administer a fourth dose of the BNT162b2 vaccine on January 2022. Thus far, sufficient real-world evidence demonstrating the effectiveness of a fourth dose against infection and severe COVID-19 are lacking. This study examined the short-term effectiveness of a fourth dose compared to three doses over the span of 10 weeks.\n\nDesignA retrospective test-negative case-control study, performing both a matched analysis and an unmatched multiple-tests analysis.\n\nSettingNationally centralized database of Maccabi Healthcare Services (MHS), an Israeli national health fund that covers 2.5 million people.\n\nParticipantsThe study population included 97,499 MHS members aged 60 or older who were eligible to receive a fourth vaccine dose and performed at least one PCR test during the study period. Of them, 27,876 received the fourth dose and 69,623 received only three doses.\n\nMain outcomes and measuresAnalyses focused on the period from January 10, 2022 (7 days after the fourth dose was first administered to eligible individuals) to March 13, 2022, an Omicron-dominant period in Israel. We evaluated two SARS-CoV-2-related outcomes: (1) breakthrough infection, defined as a positive PCR test performed 7 or more days after inoculation with the BNT162b2 vaccine; and (2) breakthrough infection resulting in a severe disease, defined as COVID-19-related hospitalization or COVID-19 associated mortality.\n\nResultsA fourth dose provided considerable additional protection against both SARS-CoV-2 infection and severe disease relative to three doses of the vaccine. However, vaccine effectiveness against infection varied over time, peaking during the third week with a VE of 64% (95% CI: 62.0%-65.9%) and declining to 29.2% (95% CI: 17.7%-39.1%) by the end of the 10-week follow-up period. Unlike VE against infection, the relative effectiveness of a fourth dose against severe COVID-19 was maintained at high level (>73%) throughout the 9-week follow-up period. Importantly, severe disease was a relatively rare event, occurring in <1% of both fourth dose and third dose only recipients.\n\nConclusionsA fourth dose of the BNT162b2 vaccine provided considerable additional protection against both SARS-CoV-2 infection and severe disease relative to three doses of the vaccine. However, effectiveness of the fourth dose against infection wanes sooner than that of the third dose.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sivan Gazit", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Yaki Saciuk", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Galit Perez", + "author_inst": "Maccabi health care servises" + }, + { + "author_name": "Asaf Peretz", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Virginia E. Pitzer", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Tal Patalon", + "author_inst": "Maccabi Healthcare Services" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.24.22272892", "rel_title": "The modified COVID-19 Yorkshire Rehabilitation Scale (C19-YRSm) patient-reported outcome measure for Long Covid or Post-COVID syndrome", @@ -365327,33 +367500,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.23.485487", - "rel_title": "In silico analysis predicts a limited impact of SARS-CoV-2 variants on CD8 T cell recognition", - "rel_date": "2022-03-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.23.485487", - "rel_abs": "Since the start of the COVID-19 pandemic, mutations have led to the emergence of new SARS-CoV-2 variants, and some of these have become prominent or dominant variants of concern. This natural course of development can have an impact on how protective the previously naturally or vaccine induced immunity is. Therefore, it is crucial to understand whether and how variant specific mutations influence host immunity. To address this, we have investigated how mutations in the recent SARS-CoV-2 variants of interest and concern influence epitope sequence similarity, predicted binding affinity to HLA, and immunogenicity of previously reported SARS-CoV-2 CD8 T cell epitopes. Our data suggests that the vast majority of SARS-CoV-2 CD8 T cell recognized epitopes are not altered by variant specific mutations. Interestingly, for the CD8 T cell epitopes that are altered due to variant specific mutations, our analyses show there is a high degree of sequence similarity between mutated and reference SARS-CoV-2 CD8 T cell epitopes. However, mutated epitopes, primarily derived from the spike protein, in SARS-CoV-2 variants Delta, AY.4.2 and Mu display reduced predicted binding affinity to their restriction element. These findings indicate that the recent SARS-CoV-2 variants of interest and concern have limited ability to escape memory CD8 T cell responses raised by vaccination or prior infection with SARS-CoV-2 early in the pandemic. The overall low impact of the mutations on CD8 T cell cross-recognition is in accordance with the notion that mutations in SARS-CoV-2 are primarily the result of receptor binding affinity and antibody selection pressures exerted on the spike protein, unrelated to T cell immunity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Olga I. Isaeva", - "author_inst": "Netherlands Cancer Institute" - }, - { - "author_name": "Steven L. C. Ketelaars", - "author_inst": "Netherlands Cancer Institute" - }, - { - "author_name": "Pia Kvistborg", - "author_inst": "Netherlands Cancer Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.22.485323", "rel_title": "Intranasal Nanoemulsion Adjuvanted S-2P Vaccine Demonstrates Protection in Hamsters and Induces Systemic, Cell-Mediated and Mucosal Immunity in Mice", @@ -366653,6 +368799,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.23.22272804", + "rel_title": "Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records", + "rel_date": "2022-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272804", + "rel_abs": "BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies.\n\nMethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death.\n\nFindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1.\n\nInterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Elsie MF Horne", + "author_inst": "University of Bristol" + }, + { + "author_name": "William J Hulme", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Ruth H Keogh", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Tom M Palmer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Elizabeth J Williamson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Edward PK Parker", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Amelia Green", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Venexia Walker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex J Walker", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Helen Curtis", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Louis Fisher", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Richard Croker", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Lisa Hopcroft", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Robin Y Park", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jon Massey", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jessica Morely", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Sebastian Bacon", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "George Hickman", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Simon Davy", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Tom Ward", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Iain Dillingham", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Miguel A Hernan", + "author_inst": "Harvard University" + }, + { + "author_name": "Jonathan AC Sterne", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.21.22272358", "rel_title": "Undiagnosed COVID-19 in households with a child with mitochondrial disease", @@ -367381,105 +369658,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.21.22272698", - "rel_title": "Assessment of cardiovascular & pulmonary pathobiology in vivo during acute COVID-19", - "rel_date": "2022-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272698", - "rel_abs": "ImportanceAcute COVID-19-related myocardial, pulmonary and vascular pathology, and how these relate to each other, remains unclear. No studies have used complementary imaging techniques, including molecular imaging, to elucidate this.\n\nObjectiveWe used multimodality imaging and biochemical sampling in vivo to identify the pathobiology of acute COVID-19.\n\nDesign, Setting and ParticipantsConsecutive patients presenting with acute COVID-19 were recruited during hospital admission in a prospective cross-sectional study. Imaging involved computed-tomography coronary-angiography (CTCA - identified coronary disease), cardiac 2-deoxy-2-[fluorine-18]fluoro-D-glucose positron-emission tomography/computed-tomography (18F-FDG-PET/CT - identified vascular, cardiac and pulmonary inflammatory cell infiltration) and cardiac magnetic-resonance (CMR - identified myocardial disease), alongside biomarker sampling.\n\nResultsOf 33 patients (median age 51 years, 94% male), 24 (73%) had respiratory symptoms, with the remainder having non-specific viral symptoms. Nine patients (35%, n=9/25) had CMR defined myocarditis. 53% (n=5/8) of these patients had myocardial inflammatory cell infiltration. Two patients (5%) had elevated troponin levels. Cardiac troponin concentrations were not significantly higher in patients with myocarditis (8.4ng/L [IQR 4.0-55.3] vs 3.5ng/L [2.5-5.5], p=0.07) or myocardial cell infiltration (4.4ng/L [3.4-8.3] vs 3.5ng/L [2.8-7.2], p=0.89). No patients had obstructive coronary artery disease or vasculitis. Pulmonary inflammation and consolidation (percentage of total lung volume) was 17% (IQR 5-31%) and 11% (7-18%) respectively. Neither were associated with presence of myocarditis.\n\nConclusions and relevanceMyocarditis was present in a third patients with acute COVID-19, and the majority had inflammatory cell infiltration. Pneumonitis was ubiquitous, but this inflammation was not associated with myocarditis. The mechanism of cardiac pathology is non-ischaemic, and not due to a vasculitic process.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the pathobiology of the cardiac, pulmonary and vascular systems during acute COVID-19 infection ?\n\nFindingsOver a third of patients with acute COVID-19 had myocarditis by cardiac MRI criteria. Myocardial inflammatory cell infiltration was present in about two thirds of patients with myocarditis. No associations were observed between the degree of pulmonary involvement and presence of myocarditis. There was no evidence of obstructive coronary artery disease or evidence of large vessel vasculitis.\n\nMeaningMyocarditis is common in acute COVID-19 infection, and may be present in the absence of significant pulmonary involvement. The cause of myocarditis is inflammatory cell infiltration in the majority of cases, but in about a third of cases this is not present. The mechanism of cardiac pathology in acute COVID-19 is non-ischaemic, and vascular thrombosis in acute COVID-19 is not due to significant coronary artery disease or a vasculitic process.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Shirjel R Alam Dr", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sudhir Vinayak Prof", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Adeel Shah Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Gemina Doolub Dr", - "author_inst": "University of Bristol" - }, - { - "author_name": "Redemptar Kimeu Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Kevin Horn Dr", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Stephen R Bowen Dr", - "author_inst": "University of Washington" - }, - { - "author_name": "Mohamed Jeilan Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Kuan Ken Lee Dr", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Sylvia Gachoka Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Felix Riunga Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Rodney D Adam Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Hubert Vesselle Dr", - "author_inst": "University of Washington" - }, - { - "author_name": "Nikhil V Joshi Dr", - "author_inst": "University of Bristol" - }, - { - "author_name": "Mariah Obino Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Khalid Makhdomi Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Kevin Onyinkwa Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Edward Nganga Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Samuel Gitau Dr", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Michael Chung Prof", - "author_inst": "Emory University" - }, - { - "author_name": "Anoop SV Shah Dr", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.03.22.22272748", "rel_title": "Venous Thromboembolism in Ambulatory Covid-19 patients: Clinical and Genetic Determinants", @@ -368355,6 +370533,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.21.485157", + "rel_title": "Stability and expression of SARS-CoV-2 spike-protein mutations", + "rel_date": "2022-03-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.21.485157", + "rel_abs": "Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen for ACE2 binding. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kristoffer T Baek", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Rukmankesh Mehra", + "author_inst": "Indian Institute of Technology Bhilai" + }, + { + "author_name": "Kasper Planeta Kepp", + "author_inst": "Technical University of Denmark" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.03.20.485044", "rel_title": "Robust and durable prophylactic protection conferred by RNA interference in preclinical models of SARS-CoV-2", @@ -369355,73 +371560,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.18.484436", - "rel_title": "High neutralizing antibody levels against SARS-CoV-2 Omicron after UB-612 booster vaccination", - "rel_date": "2022-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.18.484436", - "rel_abs": "The highly transmissible Omicron variant has caused high rates of breakthrough infections among vaccinated and convalescent individuals. Here, we demonstrate that a booster dose of UB-612 vaccine candidate delivered 7-9 months after primary vaccination increases neutralizing antibody levels by 131-, 61- and 49-fold against ancestral SARS-CoV-2, Omicron BA.1 and BA.2 variants, respectively. Based on the RBD protein binding antibody responses, we estimated a [~]95% efficacy against symptomatic COVID-19 caused by the ancestral strain after a UB-612 booster. Our results support UB-612 vaccine as a potent booster against current and emerging SARS-CoV-2 variants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Farshad Guirakhoo", - "author_inst": "Vaxxinity Inc" - }, - { - "author_name": "Shixia Wang", - "author_inst": "Vaxxinity Inc" - }, - { - "author_name": "Chang Yi Wang", - "author_inst": "United Biomedical Inc Asia" - }, - { - "author_name": "Hui-Kai Kuo", - "author_inst": "United Biomedical Inc Asia" - }, - { - "author_name": "Wen-Jiun Peng", - "author_inst": "United Biomedical Inc Asia" - }, - { - "author_name": "Hope Liu", - "author_inst": "United Biomedical Inc Asia" - }, - { - "author_name": "Lixia Wang", - "author_inst": "Vaxxinity Inc" - }, - { - "author_name": "Marina Johnson", - "author_inst": "Great Ormond Street Institute of Child Health, University College London" - }, - { - "author_name": "Adam Hunt", - "author_inst": "Great Ormond Street Institute of Child Health, University College London" - }, - { - "author_name": "Mei Mei Hu", - "author_inst": "Vaxxinity Inc" - }, - { - "author_name": "Thomas P. Monath", - "author_inst": "Vaxxinity Inc" - }, - { - "author_name": "Alexander Rumyantsev", - "author_inst": "Vaxxinity Inc" - }, - { - "author_name": "David Goldblatt", - "author_inst": "Great Ormond Street Institute of Child Health, University College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.17.22272008", "rel_title": "A SARS-CoV-2 negative antigen rapid diagnostic in RT-qPCR positive samples correlates with a low likelihood of infectious viruses in the nasopharynx.", @@ -370589,6 +372727,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.16.22272527", + "rel_title": "Severe Acute Respiratory Coronavirus-2 Antibody and T cell response after a third vaccine dose in hemodialysis patients compared with healthy controls", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272527", + "rel_abs": "1.Hemodialysis patients (HD patients) have a high health risk from Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) infection. In this study, we assess the impact of a third vaccine dose (3D) on antibody levels and T cell response in HD patients and compare the results to those of a healthy control group.\n\nWe conducted a prospective cohort study consisting of 60 HD patients and 65 healthy controls. All of them received two doses of the Comirnaty mRNA vaccine and a third mRNA vaccine dose (Spikevax or Comirnaty). The SARS-CoV-2 S antibody response in all participants was measured 6 months after the second vaccine dose and 6 to 8 weeks after administration of the 3D. We also assessed INF-{gamma} secretion 6-8 weeks after the 3D in 24 healthy controls, 17 HD patients with a normal and 20 HD patients with a low or no antibody response after the second dose. The groups were compared using univariate quantile regressions and multiple analyses. The adverse effects of vaccines were assessed via a questionnaire.\n\nAfter the 3D, the SARS-CoV-2-specific antibody and INF-{gamma} titers of most HD patients were comparable to those of healthy controls. A subgroup of HD patients who had shown a diminished antibody response after the first two vaccine doses developed a significantly lower antibody and INF-{gamma} response compared to responder HD patients and controls, even after the 3D. A new strategy is needed to protect this patient group from severe COVID-19 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Benedikt Simon", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Harald Rubey", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Martin Gromann", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Astrid Knop-Voelkerer", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Boris Hemedi", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Sonja Zehetmayer", + "author_inst": "MedUni Wien" + }, + { + "author_name": "Bernhard Kirsch", + "author_inst": "LK Mistelbach" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.03.17.22272589", "rel_title": "A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance", @@ -371405,73 +373586,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.03.15.22272441", - "rel_title": "Selection of appropriate reference genes for normalization of qRT-PCR based gene expression analysis in SARS-CoV-2, and Covid-associated Mucormycosis infection", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272441", - "rel_abs": "Selection of reference genes in quantitative PCR is critical to determine accurate and reliable mRNA expression. Despite this knowledge, not a single study has investigated the expression stability of housekeeping genes to determine their suitability to act as reference gene in SARS-CoV-2 or Covid19 associated mucormycosis (CAM) infections. Herein, we address these gaps by investigating the expression stability of nine most commonly used housekeeping genes including TBP, CypA, B2M, 18S, PGC-1, GUSB, HPRT-1, {beta}-ACTIN and GAPDH in the patients of varying severity (asymptomatic, mild, moderate and severe). We observed significant differences in the expression of candidate genes across the disease spectrum. Next, using various statistical algorithms (delta Ct, Normfinder, Bestkeeper, RefFinder and GeNorm), we observed that CypA demonstrated the most consistent expression across the patients of varying severity and emerged as the most suitable gene in Covid19, and CAM infections. Incidentally, the most commonly used reference gene GAPDH showed maximum variations and found to be the least suitable. Lastly, comparative evaluation of expression of NRF2 is performed following normalization with GAPDH and CypA to highlight the relevance of an appropriate reference gene. Our results reinforce the idea of a selection of housekeeping genes only after validation especially during infections.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sunil Kumar", - "author_inst": "Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India" - }, - { - "author_name": "Ayaan Ahmad", - "author_inst": "Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India" - }, - { - "author_name": "Namrata Kushwaha", - "author_inst": "Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India" - }, - { - "author_name": "Sheetal Negi", - "author_inst": "Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India" - }, - { - "author_name": "Kamini Gautam", - "author_inst": "Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India" - }, - { - "author_name": "Anup Singh", - "author_inst": "Department of Otorhinolaryngology-Head & Neck Surgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Pawan Tiwari", - "author_inst": "Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Rakesh Garg", - "author_inst": "Department of Onco-Anesthesiology, Intensive care, pain and Palliative Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Richa Agarwal", - "author_inst": "Department of Onco-Anesthesiology, Intensive care, pain and Palliative Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Anant Mohan", - "author_inst": "Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Anjan Trikha", - "author_inst": "Department of Onco-Anesthesiology, Intensive care, pain and Palliative Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Alok Thakar", - "author_inst": "Department of Otorhinolaryngology-Head & Neck Surgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India" - }, - { - "author_name": "Vikram Saini", - "author_inst": "Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.17.22272389", "rel_title": "Suppression of de novo antibody responses against SARS-CoV2 and the Omicron variant after mRNA vaccination and booster in patients with B cell malignancies undergoing active treatment, but maintenance of pre-existing antibody levels against endemic viruses.", @@ -372511,6 +374625,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.03.14.22272342", + "rel_title": "Tongue Coating in COVID-19 Patients: A Case-Control Study", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272342", + "rel_abs": "It has been suggested that COVID-19 patients have distinct tongue features, which may help to monitor the development of their condition. To determine if there was any specific tongue coating feature in COVID-19, this study investigated the difference in tongue coating between COVID-19 subjects and subjects with other acute inflammatory diseases characterized by fever. Tongue images taken with smartphones from three age-matched groups, namely, COVID group (n=92), non-COVID febrile group (n=92), and normal control group (n=92), were analyzed by two blinded raters according to a tongue coating scoring scheme, which assessed the levels of thick fur, slimy or greasy fur, discolored fur and composite index of tongue coating. Compared with control, significant increases in all coating indexes were found in the COVID group (P<0.001), as well as in the non-COVID febrile group (P<0.001). However, no difference was observed between COVID and non-COVID febrile groups for all coating indexes measured. In COVID-19 subjects, their scores of coating indexes had weak but significant correlations with certain inflammatory biomarkers, including WBC and neutrophil - lymphocyte ratio. It is concluded that COVID-19 subjects have pathological tongue coating patterns that are associated with inflammatory responses, and these coating patterns can help to indicate the direction of disease development.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Zhi Chun Wang", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Xi Hong Cai", + "author_inst": "The Third Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Jeremy Chan", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Yi Yi Chan", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Xiaotong Chen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ching Wan Cheng", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Donghui Huang", + "author_inst": "Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Luqi Huang", + "author_inst": "China Academy of Chinese Medical Sciences" + }, + { + "author_name": "Bei-ni Lao", + "author_inst": "Second Clinical Medical College of Guangzhou University of Chinese Medicine: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Xu-sheng Liu", + "author_inst": "Guangdong Hospital of Traditional Chinese Medicine: Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Aiping Lyu", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Wenliang Lv", + "author_inst": "China Academy of Chinese Medical Sciences" + }, + { + "author_name": "Huixian Wang", + "author_inst": "Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Helen Zhang", + "author_inst": "Hong Kong Northern District Hospital" + }, + { + "author_name": "Xuebin Zhang", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Shi Ping Zhang", + "author_inst": "Hong Kong Baptist University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.17.22272535", "rel_title": "Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data", @@ -373243,81 +375436,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.03.15.484484", - "rel_title": "Allosteric binders of ACE2 are promising anti-SARS-CoV-2 agents", - "rel_date": "2022-03-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.15.484484", - "rel_abs": "The COVID-19 pandemic has had enormous health, economic, and social consequences. Vaccines have been successful in reducing rates of infection and hospitalization, but there is still a need for an acute treatment for the disease. We investigate whether compounds that bind the human ACE2 protein can interrupt SARS-CoV-2 replication without damaging ACE2s natural enzymatic function. Initial compounds were screened for binding to ACE2 but little interruption of ACE2 enzymatic activity. This set of compounds was extended by application of quantitative structure-activity analysis, which resulted in 512 virtual hits for further confirmatory screening. A subsequent SARS-CoV-2 replication assay revealed that five of these compounds inhibit SARS-CoV-2 replication in human cells. Further effort is required to completely determine the antiviral mechanism of these compounds, but they serve as a strong starting point for both development of acute treatments for COVID-19 and research into the mechanism of infection.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/484484v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (47K):\norg.highwire.dtl.DTLVardef@173d7c9org.highwire.dtl.DTLVardef@5c0021org.highwire.dtl.DTLVardef@c9caaorg.highwire.dtl.DTLVardef@18d23_HPS_FORMAT_FIGEXP M_FIG TOC Graphic: Overall study design.\n\nC_FIG", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Joshua Earl Hochuli", - "author_inst": "University of North Carolina, Chapel Hill" - }, - { - "author_name": "Sankalp Jain", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - }, - { - "author_name": "Cleber Melo-Filho", - "author_inst": "University of North Carolina, Chapel Hill" - }, - { - "author_name": "Zoe L. Sessions", - "author_inst": "University of North Carolina, Chapel Hill" - }, - { - "author_name": "Tesia Bobrowski", - "author_inst": "University of North Carolina, Chapel Hill" - }, - { - "author_name": "Jun Choe", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - }, - { - "author_name": "Johnny Zheng", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - }, - { - "author_name": "Rich Eastman", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - }, - { - "author_name": "Daniel C. Talley", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - }, - { - "author_name": "Ganesha Rai", - "author_inst": "NIH" - }, - { - "author_name": "Anton Simeonov", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - }, - { - "author_name": "Alexander Tropsha", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Eugene Muratov", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Bolormaa Baljinnyam", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Alexey V. Zakharov", - "author_inst": "National Center for Advancing Translational Sciences, NIH" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.03.15.22272432", "rel_title": "Comorbidities Diminish the Likelihood of Seropositivity After SARS-CoV-2 Vaccination", @@ -374197,6 +376315,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.14.22272368", + "rel_title": "Area-level social and structural inequalities determine mortality related to COVID-19 diagnosis in Ontario, Canada: a population-based explanatory modeling study of 11.8 million people", + "rel_date": "2022-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272368", + "rel_abs": "ImportanceSocial determinants of health (SDOH) play an important role in COVID-19 outcomes. More research is needed to quantify this relationship and understand the underlying mechanisms.\n\nObjectivesTo examine differential patterns in COVID-19-related mortality by area-level SDOH accounting for confounders; and to compare these patterns to those for non-COVID-19 mortality, and COVID-19 case fatality (COVID-19-related death among those diagnosed).\n\nDesign, setting, and participantsPopulation-based retrospective cohort study including all community living individuals aged 20 years or older residing in Ontario, Canada, as of March 1, 2020 who were followed through to March 2, 2021.\n\nExposureSDOH variables derived from the 2016 Canada Census at the dissemination area-level including: median household income; educational attainment; proportion of essential workers, racialized groups, recent immigrants, apartment buildings, and high-density housing; and average household size.\n\nMain outcomes and measuresCOVID-19-related death was defined as death within 30 days following, or 7 days prior to a positive SARS-CoV-2 test. Cause-specific hazard models were employed to examine the associations between SDOH and COVID-19-related mortality, treating non-COVID-19 mortality as a competing risk.\n\nResultsOf 11,810,255 individuals included, 3,880 (0.03%) died related to COVID-19 and 88,107 (0.75%) died without a positive test. After accounting for demographics, baseline health, and other SDOH, the following SDOH were associated with increased hazard of COVID-19-related death (hazard ratios [95% confidence intervals]) comparing the most to least vulnerable group): lower income (1.30[1.09-1.54]), lower educational attainment (1.27[1.10-1.47]), higher proportion essential workers (1.28[1.10-1.50]), higher proportion racialized groups (1.42[1.16-1.73]), higher proportion apartment buildings (1.25[1.11-1.41]), and larger vs. medium household size (1.30[1.13-1.48]). In comparison, areas with higher proportion racialized groups were associated with a lower hazard of non-COVID-19 mortality (0.88[0.85-0.92]). With the exception of income, SDOH were not independently associated with COVID-19 case fatality.\n\nConclusions and relevanceArea-level social and structural inequalities determine COVID-19-related mortality after accounting for individual demographic and clinical factors. COVID-19 has reversed the pattern of lower non-COVID-19 mortality by racialized groups. Pandemic responses should include prioritized and community-tailored intervention strategies to address SDOH that mechanistically underpin disproportionate acquisition and transmission risks and shape barriers to the reach of, and access to prevention interventions.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSAre area-level social determinants of health factors independently associated with coronavirus disease 2019 (COVID-19)-related mortality after accounting for demographics and clinical factors?\n\nFindingsIn this population-based cohort study including 11.8 million adults residing in Ontario, Canada and 3,880 COVID-19-related death occurred between Mar 1, 2020 and Mar 2, 2021, we found that areas characterized by lower SES (including lower income, lower educational attainment, and higher proportion essential workers), greater ethnic diversity, more apartment buildings, and larger vs. medium household size were associated with increased hazard of COVID-19-related mortality compared to their counterparts, even after accounting for individual-level demographics, baseline health, and other area-level SDOH.\n\nMeaningPandemic responses should include prioritized and community-tailored intervention strategies to address SDOH that mechanistically underpin inequalities in acquisition and transmission risks, and in the reach of, and access to prevention interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Linwei Wang", + "author_inst": "Unity Health Toronto" + }, + { + "author_name": "Andrew Calzavara", + "author_inst": "ICES" + }, + { + "author_name": "Stefan Baral", + "author_inst": "JHSPH" + }, + { + "author_name": "Janet Smylie", + "author_inst": "University of Toronto" + }, + { + "author_name": "Adrienne K Chan", + "author_inst": "University of Toronto" + }, + { + "author_name": "Beate Sander", + "author_inst": "University Health Network" + }, + { + "author_name": "Peter C Austin", + "author_inst": "ICES" + }, + { + "author_name": "Jeff C Kwong", + "author_inst": "ICES" + }, + { + "author_name": "Sharmistha Mishra", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.14.22272359", "rel_title": "Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology", @@ -374957,73 +377126,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.13.484129", - "rel_title": "Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events", - "rel_date": "2022-03-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.13.484129", - "rel_abs": "The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. Although recombination events among SARS-CoV-1 and MERS-CoV were well-documented, it has been difficult to detect the recombination signatures in SARS-CoV-2 variants due to their high degree of sequence similarity. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, eighteen core mutations of BA.1 variants (frequency >99%) were identified (eight in NTD, five near the S1/S2 cleavage site, and five in S2). BA.2 variants share three additional amino acid deletions with the Alpha variants. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations (del69-70, del144) in BA.1 than BA.2, and therefore BA.1 may be phylogenetically closer to the Alpha variant. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1 subvariant. Most notably, multiple additional amino acid mutations in the Delta spike protein were also identified in the recently emerged Omicron isolates, which implied possible recombination events occurred between the Omicron and Delta variants during the on-going pandemic. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Junxian Ou", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - }, - { - "author_name": "Wendong Lan", - "author_inst": "BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University" - }, - { - "author_name": "Xiaowei Wu", - "author_inst": "BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University" - }, - { - "author_name": "Tie Zhao", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - }, - { - "author_name": "Biyan Duan", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - }, - { - "author_name": "Peipei Yang", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - }, - { - "author_name": "Yi Ren", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - }, - { - "author_name": "Lulu Quan", - "author_inst": "BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University" - }, - { - "author_name": "Wei Zhao", - "author_inst": "BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University" - }, - { - "author_name": "Donald Seto", - "author_inst": "Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University" - }, - { - "author_name": "James Chodosh", - "author_inst": "Department of Ophthalmology, Howe Laboratory Massachusetts Eye and Ear, Harvard Medical School" - }, - { - "author_name": "Jianguo Wu", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - }, - { - "author_name": "Qiwei Zhang", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.13.484037", "rel_title": "A broad and potent neutralization epitope in SARS-related coronaviruses", @@ -376019,6 +378121,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.10.22272123", + "rel_title": "Polymorphism in IFNAR contributes to glucocorticoid response and outcome in ARDS and COVID-19", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272123", + "rel_abs": "The use of glucocorticoids has given contradictory results for treating acute respiratory distress syndrome (ARDS). Here we report a novel disease association of a SNP rs9984273, which is situated in the interferon alpha/beta receptor (IFNAR2) gene in an area corresponding to a binding motif of the glucocorticoid receptor (GR). The minor allele of SNP rs9984273 associates with higher IFNAR expression, lower IFN-gamma and IL-6 levels and less severe form of coronavirus diseases (COVID-19) according to the COVID-19 Host Genetics Initiative database, and better outcome in interferon (IFN) beta treated patients with ARDS. Thus, the distribution of this SNP within clinical study arms may explain the contradictory results of multiple ARDS studies and outcomes in COVID-19 concerning type I IFN signalling and glucocorticoids.\n\nOne-Sentence SummarySingle nucleotide polymorphism in interferon receptor contributes to corticosteroid response and outcome in ARDS and COVID-19", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Juho Jalkanen", + "author_inst": "Faron Pharmaceuticals" + }, + { + "author_name": "Sofia Khan", + "author_inst": "University of Turku" + }, + { + "author_name": "Kati Elima", + "author_inst": "University of Turku" + }, + { + "author_name": "Teppo Huttunen", + "author_inst": "Estimates" + }, + { + "author_name": "Ning Wang", + "author_inst": "University of Turku" + }, + { + "author_name": "Maija Hollmen", + "author_inst": "University of Turku" + }, + { + "author_name": "Laura Elo", + "author_inst": "University of Turku" + }, + { + "author_name": "Sirpa Jalkanen", + "author_inst": "University of Turku" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.03.10.22272237", "rel_title": "Long COVID in Children and Adolescents: A Systematic Review and Meta-analyses.", @@ -376719,61 +378868,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.12.22271872", - "rel_title": "The impact of COVID-19 non-pharmaceutical interventions on future respiratory syncytial virus transmission in South Africa", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.12.22271872", - "rel_abs": "In response to the COVID-19 pandemic, the South African government employed various nonpharmaceutical interventions (NPIs) in order to reduce the spread of SARS-CoV-2. In addition to mitigating transmission of SARS-CoV-2, these public health measures have also functioned in slowing the spread of other endemic respiratory pathogens. Surveillance data from South Africa indicates low circulation of respiratory syncytial virus (RSV) throughout the 2020-2021 Southern Hemisphere winter seasons. Here we fit age-structured epidemiological models to national surveillance data to predict the 2022 RSV outbreak following two suppressed seasons. We project a 32% increase in the peak number of monthly hospitalizations among infants [≤] 2 years, with older infants (6-23 month olds) experiencing a larger portion of severe disease burden than typical. Our results suggest that hospital system readiness should be prepared for an intense RSV season in early 2022.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Samantha Bents", - "author_inst": "Princeton University" - }, - { - "author_name": "Cecile Viboud", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Bryan Grenfell", - "author_inst": "Princeton University" - }, - { - "author_name": "Alexandra Hogan", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Stefano Tempia", - "author_inst": "National Institute For Communicable Diseases of South Africa" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "National Institute For Communicable Diseases of South Africa" - }, - { - "author_name": "Jocelyn Moyes", - "author_inst": "National Institute For Communicable Diseases of South Africa" - }, - { - "author_name": "Sibongile Walaza", - "author_inst": "National Institute For Communicable Diseases of South Africa" - }, - { - "author_name": "Cheryl Cohen", - "author_inst": "National Institute For Communicable Diseases of South Africa" - }, - { - "author_name": "Rachel Baker", - "author_inst": "Princeton University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.11.22272282", "rel_title": "Development and Implementation of a Simple and Rapid Extraction-Free Saliva SARS-CoV-2 RT-LAMP Workflow for Workplace Surveillance", @@ -377877,6 +379971,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.03.09.22272113", + "rel_title": "Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination", + "rel_date": "2022-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272113", + "rel_abs": "Between November 2021 and February 2022, SARS-CoV-2 Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5-end of the viral genome was from the Delta genome, and the 3-end from Omicron including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared to the circulating Omicron lineages.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Alexandre Bolze", + "author_inst": "Helix" + }, + { + "author_name": "Tracy Basler", + "author_inst": "Helix" + }, + { + "author_name": "Simon White", + "author_inst": "Helix" + }, + { + "author_name": "Andrew Dei Rossi", + "author_inst": "Helix" + }, + { + "author_name": "Dana Wyman", + "author_inst": "Helix" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Kathleen Hayashibara", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Eric Kil", + "author_inst": "Helix" + }, + { + "author_name": "Hang Dai", + "author_inst": "Helix" + }, + { + "author_name": "Tyler Cassens", + "author_inst": "Helix" + }, + { + "author_name": "Kevin Tsan", + "author_inst": "Helix" + }, + { + "author_name": "Jason Nguyen", + "author_inst": "Helix" + }, + { + "author_name": "Jimmy Ramirez", + "author_inst": "Helix" + }, + { + "author_name": "Scotty Carter", + "author_inst": "Helix" + }, + { + "author_name": "Elizabeth T. Cirulli", + "author_inst": "Helix" + }, + { + "author_name": "Kelly Schiabor Barrett", + "author_inst": "Helix" + }, + { + "author_name": "Nicole L Washington", + "author_inst": "Helix" + }, + { + "author_name": "Pedro Belda-Ferre", + "author_inst": "Helix" + }, + { + "author_name": "Sharoni Jacobs", + "author_inst": "Helix" + }, + { + "author_name": "Efren Sandoval", + "author_inst": "Helix" + }, + { + "author_name": "David Becker", + "author_inst": "Helix" + }, + { + "author_name": "James T Lu", + "author_inst": "Helix" + }, + { + "author_name": "Magnus Isaksson", + "author_inst": "Helix" + }, + { + "author_name": "William Lee", + "author_inst": "Helix" + }, + { + "author_name": "Shishi Luo", + "author_inst": "Helix" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.10.22272197", "rel_title": "Blood group O and post-COVID-19 syndrome", @@ -378925,141 +381138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.09.22272155", - "rel_title": "Identification and Quantification of Bioactive Compounds Suppressing SARS-CoV-2 Signals in Wastewater-based Epidemiology Surveillance", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272155", - "rel_abs": "Recent SARS-CoV-2 wastewater-based epidemiology (WBE) surveillance have documented a positive correlation between the number of COVID-19 patients in a sewershed and the level of viral genetic material in the wastewater. Efforts have been made to use the wastewater SARS-CoV-2 viral load to predict the infected population within each sewershed using a multivariable regression approach. However, reported clear and sustained variability in SARS-CoV-2 viral load among treatment facilities receiving industrial wastewater have made clinical prediction challenging. Several classes of molecules released by regional industries and manufacturing facilities, particularly the food processing industry, can significantly suppress the SARS-CoV-2 signals in wastewater by breaking down the lipid-bilayer of the membranes. Therefore, a systematic ranking process in conjugation with metabolomic analysis was developed to identify the wastewater treatment facilities exhibiting SARS-CoV-2 suppression and identify and quantify the chemicals suppressing the SARS-COV-2 signals. By ranking the viral load per diagnosed case among the sewersheds, we successfully identified the wastewater treatment facilities in Missouri, USA that exhibit SARS-CoV-2 suppression (significantly lower than 5 x 1011 gene copies/reported case) and determined their suppression rates. Through both untargeted global chemical profiling and targeted analysis of wastewater samples, 40 compounds were identified as candidates of SARS-CoV-2 signal suppression. Among these compounds, 14 had higher concentrations in wastewater treatment facilities that exhibited SARS-CoV-2 signal suppression compared to the unsuppressed control facilities. Stepwise regression analyses indicated that 4-nonylphenol, palmitelaidic acid, sodium oleate, and polyethylene glycol dioleate are positively correlated with SARS-CoV-2 signal suppression rates. Suppression activities were further confirmed by incubation studies, and the suppression kinetics for each bioactive compound were determined. According to the results of these experiments, bioactive molecules in wastewater can significantly reduce the stability of SARS-CoV-2 genetic marker signals. Based on the concentrations of these chemical suppressors, a correction factor could be developed to achieve more reliable and unbiased surveillance results for wastewater treatment facilities that receive wastewater from similar industries.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Mohamed Bayati", - "author_inst": "University of Missouri" - }, - { - "author_name": "Hsin-Yeh Hsieh", - "author_inst": "University of Missouri" - }, - { - "author_name": "Shu-Yu Hsu", - "author_inst": "University of Missouri" - }, - { - "author_name": "Elizabeth Rogers", - "author_inst": "University of Missouri" - }, - { - "author_name": "Anthony Belenchia", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Sally A. Zemmer", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Todd Blanc", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Cindy LePage", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Jessica Klutts", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Melissa Reynolds", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Elizabeth Semkiw", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Hwei-Yiing Johnson", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Trevor Foley", - "author_inst": "Missouri Department of Corrections" - }, - { - "author_name": "Chris G. Wieberg", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Jeff Wenzel", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Terri Lyddon", - "author_inst": "University of Missouri" - }, - { - "author_name": "Mary LePique", - "author_inst": "University of Missouri" - }, - { - "author_name": "Clayton Rushford", - "author_inst": "University of Missouri" - }, - { - "author_name": "Braxton Salcedo", - "author_inst": "University of Missouri" - }, - { - "author_name": "Kara Young", - "author_inst": "University of Missouri" - }, - { - "author_name": "Madalyn Graham", - "author_inst": "University of Missouri" - }, - { - "author_name": "Reinier Suarez", - "author_inst": "University of Missouri" - }, - { - "author_name": "Anarose Ford", - "author_inst": "University of Missouri" - }, - { - "author_name": "Zhentian Lei", - "author_inst": "University of Missouri" - }, - { - "author_name": "Lloyd Sumner", - "author_inst": "University of Missouri" - }, - { - "author_name": "Brian P. Mooney", - "author_inst": "University of Missouri" - }, - { - "author_name": "Xing Wei", - "author_inst": "University of Missouri" - }, - { - "author_name": "C. Michael Greenlief", - "author_inst": "University of Missouri" - }, - { - "author_name": "Marc Johnson", - "author_inst": "University of Missouri" - }, - { - "author_name": "Chung-Ho Lin", - "author_inst": "University of Missouri" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.09.22272171", "rel_title": "Vaccine-induced antibody level predicts the clinical course of breakthrough infection of COVID-19 caused by delta and omicron variants: a prospective observational cohort study", @@ -380135,6 +382213,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.03.10.483790", + "rel_title": "Evolutionary safety of death by mutagenesis", + "rel_date": "2022-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.10.483790", + "rel_abs": "Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing \"death by mutagenesis\" of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of epidemiologically concerning mutated virus progeny. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of virus mutants as a function of the timing of treatment and the immune competence of patients, employing various assumptions about the vulnerability of the viral genome and its potential to generate undesired phenotypes. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against COVID-19. We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment to individuals with a low clearance rate and by designing treatments that lead to a greater increase in mutation rate. We report a simple rule to determine the fold-increase in mutation rate required to obtain evolutionary safety which is also applicable to other pathogen-treatment combinations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gabriela Aleksandra Lobinska", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Yitzhak Tzachi Pilpel", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Martin Andreas Nowak", + "author_inst": "Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.03.10.483652", "rel_title": "Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites", @@ -381155,121 +383260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.03.09.22272125", - "rel_title": "Performance evaluation of a non-invasive one-step multiplex RT-qPCR assay for detection of SARS-CoV-2 direct from human saliva", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272125", - "rel_abs": "Polymerase chain reaction (PCR) has proven to be the gold-standard for SARS-CoV-2 detection in clinical settings. The most common approaches rely on nasopharyngeal specimens obtained from swabs, followed by RNA extraction, reverse transcription and quantitative PCR. Although swab-based PCR is sensitive, swabbing is invasive and unpleasant to administer, reducing patient compliance for regular testing and resulting in an increased risk of improper sample collection. To overcome these obstacles, we developed a non-invasive one-step RT-qPCR assay performed directly on saliva specimens. The University of Nottingham Asymptomatic Testing Service (UoNATS) protocol simplifies sample collection and bypasses the need for RNA extraction, additives, or extraneous processing steps, thus helping to encourage more regular testing and reducing processing time and costs. We have evaluated the assay against the performance criteria specified by the UK regulatory bodies and attained accreditation (BS EN ISO/IEC 17025:2017) for SARS-CoV-2 diagnostic testing by the United Kingdom Accreditation Service (UKAS). We observed a sensitivity of 1 viral copy per microlitre of saliva and demonstrated a concordance of >99.4% between our results and those of other accredited testing facilities. We concluded that saliva is a stable medium with surprising longevity, and allows for a highly precise, repeatable, and robust testing method.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Harry H Jenkins", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Ana A Tellechea Lopez", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Francesco S Tarantini", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Hannah Tomlin", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Danielle Scales", - "author_inst": "University of Nottingham" - }, - { - "author_name": "I-Ning Lee", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Siyu Wu", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Ralph Hyde", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Katarzyna Lis-Slimak", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Timothy Byaruhanga", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Jamie L Thompson", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Sara Pijuan-Galito", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Lara Doolan", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Kazuyo Kaneko", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Penny Gwynne", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Caroline Reffin", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Emily Park", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Jayasree Dey", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Jack Hill", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Asta Arendt-Tranholm", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Amy Stroud", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Moira Petrie", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Chris Denning", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Andrew V Benest", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Claire Seedhouse", - "author_inst": "University of Nottingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.08.22271822", "rel_title": "Selection of optimum formulation of RBD-based protein sub-unit covid19 vaccine (Corbevax) based on safety and immunogenicity in an open-label, randomized Phase-1 and 2 clinical studies", @@ -382293,6 +384283,53 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.03.08.483429", + "rel_title": "Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting", + "rel_date": "2022-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.08.483429", + "rel_abs": "SARS-CoV-2 is currently causing an unprecedented pandemic. While vaccines are massively deployed, we still lack effective large-scale antiviral therapies. In the quest for antivirals targeting conserved structures, we focused on molecules able to bind viral RNA secondary structures. Aminoglycosides are a class of antibiotics known to interact with the ribosomal RNA of both prokaryotes and eukaryotes and have previously been shown to exert antiviral activities by interacting with viral RNA. Here we show that the aminoglycoside geneticin is endowed with antiviral activity against all tested variants of SARS-CoV-2, in different cell lines and in a respiratory tissue model at non-toxic concentrations. The mechanism of action is an early inhibition of RNA replication and protein expression related to a decrease in the efficiency of the -1 programmed ribosomal frameshift (PRF) signal of SARS-CoV-2. Using in silico modelling, we have identified a potential binding site of geneticin in the pseudoknot of frameshift RNA motif. Moreover, we have selected, through virtual screening, additional RNA binding compounds, interacting with the same site with increased potency.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Carmine Varricchio", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences" + }, + { + "author_name": "Gregory Mathez", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Trestan Pillonel", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Claire Bertelli", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Caroline Tapparel", + "author_inst": "University of Geneva" + }, + { + "author_name": "Andrea Brancale", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences" + }, + { + "author_name": "Valeria Cagno", + "author_inst": "University Hospital of Vaud (CHUV)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.01.22271721", "rel_title": "The relative impact of vaccination momentum on COVID-19 rates of death in the USA in 2020/2021. The forgotten role of population wellness.", @@ -383013,69 +385050,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.03.22271812", - "rel_title": "Culture and identification of a Deltamicron SARS-CoV-2 in a three cases cluster in southern France", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271812", - "rel_abs": "Multiple SARS-CoV-2 variants have successively, or concommitantly spread worldwide since summer 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J/AY.4-Omicron 21K/BA.1 \"Deltamicron\" recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1,163-1,421 reads and mean nucleotide diversity of 0.1-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening qPCR, we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Philippe Colson", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Pierre-Edouard Fournier", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Jeremy Delerce", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Matthieu Million", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Marielle Bedotto", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Linda Houhamdi", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Nouara Yahi", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Jeremy Bayette", - "author_inst": "LBM Inovie Labosud" - }, - { - "author_name": "Anthony LEVASSEUR", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Jacques Fantini", - "author_inst": "Aix-Marseille university" - }, - { - "author_name": "Didier Raoult", - "author_inst": "Aix-Marseille university IHU Mediterranee Infection" - }, - { - "author_name": "Bernard LA SCOLA", - "author_inst": "IHU Mediterranee Infection" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.05.483104", "rel_title": "Characterization of Hydrophobic Interactions of SARS-CoV-2 and MERS-CoV Spike Protein Fusion Peptides Using Single Molecule Force Measurements", @@ -384227,6 +386201,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.04.22271890", + "rel_title": "Protective antibodies and T cell responses to Omicron variant three months after the booster dose of BNT162b2 vaccine", + "rel_date": "2022-03-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271890", + "rel_abs": "The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when compared to the earlier variants of concern (VOC). At least three vaccine doses are required for the induction of Omicron neutralizing antibodies and further reducing the risk for hospitalization. However, most of the studies have focused on the immediate response after the booster vaccination while the duration of immune response is less known. We here studied longitudinal serum samples from the vaccinated individuals up to three months after their third dose of the BNT162b2 vaccine for their capacity to produce protective antibodies and T cell responses to Wuhan and Omicron variants. After the second dose, the antibody levels to the unmutated spike protein were significantly decreased at three months, and only 4% of the individuals were able to inhibit Omicron spike interaction compared to 47%, 38%, and 14% of individuals inhibiting wild-type, delta, and beta variants spike protein. Nine months after the second vaccination, the antibody levels were similar to the levels before the first dose and none of the sera inhibited SARS-CoV-2 wild-type or any of the three VOCs. The booster dose remarkably increased antibody levels and their ability to inhibit all variants. Three months after the booster the antibody levels and the inhibition activity were trending lower but still up and not significantly different from their peak values at two weeks after the third dose. Although responsiveness towards mutated spike peptides was lost in less than 20 % of vaccinated individuals, the wild-type spike-specific CD4+ and CD8+ memory T cells were still present at three months after the booster vaccination in the majority of studied individuals. Our data show that two doses of the BNT62b2 vaccine are not sufficient to protect against the Omicron variant, however, the spike-specific antibodies and T cell responses are strongly elicited and well maintained three months after the third vaccination dose.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Paul Naaber", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Liina Tserel", + "author_inst": "University of Tartu" + }, + { + "author_name": "Kadri Kangro", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Epp Sepp", + "author_inst": "University of Tartu" + }, + { + "author_name": "Virge Jurjenson", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Jaanika Karner", + "author_inst": "University of Tartu" + }, + { + "author_name": "Liis Haljasmagi", + "author_inst": "University of Tartu" + }, + { + "author_name": "Uku Haljasorg", + "author_inst": "University of Tartu" + }, + { + "author_name": "Marilin Kuusk", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Joachim M Gerhold", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Anu Planken", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Mart Ustav", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Kai Kisand", + "author_inst": "University of Tartu" + }, + { + "author_name": "Part Peterson", + "author_inst": "University of Tartu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.04.22271540", "rel_title": "The mutational steps of SARS-CoV-2 to become like Omicron within seven months: the story of immune escape in an immunocompromised patient.", @@ -384759,53 +386804,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.04.22271920", - "rel_title": "Patients at risk of pulmonary fibrosis Post Covid-19: Epidemiology, pulmonary sequelaes and humoral response", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271920", - "rel_abs": "BackgroundThe COVID-19 pandemic is one of the greatest public health problems. Our aims were to describe epidemiological characteristics, know the amount of protective antibodies and their permanence after a COVID-19 primary infection in patients with risk of pulmonary fibrosis.\n\nMethodsDescriptive epidemiological and follow-up study of the humoral response in patients at risk of pulmonary fibrosis Post-Covid-19 hospitalized, between March and October 2020, and who were followed up for a one year after hospital discharge.\n\nResults72 patients participated in the study, 52 showed pre-existing chronic comorbidities. COVID-19 clinical severity was rated in 6% mild, 58% as moderate and 36% as severe. After a year of follow-up, the forty percent had pulmonary sequelae, the most frequent (20%) was mild pulmonary fibrosis. Any case of reinfection was detected. All patients presented RBD IgG antibodies and 88% presented IgA antibodies after 8-9 months. The amount of RBD IgG was similar at 4-5 and 8-9 months post-Covid. There was no difference when level of RBD IgG according to the severity of the COVID-19 (p=0.441, p=0.594).\n\nConclusionsMild pulmonary fibrosis sequelae is exceptional but was detected in a high percentage. The amount of RBD IgG is maintained throughout the convalescent phase and seems to protect against new reinfections despite of emerging viral variants. However, seems not predict the developed or not of pulmonary fibrosis.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Miriam Hern\u00e1ndez Porto", - "author_inst": "Hospital Universitario de Canarias" - }, - { - "author_name": "Teresa Delgado", - "author_inst": "Hospital Universitario de Canarias" - }, - { - "author_name": "Armando Aguirre-Jaime", - "author_inst": "Institute for Healthcare research of the Nursing School of Santa Cruz de Tenerife" - }, - { - "author_name": "Maria Jose Ramos", - "author_inst": "Hospital Universitario de Canarias" - }, - { - "author_name": "Silvia Campos", - "author_inst": "Hospital Universitario de Canarias" - }, - { - "author_name": "Orlando Acosta", - "author_inst": "Hospital Universitario de Canarias" - }, - { - "author_name": "Ana Belen LLanos", - "author_inst": "Hospital Universitario de Canarias" - }, - { - "author_name": "Maria Lecuona", - "author_inst": "Hospital Universitario de Canarias" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.03.03.22271793", "rel_title": "Reasons underlying the intention to vaccinate children aged 5-11 against COVID-19: A cross-sectional study of parents in Israel, November 2021", @@ -385921,6 +387919,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.03.02.22271806", + "rel_title": "Covid-19 Exposure Assessment Tool (CEAT): Easy-to-use tool to quantify exposure based on airflow, group behavior, and infection prevalence in the community", + "rel_date": "2022-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271806", + "rel_abs": "The COVID-19 Exposure Assessment Tool (CEAT) allows users to compare respiratory relative risk to SARS-CoV-2 for various scenarios, providing understanding of how combinations of protective measures affect exposure, dose, and risk. CEAT incorporates mechanistic, stochastic and epidemiological factors including the: 1) emission rate of virus, 2) viral aerosol degradation and removal, 3) duration of activity/exposure, 4) inhalation rates, 5) ventilation rates (indoors/outdoors), 6) volume of indoor space, 7) filtration, 8) mask use and effectiveness, 9) distance between people, 10) group size, 11) current infection rates by variant, 12) prevalence of infection and immunity in the community, 13) vaccination rates of the community, and 14) implementation of COVID-19 testing procedures. Demonstration of CEAT, from published studies of COVID-19 transmission events, shows the model accurately predicts transmission. We also show how health and safety professionals at NASA Ames Research Center used CEAT to manage potential risks posed by SARS-CoV-2 exposures. Given its accuracy and flexibility, the wide use of CEAT will have a long lasting beneficial impact in managing both the current COVID-19 pandemic as well as a variety of other scenarios.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Brian Schimmoller", + "author_inst": "Signature Science LLC" + }, + { + "author_name": "Nidia S Trovao", + "author_inst": "Fogarty International Center, National Institutes of Health" + }, + { + "author_name": "Molly Isbell", + "author_inst": "Signature Science LLC" + }, + { + "author_name": "Chirag Goel", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Benjamin F Heck", + "author_inst": "Bastion Technologies, NASA Ames Research Center" + }, + { + "author_name": "Tenley C Archer", + "author_inst": "Biomea Fusion, Inc." + }, + { + "author_name": "Klint D Cardinal", + "author_inst": "Leidos, Inc., NASA Ames Research Center" + }, + { + "author_name": "Neil B Naik", + "author_inst": "Leidos, Inc., NASA Ames Research Center" + }, + { + "author_name": "Som Dutta", + "author_inst": "Mechanical & Aerospace Engineering, Utah State University" + }, + { + "author_name": "Ahleah Rohr Daniel", + "author_inst": "Space Biosciences Division, NASA Ames Research Center" + }, + { + "author_name": "Afshin Beheshti", + "author_inst": "KBR, NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.03.22271836", "rel_title": "The relationship between BMI and COVID-19: exploring misclassification and selection bias in a two-sample Mendelian randomisation study", @@ -386409,85 +388466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.02.22271724", - "rel_title": "Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking", - "rel_date": "2022-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271724", - "rel_abs": "BackgroundThe analytical sensitivities of SARS-CoV-2 diagnostic tests span 6 orders of magnitude. Optimizing sample-collection methods to achieve the most reliable detection for a given sensitivity would increase the effectiveness of testing and minimize COVID-19 outbreaks.\n\nMethodsFrom September 2020 to April 2021 we performed a household-transmission study in which participants self-collected samples every morning and evening throughout acute SARS-CoV-2 infection. Seventy mildly symptomatic participants collected saliva and, of those, 29 also collected nasal-swab samples. Viral load was quantified in 1194 saliva and 661 nasal-swab samples using a high-analytical-sensitivity RT-qPCR assay (LOD, 1,000 SARS-CoV-2 RNA copies/mL).\n\nFindingsViral loads in both saliva and nasal-swab samples were significantly higher in morning-collected samples than evening-collected samples after symptom onset. We used these quantitative measurements to infer which diagnostic tests would have detected infection (based on sample type and test analytical sensitivity). We find that morning collection would have resulted in significantly improved detection and that this advantage would be most pronounced for tests with low to moderate analytical sensitivity, which would likely have missed infections if sampling in the evening.\n\nInterpretationCollecting samples for COVID-19 testing in the morning offers a simple and low-cost improvement to clinical diagnostic sensitivity of low- to moderate-analytical-sensitivity tests. The phenomenon of higher viral loads in the morning may also have implications related to when transmission is more likely to occur.\n\nFundingBill & Melinda Gates Foundation, Ronald and Maxine Linde Center for New Initiatives (Caltech), Jacobs Institute for Molecular Engineering for Medicine (Caltech)\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSReliable COVID-19 diagnostic testing is critical to reducing transmission of SARS-CoV-2 and reducing cases of severe or fatal disease, particularly in areas with limited vaccine access or uptake. Saliva and anterior-nares nasal swabs are common sample types; however, different diagnostic tests using these sample types have a range of analytical sensitivities spanning 6 orders of magnitude, with limits of detection (LODs) between 102 and 108 genomic copy equivalents of SARS-CoV-2 RNA (copies) per mL of sample. Due to limitations in clinical laboratory capacity, many low-resource settings rely on COVID-19 tests that fall on the moderate (LODs of 104 to 105 copies/mL) to lower (LODs of 105 to 108 copies/mL) end of this spectrum of analytical sensitivity. Alterations in sample collection methods, including time of sample collection, may improve the performance of these diagnostics.\n\nAdded value of this studyThis study quantifies viral loads from saliva and nasal-swab samples that were longitudinally self-collected by symptomatic patients in the morning immediately after waking and in the evening just prior to sleeping throughout the course of acute SARS-CoV-2 infection. The study cohort was composed of mildly or moderately symptomatic individuals (outpatients). This analysis demonstrates significantly higher viral loads in samples collected in the morning, relative to those collected in the evening. When using moderate to lower analytical sensitivity test methods, these loads are inferred to result in significantly better detection of infected individuals in the morning.\n\nImplications of available evidenceThese findings suggest that samples collected in the morning immediately after waking will better detect SARS-CoV-2 infection in symptomatic individuals tested by moderate to lower analytical sensitivity COVID-19 diagnostic tests (LODs at or above 104 viral copies per mL of sample), such as many rapid antigen tests currently available.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Alexander Viloria Winnett", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Michael K. Porter", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Anna E. Romano", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Emily S. Savela", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Reid Akana", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Natasha Shelby", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Jessica A. Reyes", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Noah W. Schlenker", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Matthew M. Cooper", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Alyssa M. Carter", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Jenny Ji", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Jacob T. Barlow", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Colten Tognazzini", - "author_inst": "Pasadena Public Health Department" - }, - { - "author_name": "Matthew Feaster", - "author_inst": "Pasadena Public Health Department" - }, - { - "author_name": "Ying-Ying Goh", - "author_inst": "Pasadena Public Health Department" - }, - { - "author_name": "Rustem F. Ismagilov", - "author_inst": "California Institute of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.03.22271769", "rel_title": "The Coronavirus Calendar (CoronaCal): a Simplified SARS-CoV-2 Test System for Sampling and Retrospective Analysis", @@ -387799,6 +389777,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.23.22271355", + "rel_title": "Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19", + "rel_date": "2022-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271355", + "rel_abs": "Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals - the time between symptom onset in an infector and infectee - are fundamental, and help to define rates of transmission, estimates of reproductive numbers, and vaccination levels needed to prevent transmission. However, estimating the serial interval requires knowledge of individuals contacts and exposures (who infected whom), which is typically obtained through resource-intensive contact tracing efforts. We develop an alternate framework that uses virus sequences to inform who infected whom and thereby estimate serial intervals. The advantages are many-fold: virus sequences are often routinely collected to support epidemiological investigations and to monitor viral evolution. The genomic approach offers high resolution and cluster-specific estimates of the serial interval that are comparable with those obtained from contact tracing data. Our approach does not require contact tracing data, and can be used in large populations and over a range of time periods. We apply our techniques to SARS-CoV-2 sequence data from the first two waves of COVID-19 in Victoria, Australia. We find that serial interval estimates vary between clusters, supporting the need to monitor this key parameter and use updated estimates in onward applications. Compared to an early published serial interval estimate, using cluster-specific serial intervals can cause estimates of the effective reproduction number Rt to vary by a factor of up to 2-3. We also find that serial intervals estimated in settings such as schools and meat processing/packing plants tend to be shorter than those estimated in healthcare facilities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jessica E Stockdale", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Kurnia Susvitasari", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Paul Tupper", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Benjamin Sobkowiak", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Nicola Mulberry", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Anders Gon\u00e7alves da Silva", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Anne E Watt", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Norelle Sherry", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Corinna Minko", + "author_inst": "Victorian Department of Health, Melbourne, Victoria, Australia" + }, + { + "author_name": "Benjamin P Howden", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Courtney R Lane", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Caroline Colijn", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.17.22270791", "rel_title": "Vaccine effectiveness and duration of protection against symptomatic and severe Covid-19 during the first year of vaccination in France", @@ -388639,61 +390680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.03.01.22271684", - "rel_title": "Viral cultures, Polymerase Chain Reaction Cycle Threshold Values and Viral Load Estimation for SARS-CoV-2 Infectious Potential Assessment in Hematopoietic Stem Cell and Solid Organ Transplant Patients: A Systematic Review", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271684", - "rel_abs": "BackgroundOrgan transplant recipients are at increased vulnerability to SARS-CoV-2 due to immunosuppression and may pose a continued transmission risk especially within hospital settings. Detailed case reports including symptoms, viral load and infectiousness, defined by the presence of replication-competent viruses in culture, provide an opportunity to examine the relationship between clinical course, burden and contagiousness, and provide guidance on release from isolation.\n\nObjectivesWe performed a systematic review to investigate the relationship in transplant recipients between serial SARS-CoV-2 RT-PCR cycle threshold (Ct) value or cycle of quantification value (Cq), or other measures of viral burden and the likelihood and duration of the presence of infectious virus based on viral culture including the influence of age, sex, underlying pathologies, degree of immunosuppression, and/or vaccination on this relationship.\n\nMethodsWe searched LitCovid, medRxiv, Google Scholar and WHO Covid-19 databases, from 1 November 2019 until 31 December 2021. We included studies reporting relevant data for transplantees with SARS-CoV-2 infection: results from serial RT-PCR testing and viral culture data from the same respiratory samples. We assessed methodological quality using five criteria, and synthesised the data narratively and graphically.\n\nResultsWe included 10 case reports and case series reporting on 38 transplantees. We observed a relationship between proxies of viral burden and likelihood of shedding replication-competent SARS-CoV-2. Two individuals shed replication-competent viruses over 100 days after infection onset. Lack of standardisation of testing and reporting platforms precludes establishing a definitive viral burden cut-off. However, most transplantees stopped shedding competent viruses when the RT-PCR cycle threshold was above 30 despite differences across platforms.\n\nConclusionsViral burden is a reasonable proxy for infectivity when considered within the context of the clinical status of each patient. Standardised study design and reporting are essential to standardise guidance based on an increasing evidence base.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tom Jefferson", - "author_inst": "Department for Continuing Education, University of Oxford, UK" - }, - { - "author_name": "Elizabeth A Spencer", - "author_inst": "University of Oxford" - }, - { - "author_name": "John M Conly", - "author_inst": "Departments of Medicine, Microbiology, Immunology&Infectious Diseases, Pathology&Laboratory Medicine, Synder Institute for Chronic Diseases and OBrien Institut" - }, - { - "author_name": "Elena Cecilia Rosca", - "author_inst": "Victor Babes University of Medicine and Pharmacy of Timisoara" - }, - { - "author_name": "Susanna Maltoni", - "author_inst": "Division of Research and Innovation, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy" - }, - { - "author_name": "Jon Brassey", - "author_inst": "Trip Database Ltd, Newport, UK" - }, - { - "author_name": "IGHO ONAKPOYA", - "author_inst": "UNIVERSITY OF OXFORD" - }, - { - "author_name": "David H Evans", - "author_inst": "University of Alberta" - }, - { - "author_name": "Carl Heneghan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Annette Pluddemann", - "author_inst": "Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.01.22271662", "rel_title": "High Viral Specific Antibody Convalescent Plasma Effectively Neutralizes SARS-CoV-2 Variants of Concern", @@ -389661,6 +391647,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.02.22271385", + "rel_title": "Impact of Delta and Vaccination on SARS-CoV-2 transmission risk: Lessons for Emerging Breakthrough infections", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271385", + "rel_abs": "With the continuous emergence of SARS-CoV-2 variants of concern and implementation of mass-scale interventions like vaccination, understanding factors affecting disease transmission has critical implications for control efforts. Here we used a simple adapted N95 mask sampling method to demonstrate the impact of circulating SARS-CoV-2 variants and vaccination on 92 COVID-19 patients to expel virus into the air translating to a transmission risk. Between July and September 2021, when the Delta was the dominant circulating strain in Mumbai, we noted a two-fold increase in the proportion of people expelling virus (95%), about an eighty-fold increase in median viral load and a three-fold increase in high emitter type (41%; people expelling >1000 viral copy numbers in 30 minutes) compared to initial strains of 2020. Eight percent of these patients continued to be high emitters even after eight days of symptom onset, suggesting a probable increased transmission risk for Delta strain even at this stage. There was no significant difference in expelling pattern between partial, full and un-vaccinated individuals suggesting similar transmission risk. We noted significantly more infections among vaccinated study patients and their household members than unvaccinated, probably due to increased duration from vaccination and/or increased risk behaviour upon vaccination due to lower perceived threat. This study provides biological evidence for possible continued transmission of the Delta strain even with vaccination, emphasizing the need to continue COVID-19 appropriate behaviour. The study also indicates that the mask method may be useful for screening future vaccine candidates, therapeutics or interventions for their ability to block transmission.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Kalpana Sriraman", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Ambreen Shaikh", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Smriti Vaswani", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Tejal Mestry", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Grishma Patel", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Shalini Sakthivel", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Vikas Oswal", + "author_inst": "Vikas Nursing Home, Mumbai, India" + }, + { + "author_name": "Pratibha Kadam", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Kayzad Nilgiriwala", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Daksha Shah", + "author_inst": "Municipal Corporation of Greater Mumbai, Mumbai, India" + }, + { + "author_name": "Mangala Gomare", + "author_inst": "Municipal Corporation of Greater Mumbai,Mumbai, India" + }, + { + "author_name": "Nerges Mistry", + "author_inst": "The Foundation for Medical Research,, Mumbai, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.01.22271735", "rel_title": "Comparison of the reactogenicity and immunogenicity of a reduced and standard booster dose of the mRNA COVID-19 vaccine in healthy adults after two doses of inactivated vaccine.", @@ -390653,29 +392702,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2022.02.28.482283", - "rel_title": "Mutation patterns in SARS-COV-2 Alpha and Beta variants indicate non-neutral evolution", - "rel_date": "2022-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.28.482283", - "rel_abs": "Due to the emergence of new variants of the SARS-CoV-2 coronavirus, the question of how the viral genomes evolved, leading to the formation of highly infectious strains, becomes particularly important. Two early emergent strains, Alpha and Beta, characterized by a significant number of missense mutations, provide natural testing samples.\n\nIn this study we are exploring the history of each of the segregating sites present in Alpha and Beta variants of concern, to address the question whether defining mutations were accumulating gradually leading to the formation of sequence characteristic of these variants.\n\nOur analysis exposes data features that suggest other than neutral evolution of SARS-CoV-2 genomes, leading to emergence of variants of concern. We observe only small number of possible combinations of mutations indicating rapid evolution of genomes. In addtion, mutation patterns observed in whole genome samples of Alpha and Beta variants also indicate presence of stronger selection than in remaining genome samples.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Monika Klara Kurpas", - "author_inst": "Silesian University of Technology" - }, - { - "author_name": "Marek Kimmel", - "author_inst": "Rice University, SIlesian University of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.02.28.482377", "rel_title": "Sleep and circadian rhythm disruption alters the lung transcriptome to predispose to viral infection", @@ -391559,6 +393585,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.02.27.482153", + "rel_title": "A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2", + "rel_date": "2022-02-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.27.482153", + "rel_abs": "SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as delta and omicron are among the major challenges in finding a more permanent solution for this pandemic. The effectiveness of antivirals Molnupiravir and Paxlovid, authorized for emergency use by the FDA, are yet to be assessed at larger populations. Patients with a high risk of disease progression or hospitalization have received treatment with a combination of antibodies (antibody-cocktail). Most of the mutations leading to the new lineage of SARS-CoV-2 are found in the spike protein of this virus that plays a key role in facilitating host entry. The current study has investigated how to modify a promising peptide-based inhibitor of spike protein, LCB3, against common mutations in the target protein so that it retains its efficacy against the spike protein. LCB3 being a prototype for protein-based inhibitors is an ideal testing system to learn about protein-based inhibitors. Two common mutations N501Y and K417N are considered in this work. Using a structure-based approach that considers free energy decomposition of residues, distance, and the interactions between amino acids, we propose the substitutions of amino acid residues of LCB3 inhibitors. Our binding free energy calculations suggest a possible improvement in the binding affinity of existing inhibitor LCB3 to the mutant forms of the S-protein using simple substitutions at specific positions of the inhibitor. This approach, being general, can be used in different inhibitors and other mutations and help in fighting against SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Prerna Priya", + "author_inst": "Purnea Mahila College" + }, + { + "author_name": "Abdul Basit", + "author_inst": "School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + }, + { + "author_name": "Pradipta Bandyopadhyay", + "author_inst": "School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.02.25.481974", "rel_title": "An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques", @@ -392479,77 +394532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.28.22271562", - "rel_title": "Genetic Examination of Hematological Parameters in SARS-CoV-2 Infection and COVID-19", - "rel_date": "2022-02-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271562", - "rel_abs": "BackgroundPeople hospitalized with COVID-19 often exhibit hematological alterations, such as lower lymphocyte and platelet counts, which have been reported to associate with disease prognosis. It is unclear whether inter-individual variability in baseline hematological parameters prior to acute infection influences risk of SARS-CoV-2 infection and progression to severe COVID-19.\n\nMethodsWe assessed the association of blood cell counts and indices with incident SARS-CoV-2 infection and severe COVID-19 in UK Biobank and the Vanderbilt University Medical Center Synthetic Derivative (VUMC SD). Since genetically determined blood cell measures better represent cell abundance across the lifecourse, we used summary statistics from genome-wide association studies to assess the shared genetic architecture of baseline blood cell counts and indices on COVID-19 outcomes.\n\nResultsWe observed inconsistent associations between measured blood cell indices and both SARS-CoV-2 infection and COVID-19 hospitalization in UK Biobank and VUMC SD. In Mendelian randomization analyses using genetic summary statistics, no putative causal relationships were identified between COVID-19 related outcomes and hematological indices after adjusting for multiple testing. We observed overlapping genetic association signals between hematological parameters and COVID-19 traits. For example, we observed overlap between infection susceptibility-associated variants at PPP1R15A and red blood cell parameters, and between disease severity-associated variants at TYK2 and lymphocyte and platelet phenotypes.\n\nConclusionsWe did not find convincing evidence of a relationship between baseline hematological parameters and susceptibility to SARS-CoV-2 infection or COVID-19 severity, though this relationship should be re-examined as larger and better-powered genetic analyses of SARS-CoV-2 infection and severe COVID-19 become available.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Bryce Rowland", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Quan Sun", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Wanjiang Wang", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Tyne Miller-Fleming", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Nancy Cox", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Mariaelisa Graff", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Annika Faucon", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Megan Shuey", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Elizabeth E. Blue", - "author_inst": "University of Washington" - }, - { - "author_name": "Paul Auer", - "author_inst": "Medical College of Wisconsin" - }, - { - "author_name": "Yun Li", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Vijay G. Sankaran", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Alexander P. Reiner", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Laura M. Raffield", - "author_inst": "University of North Carolina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.02.28.22270796", "rel_title": "Real-world Effectiveness of Casirivimab and Imdevimab in Patients With COVID-19 in the Ambulatory Setting: An Analysis of Two Large US National Claims Databases", @@ -393517,6 +395499,65 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.24.481684", + "rel_title": "Dictionary learning for integrative, multimodal, and scalable single-cell analysis", + "rel_date": "2022-02-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.24.481684", + "rel_abs": "Mapping single-cell sequencing profiles to comprehensive reference datasets represents a powerful alternative to unsupervised analysis. Reference datasets, however, are predominantly constructed from single-cell RNA-seq data, and cannot be used to annotate datasets that do not measure gene expression. Here we introduce bridge integration, a method to harmonize singlecell datasets across modalities by leveraging a multi-omic dataset as a molecular bridge. Each cell in the multi-omic dataset comprises an element in a dictionary, which can be used to reconstruct unimodal datasets and transform them into a shared space. We demonstrate that our procedure can accurately harmonize transcriptomic data with independent single cell measurements of chromatin accessibility, histone modifications, DNA methylation, and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to substantially improve computational scalability, and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach aims to broaden the utility of single-cell reference datasets and facilitate comparisons across diverse molecular modalities.\n\nAvailabilityInstallation instructions, documentations, and vignettes are available at http://www.satijalab.org/seurat", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuhan Hao", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Tim Stuart", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Madeline Kowalski", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Saket Choudhary", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Paul Hoffman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Austin Hartman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Avi Srivastava", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Gesmira Molla", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Shaista Madad", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Carlos Fernandez-Granda", + "author_inst": "Center for Data Science, New York University" + }, + { + "author_name": "Rahul Satija", + "author_inst": "New York Genome Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.02.25.22271520", "rel_title": "Late-Ensemble of Convolutional Neural Networks with Test Time Augmentation for Chest XR COVID-19 Detection", @@ -394077,65 +396118,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.02.25.481966", - "rel_title": "Proteomic analysis of human milk reveals nutritional and immune benefits in the colostrum from mothers with COVID-19", - "rel_date": "2022-02-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481966", - "rel_abs": "The range of benefits breastfeeding provides neonates and infants include nutrition, improved neonatal survival, and reduced morbidity from certain diseases. It also aids maternal health by speeding postpartum recovery. However, due to concern about the risk of SARS-CoV-2 transmission and the lack of evidence of breastmilks protective effects against the virus, whether mothers with COVID-19 should be encouraged to breastfeed is under debate. Here, we present the results of proteomic and glycoproteomic studies of breast milk (colostrum and mature milk) from mothers with confirmed COVID-19. All colostrum samples exhibited significantly upregulated immune-related proteins, especially whey proteins with antiviral properties against SARS-CoV-2, and increased glycosylation levels and heterogeneity at those proteins. Such adaptive differences in milk from COVID-19 mothers tend to fade in mature milk from the same mothers one month postpartum. These results suggest the immune benefits of colostrum from mothers with COVID-19 and provide molecular-level insights that aid breastmilk feeding decisions in cases of active infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Juanjuan Guo", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Minjie Tan", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Jing Zhu", - "author_inst": "Beijing Academy of Science and Technology" - }, - { - "author_name": "Ye Tian", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Huanyu Liu", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Fan Luo", - "author_inst": "Wuhan University" - }, - { - "author_name": "Jianbin Wang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yanyi Huang", - "author_inst": "Peking University" - }, - { - "author_name": "Yuanzhen Zhang", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yuexin Yang", - "author_inst": "Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Guanbo Wang", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.02.25.481941", "rel_title": "Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)", @@ -395323,6 +397305,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.24.22271468", + "rel_title": "Clinical and Virologic Factors associated with Outcomes of COVID-19 before and after Vaccination among Veterans: Retrospective Analysis from Six New England States", + "rel_date": "2022-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.24.22271468", + "rel_abs": "BackgroundA region-wide analysis of COVID-19 outcomes in New England has not been done. We aimed to characterize clinical, demographic, and vaccination status affecting COVID-19 clinical outcomes and describe viral epidemiology.\n\nMethodsClinical variables of Veterans with COVID-19 in Veterans Administration healthcare systems in six New England states from April 8, 2020, to September 2, 2021 were correlated with outcomes of 30-day mortality, non-psychiatric hospitalization, intensive care unit admission (ICU-care), and post-vaccination infection. We sequenced 754 whole viral genomes and 197 partial genomes.\n\nResultsOf 4,170 Veterans with COVID-19, 81% were White, 8% women, mean age was 60.1 {+/-}17.7 years, and 2,399 became fully vaccinated. Overall, 19% Veterans needed hospitalization, 2.8% required ICU-care, and 3.7% died. Veterans with post-vaccination COVID-19 were older, with higher rates of tobacco/drug use, CKD, and malignancy, and 0.38% died. Among the unvaccinated, ICU-care and mortality correlated with age, while hospitalization correlated with age, male sex, black race, drug use, chronic heart disease, COPD, CKD, and chronic liver disease. Age, CKD, and alcohol use correlated with hospitalization in vaccinated patients.\n\nMost New England Veterans (>97%) were infected with B.1 sub-lineages with the D614G mutation in 2020 and early 2021. B.1.617.2 lineage (71%) predominated after July 2021, including the post-vaccination infections.\n\nConclusionIn New England Veterans with mean age of 60 years, age and CKD significantly correlated with hospitalization regardless of vaccination-status. Age correlated with mortality and ICU-care among the unvaccinated. The Delta variant of SARS-CoV-2 (B.1.617.2) dominated post-vaccination infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Megan Lee", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Danielle Cosenino", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Tassos C Kyriakides", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Tricia Cavallaro", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Gary Stack", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Shaili Gupta", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.21.481324", "rel_title": "A single-dose of the deactivated rabies virus vectored COVID-19 vaccine, CORAVAX, is highly efficacious and alleviates lung inflammation in the hamster model.", @@ -395939,45 +397960,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.22.21266830", - "rel_title": "SARS-CoV-2 Infection Breakthrough among the non-vaccinated and vaccinated: a Real World Evidence study based on Big Data", - "rel_date": "2022-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.21266830", - "rel_abs": "BackgroundSARS-CoV-2 infection after vaccination can occur because COVID-19 vaccines do not offer 100% protection. The aim of this study was to assess vaccination coverage among people nasopharyngeal swabs, disease symptoms and type of hospitalisation (Intensive Care Unit) between the non-vaccinated and the effective dose vaccinated and to evaluate vaccination trend over time.\n\nMethodsA retrospective cohort study was carried out among people tested positive for COVID-19 in Campania Region using collected information from Health Information System of Campania Region (Sinfonia).\n\nThe status of vaccination was assess according to the following timetable: \"non-vaccinated\"; \"Ineffective dose\" vaccination; \"Effective dose\" vaccination.\n\nUnivariate and multivariate logistic regression models were conducted to evaluate the association between Intensive Care Unit (ICU) to COVID-19 and gender, age groups and vaccine.\n\nTo determine vaccine coverage in subjects who received an effective dose, trend changes over time were investigated using segmented linear regression models and breakpoints estimations.\n\nVaccination coverage was assessed by analysing the trend in the percentage of covid 19 positive subjects in the 9 months after vaccination with an effective dose stratified by age group and type of vaccine. Statistical analyses were performed using R platform\n\nResultsA significant association with the risk of hospitalisation in Intensive Care Unit was the vaccination status of the subjects: subjects with ineffective dose (adjusted OR: 3.68) and subjects no-vaccination (adjusted OR: 7.14) were at three- and seven-times higher risk of hospitalisation in Intensive Care Unit, respectively, than subjects with an effective dose.\n\nRegarding subjects with an effective dose of vaccine, the vaccines ability to protect against infection in the months following vaccination decreased.\n\nThe first breakpoints is evident five months after vaccination ({beta} =1.441, p<0.001). This increase was most evident after the seventh month after vaccination ({beta} =3.110, p<0.001).\n\nConclusionsCOVID19 vaccines protect from symptomatic infection by significantly reducing the risk of ICU hospitalization for severe disease. However, it seems they have trend to decrease their fully protection against SARS-COV-2 after five months regardless age, sex or type of vaccine. Therefore it seems clear that those not undergoing vaccine had higher risk to develop clinically significant disease and being at risk of ICU stay. Thus, considering highest percentage of asymptomatic patients and that few data about their capacity to transmit SARS-CoV-2, third dose vaccination should be introduced as soon as possible while awaiting antivirals.Finally, a surveillance approach based on the use of integrated BIG Data system to match all clinical conditions too, offer a precise and real analysis with low incidence of errors in the categorization of subjects.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alessandro Perrella", - "author_inst": "AORN A.Cardarelli and Regional Task Force COVID-19, Campania Region, Naples, Italy" - }, - { - "author_name": "Massimo BIsogno", - "author_inst": "Regional Task Force COVID-19, Campania Region, Naples, Italy" - }, - { - "author_name": "Angelo D'Argenzio", - "author_inst": "Regional Task Force COVID-19, Campania Region, Naples, Italy" - }, - { - "author_name": "Ugo Trama", - "author_inst": "Regional Task Force COVID-19, Campania Region, Naples, Italy" - }, - { - "author_name": "Enrico Coscioni", - "author_inst": "Regional Task Force COVID-19, Campania Region, Naples, Italy" - }, - { - "author_name": "Valentina Orlando", - "author_inst": "CIRFF, Center of Drug Utilisation and Pharmacoeconomics, University of Naples Federico II, 80131, Naples, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.22.22271359", "rel_title": "Gestational SARS-CoV-2 infection is associated with placental expression of immune and trophoblast genes", @@ -396889,6 +398871,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.23.22271403", + "rel_title": "Quantifying antibody dynamics of severe and non-severe patients with COVID-19", + "rel_date": "2022-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271403", + "rel_abs": "COVID-19 pandemic is a major public health threat with unanswered questions regarding the role of the immune system in the severity level of the disease. In this paper, based on antibody kinetic data of patients with different disease severity, topological data analysis highlights clear differences in the shape of antibody dynamics between three groups of patients, which were non-severe, severe, and one intermediate case of severity. Subsequently, different mathematical models were developed to quantify the dynamics between the different severity groups. The best model was the one with the lowest media value of Akaike Information Criterion for all groups of patients. Although it has been reported high IgG level in severe patients, our findings suggest that IgG antibodies in severe patients may be less effective than non-severe patients due to early B cell production and early activation of the seroconversion process from IgM to IgG antibody.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fernanda Ordonez-Jimenez", + "author_inst": "UNAM" + }, + { + "author_name": "Rodolfo Blanco-Rodriguez", + "author_inst": "UNAM" + }, + { + "author_name": "Alexis Erich S. Almocera", + "author_inst": "University of the Philippines Visayas" + }, + { + "author_name": "Gustavo Chinney-Herrera", + "author_inst": "UNAM" + }, + { + "author_name": "Esteban Abelardo Hernandez Vargas", + "author_inst": "UNAM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.23.22271372", "rel_title": "Genomic surveillance of SARS-CoV-2 reveals emergence of Omicron BA.2 in Islamabad, Pakistan", @@ -397573,53 +399590,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.02.22.481430", - "rel_title": "SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses", - "rel_date": "2022-02-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.22.481430", - "rel_abs": "Delta variant of SARS-CoV-2 has caused more severe infections than its previous variants. We studied the host innate immune response to Delta, Alpha and two earlier variants to map the evolution of the recent ones. Our biochemical and transcriptomic studies reveal that Alpha and Delta have progressively evolved over the ancestral variants by silencing innate immune response, thereby limiting cytokine and chemokine production. Though Alpha silenced RLR pathway just as Delta, it failed to persistently silence the innate immune response unlike Delta. Both Alpha and Delta have evolved to resist IFN treatment while they are still susceptible to RLR activation, further highlighting the importance of RLR-mediated, IFN-independent mechanisms in restricting SARS-CoV-2. Our studies reveal that SARS-CoV-2 Delta has integrated multiple mechanisms to silence host innate immune response and evade IFN response. Deltas silent replication and sustained suppression of host innate immune response, possibly resulting in delayed or reduced intervention by the adaptive immune response, could potentially contribute to the severe symptoms and poor recovery index associated with it.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Dixit Tandel", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Vishal Sah", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Nitesh Kumar Singh", - "author_inst": "Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Poojitha Sai Potharaju", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Divya Gupta", - "author_inst": "Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Sauhard Shrivastava", - "author_inst": "Indian institute of science education and research, Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Divya Tej Sowpati", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Krishnan Harinivas Harshan", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.21.481345", "rel_title": "Mucosal Immunization of Cynomolgus Macaques with Adenoviral Vector Vaccine Elicits Neutralizing Nasal and Serum Antibody to Several SARS-CoV-2 Variants", @@ -398702,6 +400672,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.19.481107", + "rel_title": "Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron", + "rel_date": "2022-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.19.481107", + "rel_abs": "To infect cells, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds to angiotensin converting enzyme 2 (ACE2) via its spike glycoprotein (S), delivering its genome upon S-mediated membrane fusion. SARS-CoV-2 uses two distinct entry pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In investigating serine protease-independent cell-cell fusion, we found that the matrix metalloproteinases (MMPs), MMP2/9, can activate SARS-CoV-2 S fusion activity, but not that of SARS-CoV-1. Importantly, metalloproteinase activation of SARS-CoV-2 S represents a third entry pathway in cells expressing high MMP levels. This route of entry required cleavage at the S1/S2 junction in viral producer cells and differential processing of variants of concern S dictated its usage. In addition, metalloproteinase inhibitors reduced replicative Alpha infection and abrogated syncytia formation. Finally, we found that the Omicron S exhibit reduced metalloproteinase-dependent fusion and viral entry. Taken together, we identified a MMP2/9-dependent mode of activation of SARS-CoV-2 S. As MMP2/9 are released during inflammation and severe COVID-19, they may play important roles in SARS-CoV-2 S-mediated cytopathic effects, tropism, and disease outcome.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Mehdi Benlarbi", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Genevi\u00e8ve Laroche", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Corby Fink", + "author_inst": "Western University" + }, + { + "author_name": "Kathy Fu", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Rory P Mulloy", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Alexandra Phan", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Ardeshir Ariana", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Corina M Stewart", + "author_inst": "University of Ottawa" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "Redaet Daniel", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Yuxia Bo", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Julien Yockell-Leli\u00e8vre", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "William L Stanford", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "Patrick M Gigu\u00e8re", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Samira Mubareka", + "author_inst": "Sunnybrook Research Institute and University of Toronto" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Gregory A Dekaban", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Jimmy D Dikeakos", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Marceline C\u00f4t\u00e9", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.19.481089", "rel_title": "Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection", @@ -399614,53 +401679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.21.22271281", - "rel_title": "The efficacy, effectiveness and safety of SARS-CoV-2 disinfection methods (including ozone machines) in educational settings for children and young people", - "rel_date": "2022-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271281", - "rel_abs": "While evidence for the importance of transmission of SARS-CoV-2 from contaminated surfaces is limited, ozone disinfection methods have been considered for surface cleaning as a response to stopping the spread of the virus in educational settings. This rapid evidence summary aimed to search the available literature and summarise findings on the surface survival of SARS-CoV-2, efficacy and effectiveness of ozone machines against SARS-CoV-2, and benefits and harms caused by using these cleaning technologies, including their impact on health. Alternative cleaning technologies, such as light-based technologies and hydrogen peroxide vapour, were also investigated. Findings indicate that gaseous ozone can inactivate different bacteria and viruses, although there is a lack of direct evidence investigating the effect of these cleaning methods on SARS-CoV-2 in real-world settings, specifically in schools. However, regarding harm, ozone is a highly reactive oxidising agent, and high concentrations can contribute to decay of building materials, and health issues (mainly respiratory) by direct exposure or by-product formation. Therefore, leading environmental health organisations do not recommend the use of ozone cleaning technologies in real-world settings, such as schools. Research and policy focus may need to shift towards other interventions that could help reduce transmission, and consequently minimise disruption to education.\n\nFunding statementThe Wales Centre for Evidence Based Care was funded for this work by the Wales Covid-19 Evidence Centre, itself funded by Health & Care Research Wales on behalf of Welsh Government.\n\nTOPLINE SUMMARYO_ST_ABSWhat is a Rapid Evidence Summary?C_ST_ABSThis Rapid Evidence Summary was completed in two weeks to inform policy- decision making. It is based on a systematic search of the literature, conducted in September 2021. Priority is given to studies representing robust evidence synthesis. No quality appraisal or evidence synthesis are conducted, and the summary should be interpreted with caution.\n\nBackground / Aim of Rapid Evidence SummarySeveral non-touch disinfectant methods including ozone, light-based technologies, and hydrogen peroxide are being considered to reduce the risk of SARS-CoV-2 virus transmission to children and young people in educational settings. Concerns have been raised about the evidence of efficacy, effectiveness and safety of these technologies in these settings. We aimed to address the following research questions: O_LIWhat is the evidence for the surface survival of SARS-CoV-2?\nC_LIO_LIWhat is the evidence for the efficacy (in vitro) and real-life effectiveness (in situ) of ozone machines, light-based technologies and hydrogen peroxide vapour as air or surface disinfectants against SARS-CoV-2?\nC_LIO_LIWhat are the potential health effects of ozone, in particular for children and young people and the benefits and harms of using ozone machines?\nC_LI\n\nKey FindingsO_ST_ABSExtent of the evidence baseC_ST_ABSA total of 82 tertiary, secondary and primary evidence sources was included\n\nRecency of the evidence baseMost studies were published 2020-21, indirect evidence was included from earlier work from 2006 onwards\n\nSummary of findingsO_LISARS-CoV-2 fragments can be found on surfaces up to seven days later in the community but there is a lack of evidence whether these are viable\nC_LIO_LIWhen accounting for both surface survival data and real-world transmission factors, the risk of surface transmission after a person with COVID-19 has been in an indoor space is minor after 72 hours, regardless of last clean\nC_LIO_LIThere is evidence from experimental settings that ozone machines, light-based technologies and hydrogen peroxide do inactivate coronaviruses, including SARS-CoV-2\nC_LIO_LIThere is a lack of evidence for the effectiveness of ozone machines, light- based technologies and hydrogen peroxide in real-world settings\nC_LIO_LIThere are uncertainties about training requirements for staff, methods for assurance of ozone removal and monitoring of occupational exposure\nC_LIO_LIThere is strong evidence of a causal relationship between short term ozone exposure and respiratory health issues; these can occur at very low concentrations of ozone; children with asthma are more at risk\nC_LIO_LIRooms using ozone machines need to be sealed off to avoid leakage of the ozone gas which is toxic at high concentrations\nC_LIO_LIOzone may react with materials in the room to form secondary pollutants (e.g. formaldehyde)\nC_LI\n\nThe best quality evidenceO_LIThe US EPA 2021 does not recommend ozone for air cleaning and the UK SAGE EMG 2020a does not recommend technologies that \"may generate undesirable secondary chemical products that could lead to health effects such as respiratory or skin irritation (medium confidence). These devices are therefore not recommended unless their safety and efficacy can be unequivocally and scientifically demonstrated by relevant test data\" (SAGE EMG 2020a).\nC_LI\n\nPolicy implicationsO_LIThere is no direct evidence for the effectiveness and safety of using ozone machines to deactivate SARS-CoV-2 in real-world educational settings for children, young people and staff\nC_LIO_LIThere is evidence for the risk of potential harm to children and young people of ozone machines from either ozone or secondary pollutants, in particular but not only, if used in uncontrolled ways in educational settings\nC_LI\n\nStrength of Evidence to dateO_LImoderate evidence for the surface survival of SARS-CoV-2\nC_LIO_LIstrong evidence of causal relationship between short term ozone exposure and respiratory health issues\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Deborah Edwards", - "author_inst": "Cardiff University" - }, - { - "author_name": "Judit Katalin Csontos", - "author_inst": "Cardiff University" - }, - { - "author_name": "Elizabeth Gillen", - "author_inst": "Cardiff University" - }, - { - "author_name": "Ruth Lewis", - "author_inst": "Bangor University" - }, - { - "author_name": "Alison Cooper", - "author_inst": "Cardiff University" - }, - { - "author_name": "Micaela Gal", - "author_inst": "Cardiff University" - }, - { - "author_name": "Rebecca-Jane Law", - "author_inst": "Welsh Government" - }, - { - "author_name": "Adrian Edwards", - "author_inst": "Cardiff University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.02.21.22271299", "rel_title": "Psychological and financial impacts of COVID-19-related travel measures: An international cross-sectional study", @@ -400776,6 +402794,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.16.22270690", + "rel_title": "Narratives of the convalescent plasma donor in a Peruvian social security hospital: motivations, fears, expectations and experiences", + "rel_date": "2022-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22270690", + "rel_abs": "ObjectivesTo know and explore from convalescent plasma donators voices the experience in the blood donation process at a Peruvian social security hospital.\n\nMethodsQualitative study with a phenomenological design. The investigation was carried out in 01 hospitals of the social security of Peru. Semi-structured interviews were carried out.\n\nResultsEleven donors of convalescent plasma were interviewed. The main motivations for donating were being able to contribute to national research and supporting patients affected by COVID-19. Fears focus on the possible risk of contagion within the hospital. Donors emphasised the attention and support of health personnel alongside the donation procedure. The main expectations and suggestions point towards greater dissemination of donation campaigns with special emphasis on safety. Likewise, an improvement in the time of the donation procedure (from enrolment to the extraction of convalescent plasma), and the implementation of friendly spaces to encourage future blood donation campaigns were highlighted.\n\nConclusionsThe experience of the convalescent plasma donors was positive. However, improvements must be made in terms of processes and infrastructure to ensure future successful blood donation campaigns.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Silvana M Matassini Eyzaguirre", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Christian Villanueva Yapa", + "author_inst": "Servicio de Medicina Transfusional, Hospital Nacional Egdardo Rebagliati, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Ausberto Chunga Chunga", + "author_inst": "Servicio de Patolog\u00eda Cl\u00ednica, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Arturo Sagastegui Soto", + "author_inst": "Servicio de Medicina Transfusional, Hospital Nacional Egdardo Rebagliati, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Ibeth Melania Neyra Vera", + "author_inst": "Servicio de Patolog\u00eda Cl\u00ednica, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Suly Soto-Ordo\u00f1ez", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Martina Guillermo Roman", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Martin Oyanguren Miranda", + "author_inst": "Servicio de Cuidados Intensivos, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Peru" + }, + { + "author_name": "Percy Soto-Becerra", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Yamilee Hurtado-Roca", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Jorge L Magui\u00f1a", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Roger Vladimir Araujo-Castillo", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.02.17.22271142", "rel_title": "Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant", @@ -401572,77 +403653,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.17.22271116", - "rel_title": "COVID-19-related Smell and Taste Impairment with Widespread Diffusion of SARS-CoV-2 Omicron Variant", - "rel_date": "2022-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271116", - "rel_abs": "BackgroundThe aim of this study was to estimate the prevalence of self-reported chemosensory dysfunction in a study cohort of subjects who developed a mild-to-moderate COVID-19 in the period from January 17, 2022 to February 4, 2022 (Omicron proxy period) and compared that with a historical series of patients tested positive for SARS-CoV-2 infection between March and April, 2020 (comparator period).\n\nMethodsProspective study based on the sinonasal outcome tool 22 (SNOT-22), item \"sense of smell or taste\" and additional outcomes.\n\nResultsPatients characteristics and clinical presentations of COVID-19 were evaluated and compared in 779 patients, 338 of the study cohort and 441 of the historical series. The prevalence of self-reported chemosensory dysfunction during the proxy Omicron period (32.5%; 95% CI, 27.6-37.8) was significantly lower from that during the comparator period (66.9%; 95% CI, 62.3-71.3) (p<.001). 24.6% (95% CI, 20.1-29.5) of patients reported an altered sense of smell during the proxy Omicron period compared to 62.6% (95% CI, 57.9-67.1) during the comparator period (p<.001). Similarly, the prevalence of an altered sense of taste dropped from 57.4% (95% CI, 52.6-62.0) during the comparator period to 26.9% (95% CI, 22.3-32.0) during the proxy Omicron period (p<.001). The severity of chemosensory dysfunction was lower in proxy Omicron period compared to comparator period (p<.001).\n\nConclusionsThe prevalence and the severity of COVID-19 associated smell and taste dysfunction has dropped significantly with the advent of the Omicron variant.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Paolo Boscolo Rizzo", - "author_inst": "University of Trieste" - }, - { - "author_name": "Giancarlo Tirelli", - "author_inst": "University of Trieste" - }, - { - "author_name": "Pierluigi Meloni", - "author_inst": "University of Sassari" - }, - { - "author_name": "Claire Hopkins", - "author_inst": "Guys and St Thomas Hospitals, London" - }, - { - "author_name": "Giordano Madeddu", - "author_inst": "University of Sassari" - }, - { - "author_name": "Andrea De Vito", - "author_inst": "University of Sassari" - }, - { - "author_name": "Nicoletta Gardenal", - "author_inst": "University of Trieste" - }, - { - "author_name": "Romina Valentinotti", - "author_inst": "University of Trieste" - }, - { - "author_name": "Margherita Tofanelli", - "author_inst": "University fo Trieste" - }, - { - "author_name": "Daniele Borsetto", - "author_inst": "Cambridge University Hospitals" - }, - { - "author_name": "Jerome R. Lechien", - "author_inst": "Elsan Hospital, Paris" - }, - { - "author_name": "Jerry Polesel", - "author_inst": "Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano" - }, - { - "author_name": "Giacomo De Riu", - "author_inst": "University of Sassari" - }, - { - "author_name": "Luigi Angelo Vaira", - "author_inst": "University of Sassari" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.17.22271057", "rel_title": "Autoantibodies linked to autoimmune diseases associate with COVID-19 outcomes", @@ -402770,6 +404780,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.16.22271096", + "rel_title": "Analytical Sensitivity of the SalivaDirect\u2122 Assay on the Liberty16 for detecting SARS-CoV-2 B.1.1.529 Omicron", + "rel_date": "2022-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271096", + "rel_abs": "The newly emerged Omicron variant of SARS-CoV-2 has numerous mutations that are not found in other variants of concern (VOCs). Despite acquiring extended functions in adapting to the host-cell environment, the viral genetic variation exerts a potential negative impact on a molecular test, which in turn, compromises public health and safety. The Liberty16 has been clinically validated as a flexible and accessible device system for running the affordable SalivaDirect real time PCR detection assay for SARS-CoV-2 especially in low resource settings. Preliminary, based on in-silico sequence analysis, we found that Omicrons mutation at position 28,311 overlaps with the CDC 2019-nCoV_N1 probe binding region. In order to verify the performance of CDC 2019-nCoV-N1 primers-probe set in detecting the Omicron variant of SARS-CoV-2, plasmids containing Wuhan/WH01/2019 (wild-type) and B.1.1.529 (Omicron) sequences were serially diluted and subsequently directed for SalivaDirect RT-qPCR detection on Liberty16 using commercially procured reagents. Our findings provide analytical support for reports that the mutations in the Omicron variant have little or no impact on SalivaDirect assay in terms of amplification efficiency and detection sensitivity using either standard and the recently reported fast Liberty16 SalivaDirect thermal cycling protocols.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yen Pei Tan", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Mila Al-Halbouni", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Ching-Huan Chen", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "David B. Hirst", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Paul J. Pickering", + "author_inst": "Ubiquitome Limited" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.16.22271093", "rel_title": "A novel SEIR-e model for disease transmission and pathogen exposure", @@ -403498,49 +405543,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.02.14.22270109", - "rel_title": "Effectiveness and safety of PRP on persistent olfactory dysfunction related to COVID-19: towards a new therapeutic hope", - "rel_date": "2022-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270109", - "rel_abs": "Olfactory dysfunction (OD) is a well know symptom of coronavirus disease 2019 (COVID-19), accounting for 48 to 85% of patients. In 1 to 10% of cases, patients develop a chronic olfactory dysfunction (COD,) lasting more than 6 months. Recently, platelet-rich plasma (PRP) was used in patients with non-COVID-19 COD and authors reported encouraging results. In the present study, we investigated the usefulness and safety of PRP injection in 56 patients with COVID-19 COD.\n\nOur results showed that PRP in the olfactory cleft can increase the olfactory threshold one month after the injection. Moreover, our results suggest that timing of treatment may be an important factor and that PRP is a safe treatment because no adverse effects were reported throughout the study", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "younes steffens", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - }, - { - "author_name": "Serge-Daniel Lebon", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - }, - { - "author_name": "Lea Prunier", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - }, - { - "author_name": "Alexandra ruiz Rodiguez", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - }, - { - "author_name": "Jerome Lechien", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - }, - { - "author_name": "Sven Saussez", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - }, - { - "author_name": "Mihaela Horoi", - "author_inst": "Department of Otorhinolaryngology, CHU Saint-Pierre, Rue aux Laines 105 1000 Brussels, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2022.02.14.22270925", "rel_title": "Modeling COVID-19 disease processes by remote elicitation of causal Bayesian networks from medical experts", @@ -404544,6 +406546,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.11.22270843", + "rel_title": "Evaluation of test-to-return after COVID-19 diagnosis in a Massachusetts public school district", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270843", + "rel_abs": "The Centers for Disease Control allows rapid antigen testing (RAT) towards the end of a 5-day isolation for COVID-19 infection to determine eligibility to leave isolation. The impact of a test-to-return (TTR) program in schools is unknown. In January 2022 a Massachusetts school district initiated a TTR program utilizing a single school-administered RAT on days 5-9 after symptom onset or positive test, whichever was first. Of 636 students with COVID-19 infection, 408 (64.2%) participated in TTR; of these, 128 (31.4%) had a positive TTR rapid antigen test. Students who were symptomatic at any time during their infection were more likely to have a positive TTR than those who were never symptomatic (43.1% vs. 17.3%); positivity rates were lower when TTR was performed later during days 6-9. TTR may identify students who carry higher viral loads after recovery from COVID-19 infection thereby extending their isolation, while facilitating earlier return of those with negative results.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sandra B. Nelson", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Isaac Ravi Brenner", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Elizabeth Homan", + "author_inst": "Arlington Public Schools" + }, + { + "author_name": "Sarah Bott Lee", + "author_inst": "Arlington Public Schools" + }, + { + "author_name": "Christine Bongiorno", + "author_inst": "Town of Arlington, Massachusetts" + }, + { + "author_name": "Nira Pollock", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Andrea L Ciaranello", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.10.22270733", "rel_title": "Differential durability of humoral and T cell immunity after two and three BNT162b2 vaccinations in adults aged >80 years", @@ -405264,89 +407309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.11.22270831", - "rel_title": "Accuracy of rapid point-of-care antigen-based diagnostics for SARS-CoV-2: an updated systematic review and meta-analysis with meta regression analyzing influencing factors", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270831", - "rel_abs": "BackgroundComprehensive information about the accuracy of antigen rapid diagnostic tests (Ag-RDTs) for SARS-CoV-2 is essential to guide public health decision makers in choosing the best tests and testing policies. In August 2021, we published a systematic review and meta-analysis about the accuracy of Ag-RDTs. We now update this work and analyze the factors influencing test sensitivity in further detail.\n\nMethods and findingsWe registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched multiple databases (PubMed, Web of Science Core Collection, medRvix, bioRvix, and FIND) for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 until August 31, 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity with reverse transcription polymerase chain reaction (RT-PCR) testing as a reference. To evaluate factors influencing test sensitivity, we performed 3 different analyses using multivariate mixed-effects meta-regression models. We included 194 studies with 221,878 Ag-RDTs performed. Overall, the pooled estimates of Ag-RDT sensitivity and specificity were 72.0% (95% confidence interval [CI] 69.8 to 74.2) and 98.9% (95% CI 98.6 to 99.1), respectively. When manufacturer instructions were followed, sensitivity increased to 76.4% (95%CI 73.8 to 78.8). Sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values (sensitivity of 97.9% [95% CI 96.9 to 98.9] and 90.6% [95% CI 88.3 to 93.0] for Ct-values <20 and <25, compared to 54.4% [95% CI 47.3 to 61.5] and 18.7% [95% CI 13.9 to 23.4] for Ct-values [≥]25 and [≥]30) and was estimated to increase by 2.9 percentage points (95% CI 1.7 to 4.0) for every unit decrease in mean Ct-value when adjusting for testing procedure and patients symptom status. Concordantly, we found the mean Ct-value to be lower for true positive (22.2 [95% CI 21.5 to 22.8]) compared to false negative (30.4 [95% CI 29.7 to 31.1]) results. Testing in the first week from symptom onset resulted in substantially higher sensitivity (81.9% [95% CI 77.7 to 85.5]) compared to testing after 1 week (51.8%, 95% CI 41.5 to 61.9). Similarly, sensitivity was higher in symptomatic (76.2% [95% CI 73.3 to 78.9]) compared to asymptomatic (56.8% [95% CI 50.9 to 62.4]) persons. However, both effects were mainly driven by the Ct-value of the sample. With regards to sample type, highest sensitivity was found for nasopharyngeal (NP) and combined NP/oropharyngeal samples (70.8% [95% CI 68.3 to 73.2]), as well as in anterior nasal/mid-turbinate samples (77.3% [95% CI 73.0 to 81.0]).\n\nConclusionAg-RDTs detect most of the individuals infected with SARS-CoV-2, and almost all when high viral loads are present (>90%). With viral load, as estimated by Ct-value, being the most influential factor on their sensitivity, they are especially useful to detect persons with high viral load who are most likely to transmit the virus. To further quantify the effects of other factors influencing test sensitivity, standardization of clinical accuracy studies and access to patient level Ct-values and duration of symptoms are needed.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lukas E. Bruemmer", - "author_inst": "Heidelberg University Hospital" - }, - { - "author_name": "Stephan Katzenschlager", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Sean McGrath", - "author_inst": "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Stephani Schmitz", - "author_inst": "Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands" - }, - { - "author_name": "Mary Gaeddert", - "author_inst": "Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Christian Erdmann", - "author_inst": "FH Muenster University of Applied Sciences, Muenster, Germany" - }, - { - "author_name": "Marc Bota", - "author_inst": "Agaplesion Bethesda Hospital, Hamburg, Germany" - }, - { - "author_name": "Maurizio Grilli", - "author_inst": "Library, University Medical Center Mannheim, Mannheim, Germany" - }, - { - "author_name": "Jan Larmann", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Markus A. Weigand", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Nira R. Pollock", - "author_inst": "Department of Laboratory Medicine, Boston Childrens Hospital, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Aurelien Mace", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Berra Erkosar", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Sergio Carmona", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Jilian A. Sacks", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Stefano Ongarello", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.08.22270635", "rel_title": "Surveillance of Myopericarditis following COVID-19 Booster Dose Vaccination in a Large Integrated Health System", @@ -406822,6 +408784,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.14.22270958", + "rel_title": "COVID-19 mortality and excess mortality among working-age Californians, by occupational sector: March 2020 through November 2021", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270958", + "rel_abs": "BackgroundDuring the first year of the pandemic, essential workers faced higher rates of SARS-CoV-2 infection and COVID-19 mortality than non-essential workers. It is unknown whether disparities in pandemic-related mortality across occupational sectors have continued to occur, amidst SARS-CoV-2 variants and vaccine availability.\n\nMethodsWe obtained data on all deaths occurring in the state of California from 2016 through 2021. We restricted our analysis to California residents who were working age (18-65 years at time of death) and died of natural causes. Occupational sector was classified into 9 essential sectors; non-essential; or not in the labor market. We calculated the number of COVID-19 deaths in total and per capita that occurred in each occupational sector. Separately, using autoregressive integrated moving average models, we estimated total, per-capita, and relative excess natural-cause mortality by week between March 1, 2020, and November 30, 2021, stratifying by occupational sector. We additionally stratified analyses of occupational risk into regions with high versus low vaccine uptake, categorizing high-uptake regions as counties where at least 50% of the population completed a vaccination series by August 1, 2021.\n\nFindingsFrom March 2020 through November 2021, essential work was associated with higher COVID-19 and excess mortality compared with non-essential work, with the highest per-capita COVID-19 mortality in agriculture (131.8 per 100,000), transportation/logistics (107.1), manufacturing (103.3), and facilities (101.1). Essential workers continued to face higher COVID-19 and excess mortality during the period of widely available vaccines (March through November 2021). Between July and November 2021, emergency workers experienced higher per-capita COVID-19 mortality (113.7) than workers from any other sector. Essential workers faced the highest COVID-19 mortality in counties with low vaccination rates, a difference that was more pronounced during the period of the Delta surge in Summer 2021.\n\nInterpretationEssential workers have continued to bear the brunt of high COVID-19 and excess mortality throughout the pandemic, particularly in the agriculture, emergency, manufacturing, facilities, and transportation/logistics sectors. This high death toll has continued during periods of vaccine availability and the delta surge. In an ongoing pandemic without widespread vaccine coverage and anticipated threats of new variants, the US must actively adopt policies to more adequately protect essential workers.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yea-Hung Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia R Riley", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "Kate A Duchowny", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Helene E Aschmann", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ruijia Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mathew V Kiang", + "author_inst": "Stanford University" + }, + { + "author_name": "Alyssa Mooney", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrew C Stokes", + "author_inst": "Boston University" + }, + { + "author_name": "M Maria Glymour", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.02.11.22270859", "rel_title": "Clinical and economic benefits of lenzilumab plus standard of care compared with standard of care alone for the treatment of hospitalized patients with Coronavirus Disease 19 (COVID-19) from the perspective of National Health Service England", @@ -407522,101 +409539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.02.15.22270948", - "rel_title": "Fourth Dose COVID mRNA Vaccines' Immunogenicity & Efficacy Against Omicron VOC", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.15.22270948", - "rel_abs": "BACKGROUNDFollowing the emergence of the Omicron variant of concern, we investigated immunogenicity, efficacy and safety of BNT162b2 or mRNA1273 fourth dose in an open-label, clinical intervention trial.\n\nMETHODSPrimary end-points were safety and immunogenicity and secondary end-points were vaccine efficacy in preventing SARS-CoV-2 infections and COVID-19 symptomatic disease. The two intervention arms were compared to a matched control group. Eligible participants were healthcare-workers (HCW) vaccinated with three BNT162b2 doses, and whose IgG antibody levels were [≤]700 BAU (40-percentile). IgG and neutralizing titers, direct neutralization of live VOCs, and T-cell activation were assessed. All participants were actively screened for SARS-CoV-2 infections on a weekly basis.\n\nRESULTSOf 1050 eligible HCW, 154 and 120 were enrolled to receive BNT162b2 and mRNA1273, respectively, and compared to 426 age-matched controls. Recipients of both vaccine types had a [~]9-10-fold increase in IgG and neutralizing titers within 2 weeks of vaccination and an 8-fold increase in live Omicron VOC neutralization, restoring titers to those measured after the third vaccine dose. Breakthrough infections were common, mostly very mild, yet, with high viral loads. Vaccine efficacy against infection was 30% (95%CI:-9% to 55%) and 11% (95%CI:-43% to +43%) for BNT162b2 and mRNA1273, respectively. Local and systemic adverse reactions were reported in 80% and 40%, respectively.\n\nCONCLUSIONSThe fourth COVID-19 mRNA dose restores antibody titers to peak post-third dose titers. Low efficacy in preventing mild or asymptomatic Omicron infections and the infectious potential of breakthrough cases raise the urgency of next generation vaccine development.\n\nTrial registration numberclicaltrials.gov: NCT05231005, NCT05230953", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Gili Regev-Yochay", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Tal Gonen", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Mayan Gilboa", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, MOH, Sheba Medical Center" - }, - { - "author_name": "Victoria Indenbaum", - "author_inst": "Central Virology Laboratory, MOH, Sheba Medical Center" - }, - { - "author_name": "Sharon Amit", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Lilac Meltzer", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Keren Asraf", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Carmit Cohen", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ronen Fluss", - "author_inst": "Gertner Institute, Sheba Medical Center" - }, - { - "author_name": "Asaf Biber", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ital Nemet", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Limor Kliker", - "author_inst": "Central Virology Laboratory, MOH, Sheba Medical Center" - }, - { - "author_name": "Gili Joseph", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ram Doolman", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central Virology Laboratory, MOH, Sheba Medical Center" - }, - { - "author_name": "Laurence S Freedman", - "author_inst": "Gertner Institute, Sheba Medical Center" - }, - { - "author_name": "Dror Harats", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Yitshak Kreiss", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Yaniv Lustig", - "author_inst": "Central Virology Laboratory, MOH, Sheba Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.14.22270930", "rel_title": "Determinants of antibody responses to two doses of ChAdOx1 nCoV-19 or BNT162b2 and a subsequent booster dose of BNT162b2 or mRNA-1273: population-based cohort study (COVIDENCE UK)", @@ -408744,6 +410666,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.10.22270744", + "rel_title": "Coronavirus Disease 2019 (COVID-19) Vaccine Boosting in Persons Already Protected by Natural or Vaccine-Induced Immunity", + "rel_date": "2022-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270744", + "rel_abs": "BackgroundThe purpose of this study was to evaluate whether boosting healthcare personnel, already reasonably protected by prior infection or vaccination, with a vaccine developed for an earlier variant of COVID-19 protects against the Omicron variant.\n\nMethodsEmployees of Cleveland Clinic who were previously infected with or vaccinated against COVID-19, and were working in Ohio the day the Omicron variant was declared a variant of concern, were included. The cumulative incidence of COVID-19 was examined over two months during an Omicron variant surge. Protection provided by boosting (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression. Analyses were adjusted for time since proximate overt immunologic challenge (POIC) as a time-dependent covariate.\n\nResultsAmong 39 766 employees, 8037 (20%) previously infected and the remaining previously vaccinated, COVID-19 occurred in 6230 (16%) during the study. Risk of COVID-19 increased with time since POIC. In multivariable analysis, boosting was independently associated with lower risk of COVID-19 among those with vaccine-induced immunity (HR, .43; 95% CI, .41-.46) as well as those with natural immunity (HR, .66; 95% CI, .58-.76). Among those with natural immunity, receiving 2 compared to 1 dose of vaccine was associated with higher risk of COVID-19 (HR, 1.54; 95% CI, 1.21-1.97).\n\nConclusionsAdministering a COVID-19 vaccine not designed for the Omicron variant, 6 months or more after prior infection or vaccination, protects against Omicron variant infection in both previously infected and previously vaccinated individuals. There is no evidence of an advantage to administering more than 1 dose of vaccine to previously infected persons.\n\nSummaryAmong 39 766 Cleveland Clinic employees already protected by prior infection or vaccination, vaccine boosting after 6 months was associated with significantly lower risk of COVID-19. After COVID-19 infection, there was no advantage to more than one dose of vaccine.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nabin K Shrestha", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Priyanka Shrestha", + "author_inst": "Stanford University" + }, + { + "author_name": "Patrick C Burke", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Amy S Nowacki", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Paul Terpeluk", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Steven M Gordon", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.11.22270667", "rel_title": "Correlation between post-vaccination titres of combined IgG, IgA, and IgM anti-Spike antibodies and protection against breakthrough SARS-CoV-2 infection: a population-based longitudinal study (COVIDENCE UK)", @@ -409532,57 +411493,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.12.22270883", - "rel_title": "Multiple sclerosis disease-modifying therapies and COVID-19 vaccines: A practical review and meta-analysis", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.12.22270883", - "rel_abs": "ImportanceAn evidence-based appraisal of the COVID-19 vaccination policies among people with multiple sclerosis (pwMS) with respect to disease-modifying therapies (DMT) is important for our understandings and their further management.\n\nObjectiveTo synthesize the available evidence concerning the effect of DMTs on COVID-19 vaccination immunogenicity and effectiveness.\n\nData SourcesWe searched MEDLINE, Scopus, Web of Science, MedRxiv, and Google Scholar from January 2021 until January 2022.\n\nStudy SelectionThe exclusion criteria included: not a primary investigation; retracted/withdrawn; no eligible participants - people with no history/evidence of previous COVID-19 and corticosteroid administration within two months of vaccination; no eligible exposures - all nine DMT classes; and no eligible comparators - DMT-unexposed at the time of vaccination.\n\nData Extraction and SynthesisEntries were assessed independently by two reviewers for eligibility and quality. Dichotomized data was extracted by two reviewers in accordance with Cochrane guidelines, and were pooled using either Peto fixed-effects or Inverse-variance random-effects methods.\n\nMain Outcomes and MeasuresMain outcomes were i) B-cell response, measured by seroconversion odds ratio (OR); ii) T-cell response, measured by interferon-gamma release response OR, and CD4+/CD8+ activation-induced marker+ OR. Further outcomes including immunity waning speed and breakthrough COVID-19 incidence/severity were synthesized narratively.\n\nResultsData from 28 studies (5,025 pwMS and 1,635 healthy participants) after COVID-19 vaccination suggests mildly-lower B-cell responses in teriflunomide- and alemtuzumab-treated, extensively-lower B-cell responses in sphingosine-1-phosphate receptor modulator (S1PRM)- and anti-CD20 (aCD20)-treated, and lower T-cell responses in interferon-, S1PRM-, alemtuzumab- and cladribine-treated pwMS. Every ten-week increase in aCD20-to-vaccine period is associated with a 1.94-time (95%CI: 1.57, 2.41, P<0.00001) increase in odds of seroconversion. B-cell-depleting therapies seem to accelerate post-vaccination humoral waning, and booster immunogenicity is predictable with the same factors affecting the priming vaccination. Furthermore, comparatively-increased breakthrough COVID-19 incidence and severity is being observed only among S1PRM- and anti-CD20-treated pwMS - i.e., among the pwMS with extensively-blunted B-cell response, despite adequate T-cell responses in the aCD20-treated. To date, pwMS on only-T-cell-blunting DMTs have not shown increased susceptibility to breakthrough COVID-19.\n\nConclusion and RelevanceThe implemented vaccination strategy to date has been effective for pwMS on all DMTs other than S1PRM and aCD20. As B-cell immunity seems to be a more important predictor of vaccine effectiveness than T-cell immunity, optimization of humoral immunogenicity and ensuring its durability among pwMS on DMTs are the necessities of an effective COVID-19 vaccination policy.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Masoud Etemadifar", - "author_inst": "Isfahan Multiple Sclerosis Center" - }, - { - "author_name": "Hosein Nouri", - "author_inst": "Universal Scientific Education and Research Network (USERN)" - }, - { - "author_name": "Maristella Pitzalis", - "author_inst": "National Research Council" - }, - { - "author_name": "Maria Laura Idda", - "author_inst": "National Research Council" - }, - { - "author_name": "Mehri Salari", - "author_inst": "Shahid Beheshti University of Medical Sciences" - }, - { - "author_name": "Mahshid Baratian", - "author_inst": "Islamic Azad University of Najafabad" - }, - { - "author_name": "Sepide Mahdavi", - "author_inst": "Islamic Azad University of Najafabad" - }, - { - "author_name": "Amir Parsa Abhari", - "author_inst": "Universal Scientific Education and Research Network (USERN)" - }, - { - "author_name": "Nahad Sedaghat", - "author_inst": "Universal Scientific Education and Research Network (USERN)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.02.10.22270805", "rel_title": "Adequacy of serial self-performed SARS-CoV-2 rapid antigen-detection testing for longitudinal mass screening in the workplace", @@ -410557,6 +412467,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.09.22270747", + "rel_title": "Immune responses after twofold SARS-CoV-2 immunisation in elderly residents and Health Care Workers in nursing homes and homes with assisted living support - Proposal for a correlate of protection", + "rel_date": "2022-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270747", + "rel_abs": "In the present study, we were interested in the decline over time of anti SARS-CoV-2 antibodies and SARS-CoV-2 specific T-cell responses after two doses of mRNA vaccines in total and by age group and comorbidity. The second goal was to suggest an immunological correlate for protection on an individual basis and to describe the probability of protection over time after second vaccination.\n\nWe analysed blood samples from 228 residents (median age 83.8 years) and from 273 Health Care Workers (HCW; median age 49.7 years) of five nursing homes and one home for the elderly with assisted living support. Participants had received two vaccinations. The blood samples were analysed for SARS-CoV-2 specific antibody and T-cell responses. We compared outcomes in the HCW and residents in the respective institutions. No breakthrough infections occurred during the study period. The initial immune responses in the younger participants were about 30 % higher than in the older ones. Over time, all parameters dropped continuously in all groups within the maximum observation period of 232 days. Comorbidities such as coronary heart disease or diabetes mellitus reduced the initial immune responses, regardless of age. In contrast to an almost linear decline in antibody levels, we observed that the interferon-gamma response remained at a constant level between about day 120 and 180, only to decline further thereafter.\n\nBased on our data, we propose on an individual level a correlate of protection: Persons who have a neutralizing capacity of 75 % (which would correspond to approx. 200 BAU/ml) and an interferon-gamma response above 200 mIU/ml should be considered to be protected resp. sufficiently immunized.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Julia Schiffner", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Nora Eisemann", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Germany" + }, + { + "author_name": "Hannah Baltus", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Germany" + }, + { + "author_name": "Sina Jensen", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Katharina Wunderlich", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Stefan Schuesseler", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Charlotte Eicker", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Bianca Teegen", + "author_inst": "Klinisch-Immunologisches Labor Stoecker, Luebeck, Germany" + }, + { + "author_name": "Doreen Boniakowsky", + "author_inst": "Vorwerker Diakonie gemeinnuetzige GmbH, Luebeck, Germany" + }, + { + "author_name": "Werner Solbach", + "author_inst": "Center for Infection and Inflammation Research, University of Luebeck, Luebeck, Germany, German Center for Infection Research (DZIF), Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.10.22270783", "rel_title": "Implementation and economic effects of local non-pharmaceutical interventions", @@ -411305,93 +413274,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.09.479840", - "rel_title": "Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants", - "rel_date": "2022-02-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479840", - "rel_abs": "Genetic variation of SARS-CoV-2 has resulted in the emergence and rapid spread of multiple variants throughout the pandemic, of which Omicron is currently the predominant variant circulating worldwide. SARS-CoV-2 variants of concern or interest (VOC/VOI) have evidence of increased viral transmission, disease severity, or decreased effectiveness of vaccines and neutralizing antibodies. Remdesivir (RDV, VEKLURY(R)) is a nucleoside analog prodrug and the first FDA-approved antiviral treatment of COVID-19. Here we present a comprehensive antiviral activity assessment of RDV and its parent nucleoside, GS-441524, against 10 current and former SARS-CoV-2 VOC/VOI clinical isolates by nucleoprotein ELISA and plaque reduction assay.\n\nDelta and Omicron variants remained susceptible to RDV and GS-441524, with EC50 values 0.31 to 0.62-fold of those observed against the ancestral WA1 isolate. All other tested variants exhibited EC50 values ranging from 0.15 to 2.3-fold of the observed EC50 values against WA1. Analysis of nearly 6 million publicly available variant isolate sequences confirmed that Nsp12, the RNA-dependent RNA polymerase (RdRp) target of RDV and GS-441524, is highly conserved across variants with only 2 prevalent changes (P323L and G671S). Using recombinant viruses, both RDV and GS-441524 retained potency against all viruses containing frequent variant substitutions or their combination. Taken together, these results highlight the conserved nature of SARS-CoV-2 Nsp12 and provide evidence of sustained SARS-CoV-2 antiviral activity of RDV and GS-441524 across the tested variants. The observed pan-variant activity of RDV supports its continued use for the treatment of COVID-19 regardless of the SARS-CoV-2 variant.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jared Pitts", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Jiani Li", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Jason Perry", - "author_inst": "Gilead Sciences" - }, - { - "author_name": "Venice Du Pont", - "author_inst": "Gilead Sciences" - }, - { - "author_name": "Nicholas Riola", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Lauren Rodriguez", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Xianghan Lu", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Chaitanya Kurhade", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Gregory Camus", - "author_inst": "Gilead Sciences" - }, - { - "author_name": "Savrina Manhas", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Ross Martin", - "author_inst": "Gilead Sciences" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "UTMB" - }, - { - "author_name": "Tomas Cihlar", - "author_inst": "Gilead Sciences, Inc" - }, - { - "author_name": "Danielle Poulin Porter", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Hongmei Mo", - "author_inst": "Gilead Sciences" - }, - { - "author_name": "Evguenia S Maiorova", - "author_inst": "Gilead Sciences" - }, - { - "author_name": "John P Bilello", - "author_inst": "Gilead Sciences, Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.10.479924", "rel_title": "SARS-CoV-2 Nsp1 N-terminal and linker regions as a platform for host translational shutoff", @@ -412423,6 +414305,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.07.479477", + "rel_title": "The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature", + "rel_date": "2022-02-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479477", + "rel_abs": "The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Galen J Correy", + "author_inst": "Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Daniel W Kneller", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Gwyndalyn Phillips", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Swati Pant", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Silvia Russi", + "author_inst": "Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA" + }, + { + "author_name": "Aina E Cohen", + "author_inst": "Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA" + }, + { + "author_name": "George Meigs", + "author_inst": "Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "James M Holton", + "author_inst": "Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "Stefan Gahbauer", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Michael C Thompson", + "author_inst": "Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA" + }, + { + "author_name": "Alan Ashworth", + "author_inst": "Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA" + }, + { + "author_name": "Leighton Coates", + "author_inst": "Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Andrey Kovalevsky", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Flora Meilleur", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "James S Fraser", + "author_inst": "Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.02.07.479471", "rel_title": "The mechanism of RNA capping by SARS-CoV-2", @@ -413159,173 +415116,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.08.22270658", - "rel_title": "Safety and immunogenicity of inactivated whole virion vaccine CoviVac against COVID-19: a multicenter, randomized, double-blind, placebo-controlled phase I/II clinical trial", - "rel_date": "2022-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.08.22270658", - "rel_abs": "We present the results of a randomized, double-blind, placebo-controlled, multi-center clinical trial of the tolerability, safety, and immunogenicity of the inactivated whole virion concentrated purified coronavirus vaccine CoviVac in adult volunteers aged 18-60.\n\nSafety of the vaccine was assessed in 398 volunteers who received two doses of the vaccine (n=298) or placebo (n=100). The studied vaccine has shown good tolerability and safety. No deaths, serious adverse events (AE), or other significant AE related to vaccination have been detected. The most common AE in vaccinated participants was pain at the injection site (p<0.05).\n\nImmunogenicity assessment was performed in 167 volunteers (122 vaccinated and 45 in Placebo Group) separately for the participants who were anti-SARS-CoV-2 nAB negative (69/122 in Vaccine Group and 28/45 in Placebo Group) or positive (53/122 in Vaccine Group and 17/45 in Placebo Group) at screening.\n\nAt Day 42 after the first immunization the seroconversion rate in participants who were seronegative at screening was 86.9% with average the geometric mean neutralizing antibody (nAB) titer of 1:20. Statistically significant (p<0.05) increase of IFN-{gamma} production by peptide-stimulated T-cells was observed at Days 14 and 21 after the first immunization.\n\nIn participants who were seropositive at screening but had nAB titers below 1:256 the rate of 4-fold increase in nAB levels was 85.2%, while in the participants with nAB titers >1:256 the rate of 4-fold increase in nAB levels was below 45%. For the participants who were seropositive at screening the second immunization did not lead to a significant increase in nAB titers.\n\nIn conclusion, inactivated vaccine CoviVac has shown good tolerability and safety, with 86.9% seroconversion rates in participants, who were seronegative at screening. In participants who were seropositive at screening and had nAB titers below 1:256, a single immunization lead to a 4-fold increase in nAB levels in 85.2% cases.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Aydar A Ishmukhametov", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; Institu" - }, - { - "author_name": "Aleksandra A Siniugina", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Nadezhda V Yagovkina", - "author_inst": "Kirov State Medical University of the Ministry of Health of Russia, Kirov, Russia" - }, - { - "author_name": "Vladimir I Kuzubov", - "author_inst": "Healthcare Unit No. 163 of Federal Medical Biological Agency of Russia, 630559, Novosibirsk region, Russia" - }, - { - "author_name": "Konstantin A Zakharov", - "author_inst": "Eco-Safety Scientific Research Center, 196143, Saint-Petersburg, Russia" - }, - { - "author_name": "Viktor P Volok", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; Lomonos" - }, - { - "author_name": "Maria S Dodina", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Larissa V Gmyl", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Natalya A Korotina", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Rostislav D Theodorovich", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Yulia I Ulitina", - "author_inst": "RIC-Pharma, Moscow, Russia" - }, - { - "author_name": "Andrey A Tsaan", - "author_inst": "RIC-Pharma, Moscow, Russia" - }, - { - "author_name": "Tatiana V Pomaskina", - "author_inst": "Biopolis-Kirov 200, branch of the Chumakov Center for Research and Development of Immune-and-Biological Products, Kirov, Russia" - }, - { - "author_name": "Anna V Kalenskaya", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia" - }, - { - "author_name": "Irina V Solovjeva", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia" - }, - { - "author_name": "Elena V Tivanova", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia" - }, - { - "author_name": "Larissa Y Kondrasheva", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia" - }, - { - "author_name": "Antonina A Ploskireva", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia" - }, - { - "author_name": "Vasiliy G Akimkin", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 111123, Moscow, Russia" - }, - { - "author_name": "Ksenia A Subbotina", - "author_inst": "Perm State Medical University Ministry of Health of Russian Federation, Perm, Russia" - }, - { - "author_name": "Georgy M Ignatyev", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Anastasia K Korduban", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Elena Y Shustova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Ekaterina O Bayurova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Alla S Kondrashova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Darya V Avdoshina", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Anastasia N Piniaeva", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Anastasia A Kovpak", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Liliya P Antonova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Yulia V Rogova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Anna A Shishova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; Institu" - }, - { - "author_name": "Yury Y Ivin", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Svetlana E Sotskova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Konstantin A Chernov", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Elena G Ipatova", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Ekaterina A Korduban", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia" - }, - { - "author_name": "Liubov I Kozlovskaya", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; Institu" - }, - { - "author_name": "Ilya V Gordeychuk", - "author_inst": "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; Institu" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.09.22270633", "rel_title": "Increasing viral transmission paradoxically reduces progression rates to severe COVID-19 during endemic transition", @@ -414501,6 +416291,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.02.07.22270555", + "rel_title": "Clinical outcomes in hospitalized vaccine-breakthrough COVID-19 cases compared with contemporary unvaccinated hospitalized adults", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270555", + "rel_abs": "SummaryThe inactivated SARS-CoV-2 vaccine (CoronaVac(R)) has been the principal vaccine used in Chiles pre-booster immunization campaign. We compared major outcomes in 260 hospitalized vaccinated vs 507 unvaccinated adults with COVID-19 (mid-2021). The vaccinated group was much older, required less critical care, had lower hospital mortality (adjusted by age), and had shorter hospitalization than the unvaccinated. Benefits were most pronounced in those older than 59 years\n\nObjectiveTo compare major outcomes in fully vaccinated and unvaccinated adult persons hospitalized for COVID-19 in a general private hospital in Santiago, Chile during mid2021.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marcelo J Wolff Sr.", + "author_inst": "Clinica Santa Maria; U. of Chile School of Medicine;" + }, + { + "author_name": "Margarita Gilabert", + "author_inst": "Clinica Santa Maria, Santiago, Chile" + }, + { + "author_name": "Rodrigo Hernandez", + "author_inst": "Clinica Santa maria, Santiago, Chile" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.07.22270613", "rel_title": "Time to reinfection and vaccine breakthrough SARS-CoV-2 infections: a retrospective cohort study", @@ -415393,81 +417210,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.07.22270451", - "rel_title": "Anti-spike antibody trajectories in individuals previously immunised with BNT162b2 or ChAdOx1 following a BNT162b2 booster dose", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270451", - "rel_abs": "The two most commonly-used SARS-CoV-2 vaccines in the UK, BNT162b2 (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca), employ different immunogenic mechanisms. Compared to BNT162b2, two-dose immunisation with ChAdOx1 induces substantially lower peak anti-spike antibody (anti-S) levels and is associated with a higher risk of breakthrough infections. To provide preliminary indication of how a third booster BNT162b2 dose impacts anti-S levels, we performed a cross-sectional analysis using capillary blood samples from vaccinated adults (aged [≥]18 years) participating in Virus Watch, a prospective community cohort study in England and Wales. Blood samples were analysed using Roche Elecsys Anti-SARS-CoV-2 S immunoassay. We analysed anti-S levels by week since the third dose for vaccines administered on or after September 1, 2021 and stratified the results by second dose vaccine type (ChAdOx1 or BNT162b2), age, sex and clinical vulnerability. Anti-S levels peaked at two weeks post-booster for BNT162b2 (22,185 U/mL; 95%CI: 21,406-22,990) and ChAdOx1 second dose recipients (19,203 U/mL; 95%CI: 18,094-20,377). These were higher than the corresponding peak antibody levels post-second dose for BNT162b2 (12,386 U/mL; 95%CI: 9,801-15,653, week 2) and ChAdOx1 (1,192 U/mL; 95%CI: 818-1735, week 3). No differences emerged by second dose vaccine type, age, sex or clinical vulnerability. Anti-S levels declined post-booster for BNT162b2 (half-life=44 days) and ChAdOx1 second dose recipients (half-life=40 days). These rates of decline were steeper than those post-second dose for BNT162b2 (half-life=54 days) and ChAdOx1 (half-life=80 days). Our findings suggest that peak anti-S levels are higher post-booster than post-second dose, but that levels are projected to be similar after six months for BNT162b2 recipients. Higher peak anti-S levels post-booster may partially explain the increased effectiveness of booster vaccination compared to two-dose vaccination against symptomatic infection with the Omicron variant. Faster waning trajectories post third-dose may have implications for the timing of future booster campaigns or four-dose vaccination regimens for the clinically vulnerable.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Alexei Yavlinsky", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Sarah Beale", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" - }, - { - "author_name": "Vincent Nguyen", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Thomas Edward Byrne", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Cyril Geismar", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Susan J Hoskins", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Annalan Mathew Dwight Navaratnam", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Isobel Braithwaite", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Parth Patel", - "author_inst": "Institute of Health Informatics, University College London, UK" - }, - { - "author_name": "Jana Kovar", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" - }, - { - "author_name": "Andrew C Hayward", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "Institute of Health Informatics, University College London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.08.479543", "rel_title": "Spike Protein-independent Attenuation of SARS-CoV-2 Omicron Variant in Laboratory Mice", @@ -416503,6 +418245,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.06.479332", + "rel_title": "A potent SARS-CoV-2 neutralizing antibody recognizing a conserved epitope with broad mutant variant and SARS-CoV activity.", + "rel_date": "2022-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.06.479332", + "rel_abs": "COVID-19 is the deadliest respiratory virus pandemic since 1918 and the latest of several coronavirus epidemics and pandemics in recent years. Despite the unprecedented response by both the government and private sectors to develop vaccines and therapies, the evolution of SARS-CoV-2 variants resistant to these interventions reveals a crucial need for therapeutics that maintain their efficacy against current and future mutant variants. Here we describe a SARS-CoV-2 neutralizing antibody, ABP-310, with potent activity against all variants tested including the Omicron variant. ABP-310 also displays potent neutralizing activity against SARS-CoV, highlighting the conserved nature of the ABP-310 epitope. By targeting a conserved epitope, we believe that ABP-310 has therapeutic promise not only against the current SARS-CoV-2 variants but would be expected to maintain efficacy against future variants and possibly even novel coronaviruses.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Adam J Pelzek", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Sanam Ebtehaj", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "James Lulo", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Lucy Zhang", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Olivia Balduf", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Lindsay Dolan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Chaohua Zhang", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Shengqin Wan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Gang An", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Awo Kankam", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Eugene Chan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Shaun P Murphy", + "author_inst": "Abpro Corporation" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.06.479285", "rel_title": "Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques", @@ -417519,81 +419324,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.05.22270436", - "rel_title": "Molecular epidemiology of AY.28 and AY.104 delta sub-lineages in Sri Lanka", - "rel_date": "2022-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270436", - "rel_abs": "BackgroundThe worst SARS-CoV-2 outbreak in Sri Lanka was due to the two Sri Lankan delta sub-lineages AY.28 and AY.104. We proceeded to further characterize the mutations and clinical disease severity of these two sub-lineages.\n\nMethods705 delta SARS-CoV-2 genomes sequenced by our laboratory from mid-May to November 2021 using Illumina and Oxford Nanopore were included in the analysis. The clinical disease severity of 440/705 individuals were further analyzed to determine if infection with either AY.28 or AY.104 was associated with more severe disease. Sub-genomic RNA (sg-RNA) expression was analyzed using periscope.\n\nResultsAY.28 was the dominant variant throughout the outbreak, accounting for 67.7% of infections during the peak of the outbreak. AY.28 had three lineage defining mutations in the spike protein: A222V (92.80%), A701S (88.06%), and A1078S (92.04%) and seven in the ORF1a: R24C, K634N, P1640L, A2994V, A3209V, V3718A, and T3750I. AY.104 was characterized by the high prevalence of T95I (90.81%) and T572L (65.01%) mutations in the spike protein and by the absence of P1640L (94.28%) in ORF1a with the presence of A1918V (98.58%) mutation. The mean sgRNA expression levels of ORF6 in AY.28 were significantly higher compared to AY.104 (p < 0.0001) and B.1.617.2 (p < 0.01). Also, ORF3a showed significantly higher sgRNA expression in AY.28 compared to AY.104 (p < 0.0001). There was no difference in the clinical disease severity or duration of hospitalization in individuals infected with these sub lineages.\n\nConclusionsTherefore, AY.28 appears to have a fitness advantage over the parental delta variant (B.1.617.2) and AY.104 possibly due to the A222V mutation. AY.28 also had a higher expression of sg-RNA compared to other sub-lineages. The clinical implications of these should be further investigated.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Diyanath Ranasinghe", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Deshni Jayathilaka", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Chandima Jeewandara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Dumni Gunasinghe", - "author_inst": "University of Sri Jayewardenepura Faculty of Medical Sciences" - }, - { - "author_name": "Dinuka Ariyaratne", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Tibutius Jayadasa", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Heshan Kuruppu", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Ayesha Wijesinghe", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Farah Bary", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Deshan Madushanka", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Pradeep Pushpakumara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Dinuka Guruge", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka." - }, - { - "author_name": "Ruwan Wijayamuni", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Graham Ogg", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gathsaurie Neelika Malavige", - "author_inst": "University of Sri Jayewardenepura" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.05.22270481", "rel_title": "Limitations of molecular and antigen test performance for SARS-CoV-2 in symptomatic and asymptomatic COVID-19 contacts", @@ -419081,6 +420811,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.04.22270433", + "rel_title": "The usefulness of D-dimer as a predictive marker for mortality in patients with COVID-19 hospitalized during the first wave in Italy.", + "rel_date": "2022-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270433", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) presents an urgent threat to global health. Identification of predictors of poor outcomes will assist medical staff in treatment and allocating limited healthcare resources.\n\nAimsThe primary aim was to study the value of D-dimer as a predictive marker for in-hospital mortality.\n\nMethodsThis was a cohort study. The study population consisted of hospitalized patients (age >18 years), who were diagnosed with COVID-19 based on real-time PCR at 9 hospitals during the first COVID-19 wave in Lombardy, Italy (Feb-May 2020). The primary endpoint was in-hospital mortality. Information was obtained from patient records. Statistical analyses were performed using a Fine-Gray competing risk survival model. Model discrimination was assessed using Harrells C-index and model calibration was assessed using a calibration plot.\n\nResultsOut of 1049 patients, 501 patients had evaluable data. Of these 501 patients, 96 died. The cumulative incidence of in-hospital mortality within 30 days was 20% (95CI: 16%-23%), and the majority of deaths occurred within the first 10 days. A prediction model containing D-dimer as the only predictor had a C-index of 0.66 (95%CI: 0.61-0.71). Overall calibration of the model was very poor. The addition of D-dimer to a model containing age, sex and co-morbidities as predictors did not lead to any meaningful improvement in either the C-index or the calibration plot.\n\nConclusionThe predictive value of D-dimer alone was moderate, and the addition of D-dimer to a simple model containing basic clinical characteristics did not lead to any improvement in model performance.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shermarke Hassan", + "author_inst": "University of Milan" + }, + { + "author_name": "Barbara Ferrari", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Raffaella Rossio", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Vincenzo la Mura", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Andrea Artoni", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Roberta Gualtierotti", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Ida Martinelli", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Alessandro Nobili", + "author_inst": "Mario Negri Institute for Pharmacological Research Branch of Milan: Istituto di Ricerche Farmacologiche Mario Negri" + }, + { + "author_name": "Alessandra Bandera", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Andrea Gori", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Francesco Blasi", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Valter Monzani", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Giorgio Costantino", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Sergio Harari", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Frits Richard Rosendaal", + "author_inst": "Leiden Universitair Medisch Centrum: Leids Universitair Medisch Centrum" + }, + { + "author_name": "Flora Peyvandi", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "the COVID-19 Network working group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.05.22270499", "rel_title": "Comparative study of immunogenicity and safety of Gam-COVID-Vac and Sinopharm BBIBP-CorV vaccines in Belarus", @@ -419781,93 +421594,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.02.22269960", - "rel_title": "A large outbreak of COVID-19 in a UK prison, October 2020 to April 2021", - "rel_date": "2022-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22269960", - "rel_abs": "IntroductionPrisons are susceptible to outbreaks. Control measures focusing on isolation and cohorting negatively affect wellbeing. We present an outbreak of COVID-19 in a large male prison in Wales, UK, October 2020 to April 2021, and discuss control measures.\n\nMethodsWe gathered case-information, including demographics, staff-residence postcode, resident cell number, work areas/dates, test results, staff interview dates/notes and resident prison-transfer dates. Epidemiological curves were mapped by prison location. Control measures included isolation (exclusion from work or cell-isolation), cohorting (new admissions and work-area groups), asymptomatic testing (case-finding), removal of communal dining and movement restrictions. Facemask use and enhanced hygiene were already in place. Whole genome sequencing (WGS) and interviews determined genetic relationship between cases plausibility of transmission.\n\nResultsOf 453 cases, 53% (n=242) were staff, most aged 25-34 years (11.5% females, 27.15% males) and symptomatic (64%). Crude attack-rate was higher in staff (29%, 95%CI: 26-64%) than in residents (12%, 95%CI: 9-15%).\n\nConclusionsWhole genome sequencing can help differentiate multiple introductions from person-to-person transmission in prisons. It should be introduced alongside asymptomatic testing as soon as possible to control prison outbreaks. Timely epidemiological investigation, including data visualisation, allowed dynamic risk assessment and proportionate control measures, minimising reduction in resident welfare.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "James P. Adamson", - "author_inst": "Public Health Wales CDSC" - }, - { - "author_name": "Christopher Smith", - "author_inst": "Public Health Wales Health Protection" - }, - { - "author_name": "Nicole Pacchiarini", - "author_inst": "Public Health Wales CDSC" - }, - { - "author_name": "Thomas Richard Connor", - "author_inst": "Public Health Wales PenGU" - }, - { - "author_name": "Janet Wallsgrove", - "author_inst": "Group 4 Security" - }, - { - "author_name": "Ian Coles", - "author_inst": "Group 4 Security" - }, - { - "author_name": "Clare Frost", - "author_inst": "Group 4 Security" - }, - { - "author_name": "Angharad Edwards", - "author_inst": "Group 4 Security" - }, - { - "author_name": "Catherine Moore", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Jaisi Sinha", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Stephanie Perrett", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Christie Craddock", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Clare Sawyer", - "author_inst": "Public Health Wales CDSC" - }, - { - "author_name": "Alison Waldram", - "author_inst": "Public Health England" - }, - { - "author_name": "Alicia Barrasa", - "author_inst": "Public Health England" - }, - { - "author_name": "Daniel Rhys Thomas", - "author_inst": "Public Health Wales CDSC" - }, - { - "author_name": "Philip Daniels", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Heather Lewis", - "author_inst": "Public Health Wales" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.02.22270324", "rel_title": "SARS-CoV-2 and influenza co-infection throughout the COVID-19 pandemic: An assessment of co-infection rates and cohort characterization", @@ -421167,6 +422893,53 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.02.03.22270401", + "rel_title": "RISK STRATIFICATION OF PATIENTS WITH COVID-19 DISEASE THROUGH THE USE OF CLINICAL SCORES IN AN EMERGENCY DEPARTMENT. A review of the literature", + "rel_date": "2022-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270401", + "rel_abs": "DISCLAIMER STATEMENTThe authors have withdrawn the manuscript because there are some errors in the Area Under the Curve values regarding to intensive care unit admission and mortality for some scores analyzed. The article must be revised in its conclusions in order to affirm that NEWS and NEWS2 are the best clinical scores to be used in Emergency to evaluate patients with Covid-19 disease.\n\nTherefore, the authors do not wish this work to be cited as reference for one project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Simone Zanella", + "author_inst": "APSS Trento" + }, + { + "author_name": "Francesco Zanella", + "author_inst": "APSS Trento" + }, + { + "author_name": "Alena Mancosu", + "author_inst": "University of Verona" + }, + { + "author_name": "Anna Brugnolli", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Alessandro Carrara", + "author_inst": "APSS Trento" + }, + { + "author_name": "Anita Bevilacqua", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Elisa Marinelli", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Nicola Ricci", + "author_inst": "APSS Trento" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2022.02.03.22270417", "rel_title": "Fatality assessment and variant risk monitoring for COVID-19 using three new hospital occupancy related metrics", @@ -421755,77 +423528,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.02.22270341", - "rel_title": "Managing Endothelial Dysfunction in COVID-19: A Pilot, Double-Blind, Placebo-Controlled, Randomized Clinical Trial at the Lebanese American University Medical Center - Rizk Hospital (MEDIC-LAUMCRH)", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270341", - "rel_abs": "BackgroundCoronavirus disease 2019 (Covid-19) is associated with endothelial dysfunction. Pharmacologically targeting the different mechanisms of endothelial dysfunction may improve clinical outcomes and lead to reduced morbidity and mortality\n\nMethodsIn this pilot, double-blind, placebo-controlled, randomized clinical trial we assigned patients who were admitted to the hospital with mild, moderate, or severe COVID-19 infection to receive, on top of optimal medical therapy, either an endothelial protocol consisting of (Nicorandil, L-arginine, Folate, Nebivolol, and Atorvastatin) or placebo for up to 14 days. The primary outcome was time to recovery, measured by an 8 category ordinal scale and defined by the time to being discharged from the hospital or hospitalized for infection-control or other nonmedical reasons. Secondary outcomes included the composite outcome of ICU admission or the need for mechanical ventilation, all-cause mortality, and the occurrence of side effects\n\nResultsOf 42 randomized patients, 37 were included in the primary analysis. The mean age of the patients was 57 years; the mean BMI of study participants was 29.14. History of hypertension was present in 27% of the patients, obesity in 45%, and Diabetes Mellitus in 21.6%. The median(Interquartile range) time to recovery was not significantly different between the endothelial protocol group (6 [4-12] days) and the placebo group (6 [5-8]days)(p-value = 0.854). Furthermore, there were no statistically significant differences in the need for mechanical ventilation or ICU admission, all-cause mortality, and the occurrence of side effects between the endothelial protocol group and the placebo group.\n\nConclusionAmong patients hospitalized with mild, moderate, or severe COVID-19 infection, targeting endothelial dysfunction by administering Nicorandil, L-arginine, Folate, Nebivolol, and Atorvastatin on top of optimal medical therapy did not decrease time to recovery. However, this treatment protocol was associated with an excellent safety profile. Adequately sized prospective randomized controlled trials are needed for the evaluation of the role of treating endothelial dysfunction in COVID-19 infection.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kamal Matli", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Abdulrahman Al Kotob", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Wassim Jamaleddine", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Soad Al-Osta", - "author_inst": "LAU" - }, - { - "author_name": "Pascale Salameh", - "author_inst": "Lebanese University" - }, - { - "author_name": "Rami Tabbikha", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Nibal Chamoun", - "author_inst": "LAU" - }, - { - "author_name": "Ahmad Moussawi", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Jean Michel Saad", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Gibran Atwi", - "author_inst": "LAU" - }, - { - "author_name": "Tarik Abusaad", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Omar Jamal", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Jacques Mokhbat", - "author_inst": "LAUMCRH" - }, - { - "author_name": "Georges Ghanem", - "author_inst": "Lebanese American University Medical Center Rizk Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.02.02.22270278", "rel_title": "Working from home due to the COVID-19 pandemic abolished the sleep disturbance vulnerability of late chronotypes relieving their predisposition to depression", @@ -422909,6 +424611,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.02.03.22270391", + "rel_title": "Device-assessed sleep and physical activity in individuals recovering from a hospital admission for COVID-19: a prospective, multicentre study", + "rel_date": "2022-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270391", + "rel_abs": "ObjectivesTo describe physical behaviours following hospital admission for COVID-19 including associations with acute illness severity and ongoing symptoms.\n\nMethods1077 patients with COVID-19 discharged from hospital between March and November 2020 were recruited. Using a 14-day wear protocol, wrist-worn accelerometers were sent to participants after a five-month follow-up assessment. Acute illness severity was assessed by the WHO clinical progression scale, and the severity of ongoing symptoms was assessed using four previously reported data-driven clinical recovery clusters. Two existing control populations of office workers and type 2 diabetes were comparators.\n\nResultsValid accelerometer data from 253 women and 462 men were included. Women engaged in a mean{+/-}SD of 14.9{+/-}14.7 minutes/day of moderate-to-vigorous physical activity (MVPA), with 725.6{+/-}104.9 minutes/day spent inactive and 7.22{+/-}1.08 hours/day asleep. The values for men were 21.0{+/-}22.3 and 755.5{+/-}102.8 minutes/day and 6.94{+/-}1.14 hours/day, respectively. Over 60% of women and men did not have any days containing a 30-minute bout of MVPA. Variability in sleep timing was approximately 2 hours in men and women. More severe acute illness was associated with lower total activity and MVPA in recovery. The very severe recovery cluster was associated with fewer days/week containing continuous bouts of MVPA, longer sleep duration, and higher variability in sleep timing. Patients post-hospitalisation with COVID-19 had lower levels of physical activity, greater sleep variability, and lower sleep efficiency than a similarly aged cohort of office workers or those with type 2 diabetes.\n\nConclusionsPhysical activity and regulating sleep patterns are potential treatable traits for COVID-19 recovery programmes.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Tatiana Plekhanova", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Alex V Rowlands", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Rachael A Evans", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Charlotte L Edwardson", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Nicolette C Bishop", + "author_inst": "School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK" + }, + { + "author_name": "Charlotte E Bolton", + "author_inst": "University of Nottingham, Nottingham, UK" + }, + { + "author_name": "James D Chalmers", + "author_inst": "University of Dundee, Ninewells Hospital and Medical School, Dundee, UK" + }, + { + "author_name": "Melanie J Davies", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Enya Daynes", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Annemarie B Docherty", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Omer Elneima", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Neil J Greening", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Sharlene A Greenwood", + "author_inst": "King's College Hospital, Department of Physiotherapy and Renal Medicine, London, UK" + }, + { + "author_name": "Andrew P Hall", + "author_inst": "University Hospitals of Leicester NHS Trust, Leicester, UK" + }, + { + "author_name": "Victoria C Harris", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ewen M Harrison", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Joseph Henson", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ling-Pei Ho", + "author_inst": "MRC Human Immunology Unit, University of Oxford, Oxford, UK" + }, + { + "author_name": "Alex Horsley", + "author_inst": "Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK" + }, + { + "author_name": "Linzy Houchen-Wolloff", + "author_inst": "Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Olivia C Leavy", + "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Nazir I Lone", + "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Michael Marks", + "author_inst": "Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Ben Maylor", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Hamish J C McAuley", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Claire M Nolan", + "author_inst": "Harefield Respiratory Research Group, Royal Brompton and Harefield Clinical Group, Guys and St. Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Krisnah Poinasamy", + "author_inst": "Asthma UK and British Lung Foundation, London, UK" + }, + { + "author_name": "Jennifer K Quint", + "author_inst": "NHLI, Imperial College London, London, UK" + }, + { + "author_name": "Betty Raman", + "author_inst": "Radcliffe Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Matthew Richardson", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Jack A Sargeant", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ruth M Saunders", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Marco Sereno", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Aarti Shikotra", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Amisha Singapuri", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Michael Steiner", + "author_inst": "Department of Respiratory Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "David J Stensel", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Louise V Wain", + "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Julie Whitney", + "author_inst": "School of Life Course & Population Sciences, Kings College London, London, UK" + }, + { + "author_name": "Dan G Wootton", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Christopher E Brightling", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "William D-C Man", + "author_inst": "Royal Brompton and Harefield Clinical Group, Guys and St. Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Sally J Singh", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Tom Yates", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.03.22270396", "rel_title": "COVID-19 Vaccination is Associated with Decreasing Cases, Hospitalizations, and Deaths Across Age Groups and Variants over 9 months in Switzerland", @@ -423629,85 +425526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.02.22270238", - "rel_title": "The public views of and reactions to the COVID-19 pandemic in England- a qualitative study with diverse ethnicities", - "rel_date": "2022-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270238", - "rel_abs": "ObjectivesTo explore public reactions to the COVID-19 pandemic across diverse ethnic groups.\n\nDesignRemote qualitative interviews and focus groups in English or Punjabi. Data were transcribed and analysed through inductive thematic analysis.\n\nSettingEngland and Wales June-October 2020.\n\nParticipants100 participants from 19 diverse self-identified ethnic groups.\n\nResultsDismay, frustration and altruism were reported across all ethnic groups during the first six to nine months of the COVID-19 pandemic. Dismay was caused by participants reported individual, family and community risks, and loss of support networks. Frustration was caused by reported lack of recognition of the efforts of minority ethnic groups (MEGs), inaction by government to address COVID-19 and inequalities, rule breaking by government advisors, changing government rules around: border controls, personal protective equipment, social distancing, eating out, and perceived poor communication around COVID-19 and the Public Health England (PHE) COVID-19 disparities report (leading to reported increased racism and social isolation). Altruism was felt by all, in the resilience of NHS staff and their communities and families pulling together. Data, participants suggested actions, and the Behaviour Change Wheel informed suggested interventions and policies to help control COVID-19.\n\nConclusionTo maintain public trust, it is imperative that governmental bodies consider vulnerable groups, producing clear COVID-19 control guidance with contingency, fiscal, service provision and communication policies for the next rise in COVID-19 cases. This needs to be combined with public interventions including information, education, modelling and enablement of infection prevention through local community involvement and persuasion techniques or incentivisation. Government policy needs to review and include town and social planning leading to environmental restructuring that facilitates infection prevention control. This includes easy access to hand-washing facilities in homes, work, all food providers and shopping centres; toilet facilities as our Travellers mentioned, and adequate living accommodation and work environment facilitating IPC for all.\n\nStrengths and limitationsO_LIThis is amongst the largest qualitative studies on attitudes to the COVID-19 pandemic in the UK general public across ethnic groups, ages and religions, adding insights to previous smaller qualitative studies, from a broader range of participants.\nC_LIO_LIThe qualitative methodology allowed us to discuss participants responses around the COVID-19 pandemic, probing their answers to obtain detailed data to inform needs across ethnic groups.\nC_LIO_LIMost data collection was undertaken in English and therefore excludes non-English speaking sectors of the population who may have experienced the COVID-19 pandemic differently.\nC_LIO_LIWe did not obtain the views of older members of the population over 70 years, who were most at risk.\nC_LIO_LIThe data reflect public perceptions six to nine months into the pandemic when some of the social distancing rules had been relaxed in England; as the pandemic progresses attitudes and needs may well change.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Cliodna McNulty", - "author_inst": "UK Health Security Agency, PKA Public Health England" - }, - { - "author_name": "Eirwen Sides", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Amy Thomas", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Atiya Kamal", - "author_inst": "Birmingham City University" - }, - { - "author_name": "Rowshonara Syeda", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Awatif Kaissi", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Donna Lecky", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Mahendra Patel", - "author_inst": "University of Bradford" - }, - { - "author_name": "Ines Campos-Matos", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Rashmi Shukla", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Colin Brown", - "author_inst": "Public Health England" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - }, - { - "author_name": "Loretta Sollars", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Laura B Nellums", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Jane Greenway", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Leah Ffion Jones", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.01.22269931", "rel_title": "High Rates of Rapid Antigen Test Positivity After 5 Days of Isolation for COVID-19", @@ -424747,6 +426565,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.02.01.478632", + "rel_title": "Design and development of potent h-ACE2 derived peptide mimetics in SARS-CoV-2 Omicron variant therapeutics", + "rel_date": "2022-02-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.01.478632", + "rel_abs": "The pandemic of COVID-19 has become the global health challenge due to the emergence of new variants. The Receptor binding domain (RBD) of spike protein that makes direct interaction with ACE-2 has shown unique mutated residues in most of the variants of concern (VOC). Recently WHO declared the Omicron (B.1.1.529) as VOC considering it as a highly mutated variant which includes a total of 60 mutations out of which 15 mutations occurred in RBD region of SARS-CoV-2. Inhibition of Protein-protein (Omicron RBD-h-ACE2) interaction was already proved to inhibit the viral infection. In this study, by using molecular dynamic simulations efforts are made to explore the atomistic details of Omicron RBD-h-ACE2 interaction. Based on MD simulations, h-ACE2 motif is found to be interacting with omicron RBD domain. Interaction analysis had provided key residues interacting with Omicron-RBD that helped to extract h-ACE2 peptide. Here, rational design of the peptides that have resemblance with h-ACE2 is done and the peptide library is subjected for inhibition studies against Omicron-RBD. The current study helped to identify the significant peptides that can inhibit Omicron-RBD. Altogether the performed studies will provide an opportunity to develop potential therapeutic peptidomimetics effective against Omicron variant of SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Stanly M L Paul", + "author_inst": "University of Szeged" + }, + { + "author_name": "Swathi Nadendla", + "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar" + }, + { + "author_name": "Elizabeth M Sobhia", + "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.02.01.478697", "rel_title": "Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages", @@ -425463,37 +427308,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.01.26.22269928", - "rel_title": "The Age-Related Probability of Dying from COVID-19 among Those Infected: A Relative Survival Analysis", - "rel_date": "2022-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269928", - "rel_abs": "BackgroundCOVID-19 was first identified in Wuhan, the capital city of the province of Hubei in China. Due to the presentation of multiple symptoms at the same time, it is clinically important to understand the probability of dying from COVID-19 vs. the probability of dying from other causes.\n\nMethodsUsing data collected in Hubei that identified by age those who died of COVID-19 or its sequelae among the infected, we constructed a life table showing the conditional probability of dying at age x from COVID-19 and its sequela among those infected. Following the relative survival perspective, we also computed corresponding data for China that matched the format of the life table we constructed from the Hubei study. We then formed ratios of the 10-year conditional portability of dying at age x from COVID-19 for the Hubei COVID-19 victims to the ten-year conditional probability of dying at age x from all non-COVID-19 causes for those not infected by COVID-19 in China as a whole.\n\nFindingsAt every age, the conditional probability of dying from COVID-19 among those infected in Hubei is higher than the conditional probability of dying from all non-COVID-19 causes for China as a whole. Following a general age-related mortality pattern, the conditional probability of dying from COVID-19 from age 20 onward increases monotonically for those who are infected. Relative to the probability of dying in China from all other causes for those not infected, however, it declines monotonically from age 20 to age 70.\n\nInterpretationAt younger ages the relative conditional probability of dying from CVOD-19 among the infected is substantially higher than it is for those infected who dying of all other causes and while staying higher at all ages, it declines monotonically with age. The monotonic decline in the ratio from age 20 to age 70 is a result of the age-related increase in the probability of dying from one or more of a number of competing causes, which, in the case at hand is manifested in the fact that non-COVID-19 deaths in China among the uninfected were generally increasing at a faster age-related rate than were the COVID-19 deaths to the infected in Hubei.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "David A Swanson", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Dudley Poston", - "author_inst": "Texas A & M University" - }, - { - "author_name": "Steven Krantz", - "author_inst": "Washington University" - }, - { - "author_name": "Arni Rao", - "author_inst": "Medical College of Gerogia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.30.22270125", "rel_title": "Web and social media searches highlight menstrual irregularities as a global concern in COVID-19 vaccinations", @@ -426569,6 +428383,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.29.22270074", + "rel_title": "Partnering with Athletes to Assess Risk of COVID-Related Myocarditis", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270074", + "rel_abs": "BackgroundMyocarditis in athletes is a feared complication of SARS-CoV-2, yet guidelines for screening with cardiac magnetic resonance imaging are lacking. Further, stakeholder involvement in the research is rare.\n\nHypothesisWe sought to determine the rates of cardiac magnetic resonance imaging evidence of SARS-CoV-2 related myocarditis in student athletes. We hypothesized that rates of myocarditis were lower than initially reported and that including athletes on the research team would enhance participant satisfaction and scientific integrity.\n\nMethodsAccordingly, when members of a hockey team were infected with SARS-CoV-2, we invited them and their team physicians to be part of the design of a study assessing the incidence of myocarditis. We performed cardiac magnetic resonance imaging on participating hockey players infected with SARS-CoV-2 and compared them to a healthy lacrosse cohort. Participants were given an optional survey to complete at the end of the study to assess their satisfaction with it.\n\nResultsFour hockey players and two team physicians joined the study team; eight hockey players and four lacrosse players participated in the study. Zero athletes met imaging criteria for myocarditis; delayed enhancement was observed in seven cases and three controls. Athletes supported sharing the findings with the participants. No athletes reported feeling uncomfortable participating, knowing other athletes participated on the research team.\n\nConclusionRates of SARS-CoV-2 myocarditis in young athletes appears to be lower than initially reported. Partnered research is important, especially in populations with more to lose, such as collegiate athletes; future studies should include stakeholders in the study design and execution.\n\nKey pointsCardiac MRI findings of myocarditis after COVID infection in young athletes is rare. Subjects of research studies appreciate involvement in the development of the study, and this also builds trust with the research team.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Bradley William Kay", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Attila Feher", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Samuel Reinhardt", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Jason Cuomo", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Stephanie Arlis-Mayor", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Matthew Lynch", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kyle Johnson", + "author_inst": "Yale University" + }, + { + "author_name": "Phil Kemp", + "author_inst": "Yale University" + }, + { + "author_name": "Henry Wagner", + "author_inst": "Yale University" + }, + { + "author_name": "Tyler Welsh", + "author_inst": "Yale University" + }, + { + "author_name": "Jerome Lamy", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Dana Peters", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Hamid Mojibian", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lawrence Young", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Rachel Lampert", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Robert McNamara", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lauren Baldassarre", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Edward J Miller", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Erica S Spatz", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.02.01.22270170", "rel_title": "Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Quebec, Canada", @@ -427229,41 +429134,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.29.478335", - "rel_title": "SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection", - "rel_date": "2022-01-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.29.478335", - "rel_abs": "Despite much concerted effort to better understand SARS-CoV-2 viral infection, relatively little is known about the dynamics of early viral entry and infection in the airway. Here we analyzed a single-cell RNA sequencing dataset of early SARS-CoV-2 infection in a humanized in vitro model, to elucidate key mechanisms by which the virus triggers a cell-systems-level response in the bronchial epithelium. We find that SARS-CoV-2 virus preferentially enters the tissue via ciliated cell precursors, giving rise to a population of infected mature ciliated cells, which signal to basal cells, inducing further rapid differentiation. This feed-forward loop of infection is mitigated by further cell-cell communication, before interferon signaling begins at three days post-infection. These findings suggest hijacking by the virus of potentially beneficial tissue repair mechanisms, possibly exacerbating the outcome. This work both elucidates the interplay between barrier tissues and viral infections, and may suggest alternative therapeutic approaches targeting non-immune response mechanisms.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Allison M. Greaney", - "author_inst": "Yale University" - }, - { - "author_name": "Micha Sam Brickman Raredon", - "author_inst": "Yale University" - }, - { - "author_name": "Maria P. Kochugaeva", - "author_inst": "Yale University" - }, - { - "author_name": "Laura E. Niklason", - "author_inst": "Yale University" - }, - { - "author_name": "Andre Levchenko", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2022.01.30.478159", "rel_title": "An intranasal lentiviral booster broadens immune recognition of SARS-CoV-2 variants and reinforces the waning mRNA vaccine-induced immunity that it targets to lung mucosa", @@ -428231,6 +430101,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.01.30.22269980", + "rel_title": "Quantitative risk assessment of COVID-19 and serious illness among spectators at mass gathering events with vaccine-testing package implementation", + "rel_date": "2022-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22269980", + "rel_abs": "While mass gathering events have resumed in conjunction with vaccine-testing (VT) packages, their effects on reducing COVID-19 risk remain unclear. Here, we used an environmental exposure model to analyze the effects of vaccinations and proof of negative test results on reducing infection risk and serious illness among spectators at mass gathering events. We then analyzed the difference in risk with and without VT and regular seat zoning. Risk of infection and serious illness were quantified using a model incorporating parameters such as vaccination coverage, vaccine prevention effectiveness, and sensitivity of polymerase chain reaction (PCR) or qualitative antigen tests. When vaccine prevention effectiveness was 50% (corresponding to 4 months for the delta variant and 1-2 months for the omicron variant after the second vaccine dose), the risk of infection and serious illness among vaccinated spectators were 0.32-0.40 and 0.13-0.16 times of those who tested negative, respectively. In contrast, the risks of infection and serious illness among vaccinated spectators without measures such as mask wearing were 4.0 and 1.6 times higher than those among unvaccinated spectators with such measures, respectively. The risk of infection with an 80% vaccination coverage and a vaccine prevention effectiveness of 20% (corresponding to 5-6 months for the delta variant or 3-4 months for the omicron variant after the second vaccine dose) was comparable to that of a 20% vaccine coverage and a vaccine prevention effectiveness of 80% (corresponding to 1-3 months for delta variant after the second vaccine dose). Regarding zoning, there was little difference in risk with a vaccination coverage of [≥]80%. Adherence to individual measures after vaccination and maintenance of high vaccine effectiveness among spectators at stadiums are important for reducing risk of infection and serious illness. Furthermore, seat zoning did not affect overall infection risk reduction.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Michio Murakami", + "author_inst": "Osaka University; National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Tsukasa Fujita", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Yuichi Iwasaki", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Masaki Onishi", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Wataru Naito", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Seiya Imoto", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Tetsuo Yasutaka", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.29.22270094", "rel_title": "Polygenic predisposition to venous thromboembolism is associated with increased COVID-19 positive testing rates", @@ -429079,49 +430992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.27.22269865", - "rel_title": "Acute upper airway disease in children with the omicron (B.1.1.529) variant of SARS-CoV-2: a report from the National COVID Cohort Collaborative (N3C)", - "rel_date": "2022-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269865", - "rel_abs": "BackgroundReports of SARS-CoV-2 causing laryngotracheobronchitis (commonly known as croup) have been limited to small case series. Early reports suggest the Omicron (B.1.1.529) strain of SARS-CoV-2 (the dominant circulating US strain since the week of 12/25/2021) replicates more efficiently in the conducting airways. This may increase the risk of a croup phenotype in children as they have smaller airway calibers.\n\nMethodsDescription of the incidence, change over time, and characteristics of children with SARS-CoV-2 and upper airway infection (UAI) diagnoses within the National COVID Cohort Collaborative (N3C) before and during the rise of the Omicron variant. We compare the demographics, comorbidities, and clinical outcomes of hospitalized SARS-CoV-2 positive children with and without UAI.\n\nResultsSARS-CoV-2 positive UAI cases increased to the highest number per month (N = 170) in December 2021 as the Omicron variant became dominant. Of 15,806 hospitalized children with SARS-CoV-2, 1.5% (234/15,806) had an UAI diagnosis. Those with UAI were more likely to be male, younger, white, have asthma and develop severe disease as compared to those without UAI.\n\nConclusionsPediatric acute UAI cases have increased during the Omicron variant surge with many developing severe disease. Improved understanding of this emerging clinical phenotype could aid in therapeutic decision-making and healthcare resource planning.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Blake Martin", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Peter E DeWitt", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Seth Russell", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "L. Nelson Sanchez-Pinto", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Melissa A Haendel", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Richard Moffitt", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Tellen D Bennett", - "author_inst": "University of Colorado School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.01.27.22269512", "rel_title": "Investigation of air change rate and aerosol behavior during an outbreak of COVID-19 in a geriatric care facility", @@ -430229,6 +432099,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.27.22269949", + "rel_title": "Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 - January 2022", + "rel_date": "2022-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269949", + "rel_abs": "The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7-3.1 days. The mean net reproduction number rose from about 1.15 in absence of Omicron to a peak of 1.83 for symptomatic cases and 1.33 for hospitalized cases, while it remained stable for critical cases.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Paola Stefanelli", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Filippo Trentini", + "author_inst": "Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy" + }, + { + "author_name": "Daniele Petrone", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Alessia Mammone", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Luigina Ambrosio", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Mattia Manica", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Giorgio Guzzetta", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Valeria D Andrea", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Valentina Marziano", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Agnese Zardini", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Carla Molina Grane", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" + }, + { + "author_name": "Angela Di Martino", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Flavia Riccardo", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Antonino Bella", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Monica Sane Schepisi", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Francesco Maraglino", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Piero Poletti", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Anna Teresa Palamara", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Silvio Brusaferro", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Giovanni Rezza", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Patrizio Pezzotti", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.28.22270022", "rel_title": "Continuing inequalities in COVID-19 mortality in England and Wales, and the changing importance of regional, over local, deprivation", @@ -430857,29 +432834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.25.22269855", - "rel_title": "Positive attribute framing increases COVID-19 booster vaccine intention for unfamiliar vaccines", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269855", - "rel_abs": "Positive framing has been proposed as a potential intervention to increase COVID-19 vaccination intentions. However, most available research has examined fictitious or unfamiliar treatments. This pre-registered study compared positively and negatively attribute-framed side effect information for real COVID-19 booster vaccines (AstraZeneca, Pfizer, Moderna) and measured booster intentions pre- and post-intervention in 1,222 UK-based participants. As hypothesised, vaccine familiarity significantly modulated the effect of framing. While positive framing was effective for the least familiar vaccine (i.e., Moderna), standard negative framing appeared to increase intentions for familiar vaccines (AstraZeneca/Pfizer), particularly among those with low baseline intentions. These findings provide important new evidence that positive framing could improve vaccine uptake globally when switches or new developments require individuals to receive less familiar vaccines - as is currently the case for millions of booster vaccines across the world. Positive framing of familiar vaccines, however, should be treated with caution.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kirsten Barnes", - "author_inst": "University of Sydney" - }, - { - "author_name": "Ben Colagiuri", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.26.477915", "rel_title": "Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine", @@ -432031,6 +433985,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.26.22269874", + "rel_title": "General practitioner wellbeing during the COVID-19 pandemic: a qualitative interview study", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269874", + "rel_abs": "BackgroundWorkload pressures and poor job satisfaction have been reported by UK general practitioners (GPs) for some time. The COVID-19 pandemic presented new challenges, with growing international evidence of its negative impact on GPs mental health and wellbeing. While there has been wide commentary on this topic, UK research evidence is lacking. Developing greater understanding of these lived experiences and subgroup differences is important as doctor wellbeing may affect the sustainability of health care systems and quality of patient care.\n\nObjectivesTo explore the lived experience of UK GPs during COVID-19, and the pandemics impact on their psychological wellbeing.\n\nDesign and SettingIn-depth qualitative interviews, conducted remotely by telephone or video call, with NHS GPs.\n\nParticipantsGPs were sampled purposively across three career stages (early career, established and late career or retired GPs) with variation in other key demographics. A comprehensive recruitment strategy used multiple channels. Data were analysed thematically using Framework Analysis.\n\nResultsWe interviewed 40 GPs; most described generally negative sentiment and many displayed signs of psychological distress and burnout. Causes of stress and anxiety related to personal risk, workload, practice changes, public perceptions and leadership, teamworking and wider collaboration and personal challenges. GPs described facilitators of their wellbeing, including sources of support and plans to reduce clinical hours or change career path.\n\nConclusionsA range of factors detrimentally affected the wellbeing of GPs during the pandemic and we highlight the potential impact of this on workforce retention and quality of care. As the pandemic progresses and general practice faces continued challenges, urgent policy measures are now needed.\n\nStrengths and limitations of this studyO_LIWhile there is growing international evidence base demonstrating the impact of the COVID-19 pandemic on GPs wellbeing and much UK media coverage, this qualitative interview study provides much-needed research evidence of UK GPs lived experiences and wellbeing during COVID-19.\nC_LIO_LI40 GPs were sampled purposively to include GPs with different demographic and practice characteristics.\nC_LIO_LIWhile there are no easy solutions to the problems highlighted, this research provides increased contextualised understanding of how these experiences may impact future workforce retention and the sustainability of health systems longer-term.\nC_LIO_LISub-group differences by gender and age are reported; highlighting a potential need for further research and support targeted at specific groups.\nC_LIO_LIFindings are necessarily limited to the time of data collection (Spring/Summer 2021); further tensions in general practice have since arisen, particularly regarding negative and misleading media portrayal.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Laura A Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Claire Heathcote", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.01.26.22269856", "rel_title": "Antibody and T cell responses to SARS-CoV-2 mRNA vaccines during maintenance therapy for immune-mediated inflammatory diseases", @@ -432975,57 +434956,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.26.22269905", - "rel_title": "Projecting the seasonality of endemic COVID-19", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269905", - "rel_abs": "ImportanceSuccessive waves of infection by SARS-CoV-2 have left little doubt that COVID-19 will transition to an endemic disease, yet the future seasonality of COVID-19 remains one of its most consequential unknowns. Foreknowledge of spatiotemporal surges would have immediate and long-term consequences for medical and public health decision-making.\n\nObjectiveTo estimate the impending endemic seasonality of COVID-19 in temperate population centers via a phylogenetic ancestral and descendent states approach that leverages long-term data on the incidence of circulating coronaviruses.\n\nDesignWe performed a comparative evolutionary analysis on literature-based monthly verified cases of HCoV-NL63, HCoV-229E, HCoV-HKU1, and HCoV-OC43 infection within populations across the Northern Hemisphere. Ancestral and descendent states analyses on human-infecting coronaviruses provided projections of the impending seasonality of endemic COVID-19.\n\nSettingQuantitative projections of the endemic seasonality of COVID-19 were based on human endemic coronavirus infection incidence data from New York City (USA); Denver (USA); Tampere (Finland); Trondelag (Norway); Gothenburg (Sweden); Stockholm (Sweden); Amsterdam (Netherlands); Beijing (China); South Korea (Nationwide); Yamagata (Japan); Hong Kong; Nakon Si Thammarat (Thailand); Guangzhou (China); and Sarlahi (Nepal).\n\nMain Outcome(s) and Measure(s)The primary projection was the monthly relative frequency of SARS-CoV-2 infections in each geographic locale. Four secondary outcomes consisted of empirical monthly relative frequencies of the endemic human-infecting coronaviruses HCoV-NL63, -229E, -HKU1, and -OC43.\n\nResultsWe project asynchronous surges of SARS-CoV-2 across locales in the Northern Hemisphere. In New York City, SARS-CoV-2 incidence is projected in late fall and winter months (Nov.-Jan.), In Tampere, Finland; Yamagata, Japan; and Sarlahi, Nepal incidence peaks in February. Gothenburg and Stockholm in Sweden reach peak incidence between November and February. Guangzhou, China; and South Korea. In Denver, incidence peaks in early Spring (Mar.). In Amsterdam, incidence rises in late fall (Dec.), and declines in late spring (Apr.). In Hong Kong, the projected apex of infection is in late fall (Nov.-Dec.), yet variation in incidence is muted across other seasons. Seasonal projections for Nakhon Si Thammarat, Thailand and for Beijing, China are muted compared to other locations.\n\nConclusions and RelevanceThis knowledge of likely spatiotemporal surges of COVID-19 is fundamental to medical preparedness and expansions of public health interventions that anticipate the impending endemicity of this disease and mitigate COVID-19 transmission. These results provide crucial guidance for adaptive public health responses to this disease, and are vital to the long-term mitigation of COVID-19 transmission.\n\nKey Points\n\nQuestionUnder endemic conditions, what are the projected spatiotemporal seasonal surges of COVID-19?\n\nFindingsWe applied a phylogenetic ancestral and descendent states approach, leveraging long-term data on the incidence of circulating coronaviruses. We found that seasonal surges are expected in or near the winter months; dependent on the specific population center, infections are forecasted to surge in the late fall, winter, or early spring.\n\nMeaningGlobally, endemic COVID-19 surges should be expected to occur asynchronously, often coincident with local expected surges of other human-infecting respiratory viruses.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jeffrey P. Townsend", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "April D. Lamb", - "author_inst": "University of North Carolina at Charlotte" - }, - { - "author_name": "Hayley Hassler", - "author_inst": "Yale University" - }, - { - "author_name": "Pratha P. Sah", - "author_inst": "Yale University" - }, - { - "author_name": "Aia Alvarez-Nishio", - "author_inst": "Yale University" - }, - { - "author_name": "Cameron Nguyen", - "author_inst": "University of North Carolina at Charlotte" - }, - { - "author_name": "Alexandra D. Tew", - "author_inst": "University of North Carolina at Charlotte" - }, - { - "author_name": "Alison Galvani", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Alex Dornburg", - "author_inst": "University of North Carolina Charlotte" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.26.22269540", "rel_title": "Impact of voluntary risk-mitigation behaviour on transmission of the Omicron SARS-CoV-2 variant in England", @@ -434193,6 +436123,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.22269420", + "rel_title": "Immune response to third SARS-CoV-2 vaccination in seronegative kidney transplant recipients: possible improvement by mycophenolate mofetil reduction", + "rel_date": "2022-01-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269420", + "rel_abs": "BackgroundModification of vaccination strategies is needed to improve the immune response to SARS-CoV-2 vaccination in kidney transplant recipients (KTRs).\n\nMethodsThis multicenter observational study aimed to determine antibody kinetics among 60 seropositive KTRs and analyzed the effects of the third vaccination against SARS-CoV-2 in 174 previously seronegative KTRs. We investigated whether mycophenolate mofetil (MMF) dose reduction by 25-50% prior the third vaccination influences vaccination success.\n\nResults18 of 60 (30%) seropositive KTRs became seronegative in the serological assay within six months. Loss of antibodies was predicted by low initial antibody levels ([≤]206.8 BAU/ml), older age, and impaired graft function. A third vaccination in previously seronegative KTRs induced seroconversion in 56 of 174 (32.1%) KTRs with median antibody levels 119 (76-353) BAU/ml and median neutralizing capacity titer of 1:10 (0- 1:40). Multivariate logistic regression revealed that initial antibody levels (OR 1.39, 95% CI 1.09-1.76), graft function (OR 0.05, 95% CI 0.01-0.39), time after transplantation (OR 1.04, 95% CI 1.02-1.07) and MMF trough levels (OR 0.43, 95% CI 0.21-0.88) correlated with seroconversion, p<0.05. After controlling for these confounders, the effect of MMF dose reduction was calculated using propensity score matching. KTRs in the MMF reduction group had significantly lower MMF serum concentrations prior to the third vaccination and were more likely to develop antibody levels [≥]35.2 BAU/ml than their matched KTRs (p=0.02).\n\nConclusionsTemporary reduction in MMF dose might be a promising approach to improve the immune response in KTRs.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Marta Kantauskaite", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Lias Mueller", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Jonas Hillebrandt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Joshua Leon Lamberti", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Svenja Fischer", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Thilo Kolb", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Katrin Ivens", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Michael Koch", + "author_inst": "Nephrocare Mettmann" + }, + { + "author_name": "Marcel Andree", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Nadine Luebke", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Michael Schmitz", + "author_inst": "Klinikum Solingen" + }, + { + "author_name": "Tom Luedde", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Hans Martin Orth", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Torsten Feldt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Heiner Schaal", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Ortwin Adams", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Claudia Schmidt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Margarethe Kittel", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Eva Koenigshausen", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Lars Christian Rump", + "author_inst": "Heinrich-Heine University-Duesseldorf" + }, + { + "author_name": "Joerg Timm", + "author_inst": "University hospital Duesseldorf" + }, + { + "author_name": "Johannes Stegbauer", + "author_inst": "Heinrich-Heine-University Duesseldorf" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.01.20.21267627", "rel_title": "\"It affects every aspect of your life\": A qualitative study of the impact of delaying surgery during COVID-19", @@ -435077,85 +437110,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.25.22269778", - "rel_title": "Comparative immunogenicity of heterologous versus homologous 3rd SARS-CoV-2 vaccine doses in kidney transplant recipients", - "rel_date": "2022-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269778", - "rel_abs": "BackgroundSolid organ transplant recipients have attenuated immune responses to SARS-CoV-2 vaccines. Emerging evidence suggests at least equivalent immunogenicity of heterologous compared with homologous vaccine regimens in the general population. In this study, we report on immune responses to 3rd dose BNT162b2 vaccines in transplant recipients either primed with ChAdOx1 or BNT162b2.\n\nMethods700 kidney transplant recipients were prospectively screened for serological responses (median time of 33 (21-52) days) following 3 primary doses of a SARS-CoV2 vaccine. All vaccine doses were received post-transplant, and all 3rd doses were BNT162b2. All participants had serological testing performed post-2nd vaccination at a median time of 34 (IQR 26-46) days following the 2nd inoculation, and at least once prior to their 1st dose of vaccine.\n\nResults366/700 (52.3%) participants were primed with BNT162b2, whilst 334/700 (47.7) had received ChAdOx1. Overall, 139/700 (19.9%) participants had evidence of prior infection. Of 561 infection naive participants, 263 (46.9%) had no detectable anti-S following 2-doses of vaccine (V2). 134 (23.9%) participants remained seronegative post 3rd vaccine (V3); 54/291 (18.6%) and 79/270 (29.3%) of participants receiving BNT162b2 and ChAdOx1 respectively, p=0.0029. Median anti-S concentrations were significantly higher post-V3 in patients who had received BNT162b2 compared with ChAdOx1, at 612 (27-234) versus 122 (7.1-1111) BAU/ml respectively, p<0.0001.\n\nCellular responses were investigated in 30 infection naive participants at a median time of 35 (24-46) days post-V3. Eighteen of 30 (60.0%) participants had undetectable T-cell responses. There were neither qualitative or quantitative differences in T-cell responses between those patients who received BNT162b2 or ChAdOx1 as their first 2-doses, with 10/16 (62.5%) and 8/14 (57.1%) respectively having undetectable T-cell responses, p=0.77.\n\nConclusionA significant proportion of transplant recipients remain seronegative following 3 doses of SARS-CoV-2 vaccines, with anti-S concentrations lower in patients receiving heterologous versus homologous vaccinations.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Tina Thomson", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Maria Prendecki", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" - }, - { - "author_name": "Sarah Gleeson", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Paul Martin", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Katrina Spensley", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Charlotte Seneschall", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Jaslyn Gan", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Candice L Clarke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Shanice Lewis", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" - }, - { - "author_name": "Graham Pickard", - "author_inst": "Department of Infection and Immunity Sciences, Northwest London Pathology NHS Trust" - }, - { - "author_name": "David C Thomas", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" - }, - { - "author_name": "Stephen P McAdoo", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" - }, - { - "author_name": "Liz Lightstone", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London" - }, - { - "author_name": "Alison Cox", - "author_inst": "Department of Infection and Immunity Sciences, Northwest London Pathology NHS Trust" - }, - { - "author_name": "Peter Kelleher", - "author_inst": "Department of Infectious Diseases, Imperial College London" - }, - { - "author_name": "Michelle Willicombe", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2022.01.25.22269804", "rel_title": "Comparison of vaccine effectiveness against the Omicron (B.1.1.529) variant in patients receiving haemodialysis", @@ -436435,6 +438389,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.23.22269669", + "rel_title": "Effects of 12 weeks of Multi-nutrient supplementation on the Immune and Musculoskeletal systems of Older Adults in Aged-Care (The Pomerium Study): Protocol for a Randomised Controlled Trial", + "rel_date": "2022-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269669", + "rel_abs": "IntroductionImmunosenescence leads to increased morbidity and mortality associated with viral infections and weaker vaccine responses. This has been well documented for seasonal influenza and the current pandemic with Sars-Cov2, which disproportionately impact older adults, particularly those in residential aged care facilities. Inadequate nutrient intake associated with impaired immunity, respiratory and muscle function are likely to augment the effects of immunosenescence. In this study, we test whether the effects of inadequate nutrition can be reversed by multi-nutrient supplementation, consequently enhancing vaccine responses, reducing the risk of viral infections, and improving respiratory and muscle function.\n\nMethods and analysisThe Pomerium Study is a 12-week, single-blinded, randomised, placebo-controlled trial testing the effects of two daily servings of an oral multi-nutrient supplement (330 kcal, 20g protein, 1.2g CaHMB, 449mg calcium, 520IU vitamin D3, and 25 vitamins and minerals) on the immune system and muscle and respiratory function of older adults in aged-care in Melbourne, Australia. 160 older adults ([≥]75 years old) will be recruited from aged-care facilities and randomised to treatment (multi-nutrient supplement) or control (usual care). Primary outcome is the change in T-cell subsets CD8+ and CD28null counts at 4 and 12 weeks post-intervention. Secondary outcomes measured at baseline and after 12 weeks post-intervention are multiple markers of immunosenescence, body composition (bioimpedance), handgrip strength (dynamometer), physical function (short physical performance battery), respiratory function (spirometry), and quality of life (EQ-5D-3L). Incidence and complications of COVID-19 and/or viral infections (i.e., hospitalisation, complications, or death) will be recorded throughout the trial.\n\nDiscussionIf the Pomerium Study demonstrates efficacy and safety of a multi-nutrient supplement on immune, muscle and respiratory function, it may be suitable as a strategy to reduce the adverse outcomes from seasonal influenza and viral infections such as COVID-19 in older adults in aged-care.\n\nFunding, Ethics, Registration and DisseminationThe study is funded by the Australian Medical Research Future Fund. It is approved by Melbourne Health Human Research Ethics Committee (Ref No. HREC/73985/MH-2021, ERM Ref No. RMH73985, Melbourne Health Site Ref No. 2021.115), and registered at ANZCTR (12621000420842). Results will be published in peer-reviewed journals and made available to aged-care stakeholders, including providers, residents, and government bodies.\n\nArticle Summary Strengths and LimitationsO_LIThis is the first study performing a comprehensive immune, respiratory and functional assessment in aged care residents after receiving a multi-nutrient solution that is commercially available.\nC_LIO_LIOur design and tested intervention assure that the results of the study will be rapidly translated into practice.\nC_LIO_LIThe main limitation is that any biological effect observed cannot be attributed to one component of the multi-nutrient supplement.\nC_LIO_LIAnother limitation is that the potential effect of group differences in energy intake on outcomes can only be monitored by assessing regular dietary intake and weight changes during the study period.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ahmed Al Saedi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Ben Kirk", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Sandra Iuliano", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Jesse Zanker", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Sara Vogrin", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Lata Jayaram", + "author_inst": "Western Health" + }, + { + "author_name": "Shane Thomas", + "author_inst": "Australian Institute for Musculoskeletal Science (AIMSS)" + }, + { + "author_name": "Christine Golding", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Diana Navarro-Perez", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Petra Marusic", + "author_inst": "Australian Institute for Musculoskeletal Science (AIMSS)" + }, + { + "author_name": "Sean Leng", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ralph Nanan", + "author_inst": "University of Sydney" + }, + { + "author_name": "Gustavo Duque", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2022.01.23.22269626", "rel_title": "Death review caused by Covid 19 in Bangladesh", @@ -437007,69 +439028,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.24.477043", - "rel_title": "Substantial immune response in Omicron infected breakthrough and unvaccinated individuals against SARS-CoV-2 variants of concerns", - "rel_date": "2022-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.24.477043", - "rel_abs": "The recent emergence of highly mutated SARS-CoV-2 Omicron variant has debilitating effect on public health system of the affected countries worldwide. Currently India is facing third wave of COVID-19 pandemic and going through a severe crisis. Within short span of time, the variant has shown high transmissibility and capability of evading the immune response generated against natural infection and vaccination. The immune escape potential of Omicron is a serious concern and further needs to be explored. In the present study, we have assessed the IgG and neutralizing antibody (NAb) response in breakthrough individuals vaccinated with two doses ChAdOx1 nCoV-19 vaccine (n=25), breakthrough individuals vaccinated with two doses of BNT162b2 mRNA vaccine (n=8) and unvaccinated individuals (n=6). All these individuals were infected with Omicron variant. The IgG antibody activity in the sera of the ChAdOx1 nCoV-19 and BNT162b2 mRNA breakthrough individuals was comparable with S1-RBD, while it was lesser in BNT162b2 mRNA breakthrough individuals with N protein and inactivated whole antigen IgG ELISA. BNT162b2 mRNA breakthrough individuals showed moderate reduction in NAb GMTs compared to ChAdOx1 nCoV-19 against Alpha, Beta and Delta. However, 3-fold higher reduction was observed with omicron variant in BNT162b2 mRNA than ChAdOx1 nCoV-19. Apparently, Alpha variant was modestly resistant to the sera of unvaccinated individuals than Beta, Delta and Omicron. Our study demonstrated substantial immune response in the individuals infected with Omicron. The neutralizing antibodies could effectively neutralize the Omicron and other VOCs including the most prevalent Delta variant.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Pragya D Yadav", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Gajanan Sapkal", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Rima R Sahay", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Varsha Potdar", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411022" - }, - { - "author_name": "Gururaj Deshpande", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Deepak Y Patil", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Dimpal A Nyayanit", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Anita M Shete", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Jayanthi Shastri", - "author_inst": "Kasturba Hospital for Infectious Diseases, Mumbai, India Pin-400011" - }, - { - "author_name": "Pradeep Awate", - "author_inst": "State Surveillance Officer, Integrated Disease Surveillance program, Pune, Maharashtra, India Pin 411006" - }, - { - "author_name": "Bharti Malhotra", - "author_inst": "Sawai Man Singh Medical College, Jaipur, India Pin- 302004" - }, - { - "author_name": "Priya Abraham", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, IndiaPin-411021" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.21.477288", "rel_title": "Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail", @@ -437985,6 +439943,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.25.22269735", + "rel_title": "Acquired neutralizing breadth against SARS-CoV-2 variants including Omicron after three doses of mRNA COVID-19 vaccination and the vaccine efficacy", + "rel_date": "2022-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269735", + "rel_abs": "To investigate the induction of neutralizing antibodies against Omicron after two and three vaccine doses in recipients of different ages. Physicians at Kobe University Hospital who had received the second dose of the BNT162b2 mRNA vaccine. At 2 months after the second vaccinations, the positive rate of neutralizing antibody against Omicron was 28%, and the titer was significantly lower than those against other variants, 11.8-fold and 3.6-fold lower than those against D614G and Delta, respectively. Unlike Delta, that positive rates of neutralizing antibody against Omicron were low in all age groups, and there was no significant difference in titers among age groups. Seven months after the 2nd dose, the positive rate of neutralizing antibody against Omicron decreased to 6%, but after the booster,3rd vaccination, it increased to 100%, and the titer was much higher than those at 2 and 7 months post-vaccination, 32-fold and 39-fold respectively. The booster vaccination effect was also observed in the younger at 41-fold, middle-aged at 43-fold, and older at 27-fold groups compared to the 7-month titers. Surprisingly, higher-than-predicted titers of the neutralizing antibodies against Omicron were induced after the booster vaccination regardless of recipient age, while this effect was not observed after two doses, indicating the induction of antibodies against common epitopes by the booster vaccination. Three doses can be confidently recommended to suppress the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Koichi Furukawa", + "author_inst": "Kobe Unibersity" + }, + { + "author_name": "Lidya Handayani Tjan", + "author_inst": "Kobe University" + }, + { + "author_name": "Yukiya Kurahashi", + "author_inst": "Kobe University" + }, + { + "author_name": "Silvia Sutandhio", + "author_inst": "Kobe University" + }, + { + "author_name": "Mitsuhiro Nishimura", + "author_inst": "Kobe University" + }, + { + "author_name": "Jun Arii", + "author_inst": "Kobe University" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Kobe University Graduate School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.24.22269781", "rel_title": "Effects of vaccination against COVID-19 on the emotional health of Peruvian older adults", @@ -438817,89 +440818,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.23.477397", - "rel_title": "Lack of Ronapreve (REGN-CoV; casirivimab and imdevimab) virological efficacy against the SARS-CoV 2 Omicron variant (B.1.1.529) in K18-hACE2 mice", - "rel_date": "2022-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.23.477397", - "rel_abs": "BackgroundRonapreve demonstrated clinical application in post-exposure prophylaxis, mild/moderate disease and in the treatment of seronegative patients with severe COVID19 prior to the emergence of the Omicron variant in late 2021. Numerous reports have described loss of in vitro neutralisation activity of Ronapreve and other monoclonal antibodies for BA.1 Omicron and subsequent sub-lineages of the Omicron variant. With some exceptions, global policy makers have recommended against the use of existing monoclonal antibodies in COVID19. Gaps in knowledge regarding the mechanism of action of monoclonal antibodies are noted, and further preclinical study will help understand positioning of new monoclonal antibodies under development.\n\nObjectivesThe purpose of this study was to investigate the impact of Ronapreve on compartmental viral replication as a paradigm for a monoclonal antibody combination. The study also sought to confirm absence of in vivo activity against BA.1 Omicron (B.1.1.529) relative to the Delta (B.1.617.2) variant.\n\nMethodsVirological efficacy of Ronapreve was assessed in K18-hACE2 mice inoculated with either the SARS-CoV-2 Delta or Omicron variants. Viral replication in tissues was quantified using qRT-PCR to measure sub-genomic viral RNA to the E gene (sgE) as a proxy. A histological examination in combination with staining for viral antigen served to determine viral spread and associated damage.\n\nResultsRonapreve reduced sub-genomic viral RNA levels in lung and nasal turbinate, 4 and 6 days post infection, for the Delta variant but not the Omicron variant of SARS-CoV-2 at doses 2-fold higher than those shown to be active against previous variants of the virus. It also appeared to block brain infection which is seen with high frequency in K18-hACE2 mice after Delta variant infection. At day 6, the inflammatory response to lung infection with the Delta variant was altered to a mild multifocal granulomatous inflammation in which the virus appeared to be confined. A similar tendency was also observed in Omicron infected, Ronapreve-treated animals.\n\nConclusionsThe current study provides evidence of an altered tissue response to the SARS-CoV-2 after treatment with a monoclonal antibody combination that retains neutralization activity. These data also demonstrate that experimental designs that reflect the treatment use case are achievable in animal models for monoclonal antibodies deployed against susceptible variants. Extreme caution should be taken when interpreting prophylactic experimental designs when assessing plausibility of monoclonal antibodies for treatment use cases.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lee Tatham", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Anja Kipar", - "author_inst": "University of Zurich" - }, - { - "author_name": "Joanne Sharp", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Edyta Kijak", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Joanne Herriott", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Megan Neary", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Helen Box", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Eduardo Gallardo Toledo", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Anthony Valentijn", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Helen Cox", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Henry Pertinez", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Paul Curley", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Usman Arshad", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Rajith KR Rajoli", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Steve Rannard", - "author_inst": "University of Liverpool" - }, - { - "author_name": "James Stewart", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Andrew Owen", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.22.477073", "rel_title": "Bacteriophage-derived dsRNA exerts anti-SARS-CoV-2 activity in vitro and in Golden Syrian hamsters in vivo", @@ -439627,6 +441545,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.23.22269716", + "rel_title": "Evidence on the role of journal editors in the COVID19 infodemic: metascientific study analyzing COVID19 publication rates and patterns", + "rel_date": "2022-01-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269716", + "rel_abs": "ObjectiveInfodemic, a neologism characterizing an excess of fast-tracked low quality publications, has been employed to depict the scientific research response to the COVID19 crisis. The concept relies on the presumed exponential growth of research output. This study aimed to test the COVID19 infodemic claim by assessing publication rates and patterns of COVID19-related research and a control, a year prior.\n\nDesignA Reproduction Number of Publications (Rp) was conceived. It was conceptualized as a division of a week incidence of publications by the average of publications of the previous week. The publication growth rates of preprint and MEDLINE-indexed peer-reviewed literature on COVID19 were compared using the correspondent Influenza output, a year prior, as control. Rp for COVID19 and Influenza papers and preprints were generated and compared and then analyzed in light of the respective growth patterns of their papers and preprints.\n\nMain outcomesOutput growth rates and Reproduction Number of Publications (Rp).\n\nResultsCOVID19 peer-reviewed papers showed a fourteen fold increase compared to Influenza papers. COVID19 papers and preprints displayed an exponential growth curve until the 20th week. COVID19 papers displayed Rp=3.17{+/-}0.72, while the control group presented Rp=0.97{+/-}0.12. Their preprints exhibited Rp=2.18{+/-}0.54 and Rp=0.97{+/-}0.27 respectively, with no evidence of exponential growth in the control group, as its Rp remained approximately one.\n\nConclusionsCOVID19 publications displayed an epidemic pattern. As the growth patterns of COVID19 peer-reviewed articles and preprints were similar, and the majority of the COVID19 output came from indexed journals, not only authors but also editors appear to had played a significant part on the infodemic.\n\nReview protocolhttps://osf.io/q3zkw/?view_only=ff540dc4630b4c6e9a2639d732047324\n\nEthical aspectsNo ethical clarence was required as all analyzed data were publicly available.\n\nO_TEXTBOXSUMMARY BOX\n\n1. What is already known about this subject?\n\nMuch has been commented on 2020s excess of publications on COVID19. Independent studies found evidence of increased volume and speed of publication, decreased methodological quality, and qualitative variations in peer review of COVID19 papers, when compared to the scholarly output from before the pandemic. This phenomenon has been branded an infodemic, a neologism implying an epidemic of low-quality information on COVID19 when high quality scientific reports to inform health policies would have been needed the most.\n\n2. What are the new findings?\n\nNo study pushed the infodemic metaphor forward to analyze not only volume of publication but also publication rates comparing them to a control group as to clearly pinpoint an exponential phase of contagion in the infodemic (as it would take place in a real epidemic) through a mathematical analysis of the growth patterns and rates of those publications. In this paper, we were able to demonstrate that there has been an infodemic indeed and that the editor population was as susceptible to the infodemic bug as the author population because the exponential phase was shaped not only by authors but mainly by editors from PubMed-indexed journals.\n\n3.How might it impact clinical practice in the foreseeable future?\n\nThese results and conclusions are consequential to subsequent studies on rigor and depth of post publication peer review and on editorial practices within the life and health sciences research community.\n\nC_TEXTBOX", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gabriel Grisi", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Joao de Deus Barreto Segundo", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Camila Veronica Freire", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Denise Matias", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Mariana Cruz", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Larrie Rabelo Laporte", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Daniel Medina", + "author_inst": "Universidade Federal do Reconcavo da Bahia" + }, + { + "author_name": "Thiago Masashi Taniguchi", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Leticia Requiao", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Bruno Goes", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Luis Claudio Lemos Correia", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.24.22269734", "rel_title": "SARS-CoV-2 viremia precedes an IL6 response in severe COVID-19 patients: results of a longitudinal prospective cohort", @@ -440547,49 +442524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.21.22269667", - "rel_title": "Does a humoral correlate of protection exist for SARS-CoV-2? A systematic review", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269667", - "rel_abs": "BackgroundA correlate of protection (CoP) is an immunological marker associated with protection against infection. A CoP can be used to determine whether an individual is protected from infection, evaluate candidate vaccines, guide vaccination dosing intervals and policy, and understand population-level immunity against a pathogen. Despite an urgent need, a CoP for SARS-CoV-2 is currently undefined, leaving an evidence gap for informing public health policy and adapting it appropriately as new variants of concern emerge. The objective of this study was to systematically review and assess the evidence for a humoral SARS-CoV-2 CoP.\n\nMethods and FindingsWe searched OVID MEDLINE, EMBASE, Global Health, Biosis Previews and Scopus from inception to January 4, 2022 and pre-prints (using NIH iSearch COVID-19 portfolio) from inception to December 31, 2021, for studies describing SARS-CoV-2 re-infection or breakthrough infection with associated antibody measures. Two reviewers independently extracted study data and performed quality assessment. Twenty-five studies were included in our systematic review. Several studies reported re-infection or breakthrough cases that occurred in the presence of robust antibody levels. Studies that compared aggregate antibody concentrations from individuals who experienced re-infection or breakthrough compared to those who remained protected did not always find differences that were statistically significant. However, several studies found an inverse relationship between antibody levels and infection incidence, risk, or viral load, and a correlation between antibody levels and vaccine efficacy (VE). Estimates of the contribution of antibody levels to VE varied from 48.5% to 94.2%, suggesting that both humoral immunity and other immune components contribute to protection. Only two studies estimated a quantitative CoP. For Ancestral SARS-CoV-2, these included 154 (95% confidence interval (CI) 42, 559) anti-S binding antibody units/mL (BAU/mL), and 28.6% (95% CI 19.2, 29.2%) of the mean convalescent antibody level following infection. One study reported a CoP for the Alpha (B.1.1.7) variant of concern of 171 (95% CI 57, 519) BAU/mL. As of our search date, no studies reported an Omicron-specific CoP.\n\nConclusionsThe reviewed literature was limited by a wide variation in assay methodology and antibody targets. Few studies reported SARS-CoV-2 lineage. The studies included in our review suggest that if it exists, a SARS-CoV-2 CoP is likely relative, where higher antibody levels decrease the risk of infection, but do not eliminate it completely. More work is urgently needed in this area to establish a SARS-CoV-2 CoP and guide policy as the pandemic continues.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Julie A Perry", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Selma Osman", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "James Wright", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Melissa Richard-Greenblatt", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Manish Sadarangani", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Shelly Bolotin", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.17.22269394", "rel_title": "Effectiveness of mRNA COVID-19 vaccines against symptomatic SARS-CoV-2 infections during the Delta variant epidemic in Japan: Vaccine Effectiveness Real-time Surveillance for SARS-CoV-2 (VERSUS)", @@ -441741,6 +443675,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.17.475291", + "rel_title": "Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its Variants", + "rel_date": "2022-01-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.475291", + "rel_abs": "Emerging SARS-CoV-2 variants are threatening the efficacy of antibody therapies. Combination treatments including ACE2-Fc have been developed to overcome the evasion of neutralizing antibodies (NAbs) in individual cases. Here we conducted a comprehensive evaluation of this strategy by combining ACE2-Fc with NAbs of diverse epitopes on the RBD. NAb+ACE2-Fc combinations efficiently neutralized HIV-based pseudovirus carrying the spike protein of the Delta or Omicron variants, achieving a balance between efficacy and breadth. In an antibody escape assay using replication-competent VSV-SARS-CoV-2-S, all the combinations had no escape after fifteen passages. By comparison, all the NAbs without combo with ACE2-Fc had escaped within six passages. Further, the VSV-S variants escaped from NAbs were neutralized by ACE2-Fc, revealing the mechanism of NAb+ACE2-Fc combinations survived after fifteen passages. We finally examined ACE2-Fc neutralization against pseudovirus variants that were resistant to the therapeutic antibodies currently in clinic. Our results suggest ACE2-Fc is a universal combination partner to combat SARS-CoV-2 variants including Delta and Omicron.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Haoneng Tang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yong Ke", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Hang Ma", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Lei Han", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China; Jecho Institu" + }, + { + "author_name": "Lei Wang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Huifang Zong", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yunsheng Yuan", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Zhenyu Wang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Yang He", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Yunsong Chang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Shusheng Wang", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Junjun Liu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yali Yue", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Wenbo Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China" + }, + { + "author_name": "Xiaoju Zhang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Ziqi Wang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Li Yang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Hua Chen", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Yanlin Bian", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Baohong Zhang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yunji Liao", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Haiyang Yin", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yi Chen", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Clinical Research Service Center, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "En Zhang", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Xiaoxiao Zhang", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Hua Jiang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China; Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Yueqing Xie", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "John Gilly", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China; Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Mingyuan Wu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Tao Sun", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Jianwei Zhu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China; Jecho Biophar" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.01.20.477105", "rel_title": "In Silico Analysis Of The Effects Of Omicron Spike Amino Acid Changes On The Interactions With Human ACE2 Receptor And Structurally Characterized Complexes With Human Antibodies", @@ -442493,53 +444566,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.01.21.477258", - "rel_title": "Nanoformulated Remdesivir with Extremely Low Content of Poly(2-oxazoline) - Based Stabilizer for Aerosol Treatment of COVID-19", - "rel_date": "2022-01-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.21.477258", - "rel_abs": "The rise of the novel virus SARS-CoV2 which causes the disease known as COVID-19 has led to a global pandemic claiming millions of lives. With no clinically approved treatment for COVID-19, physicians initially struggled to treat the disease and there is still need for improved anti-viral therapies in this area. We conceived early in the pandemic that an inhalable formulation of the drug Remdesivir which directly targets the virus at the initial site of infection could improve therapeutic outcomes in COVID-19. We developed a set of requirements that would be conducive to rapid drug approval: 1) try to use GRAS or GRAS similar reagents 2) minimize excipient concentration and 3) achieve a working concentration of 5 mg/mL Remdesivir to achieve a deliverable dose which is 5-10% of the IV dose. In this work, we discovered that Poly(2-oxazoline) block copolymers can stabilize drug nanocrystal suspensions and provide suitable formulation characteristics for aerosol delivery while maintaining anti-viral efficacy. We believe POx block copolymers can be used as a semi-ubiquitous stabilizer for the rapid development of nanocrystal formulations for new and existing diseases.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jacob D Ramsey", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Ian E Stewart", - "author_inst": "RTI International" - }, - { - "author_name": "Emily A Madden", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Chaemin Lim", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Duhyeong Hwang", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Mark T Heise", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Anthony J Hickey", - "author_inst": "RTI International" - }, - { - "author_name": "Alexander V Kabanov", - "author_inst": "UNC Chapel Hill" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.01.21.477194", "rel_title": "ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads", @@ -443495,6 +445521,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.20.22269321", + "rel_title": "Extreme \u03b3' fibrinogen levels in COVID-19 patients", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269321", + "rel_abs": "BackgroundCOVID-19 progression can be accompanied by a \"cytokine storm\" that leads to secondary sequelae such as thrombosis and acute respiratory distress syndrome. Several inflammatory cytokines have been associated with COVID-19 progression, but have far too much daily intra-individual variability to be useful in tracking the course of the disease. In contrast, we have shown that the inflammatory biomarker {gamma} fibrinogen ({gamma} Fbg) has a 6-fold lower coefficient of variability compared to other inflammatory markers such as hs-CRP. Objectives: The aims of the study were to measure {gamma} Fbg in serial blood samples from COVID-19 patients at a tertiary care medical center in order to investigate its association with clinical measures of disease progression.\n\nMethodsCOVID-19 patients at a tertiary care medical center were retrospectively enrolled between 3/16/2020 and 8/1/2020. {gamma} Fbg was measured using a commercial ELISA. Results: Our results showed that nine out of the seventeen patients with COVID-19 had extremely high levels of {gamma} Fbg. {gamma} Fbg levels were significantly associated with the need for ECMO and with mortality.\n\nConclusionsWe found that COVID-19 patients can develop extraordinarily high levels of {gamma} Fbg. The previous highest {gamma} Fbg level that we are aware of was 80.3 mg/dL found in a study of 10,601 participants in the ARIC study. These results have several important clinical implications. {gamma} Fbg contains a high affinity binding site for thrombin that binds to anion-binding exosite II on thrombin and protects it from inactivation by heparin. High levels of {gamma} Fbg therefore provide a reservoir of heparin-resistant clot-bound thrombin when the {gamma} Fbg is clotted. These findings have potential implications regarding prophylactic anticoagulation of COVID-19 patients and suggest that heparin prophylaxis may be less effective than using other anticoagulants, particularly direct thrombin inhibitors.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "David Henry Farrell", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Matthew Hudkins", + "author_inst": "OHSU" + }, + { + "author_name": "Heather Hamilton", + "author_inst": "OHSU" + }, + { + "author_name": "Samantha J Underwood", + "author_inst": "OHSU" + }, + { + "author_name": "Elizabeth N Dewey", + "author_inst": "OHSU" + }, + { + "author_name": "Diana E Kazmierczak", + "author_inst": "OHSU" + }, + { + "author_name": "Steven C Kazmierczak", + "author_inst": "OHSU" + }, + { + "author_name": "William B Messer", + "author_inst": "OHSU" + }, + { + "author_name": "Akram Khan", + "author_inst": "OHSU" + }, + { + "author_name": "Martin A Schreiber", + "author_inst": "OHSU" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.20.22269618", "rel_title": "Molecular diagnosis of SARS-CoV-2: a validation of saliva samples", @@ -444179,113 +446260,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.01.18.476786", - "rel_title": "SARS-CoV-2 infection results in lasting and systemic perturbations post recovery", - "rel_date": "2022-01-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.18.476786", - "rel_abs": "SARS-CoV-2 has been found capable of inducing prolonged pathologies collectively referred to as Long-COVID. To better understand this biology, we compared the short- and long-term systemic responses in the golden hamster following either SARS-CoV-2 or influenza A virus (IAV) infection. While SARS-CoV-2 exceeded IAV in its capacity to cause injury to the lung and kidney, the most significant changes were observed in the olfactory bulb (OB) and olfactory epithelium (OE) where inflammation was visible beyond one month post SARS-CoV-2 infection. Despite a lack of detectable virus, OB/OE demonstrated microglial and T cell activation, proinflammatory cytokine production, and interferon responses that correlated with behavioral changes. These findings could be corroborated through sequencing of individuals who recovered from COVID-19, as sustained inflammation in OB/OE tissue remained evident months beyond disease resolution. These data highlight a molecular mechanism for persistent COVID-19 symptomology and characterize a small animal model to develop future therapeutics.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Justin J Frere", - "author_inst": "NYU Langone Health, Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Randal A Serafini", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kerri D. Pryce", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Marianna Zazhytska", - "author_inst": "Columbia University" - }, - { - "author_name": "Kohei Oishi", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Ilona Golynker", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Maryline Panis", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Jeffrey Zimering", - "author_inst": "Icahn School of Medicine at Mount Sinai: Department of Neurosurgery" - }, - { - "author_name": "Shu Horiuchi", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Daisy A Hoagland", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Rasmus Moller", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Anne Ruiz", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jonathan B Overdevest", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Albana Kodra", - "author_inst": "Columbia University" - }, - { - "author_name": "Peter D Canoll", - "author_inst": "Columbia University" - }, - { - "author_name": "James E Goldman", - "author_inst": "Columbia University" - }, - { - "author_name": "Alain C Borczuk", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Vasuretha Chandar", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Yaron Bram", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Robert Schwartz", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Stavros Lomvardas", - "author_inst": "Columbia University" - }, - { - "author_name": "Venetia Zachariou", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin tenOever", - "author_inst": "NYU Langone Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.19.476893", "rel_title": "NRP1 and furin as putative mediators of SARS-CoV-2 entry into human brain cells", @@ -445473,6 +447447,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.01.17.476644", + "rel_title": "Nirmatrelvir, an orally active Mpro inhibitor, is a potent inhibitor of SARS-CoV-2 Variants of Concern", + "rel_date": "2022-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.476644", + "rel_abs": "New variants of SARS-CoV-2 with potential for enhanced transmission, replication, and immune evasion capabilities continue to emerge causing reduced vaccine efficacy and/or treatment failure. As of January 2021, the WHO has defined five variants of concern (VOC): B.1.1.7 (Alpha, ), B.1.351 (Beta, {beta}), P.1 (Gamma, {gamma}), B.1.617.2 (Delta, {delta}), and B.1.1.529 (Omicron, o). To provide a therapeutic option for the treatment of COVID-19 and variants, Nirmatrelvir, the antiviral component of PAXLOVID, an oral outpatient treatment recently authorized for conditional or emergency use treatment of COVID-19, was developed to inhibit SARS-CoV-2 replication. Nirmatrelvir (PF-07321332) is a specific inhibitor of coronavirus main protease (Mpro, also referred to as 3CLpro), with potent antiviral activity against several human coronaviruses, including SARS-CoV-2, SARS-CoV, and MERS (Owen et al, Science 2021. doi: 10.1126/science.abl4784). Here, we evaluated PF-07321332 against the five SARS-CoV-2 VOC (, {beta}, {gamma}, {delta},, o) and two Variants of Interest or VOI, C.37 ({lambda}) and B.1.621 (), using qRT-PCR in VeroE6 cells lacking the P-glycoprotein (Pgp) multidrug transporter gene (VeroE6 P-gp knockout cells). Nirmatrelvir potently inhibited USA-WA1/2020 strain, and , {beta}, {gamma}, {lambda}, {delta}, , and o variants in VeroE6 P-gp knockout cells with mean EC50 values 38.0 nM, 41.0 nM, 127.2 nM, 24.9 nM, 21.2 nM, 15.9 nM, 25.7 nM and 16.2 nM, respectively. Sequence analysis of the Mpro encoded by the variants showed ~100% identity of active site amino acid sequences, reflecting the essential role of Mpro during viral replication leading to ability of Nirmatrelvir to exhibit potent activity across all the variants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Devendra K. Rai", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Irina Yurgelonis", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Patricia McMonagle", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Hussin A. Rothan", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Li Hao", + "author_inst": "Pfizer Worldwide Researhc, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Alexey Gribenko", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Elizabeth Titova", + "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA" + }, + { + "author_name": "Barry Kreiswirth", + "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA" + }, + { + "author_name": "Kris M. White", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA, and Global Health Emerging Pathogens Institute, Icahn School of Med" + }, + { + "author_name": "Yuao Zhu", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Annaliesa S. Anderson", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Rhonda D. Cardin", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.17.22269283", "rel_title": "ELF5 is a respiratory epithelial cell-specific risk gene for severe COVID-19", @@ -446309,53 +448346,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.01.15.476448", - "rel_title": "RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis", - "rel_date": "2022-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.15.476448", - "rel_abs": "An important component of efforts to manage the ongoing COVID19 pandemic is the Rapid Assessment of how natural selection contributes to the emergence and proliferation of potentially dangerous SARS-CoV-2 lineages and CLades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations.\n\nAvailabilityRASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl. Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl.\n\nContactDr. Sergei L Kosakovsky Pond (spond@temple.edu).\n\nSupplementary informationN/A", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alexander G Lucaci", - "author_inst": "Temple University" - }, - { - "author_name": "Jordan D Zehr", - "author_inst": "Temple University" - }, - { - "author_name": "Stephen D Shank", - "author_inst": "Temple University" - }, - { - "author_name": "Dave Bouvier", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Han Mei", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Anton Nekrutenko", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Darren P Martin", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Sergei Pond", - "author_inst": "Temple University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.01.14.475727", "rel_title": "Obesity associated with attenuated tissue immune cell responses in COVID-19", @@ -447390,6 +449380,81 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2022.01.14.22269074", + "rel_title": "Evaluation of an emergency safe supply drug and managed alcohol program in COVID-19 isolation hotel shelters for people experiencing homelessness", + "rel_date": "2022-01-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269074", + "rel_abs": "BackgroundDuring a COVID-19 outbreak in the congregate shelter system in Halifax, Nova Scotia, Canada, a multidisciplinary health care team provided an emergency \"safe supply\" of pharmaceutical-grade medications and beverage-grade alcohol to facilitate isolation in COVID-19 hotel shelters for residents who are dependent on these substances. We aimed to evaluate (a) substances and dosages provided, and (b) effectiveness and safety of the program.\n\nMethodsWe retrospectively reviewed medical records of all COVID-19 isolation hotel shelter residents during May 2021. We extracted data on medication and alcohol dosages provided each day. The primary outcome was residents prematurely leaving isolation against public health orders. Adverse events included (a) overdose; (b) intoxication; and (c) diversion, selling, or sharing of medications or alcohol.\n\nResultsOver 25 days, 77 isolation hotel residents were assessed (mean age 42 {+/-} 14 years; 24% women). Sixty-two (81%) residents were provided medications, alcohol, or cigarettes. Seventeen residents (22%) received opioid agonist treatment medications (methadone, buprenorphine, or slow-release oral morphine) and 27 (35%) received hydromorphone tablets. Thirty-one (40%) residents received stimulant tablets with methylphenidate (27; 35%), dextroamphetamine (8; 10%), or lisdexamfetamine (2; 3%). Six residents (8%) received benzodiazepines. Forty-two (55%) residents received alcohol, including 41 (53%) with strong beer, three (3%) with wine, and one (1%) with hard liquor. Over 14 days in isolation, mean daily dosages increased of hydromorphone (45 {+/-} 32 to 57 {+/-} 42mg), methylphenidate (51 {+/-} 28 to 77 {+/-} 37mg), dextroamphetamine (33 {+/-} 16 to 46 {+/-} 13mg), and alcohol (12.3 {+/-} 7.6 to 13.0 {+/-} 6.9 standard drinks). Six residents (8%) left isolation prematurely, but four of those residents returned. Over 1,059 person-days in isolation, there were zero overdoses. Documented concerns regarding intoxication occurred six times (0.005 events/person-day) and medication diversion or sharing three times (0.003 events/person-day).\n\nConclusionsAn emergency safe supply and managed alcohol program, paired with housing, was associated with low rates of adverse events and high rates of successful completion of the 14-day isolation period in COVID-19 isolation hotel shelters. This supports the effectiveness and safety of emergency safe supply prescribing and managed alcohol in this setting.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Thomas D Brothers", + "author_inst": "Dalhousie University; University College London" + }, + { + "author_name": "Malcolm Leaman", + "author_inst": "North End Community Health Centre" + }, + { + "author_name": "Matthew Bonn", + "author_inst": "Canadian Association of People who Use Drugs (CAPUD)" + }, + { + "author_name": "Dan Lewer", + "author_inst": "University College London" + }, + { + "author_name": "Jacqueline Atkinson", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "John Fraser", + "author_inst": "North End Community Health Centre" + }, + { + "author_name": "Amy Gillis", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Michael Gniewek", + "author_inst": "Dalhousie University; Direction 180" + }, + { + "author_name": "Leisha Hawker", + "author_inst": "North End Community Health Centre; Dalhousie University" + }, + { + "author_name": "Heather Hayman", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "Peter Jorna", + "author_inst": "Nova Pharmacy" + }, + { + "author_name": "David Martell", + "author_inst": "Dalhousie University; Direction 180" + }, + { + "author_name": "Tiffany O'Donnell", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre; Dalhousie University" + }, + { + "author_name": "Helen Rivers-Bowerman", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "Leah Genge", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre; Dalhousie University; Direction 180" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2022.01.16.22269377", "rel_title": "The Impact of State Paid Sick Leave Policies on Longitudinal Weekday Workplace Mobility During the COVID-19 Pandemic", @@ -448146,33 +450211,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.01.15.22269364", - "rel_title": "Waning Effectiveness of SARS-CoV-2 mRNA Vaccines in Older Adults: A Rapid Review", - "rel_date": "2022-01-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.15.22269364", - "rel_abs": "The U.S. Centers for Disease Control and Prevention (CDC) and other health agencies have recently recommended a booster dose of COVID-19 vaccines for specific vulnerable groups including adults 65 years and older. There is limited evidence whether vaccine effectiveness in older adults decreases over time, especially against severe COVID-19. We performed a rapid review of published studies available through 04 November 2021 that provide effectiveness data on mRNA vaccines approved/licensed in the United States and identified eight eligible studies which evaluated vaccine effectiveness in older adults. There is evidence of a decline in vaccine effectiveness against both SARS-CoV-2 infection and severe COVID-19 in older adults among studies which analyzed data up to July-October 2021. Our findings suggest that vaccine effectiveness diminishes in older adults, which supports the current recommendation for a booster dose in this population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Etsuro Nanishi", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Ofer Levy", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Al Ozonoff", - "author_inst": "Boston Children's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.14.22269303", "rel_title": "Development of an effective immune response in adults with Down Syndrome after SARS-CoV-2 vaccination", @@ -449072,6 +451110,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.11.22269069", + "rel_title": "Hydroxychloroquine/Chloroquine in COVID-19 With Focus on Hospitalized Patients - A Systematic Review", + "rel_date": "2022-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269069", + "rel_abs": "BackgroundIn the beginning of the COVID-19 pandemic, many hospitalized patients received empiric hydroxychloroquine/chloroquine (HC/CQ). Although some retrospective-observational trials suggested potential benefit, all subsequent randomized clinical trials (RCTs) failed to show benefit and use generally ceased. Herein, we summarize key studies that clinicians advising patients on HC/CQs efficacy:safety calculus in hospitalized COVID-19 patients would want to know about in a practical one-stop-shopping source.\n\nMethodsPubmed and Google were searched on November 4, 2021. Search words included: COVID-19, hydroxychloroquine, chloroquine, in vitro, animal studies, clinical trials, and meta-analyses. Studies were assessed for import and included if considered impactful for benefit:risk assessment.\n\nResultsThese searches led to inclusion of 12 in vitro and animal reports; 12 retrospective-observational trials, 19 interventional clinical trials (17 RCTs, 1 single-arm, 1 controlled but unblinded), and 51 meta-analyses in hospitalized patients.\n\nInconsistent efficacy was seen in vitro and in animal studies for coronaviruses and nil in SARS-CoV-2 animal models specifically. Most retrospective-observational studies in hospitalized COVID-19 patients found no efficacy; QT prolongation and increased adverse events and mortality were reported in some. All RCTs and almost all meta-analyses provided robust data showing no benefit in overall populations and subgroups, yet concerning safety issues in many.\n\nConclusionsHC/CQ have inconsistent anti-coronavirus efficacy in vitro and in animal models, and no convincing efficacy yet substantial safety issues in the overwhelming majority of retrospective-observational trials, RCTs, and meta-analyses in hospitalized COVID-19 patients. HC/CQ should not be prescribed for hospitalized COVID-19 patients outside of clinical trials.\n\nKey Summary PointsPreclinical hydroxychloroquine/chloroquine in vitro studies found inconsistent activity against coronaviruses including SARS-CoV-2.\n\nPreclinical hydroxychloroquine/chloroquine animals studies found inconsistent efficacy for coronaviruses in general and none for SARS-CoV-2.\n\nThe overhwelming majority of RCTs and retrospective-observational trials found no benefit for hydroxychloroquine/chloroquine in hospitalized COVID-19 patients, and many found concerning safety signals.\n\nThe majority of RCTs and retrospective-observational trials found no benefit for hydroxychloroquine/chloroquine in COVID-19 outpatients or for pre- or post-exposure prophylaxis, and some found concerning safety signals.\n\nThe overwhelming majority of meta-analyses found no benefit for hydroxychloroquine/chloroquine in COVID-19 inpatients, outpatients, or for prophylaxis, and many found concerning safety signals.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Daniel Freilich", + "author_inst": "Bassett Medical Center" + }, + { + "author_name": "Jennifer Victory", + "author_inst": "Bassett Research Institute" + }, + { + "author_name": "Anne Gadomski", + "author_inst": "Bassett Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.13.476204", "rel_title": "Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen", @@ -449704,169 +451769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.13.22268697", - "rel_title": "The emergence of two distinct SARS-CoV-2 Gamma related variants during the second wave of COVID-19 in Santa Catarina, Southern Brazil and the rapid spread of P.1-like-II SARS-CoV-2 variant transmission and a regionalization in the Western region", - "rel_date": "2022-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22268697", - "rel_abs": "The Western mesoregion, the State of Santa Catarina (SC), Southern Brazil, was heavily affected as a whole by the COVID-19 pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state through March 2020 to April 2021 using genomic surveillance. During this period, 23 distinct variants, including Beta and Gamma, among which, the Gamma and related lineages were predominant in the second pandemic wave within SC. A regionalization of P.1-like-II in the Western-SC region was observed, concomitant to the increase in cases, mortality, and case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 in SC transmission and highlights the importance of tracking variants, dispersion, and impact of SARS-CoV-2 on the public health systems.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Dayane A. Padilha", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Vilmar Benetti-Filho", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Renato Simoes Moreira Sr.", - "author_inst": "Federal Institute of Santa Catarina" - }, - { - "author_name": "Tatiany Soratto Teixeira Soratto", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Guilherme Augusto Maia", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Ana Paula Christoff", - "author_inst": "Biome-Hub Pesquisa e Desenvolvimento" - }, - { - "author_name": "Fernando Hartmann Barazzetti", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Marcos Andre Schorner", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Fernanda Luiza Ferrari", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Carolina Leite Martins", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Eric Kazuo Kawagoe", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Julia Kinetz Wachter", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Paula Sacchet", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Antuani Baptistella", - "author_inst": "Universidade do Oeste de Santa Catarina" - }, - { - "author_name": "Aline Daina Schlindwein", - "author_inst": "Secretaria de Estado da Saude de Santa Catarina" - }, - { - "author_name": "Bruna Kellet Coelho", - "author_inst": "Laboratorio Central do Estado da Saude de Santa Catarina" - }, - { - "author_name": "Sandra Bianchini Fernandes", - "author_inst": "Laboratorio Central do Estado da Saude de Santa Catarina" - }, - { - "author_name": "Darcita Buerger Rovaris", - "author_inst": "Laboratorio Central do Estado da Saude de Santa Catarina" - }, - { - "author_name": "Marlei Pickler Debiasi dos Anjos", - "author_inst": "Laboratorio Central do Estado da Saude de Santa Catarina" - }, - { - "author_name": "Fernanda Roesene Melo", - "author_inst": "Diretoria de Vigilancia Epidemiologica de Santa Catarina" - }, - { - "author_name": "Bianca Bittencourt", - "author_inst": "Diretoria de Vigilancia Epidemiologica de Santa Catarina" - }, - { - "author_name": "Sthefani da Cunha", - "author_inst": "Servico Nacional de Aprendizagem Industrial - Chapeco" - }, - { - "author_name": "Karine Lena Meneghetti", - "author_inst": "Servico Nacional de Aprendizagem Industrial - Chapeco" - }, - { - "author_name": "Nestor Wendt", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Tamela Zamboni Madaloz", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Marcus Vinicius Duarte Rodrigues", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Doris Sobral Marques Souza", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Milene Hoehr de Moraes", - "author_inst": "Biome-Hub Pesquisa e Desenvolvimento" - }, - { - "author_name": "Rodrigo de Paula Baptista", - "author_inst": "University of Georgia" - }, - { - "author_name": "Guilherme Toledo-Silva", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Guilherme Razzera", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Edmundo Carlos Grisard", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Patricia Hermes Stoco", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Luiz Felipe Valter de Oliveira", - "author_inst": "Biome-Hub Pesquisa e Desenvolvimento" - }, - { - "author_name": "Maria Luiza Bazzo", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Gislaine Fongaro", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Glauber Wagner", - "author_inst": "Federal University of Santa Catarina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.14.22268821", "rel_title": "The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs)", @@ -451214,6 +453116,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.12.22269048", + "rel_title": "A unique dexamethasone-dependent gene expression profile in the lungs of COVID-19 patients", + "rel_date": "2022-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269048", + "rel_abs": "Local immunopathogenesis of COVID-19 acute respiratory distress syndrome (CARDS) and the effects of systemic dexamethasone (DXM) treatment on pulmonary immunity in COVID-19 remain insufficiently understood. To provide further insight into insight into immune regulatory mechanisms in the lungs of CARDS (with and without DXM treatment) and critically ill non-COVID-19 patients (without DXM treatment), transcriptomic RNA-seq analysis of bronchoalveolar lavage fluid (BALF) was performed in these patients. Functional analysis was performed using gene ontology and a blood transcription module, and gene expression of select pro-inflammatory cytokines, interferon-stimulated genes (ISGs) and auto-IFN antibodies were assessed. We found 550 and 2173 differentially expressed genes in patients with non-DXM-CARDS and DXM-CARDS, respectively. DXM-CARDS was characterized by upregulation of genes related to pulmonary innate and adaptive immunity, notably B-cell and complement pathway activation, antigen presentation, phagocytosis and FC-gamma receptor signalling. Pro-inflammatory genes were not differentially expressed in CARDS vs. non-COVID-19, nor did they differ according to DXM. Most ISGs were specifically upregulated in CARDS, particularly in non-DXM-CARDS. Auto-IFN autoantibodies were detectable in BALF of some CARDS patients. In conclusion, DXM treatment was not associated with regulation of pro-inflammatory pathways in CARDS but with regulation of other specific local innate and adaptive immune responses.\n\nsummaryThis study identifies differentially expressed genes in bronchoalveolar fluid of COVID-19 acute respiratory distress patients with a distinct RNA expression profile of those treated with dexamethasone. These results challenge the concept of a COVID-19 specific cytokine storm.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ulrik Fahnoe", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + }, + { + "author_name": "Andreas Ronit", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre" + }, + { + "author_name": "Ronan M.G. Berg", + "author_inst": "Copenhagen University Hospital - Rigshospitalet; Copenhagen University" + }, + { + "author_name": "Sofie E.G. Joergensen", + "author_inst": "Aarhus University Hospital; Aarhus University" + }, + { + "author_name": "Trine H. Mogensen", + "author_inst": "Aarhus University Hospital; Aarhus University" + }, + { + "author_name": "Alexander P. Underwood", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre" + }, + { + "author_name": "Troels K.H. Scheel", + "author_inst": "The Rockefeller University; University of Copenahagen" + }, + { + "author_name": "Jens Bukh", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + }, + { + "author_name": "Ronni R. Plovsing", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.13.22269236", "rel_title": "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples", @@ -452162,45 +454115,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.13.22269178", - "rel_title": "People with HIV Have Higher Risk of COVID-19 Diagnosis but Similar Outcomes than the General Population", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269178", - "rel_abs": "BackgroundWe investigated the effect of HIV on COVID-19 outcomes with attention to selection bias due to differential testing and to comorbidity burden.\n\nMethodsRetrospective cohort analysis using four hierarchical outcomes: positive SARS-CoV-2 test, COVID-19 hospitalization, intensive care unit (ICU) admission, and hospital mortality. The effect of HIV status was assessed using traditional covariate-adjusted, inverse probability weighted (IPW) analysis based on covariate distributions for testing bias (testing IPWs), HIV infection status (HIV IPWs), and combined models. Among PWH, we evaluated whether CD4 count and HIV plasma viral load (pVL) discriminated between those who did or did not develop study outcomes using receiver operating characteristic analysis.\n\nResultsBetween March and November 2020, 63,319 people were receiving primary care services at UCSD, of whom 4,017 were people living with HIV (PWH). PWH had 2.1 times the odds of a positive SARS-CoV-2 test compared to those without HIV after weighting for potential testing bias, comorbidity burden, and HIV-IPW (95% CI 1.6-2.8). Relative to persons without HIV, PWH did not have an increased rate of COVID-19 hospitalization after controlling for comorbidities and testing bias [adjusted incidence rate ratio (aIRR): 0.5, 95% CI: 0.1 - 1.4]. PWH had neither a different rate of ICU admission (aIRR:1.08, 95% CI; 0.31 - 3.80) nor in-hospital death (aIRR:0.92, 95% CI; 0.08 - 10.94) in any examined model. Neither CD4 count nor pVL predicted any of the hierarchical outcomes among PWH.\n\nConclusionsPWH have a higher risk of COVID-19 diagnosis but similar outcomes compared to those without HIV.\n\nSummary pointAfter considering the effects of potential bias due to differential testing, comorbidities, and other patient characteristics, people with HIV had an increased rate of SARS-CoV-2 positivity and similar rates of hospitalization, ICU admission, and death.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Michael E Tang", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Thaidra Gaufin", - "author_inst": "Sansum Clinic" - }, - { - "author_name": "Ryan Anson", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Wenhong Zhu", - "author_inst": "University of California San Diego" - }, - { - "author_name": "William C Mathews", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Edward R Cachay", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2022.01.11.22269070", "rel_title": "Diminished capacities to make treatment decision for COVID-19 vaccination in schizophrenia", @@ -453260,6 +455174,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.11.475947", + "rel_title": "SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction", + "rel_date": "2022-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475947", + "rel_abs": "Coronavirus disease-2019 (COVID-19) is primarily a respiratory disease, however, an increasing number of reports indicate that SARS-CoV-2 infection can also cause severe neurological manifestations, including precipitating cases of probable Parkinsons disease. As microglial NLRP3 inflammasome activation is a major driver of neurodegeneration, here we interrogated whether SARS-CoV-2 can promote microglial NLRP3 inflammasome activation utilising a model of human monocyte-derived microglia. We identified that SARS-CoV-2 isolates can bind and enter microglia, triggering inflammasome activation in the absence of viral replication. Mechanistically, microglial NLRP3 could be both primed and activated with SARS-CoV-2 spike glycoprotein in a NF-{kappa}B and ACE2-dependent manner. Notably, virus- and spike protein-mediated inflammasome activation in microglia was significantly enhanced in the presence of -synuclein fibrils, which was entirely ablated by NLRP3-inhibition. These results support a possible mechanism of microglia activation by SARS-CoV-2, which could explain the increased vulnerability to developing neurological symptoms akin to Parkinsons disease in certain COVID-19 infected individuals, and a potential therapeutic avenue for intervention.\n\nSIGNIFICANCE STATEMENTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) principally affects the lungs, however there is evidence that the virus can also reach the brain and lead to chronic neurological symptoms. In this study, we examined the interaction SARS-CoV-2 with brain immune cells, by using an ex-vivo model of human monocyte-derived microglia. We identified robust activation of the innate immune sensor complex, NLRP3 inflammasome, in cells exposed to SARS-CoV-2. This was dependent on spike protein-ACE2 receptor interaction and was potentiated in the presence of -synuclein. We therefore identify a possible mechanism for SARS-CoV-2 and increased vulnerability to developing neurological dysfunction. These findings support a potential therapeutic avenue for treatment of SARS-CoV-2 driven neurological manifestations, through use of NLRP3 inflammasome or ACE2 inhibitors.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Eduardo A Albornoz", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Alberto A Amarilla", + "author_inst": "School of Chemistry and molecular Biosciences, University of Queensland" + }, + { + "author_name": "Naphak Modhiran", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Sandra Parker", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Xaria X Li", + "author_inst": "School of biomedical sciences, University of Queensland" + }, + { + "author_name": "Danushka K Wijesundara", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Adriana Pliego Zamora", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Christopher LD McMillan", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Benjamin Liang", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Nias Y.G Peng", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Julian D.J Sng", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Fatema Tuj Saima", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Devina Paramitha", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Rhys Parry", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Michael S Avumegah", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Ariel Isaacs", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Martin Lo", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Zaray Miranda-Chacon", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Daniella Bradshaw", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Constanza Salinas-Rebolledo", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Niwanthi W Rajapakse", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Trent Munro", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Alejandro Rojas-Fernandez", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Paul R Young", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Katryn J Stacey", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Alexander A Khromykh", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Keith J Chappell", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Daniel Watterson", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Trent M Woodruff", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.01.11.475327", "rel_title": "Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India", @@ -453996,65 +456041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, - { - "rel_doi": "10.1101/2022.01.10.22269009", - "rel_title": "Prevalence and determinants of persistent symptoms after infection with SARS-CoV-2: Protocol for an observational cohort study (LongCOVID-study)", - "rel_date": "2022-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.10.22269009", - "rel_abs": "BackgroundA substantial proportion of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) report persisting symptoms weeks and months following acute infection. Estimates on prevalence vary due to differences in study designs, populations, heterogeneity of symptoms and the way symptoms are measured. Common symptoms include fatigue, cognitive impairment and dyspnea. However, knowledge regarding the nature and risk factors for developing persisting symptoms is still limited. Hence in this study we aim to determine the prevalence, severity, risk factors and impact on quality of life of persisting symptoms in the first year following acute SARS-CoV-2 infection.\n\nMethodsThe LongCOVID-study is both a prospective and retrospective cohort study with a one year follow up. Participants aged 5 years and above with self-reported positive or negative tests for SARS-CoV-2 will be included in the study. The primary outcome is the prevalence and severity of persistent symptoms in participants that tested positive for SARS-CoV-2 compared to controls. Symptom severity will be assessed for fatigue using the Checklist Individual Strength (CIS subscale fatigue severity), pain (Rand-36/SF-36 subscale bodily pain), dyspnea (Medical Research Council (mMRC)) and cognitive impairment using the Cognitive Failure Questionnaire (CFQ). Secondary outcomes include loss of health-related quality of life (HRQoL) and risk factors for persisting symptoms following infection with SARS-CoV-2.\n\nDiscussionA better understanding regarding the nature of persisting symptoms following SARS-CoV-2 infection will enable better diagnosis, management and will consequently minimize negative consequences on quality of life.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Elizabeth N. Mutubuki", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Tessa van der Maaden", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Ka Yin Leung", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Albert Wong", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Anna D. Tulen", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Simeon de Bruijn", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Lotte Haverman", - "author_inst": "Amsterdam UMC, University of Amsterdam" - }, - { - "author_name": "Hans Knoop", - "author_inst": "Amsterdam UMC, University of Amsterdam" - }, - { - "author_name": "Eelco Eelco", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Albert Jan van Hoek", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Cees C. van den Wijngaard", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.11.22269017", "rel_title": "Healthcare workers' views on mandatory SARS-CoV-2 vaccination in the United Kingdom: findings from the UK-REACH prospective longitudinal cohort study", @@ -454998,6 +456984,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.07.22268883", + "rel_title": "Safety and immunogenicity of the BBIBP-CorV vaccine in adolescents aged 12-17 years in Thai population, prospective cohort study.", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268883", + "rel_abs": "IntroductionCOVID-19 pandemic affects all populations worldwide, including adolescents. Adolescents can develop a severe form of COVID-19, especially with comorbidity underlying. The prior studies of the mRNA COVID-19 vaccine showed excellent effectiveness in adolescents. Therefore, this study aimed to evaluate the safety and effectiveness of the BBIBP-CorV vaccine with the immunobridging approach in Thai adolescents.\n\nMethodsThis single-center, prospective cohort study compared the immunogenicity after 2 doses of the BBIBO-CorV vaccine with 21 days interval of participants aged 12-17 years with 18-30 years at Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand. The key eligible criteria were healthy or had stable pre-existing comorbidity participants, aged 12-17 years. The primary endpoint was the anti-receptor binding domain antibody concentration at 4 weeks after dose 2 of the vaccine. In addition, safety profiles were solicited adverse events within 7 days after each dose of vaccine and any adverse events through 1 month after dose 2 of the vaccine.\n\nResultsFour weeks after the second vaccination, the GMC of anti-RBD antibody in the adolescent cohort was 102.9 BAU/mL (95%CI; 91.0-116.4) and 36.9 BAU/mL (95%CI; 30.9-44.0) in the adult cohort. The GMR of the adolescent cohort was 2.79 (95%CI; 2.25-3.46, p-value; <0.0001) compared with the adult cohort which met non-inferiority criteria. The reactogenicity was slightly less reported in the adolescent cohort compared with the adult cohort. No serious adverse events were reported in both cohorts.\n\nConclusionVaccination with the BBIBP-CorV vaccine in the adolescent participants was safe and effective.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kriangkrai Tawinprai", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Taweegrit Siripongboonsitti", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Thachanun Porntharukchareon", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Preeda Vanichsetakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Saraiorn Thonginnetra", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Krongkwan Niemsorn", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Pathariya Promsena", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Manunya Tandhansakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Naruporn Kasemlawan", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Natthanan Ruangkijpaisal", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Narin Banomyong", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nanthida Phattraprayoon", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Teerapat Ungtrakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Kasiruck Wittayasak", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nawarat Thonwirak", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Kamonwan Soonklang", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Gaidganok Sornsamdang", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nithi Mahanonda", + "author_inst": "Chulabhorn Royal Academy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.08.22268953", "rel_title": "Anti-PEG antibodies boosted in humans by SARS-CoV-2 lipid nanoparticle mRNA vaccine", @@ -455750,101 +457823,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.09.22268986", - "rel_title": "Prevalence of Salivary IgA Reacting with SARS-CoV-2 among Japanese People Unexposed to the Virus", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268986", - "rel_abs": "While the COVID-19 pandemic caused by SARS-CoV-2 has posed a threat to public health as the number of cases and COVID-19-related deaths are increasing worldwide, the incidence of the virus infection are extremely low in Japan compared with many other countries. To explore the reason for this strange phenomenon, we hypothesized the high prevalence of \"natural\" secretory IgA in saliva as mucosal IgA reacting with SARS-CoV-2, and thus surveyed the positivity for, as well as levels of, such reactive salivary IgA in a cohort of Japanese people of a wide range of age. The major findings were that 95/180 (52.78 %) of overall individuals who had not been exposed to SARS-CoV-2 were positive for salivary IgA with the levels ranging from 0.002 to 3.272 ng/ml, and that there may be a negative trend in positivity for salivary IgA according to age. These results suggest a role of mucosal IgA in host defense against SARS-CoV-2 infection.\n\nOne Sentence Summary\"Natural\" secretory immunoglobulin A autoantibodies may play a role in mucosal defense against SARS-CoV-2.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Keiichi Tsukinoki", - "author_inst": "Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University" - }, - { - "author_name": "Tetsuro Yamamoto", - "author_inst": "EPS Research Center, EPS Holdings, Inc." - }, - { - "author_name": "Jiro Saito", - "author_inst": "Medical Station Clinic" - }, - { - "author_name": "Wakako Sakaguchi", - "author_inst": "Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University" - }, - { - "author_name": "Keiichiro Iguchi", - "author_inst": "Department of Orthodontics, Kanagawa Dental University" - }, - { - "author_name": "Yoshinori Inoue", - "author_inst": "Department of Pediatric Dentistry, Kanagawa Dental University" - }, - { - "author_name": "Shigeru Ishii", - "author_inst": "Department of Advanced Oral Surgery, KDU Yokohama Clinic" - }, - { - "author_name": "Chikatoshi Sato", - "author_inst": "Department of Orthodontics, KDU Yokohama Clinic" - }, - { - "author_name": "Mina Yokoyama", - "author_inst": "Department of Pediatric Dentistry, Kanagawa Dental University" - }, - { - "author_name": "Yuki Shiraishi", - "author_inst": "EPS Research Center, EPS Holdings, Inc" - }, - { - "author_name": "Noriaki Kato", - "author_inst": "EPS Research Center, EPS Holdings, Inc." - }, - { - "author_name": "Hiroyasu Shimada", - "author_inst": "EPS Research Center, EPS Holdings, Inc." - }, - { - "author_name": "Akio Makabe", - "author_inst": "Sites Support Section, Foods Department, EP Mediate Co., Ltd." - }, - { - "author_name": "Akihiro Saito", - "author_inst": "Sites Support Section, Foods Department, EP Mediate Co., Ltd." - }, - { - "author_name": "Masanori Tanji", - "author_inst": "EPS Research Center, EPS Holdings, Inc." - }, - { - "author_name": "Isao Nagaoka", - "author_inst": "Faculty of Health Science, Juntendo University" - }, - { - "author_name": "Juri Saruta", - "author_inst": "Department of Education Planning, Kanagawa Dental University" - }, - { - "author_name": "Tetsutaro Yamaguchi", - "author_inst": "Department of Orthodontics, Kanagawa Dental University" - }, - { - "author_name": "Shigenari Kimoto", - "author_inst": "Department of Pediatric Dentistry, Kanagawa Dental University" - }, - { - "author_name": "Hideyo Yamaguchi", - "author_inst": "Teikyo University Institute of Medical Mycology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.01.05.22268617", "rel_title": "Durability and cross-reactivity of SARS-CoV-2 mRNA vaccine in adolescent children", @@ -456755,6 +458733,117 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.07.475248", + "rel_title": "Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2", + "rel_date": "2022-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.07.475248", + "rel_abs": "SARS-CoV-2 lineages are continuously evolving. As of December 2021, the AY.4.2 Delta sub-lineage represented 20 % of sequenced strains in UK and has been detected in dozens of countries. It has since then been supplanted by the Omicron variant. AY.4.2 displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain (NTD) of the spike when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. Here, we analyzed the fusogenicity of the AY.4.2 spike and the sensitivity of an authentic AY.4.2 isolate to neutralizing antibodies. The AY.4.2 spike exhibited similar fusogenicity and binding to ACE2 than Delta. The sensitivity of infectious AY.4.2 to a panel of monoclonal neutralizing antibodies was similar to Delta, except for the anti-RBD Imdevimab, which showed incomplete neutralization. Sensitivity of AY.4.2 to sera from individuals having received two or three doses of Pfizer or two doses of AstraZeneca vaccines was reduced by 1.7 to 2.1 fold, when compared to Delta. Our results suggest that mutations in the NTD remotely impair the efficacy of anti-RBD antibodies. The temporary spread of AY.4.2 was not associated with major changes in spike function but rather to a partially reduced neutralization sensitivity.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nell Saunders", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "William Henry Bolland", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Christophe Rodriguez", + "author_inst": "AP-HP" + }, + { + "author_name": "Slim Fourati", + "author_inst": "AP-HP" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Matthieu Prot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francoise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "David Veyer", + "author_inst": "AP-HP" + }, + { + "author_name": "Helene Pere", + "author_inst": "AP-HP" + }, + { + "author_name": "Nicolas Robillard", + "author_inst": "AP-HP" + }, + { + "author_name": "Madelina Saliba", + "author_inst": "AP-HP" + }, + { + "author_name": "Artem Baidaliuk", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Aymeric Seve", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Laurent Hocqueloux", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Thierry Prazuck", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jean-Michel Pawlotsky", + "author_inst": "AP-HP" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.10.475620", "rel_title": "Strong SARS-CoV-2 N-specific CD8+ T immunity induced by engineered extracellular vesicles associates with protection from lethal infection in mice.", @@ -457715,137 +459804,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.05.21268478", - "rel_title": "Temporary hold of mycophenolate boosts SARS-CoV-2 vaccination-specific humoral and cellular immunity in kidney transplant recipients", - "rel_date": "2022-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.21268478", - "rel_abs": "Transplant recipients exhibit an impaired protective immunity after SARS-CoV-2 vaccination, potentially caused by mycophenolate (MPA) immunosuppression. Recent data from autoimmune patients suggest that temporary MPA hold might significantly improve booster vaccination outcomes. We applied a fourth dose of SARS-CoV-2 vaccine during temporary (5 weeks) MPA hold to 29 kidney transplant recipients, who had not mounted a humoral immune-response to previous vaccinations. Seroconversion until day 32 after vaccination was observed in 76% of patients, associated with acquisition of virus neutralizing capacity. Interestingly, 21/25 (84%) CNI-treated patients responded, but only 1/4 Belatacept-treated patients. In line with humoral responses, counts and relative frequencies of spike receptor binding domain (RBD) specific B cells were significantly increased on day 7 after vaccination, with an increase in RBD specific CD27++CD38+ plasmablasts. Whereas overall proportions of spike-reactive CD4+ T cells remained unaltered after the fourth dose, frequencies were positively correlated with specific IgG levels. Importantly, antigen-specific proliferating Ki67+ and in vivo activated PD1+ T cells significantly increased after re-vaccination during MPA hold, whereas cytokine production and memory differentiation remained unaffected. In summary, MPA hold was safe and augmented all arms of immunity during booster vaccination, suggesting its implementation in vaccination protocols for clinically stable transplant recipients.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Eva Schrezenmeier", - "author_inst": "Charite-Universitaetsmedizin, Berlin" - }, - { - "author_name": "Hector Rincon-Arevalo", - "author_inst": "Charite Universitaetsmedizin" - }, - { - "author_name": "Annika Jens", - "author_inst": "Charite- Universitaetesmedizin Berlin" - }, - { - "author_name": "Ana-Luisa Stefanski", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Charlotte Hammett", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Bilgin Osmanodja", - "author_inst": "Charite University, Berlin, Germany" - }, - { - "author_name": "Nadine Koch", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Bianca Zukunft", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Julia Beck", - "author_inst": "University Medical Center Gooettingen" - }, - { - "author_name": "Michael Oellerich", - "author_inst": "University Medical Center Goettingen" - }, - { - "author_name": "Vanessa Pross", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Carolin Stahl", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Mira Choi", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Friederike Bachmann", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Lutz Liefeldt", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Petra Glander", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Ekke Schuetz", - "author_inst": "Chronix Biomedical GmbH Goettingen" - }, - { - "author_name": "Kirsten Bornemann-Kolatzki", - "author_inst": "Chronix Biomedical GmbH, Goettingen" - }, - { - "author_name": "Covadonga Lopez del Moral", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Hubert Schrezenmeier", - "author_inst": "Institute of Transfusion Medicine, Ulm University" - }, - { - "author_name": "Carlin Ludwig", - "author_inst": "Institute of Transfusion Medicine, Ulm University" - }, - { - "author_name": "Bernd Jahrdoerfer", - "author_inst": "Institute of Transfusion Medicine, Ulm University" - }, - { - "author_name": "Kai Uwe Eckardt", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Nils Lachmann", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Katja Kotsch", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Thomas Doerner", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Fabian Halleck", - "author_inst": "Charite Berlin" - }, - { - "author_name": "Arne Sattler", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Klemens Budde", - "author_inst": "Charite Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2022.01.06.21268555", "rel_title": "VarLOCK - sequencing independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance", @@ -458749,6 +460707,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.01.06.475246", + "rel_title": "Climate Surveys of Biomedical PhD Students and Training Faculty Members in the Time of Covid", + "rel_date": "2022-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.06.475246", + "rel_abs": "In July 2020, four months into the disruption of normal life caused by the Covid-19 pandemic, we assessed the institutional climate within the School of Medicine. Voluntary surveys were completed by 135 graduate students in 11 PhD-granting programs and by 83 members of the graduate training faculty. Several themes emerged. PhD students work hard, but the number of hours spent on research-related activities has declined during the pandemic. The students are worried about the pandemics impact on their research productivity, consequent delays in their graduation, and diminished future job prospects. Many late stage PhD students feel they do not have adequate time or resources to plan for their future careers. Symptoms of anxiety and/or depression are prevalent in 51% of the students, based on answers to standardized questions. Most students report they have strong mentoring relationships with their faculty advisors and like their programs, but they identify to a lesser extent with the medical school as a whole. Faculty think highly of their graduate students and are also worried about the pandemics impact upon productivity and the welfare of students. Students are interested in access to an Ombuds office, which is currently being organized by the medical school. Moving forward, the school needs to address issues of bias, faculty diversity, support for mentor training, professional development, and the imposter syndrome. We must also work to create a climate in which many more graduate students feel that they are valued members of the academic medicine community.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Deepti Ramadoss", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Meghan Campbell McCord", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Johm P Horn", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2022.01.05.21268323", "rel_title": "Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey", @@ -459420,101 +461405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2022.01.05.22268785", - "rel_title": "The impact of vaccination on incidence and outcomes of SARS-CoV-2 infection in patients with kidney failure in Scotland", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268785", - "rel_abs": "BackgroundPatients with kidney failure requiring kidney replacement therapy (KRT) are at high risk of complications and death following SARS-CoV-2 infection with variable antibody responses to vaccination reported. We investigated the effects of COVID-19 vaccination on incidence of infection, hospitalization and death of COVID-19 infection.\n\nMethodsStudy design was an observational data linkage cohort study. Multiple healthcare datasets were linked to ascertain all SARS-CoV-2 testing, vaccination, hospitalization, and mortality data for all patients treated with KRT in Scotland, from the start of the pandemic over a period of 20 months. Descriptive statistics, survival analyses and vaccine effectiveness were calculated.\n\nResultsAs of 19th September 2021, 93% (n=5281) of the established KRT population in Scotland had received two doses of an approved SARS-CoV-2 vaccine. Over the study period, there were 814 cases of SARS-CoV-2 infection (15.1% of the KRT population). Vaccine effectiveness against infection and hospitalization was 33% (95% CI 0-52) and 38% (95% CI 0-57) respectively. 9.2% of fully vaccinated individuals died within 28 days of a SARS-CoV-2 positive PCR test (7% dialysis patients and 10% kidney transplant recipients). This compares to <0.1% of the vaccinated Scottish population being admitted to hospital or dying death due to COVID19 during that period.\n\nConclusionsThese data demonstrate a primary vaccine course of two doses has limited impact on COVID-19 infection and its complications in patients treated with KRT. Adjunctive strategies to reduce risk of both COVID-19 infection and its complications in this population are urgently required.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Samira Bell", - "author_inst": "University of Dundee" - }, - { - "author_name": "Jacqueline Campbell", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Emilie Lambourg", - "author_inst": "University of Dundee" - }, - { - "author_name": "Chrissie Watters", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Martin O'Neill", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Alison Almond", - "author_inst": "NHS Dumfries and Galloway" - }, - { - "author_name": "Katharine Buck", - "author_inst": "NHS Fife" - }, - { - "author_name": "Edward Carr", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Laura Clark", - "author_inst": "NHS Grampian" - }, - { - "author_name": "Zoe Cousland", - "author_inst": "NHS Lanarkshire" - }, - { - "author_name": "Mark Findlay", - "author_inst": "NHS GGC" - }, - { - "author_name": "Nicola Joss", - "author_inst": "NHS Highland" - }, - { - "author_name": "Wendy Metcalfe", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Michaela Petrie", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Elaine Spalding", - "author_inst": "NHS Ayrshire and Arran" - }, - { - "author_name": "Jamie Traynor", - "author_inst": "NHS GGC" - }, - { - "author_name": "Vinod Sanu", - "author_inst": "NHS Tayside" - }, - { - "author_name": "Peter Thomson", - "author_inst": "NHS GGC" - }, - { - "author_name": "Shona Methven", - "author_inst": "NHS Grampian" - }, - { - "author_name": "Patrick Mark", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2022.01.06.22268835", "rel_title": "An integrated lab-on-a-chip device for RNA extraction, amplification and CRISPR-Cas12a-assisted detection for COVID-19 screening in resource-limited settings", @@ -460566,6 +462456,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.03.22268704", + "rel_title": "Immune responses to inactivated and vector-based vaccines in individuals previously infected with SARS-CoV-2", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268704", + "rel_abs": "Immunity wanes in individuals previously infected with SARS-CoV-2, and vaccinating those individuals may help reduce reinfection. Herein, reactogenicity and immunogenicity following vaccination with inactivated (CoronaVac) and vector-based (ChAdOx1-S, AZD1222) vaccines were examined in previously infected individuals. Immune response was also compared between short and long intervals between first date of detection and vaccination. Adverse events were mild but were higher with AZD1222 than with CoronaVac. Baseline IgG-specific antibodies and neutralizing activity were significantly higher with shorter than longer intervals. With a single-dose vaccine, IgG and IgA-specific binding antibodies, neutralizing activity, and total interferon-gamma response peaked at 14 days. Immune response was significantly higher in recovered individuals than in infection-naive individuals. Antibody response was greater with longer than shorter intervals. AZD1222 induced higher antibody and T cell responses than those of CoronaVac. Thus, to achieve immunity, individuals with prior SARS-CoV-2 exposure may require only a single dose of AZD1222 or two doses of CoronaVac to achieve the immune response. These findings supported vaccine strategies in previously infected individuals.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.03.22268681", "rel_title": "Reported Cases of Multisystem Inflammatory Syndrome in Children Aged 12 to 20 Years in the United States Who Received COVID-19 Vaccine, December 2020 through August 2021", @@ -461230,37 +463187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.01.04.22268738", - "rel_title": "Radiological follow-up of adults hospitalised with pneumonia and SARS-CoV-2 infection, in Bristol UK, during the COVID19 pandemic", - "rel_date": "2022-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268738", - "rel_abs": "IntroductionRadiological change which may be attributed to infection can also be attributable to lung cancer. Patients with SARS-CoV-2 infection can develop groundglass lung opacification which may result in chronic lung changes. Current British Thoracic Society (BTS) guidelines recommend patients with pneumonia and COVID19 undergo repeat chest radiography.\n\nMethodsA single-centre audit of patients hospitalised with community-acquired pneumonia or COVID19 over three time periods during the COVID19 pandemic (Aug-Dec 2020, Jun-Aug 2021, Dec-Jan 2022). We assessed whether patients were eligible for radiological follow-up and if repeat radiological investigation occurred.\n\nResults1040 adults were hospitalised with infective radiological change (pneumonia=596, COVID19=444). 831/1040 patients (80%) required radiological follow-up under BTS guideline criteria: there was minimal difference between the first two time periods studied. Patients hospitalised with CAP were less likely to have radiological follow-up planned than those admitted with COVID19 disease (49% versus 59% respectively). Following a change in hospital policy, follow-up rates increased to 69% and 71% for pneumonia and COVID19. Overall, only 47% eligible patients received follow-up in line with current guidelines.\n\nConclusionBTS guideline adherence is important to avoid delay in diagnosing underlying malignancy or chronic lung disease. Radiological follow-up following CAP and COVID19 may be suboptimal, with a paucity of data. Follow-up arranged under the hospital team was more likely to occur than when the GP was responsible for instigating repeat radiological imaging. Further investigation into rates of radiological follow-up should be undertaken, including reasons for non-adherence, to ensure patients receive appropriate treatment following respiratory infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Gabriella Ruffino", - "author_inst": "Acute Medical Unit, Southmead Hospital, Bristol, UK, BS10 5NB" - }, - { - "author_name": "Rachel L Williams", - "author_inst": "Research and Innovation, North Bristol NHS Trust, Southmead Hospital, Bristol, UK, BS10 5NB" - }, - { - "author_name": "Shaney Barratt", - "author_inst": "Academic Respiratory Unit, Learning and Research, Southmead Hospital, Bristol, UK, BS10 5NB and Department of Respiratory Medicine, Southmead Hospital, Bristol," - }, - { - "author_name": "Catherine Hyams", - "author_inst": "Academic Respiratory Unit, Learning and Research, Southmead Hospital, Bristol, UK, BS10 5NB; Schools of Population Health Sciences and Cellular and Molecular Me" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.01.04.22268742", "rel_title": "COVID-19-Associated Hospitalizations Among Children Less Than 12 Years of Age in the United States", @@ -462324,6 +464250,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.05.22268637", + "rel_title": "Personal Resilience, Social Support, and Organizational Support Impact Burnout among Nurses During COVID-19", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268637", + "rel_abs": "BackgroundNurses have been under heavy workloads since the outbreak of COVID-19 and are at a high risk of infection, leading to a high level of psychosocial risk. This can adversely affect nurses both psychologically and physically. Burnout is caused by prolonged stress during work. In the nursing profession, burnout is common, potentially affecting the well-being of nurses and their productivity. The identification of factors that may contribute to maintaining mental health and reducing burnout among frontline nurses during a pandemic is essential.\n\nPurposeThe purpose of this study was to explore how personal resilience, social support, and organizational support impact burnout among frontline staff nurses.\n\nMethodsThis study involved 129 registered nurses from a COVID-19 designated hospital using four standardized scales.\n\nResultsThe mean age of the respondents was 29.46 years (standard deviation = 4.89). The mean number of years respondents worked in this organization was 5.60 years and the nursing profession was 4.16 years. Most of the respondents were female and held a bachelors degree in nursing. Multiple regression analysis was performed to predict burnout. Burnout was statistically significantly predicted by the multiple regression model (R2 = .420, F (3, 125) = 10.941, p < .0001; adjusted R2 = .406). Personal resilience, social support, and organizational support added statistically significantly to the prediction of burnout (p < .05).\n\nConclusionFindings from multiple regression analysis showed that nurses with low resilience and those who perceived inadequate social and organizational support had a higher risk of reporting more burnout. As a result of a bivariate analysis, there was no significant correlation between nurse variables and burnout level, except for age, which was negatively correlated with burnout level. Accordingly, young nurses tend to experience burnout, and nurse directors and managers must address this problem.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hanan Daghash", + "author_inst": "Al-Ghad International Colleges for Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2022.01.05.22268646", "rel_title": "SARS-CoV-2 Genetic diversity and lineage dynamics of in Egypt", @@ -463224,69 +465169,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.01.03.474825", - "rel_title": "Structural basis of Omicron neutralization by affinity-matured public antibodies", - "rel_date": "2022-01-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.03.474825", - "rel_abs": "The SARS-CoV-2 Omicron1 Variant of Concern (B.1.1.529) has spread rapidly in many countries. With a spike that is highly diverged from that of the pandemic founder, it escapes most available monoclonal antibody therapeutics2,3 and erodes vaccine protection4. A public class of IGHV3-53-using SARS-CoV-2 neutralizing antibodies5,6 typically fails to neutralize variants carrying mutations in the receptor-binding motif7-11, including Omicron. As antibodies from this class are likely elicited in most people following SARS-CoV-2 infection or vaccination, their subsequent affinity maturation is of particular interest. Here, we isolated IGHV3-53-using antibodies from an individual seven months after infection and identified several antibodies capable of broad and potent SARS-CoV-2 neutralization, extending to Omicron without loss of potency. By introducing select somatic hypermutations into a germline-reverted form of one such antibody, CAB-A17, we demonstrate the potential for commonly elicited antibodies to develop broad cross-neutralization through affinity maturation. Further, we resolved the structure of CAB-A17 Fab in complex with Omicron spike at an overall resolution of 2.6 [A] by cryo-electron microscopy and defined the structural basis for this breadth. Thus, public SARS-CoV-2 neutralizing antibodies can, without modified spike vaccines, mature to cross-neutralize exceptionally antigenically diverged SARS-CoV-2 variants.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Daniel J. Sheward", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Pradeepa Pushparaj", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Hrishikesh Das", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Changil Kim", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Sungyong Kim", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Leo Hanke", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Robert Dyrdak", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Gerald M McInerney", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jan Albert", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Ben Murrell", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Gunilla B. Karlsson Hedestam", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "B. Martin H\u00e4llberg", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.30.474592", "rel_title": "The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain", @@ -464446,6 +466328,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.02.22268629", + "rel_title": "Cognitive predictors of vaccine hesitancy and COVID-19 mitigation behaviors in a population representative sample", + "rel_date": "2022-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.02.22268629", + "rel_abs": "With the continued threat of COVID-19, predictors of vaccination hesitancy and mitigation behaviors are critical to identify. Prior studies have found that cognitive factors are associated with some COVID-19 mitigation behaviors, but few studies employ representative samples and to our knowledge no prior studies have examined cognitive predictors of vaccine hesitancy. The purpose of the present study, conducted among a large national sample of Canadian adults, was to examine associations between cognitive variables (executive function, delay discounting, and temporal orientation) and COVID-19 mitigation behaviors (vaccination, mask wearing, social distancing, and hand hygiene). Findings revealed that individuals with few executive function deficits, limited delay discounting and who adopted a generally future-orientation mindset were more likely to be double-vaccinated and to report performing COVID-19 mitigation behaviors with high consistency. The most reliable findings were for delay discounting and future orientation, with executive function deficits predicting mask wearing and hand hygiene behaviors but not distancing and vaccination. These findings identify candidate mediators and moderators for health communication messages targeting COVID-19 mitigation behaviors and vaccine hesitancy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna Hudson", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Peter A Hall", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Sara Hitchman", + "author_inst": "University of Zurich" + }, + { + "author_name": "Gang Meng", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Geoffrey T Fong", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.30.21268571", "rel_title": "Estimation the state of the Covid-19 epidemic curve in Mayotte", @@ -465222,53 +467139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2022.01.01.22268614", - "rel_title": "Executive dysfunction following SARS-CoV-2 infection: A cross-sectional examination in a population-representative sample", - "rel_date": "2022-01-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.01.22268614", - "rel_abs": "BackgroundPrior studies have documented reliable associations between SARS-CoV-2 infection and adverse cognitive impact in older adults. The current study sought to determine whether SARS-CoV-2 infection and COVID-19 symptom severity are associated with cognitive dysfunction among young adults and middled-aged adults in the general population.\n\nMethodThe Canadian COVID-19 Experiences Project (CCEP) survey involves 1,958 adults with equal representation of vaccinated and vaccine hesitant adults between the ages of 18 and 54 years. The sample comprised 1,958 adults with a mean age of 37 years (SD=10.4); 60.8% were female. The primary outcome was symptoms of cognitive dysfunction assessed via an abbreviated form of the Barkley Deficits in Executive Functioning Scale (BDEFS) and performance on a validated decision-making task.\n\nResultsYoung and middle-aged adults with a positive SARS-CoV-2 infection history reported a significantly higher number of symptoms of executive dysfunction (Madj=1.89, SE=0.08, CI: 1.74, 2.04; n=175) than their non-infected counterparts (Madj=1.63, SE=0.08, CI: 1.47,1.80; n=1,599; {beta}=0.26, p=.001). Among those infected, there was a dose-response relationship between COVID-19 symptom severity and level of executive dysfunction, with moderate ({beta}=0.23, CI: 0.003-0.46) and very/extremely severe ({beta}= 0.69, CI: 0.22-1.16) COVID-19 symptoms being associated with significantly greater dysfunction, compared to asymptomatic. These effects remained reliable and of similar magnitude after controlling for age, sex, vaccination status, income, and geographic region, and after removal of those who had been intubated during hospitalization. Similar effects were found for the decision-making task.\n\nConclusionsPositive SARS-CoV-2 infection history and COVID-19 symptom severity are associated with executive dysfunction among young and middle-aged adults with no history of medically induced coma. These findings are evident on self-reported and task-related indicators of cognitive function.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Peter A Hall", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Gang Meng", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Anna Hudson", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Mohammad Nazmus Sakib", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Sara C Hitchman", - "author_inst": "University of Waterloo" - }, - { - "author_name": "James McKillop", - "author_inst": "McMaster University" - }, - { - "author_name": "Warren Bickel", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Geoffrey T Fong", - "author_inst": "University of Waterloo" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.30.21268495", "rel_title": "Comparison of outcomes from COVID infection in pediatric and adult patients before and after the emergence of Omicron", @@ -466324,6 +468194,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.12.29.21268529", + "rel_title": "Humoral immune responses against SARS-CoV-2 variants including omicron in solid organ transplant recipients after three doses of a COVID-19 mRNA vaccine", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268529", + "rel_abs": "BackgroundSolid organ transplant recipients (SOTR), who typically receive post-transplant immunosuppression, show increased COVID-19-related mortality. It is unclear whether an additional dose of COVID-19 vaccines in SOTR can overcome the reduced immune responsiveness against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants.\n\nMethodsWe performed a prospective cohort study of 53 SOTR receiving SARS-CoV-2 vaccination into a prospective cohort study performing detailed immunoprofiling of humoral immune responses against SARS-CoV-2 and its variants.\n\nResultsPrior to the additional vaccine dose, 60.3% of SOTR showed no measurable neutralization and only 18.9% demonstrated neutralizing activity of >90% following two vaccine doses. More intensive immunosuppression, antimetabolites in particular, negatively impacted antiviral immunity. While absolute IgG levels were lower in SOTR than controls, antibody titers against microbial recall antigens were in fact higher. In contrast, SOTR showed reduced vaccine-induced IgG/IgA antibody titers against SARS-CoV-2 and its delta variants. Vaccinated SOTR showed a markedly fewer linear B cell epitopes, indicating reduced B cell diversity. Importantly, a third vaccine dose led to an increase in anti-SARS-CoV-2 antibody titers and neutralizing activity across alpha, beta and delta variants. However, we observed a significant decrease in anti-spike antibody titers with the omicron variant.\n\nConclusionsOnly a small subgroup of SOTR generated functionally relevant antibodies after completing the initial vaccine series based on dysfunctional priming of immune responses against novel antigens. An additional dose of the vaccine results in dramatically improved antibody responses against all SARS-CoV-2 variants except omicron.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Kapil K. Saharia", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Jennifer S. Husson", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Silke V. Niederhaus", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Thierry Iraguha", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Stephanie V. Avila", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Youngchae J. Yoo", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Nancy M. Hardy", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Xiaoxuan Fan", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Destiny Omili", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Alice Crane", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Amber Carrier", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Wen Y. Xie", + "author_inst": "Department of Surgery, University of Florida College of Medicine" + }, + { + "author_name": "Erica Vander Mause", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Kim Hankey", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Sheri Bauman", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Patricia Lesho", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Heather D. Mannuel", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Ashish Ahuja", + "author_inst": "Department of Medicine, University of Maryland Medical Center" + }, + { + "author_name": "Minu Mathew", + "author_inst": "Divison of Infectious Diseases, University of Maryland School of Medicine" + }, + { + "author_name": "James Avruch", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "John Baddley", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Olga Goloubeva", + "author_inst": "Department of Epidemiology and Public Health, University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Kirti Shetty", + "author_inst": "Division of Hepatology/Liver Transplantation, University of Maryland School of Medicine," + }, + { + "author_name": "Saurabh Dahiya", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Aaron P. Rapoport", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Tim Luetkens", + "author_inst": "Department of Microbiology and Immunology, University of Maryland" + }, + { + "author_name": "Djordje Atanackovic", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2021.12.30.21268565", "rel_title": "Effectiveness of COVID-19 vaccines against Omicron or Delta infection", @@ -467164,109 +469157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.30.21268540", - "rel_title": "Magnitude and breadth of neutralizing antibody responses elicited by SARS-CoV-2 infection or vaccination", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268540", - "rel_abs": "Multiple SARS-CoV-2 variants that possess mutations associated with increased transmission and antibody escape have arisen over the course of the current pandemic. While the current vaccines have largely been effective against past variants, the number of mutations found on the Omicron (B.1.529) spike appear to diminish the efficacy of pre-existing immunity. Using pseudoparticles expressing the spike of several SARS-CoV-2 variants, we evaluated the magnitude and breadth of the neutralizing antibody response over time in naturally infected and in mRNA-vaccinated individuals. We observed that while boosting increases the magnitude of the antibody response to wildtype (D614), Beta, Delta and Omicron variants, the Omicron variant was the most resistant to neutralization. We further observed that vaccinated healthy adults had robust and broad antibody responses while responses were relatively reduced in vaccinated pregnant women, underscoring the importance of learning how to maximize mRNA vaccine responses in pregnant populations. Findings from this study show substantial heterogeneity in the magnitude and breadth of responses after infection and mRNA vaccination and may support the addition of more conserved viral antigens to existing SARS-CoV-2 vaccines.\n\nOne Sentence SummaryDiminished efficacy of pre-existing immunity to highly mutated SARS-CoV-2 variants.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Benjamin L. Sievers", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Saborni Chakraborty", - "author_inst": "Stanford University" - }, - { - "author_name": "Yong Xue", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Terri Gelbart", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Joseph C. Gonzalez", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Arianna G. Cassidy", - "author_inst": "Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA," - }, - { - "author_name": "Yarden Golan", - "author_inst": "Department of Bioengineering and Therapeutic Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Mary Prahl", - "author_inst": "Division of Pediatric Infectious Diseases, Department of Pediatrics, University of California, San Francisco, CA, USA." - }, - { - "author_name": "Stephanie L. Gaw", - "author_inst": "Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA," - }, - { - "author_name": "Prabhu S Arunachalam", - "author_inst": "Stanford University" - }, - { - "author_name": "Catherine A Blish", - "author_inst": "Stanford University" - }, - { - "author_name": "Scott D. Boyd", - "author_inst": "Stanford University" - }, - { - "author_name": "Mark M Davis", - "author_inst": "Stanford University" - }, - { - "author_name": "Prasanna Jagannathan", - "author_inst": "Stanford University" - }, - { - "author_name": "Kari C. Nadeau", - "author_inst": "Stanford University" - }, - { - "author_name": "Bali Pulendran", - "author_inst": "Stanford University" - }, - { - "author_name": "Upinder Singh", - "author_inst": "Stanford University" - }, - { - "author_name": "Richard H. Scheuermann", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Matthew H. Frieman", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Sanjay Vashee", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Taia T. Wang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Gene S Tan", - "author_inst": "J. Craig Venter Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.30.21268553", "rel_title": "Performance of COVIDSeq and Swift normalase amplicon SARS-CoV-2 panels for SARS-CoV-2 Genomes Sequencing: Practical Guide and Combining FASTQ Strategy", @@ -468558,6 +470448,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.24.474110", + "rel_title": "Reduced infectivity but increased immune escape of the new SARS-CoV-2 variant of concern Omicron", + "rel_date": "2021-12-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.24.474110", + "rel_abs": "A new detected SARS-CoV-2 variant Omicron (B.1.1.529) had reported from more than 80 countries. In the past few weeks, a new wave of infection driven by Omicron is in progress. Omicron Spike (S) protein pseudotyped virus was used to determine the effect of S mutations on its capacity of infectivity and immune evasion. Our results showed the lower entry efficiency and less cleavage ability of Omicron than D614G variant. Pseudotype-based neutralizing assay was performed to analyze neutralizing antibodies elicited by previously infection or the RBD-based protein subunit vaccine ZF2001 against the Omicron variant. Sera sampled at around one month after symptom onset from 12 convalescents who were previously infected by SARS-CoV-2 original strain shows a more than 20-fold decrease of neutralizing activity against Omicron variant, when compared to D614G variant. Among 12 individuals vaccinated by RBD subunit vaccine, 58.3% (7/12) sera sampled at 15-60 days after 3rd-dose vaccination did not neutralize Omicron. Geometric mean titers (GMTs, 50% inhibitory dose [ID50]) of these sera against Omicron were 9.4-fold lower than against D614G. These results suggested a higher risk of Omicron breakthrough infections and reduced efficiency of the protective immunity elicited by existing vaccines. There are important implications about the modification and optimization of the current epidemic prevention and control including vaccine strategies and therapeutic antibodies against Omicron variant.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jie Hu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Pai Peng", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kang Wu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Quan-xin Long", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Juan Chen", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ni Tang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ailong Huang", + "author_inst": "Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.30.21268537", "rel_title": "The rich-to-poor vaccine donation game: When will self-interested countries donate their surplus vaccines during pandemics?", @@ -469318,121 +471255,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.30.474519", - "rel_title": "SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1\u03b1/XBP1 ER stress pathway in human lung-derived cells", - "rel_date": "2021-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474519", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available, or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the master UPR sensor IRE1 kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1 as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1 through autophosphorylation, but its RNase activity fails to splice XBP1. Moreover, while IRE1 was dispensable for replication in human cells for all coronaviruses tested, it was required for maximal expression of genes associated with several key cellular functions, including the interferon signaling pathway, during SARS-CoV-2 infection. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1, perhaps as a strategy to eliminate detection by the host immune system.\n\nIMPORTANCESARS-CoV-2 is the third lethal respiratory coronavirus after MERS-CoV and SARS-CoV to emerge this century, causing millions of deaths world-wide. Other common coronaviruses such as HCoV-OC43 cause less severe respiratory disease. Thus, it is imperative to understand the similarities and differences among these viruses in how each interacts with host cells. We focused here on the inositol-requiring enzyme 1 (IRE1) pathway, part of the host unfolded protein response to virus-induced stress. We found that while MERS-CoV and HCoV-OC43 fully activate the IRE1 kinase and RNase activities, SARS-CoV-2 only partially activates IRE1, promoting its kinase activity but not RNase activity. Based on IRE1-dependent gene expression changes during infection, we propose that SARS-CoV-2 prevents IRE1 RNase activation as a strategy to limit detection by the host immune system.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Long C Nguyen", - "author_inst": "University of Chicago" - }, - { - "author_name": "David M Renner", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Diane Silva", - "author_inst": "University of Chicago" - }, - { - "author_name": "Dongbo Yang", - "author_inst": "University of Chicago" - }, - { - "author_name": "Nicholas Parenti", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Kaeri M Medina", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Vlad Nicolaescu", - "author_inst": "University of Chicago" - }, - { - "author_name": "Haley Gula", - "author_inst": "University of Chicago" - }, - { - "author_name": "Nir Drayman", - "author_inst": "University of Chicago" - }, - { - "author_name": "Andrea Valdespino", - "author_inst": "University of Chicago" - }, - { - "author_name": "Adil Mohamed", - "author_inst": "University of Chicago" - }, - { - "author_name": "Christopher Dann", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kristin Wannemo", - "author_inst": "University of Chicago" - }, - { - "author_name": "Lydia Robinson-Mailman", - "author_inst": "University of Chcago" - }, - { - "author_name": "Alan Gonzalez", - "author_inst": "University of Chicago" - }, - { - "author_name": "Leticia Stock", - "author_inst": "University of Chicago" - }, - { - "author_name": "Mengrui Cao", - "author_inst": "University of Chicago" - }, - { - "author_name": "Zeyu Qiao", - "author_inst": "University of Chicago" - }, - { - "author_name": "Raymond E Moellering", - "author_inst": "University of Chicago" - }, - { - "author_name": "Savas Tay", - "author_inst": "University of Chicago" - }, - { - "author_name": "Glenn Randall", - "author_inst": "University of Chicago" - }, - { - "author_name": "Michael F Beers", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Marsha R Rosner", - "author_inst": "University of Chicago" - }, - { - "author_name": "Scott A Oakes", - "author_inst": "University of Chicago" - }, - { - "author_name": "Susan R Weiss", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.28.21268398", "rel_title": "mRNA Booster Vaccines Elicit Strong Protection Against SARS-CoV-2 Omicron Variant in Cancer Patients", @@ -470552,6 +472374,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.12.27.21268459", + "rel_title": "Immunogenicity of heterologous BNT162b2 booster in fully vaccinated individuals with CoronaVac against SARS-CoV-2 variants Delta and Omicron: the Dominican Republic Experience", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268459", + "rel_abs": "The recent emergence of the SARS-CoV-2 Omicron variant is raising concerns because of its increased transmissibility and by its numerous spike mutations with potential to evade neutralizing antibodies elicited by COVID-19 vaccines. The Dominican Republic was among the first countries in recommending the administration of a third dose COVID-19 vaccine to address potential waning immunity and reduced effectiveness against variants. Here, we evaluated the effects of a heterologous BNT162b2 mRNA vaccine booster on the humoral immunity of participants that had received a two-dose regimen of CoronaVac, an inactivated vaccine used globally. We found that heterologous CoronaVac prime followed by BNT162b2 booster regimen induces elevated virus-specific antibody levels and potent neutralization activity against the ancestral virus and Delta variant, resembling the titers obtained after two doses of mRNA vaccines. While neutralization of Omicron was undetectable in participants that had received a two-dose regimen of CoronaVac vaccine, BNT162b2 booster resulted in a 1.4-fold increase in neutralization activity against Omicron, compared to two-dose mRNA vaccine. Despite this increase, neutralizing antibody titers were reduced by 6.3-fold and 2.7-fold for Omicron compared to ancestral and Delta variant, respectively. Surprisingly, previous SARS-CoV-2 infection did not affect the neutralizing titers for Omicron in participants that received the heterologous regimen. Our findings have immediate implications for multiples countries that previously used a two-dose regimen of CoronaVac and reinforce the notion that the Omicron variant is associated with immune escape from vaccines or infection-induced immunity, highlighting the global need for vaccine boosters to combat the impact of emerging variants.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Eddy Perez-Then", + "author_inst": "Ministry of Health, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Carolina Lucas", + "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Valter Silva Monteiro", + "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Marija Miric", + "author_inst": "Two Oceans in Health, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Vivian Brache", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Leila Cochon", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Elena De la Cruz", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Aidelis Jorge", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Margarita De los Santos", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Patricia Leon", + "author_inst": "Laboratorio de Referencia, Dominican Republic." + }, + { + "author_name": "Mallery I. Breban", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Kendall Billig", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Claire Pearson", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Randy Downing", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Emily Gagnon", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Anthony Muyombwe", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Jafar Razeq", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Albert Ko", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Saad B. Omer", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Sten H. Vermund", + "author_inst": "Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.27.21268416", "rel_title": "Divergent SARS CoV-2 Omicron-specific T- and B-cell responses in COVID-19 vaccine recipients", @@ -471236,77 +473173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.12.28.21268468", - "rel_title": "Immunogenicity and safety of an inactivated SARS-CoV-2 vaccine (BBV152) in children from 2 to 18 years of age: an open-label, age-de-escalation phase 2/3 study", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268468", - "rel_abs": "BackgroundWe assessed the safety, reactogenicity, and immunogenicity of BBV152 in an open-label age de-escalation study in three age cohorts of children from 18 years of age down to 2 years of age.\n\nMethodsThis was a phase 2/3 open-label, multi-centre study done across six hospitals in India. All children received two 0.5mL doses of BBV152 (Covaxin(R), Bharat Biotech International Ltd., Hyderabad, India), which is the same formulation indicated in adults. Participants were monitored for adverse events, and post-vaccination blood draws were collected to assess neutralising antibodies. A total of 526 children were enrolled into Group 1 (ages 12 through 18 years, n=176), Group 2 (ages 6 through 12 years, n=175), Group 3 (ages 2 through 6 years, n=175).\n\nFindingsThere were no serious adverse events, deaths, or withdrawals due to an adverse event during the study. Vaccination with BBV152 was generally well tolerated, with no substantial difference in reactogenicity profiles between the different age groups. Similar immune responses were measured as microneutralisation (MNT) antibody titers in all three age groups. Vaccine-induced MNT responses in all groups were comparable to BEI reference sera run in the same assay. Seroconversion (measured by Plaque Reduction Neutralization Test (PRNT)) achieved high levels (95-98%) in all three groups four weeks after the second vaccination. The PRNT GMT ratio was 1{middle dot}76 (95%CI: 1.32 - 2.33) (GMT all children subgroup / GMT in adults) had a lower limit [≥] 1, indicating superior antibodies in children when compared to adults. Vaccine responses were skewed towards a Th1 response with IgG1/IgG4 ratios above 1.\n\nInterpretationBBV152 is well tolerated and immunogenic in children from 18 years down to 2 years of age. Immunogenicity analysis (by PRNT) shows superior antibody responses were observed in children compared to adults, suggesting that BBV152 will also be efficacious in this age group.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Krishna Mohan Vadrevu", - "author_inst": "Bharat Biotech" - }, - { - "author_name": "Siddharth Reddy", - "author_inst": "Bharat Biotech" - }, - { - "author_name": "Harsh Jogdand", - "author_inst": "Bharat Biotech" - }, - { - "author_name": "Brunda Ganneru", - "author_inst": "Bharat Biotech" - }, - { - "author_name": "Nizam Mirza", - "author_inst": "Pranaam Hospital" - }, - { - "author_name": "VN Tripathy", - "author_inst": "Prakhar Hospital" - }, - { - "author_name": "Chandramani Singh", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Vasant Khalatkar", - "author_inst": "Meditrina Institute of Medical Sciences" - }, - { - "author_name": "Siddaiah Prasanth", - "author_inst": "Cheluvamba Hospital" - }, - { - "author_name": "Sanjay Rai", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Raches Ella", - "author_inst": "Independent Consultant" - }, - { - "author_name": "William Blackwelder", - "author_inst": "WB Statistical Consulting LLC" - }, - { - "author_name": "Sai Prasad", - "author_inst": "Bharat Biotech" - }, - { - "author_name": "Krishna Ella", - "author_inst": "Bharat Biotech" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.27.21268424", "rel_title": "Waning of SARS-CoV-2 booster viral-load reduction effectiveness", @@ -472678,6 +474544,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.27.474218", + "rel_title": "Vaccine-breakthrough infection by the SARS-CoV-2 Omicron variant elicits broadly cross-reactive immune responses", + "rel_date": "2021-12-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474218", + "rel_abs": "Highly transmissible SARS-CoV-2 Omicron variant has posted a new crisis for COVID-19 pandemic control. Within a month, Omicron is dominating over Delta variant in several countries probably due to immune evasion. It remains unclear whether vaccine-induced memory responses can be recalled by Omicron infection. Here, we investigated host immune responses in the first vaccine-breakthrough case of Omicron infection in Hong Kong. We found that the breakthrough infection rapidly recruited potent cross-reactive broad neutralizing antibodies (bNAbs) against current VOCs, including Alpha, Beta, Gamma, Delta and Omicron, from unmeasurable IC50 values to mean 1:2929 at around 9-12 days, which were higher than the mean peak IC50 values of BioNTech-vaccinees. Cross-reactive spike- and nucleocapsid-specific CD4 and CD8 T cell responses were detected. Similar results were also obtained in the second vaccine-breakthrough case of Omicron infection. Our preliminary findings may have timely implications to booster vaccine optimization and preventive strategies of pandemic control.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Runhong Zhou", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Kelvin Kai-Wang To", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Qiaoli Peng", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jacky Man-Chun Chan", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Haode Huang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Dawei Yang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Bosco Hoi-Shiu Lam", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Vivien Wai-Man Chuang", + "author_inst": "Quality & Safety Division, Hospital Authority" + }, + { + "author_name": "Jian-Piao Cai", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Na Liu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ka-Kit Au", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Owen Tak-Yin Tsang", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Zhiwei Chen", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.26.472655", "rel_title": "Evaluation of maternal-infant dyad inflammatory cytokines in pregnancies affected by maternal SARS-CoV-2 infection in early and late gestation.", @@ -473586,53 +475523,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.24.474114", - "rel_title": "Impacts of the COVID-19 Pandemic on a Human Research Islet Program", - "rel_date": "2021-12-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.24.474114", - "rel_abs": "Designated a pandemic in March 2020, the spread of severe acute respiratory syndrome virus 2 (SARS-CoV2), the virus responsible for coronavirus disease 2019 (COVID-19), led to new guidelines and restrictions being implemented for individuals, businesses, and societies in efforts to limit the impacts of COVID-19 on personal health and healthcare systems. Here we report the impacts of the COVID-19 pandemic on pancreas processing and islet isolation/distribution outcomes at the Alberta Diabetes Institute IsletCore, a facility specialising in the processing and distribution of human pancreatic islets for research. While the number of organs processed was significantly reduced, organ quality and the function of cellular outputs were minimally impacted during the pandemic when compared to an equivalent period immediately prior. Despite the maintained quality of isolated islets, recipient groups reported poorer feedback regarding the samples. Our findings suggest this is likely due to disrupted distribution which led to increased transit times to recipient labs, particularly those overseas. Thus, to improve overall outcomes in a climate of limited research islet supply, prioritization of tissue recipients based on likely tissue transit times may be needed.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Tina J Dafoe", - "author_inst": "University of Alberta" - }, - { - "author_name": "Theodore dos Santos", - "author_inst": "University of Alberta" - }, - { - "author_name": "Aliya F Spigelman", - "author_inst": "University of Alberta" - }, - { - "author_name": "James Lyon", - "author_inst": "University of Alberta" - }, - { - "author_name": "Nancy Smith", - "author_inst": "University of Alberta" - }, - { - "author_name": "Austin Bautista", - "author_inst": "University of Alberta" - }, - { - "author_name": "Patrick E MacDonald", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jocelyn E Manning Fox", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "physiology" - }, { "rel_doi": "10.1101/2021.12.25.474113", "rel_title": "Clinical grade ACE2 effectively inhibits SARS-CoV-2 Omicron infections", @@ -474864,6 +476754,85 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.26.473325", + "rel_title": "Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin", + "rel_date": "2021-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.26.473325", + "rel_abs": "Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as SARS-CoV and SARS-CoV-2. It has long been suggested that bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the COVID-19 pandemic, multiple animal species were diseased by SARS-CoV-2 infection, especially in the respiratory system. Herein, single-cell transcriptomic data of the lungs of a horseshoe bat, a cat, a tiger, and a pangolin were generated. The receptor distribution of twenty-eight respiratory viruses belonging to fourteen viral families were characterized for the four species. Comparison on the immune-related transcripts further revealed limited cytokine activations in bats, which might explain the reason why bats experienced only mild diseases or even no symptoms upon virus infection. Our findings might increase our understanding of the immune background of horseshoe bats and their insensitivity to virus infections.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Xiran Wang", + "author_inst": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong L" + }, + { + "author_name": "Zhihua Ou", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China." + }, + { + "author_name": "Peiwen Ding", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Chengcheng Sun", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Daxi Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China." + }, + { + "author_name": "Jiacheng Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Wendi Wu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Yanan Wei", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Xiangning Ding", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Lihua Luo", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Meiling Li", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Wensheng Zhang", + "author_inst": "School of Basic Medical Sciences, Binzhou Medical University, No. 346, Guanhai Road, Laishan District, Yantai City, Shandong, China" + }, + { + "author_name": "Xin Jin", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Jian Sun", + "author_inst": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong L" + }, + { + "author_name": "Huan Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Dongsheng Chen", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.21.21268143", "rel_title": "Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission", @@ -475992,45 +477961,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.25.21268404", - "rel_title": "Cooccurrence of N501Y, P681R and other key mutations in SARS-CoV-2 Spike", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.25.21268404", - "rel_abs": "Analysis of circa 4.2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences on Global Initiative on Sharing All Influenza Data (GISAID) shows the spike mutations N501Y (common to Alpha, Beta, Gamma, Omicron variants) and P681R (central to Delta variants spread) have cooccurred 3,678 times between 17 October 2020 and 1 November 2021. In contrast, the N501Y+P681H combination is present in Alpha and Omicron variants and circa 1.1 million entries. Two-thirds of the 3,678 cooccurrences were in France, Turkey or US (East Coast), and the rest across 62 other countries. 55.5% and 4.6% of the cooccurrences were Alphas Q.4 and Gammas P.1.8 sub-lineages acquiring P681R; 10.7% and 3.8% were Deltas B.1.617.2 lineage and AY.33 sub-lineage acquiring N501Y; remaining 10.2% were in other variants. Despite the selective advantages individually conferred by N501Y and P681R, the N501Y+P681R combination counterintuitively didnt outcompete other variants in every instance. Although a relief to worldwide public health efforts, in vitro and in vivo studies are urgently required in the absence of a strong in silico explanation for this phenomenon. This study demonstrates a pipeline to analyse combinations of key mutations from public domain information in a systematic manner and provide early warnings of spread.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Carol Lee", - "author_inst": "CSIRO" - }, - { - "author_name": "Shruthi Mangalaganesh", - "author_inst": "Monash University" - }, - { - "author_name": "Laurence OW Wilson", - "author_inst": "CSIRO" - }, - { - "author_name": "Michael J Kuiper", - "author_inst": "CSIRO" - }, - { - "author_name": "Trevor W Drew", - "author_inst": "CSIRO" - }, - { - "author_name": "Seshadri S Vasan", - "author_inst": "Commonwealth Scientific and Industrial Research Organisation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.26.21268414", "rel_title": "Interpretable and Predictive Deep Modeling of the SARS-CoV-2 Spike Protein Sequence", @@ -477198,6 +479128,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.23.21267374", + "rel_title": "Immunogenicity and Safety Following a Homologous Booster Dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): A Phase 2 Randomized Placebo-Controlled Trial", + "rel_date": "2021-12-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21267374", + "rel_abs": "BackgroundEmerging SARS-CoV-2 variants and evidence of waning vaccine efficacy present significant obstacles toward controlling the COVID-19 pandemic. Booster doses of SARS-CoV-2 vaccines may address these concerns by both amplifying and broadening the immune responses seen with initial vaccination regimens.\n\nMethodsIn a phase 2 study, a single booster dose of a SARS-CoV-2 recombinant spike protein vaccine with Matrix-M adjuvant (NVX-CoV2373) was administered to healthy adult participants 18 to 84 years of age approximately 6 months following their primary two-dose vaccination series. Safety and immunogenicity parameters were assessed, including assays for IgG, MN50, and hACE2 receptor binding inhibition against the ancestral SARS-CoV-2 strain and select variants (B.1.351 [Beta], B.1.1.7 [Alpha], B.1.617.2 [Delta], and B.1.1.529 [Omicron]). This trial is registered with ClinicalTrials.gov, NCT04368988.\n\nFindingsAn incremental increase in the incidence of solicited local and systemic reactogenicity events was observed with subsequent vaccinations. Following the booster, incidence rates of local and systemic reactions were 82.5% (13.4% [≥] Grade 3) and 76.5% (15.3% [≥] Grade 3), respectively, compared to 70.0% (5.2% [≥] Grade 3) and 52.8% (5.6% [≥] Grade 3), respectively, following the primary vaccination series. Events were primarily mild or moderate in severity and transient in nature, with a median duration of 1.0 to 2.5 days. Immune responses seen 14 days following the primary vaccination series were compared with those observed 28 days following the booster (Day 35 and Day 217, respectively). For the ancestral SARS-CoV-2 strain, serum IgG geometric mean titers (GMTs) increased [~]4.7-fold from 43,905 ELISA units (EU) at day 35 to 204,367 EU at Day 217. Neutralization (MN50) assay GMTs showed a similar increase of [~]4.1-fold from 1,470 at day 35 to 6,023 at Day 217. A functional hACE2 receptor binding inhibition assay analyzing activity against ancestral and variant strains of SARS-CoV-2 at Day 189 vs Day 217 found 54.4-fold (Ancestral), 21.9-fold (Alpha), 24.5-fold (Beta), 24.4-fold (Delta), and 20.1-fold (Omicron) increases in titers. An anti-rS IgG activity assay comparing the same time points across the same SARS-CoV-2 strains found titers improved 61.2-fold, 85.9-fold, 65.0-fold, 92.5-fold, and 73.5-fold, respectively.\n\nInterpretationAdministration of a booster dose of NVX-CoV2373 approximately 6 months following the primary vaccination series resulted in an incremental increase in reactogenicity along with enhanced immune responses. For both the prototype strain and all variants evaluated, immune responses following the booster were notably higher than those associated with high levels of efficacy in phase 3 studies of the vaccine.\n\nFundingNovavax(R) and the Coalition for Epidemic Preparedness Innovations (CEPI(R)).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Raburn Mallory", + "author_inst": "Novavax" + }, + { + "author_name": "Neil Formica", + "author_inst": "Novavax" + }, + { + "author_name": "Susan Pfeiffer", + "author_inst": "Novavax" + }, + { + "author_name": "Bethanie Wilkinson", + "author_inst": "Novavax" + }, + { + "author_name": "Alex Marcheschi", + "author_inst": "Novavax" + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax" + }, + { + "author_name": "Heather McFall", + "author_inst": "Novavax" + }, + { + "author_name": "Michelle Robinson", + "author_inst": "Novavax" + }, + { + "author_name": "Joyce Plested", + "author_inst": "Novavax" + }, + { + "author_name": "MingZhu Zhu", + "author_inst": "Novavax" + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax" + }, + { + "author_name": "Gordon Chau", + "author_inst": "Novavax" + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax" + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax" + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.23.21268332", "rel_title": "Extending upon: What effect might border screening have on preventing importation of COVID-19 compared with other infections? - Considering the additional effect of post-arrival isolation", @@ -477762,37 +479783,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.23.473990", - "rel_title": "Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches.", - "rel_date": "2021-12-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.23.473990", - "rel_abs": "Since the SARS-CoV-2 outbreak in 2019, millions of people have been infected with the virus, and due to its high human-to-human transmission rate, there is a need for a vaccine to protect people. Although some vaccines are in use, due to the high mutation rate in the SARS-CoV-2 multiple variants, the current vaccines may not be sufficient to immunize people against new variant threats. One of the emerging variants of concern is B1.1.529 (Omicron), which carries[~]30 mutations in the Spike protein of SARS-CoV-2 is predicted to evade antibodies recognition even from vaccinated people. We used a structure-based approach along with an epitope prediction server to develop a Multi-Epitope based Subunit Vaccine (MESV) involving SARS-CoV-2 B1.1.529 variant spike glycoprotein. The predicted epitope with better antigenicity and non-toxicity were used for designing and predicting vaccine construct features and structure models. The MESV construct In-silico cloning in pET28a expression vector predicted the construct to be highly translational. The proposed MESV vaccine construct was also subjected to immune simulation prediction and was found to be highly antigenic and elicit a cell-mediated immune response. The proposed MESV in the present study has the potential to be evaluated further for vaccine production against the newly identified B1.1.529 (Omicron) variant of concern.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Meet Parmar", - "author_inst": "Institute of Advanced Research, Gandhinagar" - }, - { - "author_name": "Ritik Thumar", - "author_inst": "Institute of Advanced Research, Gandhinagar" - }, - { - "author_name": "Jigar Sheth", - "author_inst": "Institute of Advanced Research, Gandhinagar" - }, - { - "author_name": "Dhaval Patel", - "author_inst": "Institute of Advanced Research, Gandhinagar" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.23.474050", "rel_title": "SARS-CoV-2 comes up with a perfect recipe for disaster: Each mutation plays a specific role in the evolution of variants of concern", @@ -478948,6 +480938,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268265", + "rel_title": "Infrared spectroscopy enables rapid, robust, portable COVID-19 saliva screening based on pathophysiological response to SARS-CoV-2", + "rel_date": "2021-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268265", + "rel_abs": "Fourier-transform infrared (FTIR) spectroscopy provides a (bio)chemical snapshot of the sample, and was recently proposed for COVID-19 saliva screening in proof-of-concept cohort studies. As a step towards translation of this technology, we conducted controlled validation experiments in multiple biological systems. SARS-CoV-2 or UV-inactivated SARS-CoV-2 were used to infect Vero E6 cells in vitro, and K18-hACE2 mice in vivo. Potentially infectious culture supernatant or mouse oral lavage samples were treated with ethanol or Trizol to 75% (v/v) for attenuated total reflectance (ATR)-FTIR spectroscopy, or RT-PCR, respectively. The control condition, UV-inactivated SARS-CoV-2 elicited strong biochemical changes in culture supernatant/oral lavage despite lack of replication determined by RT-PCR or cell culture infectious dose 50%. Crucially, we show that active SARS-CoV-2 infection induced additional FTIR signals over the UV-inactivated SARS-CoV-2 infection, which correspond to innate immune response, aggregated proteins, and RNA. For human patient cohort prediction, we achieved high sensitivity of 93.48% on leave-on-out cross validation (n=104 participants) for predicting COVID-19 positivity using a partial least squares discriminant analysis model, in agreement with recent studies. However, COVID-19 patients negative on follow-up (RT-PCR on day of saliva sampling) were poorly predicted in this model. Importantly, COVID-19 vaccination did not lead to mis-classification of COVID-19 negatives. Meta-analysis revealed SARS-CoV-2 induced increase in Amide II band in all arms of this study and recent studies, indicative of altered {beta}-sheet structures in secreted proteins. In conclusion, ATR-FTIR is a robust, simple, portable method for COVID-19 saliva screening based on detection of pathophysiological responses to SARS-CoV-2.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Seth Kazmer", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Gunter Hartel", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Harley Robinson", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Renee S Richards", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Kexin Yan", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Sebastiaan J. Van Hal", + "author_inst": "NSW Health Pathology: New South Wales Health Pathology" + }, + { + "author_name": "Raymond Chan", + "author_inst": "NSW Health Pathology: New South Wales Health Pathology" + }, + { + "author_name": "Andrew Hind", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "David Bradley", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "Fabian Zieschang", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "Daniel J Rawle", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Thuy T Le", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "David W Reid", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Andreas Suhrbier", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Michelle M Hill", + "author_inst": "QIMR Berghofer Medical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.23.21267893", "rel_title": "Echinacea as a Potential Force against Coronavirus Infections? A Mini-Review of Randomized Controlled Trials in Adults and Children", @@ -479704,109 +481769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.24.21268377", - "rel_title": "Healthcare workers' COVID-19 Omicron variant uncertainty-related stress, resilience, and coping strategies during the first week of World Health Organization alert", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268377", - "rel_abs": "BackgroundAs the COVID-19 Omicron variant emerged and spread globally at an alarming speed, healthcare workers (HCWs) uncertainties, worries, resilience, and coping strategies warrant assessment. The COVID-19 pandemic had a severe psychological impact on HCWs, including the development of Post-Traumatic Stress symptoms. Specific subgroups of HCWs, such as front-line and female workers, were more prone to poor mental health outcomes and difficulties facing stress.\n\nMethodsThe responses to an online questionnaire among HCWs in Saudi Arabia (KSA) were collected December 1-5, 2021, aiming to assess their Omicron variants uncertainties, worries, resilience, and coping strategies. Three validated instruments were used to achieve the studys goals: the Brief Resilient Coping Scale, the Standard Stress Scale (SSS), and the Intolerance of Uncertainty Scale (IUS) - Short Form.\n\nResultsThe online survey was completed by 1285 HCWs. Females made up the majority (64%). The BRCS score of resilient coping was negatively and substantially linked with the SSS score of stress (r=-0.313, p = 0.010). Furthermore, the IUS had a positive and significant relationship with stress (r=0.326, p= 0.010). Increased stress levels were linked to a considerable drop in resilient coping scores. Furthermore, being a Saudi HCW or a nurse was linked to a significant reduction in resilient coping ratings. Coping by following healthcare authorities preventative instructions and using the WHO website as a source of information was linked to a considerable rise in resilient coping.\n\nConclusionsFollowing the emergence of the Omicron variant of SARS-CoV-2 in late 2021, a rapid investigation into the correlates of stress and resilient coping among the HCWs in KSA was conducted. The negative association between resilient coping and stress was clearly shown, as well as how underlying intolerance of uncertainty is linked to higher stress among HCWs quickly following the development of a new infectious threat. The study provides early insights to develop and promote coping strategies for emerging SARS-CoV-2 variants.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Mohamad-Hani Temsah", - "author_inst": "King Saud University" - }, - { - "author_name": "Shuliweeh Alenezi", - "author_inst": "King Saud University" - }, - { - "author_name": "Mohamad Al-Arabi", - "author_inst": "King Saud University" - }, - { - "author_name": "Fadi Aljamaan", - "author_inst": "King Saud University" - }, - { - "author_name": "Khalid Alhasan", - "author_inst": "King Saud University" - }, - { - "author_name": "Rasha Assiri", - "author_inst": "Princess Nourah bint Abdulrahman University" - }, - { - "author_name": "Rolan Bassrawi", - "author_inst": "King Saud University Medical City" - }, - { - "author_name": "Fatimah Alshahrani", - "author_inst": "King Saud University" - }, - { - "author_name": "Ali Alhaboob", - "author_inst": "King Saud University" - }, - { - "author_name": "Ali Alaraj", - "author_inst": "Qassim University" - }, - { - "author_name": "Naser S Alharbi", - "author_inst": "King Saud University" - }, - { - "author_name": "Rabih Halwani", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Amr Jamal", - "author_inst": "King Saud University" - }, - { - "author_name": "Naif Abdulmajeed", - "author_inst": "King Saud University" - }, - { - "author_name": "Lina Alfarra", - "author_inst": "Dr. Abdul Rahman Al Mishari Hospital" - }, - { - "author_name": "Wafa almashdali", - "author_inst": "Dr. Fatina Imran Medical Complex" - }, - { - "author_name": "Ayman Al-Eyadhy", - "author_inst": "King Saud University" - }, - { - "author_name": "Fahad AlZamil", - "author_inst": "King Saud University" - }, - { - "author_name": "Sarah Al-Subaie", - "author_inst": "King Saud University" - }, - { - "author_name": "Mazin Barry", - "author_inst": "King Saud University" - }, - { - "author_name": "Ziad A. Memish", - "author_inst": "Alfaisal University" - }, - { - "author_name": "Jaffar A. Al-Tawfiq", - "author_inst": "Johns Hopkins Aramco Healthcare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.23.21268319", "rel_title": "Surveillance and correlation of SARS-CoV-2 viral RNA, antigen, virus isolation, and self-reported symptoms in a longitudinal study with daily sampling", @@ -480945,6 +482907,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268021", + "rel_title": "Omicron outbreak at a private gathering in the Faroe Islands, infecting 21 of 33 triple-vaccinated healthcare workers", + "rel_date": "2021-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268021", + "rel_abs": "There are concerns that the SARS-CoV-2 Omicron variant evades immune responses due to unusually high numbers of mutations on the spike protein. Here we report a super-spreading event of Omicron infections amongst triple-vaccinated healthcare workers, infecting 21 of 33 attending a private gathering in the Faroe Islands.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gunnhild Helmsdal", + "author_inst": "General Practitioner Service, Vestmanna, Faroe Islands" + }, + { + "author_name": "Olga Kristina Hansen", + "author_inst": "Office of the Chief Medical Officer, Torshavn, Faroe Islands" + }, + { + "author_name": "Lars Fodgaard Moller", + "author_inst": "Office of the Chief Medical Officer, Torshavn, Faroe Islands" + }, + { + "author_name": "Debes Hammershaimb Christiansen", + "author_inst": "Faroese Food and Veterinary Authority, Torshavn, Faroe Islands" + }, + { + "author_name": "Maria Skaalum Petersen", + "author_inst": "The Faroese Hospital System, Torshavn, Faroe Islands" + }, + { + "author_name": "Marnar Fridheim Kristiansen", + "author_inst": "University of the Faroe Islands, Torshavn, Faroe Islands" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.22.21268274", "rel_title": "SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load, and Viral Culture Testing on a Large Sample Cohort", @@ -481713,85 +483714,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.12.23.21268298", - "rel_title": "Persistent symptoms among children and adolescents with and without anti-SARS-CoV-2 antibodies: a population-based serological study in Geneva, Switzerland", - "rel_date": "2021-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268298", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSIt is now established that a significant proportion of adults experience persistent symptoms after SARS-CoV-2 infection. However, evidence for children and adolescents is still inconclusive. In this population-based study, we examine the proportion of children and adolescents reporting persistent symptoms after SARS-CoV-2 infection, as assessed by serological status, and compare this to a seronegative control group.\n\nMethodsWe conducted a serosurvey in June-July 2021, recruiting 660 children and adolescents from 391 households selected randomly from the Geneva population. We tested participants for anti-SARS-CoV-2 antibodies targeting the nucleocapsid (N) protein to determine previous infection. A parent filled a questionnaire including questions on COVID-19-related symptoms lasting at least 2 weeks.\n\nFindingsAmong children seropositive for anti-SARS-CoV-2 antibodies, the sex- and age-adjusted prevalence of symptoms lasting longer than two weeks was 18.3%, compared to 11.1% among seronegative children (prevalence difference ({Delta}aPrev)=7.2%, 95%CI:1.5-13.0). Main symptoms declared among seropositive children were fatigue (11.5%) and headache (11.1%). For 8.6% (aPrev, 95%CI: 4.7-12.5) of seropositives, these symptoms were declared to be highly limiting of daily activities. Adolescents aged 12-17 years had a higher adjusted prevalence of persistent symptoms (aPrev=29.1%, 95%CI:19.4-38.7) than younger children. Comparing seropositive and seronegative adolescents, the estimated prevalence of symptoms lasting over four weeks is 4.4% ({Delta}aPrev, 95%CI:-3.8-13.6).\n\nInterpretationA significant proportion of children aged 12 to 17 years had symptoms lasting over two weeks after SARS-CoV-2 infection, with an estimated prevalence of symptoms lasting over 4 weeks of 4.4% in this age group. This represents a large number of adolescents in absolute terms, and should raise concern in the context of unknown long-term evolution of symptoms. Younger children appear to experience long-lasting symptoms less frequently, as no difference was observed between the seropositive and seronegative sample. Further studies with larger samples sizes are needed.\n\nFundingSwiss Federal Office of Public Health, Geneva General Directorate of Health, HUG Private Foundation, SSPH+, Fondation des Grangettes.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Roxane Dumont", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals" - }, - { - "author_name": "Mayssam Nehme", - "author_inst": "Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Elsa Lorthe", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Carlos De Mestral", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Viviane Richard", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Julien Lamour", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Helene Baysson", - "author_inst": "University of Geneva - HUG" - }, - { - "author_name": "Claire Semaani", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Francesco Pennacchio", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Anne Perrin", - "author_inst": "Division of General Pediatrics, Department of Woman, Child, and Adolescent Medicine, Geneva University Hospitals, Switzerland" - }, - { - "author_name": "Arnaud H L'Huillier", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Klara Posfay Barbe", - "author_inst": "Division of General Pediatrics, Department of Woman, Child, and Adolescent Medicine, Geneva University Hospitals, Switzerland" - }, - { - "author_name": "Nick Pullen", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Maria Eugenia Zaballa", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Silvia Stringhini", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.22.21268226", "rel_title": "A systematic review of observational methods used to quantify personal protective behaviours among members of the public during the COVID-19 pandemic, and the concordance between observational and self-report measures in infectious disease health protection", @@ -483019,6 +484941,237 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.17.473248", + "rel_title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "rel_date": "2021-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "rel_abs": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "rel_num_authors": 54, + "rel_authors": [ + { + "author_name": "Bo Meng", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Isabella Ferreira", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Adam Abdullahi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Niluka Goonawardane", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Daichi Yamasoba", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Steven A Kemp", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Guido Papa", + "author_inst": "LMB Cambridge" + }, + { + "author_name": "Saman Fatihi", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Surabhi Rathore", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Pehuen Perera Gerba", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Kumamoto Univ" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University, Kumamoto" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kuramochi Clinic Interpark" + }, + { + "author_name": "Jin Kuramochi", + "author_inst": "Kuramochi Clinic Interpark" + }, + { + "author_name": "Shigeki Mitsunaga", + "author_inst": "National Institute of Genetics, Mishima, Shizuoka" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University, Kumamoto" + }, + { + "author_name": "Oscar Charles", + "author_inst": "University College London" + }, + { + "author_name": "Dami Collier", + "author_inst": "University of Cambridge" + }, + { + "author_name": "- CITIID-NIHR BioResource COVID-19 Collaboration", + "author_inst": "-" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "-" + }, + { + "author_name": "- Ecuador-COVID19 Consortium", + "author_inst": "-" + }, + { + "author_name": "John Bradley", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Jinwook Choi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kenneth Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Elo Madissoon", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Kerstin Meyer", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Petra Mlcochova", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Rainer Doffinger", + "author_inst": "Cambridge University Hospitals NHS Trust" + }, + { + "author_name": "Sarah A Teichmann", + "author_inst": "Cambridge University" + }, + { + "author_name": "Leo James", + "author_inst": "MRC LMB" + }, + { + "author_name": "Joo Hyeon Lee", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Teresa Brevini", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Matteo Pizzuto", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Myra Hosmillo", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Donna Mallery", + "author_inst": "MRC LMB Cambridge" + }, + { + "author_name": "Samantha Zepeda", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Anshu Joshi", + "author_inst": "University of Washington" + }, + { + "author_name": "John Bowen", + "author_inst": "University of Washington" + }, + { + "author_name": "John Briggs", + "author_inst": "University of Heidelberg" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Laurelle Jackson", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Sandile Cele", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Fotios Sampaziotis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Nicholas Matheson", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ian Goodfellow", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Lipi Thukral", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Kei Sato", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Ravindra K Gupta", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.17.473140", "rel_title": "Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks", @@ -484075,65 +486228,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.20.21268096", - "rel_title": "South African Population Immunity and Severe Covid-19 with Omicron Variant", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268096", - "rel_abs": "BackgroundWe conducted a seroepidemiological survey from October 22 to December 9, 2021, in Gauteng Province, South Africa, to determine SARS-CoV-2 immunoglobulin G (IgG) seroprevalence primarily before the fourth wave of coronavirus disease 2019 (Covid-19), in which the B.1.1.529 (Omicron) variant was dominant. We evaluated epidemiological trends in case rates and rates of severe disease through to January 12, 2022, in Gauteng.\n\nMethodsWe contacted households from a previous seroepidemiological survey conducted from November 2020 to January 2021, plus an additional 10% of households using the same sampling framework. Dry blood spot samples were tested for anti-spike and anti-nucleocapsid protein IgG using quantitative assays on the Luminex platform. Daily case, hospital admission, and reported death data, and weekly excess deaths, were plotted over time.\n\nResultsSamples were obtained from 7010 individuals, of whom 1319 (18.8%) had received a Covid-19 vaccine. Overall seroprevalence ranged from 56.2% (95% confidence interval [CI], 52.6 to 59.7) in children aged <12 years to 79.7% (95% CI, 77.6 to 81.5) in individuals aged >50 years. Seropositivity was more likely in vaccinated (93.1%) vs unvaccinated (68.4%) individuals. Epidemiological data showed SARS-CoV-2 infection rates increased and subsequently declined more rapidly than in previous waves. Infection rates were decoupled from Covid-19 hospitalizations, recorded deaths, and excess deaths relative to the previous three waves.\n\nConclusionsWidespread underlying SARS-CoV-2 seropositivity was observed in Gauteng Province before the Omicron-dominant wave. Epidemiological data showed a decoupling of hospitalization and death rates from infection rate during Omicron circulation.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Shabir Madhi", - "author_inst": "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Jo" - }, - { - "author_name": "Gaurav Kwatra", - "author_inst": "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Jo" - }, - { - "author_name": "Jonathan E Myers", - "author_inst": "Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Waasila Jassat", - "author_inst": "National Institute for Communicable Diseases, Johannesburg, South Africa" - }, - { - "author_name": "Nisha Dhar", - "author_inst": "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Jo" - }, - { - "author_name": "Christian K Mukendi", - "author_inst": "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Jo" - }, - { - "author_name": "Amit Nana", - "author_inst": "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Jo" - }, - { - "author_name": "Lucille Blumberg", - "author_inst": "National Institute for Communicable Diseases, Johannesburg, South Africa" - }, - { - "author_name": "Richard Welch", - "author_inst": "National Institute for Communicable Diseases, Johannesburg, South Africa" - }, - { - "author_name": "Nicoletta Ngorima-Mabhena", - "author_inst": "ResearchLinkMe, Johannesburg, South Africa" - }, - { - "author_name": "Portia C Mutevedzi", - "author_inst": "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Jo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.19.21268069", "rel_title": "Mutational analysis of SARS-CoV-2. ORF8 and the evolution of the Delta and Omicron variants.", @@ -485264,6 +487358,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.20.21268134", + "rel_title": "Activity of convalescent and vaccine serum against a B.1.1.529 variant SARS-CoV-2 isolate", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268134", + "rel_abs": "The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in November of 2021 in South Africa and Botswana as well as in a sample of a traveler from South Africa in Hong Kong.1,2 Since then, B.1.1.529 has been detected in many countries globally. This variant seems to be more infectious than B.1.617.2 (Delta), has already caused super spreader events3 and has outcompeted Delta within weeks in several countries and metropolitan areas. B.1.1.529 hosts an unprecedented number of mutations in its spike gene and early reports have provided evidence for extensive immune escape and reduced vaccine effectiveness.2,4-6 Here, we investigated the neutralizing and binding activity of sera from convalescent, mRNA double vaccinated, mRNA boosted as well as convalescent double vaccinated and convalescent boosted individuals against wild type, B.1.351 and B.1.1.529 SARS-CoV-2 isolates. Neutralizing activity of sera from convalescent and double vaccinated participants was undetectable to very low against B.1.1.529 while neutralizing activity of sera from individuals who had been exposed to spike three or four times was maintained, albeit at strongly reduced levels. Binding to the B.1.1.529 receptor binding domain (RBD) and N-terminal domain (NTD) was reduced in convalescent not vaccinated but was mostly retained in vaccinated individuals.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Juan Manuel Carreno", + "author_inst": "ISMMS" + }, + { + "author_name": "Hala Alshammary", + "author_inst": "ISMMS" + }, + { + "author_name": "Johnstone Tcheou", + "author_inst": "ISMMS" + }, + { + "author_name": "Gagandeep Singh", + "author_inst": "ISMMS" + }, + { + "author_name": "Ariel Raskin", + "author_inst": "ISMMS" + }, + { + "author_name": "Hisaaki Kawabata", + "author_inst": "ISMMS" + }, + { + "author_name": "Levy Sominsky", + "author_inst": "ISMMS" + }, + { + "author_name": "Jordan Clark", + "author_inst": "ISMMS" + }, + { + "author_name": "Daniel C. Adelsberg", + "author_inst": "ISMMS" + }, + { + "author_name": "Dominika Bielak", + "author_inst": "ISMMS" + }, + { + "author_name": "Ana Silvia Gonzalez-Reiche", + "author_inst": "ISMMS" + }, + { + "author_name": "PSP/PARIS Study Group", + "author_inst": "ISMMS" + }, + { + "author_name": "Komal Srivastava", + "author_inst": "ISMMS" + }, + { + "author_name": "Emilia M Sordillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Goran Bajic", + "author_inst": "ISMMS" + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.20.21268124", "rel_title": "SARS-CoV-2 vaccine effectiveness and breakthrough infections in maintenance dialysis patients", @@ -486244,53 +488425,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.20.21267724", - "rel_title": "Factors associated with COVID-19 vaccine hesitancy in Senegal: a mixed study", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21267724", - "rel_abs": "IntroductionThe most effective way to control the COVID-19 pandemic in the long term is through vaccination. Two of the important components that can hinder it are vaccine hesitancy and vaccine refusal. This study, conducted before the arrival of the vaccines in Senegal, aims to assess and identify factors associated with hesitancy to the COVID-19 vaccine.\n\nMethodsThis study was an explanatory, sequential, mixed-methods design. We collected quantitative data from December 24, 2020, to January 16, 2021, and qualitative data from February 19 to March 30, 2021. We conducted a marginal quota sampling nationwide. We used a structured questionnaire to collect data for the quantitative phase and an interview guide with a telephone interview for the qualitative phase. We performed descriptive, bivariate, and multivariate analyses with R software version 4.0.5 for the quantitative phase; and performed manual content analyses for the qualitative phase.\n\nResultsWe surveyed 607 people for the quantitative phase, and interviewed 30 people for the qualitative phase. Individuals who hesitated or refused to be vaccinated represented 12.9% and 32.8%, respectively. Vaccine hesitancy was related to gender, living in large cities, having a poor attitude towards the vaccine, thinking that the vaccine would not help protect them from the virus, being influenced by people important to them, and lacking information from health professionals. Vaccine refusal was related to living in large cities, having a poor attitude towards the vaccine, thinking that the vaccine would not help protect them from the virus, thinking that the vaccine could endanger their health, trusting opinions of people who were important to them, and lacking information from health professionals.\n\nConclusionThe results of the study show that the factors associated with hesitancy and refusal to be vaccinated against COVID-19 are diverse and complex. Reducing them will help to ensure better vaccination coverage if the current challenges of vaccine accessibility are addressed. Therefore, governments and health authorities should intensify their efforts to promote vaccine confidence and reduce misinformation.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mouhamadou Faly Ba", - "author_inst": "Institute of Health and Development (ISED), Cheikh Anta Diop University, Dakar, Senegal" - }, - { - "author_name": "Adama Faye", - "author_inst": "Institute of Health and Development (ISED), Cheikh Anta Diop University, Dakar, Senegal" - }, - { - "author_name": "Babacar Kane", - "author_inst": "Institute of Health and Development (ISED), Cheikh Anta Diop University, Dakar, Senegal" - }, - { - "author_name": "Amadou Ibra Diallo", - "author_inst": "Institute of Health and Development (ISED), Cheikh Anta Diop University, Dakar, Senegal" - }, - { - "author_name": "Amandine Junot", - "author_inst": "STAPS Department, Faculty of Human and Environmental Sciences, La Reunion University, 97430 Le-Tampon, Reunion" - }, - { - "author_name": "Ibrahima Gaye", - "author_inst": "Institute of Health and Development (ISED), Cheikh Anta Diop University, Dakar, Senegal" - }, - { - "author_name": "Emmanuel Bonnet", - "author_inst": "IRD, UMR 215 Prodig, 5, cours des Humanites, Aubervilliers, France" - }, - { - "author_name": "Valery Ridde", - "author_inst": "CEPED, IRD-University of Paris, ERL INSERM SAGESUD, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.19.21268070", "rel_title": "Effectiveness of different booster regimens for preventing infection and adverse outcomes in Puerto Rico", @@ -487078,6 +489212,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.21.21267983", + "rel_title": "GB0139, an inhaled small molecule inhibitor of galectin-3, in COVID-19 pneumonitis: a randomised, controlled, open-label, phase 2a experimental medicine trial of the safety, pharmacokinetics, and potential therapeutic value", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21267983", + "rel_abs": "RationaleHigh galectin-3 levels predict poor outcomes in patients with COVID-19. Galectin-3 activates monocytes and macrophages which are directly implicated in COVID-19 immunopathology and the cytokine storm. GB0139 is a potent thiodigalactoside galectin-3 inhibitor and may reduce the severe effects of the disease. We report safety and pharmacokinetics and pharmacodynamics of the inhaled galectin-3 inhibitor, GB0139, and assess clinical outcomes and key systemic inflammatory biomarkers in hospitalised patients with COVID-19 (ClinicalTrials.gov/EudraCT identifier: NCT04473053/2020-002230-32).\n\nMethodsAdults with COVID-19 requiring oxygen, and with pneumonitis on x-ray, were randomised to receive standard of care (SOC; including dexamethasone; n=21) or SOC plus 10 mg GB0139 twice daily for 48 hours, then once daily for [≤]14 days (n=20).\n\nResultsPatients aged 27-87 years were enrolled from July 2020; the final patient completed the 90-day follow-up in April 2021. GB0139+SOC was well tolerated with no treatment-related serious adverse events reported. Incidences of adverse events were similar between treatment arms (40 with GB0139+SOC vs 35 with SOC). Plasma GB0139 was measurable in all patients after inhaled exposure, with moderate interpatient variability, and demonstrated target engagement with decreased circulating galectin (overall treatment effect post-hoc over days 2-7: p=0{middle dot}0099 vs SOC). Rate of decline in fraction of inspired oxygen (%) requirement was significantly greater in the GB0139+SOC arm with a posterior mean difference of -1{middle dot}51 (95% highest posterior density: -2{middle dot}90, -0{middle dot}189) versus SOC. Plasma levels of biomarkers associated with inflammation, coagulopathy, major organ function and fibrosis showed a downward trend versus SOC.\n\nConclusionsGB0139+SOC was well tolerated and achieved clinically relevant plasma concentrations and target engagement. This, and the reduction in markers associated with inflammatory, coagulation, fibrosis, and reduction in inspired oxygen (%) over SOC alone, indicates the therapeutic potential for inhaled GB0139 in hospitalised patients with COVID-19.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Erin Gaughan", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Tariq Sethi", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Tom Quinn", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Nikhil Hirani", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Andrew Mills", + "author_inst": "Exploristics" + }, + { + "author_name": "Annya M. Bruce", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Alison MacKinnon", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Vassilios Aslanis", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Feng Li", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Richard O'Connor", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Richard A. Parker", + "author_inst": "Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh" + }, + { + "author_name": "John Norrie", + "author_inst": "Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh" + }, + { + "author_name": "James Dear", + "author_inst": "Centre for Cardiovascular Science, University of Edinburgh" + }, + { + "author_name": "Ahsan R. Akram", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Oliver Koch", + "author_inst": "Infectious Diseases Department, NHS Lothian" + }, + { + "author_name": "Jie Wang-Jairaj", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Robert J. Slack", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Lise Gravelle", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Bertil Lindmark", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.12.19.21268028", "rel_title": "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa", @@ -488082,53 +490311,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.16.472843", - "rel_title": "SARS-COV-2 Omicron variant predicted to exhibit higher affinity to ACE-2 receptor and lower affinity to a larger range of neutralizing antibodies, using a rapid assessment platform", - "rel_date": "2021-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472843", - "rel_abs": "Rapid assessment of whether a pandemic pathogen may have increased transmissibility or be capable of evading existing vaccines and therapeutics is critical to mounting an effective public health response. Over the period of seven days, we utilized rapid computational prediction methods to evaluate potential public health implications of the emerging SARS-CoV-2 Omicron variant. Specifically, we modeled the structure of the Omicron variant, examined its interface with human angiotensin converting enzyme 2 (ACE-2) and evaluated the change in binding affinity between Omicron, ACE-2 and publicly known neutralizing antibodies. We also compared the Omicron variant to known Variants of Concern (VoC). Seven of the 15 Omicron mutations occurring in the spike protein receptor binding domain (RBD) occur at the ACE-2 cell receptor interface, and therefore may play a critical role in enhancing binding to ACE-2. Our estimates of Omicron RBD-ACE-2 binding affinities indicate that at least two of RBD mutations, Q493R and N501Y, contribute to enhanced ACE-2 binding, nearly doubling delta-delta-G (ddG) free energies calculated for other VoCs. Binding affinity estimates also were calculated for 55 known neutralizing SARS-CoV-2 antibodies. Analysis of the results showed that Omicron substantially degrades binding for more than half of these neutralizing SARS-CoV-2 antibodies, and for roughly 10 times as many of the antibodies than the currently dominant Delta variant. This early study lends support to use of rapid computational risk assessments to inform public health decision-making while awaiting detailed experimental characterization and confirmation.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Adam Zemla", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Thomas Desautels", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Edmond Lau", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Fangqiang Zhu", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Kathryn Arrildt", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Brent Segelke", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Shankar Sundaram", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Daniel Mello Faissol", - "author_inst": "Lawrence Livermore National Laboratory" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.17.473170", "rel_title": "Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions", @@ -489232,6 +491414,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.18.21267819", + "rel_title": "Knowledge, Attitude and Practices towards COVID 19 pandemic among homeless street young adults in Lusaka, Zambia: A Mixed Methods Approach", + "rel_date": "2021-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.18.21267819", + "rel_abs": "ObjectiveTo determine the knowledge, attitude and practices towards COVID-19 among homeless street young adults in Lusaka district, Zambia.\n\nMethodsA total of 89 young street adults aged between 16-35 years were sampled. A concurrent mixed methods approach was used, Structured questionnaires and focused group discussion, to achieve the objectives. STATA 13 was used to produce Descriptive statistics while thematic analysis was used to analyze the qualitative data.\n\nResultsMajority of the survey participants were male 67(78%), 55(62%) were single while 53(59%) had attained a Primary School Education. The majority of the participants received the COVID-19 information through the radio (61%). Only 44 (49%)% had adequate knowledge on Covid-19 of whom 70 (78.6%) had a positive attitude towards COVID-19. However, the 65(73%) had a low risk perception of contracting the disease. Further, 66 (74.2%) had a positive attitude towards the effectiveness of precautionary behaviors and measures. The finding also revealed that only 3(3.3%) had good practice towards the Covid-19 preventative measures overall with (SD:0).\n\nConclusionKnowledge and attitudes towards COVID-19 were quite high among homeless street adults. However, their good practices were alarmingly low. Specific strategies for them being a vulnerable group are required.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kahilu Samuyachi", + "author_inst": "Keeping Girls in School Project-Ministry of Education, Lusaka, Zambia" + }, + { + "author_name": "Mowa Zambwe", + "author_inst": "Workers Compensation Fund Control Board" + }, + { + "author_name": "Mutale Sampa", + "author_inst": "University of Zambia" + }, + { + "author_name": "Peter J. Chipimo", + "author_inst": "Zambia National Public Health Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.18.21268026", "rel_title": "Measurement of the extent of Anxiety and Depression that has occurred in college students due to the COVID 19 pandemic: An Survey based cross-sectional study.", @@ -489824,41 +492037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.12.16.21267734", - "rel_title": "The Omicron variant mutation at position 28,311 in the SARS-CoV-2 N gene does not perturb CDC N1 target detection", - "rel_date": "2021-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267734", - "rel_abs": "The emergence of new SARS-CoV-2 variants necessitates the reevaluation of current COVID-19 tests to ensure continued accuracy and reliability. The new SARS-CoV-2 variant, Omicron, is heavily mutated, with over 50 mutations within its RNA genome. Any of these mutations could adversely affect the ability of diagnostic assays to detect the virus in patient samples, potentially leading to inconclusive or false negative results. In fact, the U.S. Food and Drug Administration (FDA) has identified over two dozen diagnostic tests that contain a gene target that is expected to have \"significantly reduced sensitivity due to a mutation in the SAS-CoV-2 Omicron variant\"1. Additionally, one of the U.S. Centers for Disease Control and Prevention (CDC) Emergency Use Authorization (EUA) targets for COVID-19 tests, 2019-nCoV_N1, overlaps an Omicron mutation within the sequence targeted by the fluorescent probe. This target from the CDC has been used in many other EUA assays. Using in vitro transcribed (IVT) N gene RNA representing the wild-type (GenBank/GISAID ID MN908947.3) and Omicron variant (BA.1, GISAID ID EPI_ISL_6752027), we evaluated the performance of two different amplification protocols, both of which include the CDC 2019-nCoV_N1 primer-probe set. Both assays were able to detect the mutant N1 sequence as efficiently as the wild-type sequence. Consequently, these data suggest that diagnostic assays that use the 2019-nCoV-N1 primer-probe set are unlikely to be impacted by currently circulating Omicron lineage viruses.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yanxia Bei", - "author_inst": "New England BioLabs" - }, - { - "author_name": "Kyle B. Vrtis", - "author_inst": "New England BioLabs" - }, - { - "author_name": "Janine G. Borgaro", - "author_inst": "New England BioLabs" - }, - { - "author_name": "Bradley W. Langhorst", - "author_inst": "New England BioLabs" - }, - { - "author_name": "Nicole M. Nichols", - "author_inst": "New England BioLabs" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.12.16.21267934", "rel_title": "Predictors of SARS-CoV-2 infection in a multi-ethnic cohort of United Kingdom healthcare workers: a prospective nationwide cohort study (UK-REACH)", @@ -491158,6 +493336,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.12.17.21267968", + "rel_title": "Patients' and carers' experiences of, and engagement with remote home monitoring services for COVID-19 patients: a rapid mixed-methods study", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267968", + "rel_abs": "IntroductionRemote home monitoring models were implemented during the COVID-19 pandemic to shorten hospital length of stay, reduce unnecessary hospital admission, readmission and infection, and appropriately escalate care. Within these models, patients are asked to take and record readings and escalate care if advised. There is limited evidence on how patients and carers experience these services. This study aimed to evaluate patient experiences of, and engagement with, remote home monitoring models for COVID-19.\n\nMethodsA rapid mixed-methods study in England. We conducted a cross-sectional survey and interviews with patients and carers. Interview findings were summarised using rapid assessment procedures sheets and grouping data into themes (using thematic analysis). Survey data were analysed using descriptive statistics.\n\nResultsWe received 1069 surveys (18% response rate) and conducted interviews with patients (n=59) and carers (n=3). Care relied on support from staff members, and family/friends. Patients and carers reported positive experiences and felt that the service and human contact reassured them and was easy to engage with. Yet, some patients and carers identified problems with engagement. Engagement was influenced by: patient factors such as health and knowledge, support from family/friends and staff, availability and ease-of-use of informational and material resources (e.g. equipment), and service factors.\n\nConclusionRemote home monitoring models place responsibility on patients to self-manage symptoms in partnership with staff; yet many patients required support and preferred human contact (especially for identifying problems). Caring burden and experiences of those living alone, and barriers to engagement should be considered when designing and implementing remote home monitoring services.\n\nPatient or public contributionFor this evaluation, members of the study team met with service user and public members of the BRACE PPI group and Health and Care Panel and patient representatives from RSET in a series of workshops. These workshops informed study design, data collection tools, data interpretation and to discuss study dissemination for Phase 2. For example, patient facing documents, such as the consent form, topic guides, patient survey and patient information sheet were reviewed by this group. Additionally, PPI members helped to pilot patient surveys and interview guides with the research team. We also asked some members of the public to pilot the patient survey. Members of the PPI group were given the opportunity to comment on the manuscript. One PPI member commented on the manuscript and the manuscript was amended accordingly.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Holly Walton", + "author_inst": "University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "University College London" + }, + { + "author_name": "Nadia Crellin", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Manbinder S Sidhu", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Lauren Herlitz", + "author_inst": "University College London" + }, + { + "author_name": "Ian Litchfield", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jo Ellins", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pei Li Ng", + "author_inst": "University College London" + }, + { + "author_name": "Efthalia Massou", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Sonila M Tomini", + "author_inst": "University College London" + }, + { + "author_name": "Naomi J Fulop", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.12.16.21267932", "rel_title": "A Single Dose of COVID-19 mRNA Vaccine Induces Airway Immunity in COVID-19 Convalescent Patients", @@ -491842,85 +494079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.14.21267549", - "rel_title": "The impact of environmental mycobiomes on geographic variation in COVID-19 mortality", - "rel_date": "2021-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267549", - "rel_abs": "Mortality rates during the COVID-19 pandemic have varied by orders of magnitude across communities in the United States1. Individual, socioeconomic, and environmental factors have been linked to health outcomes of COVID-192,3,4,5. It is now widely appreciated that the environmental microbiome, composed of microbial communities associated with soil, water, atmosphere, and the built environment, impacts immune system development and susceptibility to immune-mediated disease6,7,8. The human microbiome has been linked to individual COVID-19 disease outcomes9, but there are limited data on the influence of the environmental microbiome on geographic variation in COVID-19 across populations10. To fill this knowledge gap, we used taxonomic profiles of fungal communities associated with 1,135 homes in 494 counties from across the United States in a machine learning analysis to predict COVID-19 Infection Fatality Ratios (the number of deaths caused by COVID-19 per 1000 SARS-CoV-2 infections1; IFR). Here we show that exposure to increased fungal diversity, and in particular indoor exposure to outdoor fungi, is associated with reduced SARS-CoV-2 IFR. Further, we identify seven fungal genera that are the predominant drivers of this protective signal and may play a role in suppressing COVID-19 mortality. This relationship is strongest in counties where human populations have remained stable over at least the previous decade, consistent with the importance of early-life microbial exposures11. We also assessed the explanatory power of 754 other environmental and socioeconomic factors, and found that indoor-outdoor fungal beta-diversity is amongst the strongest predictors of county-level IFR, on par with the most important known COVID-19 risk factors, including age12. We anticipate that our study will be a starting point for further integration of environmental mycobiome data with population health information, providing an important missing link in our capacity to identify vulnerable populations. Ultimately, our identification of specific genera predicted to be protective against COVID-19 mortality may point toward novel, proactive therapeutic approaches to infectious disease.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Joshua Ladau", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Katrina Abuabara", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Angelica M. Walker", - "author_inst": "University of Tennessee, Knoxville" - }, - { - "author_name": "Marcin P. Joachimiak", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Ishan Bansal", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Yulun Wu", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Eljah B. Hoffman", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Chaincy Kuo", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Nicola Falco", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Jared Streich", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Mark J. van der Lan", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Haruko M. Wainwright", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Eoin L. Brodie", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Matthias Hess", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Daniel A. Jacobson", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "James B. Brown", - "author_inst": "Lawrence Berkeley National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.14.21267800", "rel_title": "A Cloth Facemask Causes No Major Respiratory or Cardiovascular Perturbations during Moderate to Heavy Exercise", @@ -492836,6 +494994,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2021.12.16.21267902", + "rel_title": "Waning of mRNA-1273 vaccine effectiveness against SARS-CoV-2 infection in Qatar", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267902", + "rel_abs": "BACKGROUNDIn early 2021, Qatar launched a mass immunization campaign with Modernas mRNA-1273 COVID-19 vaccine. We assessed persistence of real-world mRNA-1273 effectiveness against SARS-CoV-2 infection and against COVID-19 hospitalization and death.\n\nMETHODSEffectiveness was estimated using test-negative, case-control study design, between January 1 and December 5, 2021. Effectiveness was estimated against documented infection (a PCR-positive swab, regardless symptoms), and against any severe (acute-care hospitalization), critical (ICU hospitalization), or fatal COVID-19.\n\nRESULTSBy December 5, 2021, 2,962 breakthrough infections had been recorded among those who received two mRNA-1273 doses. Of these infections, 19 progressed to severe COVID-19 and 4 to critical, but none to fatal disease. mRNA-1273 effectiveness against infection was negligible for the first two weeks after the first dose, increased to 65.5% (95% CI: 62.7-68.0%) 14 or more days after the first dose, and reached its peak at about 90% in the first three months after the second dose. Effectiveness declined gradually starting from the fourth month after the second dose and was below 50% by the 7th month after the second dose. Effectiveness against severe, critical, or fatal COVID-19 reached its peak at essentially 100% right after the second dose, and there was no evidence for declining effectiveness over time. Effectiveness against symptomatic versus asymptomatic infection demonstrated the same pattern of waning, but effectiveness against symptomatic infection was consistently higher than that against asymptomatic infection and waned more slowly.\n\nCONCLUSIONSmRNA-1273-induced protection against infection appears to wane month by month after the second dose. Meanwhile, protection against hospitalization and death appears robust with no evidence for waning for several months after the second dose.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Fatiha Benslimane", + "author_inst": "Qatar University" + }, + { + "author_name": "Heba A. Al Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad Rubayet Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.16.21267703", "rel_title": "Evaluation of SARS-CoV-2 Antibody Point of Care Devices in the Laboratory and Clinical Setting", @@ -493756,141 +496021,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.14.21267772", - "rel_title": "SARS-CoV-2 Omicron: reduction of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267772", - "rel_abs": "Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. Over this time global vaccine programs have been introduced, contributing to lowered COVID-19 hospitalisation and mortality rates, particularly in the first world. In late 2021, the Omicron (B.1.1.529) virus variant emerged, with significant genetic differences and clinical effects from other variants of concern (VOC). This variant demonstrated higher numbers of polymorphisms in the gene encoding the Spike (S) protein, and there has been displacement of the dominant Delta variant. We assessed the impact of Omicron infection on the ability of: serum from vaccinated and / or previously infected individuals; concentrated human IgG from plasma donors, and licensed monoclonal antibody therapies to neutralise virus in vitro. There was a 17 to 22-fold reduction in neutralisation titres across all donors who had a detectable neutralising antibody titre to the Omicron variant. Concentrated pooled human IgG from convalescent and vaccinated donors had greater breadth of neutralisation, although the potency was still reduced 16-fold. Of all therapeutic antibodies tested, significant neutralisation of the Omicron variant was only observed for Sotrovimab, with other monoclonal antibodies unable to neutralise Omicron in vitro. These results have implications for ongoing therapy of individuals infected with the Omicron variant.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Anupriya Aggarwal", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Alberto Ospina Stella", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Gregory Walker", - "author_inst": "Serology and Virology Division (SAViD), NSW HP SEALS, Randwick, Australia" - }, - { - "author_name": "Anoushka Akerman", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Vanessa Milogiannakis", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Alexandra Carey Hoppe", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Vennila Mathivanan", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Christina Fichter", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Samantha McAllery", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Supavadee Amatayakul-Chantler", - "author_inst": "CSL Behring" - }, - { - "author_name": "Nathan Roth", - "author_inst": "CSL Behring" - }, - { - "author_name": "Germano Coppola", - "author_inst": "CSL Behring" - }, - { - "author_name": "Mee Ling Munier", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "David Ross Darley", - "author_inst": "St Vincents Hospital" - }, - { - "author_name": "David S Khoury", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Charles S.P. Foster", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Yonghui Lu", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Peter Schofield", - "author_inst": "Garvan Institute" - }, - { - "author_name": "Jennifer Jackson", - "author_inst": "Garvan Institute" - }, - { - "author_name": "Jake Henry", - "author_inst": "Garvan Institute" - }, - { - "author_name": "Ohan Mazigi", - "author_inst": "Garvan Institute" - }, - { - "author_name": "Hans-Martin Jaeck", - "author_inst": "University of Erlangen Germany" - }, - { - "author_name": "David Langles", - "author_inst": "Garvan Institute" - }, - { - "author_name": "Deborah Cromer", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Daniel Christ", - "author_inst": "Garvan Insitute" - }, - { - "author_name": "Gail Matthews", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "William Rawlinson", - "author_inst": "Serology and Virology Division (SAViD), NSW HP SEALS, Randwick, Australia" - }, - { - "author_name": "Anthony Dominic Kelleher", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Stuart G Turville", - "author_inst": "Kirby Institute, UNSW Sydney" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.15.21267805", "rel_title": "Booster of mRNA-1273 Vaccine Reduces SARS-CoV-2 Omicron Escape from Neutralizing Antibodies", @@ -494969,6 +497099,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.13.21267368", + "rel_title": "Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations", + "rel_date": "2021-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267368", + "rel_abs": "BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis.\n\nMETHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time.\n\nFINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.\n\nCONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Ingibjorg Magnusdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Aniko Lovik", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Anna Bara Unnarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Daniel L. McCartney", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Helga Ask", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Kadri Koiv", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Lea Arregui Nordahl Christoffersen", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Sverre Urnes Johnson", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Andrew M McIntosh", + "author_inst": "Division of Psychiatry, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Anna K. Kahler", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Archie Campbell", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Arna Hauksdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Chloe Fawns-Ritchie", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Christian Erikstrup", + "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark" + }, + { + "author_name": "Dorte Helenius", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Drew Altschul", + "author_inst": "Department of Psychology, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Edda Bjork Thordardottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Elias Eythorsson", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Emma M. Frans", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Gunnar Tomasson", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Harpa Lind Jonsdottir", + "author_inst": "Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland" + }, + { + "author_name": "Harpa Runarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Henrik Hjalgrim", + "author_inst": "Danish Cancer Society Research Center, Copenhagen, Denmark" + }, + { + "author_name": "Hronn Hardardottir", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Juan Gonzalez-Hijon", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Karina Banasik", + "author_inst": "Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark" + }, + { + "author_name": "Khoa Manh Dinh", + "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark" + }, + { + "author_name": "Li Lu", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Lili Milani", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Lill Trogstad", + "author_inst": "Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Maria Didriksen", + "author_inst": "Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Omid V. Ebrahimi", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Patrick F. Sullivan", + "author_inst": "Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Per Minor Magnus", + "author_inst": "Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Qing Shen", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Ragnar Nesvag", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway." + }, + { + "author_name": "Reedik Magi", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Runolfur Palsson", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Sisse Rye Ostrowski", + "author_inst": "Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Thomas Werge", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Asle Hoffart", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "David J. Porteous", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Fang Fang", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Johanna Jakobsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Kelli Lehto", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Ole A. Andreassen", + "author_inst": "NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Ole B.V. Pedersen", + "author_inst": "Department of Clinical Immunology, Zealand University Hospital, Denmark" + }, + { + "author_name": "Thor Aspelund", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Unnur Anna Valdimarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.14.21267418", "rel_title": "COVID-19 vaccination and Guillain-Barre syndrome: analyses using the National Immunoglobulin Database", @@ -495853,69 +498194,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.14.21267562", - "rel_title": "Real-world data on immune responses following heterologous prime-boost COVID-19 vaccination schedule with Pfizer and AstraZeneca vaccines in England", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267562", - "rel_abs": "BackgroundThere are limited data on immune responses to heterologous COVID-19 immunisation schedules, especially following an extended [≥]12-week interval between doses.\n\nMethodsSARS-CoV-2 infection-naive and previously-infected adults receiving ChAd-BNT (ChAdOx1 nCoV-19, AstraZeneca followed by BNT162b2, Pfizer-BioNTech) or BNT-ChAd as part of the UK national immunisation programme provided blood samples at 30 days and 12 weeks after their second dose. Geometric mean concentrations (GMC) of anti-SARS-CoV-2 spike (S-antibody) and nucleoprotein (N-antibody) IgG antibodies and geometric mean ratios (GMR) were compared with a contemporaneous cohort receiving homologous ChAd-ChAd or BNT-BNT.\n\nResultsDuring March-October 2021, 75,827 individuals were identified as having received heterologous vaccination, 9,489 invited to participate, 1,836 responded (19.3%) and 656 were eligible. In previously-uninfected adults, S-antibody GMC at 30 days post-second dose were lowest for ChAd-ChAd (862 [95%CI, 694 - 1069]) and significantly higher for ChAd-BNT (6233 [5522-7035]; GMR 6.29; [5.04-7.85]; p<0.001), BNT-ChAd (4776 [4066-5610]; GMR 4.55 [3.56-5.81]; p<0.001) and BNT-BNT (5377 [4596-6289]; GMR 5.66 [4.49-7.15]; p<0.001). By 12 weeks after dose two, S-antibody GMC had declined in all groups and remained significantly lower for ChAd-ChAd compared to ChAd-BNT (GMR 5.12 [3.79-6.92]; p<0.001), BNT-ChAd (GMR 4.1 [2.96-5.69]; p<0.001) and BNT-BNT (GMR 6.06 [4.32-8.50]; p<0.001). Previously infected adults had higher S-antibody GMC compared to infection-naive adults at all time-points and with all vaccine schedules.\n\nConclusionsThese real-world findings demonstrate heterologous schedules with adenoviral-vector and mRNA vaccines are highly immunogenic and may be recommended after a serious adverse reaction to one vaccine product, or to increase programmatic flexibility where vaccine supplies are constrained.\n\nO_TEXTBOXWhat is already known?PubMed was searched with the terms \"COVID-19 Vaccine\" and \"heterologous\" to identify publications relating to heterologous immunisation schedules with adenoviral-vector and mRNA vaccines from 01 January 2020 until 30 November 2021. Following early reports of vaccine-induced thrombocytosis and thrombocytopenia (VITT) after the first dose of ChAd (ChAdOx1 nCoV-19), several studies reported significantly higher antibody levels, with robust neutralizing activity and cellular immune responses, in adults receiving a heterologous ChAd-mRNA schedule compared to those receiving ChAd-ChAd. Few studies, however, have compared antibody responses after both heterologous schedules (ChAd-mRNA and mRNA-ChAd) with both homologous schedules (ChAd-ChAd and mRNA-mRNA). One UK study (COMCOV) compared all four ChAd and BNT162b2 Pfizer-BioNTech (BNT; mRNA) combinations given four weeks apart and reported very high antibody and T-cell responses four weeks after the second dose for all four schedules.\n\nWhat are the new findings?We used the national immunisation register to identify adults who received a heterologous vaccine schedule as part of the national immunisation programme in England and collected blood samples to measure SARS-CoV-2 antibody responses after vaccination. We found that both heterologous schedules (ChAd-BNT and BNT-ChAd) provided superior antibody responses compared to ChAd-ChAd and similar responses to BNT-BNT at 30 days and 12 weeks after second vaccine dose. ChAd-BNT induced higher antibody levels then BNT-ChAd at both timepoints. Antibody responses after vaccination were much higher in previously infected individuals, irrespective of their immunisation schedule. A recent Swedish population-based study reported higher vaccine effectiveness against symptomatic disease with ChAd-BNT than ChAd-ChAd providing real-world confirmation of improved protection with heterologous schedules.\n\nWhat do the new findings imply?Our findings add to the growing body of evidence showing high antibody responses following heterologous vaccination schedules with ChAd and BNT, along with robust antibody neutralising activity and cellular responses, especially when compared to ChAd-ChAd. Given that globally COVID-19 vaccine demand far exceeds vaccine supply, these results have important implications for the future deployment of COVID-19 vaccine programmes; particularly where it is logistically and/or operationally difficult to administer two doses of the same vaccine product.\n\nC_TEXTBOX", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Samantha J Westrop", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Heather J Whitaker", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Annabel A Powell", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Linda Power", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Corinne Whillock", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Helen Campbell", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Ruth Simmons", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Lenesha Warrener", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Mary E Ramsay", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Shamez N Ladhani", - "author_inst": "UK Health Security Agency, London and St George's University of London, London." - }, - { - "author_name": "Kevin E Brown", - "author_inst": "UK Health Security Agency, London" - }, - { - "author_name": "Gayatri Amirthalingham", - "author_inst": "UK Health Security Agency, London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.14.21267818", "rel_title": "Performances of community pharmacists and community pharmacies during COVID-19 outbreak: a cross-sectional study", @@ -497071,6 +499349,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.10.21267574", + "rel_title": "Safety and immunogenicity of a heterologous booster of protein subunit vaccine MVC-COV1901 after two doses of adenoviral vector vaccine AZD1222", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267574", + "rel_abs": "We report the interim safety and immunogenicity results in participants administrated with a booster dose of protein subunit vaccine MVC-COV1901 at 12 or 24 weeks after two doses of AZD1222 (ChAdOx1 nCoV-19). In subjects fully vaccinated with two doses of AZD1222, waning antibody immunity was apparent within six months of the second dose of AZD1222. At one month after the MVC-COV1901 booster dose, anti-SARS-CoV-2 spike IgG antibody titers and neutralizing antibody titers were 14- and 8.6-fold increased, respectively, when compared to the titer levels on the day of the booster dose. We also observed 5.2- and 5.6-fold increases in neutralizing titer levels against wildtype and Omicron variant pseudovirus after the booster dose, respectively. These interim results support the use of MVC-COV1901 as a heterologous booster for individuals vaccinated with AZD1222.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shu-Hsing Cheng", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Yi-Chun Lin", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Cheng-Pin Chen", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Chien-Yu Cheng", + "author_inst": "Taoyuan General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.10.21267582", "rel_title": "Echinacea purpurea for the Long-term Prevention of Viral Respiratory Tract Infections during COVID-19 Pandemic: A Randomized, Open, Controlled, Exploratory Clinical Study", @@ -497975,33 +500284,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.13.472476", - "rel_title": "Potential cross-protection against SARS-CoV-2 from previous exposure to bovine coronavirus", - "rel_date": "2021-12-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.13.472476", - "rel_abs": "Humans have long shared infectious agents with cattle, and the common cold OC-43 CoV is a not-so-distant example of cross-species viral spillover. Human exposure to BCoV is certainly common, as the virus is endemic in cattle-raising regions. This article shows an in silico investigation of shared viral epitopes between BCoV and SARS-CoV-2. HLA recognition and lymphocyte reactivity were assessed using freely-available resources. Several epitopes were shared between BCoV and SARS-CoV-2, both for B and T lymphocytes. These data demonstrate that possible cross-protection is being induced by human exposure to cattle.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lana B. P. Querne", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Fernanda Z Bastos", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Breno Castello Branco Beirao", - "author_inst": "Universidade Federal do Parana" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.14.472240", "rel_title": "In silico evidence of superantigenic features in ORF8 protein from COVID-19", @@ -499173,6 +501455,141 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.11.472236", + "rel_title": "Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses", + "rel_date": "2021-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.11.472236", + "rel_abs": "The devastation caused by SARS-CoV-2 has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses and thus its promise as an agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses, but also uncovered a new antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.\n\nOne sentence summaryA monoclonal antibody that neutralizes or binds all sarbecoviruses tested and represents a reproducible antibody class.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Lihong Liu", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Sho Iketani", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Yicheng Guo", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Ryan Casner", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Eswar Reddem", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Manoj S. Nair", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Jian Yu", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Jasper Chan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Maple Wang", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Gabriele Cerutti", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Zhiteng Li", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Candace Castagna", + "author_inst": "Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA" + }, + { + "author_name": "Laura Corredor", + "author_inst": "Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA" + }, + { + "author_name": "Hin Chu", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Shuofeng Yuan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Vincent Poon", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Chris Chan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Zhiwei Chen", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Yang Luo", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Marcus Cunningham", + "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA" + }, + { + "author_name": "Alejandro Chavez", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA" + }, + { + "author_name": "Michael Yin", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA" + }, + { + "author_name": "David Perlin", + "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA" + }, + { + "author_name": "Moriya Tsuji", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Peter Kwong", + "author_inst": "Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Zizhang Sheng", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Lawrence Shapiro", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "David D. Ho", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.13.21267761", "rel_title": "SARS-CoV-2 Omicron variant escapes neutralization by vaccinated and convalescent sera and therapeutic monoclonal antibodies", @@ -499809,73 +502226,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.10.21267593", - "rel_title": "Characterization of the significant decline in humoral immune response six months post-SARS-CoV-2 mRNA vaccination: A systematic review", - "rel_date": "2021-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267593", - "rel_abs": "Accumulating evidence shows a progressive decline in the efficacy of coronavirus disease 2019 (COVID-19) mRNA vaccines such as Pfizer-BioNTech (mRNA BNT161b2) and Moderna (mRNA-1273) in preventing breakthrough infections due to diminishing humoral immunity over time. Thus, this review characterizes the kinetics of anti-SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) antibodies after the second dose of a primary cycle of COVID-19 mRNA vaccination. A systematic search of literature was performed and a total of 18 studies (N=15,980) were identified and reviewed. The percent difference of means of reported antibody titers were then calculated to determine the decline in humoral response after the peak levels post-vaccination. Findings revealed that the peak humoral response was reached at 21-28 days after the second dose, after which serum levels progressively diminished at 4-6 months post-vaccination. Additionally, results showed that regardless of age, sex, serostatus and presence of comorbidities, longitudinal data reporting antibody measurement exhibited a decline of both anti-receptor binding domain (RBD) IgG and anti-spike IgG, ranging from 94-95% at 90-180 days and 55-85% at 140-160 days, respectively, after the peak antibody response. This suggests that the rate of antibody decline may be independent of patient-related factors and peak antibody titers but mainly a function of time and antibody class/molecular target. Hence, this study highlights the necessity of more efficient vaccination strategies to provide booster administration in attenuating the effects of waning immunity, especially in the appearance of new variants of concerns (VoCs).", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Kin Israel Notarte", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Israel Guerrero-Arguero", - "author_inst": "Disease Intervention & Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Jacqueline Veronica Velasco", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Abbygail Therese Ver", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Maria Helena Santos de Oliveira", - "author_inst": "Department of Biostatistics, State University of Maringa, Brazil" - }, - { - "author_name": "Jesus Alfonso Catahay", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Md. Siddiqur Rahman Khan", - "author_inst": "Disease Intervention & Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Adriel Pastrana", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Grzegorz Juszczyk", - "author_inst": "Department of Public Health, Medical University of Warsaw, Warsaw, Poland" - }, - { - "author_name": "Jordi Torrelles", - "author_inst": "Disease Intervention & Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Giuseppe Lippi", - "author_inst": "Section of Clinical Biochemistry, University of Verona, Verona, Italy" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Disease Intervention & Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Brandon Michael Henry", - "author_inst": "Disease Intervention & Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.11.21267652", "rel_title": "Symptoms persisting after hospitalization for COVID-19: 12 months interim results of the COFLOW study", @@ -500787,6 +503137,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.12.472286", + "rel_title": "The Omicron variant is highly resistant against antibody-mediated neutralization - implications for control of the COVID-19 pandemic", + "rel_date": "2021-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.12.472286", + "rel_abs": "The rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike-protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by Sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent or BNT162b2-vaccinated individuals with 10- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1/BNT162b2-vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Nadine Kr\u00fcger", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Sebastian Schulz", + "author_inst": "Friedrich-Alexander-Universit\u00e4 Erlangen-N\u00fcrnberg" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Cheila Rocha", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fc Primatenforschung" + }, + { + "author_name": "Amy Kempf", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Inga Nehlmeier", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Luise Graichen", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Anna-Sophie Moldenhauer", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Martin Sebastian Winkler", + "author_inst": "Universit\u00e4tsmedizin G\u00f6ttingen" + }, + { + "author_name": "Martin Lier", + "author_inst": "Universit\u00e4tsmedizin G\u00f6ttingen" + }, + { + "author_name": "Alexandra Dopfer-Jablonka", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Hans-Martin J\u00e4ck", + "author_inst": "Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg" + }, + { + "author_name": "Georg Behrens", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Stefan P\u00f6hlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut f\u00fcr Primatenforschung" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.09.471735", "rel_title": "The T cell receptor repertoire reflects the dynamics of the immune response to vaccination", @@ -501711,89 +504136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.10.21267600", - "rel_title": "Incidence rates and symptomatology of community infections with SARS-CoV-2 in children and parents: The CoKids longitudinal household study", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267600", - "rel_abs": "AIMThe CoKids study aimed to estimate the community incidence of symptomatic and asymptomatic SARS-CoV-2 in children and parents and to assess the symptomatology of SARS-COV-2 infections relative to SARS-CoV-2 negative respiratory episodes.\n\nMETHODSIn this prospective study, households with at least one child <18 years were recruited from three existing Dutch cohorts. Participation included SARS-CoV-2 screening at 4-6 weeks intervals for all household members during 23 weeks of follow-up and active reporting of new onset respiratory symptoms until July 1st 2021. Follow-up was temporarily intensified following new onset respiratory symptoms in a household member or a SARS-CoV-2 positive screening test and included daily symptom recording, repeated PCR testing (nose-throat, saliva and fecal samples) and SARS-CoV-2 antibody measurement (paired dried blood spots) in all household members. Age-stratified incidence rates for SARS-CoV-2 positive and negative episodes were calculated. Symptomatology and disease burden of respiratory episodes were compared by SARS-CoV-2 status and age.\n\nRESULTSIn total 307 households were enrolled including 1209 subjects. We detected 64 SARS-CoV-2 positive and 118 SARS-CoV-2 negative respiratory outbreaks. The highest incidence rate was found in children <12 years for SARS-CoV-2 negative episodes (0.93/ person-year (PY); 95%CI: 0.88-0.96). The SARS-CoV-2 incidence in this age-group was 0.21/PY for confirmed only, and 0.41/PY if probable cases were included. SARS-CoV-2 incidence did not differ by age group (p>0.27). Nasal congestion/runny nose, with or without cough and fatigue were the three most prevalent symptom clusters for both SARS-CoV-2 positive and negative respiratory episodes. Among children, no differences were observed in the symptomatology and severity of SARS-CoV-2 positive versus negative respiratory episodes, whereas among adults, SARS-CoV-2 positive episodes had a higher number and severity of symptoms and with a longer duration p<0.001).\n\nCONCLUSIONUsing active, longitudinal household follow up, we detected a high incidence rate of SARS-CoV-2 infections in children that was similar to adults. The findings suggest that after 20 months of COVID-19 pandemic, up to 2/3 of Dutch children < 12 years have been infected with SARS-CoV-2. Symptomatology and disease severity of SARS-CoV-2 in children is similar to respiratory illness from other causes. In adults, SARS-COV-2 positive episodes are characterized by more and prolonged symptoms, and higher severity. These findings may assist decisions on COVID-19 policies targeting children.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Marieke de Hoog", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Judith Post-Sluiter", - "author_inst": "Spaarne Gasthuis Hoofddorp" - }, - { - "author_name": "Ilse Westerhof", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Elandri Fouri", - "author_inst": "Spaarne Gasthuis Hoofddorp" - }, - { - "author_name": "Valerie Heuvelman", - "author_inst": "Erasmus MC Rotterdam" - }, - { - "author_name": "Trisja Boom", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Sjoerd M Euser", - "author_inst": "Regional Public Health Laboratory Kennemerland" - }, - { - "author_name": "Paul Badoux", - "author_inst": "Regional Public Health Laboratory Kennemerland" - }, - { - "author_name": "Chantal Reusken", - "author_inst": "RIVM" - }, - { - "author_name": "Louis Bont", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Elisabeth Sanders", - "author_inst": "Wilhelmina Children's Hospital, Utrecht University Medical Centre" - }, - { - "author_name": "Vincent Jaddoe", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Bjorn Herpers", - "author_inst": "Regional Public Health Laboratory Kennemerland" - }, - { - "author_name": "Dirk Eggink", - "author_inst": "National Institute for Public Health and The Environment (RIVM)" - }, - { - "author_name": "Joanne Wildenbeest", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Liesbeth Duijts", - "author_inst": "ErasmusMC" - }, - { - "author_name": "Marlies van Houten", - "author_inst": "Spaarnegasthuis" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.10.21267363", "rel_title": "Exploring selection bias in COVID-19 research: Simulations and prospective analyses of two UK cohort studies", @@ -503033,6 +505375,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.10.21267338", + "rel_title": "Mental health indicators in Sweden over a 12-month period during the COVID-19 pandemic", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267338", + "rel_abs": "BackgroundThe ongoing COVID-19 pandemic has had an unprecedented impact on the lives of people globally and is expected to have profound effects on mental health. Yet, self-reported large-scale online surveys on mental health are still relatively uncommon. Here we aim to describe the mental health burden experienced in Sweden using baseline data of the Omtanke2020 Study.\n\nMethodSelf-reported baseline data collected over a 12-month period (June 9, 2020-June 8, 2021) from the longitudinal online survey of the Omtanke2020 Study including 27,950 adults in Sweden. Participants were volunteers or actively recruited through existing cohorts and after providing informed consent responded to monthly online questionnaires on socio-demographics, mental and physical health, COVID-19 infection, and impact. Poisson regression was fitted to assess the relative risk of high mental health burden (depression, anxiety, and COVID-19 specific PTSD).\n\nResultThe overall proportion of persons with high level of symptoms was 15.6%, 9.5% and 24.5% for depression, anxiety, and COVID-19 specific PTSD, respectively. Overall, 43.4% of the participants had significant, clinically relevant symptoms for at least one mental health outcome and 7.3% had significant symptoms for all three outcomes. We also observed differences in the prevalence of these symptoms across strata of sex, age, recruitment type, COVID-19 status, region, and seasonality.\n\nConclusionWhile the proportion of persons with high mental health burden remains higher than in pre-pandemic publications, our estimates are lower than previously reported levels of depression, anxiety, and PTSD during the pandemic in Sweden and elsewhere.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Anik\u00f3 Lovik", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anna K. K\u00e4hler", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Unnur A. Valdimarsd\u00f3ttir", + "author_inst": "University of Iceland, Karolinska Institutet" + }, + { + "author_name": "Emma M. Frans", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Nancy L. Pedersen", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Per Hall", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kamila Czene", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Patrick F. Sullivan", + "author_inst": "University of North Carolina, Karolinska Institutet" + }, + { + "author_name": "Fang Fang", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.12.09.21267349", "rel_title": "Down-regulation of SARS-CoV-2 neutralizing antibodies in vaccinated smokers", @@ -503761,153 +506158,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.08.21267417", - "rel_title": "SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection", - "rel_date": "2021-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267417", - "rel_abs": "The emergence of SARS-CoV-2 Omicron, first identified in Botswana and South Africa, may compromise vaccine effectiveness and the ability of antibodies triggered by previous infection to protect against re-infection (1). Here we investigated whether Omicron escapes antibody neutralization in South Africans, either previously SARS-CoV-2 infected or uninfected, who were vaccinated with Pfizer BNT162b2. We also investigated if Omicron requires the ACE2 receptor to infect cells. We isolated and sequence confirmed live Omicron virus from an infected person in South Africa and compared plasma neutralization of this virus relative to an ancestral SARS-CoV-2 strain with the D614G mutation, observing that Omicron still required ACE2 to infect. For neutralization, blood samples were taken soon after vaccination, so that vaccine elicited neutralization was close to peak. Neutralization capacity of the D614G virus was much higher in infected and vaccinated versus vaccinated only participants but both groups had 22-fold Omicron escape from vaccine elicited neutralization. Previously infected and vaccinated individuals had residual neutralization predicted to confer 73% protection from symptomatic Omicron infection, while those without previous infection were predicted to retain only about 35%. Both groups were predicted to have substantial protection from severe disease. These data support the notion that high neutralization capacity elicited by a combination of infection and vaccination, and possibly boosting, could maintain reasonable effectiveness against Omicron. A waning neutralization response is likely to decrease vaccine effectiveness below these estimates. However, since protection from severe disease requires lower neutralization levels and involves T cell immunity, such protection may be maintained.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Sandile Cele", - "author_inst": "Africa Health Research Institute; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" - }, - { - "author_name": "Laurelle Jackson", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Khadija Khan", - "author_inst": "Africa Health Research Institute; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" - }, - { - "author_name": "David S Khoury", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Thandeka Moyo-Gwete", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Rese" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform; Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stell" - }, - { - "author_name": "Cathrine Scheepers", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Rese" - }, - { - "author_name": "Daniel Amoako", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Rese" - }, - { - "author_name": "Farina Karim", - "author_inst": "Africa Health Research Institute; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" - }, - { - "author_name": "Mallory Bernstein", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Gila Lustig", - "author_inst": "Centre for the AIDS Programme of Research in South Africa" - }, - { - "author_name": "Derseree Archary", - "author_inst": "Centre for the AIDS Programme of Research in South Africa; Department of Medical Microbiology, University of KwaZulu-Natal" - }, - { - "author_name": "Muneerah Smith", - "author_inst": "Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Yashica Ganga", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Zesuliwe Jule", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Kajal Reedoy", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "James Emmanuel San", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Shi-Hsia Hwa", - "author_inst": "Africa Health Research Institute; Division of Infection and Immunity, University College London" - }, - { - "author_name": "Jennifer Giandhari", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" - }, - { - "author_name": "Jonathan Blackburn", - "author_inst": "Department of Integrative Biomedical Sciences; Institute of Infectious Disease and Molecular Medicine; Sengenics Corporation" - }, - { - "author_name": "Bernadett I Gosnell", - "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Salim Abdool Karim", - "author_inst": "Centre for the AIDS Programme of Research in South Africa; Department of Epidemiology, Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Willem Hanekom", - "author_inst": "Africa Health Research Institute; Division of Infection and Immunity, University College London" - }, - { - "author_name": "- NGS-SA", - "author_inst": "" - }, - { - "author_name": "- COMMIT-KZN Team", - "author_inst": "" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Resea" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Rese" - }, - { - "author_name": "Richard Lessells", - "author_inst": "School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa" - }, - { - "author_name": "Mahomed-Yunus S Moosa", - "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa" - }, - { - "author_name": "Penny L. Moore", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Rese" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.06.21266926", "rel_title": "Opening up safely: public health system requirements for ongoing COVID-19 management based on evaluation of Australia's surveillance system performance", @@ -504839,6 +507089,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.07.471590", + "rel_title": "A novel bacterial protease inhibitor adjuvant in RBD-based COVID-19 vaccine formulations increases neutralizing antibodies, specific germinal center B cells and confers protection against SARS-CoV-2 infection.", + "rel_date": "2021-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.07.471590", + "rel_abs": "In this work we evaluated recombinant receptor binding domain (RBD) based vaccine formulation prototypes with potential for further clinical development. We assessed different formulations containing RBD plus Alum, AddaS03, AddaVax or the combination of Alum and U-Omp19: a novel Brucella spp. protease inhibitor vaccine adjuvant. Results show that the vaccine formulation composed of U-Omp19 and Alum as adjuvants have a better performance: it significantly increased mucosal and systemic neutralizing antibodies in comparison to antigen plus Alum, AddaVax or AddaS03. Antibodies induced with the formulation containing U-Omp19 not only increased their neutralization capacity against the wild-type virus but also cross neutralized alpha, lambda and gamma variants with similar potency. Also, addition of U-Omp19 to vaccine formulation increased the frequency of RBD-specific geminal center B cells and plasmablasts. Additionally, U-Omp19+Alum formulation induced RBD-specific Th1 and CD8+ T cell responses in spleens and lungs. Finally, this vaccine formulation conferred protection against an intranasal SARS-CoV-2 challenge of K18-hACE2 mice.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Lorena M Coria", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Lucas M Saposnik", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Celeste Pueblas Castro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Eliana F Castro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Laura A Bruno", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "William B Stone", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Paula S Perez", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "M. Laura Darriba", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Lucia B Chemes", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Julieta Alcain", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Ignacio Mazzitelli", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Augusto Varese", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Melisa Salvatori", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Albert J Auguste", + "author_inst": "Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Diego E Alvarez", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Karina A Pasquevich", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Juliana Cassataro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.08.471814", "rel_title": "Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses", @@ -505543,29 +507876,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.08.21267475", - "rel_title": "The unequal impact of the COVID-19 pandemic on life expectancy across Chile", - "rel_date": "2021-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267475", - "rel_abs": "ObjectivesTo quantify the effect of the COVID-19 pandemic on life expectancy in Chile categorized by rural and urban, and to correlate life expectancy changes with socioeconomic factors at the municipal level.\n\nDesignRetrospective cross-sectional demographic analysis using aggregated data.\n\nSettingVital and demographic statistics from the national institute of statistics and department of vital statistics of ministry of health.\n\nParticipantsAggregated national all-cause death data stratified by year (2000-2020), sex, and municipality.\n\nMain Outcome measuresStratified mortality rates using a Bayesian methodology. With this, we assessed the unequal impact of the pandemic in 2020 on life expectancy across Chilean municipalities for men and women and analyzed previous mortality trends since 2010.\n\nResultsLife expectancy declined for both men and women in 2020. Urban areas were the most affected, with males losing 1.89 and females 1.33 in 2020. The strength of the decline in life expectancy correlated with indicators of social deprivation and poverty. Also, inequality in life expectancy between municipalities increased, largely due to excess mortality among the working-age population in socially disadvantaged municipalities.\n\nConclusionsNot only do people in poorer areas live shorter lives, they also have been substantially more affected by the COVID-19 pandemic, leading to increased population health inequalities. Quantifying the impact of the COVID-19 pandemic on life expectancy provides a more comprehensive picture of the toll.\n\nStrengths and limitationsO_LIFirst study to analyze changes in life expectancy in Chile with small-area resolution.\nC_LIO_LIWe applied a hierarchical Bayesian methodology to estimate life expectancies in the past 20 years.\nC_LIO_LIWe show that COVID-19 led to declines in life expectancy in Chile greater than a year in magnitude. These declines correlated with poverty levels, indicating that socially deprived populations were hit the hardest.\nC_LIO_LIWe also show that inequality in life expectancy between municipalities increased due to excess mortality among the working-age population in socially disadvantaged municipalities.\nC_LIO_LIThe main limitation is that our estimates depend on accurate small-area stratified population estimates. We implemented several estimates and showed that our findings are robust to the choice of them.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Gonzalo E Mena", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jose Manuel Aburto", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.09.21267295", "rel_title": "Population Optimally Immunized after Accounting for Type-Specific COVID-19 Vaccine Waning Intervals: State-Level Prevalence and Trends", @@ -506389,6 +508699,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.06.471215", + "rel_title": "The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta Variants: a computational approach", + "rel_date": "2021-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.06.471215", + "rel_abs": "The newly discovered COVID variant B.1.1.529 in Botswana has more than 30 mutations in spike and many other in non-spike proteins, far more than any other SARS-CoV-2 variant accepted as a variant of concern by the WHO and officially named Omicron, and has sparked concern among scientists and the general public. Our findings provide insights into structural modification caused by the mutations in the Omicrons receptor-binding domain and look into the effects on interaction with the hosts neutralising antibodies CR3022, B38, CB6, P2B-2F6, and REGN, as well as ACE2R using an in silico approach. We have employed secondary structure prediction, structural superimposition, protein disorderness, molecular docking, and MD simulation to investigate host-pathogen interactions, immune evasion, and transmissibility caused by mutations in the RBD region of the spike protein of the Omicron variant and compared it to the Delta variants (AY.1, AY.2, & AY.3) and wild type. Computational analysis revealed that the Omicron variant has a higher binding affinity for the human ACE2 receptor than the wild and Delta (AY.1 and AY.2 strains), but lower than the Delta AY.3 strain. MD simulation and docking analysis suggest that the omicron and Delta AY.3 were found to have relatively unstable and compact RBD structures and hampered interactions with antibodies more than wild and Delta (AY.1 and AY.2), which may lead to relatively more pathogenicity and antibody escape. In addition, we observed lower binding affinity of Omicron for human monoclonal antibodies (CR3022, B38, CB6, and P2B2F6) when compared to wild and Delta (AY.1 & AY.2). However, the binding affinity of Omicron RBD variants for CR3022, B38, and P2B2F6 antibodies is lower as compared to Delta AY.3, which might promote immune evasion and reinfection and needs further experimental investigation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Prashant Ranjan", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Neha", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Chandra Devi", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Kaviyapriya Arulmozhi Devar", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Parimal Das", + "author_inst": "Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.07.21267442", "rel_title": "Dynamic analysis and evaluation of asymptomatic infection in the spread of COVID-19", @@ -507209,77 +509554,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.07.21267431", - "rel_title": "Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267431", - "rel_abs": "In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Deltas increased epidemic growth in times of waning vaccine protection.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ralf Duerr", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Dacia Dimartino", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Christian Marier", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Paul Zappile", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Samuel Levine", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Fritz Francois", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Eduardo Iturrate", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Guiqing Wang", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Meike Dittmann", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Jennifer Lighter", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Brian Elbel", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Andrea B Troxel", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Keith S Goldfeld", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Adriana Heguy", - "author_inst": "NYU Langone Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.08.21267353", "rel_title": "The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination", @@ -508431,6 +510705,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.05.471290", + "rel_title": "Constructing a multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and co-infecting microbes", + "rel_date": "2021-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.05.471290", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused millions of deaths worldwide. Many efforts have focused on unraveling the mechanism of the viral infection to develop effective strategies for treatment and prevention. Previous studies have provided some clarity on the protein-protein interaction linkages occurring during the life cycle of viral infection; however, we lack a complete understanding of the full interactome, comprising human miRNAs and protein-coding genes and co-infecting microbes. To comprehensively determine this, we developed a statistical modeling method using latent Dirichlet allocation (called MLCrosstalk, for multiple-layer crosstalk) to fuse many types of data to construct the full interactome of SARS-CoV-2. Specifically, MLCrosstalk is able to integrate samples with multiple layers of information (e.g., miRNA and microbes), enforce a consistent topic distribution on all data types, and infer individual-level linkages (i.e., differing between patients). We also implement a secondary refinement with network propagation to allow our microbe-gene linkages to address larger network structures (e.g., pathways). Using MLCrosstalk, we generated a list of genes and microbes linked to SARS-CoV-2. Interestingly, we found that two of the identified microbes, Rothia mucilaginosa and Prevotella melaninogenica, show distinct patterns representing synergistic and antagonistic relationships with the virus, respectively. We also identified several SARS-COV-2-associated pathways, including the VEGFA-VEGFR2 and immune response pathways, which may provide potential targets for drug design.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shaoke Lou", + "author_inst": "Yale University" + }, + { + "author_name": "Tianxiao Li", + "author_inst": "Yale University" + }, + { + "author_name": "Mark Gerstein", + "author_inst": "Yale university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.05.471277", "rel_title": "A zebrafish model of COVID-19-associated cytokine storm syndrome reveals differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern.", @@ -509223,57 +511524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.06.21266524", - "rel_title": "Effect of perceived discrimination on depression and suicidal ideation during the COVID-19 pandemic: A large-scale, repeated-measures study in the All of Us Research Program", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21266524", - "rel_abs": "ObjectiveThe COVID-19 pandemic has coincided with an increase in depressive symptoms as well as a growing awareness of health inequities and structural racism in the United States. Here, we examine the mental health impact of everyday discrimination during the pandemic in a large and diverse cohort of the All of Us Research Program.\n\nMethodsUsing repeated assessments of 62,651 participants in May to July of 2020, we fitted mixed-effects models to assess the effect of everyday discrimination on moderate to severe depression (Patient Health Questionnaire (PHQ)-9 [≥] 10) and suicidal ideation (PHQ-9 item 9 > 0), and applied inverse probability weights to account for non-random probabilities of completing the voluntary survey.\n\nResultsEveryday discrimination was associated with increased odds of depression (adjusted odds ratio (aOR) [95% CI]: 1.21 [1.20 -1.22]) and suicidal ideation (1.17 [1.16-1.18]). For depression, the effects were larger in earlier phases of the pandemic (interaction p=8.2x10-5), which varied by main reason for discrimination and self-reported race and ethnicity. Among those who identified race or ancestry/national origin(s) as a primary reason for discrimination, Asian and Black or African American participants had 24% and 17% increase in the odds of depression in May of 2020 (1.24 [1.17-1.31] and 1.17 [1.12-1.22]), respectively, versus a 3% and 7% increase in July (1.03 [0.96-1.10] and 1.07 [1.02-1.12]).\n\nConclusionIn this large and diverse sample, increased levels of everyday discrimination were associated with higher odds of depression, particularly during the early phase of the pandemic among participants self-identifying as Asian or Black.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Younga Heather Lee", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Zhaowen Liu", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Daniel Fatori", - "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" - }, - { - "author_name": "Joshua R. Bauermeister", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rebecca A. Luh", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Cheryl R. Clark", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Sarah Bauermeister", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andr\u00e9 R. Brunoni", - "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" - }, - { - "author_name": "Jordan W. Smoller", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.07.21267415", "rel_title": "Covid-19 social distancing: when less is more", @@ -510129,6 +512379,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.06.21267289", + "rel_title": "Testing the Validity of the Modified Vaccine Attitude Question Battery across 22 Languages with a Large-scale International Survey Dataset", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267289", + "rel_abs": "In this study, we tested the validity of the modified version of the Vaccine Attitude Question Battery (VAQB) across 22 different languages. Validity test was conducted with a large-scale international survey dataset, COVIDiSTRESSII Global Survey, collected from 20,601 participants from 62 countries. We employed exploratory and confirmatory factor analysis, measurement invariance test, and measurement alignment for internal validity test. Moreover, we examined correlation between the VAQB score, vaccination intent, compliance with preventive measures, and trust in public health-related agents. The results reported that the modified VAQB, which included five items, showed good validity across 22 languages with measurement alignment. Furthermore, the VAQB score showed negative association with vaccination intent, compliance, and trust as expected. The findings from this study provide additional evidence supporting the validity of the modified VAQB in 22 languages for future large-scale international research on COVID-19 and vaccination.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hyemin Han", + "author_inst": "University of Alabama" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.06.21267101", "rel_title": "SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia", @@ -511117,33 +513386,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.06.21267351", - "rel_title": "Proactive vs. reactive country responses to the COVID19 pandemic shock", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267351", - "rel_abs": "The infection caused by SARS-CoV-2, responsible for the COVID-19 pandemic, is characterized by an infectious period with either asymptomatic or pre-symptomatic phases, leading to a rapid surge of mild and severe cases putting national health systems under serious stress. To avoid their collapse, and in the absence of pharmacological treatments, during the early pandemic phase countries worldwide were forced to adopt strategies, from elimination to mitigation, based on non-pharmacological interventions which, in turn, overloaded social, educational and economic systems. To date, the heterogeneity and incompleteness of data sources does not allow to quantify the multifaceted impact of the pandemic at country level and, consequently, to compare the effectiveness of country responses. Here, we tackle this challenge from a complex systems perspective, proposing a model to evaluate the impact of systemic failures in response to the pandemic shock. We use health, behavioral and economic indicators for 44 countries to build a shock index quantifying responses in terms of robustness and resilience, highlighting the crucial advantage of proactive policy and decision making styles over reactive ones.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pierluigi Sacco", - "author_inst": "IULM University, Milan" - }, - { - "author_name": "Francesco Valle", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Manlio De Domenico", - "author_inst": "University of Padua" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.01.21267121", "rel_title": "Impact of COVID-19 on healthcare access for Australian adolescents and young adults", @@ -512231,6 +514473,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.12.03.21267281", + "rel_title": "Safety and immunogenicity of the third booster dose with inactivated, viral vector, and mRNA COVID-19 vaccines in fully immunized healthy adults with inactivated vaccine", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267281", + "rel_abs": "The coronavirus disease-2019 (COVID-19) pandemic has become a severe healthcare problem worldwide since the first outbreak in late December 2019. Currently, the COVID-19 vaccine has been used in many countries, but it is still unable to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection despite patients receiving full vaccination doses. Therefore, we aimed to appraise the booster effect of the different platforms of vaccines, including inactivated vaccine (BBIBP), viral vector vaccine (AZD122), and mRNA vaccine (BNT162b2) in healthy adults who received the full dose of inactivated vaccine (CoronaVac). The booster dose was safe with no serious adverse events. Moreover, the immunogenicity indicated that the booster dose with viral vector and mRNA vaccine achieved a significant proportion of Ig anti-receptor binding domain (RBD), IgG anti-RBD, and IgA anti-S1 booster response. In contrast, inactivated vaccine achieved a lower booster response than others. Consequently, the neutralization activity of vaccinated serum had a high inhibition of over 90% against SARS-CoV-2 wild-type and their variants (B.1.1.7-alpha, B.1.351-beta, and B.1.617.2-delta). In addition, IgG anti-nucleocapsid was observed only among the group that received the BBIBP booster. Our study found a significant increase in levels of interferon gamma-secreting T-cell response after the additional viral vector or mRNA booster vaccination. This study showed that administration with either viral vector (AZD1222) or mRNA (BNT162b2) boosters in individuals with a history of two doses of inactivated vaccine (CoronaVac) obtained great immunogenicity with acceptable adverse events.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn Univ" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn Univ" + }, + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sirapa Klinfueng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sittisak Honsawek", + "author_inst": "Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospita" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Thailand and FRS(T), the Royal Society of Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.12.04.21267294", "rel_title": "Characteristics of Patients Referred to a Cardiovascular Disease Clinic for Post-Acute Sequelae of SARS-CoV-2 Infection", @@ -512887,41 +515204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.03.21267250", - "rel_title": "Cellular and humoral responses to SARS-CoV-2 vaccination in immunosuppressed patients", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267250", - "rel_abs": "ObjectiveSARS-CoV-2 vaccinations have demonstrated vaccine immunogenicity in healthy volunteers, however, efficacy in immunosuppressed patients is less well characterised. Subsequently, there is an urgent need to address the impact of immunosuppression on vaccine immunogenicity.\n\nMethodsSerological, T-cell ELISpot, cytokines and immunophenotyping investigations were used to assess vaccine responses (either BNT162b2 mRNA or ChAdOx1 nCoV-19) in double-vaccinated patients receiving immunosuppression for renal transplants or haematological malignancies (n=13). Immunological responses in immunosuppressed patients (VACC-IS) were compared to immunocompetent vaccinated (VACC-IC, n=12), unvaccinated (UNVACC, n=11) and infection-naive unvaccinated (HC, n=3) cohorts. All participants, except HC, had prior COVID-19 infection.\n\nResultsT-cell responses were identical between VACC-IS and VACC-IC (92%) to spike-peptide (S) stimulation. UNVACC had the highest T-cell non-responders (n=3), whereas VACC-IC and VACC-IS both had one T-cell non-responder. No significant differences in humoral responses were observed between VACC-IC and VACC-IS, with 92% (12/13) of VACC-IS patients demonstrating seropositivity. One VACC-IS failed to seroconvert, however had detectable T-cell responses. All VACC-IC participants were seropositive for anti-spike antibodies. Furthermore, both VACC-IS and VACC-IC participants elicited strong Th1 cytokine response with immunodominance towards S-peptide. Differences in T-cell immunophenotyping were seen between VACC-IS and VACC-IC, with lower CD8+ activation and T-effector memory phenotype observed in VACC-IS.\n\nConclusionSARS-CoV-2 vaccines are immunogenic in patients receiving immunosuppressive therapy, with responses comparable to vaccinated immunocompetent participants. Lower humoral responses were seen in patients treated with B-cell depleting therapeutics, but with preserved T-cell responses. We suggest further work to correlate both protective immunity and longevity of these responses in both healthy and immunosuppressed patients.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dinesh Mohanraj", - "author_inst": "Faculty of Medicine, Biology and Health. The University of Manchester, Manchester, UK" - }, - { - "author_name": "Samuel Baldwin", - "author_inst": "Department of Blood Sciences, Portsmouth Hospital University NHS Trust, Portsmouth, UK" - }, - { - "author_name": "Satbeer Singh", - "author_inst": "Department of Blood Sciences, Portsmouth Hospital University NHS Trust, Portsmouth, UK" - }, - { - "author_name": "Alun Gordon", - "author_inst": "Department of Blood Sciences, Portsmouth Hospital University NHS Trust, Portsmouth, UK" - }, - { - "author_name": "Alison Whitelegg", - "author_inst": "Department of Clinical Immunology, University Hospital Southampton NHS Trust, Southampton, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.12.02.21266871", "rel_title": "Impact of individual-level characteristics and transmission mitigation behaviors on SARS-CoV-2 infection and seroprevalence in a large Northern California Bay Area cohort", @@ -513953,6 +516235,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.12.03.21266538", + "rel_title": "Introduction and community transmission of SARS-CoV-2 lineage A.2.5 in Florida with novel spike INDELS", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21266538", + "rel_abs": "SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah E Schmedes", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Taj Azarian", + "author_inst": "Burnett School of Biomedical Sciences, University of Central Florida" + }, + { + "author_name": "Eleonora Cella", + "author_inst": "Burnett School of Biomedical Sciences, University of Central Florida" + }, + { + "author_name": "Jessy Motes", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Omer Tekin", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "James Weiss", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Nancimae Miller", + "author_inst": "Pathology Consultants of South Broward, Memorial Healthcare System" + }, + { + "author_name": "Jason Blanton", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.03.21267155", "rel_title": "High viral loads: what drives fatal cases of COVID-19 in vaccinees? an autopsy study", @@ -514681,37 +517010,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.12.02.471030", - "rel_title": "Drug repurposing screening identified tropifexor as a SARS-CoV-2 papain-like protease inhibitor", - "rel_date": "2021-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.02.471030", - "rel_abs": "The global COVID-19 pandemic underscores the dire need of effective antivirals. Encouraging progress has been made in developing small molecule inhibitors targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and main protease (Mpro). However, the development of papain-like protease (PLpro) inhibitors faces several obstacles. Nevertheless, PLpro represents a high-profile drug target given its multifaceted roles in viral replication. PLpro is involved in not only the cleavage of viral polyprotein but also modulation of host immune response. In this study, we conducted a drug-repurposing screening of PLpro against the MedChemExpress bioactive compound library and identified three hits, EACC, KY-226, and tropifexor, as potent PLpro inhibitors with IC50 values ranging from 3.39 to 8.28 {micro}M. The three hits showed dose-dependent binding to PLpro in the thermal shift assay. In addition, tropifexor inhibited the cellular PLpro activity in the FlipGFP assay with an IC50 of 10.6 {micro}M. Gratifyingly, tropifexor showed antiviral activity against SARS-CoV-2 in Calu-3 cells with an EC50 of 4.03 {micro}M, a 7.8-fold increase compared to GRL0617 (EC50 = 31.4 {micro}M). Overall, tropifexor represents a novel PLpro inhibitor that can be further developed as SARS-CoV-2 antivirals.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chunlong Ma", - "author_inst": "University of Arizona" - }, - { - "author_name": "Yuyin Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Juliana Choza", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jun Wang", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.12.02.470978", "rel_title": "Secreted ORF8 is a pathogenic cause of severe Covid-19 and potentially targetable with select NLRP3 inhibitors", @@ -515751,6 +518049,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.02.21267185", + "rel_title": "Tajima D test accurately forecasts Omicron / COVID-19 outbreak", + "rel_date": "2021-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267185", + "rel_abs": "On 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (-2.814, p<0.001) and Zengs E (0.0583, p=1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous (Dsyn) and nonsynonymous (Dnonsyn) polymorphisms of the Omicron variant spike gene were estimated with Tajimas D statistic to eliminate homogenous effects. Both D ratio (Dnonsyn/Dsyn, 1.57) and {Delta}D (Dsyn-Dnonsyn, 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (-2.709, p<0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajimas D test score, with a threshold value as -2.50, as an accurate predictor of new COVID-19 outbreaks.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ting-Yu Yeh", + "author_inst": "Institute of Marine and Environmental Technology" + }, + { + "author_name": "Gregory P. Contreras", + "author_inst": "Auxergen Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.30.21267071", "rel_title": "Increased risk of psychiatric sequelae of COVID-19 is highest early in the clinical course", @@ -516211,49 +518532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.01.21267145", - "rel_title": "Medical Students' Perceptions of Learning and Working on the COVID-19 Frontlines: \"...a confirmation that I am in the right place professionally.\"", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21267145", - "rel_abs": "IntroductionThe COVID-19 pandemic caused complex and enduring challenges for health care providers and medical educators and changed the medical education landscape for learners. Medical students were required to adapt and learn in a novel learning environment while universities paused their formal medical training. The current study sought to investigate medical students experiences working on a pandemic frontline to understand how they perceived this novel learning environment influenced both their learning and their developing professional identity.\n\nMethodsWe conducted semi-structured interviews with 21 medical students who worked in a COVID-19 testing facility at the University Hospital of Basel. Using constructivist grounded theory methodology, we collected and analyzed data iteratively using a constant comparative approach to develop codes and theoretical categories.\n\nResultsParticipants described improvements in their technical and communication skills, consequently impacting their professional development. The presence of a perceived flat hierarchy between the physicians and medical students promoted professional identity development amongst the medical students. Most participants perceived working on the pandemic frontlines as a positive learning experience, which seemed supported by a flatter hierarchy and open communication compared to their usual learning environment.\n\nConclusionSince medical students reported that their work on the pandemic frontlines positively affected their learning, the need to create hands-on learning opportunities for medical students challenge curriculum developers. Medical students wish to feel like full-fledged care team members rather than observing learners. Performing simple clinical tasks and collaborative moments in a supportive learning environment may promote learning and professional development.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jennifer M Klasen MD", - "author_inst": "University Hospital of Basel" - }, - { - "author_name": "Zoe Schoenbaechler", - "author_inst": "University of Basel" - }, - { - "author_name": "Bryce Bogie", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Andrea Meienberg MD", - "author_inst": "University Hospital of Basel" - }, - { - "author_name": "Christian Nickel MD", - "author_inst": "University Hospital of Basel" - }, - { - "author_name": "Roland Bingisser MD", - "author_inst": "University Hospital of Basel" - }, - { - "author_name": "Kori LaDonna PhD", - "author_inst": "University of Ottawa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.11.25.21266853", "rel_title": "Digital exclusion predicts worse mental health among adolescents during COVID-19", @@ -517469,6 +519747,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.11.29.21267041", + "rel_title": "COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme", + "rel_date": "2021-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267041", + "rel_abs": "Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here we present the development and validation of a rapid COVID-19 variant DETECTR(R) assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations that are associated with nearly all circulating viral lineages and identifies the two circulating variants of concern, Delta and Omicron. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 139 clinical samples yielded an overall SNP concordance of 98% and agreement with SARS-CoV-2 lineage classification of 138/139 compared to viral whole-genome sequencing. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR(R) as a faster and simpler diagnostic than sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Clare L Fasching", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Venice Servellita", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Bridget McKay", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Vaishnavi Nagesh", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "James P Broughton", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Noah Brazer", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Baolin Wang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Kevin Reyes", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Rachel N Deraney", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Emma Stanfield", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Carley G Hendriks", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Steve Miller", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jesus Ching", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Janice S Chen", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.29.21267042", "rel_title": "Favipiravir for the Treatment of Coronavirus Disease 2019; a propensity score-matched cohort study", @@ -518457,41 +520818,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.11.26.470157", - "rel_title": "A large-scale systematic survey of SARS-CoV-2 antibodies reveals recurring molecular features", - "rel_date": "2021-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.26.470157", - "rel_abs": "In the past two years, the global research in combating COVID-19 pandemic has led to isolation and characterization of numerous human antibodies to the SARS-CoV-2 spike. This enormous collection of antibodies provides an unprecedented opportunity to study the antibody response to a single antigen. From mining information derived from 88 research publications and 13 patents, we have assembled a dataset of [~]8,000 human antibodies to the SARS-CoV-2 spike from >200 donors. Analysis of antibody targeting of different domains of the spike protein reveals a number of common (public) responses to SARS-CoV-2, exemplified via recurring IGHV/IGK(L)V pairs, CDR H3 sequences, IGHD usage, and somatic hypermutation. We further present a proof-of-concept for prediction of antigen specificity using deep learning to differentiate sequences of antibodies to SARS-CoV-2 spike and to influenza hemagglutinin. Overall, this study not only provides an informative resource for antibody and vaccine research, but fundamentally advances our molecular understanding of public antibody responses to a viral pathogen.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yiquan Wang", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Jian Peng", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Nicholas C. Wu", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.28.470293", "rel_title": "Protective immunity of the primary SARS-CoV-2 infection reduces disease severity post re-infection with Delta variants in Syrian hamsters", @@ -519347,6 +521673,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.25.21266875", + "rel_title": "COVID-19 trends and severity among symptomatic children aged 0 to 17 years in ten EU countries, 3 August 2020 to 3 October 2021", + "rel_date": "2021-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.25.21266875", + "rel_abs": "To guide evidence-based prevention of COVID-19 in children, we estimated risks of severe outcomes in 820,404 symptomatic paediatric cases reported by 10 EU Member States between August 2020 and October 2021. Case and hospitalisation rates rose as overall transmission increased but severe outcomes were rare: 9,611 (1.2%) were hospitalised, 640 (0.08%) required intensive care and 84 (0.01%) died. Despite increased individual risk (aOR; 95% CI for hospitalisation: 7.3; 3.3 - 16.2, ICU: 8.7; 6.2 - 12.3) in cases with comorbidities such as cancer, diabetes, cardiac or lung disease, most (83.7%) hospitalised children had no reported comorbidity.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nick Bundle", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Nishi Dave", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Gianfranco Spiteri", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Charlotte Deogan", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "- Study group members", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.21266976", "rel_title": "Impact of the COVID-19 pandemic on the malaria burden in northern Ghana: Analysis of routine surveillance data", @@ -520143,41 +522512,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.26.21266896", - "rel_title": "The relationship of COVID-19 related stress and media consumption with schizotypy, depression and anxiety", - "rel_date": "2021-11-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.26.21266896", - "rel_abs": "Studies report a strong impact of the COVID-19 pandemic and related stressors on the mental wellbeing of general population. In this paper, we investigated whether COVID-19 related concerns and social adversity affected schizotypal traits, anxiety and depression using structural equational modelling. In mediation analyses, we furthermore explored whether these associations were mediated by healthy (sleep and physical exercise) or unhealthy behaviours (drug and alcohol consumption, excessive media use).\n\nWe assessed schizotypy, depression and anxiety as well as, healthy and unhealthy behaviours and a wide range of sociodemographic scores using online surveys from residents of Germany and the United Kingdom over one year during the COVID-19 pandemic. Four independent samples were collected (April/ May 2020: N=781, September/ October 2020: N=498, January/ February 2021: N=544, May 2021: N= 486). The results revealed that COVID-19 related life concerns were significantly associated with schizotypy in the autumn 2020 and spring 2021 surveys, and with anxiety and depressive symptoms in all surveys; and social adversity significantly affected the expression of schizotypal traits in all but the spring 2020 survey, and depressive and anxiety symptoms in all samples. Importantly, we found that excessive media consumption (>4h per day) fully mediated the relationship of COVID-19 related life concerns and schizotypal traits in the winter 2021 survey. Furthermore, several of the surveys showed that excessive media consumption was associated with increased depressive and anxiety- related symptoms in people burdened by COVID-19 related life.\n\nThe ongoing uncertainties of the pandemic and the restrictions on social life have a strong impact on mental well-being and especially the expression of schizotypal traits. The negative impact is further boosted by excessive media consumption, which is especially critical for people with high schizotypal traits.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sarah Daimer", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Lorenz Mihatsch", - "author_inst": "Ludwig-Maximillians University Munich" - }, - { - "author_name": "Sharon AS Neufeld", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Graham K Murray", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Franziska Knolle", - "author_inst": "Technical University of Munich" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.11.27.21266927", "rel_title": "Variations of the quality of care during the COVID-19 pandemic affected the mortality rate of non-COVID patients with hip fracture", @@ -521169,6 +523503,125 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.11.24.21266812", + "rel_title": "SARS-CoV-2 Convalescent Sera Binding and Neutralizing Antibody Concentrations Compared with COVID-19 Vaccine Efficacy Estimates Against Symptomatic Infection", + "rel_date": "2021-11-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266812", + "rel_abs": "Previous vaccine efficacy (VE) studies have estimated neutralizing and binding antibody concentrations that correlate with protection from symptomatic infection; how these estimates compare to those generated in response to SARS-CoV-2 infection is unclear. Here, we assessed quantitative neutralizing and binding antibody concentrations using standardized SARS-CoV-2 assays on 3,067 serum specimens collected during July 27, 2020-August 27, 2020 from COVID-19 unvaccinated persons with detectable anti-SARS-CoV-2 antibodies using qualitative antibody assays. Quantitative neutralizing and binding antibody concentrations were strongly positively correlated (r=0.76, p<0.0001) and were noted to be several fold lower in the unvaccinated study population as compared to published data on concentrations noted 28 days post-vaccination. In this convenience sample, [~]88% of neutralizing and [~]63-86% of binding antibody concentrations met or exceeded concentrations associated with 70% COVID-19 VE against symptomatic infection from published VE studies; [~]30% of neutralizing and 1-14% of binding antibody concentrations met or exceeded concentrations associated with 90% COVID-19 VE. These data support observations of infection-induced immunity and current recommendations for vaccination post infection to maximize protection against symptomatic COVID-19.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Amy J. Schuh", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Panayampalli S. Satheshkumar", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Stephanie Dietz", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Lara Bull-Otterson", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Myrna Charles", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Chris Edens", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Jefferson M. Jones", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristina L. Bajema", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristie E.N. Clarke", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "L. Clifford McDonald", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Sadhna Patel", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kendra Cuffe", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Jarad Schiffer", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kelly Chun", + "author_inst": "Labcorp" + }, + { + "author_name": "Monique Bastidas", + "author_inst": "Labcorp" + }, + { + "author_name": "Manory Fernando", + "author_inst": "Labcorp" + }, + { + "author_name": "Christos J. Petropoulos", + "author_inst": "Labcorp" + }, + { + "author_name": "Terri Wrin", + "author_inst": "Labcorp" + }, + { + "author_name": "Suqin Cai", + "author_inst": "Labcorp" + }, + { + "author_name": "Dot Adcock", + "author_inst": "Labcorp" + }, + { + "author_name": "Deborah Sesok-Pizzini", + "author_inst": "Labcorp" + }, + { + "author_name": "Stanley Letovsky", + "author_inst": "Labcorp" + }, + { + "author_name": "Alicia M. Fry", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Aron J. Hall", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Adi V. Gundlapalli", + "author_inst": "United States Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.21.21266633", "rel_title": "SARS-CoV-2 vaccination predicts COVID-19 progression and outcomes in hospitalized patients", @@ -522001,65 +524454,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.11.25.21266090", - "rel_title": "Synthesis of High-Resolution Research-Quality MRI Data from Clinical MRI Data in Patients with COVID-19", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.25.21266090", - "rel_abs": "Pathophysiological mechanisms of neurological disorders in patients with coronavirus disease 2019 (COVID-19) are poorly understood, partly because of a lack of high-resolution neuroimaging data. We applied SynthSR, a convolutional neural network that synthesizes high-resolution isotropic research-quality data from thick-slice clinical MRI data, to a cohort of 11 patients with severe COVID-19. SynthSR successfully synthesized T1-weighted MPRAGE data at 1 mm spatial resolution for all 11 patients, each of whom had at least one brain lesion. Correlations between volumetric measures derived from synthesized and acquired MPRAGE data were strong for the cortical grey matter, subcortical grey matter, brainstem, hippocampus, and hemispheric white matter (r=0.84 to 0.96, p[≤]0.001), but absent for the cerebellar white matter and corpus callosum (r=0.04 to 0.17, p>0.61). SynthSR creates an opportunity to quantitatively study clinical MRI scans and elucidate the pathophysiology of neurological disorders in patients with COVID-19, including those with focal lesions.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ryan J Cali", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Holly J Freeman", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Benjamin Billot", - "author_inst": "University College London" - }, - { - "author_name": "Megan E Barra", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "David Fischer", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "William R Sanders", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Susie Y Huang", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "John Conklin", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Bruce Fischl", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Juan Eugenio Iglesias", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Brian L Edlow", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.11.24.21266824", "rel_title": "Synergetic measures needed to control infection waves and contain SARS-CoV-2 transmission", @@ -523083,6 +525477,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.22.21266692", + "rel_title": "Serological responses to COVID-19 booster vaccine in England", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266692", + "rel_abs": "IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca).\n\nMethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared.\n\nResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants.\n\nConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Georgina Ireland", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Heather Whitaker", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Shamez N Ladhani", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Frances Baawuah", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Vani Subbarao", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Ezra Linley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Lenesha Warrener", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Michelle O'Brien", + "author_inst": "Brondesbury Medical Centre, Kilburn, London, United Kingdom" + }, + { + "author_name": "Corrine Whillock", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Paul Moss", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Mary E Ramsay", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Gayatri Amirthalingam", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Kevin E Brown", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.22.21266713", "rel_title": "In Vitro Nasal Tissue Model for the Validation of Nasopharyngeal and Mid-turbinate Swabs for SARS-CoV-2 Testing", @@ -523715,41 +526176,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.11.24.21266807", - "rel_title": "A population framework for predicting the proportion of people infected by the far-field airborne transmission of SARS-CoV-2 indoors", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266807", - "rel_abs": "The number of occupants in a space influences the risk of far-field airborne transmission of SARS-CoV-2 because the likelihood of having infectious and susceptible people both correlate with the number of occupants. This paper explores the relationship between occupancy and the probability of infection, and how this affects an individual person and a population of people. Mass-balance and dose-response models determine far-field transmission risks for an individual person and a population of people after sub-dividing a large reference space into 10 identical comparator spaces.\n\nFor a single infected person, the dose received by an individual person in the comparator space is 10-times higher because the equivalent ventilation rate per infected person is lower when the per capita ventilation rate is preserved.\n\nHowever, accounting for population dispersion, such as the community prevalence of the virus, the probability of an infected person being present and uncertainty in their viral load, shows the transmission probability increases with occupancy and the reference space has a higher transmission risk. Also, far-field transmission is likely to be a rare event that requires a high emission rate, and there are a set of Goldilocks conditions that are just right when ventilation is effective at mitigating against transmission. These conditions depend on the viral load, because when they are very high or low, ventilation has little effect on transmission risk.\n\nNevertheless, resilient buildings should deliver the equivalent ventilation rate required by standards as minimum.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christopher Iddon", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Benjamin Jones", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Patrick Sharpe", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Muge Cevik", - "author_inst": "University of St Andrews" - }, - { - "author_name": "Shaun Fitzgerald", - "author_inst": "Cambridge University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.23.469755", "rel_title": "Distinct SARS-CoV-2 sensing pathways in pDCs driving TLR7-antiviral vs. TLR2-immunopathological responses in COVID-19", @@ -524797,6 +527223,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.11.24.21266401", + "rel_title": "Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission - a prospective cohort study in England", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266401", + "rel_abs": "BackgroundThe ability of SARS-CoV-2 vaccines to protect against infection and onward transmission determines whether immunisation can control global circulation. We estimated effectiveness of BNT162b2 and ChAdOx1 vaccines against acquisition and transmission of the Alpha and Delta variants in a prospective household study in England.\n\nMethodsAdult index cases in the community and their household contacts took oral-nasal swabs on days 1, 3 and 7 after enrolment. Swabs were tested by RT-qPCR with genomic sequencing conducted on a subset. We used Bayesian logistic regression to infer vaccine effectiveness against acquisition and transmission, adjusted for age, vaccination history and variant.\n\nFindingsBetween 2 February 2021 and 10 September 2021 213 index cases and 312 contacts were followed up. After excluding households lacking genomic proximity (N=2) or with unlikely serial intervals (N=16), 195 households with 278 contacts remained of whom 113 (41%) became PCR positive. Delta lineages had 1.64 times the risk (95% Credible Interval: 1.15 - 2.44) of transmission than Alpha; contacts older than 18 years were 1.19 times (1.04 - 1.52) more likely to acquire infection than children. Effectiveness of two doses of BNT162b2 against transmission of Delta was 31% (-3%, 61%) and 42% (14%, 69%) for ChAdOx1, similar to their effectiveness for Alpha. Protection against infection with Alpha was higher than for Delta, 71% (12%,95%) vs 24% (-2%, 64%) respectively for BNT162b2 and 26% (-39%, 73%) vs 14% (-5%, 46%) respectively for ChAdOx1.\n\nInterpretationBNT162b2 and ChAdOx1 reduce transmission of the Delta variant from breakthrough infections in the household setting though their protection against infection is low.\n\nFundingThis study was funded by the UK Health Security Agency (formerly Public Health England) as part of the COVID-19 response.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Samuel Clifford", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Pauline Waight", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jada Hackman", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stephane Hue", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Charlotte M Gower", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Freja CM Kirsebom", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Catriona Skarnes", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Louise Letley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Elizabeth Miller", + "author_inst": "London School of Hygiene and Tropical Medicine, UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.22.21266599", "rel_title": "Modeling on Wastewater Treatment Process in Saudi Arabia: a perspective of Covid-19", @@ -525341,201 +527830,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.11.22.469117", - "rel_title": "Preclinical efficacy, safety, and immunogenicity of PHH-1V, a second-generation COVID-19 vaccine candidate based on a novel recombinant RBD fusion heterodimer of SARS-CoV-2.", - "rel_date": "2021-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.22.469117", - "rel_abs": "Current C0VID-19 vaccines have been associated with a decline in infection rates, prevention of severe disease and a decrease in mortality rates. However, SARS-CoV-2 variants are continuously evolving, and development of new accessible COVID-19 vaccines is essential to mitigate the pandemic. Here, we present data on preclinical studies in mice of a receptor-binding domain (RBD)-based recombinant protein vaccine (PHH-1V) consisting of an RBD fusion heterodimer comprising the B.1.351 and B.1.1.7 SARS-CoV-2 variants formulated in SQBA adjuvant, an oil-in-water emulsion. A prime-boost immunisation with PHH-1V in BALB/c and K18-hACE2 mice induced a CD4+ and CD8+ T cell response and RBD-binding antibodies with neutralising activity against several variants, and also showed a good tolerability profile. Significantly, RBD fusion heterodimer vaccination conferred 100% efficacy, preventing mortality in SARS-CoV-2 infected K18-hACE2 mice, but also reducing Beta, Delta and Omicron infection in lower respiratory airways. These findings demonstrate the feasibility of this recombinant vaccine strategy.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Antonio Barreiro", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Antoni Prenafeta", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Gregori Bech-Sabat", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Merce Roca", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Eva Perozo", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Ricard March", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Luis Gonzalez-Gonzalez", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Laia Madrenas", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Julia Corominas", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Alex Fernandez", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Alexandra Moros", - "author_inst": "HIPRA SCIENTIFIC S.L.U" - }, - { - "author_name": "Merce Molas", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Thais Pentinat-Pelegrin", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Clara Panosa", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Alberto Moreno", - "author_inst": "HIPRA SCIENTIFIC S. L. U" - }, - { - "author_name": "Ester Puigvert", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Eva Pol", - "author_inst": "HIPRA SCIENTIFIC S.L.U" - }, - { - "author_name": "Jordi Palmada", - "author_inst": "HIPRA SCIENTIFIC S.L.U" - }, - { - "author_name": "Carme Garriga", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Teresa Prat", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - }, - { - "author_name": "Javier Iglesias-Fernandez", - "author_inst": "Nostrum biodiscovery" - }, - { - "author_name": "Julia Vergara-Alert", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB)" - }, - { - "author_name": "Cristina Lorca-Oro", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Campus de la UAB (CReSA, IRTA-UAB)" - }, - { - "author_name": "Nuria Roca", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Campus de la UAB (CReSA, IRTA-UAB)" - }, - { - "author_name": "Leira Fernandez-Bastit", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Campus de la UAB (CReSA, IRTA-UAB)" - }, - { - "author_name": "Jordi Rodon", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Campus de la UAB (CReSA, IRTA-UAB)" - }, - { - "author_name": "Monica Perez", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Campus de la UAB (CReSA, IRTA-UAB)" - }, - { - "author_name": "Joaquim Segales", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agraroalimentaries (IRTA), Campus de la UAB (CReSA, IRTA-UAB); Departament de Sani" - }, - { - "author_name": "Edwards Pradenas", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Silvia Marfil", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Benjamin Trinite", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Raquel Ortiz", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP); University of Vic-Central University of Catalonia (UVic-UCC)" - }, - { - "author_name": "Julia Blanco", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP); University of Vic-Central University of Catalonia (UVic-UCC)" - }, - { - "author_name": "Jorge Diaz Pedroza", - "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Rosa Ampudia Carrasco", - "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Yaiza Rosales Salgado", - "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Jordina Loubat Casanovas", - "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Sara Capdevila Larripa", - "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Julia Garcia Prado", - "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Jordi Barretina Ginesta", - "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Germans Trias i Pujol Research Institute (IGTP)" - }, - { - "author_name": "Marta Sistere-Oro", - "author_inst": "Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)" - }, - { - "author_name": "Paula Cebollada Rica", - "author_inst": "Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)" - }, - { - "author_name": "Andreas Meyerhans", - "author_inst": "Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF); ICREA" - }, - { - "author_name": "Laura Ferrer", - "author_inst": "HIPRA SCIENTIFIC S.L.U." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.21.469172", "rel_title": "Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein", @@ -526611,6 +528905,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.19.21266580", + "rel_title": "COVID-19 cases and hospitalizations averted by case investigation and contact tracing in the United States", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266580", + "rel_abs": "ImportanceEvidence of the impact of COVID-19 Case Investigation and Contact Tracing (CICT) programs is lacking. Policymakers need this evidence to assess its value.\n\nObjectiveEstimate COVID-19 cases and hospitalizations averted nationwide by US states CICT programs.\n\nDesignWe combined data from US CICT programs (e.g., proportion of cases interviewed, contacts notified or monitored, and days to case and contact notification) with incidence data to model CICT impacts over 60 days period (November 25, 2020 to January 23, 2021) during the height of the pandemic. We estimated a range of impacts by varying assumed compliance with isolation and quarantine recommendations.\n\nSettingUS States and Territories\n\nParticipantsFifty-nine state and territorial health departments that received federal funding supporting COVID-19 pandemic response activities were eligible for inclusion. Of these, 22 states and 1 territory reported all measures necessary for the analysis. These 23 jurisdictions covered 42.5% of the US population (140 million persons), spanned all 4 census regions, and reported data that reflected all 59 federally funded CICT programs.\n\nInterventionPublic health case investigation and contact tracing\n\nMain Outcomes and MeasuresCases and hospitalizations averted; percent of cases averted among cases not prevented by vaccination and other non-pharmaceutical interventions (other NPIs).\n\nResultsWe estimated 1.11 million cases and 27,231 hospitalizations were averted by CICT programs under a scenario where 80% of interviewed cases and monitored contacts, and 30% of notified contacts fully complied with isolation and quarantine guidance, eliminating their contributions to future transmission. As many as 1.36 million cases and 33,527 hospitalizations could have been prevented if all interviewed cases and monitored contacts had entered into and fully complied with isolation and quarantine guidelines upon being interviewed or notified. Across all scenarios and jurisdictions, CICT averted a median of 21.2% (range: 1.3% - 65.8%) of the cases not prevented by vaccination and other NPIs.\n\nConclusions and RelevanceCICT programs likely had a substantial role in curtailing the pandemic in most jurisdictions during the winter 2020-2021 peak. Differences in impact across jurisdictions indicate an opportunity to further improve CICT effectiveness. These estimates demonstrate the potential benefits from sustaining and improving these programs.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat were the health impacts of COVID-19 case investigation and contact tracing programs (CICT) in the US?\n\nFindingsBy combining CICT program data from 22 states and 1 territory with mathematical modeling, we estimate CICT averted between 1.11 to 1.36 million cases and 27,231 to 33,527 hospitalizations over 60 days during the height of the pandemic (winter 2020-21). The upper estimate assumes all interviewed cases and monitored contacts complied with isolation and quarantine guidelines, while the lower estimate assumes fractions of interviewed cases and monitored or notified contacts did so.\n\nMeaningCICT programs likely played a critical role in curtailing the pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Gabriel Rainisch", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Seonghye Jeon", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Danielle Pappas", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kimberly Spencer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Leah S Fischer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bishwa Adhikari", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melanie Taylor", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bradford Greening Jr.", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Patrick Moonan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John Oeltmann", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emily B Kahn", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michael Washington", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Martin I Meltzer", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.19.21266581", "rel_title": "Baseline hypocapnia is associated with intubation in COVID-19 diagnosed patients", @@ -527375,41 +529736,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.17.21266472", - "rel_title": "An integrative method for COVID-19 patients classification from chest X-ray using deep learning network with image visibility graph as feature extractor", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266472", - "rel_abs": "We propose a method by integrating image visibility graph and deep neural network (DL) for classifying COVID-19 patients from their chest X-ray images. The computed assortative coefficient from each image horizonal visibility graph (IHVG) is utilized as a physical parameter feature extractor to improve the accuracy of our image classifier based on Resnet34 convolutional neural network (CNN). We choose the most optimized recently used CNN deep learning model, Resnet34 for training the pre-processed chest X-ray images of COVID-19 and healthy individuals. Independently, the preprocessed X-ray images are passed through a 2D Haar wavelet filter that decomposes the image up to 3 labels and returns the approximation coefficients of the image which is used to obtain the horizontal visibility graph for each X-ray image of both healthy and COVID-19 cases. The corresponding assortative coefficients are computed for each IHVG and was subsequently used in random forest classifier whose output is integrated with Resnet34 output in a multi-layer perceptron to obtain the final improved prediction accuracy. We employed a multilayer perceptron to integrate the feature predictor from image visibility graph with Resnet34 to obtain the final image classification result for our proposed method. Our analysis employed much larger chest X-ray image dataset compared to previous used work. It is demonstrated that compared to Resnet34 alone our integrative method shows negligible false negative conditions along with improved accuracy in the classification of COVID-19 patients. Use of visibility graph in this model enhances its ability to extract various qualitative and quantitative complex network features for each image. Enables the possibility of building disease network model from COVID-19 images which is mostly unexplored. Our proposed method is found to be very effective and accurate in disease classification from images and is computationally faster as compared to the use of multimode CNN deep learning models, reported in recent research works.\n\nSignificanceAn integrative method is proposed combining convolutional neural networks and 2D visibility graphs through a multilayer perceptron, for effective classification of COVID-19 patients from the chest x-ray images. In our study, the computed assortative coefficient from the horizontal visibility graph of each wavelet filtered X-ray image is used as a physical feature extractor. We demonstrate that compared to Resnet34 alone, our proposed integrative approach shows significant reduction in false negative conditions and higher accuracy in the classification of COVID-19 patients. The method is computationally faster and with the use of visibility graph, it also enables one to extract complex network based qualitative and quantitative parameters for each subject for additional understandings like disease network model building and its structures etc.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mayukha Pal", - "author_inst": "ABB Ability Innovation Center" - }, - { - "author_name": "Yash Tiwari", - "author_inst": "Indian Institute of Technology Hyderabad" - }, - { - "author_name": "T Vineeth Reddy", - "author_inst": "IIT Hyderabad" - }, - { - "author_name": "Sai Ram Aditya Parisineni", - "author_inst": "IIT Hyderabad" - }, - { - "author_name": "Prasanta K Panigrahi", - "author_inst": "IISER Kolkata" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.11.18.21266501", "rel_title": "Risk factors for workplace bullying, severe psychological distress, and suicidal ideation during the COVID-19 pandemic: a nationwide internet survey for the general working population in Japan", @@ -528317,6 +530643,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.17.21266488", + "rel_title": "Enoxaparin for thromboprophylaxis in hospitalized COVID-19 patients: comparison of 40 mg o.d. vs 40 mg b.i.d. The X-COVID19 Randomized Clinical Trial", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266488", + "rel_abs": "It is uncertain whether higher doses of anticoagulants than recommended for thromboprophylaxis are necessary in COVID-19 patients hospitalized in general wards. This is a multicentre, open-label, randomized trial performed in 9 Italian centres, comparing 40 mg b.i.d. vs 40 mg o.d. enoxaparin in COVID-19 patients, between April 30, 2020 and April 25, 2021. Primary efficacy outcome was in-hospital incidence of venous thromboembolism (VTE): asymptomatic or symptomatic proximal deep vein thrombosis (DVT) diagnosed by serial compression ultrasonography (CUS), and/or symptomatic pulmonary embolism (PE) diagnosed by computed tomography angiography (CTA). Secondary endpoints included each individual component of the primary efficacy outcome and a composite of death, VTE, mechanical ventilation, stroke, myocardial infarction, admission to ICU. Safety outcomes included major bleeding. The study was interrupted prematurely due to slow recruitment. We included 183 (96%) of the 189 enrolled patients in the primary analysis (91 in b.i.d., 92 in o.d.). Primary efficacy outcome occurred in 6 patients (6{middle dot}5%, 0 DVT, 6 PE) in the o.d. group and 0 in the b.id. group (ARR 6{middle dot}5, 95% CI, 1{middle dot}5-11{middle dot}6). Absence of concomitant DVT and imaging characteristics suggest that most pulmonary artery occlusions were actually caused by local thrombi rather than PE. Statistically non-significant differences in secondary and safety endpoints were observed, with two major bleeding events in each arm. In conclusion, no DVT developed in COVID-19 patients hospitalized in general wards, independently of enoxaparin dosing used for thromboprophylaxis. Pulmonary artery occlusions developed only in the o.d. group. Our trial is underpowered and with few events.\n\nREGISTRATIONClinicalTrials.gov Identifier: NCT04366960\n\nEthics Commettee approvation number75/2020", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nuccia Morici", + "author_inst": "ASST GRANDE OSPEDALE METROPOLITANO NIGUARDA" + }, + { + "author_name": "Gian Marco Podda", + "author_inst": "University of Milan; Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + }, + { + "author_name": "Simone Birocchi", + "author_inst": "Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + }, + { + "author_name": "Luca Bonacchini", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Marco Merli", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Michele Trezzi", + "author_inst": "Struttura Operativa Complessa (SOC) Malattie Infettive II, AUSL Toscana Centro, Ospedale San Jacopo, Pistoia, Italy" + }, + { + "author_name": "Gianluca Massaini", + "author_inst": "Struttura Operativa Semplice (SOS) Chirurgia vascolare, AUSL Toscana Centro, Ospedale San Jacopo, Pistoia, Italy" + }, + { + "author_name": "Marco Agostinis", + "author_inst": "Emergency Department, Ospedale San Carlo Borromeo, ASST Santi Paolo e Carlo, Milano, Italy" + }, + { + "author_name": "Giulia Carioti", + "author_inst": "Emergency Department, Ospedale San Carlo Borromeo, ASST Santi Paolo e Carlo, Milano, Italy" + }, + { + "author_name": "Francesco Saverio Serino", + "author_inst": "ASL 4 Veneto, Covid Hospital, Jesolo, Italy" + }, + { + "author_name": "Gianluca Gazzaniga", + "author_inst": "Postgraduate School of Clinical Pharmacology and Toxicology, Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy" + }, + { + "author_name": "Daniela Barberis", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Laura Antolini", + "author_inst": "Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Maria Grazia Valsecchi", + "author_inst": "Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Marco Cattaneo", + "author_inst": "University of Milan; Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.17.21266367", "rel_title": "A prospective study of asymptomatic SARS-CoV-2 infection among individuals involved in academic research under limited operations during the COVID-19 pandemic", @@ -528909,77 +531310,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.11.17.21266437", - "rel_title": "Experiences of staff providing specialist palliative care during COVID-19: A multiple qualitative case study.", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266437", - "rel_abs": "ObjectivesTo explore the experiences of, and impact on, staff working in palliative care during the COVID-19 pandemic.\n\nDesignQualitative multiple case study using semi-structured interviews between November 2020 and April 2021 as part of the CovPall study. Data were analysed using thematic framework analysis.\n\nSettingOrganisations providing specialist palliative services in any setting.\n\nParticipantsStaff working in specialist palliative care, purposefully sampled by the criteria of role, care setting and COVID-19 experience.\n\nMain outcome measuresExperiences of working in palliative care during the COVID-19 pandemic.\n\nResultsFive cases and 24 participants were recruited (n=12 nurses, 4 clinical managers, 4 doctors, 2 senior managers, 1 healthcare assistant, 1 allied healthcare professional). Central themes demonstrate how infection control constraints prohibited and diluted participants ability to provide care that reflected their core values, resulting in experiences of moral distress. Despite organisational, team, and individual support strategies, continually managing these constraints led to a crescendo effect in which the impacts of moral distress accumulated over time, sometimes leading to burnout. Solidarity with colleagues and making a valued contribution provided moral comfort for some.\n\nConclusionsThis study provides a unique insight into why and how healthcare staff have experienced moral distress during the pandemic, and how organisations have responded. Despite their experience of dealing with death and dying, the mental health and well-being of palliative care staff was affected by the pandemic. Organisational, structural, and policy changes are urgently required to mitigate and manage these impacts.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Andy Bradshaw", - "author_inst": "University of Hull, Hull York Medical School" - }, - { - "author_name": "Lesley Dunleavy", - "author_inst": "Lancaster University" - }, - { - "author_name": "Ian Garner", - "author_inst": "Lancaster University" - }, - { - "author_name": "Nancy Preston", - "author_inst": "Lancaster University" - }, - { - "author_name": "Sabrina Bajwah", - "author_inst": "King's College London" - }, - { - "author_name": "Rachel Cripps", - "author_inst": "King's College London" - }, - { - "author_name": "Lorna K Fraser", - "author_inst": "University of York" - }, - { - "author_name": "Matthew Maddocks", - "author_inst": "King's College London" - }, - { - "author_name": "Mevhibe Hocaoglu", - "author_inst": "King's College London" - }, - { - "author_name": "Fliss E Murtagh", - "author_inst": "University of Hull, Hull York Medical School" - }, - { - "author_name": "Adejoke O Oluyase", - "author_inst": "King's College London" - }, - { - "author_name": "Katherine E Sleeman", - "author_inst": "King's College London" - }, - { - "author_name": "Irene J Higginson", - "author_inst": "King's College London" - }, - { - "author_name": "Catherine Walshe", - "author_inst": "Lancaster University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "palliative medicine" - }, { "rel_doi": "10.1101/2021.11.12.21265796", "rel_title": "Transmission potential of vaccinated and unvaccinated persons infected with the SARS-CoV-2 Delta variant in a federal prison, July-August 2021", @@ -529899,6 +532229,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.14.21266334", + "rel_title": "Attenuation of antibody titres during 3-6 months after the second dose of the BNT162b2 vaccine depends on sex, with age and smoking as risk factors for lower antibody titres at 6 months", + "rel_date": "2021-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266334", + "rel_abs": "ObjectiveWe aimed to determine antibody titres at 6 months and their rate of change during 3-6 months after the second dose of the BNT162b2 coronavirus disease 2019 (COVID-19) mRNA vaccine (Pfizer/BioNTech) and to explore clinical variables associated with titres in Japan.\n\nMethodsWe enrolled 365 healthcare workers (250 women, 115 men) whose 3-month antibody titres were analyzed in our previous study and whose blood samples were collected 183 {+/-} 15 days after the second dose. Participant characteristics collected previously were used. The relationships of these factors with antibody titres at 6 months and rates of change in antibody titres during 3-6 months were analyzed.\n\nResultsMedian age was 44 years. Median antibody titre at 6 months was 539 U/mL. Older participants had significantly lower antibody titres (20s, 752 U/mL; 60s-70s, 365 U/mL). In age-adjusted analysis, smoking was the only factor associated with lower antibody titres. Median rate of change in antibody titres during 3-6 months was -29.4%. The only factor significantly associated with the rate of change in Ab titres was not age or smoking, but sex (women, -31.6%; men, -25.1%).\n\nConclusionThe most important factors associated with lower antibody titres at 6 months were age and smoking, as at 3 months, probably reflecting their effect on peak antibody titres. However, antibody titres significantly attenuated during 3-6 months in women alone, which reduced the sex difference in antibody titres seen during the first 3 months. Antibody titres may be affected by different factors at different time points.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yushi Nomura", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Michiru Sawahata", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Yosikazu Nakamura", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Ryousuke Koike", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Otohiro Katsube", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Koichi Hagiwara", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Seiji Niho", + "author_inst": "Dokkyo Medical University" + }, + { + "author_name": "Norihiro Masuda", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Takaaki Tanaka", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Kumiya Sugiyama", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.16.21266414", "rel_title": "Unraveling the spatiotemporal spread of COVID-19 in Brazil through spatial network connectivity", @@ -530607,53 +532992,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.16.468834", - "rel_title": "Global Mutational Sweep of SARS-CoV-2: from Chaos to Order", - "rel_date": "2021-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.16.468834", - "rel_abs": "Analysis of large-scale genome sequences demonstrates the mutation of SARS-CoV-2 has been undergoing significant sweeps. Driven by emerging variants, global sweeps are accelerated and purified over time. This may prolong the pandemic with repeating epidemics, presenting challenges to the control and prevention of SARS-CoV-2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Xin Wang", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Mingda Hu", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Yuan Jin", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Boqian Wang", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Yunxiang Zhao", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Long Liang", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Junjie Yue", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - }, - { - "author_name": "Hongguang Ren", - "author_inst": "Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.11.16.468802", "rel_title": "NUDT18 catalyzes hydrolysis of active metabolites of the antivirals Remdesivir and Ribavirin", @@ -531609,6 +533947,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.11.15.21265526", + "rel_title": "COVID-19 in the Republic of Belarus: pandemic features and the interim safety and efficacy assessment of the Gam-COVID-Vac vaccine", + "rel_date": "2021-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21265526", + "rel_abs": "ObjectiveTo study the COVID-19 pandemic features among the population of the Republic of Belarus from February 2020 to September 2021 and assess the safety (tolerance) and epidemiological efficacy of the Gam-COVID-Vac vaccine (Sputnik V).\n\nMaterials and methodsA retrospective analysis of COVID-19 cases in the Republic of Belarus from the beginning of registration (February 28, 2020) to September 12, 2021 was performed. To assess the COVID-19 case detection dynamics, official registration data available on the website of the Ministry of Health of the Republic of Belarus were used.\n\nVaccine safety (tolerance) and efficacy were assessed in an observational study. Safety (tolerance) was assessed by presence/absence of adverse reactions: general and local ones.\n\nThe efficacy rate (E) and the epidemiological efficacy index (K) was calculated according to the formula: E(%)=100*(b-a)/b, K=b/a.\n\nResultsOur data show that The COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: the first is the absence of COVID-19 cases in the country; the second is the registration of individual infection cases that came from abroad followed by local pathogen spread among the countrys population; the third is a local spread of COVID-19 among individuals who had contact with infected people; the fourth is the detection of cases where patients had no history of exposure to COVID-19 patients.\n\nAs of calendar week 26, 2021 Delta variant of SARS-CoV-2 has become the prevalent in the country.\n\nFollow-up results in January-August 2021 showed that the Sputnik V vaccine was well tolerated, with 80,832 adverse reactions reported (2.99% (95% CI 2.9-3.0) of the total number of vaccine doses administered). In terms of severity, adverse reactions were mild (91.4% (95% CI 91.2-91.6)) and moderate (8.6% (95% CI 8.6-8.8)). The epidemiological efficacy rate was 96.3%, the epidemiological efficacy index was 26.7. Thus, the results obtained testify to high prophylactic efficacy of the Sputnik V vaccine.\n\nConclusionsThe COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: from no cases in early 2020 to detected cases where most individuals had no history of contact with COVID-19 patients; periods of rising and falling incidence. The Sputnik V vaccine has demonstrated a high safety profile and epidemiological efficacy throughout mass vaccination in the Republic of Belarus.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ala M Dashkevich", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Veronika S Vysotskaya", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Iryna N Hlinskaya", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Anzhela L Skuranovich", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Aliaksandr A Tarasenka", + "author_inst": "Ministry of Health of the Republic of Belarus" + }, + { + "author_name": "Inna A Karaban", + "author_inst": "Ministry of Health of the Republic of Belarus" + }, + { + "author_name": "Natalia D Kolomiets", + "author_inst": "Belarusian Medical Academy of Postgraduate Education" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.16.21266391", "rel_title": "From online data collection to identification of disease mechanisms: The IL-1beta, IL-6 and TNF-alpha; cytokine triad is associated with post-acute sequelae of COVID-19 in a digital research cohort", @@ -532549,93 +534930,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.11.11.468228", - "rel_title": "Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro", - "rel_date": "2021-11-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.11.468228", - "rel_abs": "In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like (3CLpro) protease can cleave human immune signaling proteins, like NF-{kappa}B Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.14 [A] resolution crystal structure of 3CLpro C145S bound to NEMO226-235 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro- NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for in the pathology of COVID-19.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Mikhail Ali Hameedi", - "author_inst": "Stanford University" - }, - { - "author_name": "Erica Teixeira Prates", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Michael R Garvin", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Irimpan Mathews", - "author_inst": "SLAC National Accelerator Laboratory" - }, - { - "author_name": "B Kirtley Amos", - "author_inst": "University of Kentucky" - }, - { - "author_name": "Omar Demerdash", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Mark Bechthold", - "author_inst": "Stanford University" - }, - { - "author_name": "Mamta Iyer", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Simin Rahighi", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Daniel W. Kneller", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Andrey Kovalevsky", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Stephan Irle", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Van-Quan Vuong", - "author_inst": "University of Tennessee Knoxville" - }, - { - "author_name": "Julie C Mitchell", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Audrey Labbe", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Stephanie Galanie", - "author_inst": "Merck & Co., Inc." - }, - { - "author_name": "Soichi Wakatsuki", - "author_inst": "Stanford University" - }, - { - "author_name": "Daniel Jacobson", - "author_inst": "Oak Ridge National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.11.13.21266289", "rel_title": "AI/ML Models to Aid in the Diagnosis of COVID-19 Illness from Forced Cough Vocalizations: Good Machine Learning Practice and Good Clinical Practices from Concept to Consumer for AI/ML Software Devices", @@ -533811,6 +536105,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.11.12.21266292", + "rel_title": "Covid-19 Pandemic and its Effect on Residents' Mental Well-Being", + "rel_date": "2021-11-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266292", + "rel_abs": "Concerns about COVID-19s long-term consequences on the mental health of frontline health professionals are mounting as the entire world strives anew to contain it. The primary objective of this research is to describe the impact of working during the COVID-19 pandemic on junior doctors mental health and to investigate the effect of the COVID-19 pandemic on junior doctors training and professional performance. A cross-sectional online survey using the Google Forms platform was conducted from May 1st to May 30th, 2021, in 311 healthcare workers who were currently enrolled in a residency program at the Kuwait Institutional of Medical Specialization (KIMS). Socio-demographic details of each health worker were collected and the scores related to depression, anxiety, and stress were measured using the previously validated depression anxiety stress scale-21 (DASS-21). Higher stress scores were seen in those who were devoid of the option to work with COVID-19 patients (adjusted {beta} 5.1 (95%CI:1.2-9);p=0.01), who reported that working during the pandemic affected their study schedule (adjusted {beta} 4.8 (95%CI:1.6-8.1);p= 0.004), and who lost off service training time (adjusted {beta} 2.7 (95%CI:0.13-5.2); p=0.034). Further, the anxiety scores were significantly higher in females. The impact of the ongoing pandemic on residents mental health is grave, necessitating psychological treatment and support. The study discovered various factors linked to depression, anxiety, and stress. As a result, these aspects must be regarded to protect the residents mental health.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Anwar Yazdani", + "author_inst": "Anesthesia and ICU Department, AlSabah Hospital, Kuwait" + }, + { + "author_name": "Hend Esmaeili", + "author_inst": "Department of Anesthesia and Critical Care, Farwaniya Hospital, Kuwait" + }, + { + "author_name": "Abdulla K AlSaleh", + "author_inst": "Anesthesia and ICU Department, Amiri Hospital, Kuwait" + }, + { + "author_name": "Ahmed Sultan", + "author_inst": "Anesthesia and ICU Department, Amiri Hospital, Kuwait" + }, + { + "author_name": "Esam Alamad", + "author_inst": "Anesthesia and ICU Department, Al Adan Hospital, Kuwait" + }, + { + "author_name": "Ali Bandar", + "author_inst": "Department of Anesthesia and critical care, Jaber Hospital, Kuwait" + }, + { + "author_name": "Hanouf Rawdhan", + "author_inst": "Department of Anesthesia Kuwait Cancer Control Center" + }, + { + "author_name": "Mariam Ayed", + "author_inst": "Ministry of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.11.10.21266063", "rel_title": "Case Series of Thrombosis with Thrombocytopenia Syndrome following COVID-19 vaccination--United States, December 2020-August 2021", @@ -534643,53 +536984,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.11.10.468147", - "rel_title": "Nebulized delivery of a broadly neutralizing SARS-CoV-2 RBD-specific nanobody prevents clinical, virological and pathological disease in a Syrian hamster model of COVID-19", - "rel_date": "2021-11-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.10.468147", - "rel_abs": "There remains an unmet need for globally deployable, low-cost therapeutics for the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Previously, we reported on the isolation and in vitro characterization of a potent single-domain nanobody, NIH-CoVnb-112, specific for the receptor binding domain (RBD) of SARS-CoV-2. Here, we report on the molecular basis for the observed broad in vitro neutralization capability of NIH-CoVnb-112 against variant SARS-CoV-2 pseudoviruses, including the currently dominant Delta variant. The structure of NIH-CoVnb-112 bound to SARS-CoV-2 RBD reveals a large contact surface area overlapping the angiotensin converting enzyme 2 (ACE2) binding site, which is largely unencumbered by the common RBD mutations. In an in vivo pilot study, we demonstrate effective reductions in weight loss, viral burden, and lung pathology in a Syrian hamster model of COVID-19 following nebulized delivery of NIH-CoVnb-112. These findings support the further development of NIH-CoVnb-112 as a potential adjunct preventative therapeutic for the treatment of SARS-CoV-2 infection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thomas J Esparza", - "author_inst": "National Institutes of Health - NINDS" - }, - { - "author_name": "Yaozong Chen", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Negin P Martin", - "author_inst": "National Institutes of Health - NIEHS" - }, - { - "author_name": "Helle Bielefeldt-Ohmann", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Richard A Bowen", - "author_inst": "Colorado State University" - }, - { - "author_name": "William D Tolbert", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Marzena J Pazgier", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "David L Brody", - "author_inst": "National Institutes of Health - NINDS" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.11.10.468129", "rel_title": "CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses", @@ -535685,6 +537979,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.11.21266216", + "rel_title": "Effectiveness of non-pharmaceutical measures (NPIs) on COVID-19 in Europe: A systematic literature review", + "rel_date": "2021-11-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266216", + "rel_abs": "BackgroundThe study objective was to conduct a systematic review to assess the effectiveness of non-pharmaceutical interventions (NPIs) to reduce the transmission of SARS-CoV-2 in Europe during the first wave of the pandemic.\n\nMethodsWe searched OVID Medline, EMBASE, and the Cochrane and Campbell Databases for Systematic Reviews published up to April 15th 2021. Focusing on community (meso-level) and society (macro-level) level NPIs, we included all study designs, while a geographic restriction was limited to the EU, UK and European Economic Area (EEA) countries. Using the PICO framework, two reviewers independently extracted data and assessed quality using appropriate quality appraisal tools. A qualitative synthesis was performed, with NPIs grouped initially by a) Physical Distancing measures, b) Case detection and management measures, and c) hygiene measures and subsequently by country.\n\nResultsOf 17,692 studies initially assessed, 45 met all inclusion criteria. Most studies (n=30) had a modelling study design, while 13 were observational, one quasi-experimental and one experimental. Evidence from across the European continent, presented by country, indicates that the implementations of physical distancing measures (i.e., lockdowns/quarantines), preferably earlier in the pandemic, reduce the number of cases and hospitalisation across settings and for which the timing and duration are essential parameters. Case detection and management measures were also identified as effective measures at certain levels of testing and incidence, while hygiene and safety measures complemented the implementation of physical distancing measures.\n\nConclusionsThis literature review represents a comprehensive assessment of the effectiveness of NPIs in Europe up to April 2021. Despite heterogeneity across studies, NPIs, as assessed within the context of this systematic review at the macro and meso level, are effective in reducing SARS-CoV-2 transmission rates and COVID-19 hospitalisation rates and deaths in the European Region and may be applied as response strategies to reduce the burden of COVID-19 in forthcoming waves.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Constantine Vardavas", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Aslanoglou", + "author_inst": "University of Crete" + }, + { + "author_name": "Michele Hilton Boon", + "author_inst": "WISE Centre for Economic Justice, Glasgow Caledonian University" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Climate Change and Health Group, Public Health England, United Kingdom" + }, + { + "author_name": "Jo Leonardi-Bee", + "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Gkikas Magiorkinis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Paraskevi Katsaounou", + "author_inst": "Department of Respiratory Medicine, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Ettore Severi", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.10.21266124", "rel_title": "Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study", @@ -536333,109 +538686,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.11.10.21266134", - "rel_title": "SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266134", - "rel_abs": "BackgroundSARS-CoV-2 Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals.\n\nMethodsBetween October 2020 and July 2021, we sequenced 4,439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral load (VL) level and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals.\n\nResultsThe majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about three months (104 {+/-} 57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, three of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad VL values during acute infection (IQR 1.2 - 8.64 Log copies/ml), on average 38% lower than matched unvaccinated patients (3.29 - 10.81 Log copies/ml, p<0.00001). Nevertheless, 49-50% of all breakthroughs, and 56-60% of Delta-infected breakthroughs exhibited VL above the transmissibility threshold (4 Log copies/ml) irrespective of time post vaccination.\n\nConclusionsDelta infection transmissibility and general VL patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should address whether extra vaccine doses might curb breakthrough contribution to epidemic spread.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Brittany Rife Magalis", - "author_inst": "University of Florida" - }, - { - "author_name": "Shannan Rich", - "author_inst": "University of Florida" - }, - { - "author_name": "Massimiliano S Tagliamonte", - "author_inst": "University of Florida" - }, - { - "author_name": "Carla Mavian", - "author_inst": "University of Florida" - }, - { - "author_name": "Melanie N. Cash", - "author_inst": "University of Florida College of Medicine" - }, - { - "author_name": "Alberto Riva", - "author_inst": "University of Florida" - }, - { - "author_name": "Simone Marini", - "author_inst": "University of Florida" - }, - { - "author_name": "David Moraga Amador", - "author_inst": "University of Florida" - }, - { - "author_name": "Yanping Zhang", - "author_inst": "University of Florida" - }, - { - "author_name": "Jerne Shapiro", - "author_inst": "University of Florida" - }, - { - "author_name": "Amelia Horine", - "author_inst": "University of Florida" - }, - { - "author_name": "Petr Starostik", - "author_inst": "University of Florida" - }, - { - "author_name": "Maura Pieretti", - "author_inst": "BayCare Laboratories LLC" - }, - { - "author_name": "Samantha Vega", - "author_inst": "BayCare Laboratories LLC" - }, - { - "author_name": "Ana Paula Lacombe", - "author_inst": "University of Miami" - }, - { - "author_name": "Jessica Salinas", - "author_inst": "University of Miami" - }, - { - "author_name": "MARIO STEVENSON", - "author_inst": "University of Miami Medical School" - }, - { - "author_name": "Paul Myers", - "author_inst": "Florida Department of Health" - }, - { - "author_name": "John Glenn Morris Jr.", - "author_inst": "University of Florida" - }, - { - "author_name": "Michael Lauzardo", - "author_inst": "University of Florida" - }, - { - "author_name": "Mattia Prosperi", - "author_inst": "University of Florida" - }, - { - "author_name": "Marco Salemi", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.10.468057", "rel_title": "SARS-CoV-2 ORF8 encoded protein contains a histone mimic, disrupts chromatin regulation, and enhances replication", @@ -537607,6 +539857,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.09.21266145", + "rel_title": "Viral kinetic modeling and clinical trial simulation predicts disruption of respiratory disease trials by non-pharmaceutical COVID-19 interventions", + "rel_date": "2021-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266145", + "rel_abs": "Clinical research in infectious respiratory diseases has been profoundly affected by non-pharmaceutical interventions (NPIs) against COVID-19. On top of trial delays or even discontinuation which have been observed in all disease areas, NPIs altered transmission pattern of many seasonal respiratory viruses which followed regular patterns for decades before the pandemic. Clinical trial design based on pre-pandemic historical data therefore needs to be put in question. In this article, we show how knowledge-based mathematical modeling can be used to address this issue. We set up an epidemiological model of respiratory tract infection (RTI) sensitive to a time dependent between-host transmission rate and coupled this model to a mechanistic description of viral RTI episodes in an individual patient. By reducing the transmission rate when the lockdown was introduced in the United Kingdom in March 2020, we were able to reproduce the perturbed 2020 RTI disease burden data. Using this setup, we simulated several NPIs scenarios of various strength (none, mild, medium, strong) and conducted placebo-controlled in silico clinical trials in pediatric patients with recurrent RTIs (RRTI) quantifying annual RTI rate distributions. In interventional arms, virtual patients aged 1-5 years received the bacterial lysate OM-85 (approved in several countries for the prevention of pediatric RRTIs) through a pro-type I immunomodulation mechanism of action described by a physiologically based pharmacokinetics and pharmacodynamics approach (PBPK/PD). Our predictions showed that sample size estimates based on the ratio of RTI rates (or the post-hoc power of fixed sample size trials) are not majorly impacted under NPIs which are less severe (none, mild and medium NPIs) than a strict lockdown (strong NPI). However, NPIs show a stronger impact on metrics more relevant for assessing the clinical relevance of the effect such as absolute benefit. This dichotomy shows the risk that successful trials (even with their primary endpoints being met) still get challenged in risk benefit assessment during the review of market authorization. Furthermore, we found that a mild NPI scenario already affected the time to recruit significantly when sticking to eligibility criteria complying with historical data. In summary, our model predictions can help rationalize and forecast post-COVID-19 trial feasibility. They advocate for gauging absolute and relative benefit metrics as well as clinical relevance for assessing efficacy hypotheses in trial design and they question eligibility criteria misaligned with the actual disease burden.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Simon Ars\u00e8ne", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Claire Couty", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Igor Faddeenkov", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Natacha Go", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Sol\u00e8ne Granjeon-Noriot", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Daniel \u0160m\u00edt", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Riad Kahoul", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Ben Illigens", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Jean-Pierre Boissel", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Aude Chevalier", + "author_inst": "OM Pharma" + }, + { + "author_name": "Lorenz Lehr", + "author_inst": "OM Pharma" + }, + { + "author_name": "Christian Pasquali", + "author_inst": "OM Pharma" + }, + { + "author_name": "Alexander Kulesza", + "author_inst": "Novadiscovery" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.09.467827", "rel_title": "A novel histone deacetylase inhibitor-based approach to eliminate microglia and retain astrocyte properties in glial cell culture.", @@ -538302,41 +540619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.11.08.21266037", - "rel_title": "Third dose vaccine With BNT162b2 and its response on Long COVID after Breakthrough infections", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266037", - "rel_abs": "BackgroundBreakthrough events are not rare after emerging of Delta variant. On the other hand, long COVID is an unsolved issue where sufferers suffer a lot. Some study has shown that COVID-19 vaccine has improved some clinical and libratory parameters in long COVID. But what will be the possible measures against long COVID after the breakthrough event is still a burning question.\n\nMethodWe have observed the third dose by BNT162b2 in a small group(n=20) who were diagnosed as long COVID after breakthrough infections, in Sheikh Hasina National Institute of Burn & Plastic Surgery Institute, Dhaka, Bangladesh. CRP(C-reactive protein) and Anti S1 RBD IgG responses were measured.\n\nResultAll 20 participants in the study received both dosage of \"ChAdOx1-nCoV-19\" in between February 2021 to April 2021 and had breakthrough infection in the same or following month which led to long COVID syndrome. They all received a third dose of \"BNT162b2\". A before and after 3rd dose (14 days after) CRP from participants serum was measured. A Wilcoxon matched paired signed rank test revealed significant (P value <0.05) reduction of inflammatory marker (CRP) after receiving the 3rd vaccine dose. Pre and post 3rd dose quantitative anti S1-RBD IgG response was measured and compared that revealed significant boosting effect that clearly correlates with the CRP response.\n\nConclusionCoverage of vaccines all over the world is still not expected level to control this pandemic. WHO has not recommended the use of a third/booster dose of COVID vaccines. Though our results show some sort of hope for the long COVID in breakthrough events after getting the third dose more study is needed to conclude this issue.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "ashraful hoque", - "author_inst": "Sheikh Hasina National Institute of Burn & Plastic Surgery" - }, - { - "author_name": "Marufur Rahman", - "author_inst": "The Medical School, University of Sheffield, UK" - }, - { - "author_name": "Hossain Imam", - "author_inst": "Sheikh Hasina National Institute of Burn & Plastic Surgery" - }, - { - "author_name": "Nurun Nahar", - "author_inst": "Dhaka Medical College Hospital" - }, - { - "author_name": "Forhad Uddin Hasan Chowdhury", - "author_inst": "Dhaka Medical College Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.11.08.21265884", "rel_title": "Favipiravir In Adults with Moderate to Severe COVID-19: A Phase 3 Multicentre, Randomized, Double-Blind, Placebo-Controlled Trial.", @@ -539196,6 +541478,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.11.09.21266122", + "rel_title": "The effects of the first national lockdown in England on geographical inequalities in the evolution of COVID-19 case rates: An ecological study", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266122", + "rel_abs": "BackgroundSocio-economic inequalities in COVID-19 case rates have been noted worldwide. Previous studieshave compared case rates over set phases. There has been no analysis of how inequalities in cases changed overtime and were shaped by national mitigation strategies (e.g. lock downs). This paper provides the first analysis of the evolution of area-level inequalities in COVID-19 cases by deprivation levels in the first wave of the pandemic (January to July 2020) in England - with a focus on the effects of the first national lockdown (March - July 2020).\n\nMethodsWeekly case rates per Middle Super Output Area (MSOA, n=4412) in England from 2020-03-15 to 2020-07-04 were obtained, and characteristics of local epidemics were calculated, e.g. the highest case rate per area. Simple linear and logistic regression analyses were employed to assess the association of these metrics with index of multiple deprivation (IMD). Local authority-level (n=309) cases were used similarly in a sensitivity analysis, as these data were available daily and extended further back in time. The impact of lockdown was assessed by comparing the cumulative case rate in the most deprived 20% of MSOAs to the least deprived 20%, for the periods before the lockdown, and by the end of lockdown.\n\nFindingsLess deprived areas began recording COVID-19 cases earlier than more deprived areas and were more likely to have peaked by March 2020. More deprived areas case rates grew faster and peaked higher than less deprived areas. During the first national lockdown in the UK, the relative excess in case rates in the most deprived areas increased to 130% of that of the least deprived ones.\n\nInterpretationThe pattern of disease spread in England confirm the hypothesis that initial cases of a novel infectious disease are likely to occur in more affluent communities, but more deprived areas will overtake them once national mitigation strategies begin, and bear the brunt of the total case load. The strict first national lockdown served to increase case rate inequalities in England.\n\nFundingThis work was supported by a grant from The Health Foundation (Ref: 2211473), who took no part in the design, analysis or writing of this study.\n\nResearch in Context\n\nEvidence before this studyThe magnitude and distribution of deprivation-related inequalities in COVID-19 cases have been reported for England and many other countries, however, none have yet investigated the initial evolution of these inequalities, nor the effects of the first national lockdown.\n\nAdded value of this studyWe leverage the benefits of two separate datasets of COVID-19 case counts to investigate the initiation and evolution in inequalities in disease burden by deprivation. We found that cases were first recorded in less deprived areas before rising faster in more deprived areas. The first national lockdown led to an increase in these geographical inequalities.\n\nImplications of all the available evidenceNational lockdowns are an important tool in the armoury of pandemic control, but their timing and duration must be carefully decided and be locally specific. Because case rate inequalities were already present before lockdown in England, movement restrictions served to further increase them.\n\nSummary Box\n\nSection 1: What is already known on this subjectGeographical inequalities in COVID-19 case rates have been noted worldwide, and in England. However, how these inequalities were affected by policy responses - such as national lockdowns - has yet to be investigated.\n\nSection 2: What this study addsWe examined geographical inequalities in COVID-19 case rates by deprivation during the first English lock down (March - July, 2020). We find that cases were first reported in the less deprived areas of England, but this pattern quickly reversed and large excesses of cases occurred in the most deprived areas during the first national lockdown. Case rates in more deprived areas also rose more sharply, peaked higher, and then dropped faster than in less deprived areas. Inequality in cumulative case rates grew over the lockdown, increasing inequalities in disease burden.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Claire E Welsh", + "author_inst": "Newcastle University" + }, + { + "author_name": "Viviana Albani", + "author_inst": "Newcastle University" + }, + { + "author_name": "Fiona E Matthews", + "author_inst": "Newcastle University" + }, + { + "author_name": "Clare Bambra", + "author_inst": "Newcastle University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.08.21266055", "rel_title": "Immunity to COVID-19 in India through vaccination and natural infection", @@ -539804,37 +542117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.05.21265969", - "rel_title": "COVID-19: a study about the impact of coronavirus on physicians of La Plata, Argentina", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265969", - "rel_abs": "BackgroundIn Argentina, the burden of COVID-19 on health systems and physicians was substantial with difficulties on daily triage decisions which have to be made in the context of grave shortages of basic equipment and consumables.\n\nPurposethis study was performed to understand what physicians were experiencing during the COVID-19 pandemic in La Plata (capital city of Buenos Aires province, Argentina).\n\nMethodsA cross-sectional study was performed; a questionnaire was sent by e-mail to physicians who work in this city during November 2020. The questionnaire was made based on Medscape US and International Physicians COVID-19 Experience Report: Risk, Burnout, Loneliness.\n\nStatistical analysistest for normality was performed employing the Kolmogorov-Smirnov test while Chi-square test of independence to examine the relationship between sex and workplace with nominal variables. For categorical variables, Kendalls tau correlation was performed to test for independence. ANOVA was developed to examine differences between physicians age. Statistical significance was set to p < 0.05 in all cases. All statistical analysis was done employing SPSS Statistics, Version 24 (IBM, USA).\n\nResults203 physicians answered the questionnaire; the majority of physicians (96%) considered stressful their experience during pandemic and reported distress episodes being for more than 60% the most stressful of their practices, 30% presented depression and were medically treated, while 32.7% felt loneliness with 4 physicians with suicidal thoughts.\n\nConclusionThe results highlight the need to protect the psychological well-being of the healthcare community, and to invest resources to significantly promote the mental health of professionals.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Virginia Croce", - "author_inst": "Universidad Nacional de La Plata" - }, - { - "author_name": "Elsa Chiappa", - "author_inst": "Universidad Nacional de La Plata" - }, - { - "author_name": "Adriana Moiso", - "author_inst": "Universidad Nacional de La Plata" - }, - { - "author_name": "Martin Enrique Rabassa", - "author_inst": "Universidad Nacional de La Plata" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.08.467773", "rel_title": "A self-amplifying mRNA COVID-19 vaccine drives potent and broad immune responses at low doses that protects non-human primates against SARS-CoV-2", @@ -541098,6 +543380,101 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.11.03.21265533", + "rel_title": "Effect of the Neutralizing SARS-CoV-2 Antibody Sotrovimab in Preventing Progression of COVID-19: A Randomized Clinical Trial", + "rel_date": "2021-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265533", + "rel_abs": "ImportanceOlder patients and those with underlying comorbidities infected with SARS-CoV-2 may be at increased risk of hospitalization and death from COVID-19. Sotrovimab is a neutralizing antibody designed for treatment of high-risk patients to prevent COVID-19 progression.\n\nObjectiveTo evaluate the efficacy and safety of sotrovimab in preventing progression of mild to moderate COVID-19 to severe disease.\n\nDesignRandomized, double-blind, multicenter, placebo-controlled, phase 3 study.\n\nSetting57 centers in 5 countries.\n\nParticipantsNonhospitalized patients with symptomatic, mild to moderate COVID-19 and at least 1 risk factor for disease progression.\n\nInterventionPatients were randomized (1:1) to an intravenous infusion of sotrovimab 500 mg or placebo.\n\nMain Outcomes and MeasuresThe primary efficacy outcome was the proportion of patients with COVID-19 progression, defined as all-cause hospitalization longer than 24 hours for acute illness management or death through day 29. Key secondary outcomes included the proportion of patients with COVID-19 progression, defined as emergency room visit, hospitalization of any duration, or death, and proportion of patients developing severe/critical respiratory COVID-19 requiring supplemental oxygen.\n\nResultsAmong 1057 patients randomized (sotrovimab, 528; placebo, 529), all-cause hospitalization longer than 24 hours or death was significantly reduced with sotrovimab (6/528 [1%]) vs placebo (30/529 [6%]) by 79% (95% CI, 50% to 91%; P<.001). Secondary outcome results further demonstrated the effect of sotrovimab in reducing emergency room visits, hospitalization of any duration, or death, which was reduced by 66% (95% CI, 37% to 81%; P<.001), and severe/critical respiratory COVID-19, which was reduced by 74% (95% CI, 41% to 88%; P=.002). No patients receiving sotrovimab required high-flow oxygen, oxygen via nonrebreather mask, or mechanical ventilation compared with 14 patients receiving placebo. The proportion of patients reporting adverse events was similar between treatment groups; sotrovimab was well tolerated, and no safety concerns were identified.\n\nConclusions and RelevanceAmong nonhospitalized patients with mild to moderate COVID-19, a single 500-mg intravenous dose of sotrovimab prevented progression of COVID-19, with a reduction in hospitalization and need for supplemental oxygen. Sotrovimab is a well-tolerated, effective treatment option for patients at high risk for severe morbidity and mortality from COVID-19.\n\nTrial RegistrationClinicalTrials.gov Identifier: NCT04545060", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anil Gupta", + "author_inst": "Albion Finch Medical, William Osler Health Centre" + }, + { + "author_name": "Yaneicy Gonzalez-Rojas", + "author_inst": "Optimus U, Corp." + }, + { + "author_name": "Erick Juarez", + "author_inst": "Florida International Medical Research" + }, + { + "author_name": "Manuel Crespo", + "author_inst": "Alvaro Cunqueiro Hospital, IIS Galicia Sur" + }, + { + "author_name": "Jaynier Moya", + "author_inst": "Pines Care Research Center" + }, + { + "author_name": "Diego Falci", + "author_inst": "Hospital de Clinicas de Porto Alegre" + }, + { + "author_name": "Elias Sarkis", + "author_inst": "Sarkis Clinical Trials" + }, + { + "author_name": "Joel Solis", + "author_inst": "Centex Studies" + }, + { + "author_name": "Hanzhe Zheng", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Nicola Scott", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Andrea L. Cathcart", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Sergio Parra", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Jennifer E. Sager", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Daren J Austin", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Amanda Peppercorn", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Elizabeth Alexander", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Wendy W. Yeh", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Cynthia Brinson", + "author_inst": "Central Texas Clinical Research" + }, + { + "author_name": "Melissa Aldinger", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Adrienne E Shapiro", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.05.21265763", "rel_title": "Surveillance of COVID-19 in a Vaccinated Population: A Rapid Literature Review", @@ -541830,97 +544207,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.11.05.21265853", - "rel_title": "A SARS-CoV-2 variant of concern triggers Fc effector function with increased cross-reactivity", - "rel_date": "2021-11-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265853", - "rel_abs": "SARS-CoV-2 variants of concern (VOCs) exhibit escape from neutralizing antibodies, causing concern about vaccine effectiveness. However, while non-neutralizing cytotoxic functions of antibodies are associated with decreased disease severity and vaccine protection, Fc effector function escape from VOCs is poorly defined. Furthermore, whether VOCs trigger Fc functions with altered specificity, as has been reported for neutralization, is unknown. Here, we demonstrate that the Beta VOC partially evades Fc effector activity in individuals infected with the original (D614G) variant. However, not all functions are equivalently affected, suggesting differential targeting by antibodies mediating distinct Fc functions. Furthermore, Beta infection triggered responses with significantly improved Fc cross-reactivity against global VOCs compared to either D614G infected or Ad26.COV2.S vaccinated individuals. This suggests that, as for neutralization, the infecting spike sequence impacts Fc effector function. These data have important implications for vaccine strategies that incorporate VOCs, suggesting these may induce broader Fc effector responses.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Simone I Richardson", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Nelia P Manamela", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Boitumelo M Motsoeneng", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Haajira Kaldine", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Frances Ayres", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Zanele Makhado", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Mathilda Mennen", - "author_inst": "Cape Heart Institute, Faculty of Health Sciences, University of Cape Town" - }, - { - "author_name": "Sango Skelem", - "author_inst": "Cape Heart Institute, Faculty of Health Sciences, University of Cape Town" - }, - { - "author_name": "Noleen Williams", - "author_inst": "Cape Heart Institute, Faculty of Health Sciences, University of Cape Town" - }, - { - "author_name": "Nancy J Sullivan", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "John Misasi", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Glenda G Gray", - "author_inst": "The South African Medical Research Council" - }, - { - "author_name": "Linda-Gail Bekker", - "author_inst": "The Desmond Tutu HIV Centre, University of Cape Town" - }, - { - "author_name": "Veronica Ueckermann", - "author_inst": "Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria" - }, - { - "author_name": "Theresa Rossouw", - "author_inst": "Department of Immunology, Faculty of Health Sciences, University of Pretoria" - }, - { - "author_name": "Michael T Boswell", - "author_inst": "Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria" - }, - { - "author_name": "Ntobeko A B Ntusi", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, University of Cape Town" - }, - { - "author_name": "Wendy A Burgers", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, University of Cape Town" - }, - { - "author_name": "Penelope Linda Moore", - "author_inst": "National Institute for Communicable Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.05.21265698", "rel_title": "The COVID19 pandemic has changed women's experiences of pregnancy in the UK", @@ -542916,6 +545202,33 @@ "type": "new results", "category": "synthetic biology" }, + { + "rel_doi": "10.1101/2021.11.04.21265937", + "rel_title": "Estimation of the basic reproduction number of COVID-19 from the incubation period distribution", + "rel_date": "2021-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265937", + "rel_abs": "BackgroundThe estimates of future course of spreading of the SARS-CoV-2 virus are frequently based on Markovian models in which the transitions between the compartments are exponentially distributed. Specifically, the basic reproduction number R0 is also determined from formulae where it is related to the parameters of such models. The observations show that the start of infectivity of an individual appears nearly at the same time as the onset of symptoms, while the distribution of the incubation period is not an exponential.\n\nMethodsWe propose a method for estimation of R0 for COVID-19 based on the empirical incubation period distribution and assumed very short infectivity period that lasts only few days around the onset of symptoms. It is tested on daily new cases in six major countries in Europe, in the first wave of epidemic in spring, 2020.\n\nResultsThe calculations show that even if the infectivity starts two days before the onset of symptoms and stops immediately when they appear, the value of R0 is larger than that from the classical, Markovian approach. For more realistic cases, when only individuals with mild symptoms spread the virus for few days after onset of symptoms, the respective values are even larger.\n\nConclusionsThe calculations of R0 and other characteristics of spreading of COVID-19 based on the classical, Markovian approaches should be taken very cautiously. Instead, non-Markovian models with general distribution functions of transition between compartments should be considered as more appropriate.\n\nKey messagesO_LIAlthough formulae for estimate of the basic reproduction number R0, by using general-form functions of infectivity are known since the earliest works in epidemiology, majority of studies are based on exponential distribution function.\nC_LIO_LIWe introduce a new methodology of calculating R0 with an infectivity function obtained by combining empirical incubation period distribution with infectivity window function that is localized around the onset of symptoms.\nC_LIO_LIEstimates of R0 for the first wave of COVID - 19 in the spring 2020, by the proposed methodology are larger than those from the classical SIR model.\nC_LIO_LIWhen possible, the estimates of R0 should be based on empirical distributions of the infectivity functions, while the values obtained with the conventional epidemic spreading models should be taken with caution.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lasko Basnarkov", + "author_inst": "SS Cyril and Methodius University in Skopje, Macedonia" + }, + { + "author_name": "Igor Tomovski", + "author_inst": "Macedonian Academy of Sciences and Arts" + }, + { + "author_name": "Florin Avram", + "author_inst": "Universite de Pau, France" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.04.21265910", "rel_title": "SARS-CoV-2 Aerosol Transmission Indoors: A Closer Look at Viral Load, Infectivity, the Effectiveness of Preventive Measures and a Simple Approach for Practical Recommendations", @@ -543688,45 +546001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.03.467065", - "rel_title": "Clinically observed deletions in SARS-CoV-2 Nsp1 affect protein stability and its ability to inhibit translation", - "rel_date": "2021-11-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.03.467065", - "rel_abs": "Nonstructural protein 1 (Nsp1) is a major pathogenicity factor of SARS-CoV-2. It inhibits host-cell translation, primarily through a direct interaction between its C-terminal domain and the mRNA entry channel of the 40S small ribosomal subunit, with an N-terminal {beta}-barrel domain fine-tuning the inhibition and promoting selective translation of viral mRNA. SARS-CoV-2 nsp1 is a target of recurring deletions, some of which are associated with altered COVID-19 disease progression. To provide the biochemical basis for this, it is essential to characterize the efficiency of translational inhibition by the said protein variants. Here, we use an in vitro translation system to investigate the translation inhibition capacity of a series of clinically observed Nsp1 deletion variants. We find that a frequently observed deletion of residues 79-89 destabilized the N-terminal domain (NTD) and severely reduced the capacity of Nsp1 to inhibit translation. Interestingly, shorter deletions in the same region have been reported to effect the type I interferon response but did not affect translation inhibition, indicating a possible translation-independent role of the Nsp1 NTD in interferon response modulation. Taken together, our data provide a mechanistic basis for understanding how deletions in Nsp1 influence SARS-CoV-2 induction of interferon response and COVID-19 progression.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Pravin Kumar", - "author_inst": "Umea University" - }, - { - "author_name": "Erin Schexnaydre", - "author_inst": "Umea University" - }, - { - "author_name": "Karim Rafie", - "author_inst": "Umea University" - }, - { - "author_name": "Ilya Terenin", - "author_inst": "Lomonosov Moscow State University" - }, - { - "author_name": "Vasili Hauryliuk", - "author_inst": "Lund University" - }, - { - "author_name": "Lars-Anders Carlson", - "author_inst": "Umea University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.11.02.466971", "rel_title": "Protein arginylation is regulated during SARS-CoV-2 infection", @@ -544794,6 +547068,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.02.466951", + "rel_title": "Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2", + "rel_date": "2021-11-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.02.466951", + "rel_abs": "The SARS-Cov-2 non-structural protein 1 (Nsp1) contains an N-terminal domain and C-terminal helices connected by a short linker region. The C-terminal helices of Nsp1 (Nsp1-C-ter) from SARS-Cov-2 bind in the mRNA entry channel of the 40S ribosomal subunit and block the entry of mRNAs thereby shutting down host protein synthesis. Nsp1 suppresses the host immune function and is vital for viral replication. Hence, Nsp1 appears to be an attractive target for therapeutics. In this study, we have in silico screened Food and Drug Administration (FDA)-approved drugs against Nsp1-C-ter and find that montelukast sodium hydrate binds to Nsp1-C-ter with a binding affinity (KD) of 10.8{+/-}0.2 M in vitro and forms a stable complex with it in simulation runs with a binding energy of -76.71{+/-}8.95 kJ/mol. The drug also rescues the inhibitory effect of Nsp1 in host protein synthesis as demonstrated by the expression of firefly luciferase reporter gene in cells. Importantly, montelukast sodium hydrate demonstrates antiviral activity against SARS-CoV-2 with reduced viral replication in HEK cells expressing ACE2 and Vero-E6 cells. We therefore propose montelukast sodium hydrate may help in combatting SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tanweer Hussain", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Mohammad Afsar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rohan Narayan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Md Noor Akhtar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Huma Rahil", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Sandeep Eswarappa", + "author_inst": "Indian Institute of Science Bangalore" + }, + { + "author_name": "Shashank Tripathi", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.11.03.21265876", "rel_title": "Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility", @@ -546110,77 +548427,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.01.21265660", - "rel_title": "Estimating the relationship between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana", - "rel_date": "2021-11-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265660", - "rel_abs": "BackgroundGovernments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts.\n\nMethodsIn this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of Rt, a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana.\n\nFindingsWe observe a relationship between reductions in human mobility and decreases in Rt during the early stages of the COVID-19 epidemic in Ghana. We find that the strength of this relationship varies through time, decreasing after the most stringent period of interventions in the early epidemic.\n\nInterpretationOur findings demonstrate how the association of NPI and mobility indicators with COVID-19 transmission may vary through time. Further, we demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity and monitor the impact of NPI policies.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and preprint archives for articles published in English that contained information about the COVID-19 pandemic published up to Nov 1, 2021, using the search terms \"coronavirus\", \"CoV\", \"COVID-19\", \"mobility\", \"movement\", and \"flow\". The data thus far suggests that NPI measures including physical distancing, reduction of travel, and use of personal protective equipment have been demonstrated to reduce COVID-19 transmission. Much of the existing research focuses on comparisons of NPI stringency with COVID-19 transmission among different high-income countries, or on high-income countries, leaving critical questions about the applicability of these findings to low- and middle-income settings.\n\nAdded value of this studyWe used a detailed COVID-19 surveillance dataset from Ghana, and unique high resolution spatial data on human mobility from Vodafone Ghana as well as Google smartphone GPS location data. We show how human mobility and NPI stringency were associated with changes in the effective reproduction number (Rt). We further demonstrate how this association was strongest in the early COVID-19 outbreak in Ghana, decreasing after the relaxation of national restrictions.\n\nImplications of all the available evidenceThe change in association between human mobility, NPI stringency, and Rt may reflect a \"decoupling\" of NPI stringency and human mobility from disease transmission in Ghana as the COVID-19 epidemic progressed. This finding provides public health decision makers with important insights for the understanding of the utility of mobility data for predicting the spread of COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Hamish Gibbs", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Yang Liu", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Isaac Baffoe-Nyarko", - "author_inst": "Ghana Health Service" - }, - { - "author_name": "Dennis O. Laryea", - "author_inst": "Ghana Health Service" - }, - { - "author_name": "Ernest Akyereko", - "author_inst": "Ghana Health Service" - }, - { - "author_name": "Patrick Kuma-Aboagye", - "author_inst": "Ghana Health Service" - }, - { - "author_name": "Ivy Asante", - "author_inst": "University of Ghana Noguchi Memorial Institute for Medical Research" - }, - { - "author_name": "Oriol Mitja", - "author_inst": "Fight Against AIDS Foundation" - }, - { - "author_name": "- LSHTM CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "William Ampofo", - "author_inst": "University of Ghana Noguchi Memorial Institute for Medical Research" - }, - { - "author_name": "Franklin Asiedu-Bekoe", - "author_inst": "Ghana Health Service" - }, - { - "author_name": "Michael Marks", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.01.21265761", "rel_title": "The Brief Observation of Symptoms of Autism (BOSA): Development of a New Adapted Assessment Measure for Remote Telehealth Administration through COVID-19 and Beyond", @@ -547172,6 +549418,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.01.21265653", + "rel_title": "Modelling COVID-19 Pandemic Dynamics Using Transparent, Interpretable, Parsimonious and Simulatable (TIPS) Machine Learning Models: A Case Study from Systems Thinking and System Identification Perspectives", + "rel_date": "2021-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265653", + "rel_abs": "Since the outbreak of COVID-19, an astronomical number of publications on the pandemic dynamics appeared in the literature, of which many use the susceptible infected removed (SIR) and susceptible exposed infected removed (SEIR) models, or their variants, to simulate and study the spread of the coronavirus. SIR and SEIR are continuous-time models which are a class of initial value problems (IVPs) of ordinary differential equations (ODEs). Discrete-time models such as regression and machine learning have also been applied to analyze COVID-19 pandemic data (e.g. predicting infection cases), but most of these methods use simplified models involving a small number of input variables pre-selected based on a priori knowledge, or use very complicated models (e.g. deep learning), purely focusing on certain prediction purposes and paying little attention to the model interpretability. There have been relatively fewer studies focusing on the investigations of the inherent time-lagged or time-delayed relationships e.g. between the reproduction number (R number), infection cases, and deaths, analyzing the pandemic spread from a systems thinking and dynamic perspective. The present study, for the first time, proposes using systems engineering and system identification approach to build transparent, interpretable, parsimonious and simulatable (TIPS) dynamic machine learning models, establishing links between the R number, the infection cases and deaths caused by COVID-19. The TIPS models are developed based on the well-known NARMAX (Nonlinear AutoRegressive Moving Average with eXogenous inputs) model, which can help better understand the COVID-19 pandemic dynamics. A case study on the UK COVID-19 data is carried out, and new findings are detailed. The proposed method and the associated new findings are useful for better understanding the spread dynamics of the COVID-19 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hua-Liang Wei", + "author_inst": "The University Of Sheffield" + }, + { + "author_name": "Stephen A Billings", + "author_inst": "The University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.01.21265729", "rel_title": "Quantifying the effects of non-pharmaceutical and pharmaceutical interventions against COVID-19 epidemic in the Republic of Korea: Mathematical model-based approach considering age groups and the Delta variant", @@ -547956,57 +550225,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.29.21265669", - "rel_title": "Correlates of COVID-19 Vaccine Hesitancy among People who Inject Drugs in the San Diego-Tijuana Border Region", - "rel_date": "2021-10-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.29.21265669", - "rel_abs": "BackgroundPeople who inject drugs (PWID) are vulnerable to acquiring SARS-CoV-2 but their barriers to COVID-19 vaccination are under-studied. We examined correlates of COVID-19 vaccine hesitancy among PWID in the U.S.-Mexico border region, of whom only 7.6% had received [≥]one COVID-19 vaccine dose by September, 2021.\n\nMethodsBetween October, 2020 and September, 2021, participants aged [≥]18 years from San Diego, California, USA and Tijuana, Baja California, Mexico who injected drugs within the last month completed surveys and SARS-CoV-2, HIV, and HCV serologic testing. Logistic regressions with robust standard error estimation via generalized estimating equations identified factors associated with COVID-19 vaccine hesitancy, defined as being unsure or unwilling to receive COVID-19 vaccines.\n\nResultsOf 393 participants, 127 (32.3%) were vaccine hesitant. Older participants, those with greater food insecurity, and those with greater concern about acquiring SARS-CoV-2 were more willing to be vaccinated. Higher numbers of chronic health conditions, having access to a smart phone or computer, and citing social media as ones most important source of COVID-19 information were independently associated with vaccine hesitancy. COVID-19-related disinformation was independently associated with vaccine hesitancy (adjusted odds ratio: 1.51 per additional conspiracy theory endorsed; 95% confidence interval: 1.31-1.74).\n\nConclusionsNearly one third of PWID in the San Diego-Tijuana border region reported COVID-19 vaccine hesitancy, which was significantly influenced by exposure to disinformation. Interventions that improve accurate knowledge and trust in COVID-19 vaccines are needed to increase vaccination in this vulnerable population.\n\nSummaryNearly one third of people who inject drugs in the U.S.-Mexico border region reported COVID-19 vaccine hesitancy, which was significantly influenced by exposure to disinformation and social media and inversely associated with food insecurity and high perceived threat of COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Steffanie Ann Strathdee", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Daniela Abramovitz", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Alicia Y. Harvey-Vera", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Carlos Vera", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Gudelia Rangel", - "author_inst": "El Colegio de la Frontera Norte" - }, - { - "author_name": "Irina Artamonova", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Thomas L. Patterson", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Rylie Mitchell", - "author_inst": "Guelph University" - }, - { - "author_name": "Angela R. Bazzi", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.28.21265629", "rel_title": "An Objective Search for Unrecognized Bias in Validated COVID-19 Prediction Models", @@ -548846,6 +551064,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.10.28.21265499", + "rel_title": "Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers", + "rel_date": "2021-10-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265499", + "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global crisis with unprecedented challenges for public health. Vaccinations against SARS-CoV-2 have slowed the incidence of new infections and reduced disease severity. As the time-of-day of vaccination has been reported to influence host immune responses to multiple pathogens, we quantified the influence of SARS-CoV-2 vaccination time, vaccine type, age, sex, and days post-vaccination on anti-Spike antibody responses in healthcare workers. The magnitude of the anti-Spike antibody response associated with the time-of-day of vaccination, vaccine type, participant age, sex, and days post vaccination. These results may be relevant for optimizing SARS-CoV-2 vaccine efficacy.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wei Wang", + "author_inst": "Division of Sleep and Circadian Disorders, Brigham and Womens Hospital; Division of Sleep Medicine, Harvard Medical School, US." + }, + { + "author_name": "Peter Balfe", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sheila F Lumley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Denise O'Donnell", + "author_inst": "Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Fiona Warren", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Derrick W Crook", + "author_inst": "NIHR Oxford Biomedical Research Centre" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, and\tRadcliffe Department of Medic" + }, + { + "author_name": "Philippa C Matthews", + "author_inst": "Nuffield Department of Medicine, and 4.\tDepartment of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hos" + }, + { + "author_name": "Elizabeth B Klerman", + "author_inst": "Massachusetts General Hospital/Harvard Medical School" + }, + { + "author_name": "Jane McKeating", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.28.21265544", "rel_title": "In vitro characterisation and clinical evaluation of the diagnostic accuracy of a new antigen test for SARS-CoV-2 detection.", @@ -549698,97 +551975,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.10.27.466206", - "rel_title": "A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity", - "rel_date": "2021-10-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.27.466206", - "rel_abs": "BackgroundCOVID-19 symptoms range from mild to severe illness; the cause for this differential response to infection remains unknown. Unravelling the immune mechanisms acting at different levels of the colonization process might be key to understand these differences.\n\nMethods and findingsWe carried out a multi-tissue (nasal, buccal and blood; n = 156) gene expression analysis of immune-related genes from patients affected by different COVID-19 severities, and healthy controls through the nCounter technology. We then used a differential expression approach and pathways analysis to detect tissue specific immune severity signals in COVID-19 patients.\n\nMild and asymptomatic cases showed a powerful innate antiviral response in nasal epithelium, characterized by activation of interferon (IFN) pathway and downstream cascades, successfully controlling the infection at local level. In contrast, weak macrophage/monocyte driven innate antiviral response and lack of IFN signalling activity were shown in severe cases. Consequently, oral mucosa from severe patients showed signals of viral activity, cell arresting and viral dissemination to the lower respiratory tract, which ultimately could explain the exacerbated innate immune response and impaired adaptative immune responses observed at systemic level. Results from saliva transcriptome suggest that the buccal cavity might play a key role in SARS-CoV-2 infection and dissemination in patients with worse prognosis.\n\nConclusionsWe found severity-related signatures in patient tissues mainly represented by genes involved in the innate immune system and cytokine/chemokine signalling. Local immune response could be key to determine the course of the systemic response and thus COVID-19 severity. Our findings provide a framework to investigate severity host gene biomarkers and pathways that might be relevant to diagnosis, prognosis, and therapy.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Alberto Gomez-Carballa", - "author_inst": "SERGAS" - }, - { - "author_name": "Irene Rivero-Calle", - "author_inst": "SERGAS" - }, - { - "author_name": "Jacobo Pardo-Seco", - "author_inst": "SERGAS" - }, - { - "author_name": "Jose Gomez-Rial", - "author_inst": "SERGAS" - }, - { - "author_name": "Carmen Rivero-Velasco", - "author_inst": "SERGAS" - }, - { - "author_name": "Nuria Rodriguez-Nunez", - "author_inst": "SERGAS" - }, - { - "author_name": "Gema Barbeito-Castineiras", - "author_inst": "SERGAS" - }, - { - "author_name": "Hugo Perez-Freixo", - "author_inst": "SERGAS" - }, - { - "author_name": "Miriam Cebey-Lopez", - "author_inst": "SERGAS" - }, - { - "author_name": "Ruth Barral-Arca", - "author_inst": "SERGAS" - }, - { - "author_name": "Carmen Rodriguez-Tenreiro", - "author_inst": "SERGAS" - }, - { - "author_name": "Ana Dacosta-Urbieta", - "author_inst": "SERGAS" - }, - { - "author_name": "Xabier Bello", - "author_inst": "SERGAS" - }, - { - "author_name": "Sara Pischedda", - "author_inst": "SERGAS" - }, - { - "author_name": "Maria Jose Curras-Tuala", - "author_inst": "SERGAS" - }, - { - "author_name": "Sandra Viz-Lasheras", - "author_inst": "SERGAS" - }, - { - "author_name": "Federico Martinon-Torres", - "author_inst": "SERGAS" - }, - { - "author_name": "Antonio Salas", - "author_inst": "SERGAS" - }, - { - "author_name": "- GEN-COVID", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.10.26.466002", "rel_title": "Whole-genome sequencing of Vero E6 (C1008) and comparative analysis of four Vero cell sublines", @@ -550712,6 +552898,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.27.21265574", + "rel_title": "Boosting of Cross-Reactive Antibodies to Endemic Coronaviruses by SARS-CoV-2 Infection but not Vaccination with Stabilized Spike", + "rel_date": "2021-10-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.27.21265574", + "rel_abs": "Pre-existing antibodies to endemic coronaviruses (CoV) that cross-react with SARS-CoV-2 have the potential to influence the antibody response to COVID-19 vaccination and infection for better or worse. In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross reactivity against endemic CoV spike (S) protein at subdomain resolution. Elevated responses, particularly to the {beta}-CoV OC43, were observed in all natural infection cohorts tested and were correlated with the response to SARS-CoV-2. The kinetics of this response and isotypes involved suggest that infection boosts preexisting antibody lineages raised against prior endemic CoV exposure that cross react. While further research is needed to discern whether this recalled response is desirable or detrimental, the boosted antibodies principally targeted the better conserved S2 subdomain of the viral spike and were not associated with neutralization activity. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. In sum, this study provides evidence that antibodies targeting endemic CoV are robustly boosted in response to SARS-CoV-2 infection but not to vaccination with stabilized S, and that depending on conformation or other factors, the S2 subdomain of the spike protein triggers a rapidly recalled, IgG-dominated response that lacks neutralization activity.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/21265574v1_figA1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@168d38aorg.highwire.dtl.DTLVardef@1183afcorg.highwire.dtl.DTLVardef@1c88b77org.highwire.dtl.DTLVardef@13c6e0a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Antibody responses to SARS-CoV-2 and endemic CoV spike proteins were measured in diverse cohorts. While antibodies to SARS-CoV-2 were induced across all isotypes, only IgA and IgG responses to endemic CoV were robustly boosted, and only among naturally-infected but not vaccinated individuals. These recalled, cross-reactive responses to endemic CoV primarily recognized the better conserved S2 domain and were non-neutralizing. While other antiviral activities of broadly cross-reactive S2-specifc antibodies are not known, the differing antigenicity of natural infection and vaccination with stabilized pre-fusion spike has potential implications for the breadth and level of protection afforded by each.\n\nC_FIG", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Andrew R Crowley", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Harini Natarajan", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Andrew P Hederman", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Carly A Bobak", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Joshua A Weiner", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Wendy F. Wieland-Alter", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Jiwon Lee", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Evan M Bloch", + "author_inst": "Johns Hopkins Medicine" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Andrew Redd", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joel N. Blankson", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Dana Wolf", + "author_inst": "Hadassah University Medical Center" + }, + { + "author_name": "Tessa Goetghebuer", + "author_inst": "CHU St. Pierre" + }, + { + "author_name": "Arnaud Marchant", + "author_inst": "Universite libre de Bruxelles" + }, + { + "author_name": "Ruth I Connor", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Peter F Wright", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Margaret E Ackerman", + "author_inst": "Dartmouth College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.27.21265591", "rel_title": "How many lives do COVID vaccines save? Evidence from Israel.", @@ -551512,33 +553781,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.24.21265344", - "rel_title": "Impact of biologics and small molecules for Inflammatory Bowel Disease on COVID-19 Related Hospitalization: A Systematic Review and Meta-analysis", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.24.21265344", - "rel_abs": "BackgroundThe use of biological therapies and small molecules have been a concern for patients with inflammatory bowel disease (IBD) during COVID-19 pandemic. We aim to assess the association between risk of COVID-19 related hospitalization and these agents.\n\nMethodA systematic review and meta-analysis of all published studies from December 2019 to September 2021 was performed to identify studies that reported COVID-19 related hospitalization in IBD patients receiving biological therapies or tofacitinib. The risk ratio (RR) was calculated to compare the relative risk of COVID-19 related hospitalization in patients receiving these medications to those who were not, at the time of the study.\n\nResults18 studies were included. The relative risk of hospitalization was significantly lower in patients with IBD and COVID-19 who were receiving biologic therapy with RR of 0.47 (95% CI: 0.42-0.52, p < 0.00001). The RR was lower in patients receiving anti-TNFs compared to those who did not [RR= 0.48 (95% CI: 0.41-0.55, p < 0.00001)]. Similar finding was observed in patients taking ustekinumab [RR= 0.55 (95% CI: 0.43-0.72, p < 0.00001)]. Combination therapy of anti-TNF and an immunomodulator did not lower the risk of COVID-19 related hospitalization [RR= 0.98 (95% CI: 0.82-1.18, p =0.84]. The use of vedolizumab [RR= 1.13 (95% CI: 0.75-1.73, p =0.56] and tofacitinib [RR= 0.81 (95% CI: 0.49-1.33, p =0.40] was not associated with lower risk of COVID-19 related hospitalization.\n\nConclusionRegarding COVID-19 related hospitalization in IBD, anti-TNFs and ustekinumab were associated with favorable outcomes. In addition, vedolizumab and tofacitinib were not associated with COVID-19 related hospitalization.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Fatema Alrashed", - "author_inst": "Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences (MCPHS) University, Boston, USA" - }, - { - "author_name": "Hajer Alasfour", - "author_inst": "Department of Pharmacy Practice, Kuwait University, Kuwait." - }, - { - "author_name": "Mohammad Shehab", - "author_inst": "Mubarak Alkaber Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.10.23.21265421", "rel_title": "Assessing the potential impact of immunity waning on the dynamics of COVID-19: an endemic model of COVID-19", @@ -552490,6 +554732,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.25.465714", + "rel_title": "Nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants", + "rel_date": "2021-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.25.465714", + "rel_abs": "We are in the midst of the historic coronavirus infectious disease 2019 (COVID-19) pandemic caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Although countless efforts to control the pandemic have been attempted--most successfully, vaccination1-3--imbalances in accessibility to vaccines, medicines, and diagnostics among countries, regions, and populations have been problematic. Camelid variable regions of heavy chain-only antibodies (VHHs or nanobodies)4 have unique modalities: they are smaller, more stable, easier to customize, and, importantly, less expensive to produce than conventional antibodies5, 6. We present the sequences of nine alpaca nanobodies that detect the spike proteins of four SARS-CoV-2 variants of concern (VOCs)--namely, the alpha, beta, gamma, and delta variants. We show that they can quantify or detect spike variants via ELISA and lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays7. The panel of nanobodies broadly neutralized viral infection by pseudotyped SARS-CoV-2 VOCs. Structural analyses showed that a P86 clone targeted epitopes that were conserved yet unclassified on the receptor-binding domain (RBD) and located inside the N-terminal domain (NTD). Human antibodies have hardly accessed both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins undetected by conventional antibodies and maintains activity against spike proteins carrying escape mutations.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ryota Maeda", + "author_inst": "Kyoto University & COGNANO Inc." + }, + { + "author_name": "Junso Fujita", + "author_inst": "Osaka University" + }, + { + "author_name": "Yoshinobu Konishi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yasuhiro Kazuma", + "author_inst": "Kyoto University" + }, + { + "author_name": "Hiroyuki Yamazaki", + "author_inst": "COGNANO Inc." + }, + { + "author_name": "Itsuki Anzai", + "author_inst": "Osaka University" + }, + { + "author_name": "Keishi Yamaguchi", + "author_inst": "Osaka University" + }, + { + "author_name": "Kazuki Kasai", + "author_inst": "Kyoto University & COGNANO Inc." + }, + { + "author_name": "Kayoko Nagata", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yutaro Yamaoka", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kotaro Shirakawa", + "author_inst": "Kyoto University" + }, + { + "author_name": "Fumiaki Makino", + "author_inst": "Osaka University & JEOL Ltd." + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Tsuyoshi Inoue", + "author_inst": "Osaka University" + }, + { + "author_name": "Akihiro Imura", + "author_inst": "COGNANO Inc." + }, + { + "author_name": "Keiichi Namba", + "author_inst": "Osaka University & JEOL YOKOGUSHI Research Alliance Laboratories & RIKEN Center for Biosystems Dynamics Research and SPring-8 Center" + }, + { + "author_name": "Akifumi Takaori-Kondo", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.10.22.21265188", "rel_title": "Response to the coronavirus disease 2019 (COVID-19) pandemic at private retail pharmacies in Kenya: a mixed methods study", @@ -553074,65 +555407,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.26.21265510", - "rel_title": "Virtual reality exercise to help COVID patients with refractory breathlessness", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265510", - "rel_abs": "BackgroundImmersive virtual reality (iVR)-based digital therapeutics (DTx) are gaining clinical attention in the field of pain management. Based on known analogies between pain and dyspnea, we investigated the effects of visual-respiratory feedback, on persistent dyspnea in patients recovering from COVID-19 pneumonia.\n\nMethodsWe performed a controlled, randomized, single-blind, cross-over clinical study to evaluate an iVR-based intervention to alleviate dyspnea in patients recovering from COVID-19 pneumonia. Included patients reported persistent dyspnea ([≥]5 on a 10-point scale) and preserved cognitive function (MoCA>24). Assignment was random and concealed. Patients received synchronous (intervention) or asynchronous (control) feedback of their breathing, embodied via a gender-matched virtual body. Outcomes were assessed using questionnaires and breathing recordings. COVVR is registered with ClinicalTrials.gov (NCT04844567).\n\nFindingsStudy enrollment was open between November 2020 and April 2021. Twenty-six patients were enrolled (27% women; age: median=55, interquartile range (IQR)=18). Data were available for 24 of 26 patients. The median (IQR) rating on a 7-point Likert-scale of breathing comfort improved from 1(2) at baseline, to 2(1) for synchronous feedback, but remained unchanged at 1(1.5) for asynchronous feedback (p<0.05) between iVR conditions). Moreover, 91.2% of all patients were satisfied with the intervention (p<0.0001) and 66.7% perceived it as beneficial for their breathing (p<0.05). No adverse events were reported.\n\nInterpretationBased on these findings, our iVR-based DTx presents a feasible and safe respiratory rehabilitation tool that improves breathing comfort in patients recovering from COVID-19 infection presenting with persistent dyspnea. Future research should investigate the DTxs generalizability to persistent dyspnea with other etiologies and its potential for preventing chronification.\n\nFundingMarie Sklodowska-Curie Individual Fellowship (H2020-MSCA-IF-2019 894111/ RESPVR), Bertarelli Foundation", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sophie J A Betka", - "author_inst": "EPFL" - }, - { - "author_name": "Oliver A Kannape", - "author_inst": "EPFL" - }, - { - "author_name": "Jemina Fasola", - "author_inst": "EPFL" - }, - { - "author_name": "Florian Lance", - "author_inst": "EPFL" - }, - { - "author_name": "Sylvain Cardin", - "author_inst": "MindMaze" - }, - { - "author_name": "Aline Schmid", - "author_inst": "Division of Lung Diseases, University Hospital and Geneva Medical School, University of Geneva, Switzerland" - }, - { - "author_name": "Thomas Similowski", - "author_inst": "Sorbonne University" - }, - { - "author_name": "Marina Paola Soccal", - "author_inst": "Division of Lung Diseases, University Hospital and Geneva Medical School, University of Geneva, Switzerland" - }, - { - "author_name": "Bruno Herbelin", - "author_inst": "EPFL" - }, - { - "author_name": "Dan Adler", - "author_inst": "Division of Lung Diseases, University Hospital and Geneva Medical School, University of Geneva, Switzerland" - }, - { - "author_name": "Olaf Blanke", - "author_inst": "EPFL" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.10.25.21265304", "rel_title": "Effectiveness of Covid-19 Vaccines in the United States Over 9 Months: Surveillance Data from the State of North Carolina", @@ -554416,6 +556690,189 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.18.21264530", + "rel_title": "Integrated Genomic Surveillance reveals extensive onward transmission of travel-imported SARS-CoV-2 infections in the community", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21264530", + "rel_abs": "Integration of genomic surveillance with contact tracing provides a powerful tool for the reconstruction of person-to-person pathogen transmission chains. We report two large clusters of SARS-CoV-2 cases (\"Delta\" clade, 110 cases combined) detected in July 2021 by Integrated Genomic Surveillance in Dusseldorf. Structured interviews and deep contact tracing demonstrated an association to a single SARS-CoV-2 infected return traveller (Cluster 1) and to return travel from Catalonia and other European countries (Cluster 2), highlighting the importance of containing travel-imported SARS-CoV-2 infections.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Torsten Houwaart", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Samir Belhaj", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Emran Tawalbeh", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Dirk Nagels", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Patrick Finzer", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany; Zotz | Klimas, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lisa Stiller", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jacqueline Blum", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Christian Lange", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Yara Fr\u00f6hlich", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Assia Benmoumene", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Dounia Asskali", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Hussein Haidar", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Janina von Dahlen", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Carla Adelmann", + "author_inst": "Solingen Health Authority (Gesundheitsamt Solingen)" + }, + { + "author_name": "Britta Schroer", + "author_inst": "Solingen Health Authority (Gesundheitsamt Solingen)" + }, + { + "author_name": "Ute Osmers", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Christiane Grice", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Phillipp P. Kirfel", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Hassan Jomaa", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Moritz Pigulla", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Pascal Kreuzer", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Alona Tyshaieva", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jonas Weber", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Daniel Strelow", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jessica Nicolai", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Tobias Wienemann", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Malte Kohns Vasconcelos", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lisanna H\u00fclse", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Katrin Hoffmann", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Nadine L\u00fcbke", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Sandra Hauka", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Marcel Andree", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Claus J\u00fcrgen Scholz", + "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Nathalie Jazmati", + "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Klaus G\u00f6bels", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Rainer Zotz", + "author_inst": "Zotz | Klimas, D\u00fcsseldorf, Germany; Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Klaus Pfeffer", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "J\u00f6rg Timm", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lutz Ehlkes", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Andreas Walker", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Alexander T. Dilthey", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "- German COVID-19 OMICS Initiative (DeCOI)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.24.465626", "rel_title": "SARS-CoV-2 infects human adipose tissue and elicits an inflammatory response consistent with severe COVID-19", @@ -555104,45 +557561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.21.21265354", - "rel_title": "The effect of social restrictions, loss of social support, and loss of maternal autonomy on postpartum depression in 1 to 12-months postpartum women during the COVID-19 pandemic", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265354", - "rel_abs": "BackgroundThis study focuses on postpartum women, who are one of the most vulnerable populations during the COVID-19 pandemic, aiming to reveal mental health consequences of social restrictions, loss of social support, or loss of autonomy.\n\nMethodsA cross-sectional study for postpartum women was conducted in October 2020 (N = 600). The Edinburgh Postpartum Depression Scale (EPDS) was used to measure postpartum depression. The prevalence ratios were estimated by log-binomial regression models, adjusting for age, education, household income, residence area, parity, the timing of delivery, and a prior history of depression.\n\nResultsThe prevalence of postpartum depression was 28.7% (EPDS [≥] 9), 18.6% ([≥] 11), and 13.1% ([≥] 13). Social restrictions including cancellation of home visits by health care professionals, or cancellation of infant checkups or vaccinations, loss of support during pregnancy or after delivery including loss of opportunities to consult with health care professionals or friends, or cancellation of parents or other family members visits to support, and loss of autonomy about delivery or breastfeeding, were associated with postnatal depression.\n\nConclusionAbout 30% of women who delivered and raised a baby during the COVID-19 pandemic had postpartum depression, which is much higher than a pre-pandemic meta-analysis. COVID-19 related social restrictions or loss of social support from healthcare professionals, family, and friends were significantly associated with postpartum depression. Also, loss of maternal autonomy in delivery and breastfeeding is associated with postpartum depression. The results indicate that both formal and informal support should not be limited to prevent postpartum depression during the pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kanami Tsuno", - "author_inst": "Kanagawa University of Human Services" - }, - { - "author_name": "Sumiyo Okawa", - "author_inst": "Institute for Global Health Policy Research" - }, - { - "author_name": "Midori Matsushima", - "author_inst": "the University of Tsukuba" - }, - { - "author_name": "Daisuke Nishi", - "author_inst": "the University of Tokyo" - }, - { - "author_name": "Yuki Arakawa", - "author_inst": "the University of Tokyo" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Osaka International Cancer Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.10.21.21265349", "rel_title": "Safety and Effectiveness of COVID-19 SPUTNIK V Vaccine in Dialysis Patients", @@ -556394,6 +558812,145 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.10.22.465476", + "rel_title": "The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2", + "rel_date": "2021-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.22.465476", + "rel_abs": "Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Ying Fu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Juliana da Fonseca Rezende e Mello", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Bryan D Fleming", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Alex Renn", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Catherine Z. Chen", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Xin Hu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Miao Xu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Kirill Gorshkov", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Quinlin Hanson", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Emily M Lee", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Lalith Perera", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Robert Petrovich", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Richard T Eastman", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Zina Itkin", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Thomas Stanley", + "author_inst": "National Institute of Environmental Health Services" + }, + { + "author_name": "Allen Hsu", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Venkata Dandey", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "William Gillette", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Troy Taylor", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Nitya Ramakrishnan", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Shelley Perkins", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Eunkeu Oh", + "author_inst": "Naval Research Laboratory" + }, + { + "author_name": "Kimihiro Susumu", + "author_inst": "Jacobs Corporation" + }, + { + "author_name": "Mason Wolak", + "author_inst": "Naval Research Laboratory" + }, + { + "author_name": "Marc Ferrer", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Matthew D. Hall", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Mario J Borgnia", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Anton Simeonov", + "author_inst": "National Center for Advancing Translational Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2021.10.23.465542", "rel_title": "Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway", @@ -557306,61 +559863,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.21.21265313", - "rel_title": "Clinical characteristics of pregnant women infected with Coronavirus Disease 2019 in China: a nationwide case-control study", - "rel_date": "2021-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265313", - "rel_abs": "OBJECTIVETo formally compare the clinical course of Coronavirus disease 2019 (COVID-19) in pregnant women with their nonpregnant counterparts.\n\nMETHODSClinical data of pregnant women with confirmed COVID-19 in the designated hospitals of mainland China were retrieved up to April 12, 2020 through an epidemic reporting system maintained at the National Health Commission of the Peoples Republic China. Each pregnant patient was randomly matched to a nonpregnant woman with confirmed COVID-19 in the same hospital as control, then their clinical courses were formally compared.\n\nRESULTS138 pregnant women had been identified as confirmed COVID-19 cases. Among them, 17 severe cases and 1 maternal death were recorded, which was less than their nonpregnant peers (23 severe cases and 3 death). 57.2% had been infected with SARS-CoV-2 during the third trimester, including 13 severe cases and 1 maternal death. 7.3% of pregnant patients had diarrhea and 3.6% had nausea or vomiting, compared with related proportion as 15.2% (OR: 0.38, 95%CI: 0.15, 0.96) and 10.1% (OR: 0.25, 95%CI: 0.07, 0.89) in nonpregnant patients. Pregnant patients infected with SARS-CoV-2 in early pregnancy presented similar laboratory tests with their nonpregnant peers, however, with pregnancy progresses, increased inflammation, coagulation and hepatic injury markers happened more and more frequently (p<0.001) in pregnant patients.\n\nCONCLUSIONSBeing pregnant did not represent a risk for severe condition when compared with their nonpregnant peers. Patients infected with SARS-CoV-2 in early pregnancy were even at lower risk of severe illness than those infected in late pregnancy.\n\nWhat are the novel findings of this work?Compared with non-pregnant COVID-19 patients, pregnant patients tend to present less symptom, had unique laboratory findings, and tend to at lower risk of COVID-19-related death. Patients infected with SARS-CoV-2 in the early pregnancy tend to be in the less severe condition of illness than those infected in late pregnancy.\n\nWhat are the clinical implications of this work?Vital comparisons of the clinical course upon COVID-19 between pregnant and nonpregnant women in childbearing age are, unfortunately, lacking. Through formally comparisons between the two groups, the present study provides more reliable evidence towards the management of pregnant women with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Qin Li", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Lian Chen", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Hai Jiang", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Danni Zheng", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Yuanyuan Wang", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Jie Mei", - "author_inst": "Department of Obstetrics and Gynecology, Sichuan Province Peoples Hospital, Chengdu, China" - }, - { - "author_name": "Xudong Ma", - "author_inst": "National Health Commission of the Peoples Republic China, Beijing, China" - }, - { - "author_name": "Yuan Wei", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Yangyu Zhao", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - }, - { - "author_name": "Jie Qiao", - "author_inst": "National Clinical Research Center for Obstetrical and Gynecology, National Center for Healthcare Quality Management in Obstetrics, Department of Obstetrics and " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.10.22.465399", "rel_title": "Nanoviricides Platform Technology based NV-387 polymer Protects Remdesivir from Plasma-Mediated Catabolism in vitro:Importance of its increased lifetime for in vivo action", @@ -558343,6 +560845,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.10.20.21265149", + "rel_title": "Differences in COVID-19 Risk by Race and County-Level Social Determinants of Health Among Veterans", + "rel_date": "2021-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265149", + "rel_abs": "COVID-19 disparities by area-level social determinants of health (SDH) may be impacting U.S. Veterans. This retrospective analysis utilized COVID-19 data from the U.S. Department of Veterans Affairs (VA)s EHR and geographically linked county-level data from 18 area-based socioeconomic measures. The risk of testing positive with Veterans county-level SDHs adjusting for demographics, comorbidities, and facility characteristics was calculated using generalized linear models. We found an exposure-response relationship whereby individual COVID-19 infection risk increased with each increasing quartile of adverse county-level SDH such as the percentage of residents in a county without a college degree, eligible for Medicaid, and living in crowded housing.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hoda S. Abdel Magid", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Jacqueline M Ferguson", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Raymond V Cleve", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Amanda Purnell", + "author_inst": "Veterans Affairs Central Office" + }, + { + "author_name": "Thomas F Osborne", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.21.21265133", "rel_title": "Post COVID-19 in children, adolescents, and adults: results of a matched cohort study including more than 150,000 individuals with COVID-19", @@ -559183,37 +561720,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.13.21264693", - "rel_title": "Modeling brings additional insights into the kinetics of SARS-CoV-2 neutralizing antibody", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264693", - "rel_abs": "Following the paper by Seow et al. published in Nature Microbiology, we reanalyzed the publicly available data using dynamical models of humoral response. The main conclusion is that, from available data, we can demonstrate that the decline of neutralizing antibodies (as measured with ID50) is biphasic, which is compatible with two types of antibody secreting cells (short lived and long lived). We found that lower bound of half life of the long-lived antibody secreting cells is 450 days. Moreover, our model predicts that the neutralizing antibody response could be more durable than suggested (up to 129 days for individuals with no requirement of supplemental oxygen and up to 175 days for others). A result which adds insight on the longevity of immune response.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Melanie Prague", - "author_inst": "Univ. Bordeaux, Inria, Inserm U1219, SISTM, Vaccine research institute, France" - }, - { - "author_name": "Quentin Clairon", - "author_inst": "Univ. Bordeaux, Inria, Inserm U1219, SISTM, Vaccine research institute, France" - }, - { - "author_name": "Jeremie Guedj", - "author_inst": "Inserm IAME, Paris, France" - }, - { - "author_name": "Rodolphe Thiebaut", - "author_inst": "Univ. Bordeaux, Inria, Inserm U1219, SISTM, Vaccine research institute, France" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.19.21265062", "rel_title": "Mutations on non-structural proteins of SARS-CoV-2 are possibly responsible for adverse clinical outcomes in a real-life practice", @@ -560489,6 +562995,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.18.21265057", + "rel_title": "Impact of routine asymptomatic screening on COVID-19 incidence in a highly vaccinated university population", + "rel_date": "2021-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265057", + "rel_abs": "BackgroundWith the return of in-person classes, an understanding of COVID-19 transmission in vaccinated university campuses is essential. Given the context of high anticipated vaccination rates and other measures, there are outstanding questions of the potential impact of campus-based asymptomatic screening.\n\nMethodsWe estimated the expected number of cases and hospitalizations in one semester using rates derived for British Columbia (BC), Canada up to September 15th, 2021 and age-standardizing to a University population. To estimate the expected number of secondary cases averted due to routine tests of unvaccinated individuals in a BC post-secondary institution, we used a probabilistic model based on the incidence, vaccination effectiveness, vaccination coverage and R0. We examined multiple scenarios of vaccine coverage, screening frequency, and pre-vaccination R0.\n\nResultsFor one 12 week semester, the expected number of cases is 67 per 50,000 for 80% vaccination coverage and 37 per 50,000 for 95% vaccination coverage. Screening of the unvaccinated population averts an expected 6-16 cases per 50,000 at 80% decreasing to 1-2 averted cases per 50,000 at 95% vaccination coverage for weekly to daily screening. Further scenarios can be explored using a web-based application.\n\nInterpretationRoutine screening of unvaccinated individuals may be of limited benefit if vaccination coverage is 80% or greater within a university setting.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rebeca Cardim Falcao", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michael Otterstatter", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "May A. Ahmed", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michelle Spencer", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Sarafa Iyaniwura", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Naveed Z. Janjua", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Geoff McKee", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michael A. Irvine", + "author_inst": "BC Centre for Disease Control" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.15.21265037", "rel_title": "Extreme COVID-19 waves reveal hyperexponential growth and finite-time singularity", @@ -561229,57 +563782,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.10.14.21265004", - "rel_title": "Adapting cleft care protocols in low- and middle-income countries during and after COVID-19: a process-driven review with recommendations", - "rel_date": "2021-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21265004", - "rel_abs": "ObjectiveA consortium of global cleft professionals, predominantly from low- and middle-income countries, identified adaptions to cleft care protocols during and after COVID as a priority learning area of need.\n\nDesignA multidisciplinary international working group met on a videoconferencing platform in a multi-staged process to make consensus recommendations for adaptions to cleft protocols within resource-constrained settings. Feedback was sought from a roundtable discussion forum and global organisations involved in comprehensive cleft care.\n\nResultsFoundational principles were agreed to enable recommendations to be globally relevant and two areas of focus within the specified topic were identified. First the safety aspects of cleft surgery protocols were scrutinised and COVID adaptions, specifically in the pre and peri-operative periods, were highlighted. Second, surgical operations and access to services were prioritized according to their relationship to functional outcomes and time-sensitivity. The operations assigned the highest priority were emergent interventions for breathing and nutritional requirements and primary palatoplasty. The cleft services assigned the highest priority were new-born assessments, paediatric support for children with syndromes, management of acute dental or auditory infections and speech pathology intervention.\n\nConclusionsA collaborative, interdisciplinary and international working group delivered consensus recommendations to assist with the provision of cleft care in low- and middle-income countries. At a time of global cleft care delays due to COVID-19, a united approach amongst global cleft care providers will be advantageous to advocate for children born with cleft lip and palate in resource-constrained settings.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Matthew John Fell", - "author_inst": "University of Bristol" - }, - { - "author_name": "Michael Goldwasser", - "author_inst": "Operation Smile" - }, - { - "author_name": "BS Jayanth", - "author_inst": "ABMSS" - }, - { - "author_name": "Rui Manuel Rodrigues Pereira", - "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo," - }, - { - "author_name": "Christian Tshisuz Nawej", - "author_inst": "Cliniques Universitaires de Lubumbashi," - }, - { - "author_name": "Rachel Winer", - "author_inst": "Transforming Faces" - }, - { - "author_name": "Neeti Daftari", - "author_inst": "Transforming Faces" - }, - { - "author_name": "Hugh Brewster", - "author_inst": "Transforming Faces" - }, - { - "author_name": "Karen Goldschmied", - "author_inst": "Hospital Dr Luis Calvo Mackenna" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.10.12.21264136", "rel_title": "Accuracy of emergency medical service telephone triage of need for an ambulance response in suspected COVID-19: An observational cohort study", @@ -562294,6 +564796,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.13.21264919", + "rel_title": "Agile design and development of a high throughput cobas(R) SARS-CoV-2 RT-PCR diagnostic test", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264919", + "rel_abs": "Diagnostic testing is essential for management of the COVID-19 pandemic. An agile assay design methodology, optimized for the cobas(R) 6800/8800 system, was used to develop a dual-target, qualitative SARS-CoV-2 RT-PCR test using commercially available reagents and existing sample processing and thermocycling profiles. The limit of detection was 0.004 to 0.007 TCID50/mL for USA-WA1/2020. Assay sensitivity was confirmed for SARS-CoV-2 variants Alpha, Beta, Gamma, Delta and Kappa. The coefficients of variation of the cycle threshold number (Ct) were between 1.1 and 2.2%. There was no difference in Ct using nasopharyngeal compared to oropharyngeal swabs in universal transport medium (UTM). A small increase in Ct was observed with specimens collected in cobas(R) PCR medium compared to UTM. In silico analysis indicated that the dual-target test is capable of detecting all >1,800,000 SARS-CoV-2 sequences in the GISAID database. Our agile assay design approach facilitated rapid development and deployment of this SARS-CoV-2 RT-PCR test.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Chitra Manohar", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Jingtao Sun", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Peter Schlag", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Chris Santini", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Marcel Fontecha", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Pirmin Lotscher", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Carolin Bier", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Kristina Goepfert", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Dana Duncan", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Gene Spier", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Daniel Jarem", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Dmitriy Kosarikov", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.14.21265010", "rel_title": "How frequent are acute reactions to COVID-19 vaccination and who is at risk?", @@ -562802,41 +565367,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.15.21264970", - "rel_title": "Prediction of severe COVID-19 infection at the time of testing: A machine learning approach", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.15.21264970", - "rel_abs": "Early and effective detection of severe infection cases during a pandemic can significantly help patient prognosis and resource allocation. We develop a machine learning framework for detecting severe COVID-19 cases at the time of RT-PCR testing. We retrospectively studied 988 patients from a small Canadian province that tested positive for SARS-CoV-2 where 42 (4%) cases were at-risk (i.e., resulted in hospitalization, admission to ICU, or death), and 8 (< 1%) cases resulted in death. The limited information available at the time of RT-PCR testing included age, comorbidities, and patients reported symptoms, totaling 27 features. Vaccination status was unavailable. Due to the severe class imbalance and small dataset size, we formulated the problem of detecting severe COVID as anomaly detection and applied three models: one-class support vector machine (OCSVM), weight-adjusted XGBoost, and weight-adjusted Ad-aBoost. The OCSVM was the best performing model for detecting the deceased cases with an average 95% true positive rate (TPR) and 27.2% false positive rate (FPR). Meanwhile, the XGBoost provided the best performance for detecting the at-risk cases with an average 96.2% TPR and 19% FPR. In addition, we developed a novel extension to SHAP interpretability to explain the outputs from the models. In agreement with conventional knowledge, we found that comorbidities were influential in predicting severity, however, we also found that symptoms were generally more influential, noting that machine learning combines all available data and is not a single-variate statistical analysis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Faraz Khoshbaktian", - "author_inst": "University of Toronto" - }, - { - "author_name": "Ardian Lagman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Dionne M Aleman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Randy Giffen", - "author_inst": "IBM Canada" - }, - { - "author_name": "Proton Rahman", - "author_inst": "Memorial University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.14.21264992", "rel_title": "Estimating COVID-19 Hospitalizations in the United States with surveillance data using a Bayesian Hierarchical model", @@ -563864,6 +566394,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.17.21265101", + "rel_title": "Time-varying effectiveness of the mRNA-1273, BNT162b2 and Ad26.COV2.S vaccines against SARS-CoV-2 infections and COVID-19 hospitalizations and deaths: an analysis based on observational data from Puerto Rico", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.17.21265101", + "rel_abs": "BackgroundAs of October 1, 2021 2,217,547 individuals were fully vaccinated against COVID-19 in Puerto Rico. Since the vaccination process commenced on December 15, 2020 111,052 laboratory-confirmed SARS-CoV-2 infections have been reported. These data permitted us to quantify the benefits of the immunization campaign and to compare effectiveness of the mRNA-1273 (Moderna), BNT162b2 (Pfizer), and Ad26.COV2.S (J&J) vaccines.\n\nMethodsDepartment of Health databases holding vaccination status, SARS-CoV-2 test results, and COVID-19 hospitalizations and deaths were integrated. We fit a statistical model that adjusted for time-varying incidence rates and age to estimate vaccine effectiveness and hospitalization and death relative risks. Code and data are provided here: https://github.com/rafalab/vax-eff-pr.\n\nResultsAt the peak of their protection, mRNA-1273, BNT162b2, and Ad26.COV2.S had an effectiveness of 90% (88%-91%), 87% (85%-89%), and 58% (51%-65%), respectively. After four months, effectiveness waned to about 70%, 60%, and 30%. We found no evidence that effectiveness was different after the Delta variant became dominant. For those infected, the vaccines provided further protection against hospitalization and deaths across all age groups. All vaccines had a lower effectiveness for those over 85 years, with a larger decrease for the Ad26.COV2.S vaccine. Overall, thousands of hospitalizations and deaths were avoided thanks to the vaccines.\n\nConclusionsThe mRNA-1273 and BNT162b2 vaccines were highly effective across all age groups. They were still effective after four months although the protection waned. The Ad26.COV2.S vaccine was effective but to a lesser degree, especially for older age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Monica M. Robles-Fontan", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Elvis G. Nieves", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Iris Cardona-Gerena", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Rafael A Irizarry", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.18.21265046", "rel_title": "Comparative assessment of methods for short-term forecasts of COVID-19 admissions in England at the local level", @@ -564439,65 +567000,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.12.21264707", - "rel_title": "Evaluation of COVID-19 vaccine breakthrough infections among immunocompromised patients fully vaccinated with BNT162b2", - "rel_date": "2021-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264707", - "rel_abs": "ObjectiveTo evaluate COVID-19 vaccine breakthrough infections among immunocompromised (IC) individuals.\n\nMethodsIndividuals vaccinated with BNT162b2 were selected from the US HealthVerity database (12/10/2020-7/8/2021). COVID-19 vaccine breakthrough infections were examined in fully vaccinated ([≥]14 days after 2nd dose) IC individuals (IC cohort), 12 mutually exclusive IC condition groups, and a non-IC cohort. IC conditions were identified using an algorithm based on diagnosis codes and immunosuppressive (IS) medication usage.\n\nResultsOf 1,277,747 individuals [≥]16 years of age who received 2 BNT162b2 doses, 225,796 (17.7%) were identified as IC (median age: 58 years; 56.3% female). The most prevalent IC conditions were solid malignancy (32.0%), kidney disease (19.5%), and rheumatologic/inflammatory conditions (16.7%). Among the fully vaccinated IC and non-IC cohorts, a total of 978 breakthrough infections were observed during the study period; 124 (12.7%) resulted in hospitalization and 2 (0.2%) were inpatient deaths. IC individuals accounted for 38.2% (N=374) of all breakthrough infections, 59.7% (N=74) of all hospitalizations, and 100% (N=2) of inpatient deaths. The proportion with breakthrough infections was 3 times higher in the IC cohort compared to the non-IC cohort (N=374 [0.18%] vs. N=604 [0.06%]; unadjusted incidence rates were 0.89 and 0.34 per 100 person-years, respectively. Organ transplant recipients had the highest incidence rate; those with >1 IC condition, antimetabolite usage, primary immunodeficiencies, and hematologic malignancies also had higher incidence rates compared to the overall IC cohort. Incidence rates in older ([≥]65 years old) IC individuals were generally higher versus younger IC individuals (<65).\n\nLimitationsThis retrospective analysis relied on coding accuracy and had limited capture of COVID-19 vaccine receipt.\n\nConclusionsCOVID-19 vaccine breakthrough infections are rare but are more common and severe in IC individuals. The findings from this large study support FDA authorization and CDC recommendations to offer a 3rd vaccine dose to increase protection among IC individuals.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Manuela Di Fusco", - "author_inst": "Pfizer Inc., New York, NY USA" - }, - { - "author_name": "Mary M Moran", - "author_inst": "Pfizer Inc., Collegeville, PA, USA" - }, - { - "author_name": "Alejandro Cane", - "author_inst": "Pfizer Inc., New York, NY USA" - }, - { - "author_name": "Daniel Curcio", - "author_inst": "Pfizer Inc., New York, NY USA" - }, - { - "author_name": "Farid Khan", - "author_inst": "Pfizer Inc., Collegeville, PA, USA" - }, - { - "author_name": "Deepa Malhotra", - "author_inst": "Pfizer Inc., New York, NY USA" - }, - { - "author_name": "Andy Surinach", - "author_inst": "Genesis Research, Hoboken, NJ, USA" - }, - { - "author_name": "Amanda Miles", - "author_inst": "Pfizer Inc., New York, NY USA" - }, - { - "author_name": "David Swerdlow", - "author_inst": "Pfizer Inc., Collegeville, PA, USA" - }, - { - "author_name": "John M McLaughlin", - "author_inst": "Pfizer Inc., Collegeville, PA, USA" - }, - { - "author_name": "Jennifer L Nguyen", - "author_inst": "Pfizer Inc., New York, NY USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.13.21264932", "rel_title": "The role of educational settings in the transmission chain of SARS-CoV-2 in 2020: a systematic review", @@ -565885,6 +568387,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.10.11.21264709", + "rel_title": "Quantitative chest CT combined with plasma cytokines predict outcomes in COVID-19 patients", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264709", + "rel_abs": "Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest CT in combination with plasma cytokines using a machine learning approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n=152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within 5 days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-) were collected from the electronic medical record. We found that chest CT combined with plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82), whereas CT quantitative was better at predicting severity (AUC 0.81 vs 0.70) while cytokine measurements better predicted death (AUC 0.70 vs 0.66). Finally, we provide a simple scoring system using plasma IL-6, IL-8, TNF-, GGO to aerated lung ratio and age as novel metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Guillermo Carbonell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar E Gonzalez-Kozlova", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Brett Marinelli", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emma Klein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Maria El Homsi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Daniel Stocker", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael Chung", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam Bernheim", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicole Simons", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jiani Xiang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sharon Nirenberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sara Lewis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bachir Taouli", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.10.12.21264890", "rel_title": "Breastfeeding infants receive neutralizing antibodies and cytokines from mothers immunized with a COVID-19 mRNA vaccine", @@ -566593,65 +569178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.12.21264840", - "rel_title": "Effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines for reducing susceptibility to infection with the Delta variant(B.1.617.2) of SARS-CoV-2", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264840", - "rel_abs": "BackgroundFrom January to May 2021 the alpha variant (B.1.1.7) of SARS-CoV-2 was the most commonly detected variant in the UK, but since then the Delta variant (B.1.617.2), first detected in India, has become the predominant variant. The UK COVID-19 vaccination programme started on 8th December 2020. Most vaccine effectiveness studies to date have focused on the alpha variant. We therefore aimed to estimate the effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines in preventing infection with respect to the Delta variant in a UK setting.\n\nMethodsWe used anonymised public health record data linked to infection data (PCR) using the Combined Intelligence for Population Health Action resource. We then constructed an SIR epidemic model to explain SARS-CoV-2 infection data across the Cheshire and Merseyside region of the UK.\n\nResultsWe determined that the effectiveness of the Oxford-AstraZeneca vaccine in reducing susceptibility to infection is 39% (95% credible interval [34,43]) and 64% (95% credible interval [61,67]) for a single dose and a double dose respectively. For the Pfizer-BioNTech vaccine, the effectiveness is 20% (95% credible interval [10,28]) and 84% (95% credible interval [82,86]) for a single-dose and a double dose respectively.\n\nConclusionVaccine effectiveness for reducing susceptibility to SARS-CoV-2 infection shows noticeable improvement after receiving two doses of either vaccine. Findings also suggest that a full course of the Pfizer-BioNTech provides the optimal protection against infection with the Delta variant. This would advocate for completing the full course programme to maximise individual protection and reduce transmission.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Karan Pattni", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Dan Hungerford", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Sarah Adams", - "author_inst": "Graphnet Health" - }, - { - "author_name": "Iain Buchan", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Christopher P Cheyne", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marta Garc\u00eda-Fi\u00f1ana", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Ian Hall", - "author_inst": "University of Manchester" - }, - { - "author_name": "David M Hughes", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Christopher Overton", - "author_inst": "University of Manchester" - }, - { - "author_name": "Xingna Zhang", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Kieran J Sharkey", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.12.21264902", "rel_title": "COVID-19 and Mental Health: Predicted Mental Health Status is Associated with Clinical Symptoms and Pandemic-Related Psychological and Behavioral Responses", @@ -567707,6 +570233,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.13.21264975", + "rel_title": "Disparities in SARS-CoV-2 exposure: evidence from a citywide seroprevalence study in Holyoke, Massachusetts, USA", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264975", + "rel_abs": "BackgroundSeroprevalence studies are important tools to estimate the prevalence of prior or recent SARS-CoV-2 infections, identifying hotspots and high-risk groups and informing public health responses to the COVID-19 pandemic. We conducted a city-level seroprevalence study in Holyoke, Massachusetts, USA to estimate the seroprevalence of SARS-CoV-2 antibodies and risk factors for seropositivity.\n\nMethodsWe invited inhabitants of 2,000 randomly sampled addresses between November 5 and December 31, 2020. Participants completed questionnaires measuring sociodemographic and health characteristics, and COVID-19 exposure history, and provided dried blood spots for measurement of SARS-CoV-2 IgG and IgM antibodies. We calculate total and subgroup seroprevalence estimates based on presence of IgG antibodies using a Bayesian procedure that incorporates uncertainty in antibody test sensitivity and specificity. We account for clustering by household and weighting based on demographic characteristics to ensure estimates represented the citys population.\n\nFindingsWe enrolled 280 households including 472 individuals. 328 underwent antibody testing. The citywide seroprevalence estimate of SARS-CoV-2 IgG was 13.1% (95%CI 6.9-22.3) compared to 9.8% based on publicly reported case counts. Seroprevalence was 16.1% (95%CI 6.2-31.8) among individuals identifying as Hispanic compared to 9.4% (95%CI 4.6-16.4) among those identifying as non-Hispanic white. Seroprevalence was higher among Spanish speaking households (21.9%; 95% CI 8.3-43.9) compared to English speaking households (10.2%; 95% CI 5.2-18.0) and among individuals living in high vulnerability areas (14.4%; 95% CI 7.1-25.5) compared to low vulnerability areas (8.2%; 95% CI 3.1-16.9).\n\nInterpretationThe measured SARS-CoV-2 seroprevalence of IgG antibodies in Holyoke was only 13.1% during the second surge of SARS-CoV-2 in this region, far from accepted thresholds for \"herd immunity.\" Already vulnerable communities were at highest risk of prior infection. Implementation of local serosurveys in tandem with proactive public health interventions that address disparities in SARS-CoV-2 exposure are crucial to ensure at-risk communities have appropriate educational materials and access to vaccines, testing, and timely treatment.\n\nFundingThe Sullivan Family Foundation, Harvard Data Science Institute Bias2 program, the US Centers for Disease Control and Prevention.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wilfredo Rafael Matias", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Division of Infectious Diseases, Brigham and Womens Hospital, Boston, MA; Center fo" + }, + { + "author_name": "Isabel R Fulcher", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA; Harvard Data Science Initiative, Cambridge, MA" + }, + { + "author_name": "Sara M Sauer", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Cody P Nolan", + "author_inst": "Department of Medicine, Brigham and Womens Hospital, Boston, MA" + }, + { + "author_name": "Yodeline Guillaume", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Jack Zhu", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Francisco J Molano", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Elizabeth Uceta", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Shannon Collins", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Damien M Slater", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Vanessa M Sanchez", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Serina Moheed", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Jason B Harris", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Richelle C Charles", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Ryan M Paxton", + "author_inst": "Holyoke Board of Health, Holyoke, MA" + }, + { + "author_name": "Sean F Gonsalves", + "author_inst": "Holyoke Board of Health, Holyoke, MA" + }, + { + "author_name": "Molly F Franke", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Louise C Ivers", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Center for Global Health, Massachusetts General Hospital, Boston, MA; Department of" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.13.21264901", "rel_title": "Soluble angiotensin-converting enzyme 2 as a prognostic biomarker for disease progression in patients infected with SARS-CoV-2", @@ -568395,165 +571008,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.10.21264827", - "rel_title": "Heterologous SARS-CoV-2 Booster Vaccinations: Preliminary Report", - "rel_date": "2021-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264827", - "rel_abs": "BackgroundWhile Coronavirus disease 2019 (Covid-19) vaccines are highly effective, breakthrough infections are occurring. Booster vaccinations have recently received emergency use authorization (EUA) for certain populations but are restricted to homologous mRNA vaccines. We evaluated homologous and heterologous booster vaccination in persons who had received an EUA Covid-19 vaccine regimen.\n\nMethodsIn this phase 1/2 open-label clinical trial conducted at ten U.S. sites, adults who received one of three EUA Covid-19 vaccines at least 12 weeks prior to enrollment and had no reported history of SARS-CoV-2 infection received a booster injection with one of three vaccines (Moderna mRNA-1273 100-g, Janssen Ad26.COV2.S 5x1010 virus particles, or Pfizer-BioNTech BNT162b2 30-g; nine combinations). The primary outcomes were safety, reactogenicity, and humoral immunogenicity on study days 15 and 29.\n\nResults458 individuals were enrolled: 154 received mRNA-1273, 150 received Ad26.CoV2.S, and 153 received BNT162b2 booster vaccines. Reactogenicity was similar to that reported for the primary series. Injection site pain, malaise, headache, and myalgia occurred in more than half the participants. Booster vaccines increased the neutralizing activity against a D614G pseudovirus (4.2-76-fold) and binding antibody titers (4.6-56-fold) for all combinations; homologous boost increased neutralizing antibody titers 4.2-20-fold whereas heterologous boost increased titers 6.2-76-fold. Day 15 neutralizing and binding antibody titers varied by 28.7-fold and 20.9-fold, respectively, across the nine prime-boost combinations.\n\nConclusionHomologous and heterologous booster vaccinations were well-tolerated and immunogenic in adults who completed a primary Covid-19 vaccine regimen at least 12 weeks earlier.\n\n(Funded by National Institute of Allergy and Infectious Diseases; Clinical Trials.gov number, NCT04889209)", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Robert L Atmar", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Kirsten E Lyke", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Meagan E Deming", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Lisa A Jackson", - "author_inst": "Kaiser Permanente Washington Health Research Institute" - }, - { - "author_name": "Angela R Branche", - "author_inst": "University of Rochester" - }, - { - "author_name": "Hana M El Sahly", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Christina A Rostad", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Judith M Martin", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Christine Johnston", - "author_inst": "University of Washington" - }, - { - "author_name": "Richard E Rupp", - "author_inst": "University of Texas Medical Branch-Galveston" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Rebecca C Brady", - "author_inst": "Cincinnati Childrens Hospital Medical Center" - }, - { - "author_name": "Robert W Frenck Jr.", - "author_inst": "Cincinnati Childrens Hospital Medical Center" - }, - { - "author_name": "Martin Backer", - "author_inst": "NYU Long Island School of Medicine" - }, - { - "author_name": "Angelica C Kottkamp", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Tara M Babu", - "author_inst": "University of Washington" - }, - { - "author_name": "Kumaravel Rajakumar", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Srilatha Edupuganti", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "David Dobryzynski", - "author_inst": "University of Rochester" - }, - { - "author_name": "Christine M Posavad", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Janet I Archer", - "author_inst": "FHI360" - }, - { - "author_name": "Sonja Crandon", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Seema U Nayak", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Daniel Szydlo", - "author_inst": "Statistical Center for HIV/AIDS Research and Prevention (SCHARP)" - }, - { - "author_name": "Jillian Zemanek", - "author_inst": "Statistical Center for HIV/AIDS Research and Prevention (SCHARP)" - }, - { - "author_name": "Clara P Dominguez Islas", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Elizabeth R Brown", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Mehul S Suthar", - "author_inst": "Emory School of Medicine" - }, - { - "author_name": "M Juliana McElrath", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Adrian B McDermott", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "David C Montefiori", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Amanda Eaton", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Kathleen M Neuzil", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "David S Stephens", - "author_inst": "Emory University" - }, - { - "author_name": "Paul C Roberts", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "John Beigel", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.10.21264779", "rel_title": "Genetically determined serum testosterone level and Covid-19 illness level: A mendelian randomization study", @@ -569489,6 +571943,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.10.09.21264794", + "rel_title": "Covid-19 Epidemic Prediction in France: the Multimodal Case.", + "rel_date": "2021-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264794", + "rel_abs": "In two previous papers we have proposed models to estimate the Covid-19 epidemic when the number of daily positive cases has a bell shaped form that we call a mode. We have observed that each Covid variant produces this type of epidemic shape at a different moment, resulting in a multimodal epidemic shape. We will show in this document that each mode can still be estimated with models described in the two previous papers provides we replace the cumulated number of positive cases y by the cumulated number of positive cases reduced by a parameter P to be estimated. Therefore denoting z the logarithm of y -P, z follows approximately the differential equation [z] = b -azr where a, b, r have also to be estimated from the observed data. We will show the obtained predictions on the four French modes April, November 2020, May and September 2021. The comparison between the prediction obtained before the containment decisions made by the French government and the observed data afterwards suggests the inefficiency of the epidemic lockdowns.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jean-Pierre Quadrat", + "author_inst": "Retired from INRIA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.11.463917", "rel_title": "Secondary structure of subgenomic RNA M of SARS-CoV-2", @@ -570120,57 +572593,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.08.21264699", - "rel_title": "Cardiovascular Mortality during the COVID-19 Pandemics in a Large Brazilian City: a Comprehensive Analysis", - "rel_date": "2021-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264699", - "rel_abs": "IntroductionThe impact of COVID-19 pandemics on cardiovascular diseases (CVD) may be caused by health system reorganization and/or collapse, or from changes in the behaviour of individuals. In Brazil, municipalities were empowered to define regulatory measures, potentially resulting in diverse effects on CVD morbimortality.\n\nObjectiveTo analyse the impact of COVID-19 pandemics on CVD outcomes in Belo Horizonte (BH), the 6th greater capital city in Brazil, including: mortality, mortality at home, hospitalizations, intensive care unit utilization, and in-hospital mortality; and the differential effect according to sex, age range, social vulnerability, and pandemics phase.\n\nMethodsEcological study analysing data from the Mortality and Hospital Information System of BH residents aged [≥]30 years. CVD was defined as in Chapter IX from ICD-10. Social vulnerability was classified by a composite socioeconomic index as high, medium and low. The observed age-standardized rates for epidemiological weeks 10-48, 2020, were compared to the expected rates (mean of 2015-2019). Wilcoxon rank-sum test was used to test differences, and risk ratios with their 95% confidence intervals were calculated. National demographic estimates was used to calculate rates.\n\nResultsWe found no changes in CVD mortality rates (RiR 1.01, 95%CI 0.96-1.06). However, CVD deaths occurred more at homes (RiR 1.32, 95%CI 1.20-1.46) than in hospitals (RiR 0.89, 95%CI 0.79-0.99), as a result of a substantial decline in hospitalization rates, even though proportional in-hospital deaths increased. The rise in home deaths was greater in older adults and in had an increasing gradient in those more socially vulnerable (RiR 1.45); for high (RiR 1.45), medium (RiR 1.32) and low vulnerability (RiR 1.21).\n\nConclusionThe greater occurrence of CVD deaths at home, in parallel with lower hospitalization rates, suggests that CVD care was disrupted during the COVID-19 pandemics, which more adversely affected older and more socially vulnerable individuals, exacerbating health inequities in BH.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Luisa Campos Caldeira Brant", - "author_inst": "School of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" - }, - { - "author_name": "Pedro C Pinheiro", - "author_inst": "School of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" - }, - { - "author_name": "Antonio L P Ribeiro", - "author_inst": "School of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" - }, - { - "author_name": "Isis E Machado", - "author_inst": "Municipal Health Secretariat, Belo Horizonte, MG, Brazil" - }, - { - "author_name": "Paulo R L Correa", - "author_inst": "School of Medicine, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil" - }, - { - "author_name": "Mayara R Santos", - "author_inst": "School of Medicine, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil" - }, - { - "author_name": "Maria de Fatima M de Souza", - "author_inst": "Vital Strategies, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Deborah C Malta", - "author_inst": "Nursing School, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" - }, - { - "author_name": "Valeria M A Passos", - "author_inst": "School of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.10.07.21264711", "rel_title": "Differential anchoring effects of vaccination comparator selection: characterizing a potential bias due to healthcare utilization in COVID-19 versus influenza", @@ -571418,6 +573840,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.07.21264419", + "rel_title": "Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy", + "rel_date": "2021-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264419", + "rel_abs": "With a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We used a matching procedure designed to create groups of counties that are aligned along age, race, income, population, and urban/rural categories--socio-demographic variables that have been shown to be correlated with COVID-19 outcomes. We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. We complement the statistical analysis with a case study of IHEs in Massachusetts--a rich data state in our dataset--which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in the general population.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brennan Klein", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Nicholas Generous", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Zarana Bhadricha", + "author_inst": "Northeastern University" + }, + { + "author_name": "Rishab Gunashekar", + "author_inst": "Northeastern University" + }, + { + "author_name": "Preeti Kori", + "author_inst": "Northeastern University" + }, + { + "author_name": "Bodian Li", + "author_inst": "Northeastern University" + }, + { + "author_name": "Stefan McCabe", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jon Green", + "author_inst": "Northeastern University" + }, + { + "author_name": "David Lazer", + "author_inst": "Northeastern University" + }, + { + "author_name": "Christopher R. Marsicano", + "author_inst": "Davidson College" + }, + { + "author_name": "Samuel V. Scarpino", + "author_inst": "The Rockefeller Foundation Pandemic Prevention Institute" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.08.21264749", "rel_title": "Longitudinal changes in home confinement and mental health implications: A 17-month follow-up study in England during the COVID-19 pandemic", @@ -572098,37 +574587,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.10.07.463611", - "rel_title": "A bacteria-based assay to study SARS-CoV-2 protein-protein interactions", - "rel_date": "2021-10-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.07.463611", - "rel_abs": "Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of COVID-19, an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of SARS-CoV-2-encoded proteins. Here we describe the use of a convenient bacteria-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identify sixteen distinct intraviral protein-protein interactions (PPIs), involving sixteen proteins. We find that many of the identified proteins interact with more than one partner. We further show how our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm and we use this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examine how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.\n\nImportanceUnderstanding how virally encoded proteins interact with one another is essential in elucidating basic viral biology, providing a foundation for therapeutic discovery. Here we describe the use of a versatile bacteria-based system to investigate the interactions of the protein set encoded by SARS-CoV-2, the virus responsible for the current pandemic. We identify sixteen distinct intraviral protein-protein interactions, involving sixteen proteins, many of which interact with more than one partner. Our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified version of our bacteria-based system that permits detection of the interaction between the SARS-CoV-2 spike protein (specifically its receptor binding domain) and its cognate human cell surface receptor ACE2 and we investigate the effects of spike mutations found in currently circulating SARS-CoV-2 variants. Our findings illustrate the general utility of our system for probing the interactions of virally encoded proteins.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ann Hochschild", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Benjamin L Springstein", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Padraig Deighan", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Grzegorz Grabe", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.10.07.463402", "rel_title": "Inhibition of SARS-CoV-2 spike protein palmitoylation reduces virus infectivity", @@ -573324,6 +575782,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.04.21264540", + "rel_title": "Detailed reconstruction of the Iranian COVID-19 epidemic reveals high attack rates of SARS-CoV-2 in several provinces", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264540", + "rel_abs": "Detailed reconstruction of the SARS-CoV-2 transmission dynamics and assessment of its burden in several parts of the world has still remained largely unknown due to the scarcity of epidemiological analyses and limited testing capacities of different countries to identify cases and deaths attributable to COVID-19 [1-4]. Understanding the true burden of the Iranian COVID-19 epidemic is subject to similar challenges with limited clinical and epidemiological studies at the subnational level [5-9]. To address this, we develop a new quantitative framework that enables us to fully reconstruct the transmission dynamics across the country and assess the level of under-reporting in infections and deaths using province-level, age-stratified all-cause mortality data. We show that excess mortality aligns with seroprevalence estimates in each province and subsequently estimate that as of 2021-10-22, only 48% (95% confidence interval: 43-55%) of COVID-19 deaths in Iran have been reported. We find that in the most affected provinces such as East Azerbaijan, Qazvin, and Qom approximately 0.4% of the population have died of COVID-19 so far. We also find significant heterogeneity in the estimated attack rates across the country with 11 provinces reaching close to or higher than 100% attack rates. Despite a relatively young age structure in Iran, our analysis reveals that the infection fatality rate in most provinces is comparable to high-income countries with a larger percentage of older adults, suggesting that limited access to medical services, coupled with undercounting of COVID-19-related deaths, can have a significant impact on accurate estimation of COVID-19 fatalities. Our estimation of high attack rates in provinces with largely unmitigated epidemics whereby, on average, between 10% to 25% individuals have been infected with COVID-19 at least twice over the course of 20 months also suggests that, despite several waves of infection, herd immunity through natural infection has not been achieved in the population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ariel Karlinsky", + "author_inst": "Hebrew University of Jerusalem" + }, + { + "author_name": "Luca Ferretti", + "author_inst": "Nuffield Department of Medicine" + }, + { + "author_name": "Aris Katzourakis", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.06.21264645", "rel_title": "A joint hierarchical model for the number of cases and deaths due to COVID-19 across the boroughs of Montreal", @@ -574196,49 +576689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.10.06.21264569", - "rel_title": "Predicting increases in COVID-19 incidence to identify locations for targeted testing in West Virginia: A machine learning enhanced approach", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264569", - "rel_abs": "During the COVID-19 pandemic, West Virginia developed an aggressive SARS-CoV-2 testing strategy which included utilizing pop-up mobile testing in locations anticipated to have near-term increases in SARS-CXoV-2 infections. In this study, we describe and compare two methods for predicting near-term SARS-CoV-2 incidence in West Virginia counties. The first method, Rt Only, is solely based on producing forecasts for each county using the daily instantaneous reproductive numbers, Rt. The second method, ML+ Rt, is a machine learning approach that uses a Long Short-Term Memory network to predict the near-term number of cases for each county using epidemiological statistics such as Rt, county population information, and time series trends including information on major holidays, as well as leveraging statewide COVID-19 trends across counties and county population size. Both approaches used daily county-level SARS-CoV-2 incidence data provided by the West Virginia Department Health and Human Resources beginning April 2020. The methods are compared on the accuracy of near-term SARS-CoV-2 increases predictions by county over 17 weeks from January 1, 2021-April 30, 2021. Both methods performed well (correlation between forecasted number of cases and the actual number of cases week over week is 0.872 for the ML+Rt method and 0.867 for the Rt Only method) but differ in performance at various time points. Over the 17-week assessment period, the ML+Rt method outperforms the Rt Only method in identifying larger spikes. We also find that both methods perform adequately in both rural and non-rural predictions. Finally, we provide a detailed discussion on practical issues regarding implementing forecasting models for public health action based on Rt, and the potential for further development of machine learning methods that are enhanced by Rt.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Bradley S Price", - "author_inst": "West Virginia University" - }, - { - "author_name": "Maryam Khodaverdi", - "author_inst": "West Virginia University" - }, - { - "author_name": "Adam Halasz", - "author_inst": "West Virginia University" - }, - { - "author_name": "Brian Hendricks", - "author_inst": "West Virginia University" - }, - { - "author_name": "Wesley Kimble", - "author_inst": "West Virginia University" - }, - { - "author_name": "Gordon S Smith", - "author_inst": "West Virginia University" - }, - { - "author_name": "Sally L Hodder", - "author_inst": "West Virginia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.10.06.21264535", "rel_title": "Analytical performance of eleven SARS-CoV-2 antigen-detecting rapid tests for Delta variant", @@ -575482,6 +577932,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.05.21264548", + "rel_title": "Feasibility and acceptability of daily testing at school as an alternative to self-isolation following close contact with a confirmed case of COVID-19: A qualitative analysis", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264548", + "rel_abs": "BackgroundDaily testing using a rapid Lateral Flow Device (LFD) has been suggested as an alternative to self-isolation. A randomised trial comparing daily contact testing (DCT) in schools with self-isolation found that SARS-CoV-2 transmission within school was comparable and low in both groups. However, if this approach is to be adopted widely, it is critical that we understand the perspective of those who will be delivering and receiving DCT. The aim of this qualitative process study embedded in the randomised controlled trial (RCT) was to improve understanding of a range of behavioural factors that could influence implementation.\n\nMethodsInterviews were conducted with 63 participants, including staff, students, and parents of students who had been identified as being in close contact with someone with COVID-19. The topic guide explored perceptions of daily testing, understanding of positive and negative test results, and adherence to guidance. Data were analysed using an inductive thematic approach.\n\nResultsResults were organised under three main headings: (1) factors influencing daily testing (2) interpretation of test results (3) behaviour during testing period. Participants recognized that daily testing may allow students to remain in school, which was viewed as necessary for both education and social needs. Whilst some felt safer as a result of daily testing, others raised concerns about safety. Participants did not always understand how to interpret and respond to test results, and although participants reported high levels of adherence to the guidance, improved communications were desired.\n\nConclusionDaily testing may be a feasible and acceptable alternative to self-isolation among close contacts of people who test positive. However, improved communications are needed to ensure that all students and parents have a good understanding of the rationale for testing, what test results mean, how test results should be acted on, and how likely students are to test positive following close contact. Support is needed for students and parents of students who have to self-isolate and for those who have concerns about the safety of daily testing.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah Denford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lauren Towler", + "author_inst": "University of Southampton" + }, + { + "author_name": "Behiye Ali", + "author_inst": "University of Bristol" + }, + { + "author_name": "Georgia Treneman-Evans", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rachael Bloomer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Tim E Peto", + "author_inst": "oxford university" + }, + { + "author_name": "Bernadette C Young", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.05.463205", "rel_title": "SARS-CoV-2 causes human BBB injury and neuroinflammation indirectly in a linked organ chip platform", @@ -576402,61 +578899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.04.21264513", - "rel_title": "Use of an EHR to inform an administrative data algorithm to categorize inpatient COVID-19 severity", - "rel_date": "2021-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264513", - "rel_abs": "STRUCTURED ABSTRACTO_ST_ABSImportanceC_ST_ABSAlgorithms for classification of inpatient COVID-19 severity are necessary for confounding control in studies using real-world data (RWD).\n\nObjectiveTo explore use of electronic health record (EHR) data to inform an administrative data algorithm for classification of supplemental oxygen or noninvasive ventilation (O2/NIV) and invasive mechanical ventilation (IMV) to assess disease severity in hospitalized COVID-19 patients.\n\nDesignIn this retrospective cohort study, we developed an initial procedure-based algorithm to identify O2/NIV, IMV, and NEITHER O2/NIV nor IMV in two inpatient RWD sources. We then expanded the algorithm to explore the impact of adding diagnoses indicative of clinical need for O2/NIV (hypoxia, hypoxemia) or IMV (acute respiratory distress syndrome) and O2-related patient vitals available in the EHR. Observed changes in severity categorization were used to augment the administrative algorithm.\n\nSettingOptum de-identified COVID-19 EHR data and HealthVerity claims and chargemaster data (March - August 2020).\n\nParticipantsAmong patients hospitalized with COVID-19 in each RWD source, our motivating example selected dexamethasone (DEX+) initiators and a random selection of patients who were non-initiators of a corticosteroid of interest (CSI-) matched on date of DEX initiation, age, sex, baseline comorbidity score, days since admission, and COVID-19 severity level (NEITHER, O2/NIV, IMV) on treatment index.\n\nMain Outcome and MeasuresInpatient COVID-19 severity was defined using the algorithms developed to classify respiratory support requirements among hospitalized COVID-19 patients (NEITHER, O2/NIV, IMV). Measures were reported as the treatment-specific distributions of patients in each severity level, and as observed changes in severity categorization between the initial procedure-based and expanded algorithms.\n\nResultsIn the administrative data cohort with 5,524 DEX+ and CSI- patient pairs matched using the initial procedure-based algorithm, 30% were categorized as O2/NIV, 5% as IMV, and 65% as NEITHER. Among patients assigned NEITHER via the initial algorithm, use of an expanded algorithm informed by the EHR-based algorithm shifted 54% DEX+ and 28% CSI- to O2/NIV, and 2% DEX+ and 1% CSI- to IMV. Among patients initially assigned O2/NIV, 7% DEX+ and 3% CSI- shifted to IMV.\n\nConclusions and RelevanceApplication of learnings from an EHR-based exploration to our administrative algorithm minimized treatment-differential misclassification of COVID-19 severity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elizabeth M Garry", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "Andrew R Weckstein", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "Kenneth Quinto", - "author_inst": "Office of Medical Policy, Center for Drug Evaluation and Research, U.S. Food and Drug Administration" - }, - { - "author_name": "Tamar Lasky", - "author_inst": "Office of the Commissioner, U.S. Food and Drug Administration" - }, - { - "author_name": "Aloka Chakravarty", - "author_inst": "Office of the Commissioner, U.S. Food and Drug Administration" - }, - { - "author_name": "Sandy Leonard", - "author_inst": "Partnerships and RWD, HealthVerity" - }, - { - "author_name": "Sarah E Vititoe", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "Imaani J Easthausen", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "Jeremy A Rassen", - "author_inst": "Aetion, Inc." - }, - { - "author_name": "Nicolle M Gatto", - "author_inst": "Aetion, Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.04.21264015", "rel_title": "Circulating proteins to predict adverse COVID-19 outcomes", @@ -577880,6 +580322,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.10.02.21264210", + "rel_title": "SARS-CoV-2 multi-variant graphene biosensor based on engineered dimeric ACE2 receptor", + "rel_date": "2021-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.02.21264210", + "rel_abs": "Fast, reliable and point-of-care systems to detect the SARS-CoV-2 infection are crucial to contain viral spreading and to adopt timely clinical treatments. Many of the rapid detection tests currently in use are based on antibodies that bind viral proteins1. However, newly appearing virus variants accumulate mutations in their RNA sequence and produce proteins, such as Spike, that may show reduced binding affinity to these diagnostic antibodies, resulting in less reliable tests and in the need for continuous update of the sensing systems2. Here we propose a graphene field-effect transistor (gFET) biosensor which exploits the key interaction between the Spike protein and the human ACE2 receptor. This interaction is one of the determinants of host infections and indeed recently evolved Spike variants were shown to increase affinity for ACE2 receptor3. Through extensive computational analyses we show that a chimeric ACE2-Fc construct mimics the ACE2 dimer, normally present on host cells membranes, better than its soluble truncated form. We demonstrate that ACE2-Fc functionalized gFET is effective for in vitro detection of Spike and outperforms the same chip functionalized with either a diagnostic antibody or the soluble ACE2. Our sensor is implemented in a portable, wireless, point-of-care device and successfully detected both alpha and gamma virus variants in patients clinical samples. As incomplete immunization, due to vaccine roll-out, may offer new selective grounds for antibody-escaping virus variants4, our biosensor opens to a class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Mattia D'Agostino", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Eleonora Pavoni", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Alice Romagnoli", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Chiara Ardiccioni", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Stefano Motta", + "author_inst": "Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy." + }, + { + "author_name": "Paolo Crippa", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Giorgio Biagetti", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Valentina Notarstefano", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Simone Barocci", + "author_inst": "Department of Clinical Pathology, ASUR Marche AV1, Urbino, PU, Italy." + }, + { + "author_name": "Brianna K Costabile", + "author_inst": "Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA." + }, + { + "author_name": "Gabriele Colasurdo", + "author_inst": "OMME GEARS, Falconara M.am, Zona Ind. CIAF, 60015, Ancona, Italy." + }, + { + "author_name": "Sara Caucci", + "author_inst": "Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy." + }, + { + "author_name": "Davide Mencarelli", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Claudio Turchetti", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Marco Farina", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Luca Pierantoni", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Anna La Teana", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Richard Al Hadi", + "author_inst": "Alcatera Inc, Los Angeles, CA 90024, USA." + }, + { + "author_name": "Mauro Chinappi", + "author_inst": "Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy." + }, + { + "author_name": "Emiliano Trucchi", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Filippo Mancia", + "author_inst": "Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA." + }, + { + "author_name": "Blasco Morozzo della Rocca", + "author_inst": "Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy." + }, + { + "author_name": "Ilda D'Annessa", + "author_inst": "Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, 20131, Milan, Italy." + }, + { + "author_name": "Daniele Di Marino", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.01.452232", "rel_title": "Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach", @@ -578312,89 +580865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.03.21264480", - "rel_title": "Clinical evaluation of a RT-LAMP SARS-CoV-2 test for the Point-Of-Care, rapid, low-cost, integrating sample solid phase extraction and on which reagents are lyophilized.", - "rel_date": "2021-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.03.21264480", - "rel_abs": "ObjectivesDetermine the sensitivity and specificity of a Point-Of-Care test ( COVIDISC) for SARS-COV2. The novelty of the test is to integrate, on the same (low-cost) compact plastic/paper device, solid phase RNA extraction and RT-LAMP amplification, all reagents being freeze-dried on it.\n\nMethodRetrospective study with a cohort of 99 patients characterized by real-time RT-PCR. The 37 positive naso-pharyngeal samples cover a broad range of viral loads (from 5 gc /{micro}L to 2 106 gc/ {micro}L of sample).\n\nResultsThe COVIDISC found 36 positives (out of 37 by IP4 RT-PCR protocols) and 63 negatives (out of 62 by RT-PCR).\n\nConclusionThe sensitivity of the COVIDISC, found in this 99-patient retrospective study, is 97% and the specificity 100%.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Etienne Coz", - "author_inst": "MMN, ESPCI, 6 rue Jean Calvin, Paris 5 , France" - }, - { - "author_name": "Pierre Garneret", - "author_inst": "MMN, CBI, ESPCI, 6 rue Jean Calvin, Paris 5 , France" - }, - { - "author_name": "Elian Martin", - "author_inst": "MMN, CBI, ESPCI, 6 rue Jean Calvin, Paris 5 , France" - }, - { - "author_name": "Debora Freitas do Nascimento", - "author_inst": "MMN, CBI, ESPCI, 6 rue Jean Calvin, Paris 5 , France" - }, - { - "author_name": "Alexandre Vilquin", - "author_inst": "Gulliver CNRS UMR 7083, PSL Research University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France" - }, - { - "author_name": "Damien Hoinard", - "author_inst": "CIBU, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Maxence Feher", - "author_inst": "CIBU, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Quentin Grassin", - "author_inst": "CIBU, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Jessica Vanhomwegen", - "author_inst": "CIBU, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Jean-Claude Manuguerra", - "author_inst": "CIBU, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Sudavip Mukherjee", - "author_inst": "Bioimage Analysis Unit, Institut Pasteur, 25-28 rue du Dr Roux, Paris 153" - }, - { - "author_name": "Jean-Christophe Olivo-Marin", - "author_inst": "Bioimage Analysis Unit, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Elodie Brient-Litzler", - "author_inst": "Innovation Office, Institut Pasteur, 25-28 rue du Dr Roux, Paris 15" - }, - { - "author_name": "Messaouda Merzoug", - "author_inst": "CMC Ambroise Pare, 25 Boulevard Victor Hugo, 92200 Neuilly sur Seine" - }, - { - "author_name": "elodie collin", - "author_inst": "Hopital Ballanger, Blvd Robert Ballanger, 93600 Aulnay-Sous-Bois" - }, - { - "author_name": "Patrick Tabeling", - "author_inst": "ESPCI" - }, - { - "author_name": "benjamin rossi", - "author_inst": "Hopital Ballanger, Blvd Robert Ballanger, 93600 Aulnay-Sous-Bois" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.03.21264492", "rel_title": "Non-pharmaceutical interventions and vaccinating school children required to contain SARS-CoV-2 Delta variant outbreaks in Australia: a modelling analysis", @@ -579466,6 +581936,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.01.21264412", + "rel_title": "Initial SARS-CoV-2 viral load is associated with disease severity: a retrospective cohort study", + "rel_date": "2021-10-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264412", + "rel_abs": "BackgroundWe aimed to assess the association between initial SARS-CoV-2 viral load and the subsequent hospital and intensive care unit (ICU) admission and overall survival.\n\nMethodsAll persons with a positive SARS-CoV-2 RT-PCR result from a combined nasopharyngeal (NP) and oropharyngeal (OP) swab (first samples from unique persons only) that was collected between March 17, 2020, and March 31, 2021, in Public Health testing facilities in the region Kennemerland, province of North Holland, the Netherlands were included. Data on hospital (and ICU) admission were collected from the two large teaching hospitals in the region Kennemerland.\n\nResultsIn total, 20,207 SARS-CoV-2 positive persons were included in this study, of whom 310 (1.5%) were hospitalized in a regional hospital within 30 days of their positive SARS-CoV-2 RT-PCR test. When persons were categorized in three SARS-CoV-2 viral load groups, the high viral load group (Cp < 25) was associated with an increased risk of hospitalization as compared to the low viral load group (Cp > 30) (ORadjusted [95%CI]: 1.57 [1.11-2.26], p-value=0.012), adjusted for age and sex. The same association was seen for ICU admission (ORadjusted [95%CI]: 7.06 [2.15-43.57], p-value=0.007). For a subset of 243 of the 310 hospitalized patients, the association of initial SARS-CoV-2 Cp-value with in-hospital mortality was analyzed. The initial SARS-CoV-2 Cp-value of the 17 patients who deceased in the hospital was significantly lower (indicating a higher viral load) compared to the 226 survivors: median Cp-value [IQR]: 22.7 [3.4] vs. 25.0 [5.2], OR[95%CI]: 0.81 [0.68-0.94], p-value = 0.010.\n\nConclusionsOur data show that higher initial SARS-CoV-2 viral load is associated with an increased risk of hospital admission, ICU admission, and in-hospital mortality. We believe that our findings emphasize the added value of reporting SARS-CoV-2 viral load based on Cp-values to identify persons who are at the highest risk of adverse outcomes such as hospital or ICU admission and who therefore may benefit from more intensive monitoring.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Dennis Souverein", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Karlijn van Stralen", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Steven van Lelyveld", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Claudia van Gemeren", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Milly Haverkort", + "author_inst": "Public Health Service Kennemerland" + }, + { + "author_name": "Dominic Snijders", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Robin Soetekouw", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Erik Kapteijns", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Evelien de Jong", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Gonneke Hermanides", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Sem Aronson", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Alex Wagemakers", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Sjoerd Euser", + "author_inst": "Regional Public Health Laboratory Kennemerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.01.21264428", "rel_title": "Risk factors for infection, predictors of severe disease and antibody response to COVID-19 in patients with rheumatic diseases in Portugal - a multicentre, nationwide study", @@ -580230,25 +582767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.29.21264323", - "rel_title": "Importation Risk Stratification for COVID19 using Quantitative Serology", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264323", - "rel_abs": "Recent work (Khoury et al.,Nature Medicine 2021, 27 (7), 1205-1211) has shown that measurement of IgG antibody concentration in blood correlates well with vaccine efficacy. The present communication builds on this work and considers the probability of infection given immunity, taking into account the distribution across the population of antibody concentration in vaccinated or convalescent people. The model is consistent with the observed rates of breakthrough infection following vaccination or previous infection. The model is then developed to consider the use of quantitative measurement of antibody concentration on arrival as an aid to risk stratification of travellers. The model indicates that such a measurement could significantly decrease the quarantine time required to achieve a given level of importation risk.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "David Edward Williams", - "author_inst": "University of Auckland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.29.21264315", "rel_title": "Characteristics associated with COVID-19 vaccination status among staff and faculty of a large, diverse University in Los Angeles.", @@ -581188,6 +583706,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.01.21264382", + "rel_title": "COVID-19 Pandemic Response in a Migrant Farmworker Community: Excess Mortality, Testing Access and Contact Tracing in Immokalee, Florida", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264382", + "rel_abs": "IntroductionWe aim to estimate the impact of COVID-19 in Immokalee, FL and assess community experiences with workplace conditions, access to testing, sources of information, and contact tracing to inform and strengthen local public health sector efforts in reaching and providing high-quality care to the community.\n\nMethodsWe conducted a descriptive analysis of data on COVID-19 deaths for Collier County from May-August 2020. We surveyed a cross-sectional, randomized representative sample of 318 adults living in Immokalee from March-November 2020 to assess socio-demographics, sources of information, ability to follow guidelines, and experiences with local programs. Results were compared across language groups.\n\nResultsAverage excess mortality in Collier County was 108%. The majority surveyed in Immokalee had socio-demographic factors associated with higher COVID risk. Non-English speakers had higher workplace risk due to less ability to work from home. Haitian Creole speakers were less likely to be tested, though all participants were willing to get symptomatic testing and quarantine. Those participants who tested positive or had COVID-19 exposures had low engagement with the contact tracing program, and Spanish-speakers reported lower quality of contact tracing than English speakers.\n\nConclusionsThe community of Immokalee, FL is a vulnerable population that suffered disproportionate deaths from COVID-19. This study reveals language inequities in COVID testing and contact tracing should be targeted in future pandemic response in Immokalee and other migrant farmworker communities.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Neha Limaye", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Brennan Ninesling", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Frantzso Marcelin", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Cody Nolan", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Walter Sobba", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Matthew Hing", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Emily Ptaszek", + "author_inst": "Healthcare Network of Southwest Florida" + }, + { + "author_name": "Fernet Leandre", + "author_inst": "Partners in Health" + }, + { + "author_name": "Daniel Palazuelos", + "author_inst": "Brigham and Women's Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.01.462460", "rel_title": "ZBP1 induces inflammatory signaling via RIPK3 and promotes SARS-CoV-2-induced cytokine expression", @@ -582004,157 +584573,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.30.462420", - "rel_title": "SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies", - "rel_date": "2021-09-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.30.462420", - "rel_abs": "SARS-CoV-2 Beta variant of concern (VOC) resists neutralization by major classes of antibodies from non-VOC COVID-19 patients and vaccinated individuals. Here, serum of Beta variant infected patients revealed reduced cross-neutralization of non-VOC virus. From these patients, we isolated Beta-specific and cross-reactive receptor-binding domain (RBD) antibodies. The Beta-specificity results from recruitment of novel VOC-specific clonotypes and accommodation of VOC-defining amino acids into a major non-VOC antibody class that is normally sensitive to these mutations. The Beta-elicited cross-reactive antibodies share genetic and structural features with non-VOC-elicited antibodies, including a public VH1-58 clonotype targeting the RBD ridge independent of VOC mutations. These findings advance our understanding of the antibody response to SARS-CoV-2 shaped by antigenic drift with implications for design of next-generation vaccines and therapeutics.\n\nOne sentence summarySARS-CoV-2 Beta variant elicits lineage-specific antibodies and antibodies with neutralizing breadth against wild-type virus and VOCs.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "S Momsen Reincke", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Meng Yuan", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" - }, - { - "author_name": "Hans-Christian Kornau", - "author_inst": "Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t B" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Virology, Berlin, Germany and " - }, - { - "author_name": "Scott van Hoof", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Elisa S\u00e1nchez-Sendin", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Melanie Ramberger", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Wenli Yu", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" - }, - { - "author_name": "Yuanzi Hua", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" - }, - { - "author_name": "Henry Tien", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" - }, - { - "author_name": "Marie Luisa Schmidt", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Virology, Berlin, Germany and " - }, - { - "author_name": "Tatjana Schwarz", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Virology, Berlin, Germany and " - }, - { - "author_name": "Lara Maria Jeworowski", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Virology, Berlin, Germany and " - }, - { - "author_name": "Sarah E Brandl", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Helle Foverskov Rasmussen", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Marie A Homeyer", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Laura St\u00f6ffler", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Martin Barner", - "author_inst": "Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany" - }, - { - "author_name": "D\u00e9sir\u00e9e Kunkel", - "author_inst": "Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin, Flow & Mass Cytometry Core Facility, Berlin, Germany" - }, - { - "author_name": "Shufan Huo", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Johannes Horler", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Niels von Wardenburg", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - }, - { - "author_name": "Inge Kroidl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany" - }, - { - "author_name": "Tabea M Eser", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany" - }, - { - "author_name": "Andreas Wieser", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany" - }, - { - "author_name": "Christof Geldmacher", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany" - }, - { - "author_name": "Michael Hoelscher", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany" - }, - { - "author_name": "Hannes G\u00e4nzer", - "author_inst": "Department of Internal Medicine, BKH Schwaz, Schwaz, Austria" - }, - { - "author_name": "G\u00fcnter Weiss", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Dietmar Schmitz", - "author_inst": "Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t B" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Virology, Berlin, Germany and " - }, - { - "author_name": "Harald Pr\u00fcss", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Virology, Berlin, Germany and " - }, - { - "author_name": "Ian A Wilson", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA" - }, - { - "author_name": "Jakob Kreye", - "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Neurology and Experimental Ne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.09.30.462514", "rel_title": "Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters", @@ -583450,6 +585868,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.27.21264174", + "rel_title": "Counter-intuitive COVID-19 Trajectories - Explanations, Early Warning Indicator and Mitigation Strategies", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264174", + "rel_abs": "The COVID-19 trajectories worldwide have shown several surprising features which are outside the purview of classical epidemiological models. These include (a) almost constant and low daily case rates over extended periods of time, (b) sudden waves emerging from the above solution despite no or minimal change in the level of non-pharmaceutical interventions (NPI), and (c) reduction or flattening of case counts even after relaxation of NPI. To explain these phenomena, we add contact tracing to our recently developed cluster seeding and transmission (CST) model, which is predicated on heterogeneous rather than homogeneous mixing of people in society. With this addition, we find no fewer than four effects which make prediction of epidemic trajectories uncertain. These are (a) cryptogenic instability, where a small increase in population-averaged contact rate causes a large increase in cases, (b) critical mass effect, where a wave can manifest after weeks of quiescence with no change in parameter values, (c) knife-edge effect, where a small change in parameter across a critical value can cause a huge change in the response of the system, and (d) hysteresis effect, where the timing and not just the strength of a particular NPI determines the subsequent evolution of the epidemic. Despite these effects however, it is a robust conclusion that a good contact tracing program can effectively substitute for much more invasive measures. We further find that the contact tracing capacity ratio - a metric of the stress to which the tracers are subject - can act as a reliable early warning indicator of an imminent epidemic wave. Extensive simulations demonstrate that whenever there is a drop in capacity ratio during a period of low daily infections, there is a very high probability of the case counts rising significantly in the immediate future.\n\nAuthor summaryClose to two years into the pandemic, the trajectories of COVID-19 in different places and at different times have shown wild variations and confounded modeling and forecasting efforts. Our new mathematical model can help to explain these variations. Some solutions of our model are non-standard but realistic. For example, we find an epidemic curve where daily cases remain on a plateau for a long time before suddenly exploding into a wave, despite interventions remaining constant throughout. We also find solutions showing that a specific intervention, for example capacity reduction at public gatherings, is very effective if implemented early on in a wave but useless if implemented a little later. Our proposed early warning indicator can be a game-changer for epidemic forecasting and model-based intervention strategies. Current forecasting algorithms have the weakest performance at the inflection points where there is an abrupt change in trend in the daily infection rates. The early warning indicator can give us advance notice of an approaching inflection point, and enable the authorities to take preventive measures before a wave actually arrives. Our results indicate that close communication between contact tracing personnel and public health authorities can achieve synergistic mitigation of the pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Mohit Manoj Sharma", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.29.21264261", "rel_title": "World Science against COVID-19: Gender and Geographical Distribution of Research.", @@ -584422,45 +586863,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.27.21264225", - "rel_title": "Impact of long-COVID on health-related quality of life in Japanese COVID-19 patients", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264225", - "rel_abs": "BackgroundThe empirical basis for a quantitative assessment of the disease burden imposed by long-COVID is currently scant. We aimed to assess the disease burden caused by long-COVID in Japan.\n\nMethodsWe conducted a cross sectional self-report questionnaire survey. The questionnaire was mailed to 530 eligible patients, who were recovered from acute COVID-19 in April 2021. Answers were classified into two groups; participants who have no symptom and those who have any ongoing symptoms that lasted longer than four weeks at the time of the survey. We compared health-related quality of life scores estimated by the EQ-5D-3L questionnaire between these two groups after adjusting basic characteristics of the participants by propensity score matching.\n\nResults349 participants reported no symptoms and 108 reported any symptoms at the time of the survey. The participants who reported any symptoms showed a lower value on a Visual Analogue Scale (median 70 [IQR 60-80]) and on the EQ-5D-3L (median 0.81 [IQR 0.77-1.0]) than those reporting no symptoms (median 85 [IQR 75-90] and 1.0 [IQR 1.0-1.0], respectively). After adjusting for background characteristics, these trends did not change substantially (Visual Analog Scale: median 70 [IQR 60-80] vs 80 [IQR 77-90], EQ-5D-3L: median 0.81 [IQR 0.76-1.0] vs 1.0 [IQR 1.0-1.0]).\n\nConclusionsDue to their long duration, long-COVID symptoms represent a substantial disease burden expressed in impact on health-related quality of life.\n\nTrial registrationNot applicable.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shinya Tsuzuki", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Yusuke Miyazato", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Mari Terada", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Shinichiro Morioka", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Norio Ohmagari", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Philippe Beutels", - "author_inst": "University of Antwerp" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.27.21264219", "rel_title": "Mucosal antibody response to SARS-CoV-2 in paediatric and adult patients: a longitudinal study", @@ -585592,6 +587994,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.27.21264044", + "rel_title": "Sub-Saharan African Countries' COVID-19 Research: An analysis of the External and Internal Contributions, Collaboration Patterns and Funding Sources", + "rel_date": "2021-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264044", + "rel_abs": "This study aims at providing some evidence-based insight into Sub-Saharan Africas first eighteen months of COVID-19 research by evaluating its research contributions, patterns of collaboration, and funding sources. Eighteen months (2020 January 1-2021 June 30) COVID-19 publication data of 46 Sub-Saharan African countries was collected from Scopus for analysis. Country of affiliation of the authors and funding agencies data was analyzed to understand country contributions, collaboration pattern and funding sources. USA (23.08%) and the UK (19.63%), the top two external contributors, collaborated with Sub-Saharan African countries about three times more than other countries. Collaborative papers between Sub-Saharan African countries - without contributions from outside the region-made up less than five percent of the sample, whereas over 50% of the papers were written in collaboration with researchers from outside the region. Organizations that are in USA and the UK funded 45% of all the COVID-19 research from Sub-Saharan Africa. 53.44% of all the funding from Sub-Saharan African countries came from South African organizations. This study provides evidence that pan-African COVID-19 research collaboration is low, perhaps due to poor funding and lack of institutional support within Sub-Saharan Africa. This mirrors the collaborative features of science in Sub-Saharan Africa before the COVID-19 pandemic. The high volume of international collaboration during the pandemic is a good development. There is also a strong need to forge more robust pan-African research collaboration networks, through funding from Africas national and regional government organizations, with the specific objective of meeting local COVID-19 and other healthcare needs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Toluwase Victor Asubiaro", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Hafsah Shaik", + "author_inst": "Independent Researcher" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.27.21264130", "rel_title": "Effectiveness of the mRNA BNT162b2 vaccine against SARS-CoV-2 severe infections in the Israeli over 60 population: a temporal analysis done by using the national surveillance data.", @@ -586140,45 +588565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.26.21264142", - "rel_title": "Non-Pharmaceutical Interventions and COVID-19 Burden in the United States", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264142", - "rel_abs": "BackgroundNon-pharmaceutical interventions (NPIs) are mitigation strategies used to reduce the spread of transmissible diseases. The relative effectiveness of specific NPIs remains uncertain.\n\nMethodsWe used state-level Coronavirus disease 2019 (COVID-19) case and mortality data between January 19, 2020 and March 7, 2021 to model NPI policy effectiveness. Empirically derived breakpoints in case and mortality velocities were used to identify periods of stable, decreasing, or increasing COVID-19 burden. The associations between NPI adoption and subsequent decreases in case or death velocities were estimated using generalized linear models accounting for weekly variability shared across states. State-level NPI policies included: stay at home order, indoor public gathering ban (mild >10 or severe [≤]10), indoor restaurant dining ban, and public mask mandate.\n\nResults28,602,830 cases and 511,899 deaths were recorded. The odds of a decrease in COVID-19 case velocity were significantly elevated for stay at home (OR 2.02, 95% CI 1.63-2.52), indoor dining ban (OR 1.62, 95% CI 1.25-2.10), public mask mandate (OR 2.18, 95% CI 1.47-3.23), and severe gathering ban (OR 1.68, 95% CI 1.31-2.16). In mutually adjusted models, odds remained elevated for stay at home (AOR 1.47, 95% CI 1.04-2.07) and public mask mandate (AOR = 2.27, 95% CI 1.51-3.41). Stay at home (OR 2.00, 95% CI 1.53-2.62; AOR 1.89, 95% CI 1.25-2.87) was also associated with greater likelihood of decrease in death velocity in unadjusted and adjusted models.\n\nConclusionsNPIs employed in the U.S. during the COVID-19 pandemic, most significantly stay at home orders, were associated with decreased COVID-19 burden.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Michael Ahlers", - "author_inst": "UCLA Medical Center" - }, - { - "author_name": "Hilary Aralis", - "author_inst": "Department of Biostatistics, UCLA Fielding School of Public Health" - }, - { - "author_name": "Wilson Tang", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Jeremy Sussman", - "author_inst": "Department of Internal Medicine, University of Michigan" - }, - { - "author_name": "Gregg Fonarow", - "author_inst": "Division of Cardiology, David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Boback Ziaeian", - "author_inst": "Division of Cardiology, David Geffen School of Medicine at UCLA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.27.21264000", "rel_title": "Pre-pandemic SARS-CoV-2 serological reactivity in rural malaria-experienced Cambodians", @@ -587142,6 +589528,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.25.21264082", + "rel_title": "Contact surveys reveal heterogeneities in age-group contributions to SARS-CoV-2 dynamics in the United States", + "rel_date": "2021-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.25.21264082", + "rel_abs": "SARS-CoV-2 is spread primarily through person-to-person contacts. Quantifying population contact rates is important for understanding the impact of physical distancing policies and for modeling COVID-19, but contact patterns have changed substantially over time due to shifting policies and behaviors. There are surprisingly few empirical estimates of age-structured contact rates in the United States both before and throughout the COVID-19 pandemic that capture these changes. Here, we use data from six waves of the Berkeley Interpersonal Contact Survey (BICS), which collected detailed contact data between March 22, 2020 and February 15, 2021 across six metropolitan designated market areas (DMA) in the United States. Contact rates were low across all six DMAs at the start of the pandemic. We find steady increases in the mean and median number of contacts across these localities over time, as well as a greater proportion of respondents reporting a high number of contacts. We also find that young adults between ages 18 and 34 reported more contacts on average compared to other age groups. The 65 and older age group consistently reported low levels of contact throughout the study period. To understand the impact of these changing contact patterns, we simulate COVID-19 dynamics in each DMA using an age-structured mechanistic model. We compare results from models that use BICS contact rate estimates versus commonly used alternative contact rate sources. We find that simulations parameterized with BICS estimates give insight into time-varying changes in relative incidence by age group that are not captured in the absence of these frequently updated estimates. We also find that simulation results based on BICS estimates closely match observed data on the age distribution of cases, and changes in these distributions over time. Together these findings highlight the role of different age groups in driving and sustaining SARS-CoV-2 transmission in the U.S. We also show the utility of repeated contact surveys in revealing heterogeneities in the epidemiology of COVID-19 across localities in the United States.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Taylor Chin", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Dennis M. Feehan", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Caroline O. Buckee", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Ayesha S. Mahmud", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.26.21264145", "rel_title": "Racial and ethnic inequalities in COVID-19 mortality within carceral settings: An analysis of Texas prisons and jails", @@ -587978,93 +590395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.09.24.21263996", - "rel_title": "Acquired peripheral nerve injuries associated with severe COVID-19", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.24.21263996", - "rel_abs": "We diagnosed 66 peripheral nerve injuries in 34 patients who survived severe COVID-19. We combine our latest data with published case series re-analyzed here (117 nerve injuries; 58 patients) to provide a comprehensive accounting of lesion sites. The most common are ulnar (25.1%), common fibular (15.8%), sciatic (13.1%), median (9.8%), brachial plexus (8.7%) and radial (8.2%) nerves at sites known to be vulnerable to mechanical loading. Protection of peripheral nerves should be prioritized in the care of COVID-19 patients. To this end, we report proof of concept data of a wearable, wireless pressure sensor to provide real time monitoring in the intensive care unit setting.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Colin K. Franz", - "author_inst": "Shirley Ryan AbilityLab" - }, - { - "author_name": "Nikhil K. Murthy", - "author_inst": "Northwestern University" - }, - { - "author_name": "George Ross Malik", - "author_inst": "Hospital for Special Surgery" - }, - { - "author_name": "Jean W. Kwak", - "author_inst": "Northwestern University" - }, - { - "author_name": "Dom D'Andrea", - "author_inst": "Shirley Ryan AbilityLab" - }, - { - "author_name": "Alexis R. Wolfe", - "author_inst": "Northwestern University" - }, - { - "author_name": "Ellen Farr", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Melanie A. Stearns", - "author_inst": "Marionjoy Rehabilitation Hospital" - }, - { - "author_name": "Swati Deshmukh", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jinny O. Tavee", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Fang Sun", - "author_inst": "Northwestern University" - }, - { - "author_name": "Kevin N. Swong", - "author_inst": "Northwestern University" - }, - { - "author_name": "Leslie Rydberg", - "author_inst": "Shirley Ryan AbilityLab" - }, - { - "author_name": "Ronald James Cotton", - "author_inst": "Shirley Ryan AbilityLab" - }, - { - "author_name": "Lisa F. Wolfe", - "author_inst": "Northwestern University" - }, - { - "author_name": "James M. Walter", - "author_inst": "Northwestern University" - }, - { - "author_name": "John M. Coleman III", - "author_inst": "Northwestern University" - }, - { - "author_name": "John A. Rogers", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.09.24.21263853", "rel_title": "Multi-omics approach identifies novel age-, time- and treatment-related immunopathological signatures in MIS-C and pediatric COVID-19", @@ -589276,6 +591606,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.23.21264014", + "rel_title": "Neutralizing efficacy of vaccines against the SARS-CoV-2 Mu variant", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21264014", + "rel_abs": "The rise of mutant strains of SARS-CoV-2 poses an additional problem to the existing pandemic of COVID-19. There are rising concerns about the Mu variant which can escape humoral immunity acquired from infections from previous strains or vaccines. We examined the neutralizing efficacy of the BNT162b2 mRNA vaccine against the Mu variant and report that the vaccine has 76% neutralizing effectiveness against the Mu compared to 96% with the original strain. We also show that Mu, similar to the Delta variant, causes cell-to-cell fusion which can be an additional factor for the variant to escape vaccine-mediated humoral immunity. Despite the rise in vaccine escape strains, the vaccine still possesses adequate ability to neutralize majority of the mutants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University School of Medicine" + }, + { + "author_name": "Sundararaj Stanleyraj Jeremiah", + "author_inst": "Yokohama City University School of Medicine" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University Hospital" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.21.21263902", "rel_title": "Quantification and prognostic significance of interferon-\u03b3 secreting SARS-CoV-2 responsive T cells in hospitalised patients with acute COVID-19", @@ -589888,45 +592249,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.09.26.21263691", - "rel_title": "SARS-CoV-2 vaccines breakthrough infection hospitalizations after one dose in Libya: cohort study", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21263691", - "rel_abs": "SARS-CoV-2 infection is widely spread over people, from youth to the elderly. Vaccination against SARS-CoV-2 is an important preventive measurement to help end the SARS-CoV-2 pandemic. From 30 April to 15 July, we collected the number of people infected with SARS-COV-2 and the mortality rate from daily reports issued by the National Center for Disease Control of Libya (NCDC). Approximately 445000 doses have been administered in Libya since 10 April, and 5 thousand doses are now being administered during this period on a daily basis. To estimate the rate of breakthrough vaccine infection of the SARS-COV-2 in Libya. We found that one dose of the three different types of vaccines had decreased the virus transmission across people and mortality rate until 10 weeks after the first dose. This study highlights the dramatic success of the early months of the nations coronavirus vaccines rollout.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mohamed Hadi Mohamed Abdelhamid", - "author_inst": "Biotechnology Research Center" - }, - { - "author_name": "Iman Amin Al msellati", - "author_inst": "Primary Health Care - NCDC" - }, - { - "author_name": "Badereddin B Annajar", - "author_inst": "Department of Public Health, Faculty of Medical Technology, University of Tripoli, Tripoli 13662, Libya." - }, - { - "author_name": "Alaa Hadi Abdelhamid", - "author_inst": "Department of Cardiology, Tripoli University Hospital, Tripoli, Libya" - }, - { - "author_name": "Hafsa alemam", - "author_inst": "Department of Environment, Biotechnology Research Center (BTRC), Tripoli - Libya" - }, - { - "author_name": "Mohammed Eltikar", - "author_inst": "National Center of Disease Control (NCDC), Tripoli - Libya." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.23.21264032", "rel_title": "Modeling the transmission of the SARS-CoV-2 delta variant in a partially vaccinated population", @@ -590994,6 +593316,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.23.461605", + "rel_title": "Apixaban, an orally available anticoagulant, inhibits SARS-CoV-2 replication by targeting its major protease in a non-competitive way", + "rel_date": "2021-09-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.23.461605", + "rel_abs": "Anticoagulants are associated with clinical benefit against the 2019 coronavirus disease (COVID-19), preventing COVID-19 associated coagulopathy. Blood coagulation factor Xa (FXa) and SARS-CoV-2 major protease (Mpro) share over 80% homology at the three-dimensional protein level. Thus, it is worth interrogating whether there is crosstalk between inhibitors and substrates between these enzymes. Here, we found that the clinically-approved FXa inhibitor apixaban targets SARS-CoV-2 Mpro with a 21-fold higher potency than boceprevir (GC376). Apixaban displayed a non-competitive mechanism of inhibition towards Mpro, since it targets the enzyme/substrate complex and the allosteric site onto the viral protease. Enzymatic assays were further validated in infected Calu-3 cells, which reveal that apixaban decreases the production of infectious viral particles in a dose-dependent manner, with an inhibitory potency in the micromolar range. Our results are in line with the proposed early use of anticoagulants, including FXa inhibitors, to improve clinical outcome of COVID-19 patients. In this context, apixaban may display a dual mechanism of action by targeting FXa to prevent coagulopathy and, at some level, SARS-CoV-2 Mpro.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Otavio Augusto Chaves", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Carolina Q. Sacramento", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Natalia Fintelman-Rodrigues", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Jairo Ramos Temerozo", + "author_inst": "Oswaldo Cruz Institute" + }, + { + "author_name": "Filipe Pereira-Dutra", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Daniella M. Mizurini", + "author_inst": "UFRJ" + }, + { + "author_name": "Robson Q. Monteiro", + "author_inst": "UFRJ" + }, + { + "author_name": "Leonardo Vazquez", + "author_inst": "Fiocruz" + }, + { + "author_name": "Patricia T. Bozza", + "author_inst": "Lab Imunofarmacologia, Instituto Oswaldo Cruz, FIOCRUZ" + }, + { + "author_name": "Hugo Caire Castro-Faria-Neto", + "author_inst": "Fiocruz" + }, + { + "author_name": "Thiago Moreno L. Souza", + "author_inst": "Oswaldo Cruz Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.23.21262822", "rel_title": "Plasma S-Adenosylmethionine is Associated with Lung Injury in COVID-19", @@ -591846,29 +594227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.20.21263823", - "rel_title": "Effects of testing and vaccination levels on the dynamics of the COVID-19 pandemic and the prospects for its termination", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263823", - "rel_abs": "A simple statistical analysis of the accumulated and daily numbers of new COVID-19 cases and deaths per capita was performed with the use of recent datasets for European and some other countries and regions. It was shown that vaccination can significantly reduce the likelihood of deaths. However, existing vaccines do not prevent new infections, and vaccinated individuals can spread the infection as intensely as unvaccinated ones. Therefore, it is too early to lift quarantine restrictions in Europe and most other countries. The constant appearance of new cases due to re-infection increases the likelihood of new coronavirus strains, including very dangerous. As existing vaccines are not able to prevent this, it remains to increase the number of tests per registered case. If the critical value of 520 is exceeded, one can hope to stop the occurrence of new cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Igor Nesteruk", - "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" - }, - { - "author_name": "Oleksii Rodionov", - "author_inst": "Private consulting office, Kyiv, Ukraine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.21.21263568", "rel_title": "Risk Factors for Low Humoral Response to BNT-162b2 In Hemodialysis Patients", @@ -592704,6 +595062,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.09.18.21263773", + "rel_title": "COVID-19 Acceleration and Vaccine Status in France - August 2021", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263773", + "rel_abs": "ObjectivesThis note provides an assessment of COVID-19 acceleration among groups with different vaccine status in France.\n\nMethodsWe assess viral acceleration using a novel indicator introduced in Baunez et al. (2021). The acceleration index relates the percentage change of tests that have been performed on a given day to the percentage change in the associated positive cases that same day. We compare viral acceleration among vaccinated and unvaccinated individuals in France over the period May 31st - August 29, 2021.\n\nResultsOnce the state of the epidemic within each groups is accounted for, it turns out that viral acceleration has since mid-July converged to similar levels among vaccinated and unvaccinated individuals in France, even though viral speed is larger for the latter group compared to the former.\n\nConclusionOur results call for an increasing testing effort for both vaccinated and unvaccinated individuals, in view of the fact that viral circulation is currently accelerating at similar levels for both groups in France.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christelle Baunez", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Mickael Degoulet", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille School of Economics" + }, + { + "author_name": "Patrick Pintus", + "author_inst": "Aix-Marseille University and CNRS" + }, + { + "author_name": "Miriam Teschl", + "author_inst": "Aix-Marseille School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.09.19.21262487", "rel_title": "Genomic analysis of SARS-CoV-2 breakthrough infections from Varanasi, India", @@ -593492,33 +595885,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.09.15.21263653", - "rel_title": "Toward Using Twitter Data to Monitor Covid-19 Vaccine Safety in Pregnancy", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263653", - "rel_abs": "BackgroundCoronavirus Disease 2019 (Covid-19) during pregnancy is associated with an increased risk of maternal death, intensive care unit (ICU) admission, and preterm birth; however, many people who are pregnant refuse to receive Covid-19 vaccination because of a lack of safety data.\n\nObjectiveThe objective of this preliminary study was to assess whether we could identify (1) users who have reported on Twitter that they received Covid-19 vaccination during pregnancy or the periconception period, and (2) reports of their pregnancy outcomes.\n\nMethodsWe searched for reports of Covid-19 vaccination in a large collection of tweets posted by users who have announced their pregnancy on Twitter. To help determine if users were vaccinated during pregnancy, we drew upon a natural language processing (NLP) tool that estimates the timeframe of the prenatal period. For users who posted tweets with a timestamp indicating they were vaccinated during pregnancy, we drew upon additional NLP tools to help identify tweets that report their pregnancy outcomes.\n\nResultsUpon manually verifying the content of tweets detected automatically, we identified 150 users who reported on Twitter that they received at least one dose of Covid-19 vaccination during pregnancy or the periconception period. Among the 60 completed pregnancies, we manually verified at least one reported outcome for 45 (75%) of them.\n\nConclusionsGiven the limited availability of data on Covid-19 vaccine safety in pregnancy, Twitter can be a complementary resource for potentially increasing the acceptance of Covid-19 vaccination in pregnant populations. Directions for future work include developing machine learning algorithms to detect a larger number of users for observational studies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ari Z Klein", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Karen O'Connor", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Graciela Gonzalez-Hernandez", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.09.20.21263794", "rel_title": "Development and evaluation of a machine learning-based in-hospital COvid-19 Disease Outcome Predictor (CODOP): a multicontinental retrospective study", @@ -594670,6 +597036,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.09.16.21263576", + "rel_title": "Impact of prior SARS-CoV-2 infection on post-vaccination SARS-CoV-2 spike IgG antibodies in a longitudinal cohort of healthcare workers", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263576", + "rel_abs": "Waning serum antibodies against SARS-CoV-2 have sparked discussions about long-term immunity and need for vaccine boosters. We examined SARS-CoV-2 spike IgG antibodies in a longitudinal cohort, comparing antibody decay in individuals who received an mRNA SARS-CoV-2 vaccine, with and without prior SARS-CoV-2 infection. We completed a longitudinal cohort of healthcare workers (HWs) between June 2020 and September 2021. HWs were included if they had a serum sample collected after SARS-CoV-2 infection and/or a serum sample collected [≥] 14 days after second dose of an mRNA SARS-CoV-2 vaccine. Linear regression models adjusting for vaccine type, age, and sex were used to compare post-vaccination antibody levels between 1) HWs with and without prior SARS-CoV-2 infection and 2) HWs with prior SARS-CoV-2 infection [≤] 90 days and > 90 days prior to first vaccine. Serum was collected from 98 HWs after SARS-CoV-2 infection and before vaccine, and 1960 HWs [≥] 14 days following second vaccine dose. Serum spike antibody levels were higher after vaccination than after natural infection. Compared to SARS-CoV-2 naive individuals, those with prior infection maintained higher post-vaccination mean spike IgG values at 1, 3, and 6 months, after adjusting for age, sex, and vaccine type. Individuals with PCR-confirmed infection > 90 days before vaccination had higher post-vaccination antibody levels than individuals infected [≤] 90 days before vaccination. Individuals with three exposures to spike protein maintain the highest antibody levels particularly when first and second exposures were greater than 90 days apart. A booster dose provides a third exposure and may similarly induce a more durable antibody response.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Diana Zhong", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shaoming Xiao", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Amanda K Debes", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Emily R Egbert", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Patrizio Caturegli", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Elizabeth Colantuoni", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Aaron M Milstone", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.20.21263875", "rel_title": "Comparative single-dose mRNA and ChAdOx1 vaccine effectiveness against SARS-CoV-2, including early variants of concern: a test-negative design, British Columbia, Canada", @@ -595151,81 +597560,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.14.21263556", - "rel_title": "Immunogenicity and safety of an inactivated SARS-CoV-2 vaccine in people living with HIV-1", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263556", - "rel_abs": "BackgroundIt has been proven that inactivated COVID-19 vaccines are safe and effective in general population with intact immunity. However, their safety and immunogenicity have not been demonstrated in people living with HIV (PLWH).\n\nMethods42 HIV-1 infected individuals who were stable on cART and 28 healthy individuals were enrolled in this study. Two doses of an inactivated COVID-19 vaccine (BIBP-CorV) were given 4 weeks apart. The safety and reactogenicity of the vaccine were evaluated by observing clinical adverse events and solicited local and systemic reactions. Humoral responses were measured by anti-spike IgG ELISA and surrogate neutralization assays. Cell-mediated immune responses and vaccine induced T cell activation were measured by flow cytometry.\n\nFindingsAll the HIV-1 infected participants had a CD4+ T cell count of above 200 cells/L both at baseline and 4 weeks after vaccination. No solicited adverse reaction was observed among all participants. Similar binding antibody, neutralizing antibody and S protein specific T cell responses were elicited in PLWH and healthy individuals. Further analyses showed that PLWH with low baseline CD4+/CD8+ T cell ratios (<0{middle dot}6) generated lower antibody responses after vaccination than PLWH with medium (0{middle dot}6[~]1{middle dot}0) or high ([≥]1{middle dot}0) baseline CD4+/CD8+ T cell ratios (P<0{middle dot}01). The CD3+, CD4+ and CD8+ T cell counts of PLWH decreased significantly after vaccination, but it did not lead to any adverse clinical manifestation. Moreover, we found that the general burden of HIV-1 among the PLWH cohort decreased significantly (P=0{middle dot}0192) after vaccination. And the alteration of HIV-1 viral load was not significantly associated with the vaccine induced CD4+ T cell activation.\n\nInterpretationOur data demonstrate that the inactivated COVID-19 vaccine is safe and immunogenic in PLWH who are stable on cART with unsuppressed CD4 counts.\n\nFundingThis work was funded by the National Natural Science Foundation of China (Grant No. 81971559, 82041010).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe safety and efficacy of inactivated COVID-19 vaccines have been validated in general population with intact immunity. However, their safety and immunogenicity have not been demonstrated in people living with HIV (PLWH).\n\nAdded value of this studyOur study provides the first evidence to show humoral and cellular immune responses to an inactivated vaccine in PLWH who have been stable on cART with good CD4 cell counts. We found that participants with HIV-1 generated antibody and T cell responses comparable with those of healthy individuals after two-dose vaccination. The baseline CD4/CD8 ratios while not the absolute CD4+ T cell counts were shown to be associated with the magnitudes of vaccine induced antibody responses. Moreover, we showed that the vaccine induced T cell activation did not increase the viral burden in PLWH on cART. On the contrary, the levels of plasma HIV-1 RNA decreased among a significant percentage of PLWH.\n\nImplications of all the available evidenceOur data demonstrate that the inactivated COVID-19 vaccine is safe and immunogenic in PLWH who are stable on cART with unsuppressed CD4 counts and indicate that this vaccine might be protective and efficacious against COVID-19 for people with HIV.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Yanmeng Feng", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Yifan Zhang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Zhangyufan He", - "author_inst": "Fudan University, Huashan hospital" - }, - { - "author_name": "Haojie Huang", - "author_inst": "Wuhan Pioneer Social Work Service Center" - }, - { - "author_name": "Xiangxiang Tian", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Gang Wang", - "author_inst": "Shanghai Public Health Clinical Center" - }, - { - "author_name": "Daihong Chen", - "author_inst": "Shanghai Public Health Clinical Center" - }, - { - "author_name": "Yanqin Ren", - "author_inst": "Fudan University, Huashan Hospital" - }, - { - "author_name": "Liqiu Jia", - "author_inst": "Fudan University, Huashan Hospital" - }, - { - "author_name": "Wanhai Wang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Jing Wu", - "author_inst": "Huashan hospital, Fudan University" - }, - { - "author_name": "Lingyun Shao", - "author_inst": "Fudan University, Huashan Hospital" - }, - { - "author_name": "Wenhong Zhang", - "author_inst": "Fudan University, Huashan hospital" - }, - { - "author_name": "Heng Tang", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Yanmin Wan", - "author_inst": "Fudan University, Huashan hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2021.09.15.21263597", "rel_title": "High- Versus Low-Dose Dexamethasone for the Treatment of COVID-19-related Acute Respiratory Distress Syndrome: A Multicenter and Randomized Open-label Clinical Trial", @@ -596133,6 +598467,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.17.21263723", + "rel_title": "Optimized Post-Vaccination Strategies and Preventative Measures for SARS-CoV-2", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263723", + "rel_abs": "IntroductionSince March of 2020, over 210 million SARS-CoV-2 cases have been reported and roughly five billion doses of a SARS-CoV-2 vaccine have been delivered. The rise of the more infectious delta variant has recently indicated the value of reinstating previously relaxed non-pharmacological and test-driven preventative measures. These efforts have been met with resistance, due, in part, to a lack of site-specific quantitative evidence which can justify their value. As vaccination rates continue to increase, a gap in knowledge exists regarding appropriate thresholds for escalation and de-escalation of COVID-19 preventative measures.\n\nMethodsWe conducted a series of simulation experiments, trialing the spread of SARS-CoV-2 virus in a hypothesized working environment that is subject to COVID-19 infections from the surrounding community. We established cohorts of individuals who would, in simulation, work together for a set period of time. With these cohorts, we tested the rates of workplace and community acquired infections based on applied isolation strategies, community infection rates (CIR), scales of testing, non-pharmaceutical interventions, variant predominances and testing strategies, vaccination coverages, and vaccination efficacies of the members included. Permuting through each combination of these variables, we estimated expected case counts for 33,462 unique workplace scenarios.\n\nResultsWhen the CIR is 5 new confirmed cases per 100,000 or fewer, and at 50% of the workforce is vaccinated with a 95% efficacious vaccine, then testing daily with an antigen-based or PCR based test in only unvaccinated workers will result in less than one infection through 4,800 person weeks. When the community infection rate per 100,000 persons is less than or equal to 60, and the vaccination coverage of the workforce is 100% with 95% vaccine efficacy then no masking or routine testing + isolation strategies are needed to prevent workplace acquired infections regardless of variant predominance. Identifying and isolating workers with antigen-based SARS-CoV-2 testing methods results in the same or fewer workplace acquired infections than testing with polymerase chain reaction (PCR) methods.\n\nConclusionsSpecific scenarios exist in which preventative measures taken to prevent SARS-CoV-2 spread, including masking, and testing plus isolation strategies can safely be relaxed. Further, efficacious testing with quarantine strategies exist for implementation in only unvaccinated cohorts in a workplace. Due to shorter turnaround time, antigen-based testing with lower sensitivity is more effective than PCR testing with higher sensitivities in comparable testing strategies. The general reference interactive heatmap we provide can be used for site specific, immediate, parameter-based case count predictions to inform appropriate institutional policy making.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rowland W Pettit", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Bo Peng", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Patrick Yu", + "author_inst": "Corporate Medical Advisors, Houston, Texas, USA" + }, + { + "author_name": "Peter Matos", + "author_inst": "Corporate Medical Advisors, Houston, Texas, USA" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "Laboratory Medicine, University of Washington" + }, + { + "author_name": "Julie McCashin", + "author_inst": "International S.O.S., Houston, TX" + }, + { + "author_name": "Christopher Ian Amos", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.09.16.21263714", "rel_title": "The Relationship of Vaccine Uptake and COVID-19 Infections among Nursing Home Staff and Residents in Missouri", @@ -596749,49 +599126,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.09.16.21263477", - "rel_title": "Absence of Excess Mortality in a Highly Vaccinated Population During the Initial Covid-19 Delta Period.", - "rel_date": "2021-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263477", - "rel_abs": "BackgroundAll-cause excess mortality (the number of deaths that exceed projections in any period) has been widely reported during the Covid-19 pandemic. Whether excess mortality has occurred during the Delta wave is less well understood.\n\nMethodsWe performed an observational study using data from the Massachusetts Department of Health. Five years of US Census population data and CDC mortality statistics were applied to a seasonal autoregressive integrated moving average (sARIMA) model to project the number of expected deaths for each week of the pandemic period, including the Delta period (starting in June 2021, extending through August 28th 2021, for which mortality data are >99% complete). Weekly Covid-19 cases, Covid-19-attributed deaths, and all-cause deaths are reported. County-level excess mortality during the vaccine campaign are also reported, with weekly rates of vaccination in each county that reported 100 or more all-cause deaths during any week included in the study period.\n\nResultsAll-cause mortality was not observed after March 2021, by which time over 75% of persons over 65 years of age in Massachusetts had received a vaccination. Fewer deaths than expected (which we term deficit mortality) occurred both during the summer of 2020, the spring of 2021 and during the Delta wave (beginning June 13, 2021 when Delta isolates represented >10% of sequenced cases). After the initial wave in the spring of 2020, more Covid-19-attributed deaths were recorded that all-cause excess deaths, implying that Covid-19 was misattributed as the underlying cause, rather than a contributing cause of death in some cases.\n\nConclusionIn a state with high vaccination rates, excess mortality has not been recorded during the Delta period. Deficit mortality has been recorded during this period.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jeremy S Faust", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Chengan Du", - "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" - }, - { - "author_name": "Katherine Dickerson Mayes", - "author_inst": "Harvard Affiliated Emergency Medicine Residency, Boston, Massachusetts" - }, - { - "author_name": "Benjamin Renton", - "author_inst": "Ariadne Labs" - }, - { - "author_name": "Shu-Xia Li", - "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.12.21263461", "rel_title": "Equivalency of Protection from Natural Immunity in COVID-19 Recovered Versus Fully Vaccinated Persons: A Systematic Review and Pooled Analysis", @@ -597743,6 +600077,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.14.21262977", + "rel_title": "Spatiotemporal analyses illuminate the competitive advantage of a SARS-CoV-2 variant of concern over a variant of interest", + "rel_date": "2021-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21262977", + "rel_abs": "The emergence of novel SARS-CoV-2 variants in late 2020 and early 2021 raised alarm worldwide and prompted reassessment of the management, surveillance, and projected future of COVID-19. Mutations that confer competitive advantages by increasing transmissibility or immune evasion have been associated with the localized dominance of single variants. Thus, elucidating the evolutionary and epidemiological dynamics among novel variants is essential for understanding the trajectory of the COVID-19 pandemic. Here we show the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) in New York (NY) from December 2020 to April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 likely evolved in the Bronx in late 2020, providing opportunity for an initial foothold in the heavily interconnected New York City (NYC) region, as evidenced by numerous exportations to surrounding locations. In contrast, B.1.1.7 became dominant in regions of upstate NY where B.1.526 had limited presence, suggesting that B.1.1.7 was able to spread more efficiently in the absence of B.1.526. Clusters discovered from the spatial-time scan analysis supported the role of competition between B.1.526 and B.1.1.7 in NYC in March 2021 and the outsized presence of B.1.1.7 in upstate NY in April 2021. Although B.1.526 likely delayed the rise of B.1.1.7 in NYC, B.1.1.7 became the dominant variant in the Metro region by the end of the study period. These results reveal the advantages endemicity may grant to a variant (founder effect), despite the higher fitness of an introduced lineage. Our research highlights the dynamics of inter-variant competition at a time when B.1.617.2 (Delta) is overtaking B.1.1.7 as the dominant lineage worldwide. We believe our combined spatiotemporal methodologies can disentangle the complexities of shifting SARS-CoV-2 variant landscapes at a time when the evolution of variants with additional fitness advantages is impending.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alexis Russell", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Collin O'Connor", + "author_inst": "Division of Epidemiology, New York State Department of Health" + }, + { + "author_name": "Erica Lasek-Nesselquist", + "author_inst": "Bioinformatics Core, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Jonathan Plitnick", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "John P Kelly", + "author_inst": "Applied Genomic Technology Core, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Daryl M Lamson", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Kirsten St George", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.14.21263153", "rel_title": "Evolution of COVID-19 mortality over time: results from the Swiss hospital surveillance system (CH-SUR)", @@ -598931,29 +601308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.13.21263458", - "rel_title": "Masking significantly reduces, but does not eliminate COVID-19 infection in a spatial agent-based simulation of a University dormitory floor", - "rel_date": "2021-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263458", - "rel_abs": "COVID-ADAPT is a stochastic, discrete-space, agent-based simulation model of airborne infection and public health interventions, capable of modeling SARS-CoV-2 transmission. Using a map of a real university dormitory floor, the model simulates agents moving about and potentially infecting each other. Health interventions tested are vaccination and masking, including whether the solitary initial infectious agent was masked. Universal masking with N95 masks and 100% vaccination of susceptible people resulted in significantly lower prevalence after 3 weeks compared to all other scenarios, but still led to a substantial number of infections. Increased vaccination levels from 52% to 100% by itself did not result in a significant difference in prevalence due to symptomatic and asymptomatic breakthrough infections. These results suggest that vaccination alone is insufficient to stem outbreaks, and the best way to reduce COVID-19 infections is to ensure that all infectious people are masked. However, because asymptomatic infections are common, the only way to ensure this is universal masking, which also reduces prevalence by protecting susceptible individuals from infection. Universal masking is the best way forward, especially under threat of the Delta variant, to keep facilities open and safe for occupants, while minimizing the number of infections.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Roxanne McPeck", - "author_inst": "Eastern Washington University" - }, - { - "author_name": "Krisztian Magori", - "author_inst": "Eastern Washington University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.19.460976", "rel_title": "Planning and Conducting an Online Conference at the time of COVID-19: Lessons Learned from EGREPA 2021", @@ -600145,6 +602499,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.13.21263487", + "rel_title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "rel_date": "2021-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "rel_abs": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jia Wei", + "author_inst": "University of Oxford" + }, + { + "author_name": "Koen B. Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa C. Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Duncan Cook", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John I Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John N Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Alison Howarth", + "author_inst": "University of Oxford" + }, + { + "author_name": "Brian D. Marsden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Hoosdally", + "author_inst": "University of Oxford" + }, + { + "author_name": "E Yvonne Jones", + "author_inst": "University of Oxford" + }, + { + "author_name": "David I Stuart", + "author_inst": "University of Oxford" + }, + { + "author_name": "Derrick W. Crook", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tim E.A. Peto", + "author_inst": "University of Oxford" + }, + { + "author_name": "A.Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "David W. Eyre", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.09.21263348", "rel_title": "Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach", @@ -600885,65 +603334,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.13.21263371", - "rel_title": "Spread of SARS-CoV-2 Delta variant infections bearing the S:E484Q and S:T95I mutations in July and August 2021 in France", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263371", - "rel_abs": "Analysing 92,598 variant screening tests performed on SARS-CoV-2 positive samples collected in France between 1 July and 31 August 2021 shows an increase of Kappa-like infections. Full genome sequencing reveals that these correspond to Delta variants bearing the S:E484Q mutation. Most of these sequences belong to a phylogenetic cluster and also bear the S:T95I mutation. Further monitoring is needed to determine if this trend is driven by undocumented superspreading events or an early signal of future viral evolutionary dynamics.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Laura Verdume", - "author_inst": "CERBA" - }, - { - "author_name": "Gonch\u00e9 Danesh", - "author_inst": "CNRS" - }, - { - "author_name": "Sabine Trombert", - "author_inst": "CERBA" - }, - { - "author_name": "Mircea T. Sofonea", - "author_inst": "Univ. Montpellier" - }, - { - "author_name": "Val\u00e9rie Noel", - "author_inst": "CNRS" - }, - { - "author_name": "Vincent Foulongne", - "author_inst": "CHU de Montpellier" - }, - { - "author_name": "Brigitte Mont\u00e8s", - "author_inst": "CHU de Montpellier" - }, - { - "author_name": "Edouard TUAILLON", - "author_inst": "Montpellier University" - }, - { - "author_name": "St\u00e9phanie Haim-Boukobza", - "author_inst": "CERBA" - }, - { - "author_name": "B\u00e9n\u00e9dicte Roquebert", - "author_inst": "Cerba Laboratory" - }, - { - "author_name": "Samuel Alizon", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.13.21263214", "rel_title": "Detailed Overview of the Buildout and Integration of an Automated High-Throughput CLIA Laboratory for SARS-CoV-2 Testing on a Large Urban Campus", @@ -602187,6 +604577,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.10.21263072", + "rel_title": "VALIDATION OF A SALIVA-BASED TEST FOR THE MOLECULAR DIAGNOSIS OF SARS-CoV-2 INFECTION", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21263072", + "rel_abs": "BackgroundSince the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve screening and diagnosis of SARS-CoV-2 infection (Y. Yang et al., medRxiv 2020; W. Wang et al., 2020.3786; A Senok et al., Infect Drug Resist 2020). Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab (N. Sethuraman et al., JAMA 2020; A.J. Jamal et al Clinical Infect Disease 2021). Saliva samples, however, offer clear practical and logistical advantages (K.K.W To et al, Clinical Microb and Infect; A.L. Wylle et al. N Engl J Med 2020; N. Matic et al, Eur J Clin 2021) but due to lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool (D. Esser et al., Biomark Insights 2008; E. Kaufman et al., Crit Rev Oral Biol Med2002). With this study, we aimed to validate an intra-laboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage saline solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests.\n\nMethodsIn this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples.\n\nResultsThe identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohens Kappa=0.86; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples.\n\nConclusionsRT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturing properties of the solution reduce the infective risks belonging to sample manipulation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michela Bulfoni", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy; Institute of Pathology, ASU FC, Udine, Italy" + }, + { + "author_name": "Emanuela Sozio", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Barbara Marcon", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Maria De Martino", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Daniela Cesselli", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy; Institute of Pathology, ASU FC, Udine, Italy" + }, + { + "author_name": "Chiara De Carlo", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Romina Martinella", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Angelica Migotti", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Eleonora Vania", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Agnese Zanus-Fortes", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Jessica De Piero", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Emanuele Nencioni", + "author_inst": "Biofarma Srl" + }, + { + "author_name": "Carlo Tascini", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy; Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Miriam Isola", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Francesco Curcio", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy; Department of Medicine, University of Udine, Udine, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.14.460356", "rel_title": "Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display", @@ -602919,65 +605384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.10.21263332", - "rel_title": "Scale-free dynamics of Covid-19 in a Brazilian city", - "rel_date": "2021-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21263332", - "rel_abs": "Mathematical models can provide insights into the control of pandemic COVID-19, which remains a global priority. The dynamics of directly-transmitted infectious diseases, such as COVID-19, are usually described by compartmental models where individuals are classified as susceptible, infected and removed. These SIR models typically assume homogenous transmission of infection, even in large populations, a simplification that is convenient but inconsistent with observations. Here we use original data on the dynamics of COVID-19 spread in a Brazilian city to investigate the structure of the transmission network. We find that transmission can be described by a network in which each infectious individual has a small number of susceptible contacts, of the order of 2-5, which is independent of total population size. Compared with standard models of homogenous mixing, this scale-free, fractal infection process gives a better description of COVID-19 dynamics through time. In addition, the contact process explains the geographically localized clusters of disease seen in this Brazilian city. Our scale-free model can help refine criteria for physical and social distancing in order to more effectively mitigate the spread of COVID-19. We propose that scale-free COVID-19 dynamics could be a widespread phenomenon, a topic for further investigation.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Josue M. P. Policarpo", - "author_inst": "Instituto de Fisica da Universidade de Sao Paulo" - }, - { - "author_name": "Arthur A. G. F. Ramos", - "author_inst": "Intituto de Fisica da Universidade de Sao Paulo" - }, - { - "author_name": "Christopher Dye", - "author_inst": "Department of Zoology, University of Oxford" - }, - { - "author_name": "Nuno R Faria", - "author_inst": "Imperial Coll London, MRC Ctr Global Infect Dis Anal, Sch Publ Helth" - }, - { - "author_name": "Fabio E Leal", - "author_inst": "Universidade de Sao Caetano do Sul, Sao Caetano do Sul and Programa de Oncovirologia Instituto Nacional de Cancer" - }, - { - "author_name": "Osmar J S Moraes", - "author_inst": "Instituto de Fisica - Universidade de Sao Paulo" - }, - { - "author_name": "Kris V Parag", - "author_inst": "MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London" - }, - { - "author_name": "Pedro S Peixoto", - "author_inst": "Instituto de Matematica e Estatistica, Universidade de Sao Paulo" - }, - { - "author_name": "Ester C Sabino", - "author_inst": "Faculdade de Medicina - Universidade de Sao Paulo" - }, - { - "author_name": "Vitor H Nascimento", - "author_inst": "Escola Politecnica - Universidade de Sao Paulo" - }, - { - "author_name": "Airton Deppman", - "author_inst": "Instituto de Fisica da Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.12.21263451", "rel_title": "What pushed Israel out of herd immunity? Modeling COVID-19 spread of Delta and Waning immunity", @@ -603901,6 +606307,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.07.21262725", + "rel_title": "SARS-COV2 mutant-specific T cells and neutralizing antibodies after vaccination and up to 1 year after infection", + "rel_date": "2021-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21262725", + "rel_abs": "ObjectiveWe investigated blood samples from fully SARS-CoV2-vaccinated subjects and from previously positive tested patients up to one year after infection with SARS-CoV2, and compared short- and long-term T cell and antibody responses, with a special focus on the recently emerged delta variant (B.1.617.2).\n\nMethods and ResultsIn 23 vaccinated subjects, we documented high anti-SARS-CoV2 spike protein receptor binding domain (RBD) antibody titers. Average virus neutralization by antibodies, assessed as inhibition of ACE2 binding to RBD, was 2.2-fold reduced for delta mutant vs. wild type (wt) RBD. The mean specific antibody titers were lower one year after natural infection than after vaccination; ACE2 binding to delta mutant vs. wt RBD was 1.65-fold reduced. In an additional group, omicron RBD binding was reduced compared to delta.\n\nSpecific CD4+ T cell responses were measured after stimulation with peptides pools from wt, alpha, beta, gamma, or delta variant SARS-CoV2 spike proteins by flow cytometric intracellular cytokine staining. There was no significant difference in cytokine production of IFN-{gamma}, TNF-, or IL-2 between vaccinated subjects. T cell responses to wt or mutant SARS-CoV2 spike were significantly weaker after natural occurring infections compared to those in vaccinated individuals.\n\nConclusionAntibody neutralisation of the delta mutant was reduced compared to wt, as assessed in a novel inhibition assay with a finger prick blood drop. Strong CD4 T cell responses were present against wt and mutant SARS-CoV2 variants, including the delta (B.1.617.2) strain, in fully vaccinated individuals, whereas they were partly weaker 1 year after natural infection. Hence, immune responses after vaccination are stronger compared to those after naturally occurring infection, pointing out the need of the vaccine to overcome the pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jennifer R Richardson", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Ralph Goetz", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Vanessa Mayr", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Martin J Lohse", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Hans-Peter Holthoff", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Martin Ungerer", + "author_inst": "ISAR Bioscience" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.09.10.21262710", "rel_title": "Antibody responses to BNT162b2 mRNA vaccine: infection-naive individuals with abdominal obesity warrant attention", @@ -605037,33 +607482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.09.07.21263196", - "rel_title": "Implicit, Intrinsic, Extrinsic, and Host Factors Attributing the Covid-19 Pandemic. Part 1- Intrinsic Factor Nitrous Oxide Emissions: A Systematic Analysis", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263196", - "rel_abs": "Despite Nitrous oxide (N2O) being the most widely used anesthetics in dental and other medical applications, it is associated with global warming and stratospheric ozone destruction. With globalization, a larger amount of N2O emissions arearticulated especially from human activities (30%, 6.7 Tg N per year), which are primarily dominated by agriculture that is even above the emissions of all oceans (26%). The synthesis of N2O reflects the general chemistry and readily from a substrate Nitric oxide (NO) in the environment. The modeling of infectious disease dynamics covering common pathogen-transmission factors, for example intrinsic (or microbes nutrient supply) at a population level, is indeed imperative to curb the menace of any disease. Nonetheless, in areas where novel coronavirus disease (COVID-19) was at its worst, for example, Wuhan China, Mumbai India, Milan Italy, Washington USA etc., the reduction in N2O emissions was well noticed. Nonetheless, viruses exhibit greater mobility than humans and hijack nutrients including nitrogen to complete their epidemiological cycle all due to limited sequence space of viral genomes, the high probability of genetic drift, extremely large population sizes, the high mutation and recombination rates. In consequence of drastic fall in N2O emissions, lower human transport can not be an all alone contributor, but contrarily it may also be associated with coronavirus intrinsic factors. This prompted us to analyze freely accessible and large global data from two authenticated sources, the World Health Organization and World Bank. We hereby argue that intrinsic factor N2O emissions fueling the COVID-19 progression significantly. Entire predictions were found consistent with the recently observed shreds of evidence. These insights enhanced scientific ability to interrogate viral epidemiology and recommended a 7-points framework covering all-natural lifestyle and dietary supplements for COVID-19 prevention before the arrival of a front-line therapeutic(s) or preventable vaccine.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nikita Thapliyal", - "author_inst": "Graphic Era Hill University" - }, - { - "author_name": "Gaurav Joshi", - "author_inst": "Graphic Era Hill University" - }, - { - "author_name": "Prashant Gahtori", - "author_inst": "Graphic Era Hill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.09.21263347", "rel_title": "Implicit, Intrinsic, Extrinsic (or Environmental), and Host Factors Attributing the Covid-19 Pandemic. Part 2- Implicit Factor Pesticide Use: A Systematic Analysis", @@ -606083,6 +608501,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.13.460111", + "rel_title": "Therapeutic efficacy of an oral nucleoside analog of remdesivir against SARS-CoV-2 pathogenesis in mice.", + "rel_date": "2021-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.13.460111", + "rel_abs": "The COVID-19 pandemic remains uncontrolled despite the rapid rollout of safe and effective SARS-CoV-2 vaccines, underscoring the need to develop highly effective antivirals. In the setting of waning immunity from infection and vaccination, breakthrough infections are becoming increasingly common and treatment options remain limited. Additionally, the emergence of SARS-CoV-2 variants of concern with their potential to escape therapeutic monoclonal antibodies emphasizes the need to develop second-generation oral antivirals targeting highly conserved viral proteins that can be rapidly deployed to outpatients. Here, we demonstrate the in vitro antiviral activity and in vivo therapeutic efficacy of GS-621763, an orally bioavailable prodrug of GS-441524, the parental nucleoside of remdesivir, which targets the highly conserved RNA-dependent RNA polymerase. GS-621763 exhibited significant antiviral activity in lung cell lines and two different human primary lung cell culture systems. The dose-proportional pharmacokinetic profile observed after oral administration of GS-621763 translated to dose-dependent antiviral activity in mice infected with SARS-CoV-2. Therapeutic GS-621763 significantly reduced viral load, lung pathology, and improved pulmonary function in COVID-19 mouse model. A direct comparison of GS-621763 with molnupiravir, an oral nucleoside analog antiviral currently in human clinical trial, proved both drugs to be similarly efficacious. These data demonstrate that therapy with oral prodrugs of remdesivir can significantly improve outcomes in SARS-CoV-2 infected mice. Thus, GS-621763 supports the exploration of GS-441524 oral prodrugs for the treatment of COVID-19 in humans.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Alexandra Schafer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "David R Martinez", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "John J Won", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Fernanado R Moreira", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ariane J Brown", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kendra L Gully", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rao Kalla", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Kwon Chun", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Venice Du Pont", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Darius Babusis", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Jennifer Tang", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Eisuke Murakami", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Raju Subramanian", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Kimberly T Barrett", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Blake J. Bleier", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Roy Bannister", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Joy Y. Feng", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "John P. Bilello", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Tomas Cihlar", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Richard L. Mackman", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Stephanie A. Montgomery", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Timothy P. Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.13.460130", "rel_title": "Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods", @@ -606771,65 +609296,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.09.21262951", - "rel_title": "Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences", - "rel_date": "2021-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21262951", - "rel_abs": "We are reporting on the observation of a large, under-sequenced region of the S gene of the SARS-CoV2 Delta variant genomes, identified in sequences originating from various sequencing centres worldwide (e.g. USA, India, England, Switzerland, France, Germany). This poorly sequenced region was identified from the early phases of the Delta variant spread and the phenomenon is still ongoing. As many commonly-used protocols rely on amplicon-based sequencing procedures, we investigated the likely origin of the issue. We established its biological origin as resulting from mutations in the viral genomes at primer binding sites. We designed and evaluated new PCR primers to circumvent this issue in order to complement the ARTIC v3 set, and validated their performance for the sequencing of circulating Delta variants.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lo\u00efc Borcard", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Sonja Gempeler", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Miguel A Terrazos Miani", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Christian Baumann", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Carole Gr\u00e4del", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Ronald Dijkman", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Franziska Suter-Riniker", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Stephen L Leib", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Pascal Bittel", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Stefan Neuenschwander", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Alban Ramette", - "author_inst": "University of Bern" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.09.21263315", "rel_title": "Professional practice for COVID-19 risk reduction among health care workers : a Cross-Sectional Study with Matched Case-Control Comparison", @@ -607689,6 +610155,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.09.11.459891", + "rel_title": "Phylogenetic evidence for asparagine to aspartic acid protein editing of N-glycosylated SARS-CoV-2 viral proteins by NGLY1 deglycosylation/deamidation suggests an unusual vaccination strategy", + "rel_date": "2021-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.11.459891", + "rel_abs": "Many viral proteins, including multiple SARS-CoV-2 proteins, are secreted via the endoplasmic reticulum, and viral particles are assembled and exported in ER-associated replication compartments. Viral coat proteins such as the SARS-CoV-2 Spike protein are N-glycosylated at NxS/T sites as they enter the ER. N-glycosylated sites in many eukaryotic proteins are deglycosylated by the NGLY1/PNG-1 deglycosylation enzyme which also deamidates the N-glycosylated asparagine to aspartic acid, thus editing the target protein sequence. Proteomic analysis of mammalian cell lines has revealed deamidation of many host N-glycosylated asparagines to aspartic acid by NGLY1/PNG-1 on peptides that are presented by mammalian HLA for immune surveillance. The key client protein for NGLY1/PNG-1 deglycosylation and N to D protein editing was revealed by genetic analysis of C. elegans proteasome regulation to be the intact endoplasmic reticulum-transiting SKN-1A transcription factor. Strikingly, an analysis of cancer cell genetic dependencies for growth revealed that the mammalian orthologue of SKN-1A, NRF1 (also called NFE2L1) is required by a highly correlated set of cell lines as NGLY1/PNG-1, supporting that NGLY1/PNG-1 and NRF1 act in the same pathway. NGLY1/PNG-1 edits N-glycosylated asparagines on the intact SKN-1 protein as it is retrieved by ERAD from the ER to in turn activate the transcription of target proteasomal genes. The normal requirement for NGLY1/PNG-1 editing of SKN-1A can be bypassed by a genomic substituion of N to D in four NxS/T N-glycosylation motifs of SKN-1A. Thus NGLY1/PNG-1-mediated N to D protein editing is more than a degradation step for the key client protein for proteasomal homeostasis in C. elegans or tumor growth in particular mammalian cell lines, SKN-1A/NRF1. In addition, such N to D substitutions in NxS/T N-glycosylation motifs occur in evolution: N to D substitutions are observed in phylogenetic comparisons of SKN-1A between nematode species that diverged hundreds of millions of years ago or of the vertebrate NRF1 between disparate vertebrates. Genomic N to D mutations bypass the many steps in N-glycosylation in the ER and deglycosylation-based editing of N to D, perhaps based on differences in the competency of divergent species for various N-glycosylation or deglycosylation steps.\n\nWe surveyed the N-glycosylation sites in coronavirus proteins for such phylogenetic evidence for N to D protein editing in viral life cycles, and found evidence for preferential N to D residue substitutions in NxS/T N-glycosylation sites in comparisons of the genome sequences of hundreds of coronaviruses. This suggests that viruses use NGLY1/PNG-1 in some hosts, for example humans, to edit particular N-glycosylated residues to aspartic acid, but that in other hosts, often in bats, an N to D substitution mutation in the virus genome is selected. Single nucleotide mutations in Asp or Asn codons can produce viruses with N to D or D to N substitutions that might be selected in different animal hosts from the population of viral variants produced in any previous host. NGLY1/PNG-1 has been implicated in viral immunity in mammalian cell culture, favoring this hypothesis.\n\nBecause of the phylogenetic evidence that the NGLY1/PNG-1 editing of protein sequences has functional importance for SKN-1A/NRF1 and viruses, and because most immunization protocols do not address the probable editing and functional importance of N-glycosylated aspargines to aspartic acid in normal viral infections, we suggest that immunization with viral proteins engineered to substitute D at genomically encoded NxS/T sites of N-glycosylated viral proteins that show a high frequency of N to D substitution in viral phylogeny may enhance immunological response to peptide antigens. Such genomically-edited peptides would not require ER-localization for N-glycosylation or other cell compartment localization for NGLY1/PNG-1 N to D protein editing. In addition, such N to D edited protein vaccines could be produced in bacteria since N-glycosylation and deglycosylation which do not occur in bacteria would no longer be required to immunize with a D-substituted peptide. Bacterially-expressed vaccines would be much lower cost and with fewer failure modes than attenuated viral vaccines or recombinant animal viruses produced in chicken eggs, mammalian tissue culture cells, or delivered by mRNA vectors to the patient directly. Because N to D edited peptides are clearly produced by NGLY1/PNG-1, and may be and presented by mammalian HLA, such peptides may more robustly activate T-cell killing or B-cell maturation to mediate more robust viral immunity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gary Ruvkun", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Ruslan Sadreyev", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Fei Ji", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.09.06.21263168", "rel_title": "Coronavirus disease (COVID-19) associated Mucormycosis: An Anaesthesiologist's Perspective", @@ -608253,89 +610746,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.08.21263095", - "rel_title": "Exposures to different SARS-CoV-2 spike variants elicit neutralizing antibody responses with differential specificity towards established and emerging strains", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263095", - "rel_abs": "The wide spectrum of SARS-CoV-2 variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of the immune response to different spike protein versions. Here, we compare the neutralization of variants of concern, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure. We also observe that exposure to multiple spike variants increases the breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.\n\nSUMMARYThis study characterizes neutralization of eight different SARS-CoV-2 variants, including Delta and Omicron, with respect to nine different prior exposures, including vaccination, booster, and infections with Delta, Epsilon, and others. Different exposures were found to confer substantially differing neutralization specificity.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Matthew T Laurie", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA" - }, - { - "author_name": "Jamin Liu", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; University of California, Berkeley-University of California, S" - }, - { - "author_name": "Sara Sunshine", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA" - }, - { - "author_name": "James Peng", - "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA" - }, - { - "author_name": "Douglas Black", - "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA" - }, - { - "author_name": "Anthea M Mitchell", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA" - }, - { - "author_name": "Sabrina A Mann", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA" - }, - { - "author_name": "Genay Pilarowski", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA" - }, - { - "author_name": "Kelsey C Zorn", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA" - }, - { - "author_name": "Luis Rubio", - "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA" - }, - { - "author_name": "Sara Bravo", - "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA" - }, - { - "author_name": "Joseph J Sabatino", - "author_inst": "Weill Institute for Neurosciences, Department of Neurology, San Francisco, CA 94158, USA" - }, - { - "author_name": "Kristen Mittl", - "author_inst": "Weill Institute for Neurosciences, Department of Neurology, San Francisco, CA 94158, USA" - }, - { - "author_name": "Carina Marquez", - "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA" - }, - { - "author_name": "Maya Petersen", - "author_inst": "Division of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA" - }, - { - "author_name": "Diane Havlir", - "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA" - }, - { - "author_name": "Joseph DeRisi", - "author_inst": "Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.06.21263149", "rel_title": "Reduced magnitude and durability of humoral immune responses by COVID-19 mRNA vaccines among older adults", @@ -609747,6 +612157,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.02.21263033", + "rel_title": "Epidemic Models for COVID-19 during the First Wave from February to May 2020: a Methodological Review", + "rel_date": "2021-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263033", + "rel_abs": "We review epidemiological models for the propagation of the COVID-19 pandemic during the early months of the outbreak: from February to May 2020. The aim is to propose a methodological review that highlights the following characteristics: (i) the epidemic propagation models, (ii) the modeling of intervention strategies, (iii) the models and estimation procedures of the epidemic parameters and (iv) the characteristics of the data used. We finally selected 80 articles from open access databases based on criteria such as the theoretical background, the reproducibility, the incorporation of interventions strategies, etc. It mainly resulted to phenomenological, compartmental and individual-level models. A digital companion including an online sheet, a Kibana interface and a markdown document is proposed. Finally, this work provides an opportunity to witness how the scientific community reacted to this unique situation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Marie Garin", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, F-91190 Gif-sur-Yvette, France" + }, + { + "author_name": "Myrto Limnios", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, F-91190 Gif-sur-Yvette, France" + }, + { + "author_name": "Alice Nicolai", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Ioannis Bargiotas", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Olivier Boulant", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Stephen E. Chick", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France" + }, + { + "author_name": "Amir Dib", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Theodoros Evgeniou", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France" + }, + { + "author_name": "Mathilde Fekom", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Argyris Kalogeratos", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Christophe Labourdette", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Anton Ovchinnikov", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France and Smith School of Business, Queen's University, Kingston, ON, K7L3N6, Canada" + }, + { + "author_name": "Rapha\u00ebl Porcher", + "author_inst": "Universit\u00e9 de Paris CRESS, INSERM, INRA, 75004 Paris, France" + }, + { + "author_name": "Camille Pouchol", + "author_inst": "MAP5 Laboratory, FP2M, CNRS FR 2036, Universit\u00e9 de Paris, 75006 Paris, France" + }, + { + "author_name": "Nicolas Vayatis", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.09.21263328", "rel_title": "COVID-19 Vaccine Concerns about Safety, Effectiveness and Policies in the United States, Canada, Sweden, and Italy among Unvaccinated Individuals", @@ -610519,53 +613004,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.08.459535", - "rel_title": "SARS-CoV-2 triggers DNA damage response in Vero E6 cells", - "rel_date": "2021-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459535", - "rel_abs": "The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for the current COVID-19 pandemic and has now infected more than 200 million people with more than 4 million deaths globally. Recent data suggest that symptoms and general malaise may continue long after the infection has ended in recovered patients, suggesting that SARS-CoV-2 infection has profound consequences in the host cells. Here we report that SARS-CoV-2 infection can trigger a DNA damage response (DDR) in African green monkey kidney cells (Vero E6). We observed a transcriptional upregulation of the Ataxia telangiectasia and Rad3 related protein (ATR) in infected cells. In addition, we observed enhanced phosphorylation of CHK1, a downstream effector of the ATR DNA damage response, as well as H2AX. Strikingly, SARS-CoV-2 infection lowered the expression of TRF2 shelterin-protein complex, and reduced telomere lengths in infected Vero E6 cells. Thus, our observations suggest SARS-CoV-2 may have pathological consequences to host cells beyond evoking an immunopathogenic immune response.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Joshua Victor", - "author_inst": "University of Vermont" - }, - { - "author_name": "Jamie Deutsch", - "author_inst": "University of Vermont" - }, - { - "author_name": "Annalis Whitaker", - "author_inst": "University of Vermont" - }, - { - "author_name": "Erica N Lamkin", - "author_inst": "University of Vermont" - }, - { - "author_name": "Anthony March", - "author_inst": "University of Vermont" - }, - { - "author_name": "Pei Zhou", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Jason W Botten", - "author_inst": "University of Vermont" - }, - { - "author_name": "Nimrat Chatterjee", - "author_inst": "University of Vermont" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cancer biology" - }, { "rel_doi": "10.1101/2021.09.09.459641", "rel_title": "Targeting Stem-loop 1 of the SARS-CoV-2 5'UTR to suppress viral translation and Nsp1 evasion", @@ -611857,6 +614295,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.08.459480", + "rel_title": "Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses", + "rel_date": "2021-09-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459480", + "rel_abs": "The emergence of current SARS-CoV-2 variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy 1-7. Development of broadly effective coronavirus vaccines that can mitigate these threats is needed 8, 9. Notably, several recent studies have revealed that vaccination of recovered COVID-19 donors results in enhanced nAb responses compared to SARS-CoV-2 infection or vaccination alone 10-13. Here, we utilized a targeted donor selection strategy to isolate a large panel of broadly neutralizing antibodies (bnAbs) to sarbecoviruses from two such donors. Many of the bnAbs are remarkably effective in neutralization against sarbecoviruses that use ACE2 for viral entry and a substantial fraction also show notable binding to non-ACE2-using sarbecoviruses. The bnAbs are equally effective against most SARS-CoV-2 VOCs and many neutralize the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor binding domain (RBD) as opposed to strain-specific nAbs to the receptor binding site that are commonly elicited in SARS-CoV-2 infection and vaccination 14-18. Consistent with targeting of conserved sites, select RBD bnAbs exhibited in vivo protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model. The generation of a large panel of potent bnAbs provides new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and, importantly, provides a molecular basis for effective design of pan-sarbecovirus vaccines.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Wan-ting He", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Rami Musharrafieh", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ge Song", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Katharina Dueker", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Longping V. Tse", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "David R. Martinez", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Alexandra Schafer", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Sean Callaghan", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Peter Yong", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Nathan Beutler", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Jonathan L. Torres", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Reid M. Volk", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Panpan Zhou", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Meng Yuan", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Hejun Liu", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Fabio Anzanello", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Mara Parren", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Elijah Garcia", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Stephen A. Rawlings", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Davey M. Smith", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Yana Safonova", + "author_inst": "Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA" + }, + { + "author_name": "Andrew B. Ward", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Thomas Rogers", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Lisa E. Gralinski", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Dennis R. Burton", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.08.459260", "rel_title": "Artemisia annua hot-water extracts show potent activity in vitro against Covid-19 variants including delta", @@ -612509,33 +615078,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21263050", - "rel_title": "Two new compartmental epidemiological models and their equilibria", - "rel_date": "2021-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263050", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWCompartmental models have long served as important tools in mathematical epidemiology, with their usefulness highlighted by the recent COVID-19 pandemic. However, most of the classical models fail to account for certain features of this disease and others like it, such as the ability of exposed individuals to recover without becoming infectious, or the possibility that asymptomatic individuals can indeed transmit the disease but at a lesser rate than the symptomatic. Furthermore, the rise of new disease variants and the imperfection of vaccines suggest that concept of endemic equilibrium is perhaps more pertinent than that of herd immunity.\n\nHere we propose a new compartmental epidemiological model and study its equilibria, characterizing the stability of both the endemic and disease-free equilibria in terms of the basic reproductive number. Moreover, we introduce a second compartmental model, generalizing our first, which accounts for vaccinated individuals, and begin an analysis of its equilibria.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jonas Balisacan", - "author_inst": "University of Hawai'i at Manoa" - }, - { - "author_name": "Monique Chyba", - "author_inst": "University of Hawai'i at Manoa" - }, - { - "author_name": "Corey Shanbrom", - "author_inst": "Sacramento State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.03.21263103", "rel_title": "The prevalence of adaptive immunity to COVID-19 and reinfection after recovery, a comprehensive systematic review and meta-analysis of 12 011 447 individuals", @@ -613547,6 +616089,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.03.21257002", + "rel_title": "Long COVID: Assessment of Neuropsychiatric Symptoms in Children and Adolescents - A Clinical Data Analysis", + "rel_date": "2021-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21257002", + "rel_abs": "COVID-19 infections in adults often result in medical, neuropsychiatric, and unspecific symptoms, called Long COVID, and the premorbid functional status cannot be achieved. Regarding the course in children and adolescents, however, reliable data are not yet available.\n\nObjective380 children and adolescents/young adults aged between 6 and 21 years, being treated for various psychiatric diseases in an outpatient clinical service, were examined for COVID-19 infections and Long COVID symptoms following a structured protocol.\n\nResultsThree patients had COVID-19; one patient had symptoms of Long COVID in his medical history, but they could not be objectivized in an in-depth neuropsychiatric and neuropsychological assessment.\n\nConclusionsLong COVID seems to occur rarely in children and adolescents. Objectivizing the symptoms is a difficult task that requires various diagnostic considerations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jan Froelich", + "author_inst": "Central Institute of Mental Health Department of Child and Adolescent Psychiatry, University of Heidelberg - Faculty of Medicine Mannheim" + }, + { + "author_name": "Tobias Banaschewski", + "author_inst": "Central Institute of Mental Health Department of Child and Adolescent Psychiatry, University of Heidelberg - Faculty of Medicine Mannheim" + }, + { + "author_name": "Annabelle Ulmer", + "author_inst": "Practice for Child and Adolescent Psychiatry and Psychotherapy Dr. Dr. Jan Froelich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.09.02.21263038", "rel_title": "COVID-19 Vaccine Efficacy in a Diverse Urban Healthcare Worker Population", @@ -614115,41 +616684,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.02.21262808", - "rel_title": "COVID-19 vaccination did not improve employee mental health: A prospective study in an early phase of vaccination in Japan", - "rel_date": "2021-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21262808", - "rel_abs": "The effect of the COVID-19 vaccination as an individual-based preventive measure on mental health is largely unclear in the literature. The authors report a preliminary finding on whether vaccination effectively improves mental health among employees in Japan based on a prospective study (E-COCO-J). Of the total sample (N=948), 105 (11.1%) were vaccinated at least once at the follow-up survey (June 2021). There was no significant effect of vaccination on the change of psychological distress at baseline (February 2021) and follow-up (June 2021), after adjusting for gender, age, marital status, education, chronic disease, company size, industry, and occupation (healthcare workers or non-HCWs). Providing continuous mental health care for employees is important in an early vaccination phase.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Natsu Sasaki", - "author_inst": "Department of Mental Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan" - }, - { - "author_name": "Reiko Kuroda", - "author_inst": "Division for Environment, Health, and Safety, The University of Tokyo, Tokyo, Japan" - }, - { - "author_name": "Kanami Tsuno", - "author_inst": "School of Health Innovation, Kanagawa University of Human Services, Kanagawa, Japan" - }, - { - "author_name": "Kotaro Imamura", - "author_inst": "Department of Mental Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan" - }, - { - "author_name": "Norito Kawakami", - "author_inst": "The University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.09.01.21262387", "rel_title": "Simultaneous detection of SARS-CoV-2 RNA and host antibodies enabled by a multiplexed electrochemical sensor platform", @@ -615065,6 +617599,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.09.03.458854", + "rel_title": "The genetics of eating behaviors: research in the age of COVID-19", + "rel_date": "2021-09-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.03.458854", + "rel_abs": "How much pleasure we take in eating is more than just how much we enjoy the taste of food. Food involvement - the amount of time we spend on food beyond the immediate act of eating and tasting - is key to the human food experience. We took a biological approach to test whether food-related behaviors, together capturing food involvement, have genetic components and are partly due to inherited variation. We collected data via an internet survey from a genetically informative sample of 419 adult twins (114 monozygotic twin pairs, 31 dizygotic twin pairs, and 129 singletons). Because we conducted this research during the pandemic, we also ascertained how many participants had experienced COVID-19-associated loss of taste and smell. Since these respondents had previously participated in research in person, we measured their level of engagement to evaluate the quality of their online responses. Additive genetics explained 16-44% of the variation in some measures of food involvement, most prominently various aspects of cooking, suggesting some features of the human food experience may be inborn. Other features reflected shared (early) environment, captured by respondents twin status. About 6% of participants had a history of COVID-19 infection, many with transitory taste and smell loss, but all but one had recovered before the survey. Overall, these results suggest that people may have inborn as well as learned variations in their involvement with food. We also learned to adapt to research during a pandemic by considering COVID-19 status and measuring engagement in online studies of human eating behavior.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mackenzie E. Hannum", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Cailu Lin", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Katherine A Bell", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Aurora K Toskala", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Riley R Koch", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Tharaka Galaniha", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Alissa Nolden", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Danielle R. Reed", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Paule Valery Joseph", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.08.27.21262422", "rel_title": "Characteristics associated with COVID-19 vaccine uptake among adults in England (08 December to 17 May 2021)", @@ -615825,137 +618410,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.01.21262953", - "rel_title": "Severe COVID-19 is characterised by inflammation and immature myeloid cells early in disease progression", - "rel_date": "2021-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262953", - "rel_abs": "SARS-CoV-2 infection causes a wide spectrum of disease severity. Immune changes associated with severe disease include pro-inflammatory cytokine production and expansion of immature myeloid populations. The relative importance of the immunological changes in driving progression to severe disease remain poorly understood.\n\nWe aimed to identify and rank clinical and immunological features associated with progression to severe COVID-19. We sought to use tests available in an on-site diagnostic hospital laboratory to identify an immunological signature for severe disease development which could be detected prior to peak severity thereby allowing initiation of therapeutic interventions. We used univariate and multivariate analysis, including unbiased machine learning, to investigate the relationships between clinical and demographic characteristics, inflammatory markers, and leukocyte immunophenotypes with progression to severe disease in 108 patients and to rank these in importance. A combination of four features (elevated levels of interleukin-6 and C-reactive protein, coupled with reduced monocyte HLA-DR expression and reduced neutrophil CD10 expression), were strongly predictive of severe disease with an average prediction score of 0.925.\n\nHighlightsO_LISevere COVID-19 can be predicted by a combination of emergency myelopoiesis (CD10-neutrophils and HLA DR-monocytes) and inflammation (raised IL-6 and CRP)\nC_LIO_LIThese changes can be identified from tests carried out prior to peak illness severity in a diagnostic laboratory\nC_LIO_LIThis predictive model was derived from a cohort of patients with a wide range of ages, frailty and COVID-19 severity\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC=\"FIGDIR/small/21262953v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@16c6947org.highwire.dtl.DTLVardef@73ba2corg.highwire.dtl.DTLVardef@1c3dd82org.highwire.dtl.DTLVardef@3a48f_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Liam Townsend", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Adam H Dyer", - "author_inst": "School of Medicine, Trinity Translational Medicine Institute" - }, - { - "author_name": "Aifric Naughton", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Sultan Imangaliyev", - "author_inst": "Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity College Dublin, Ireland" - }, - { - "author_name": "Jean Dunne", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Rachel Kiersey", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Dean Holden", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Aoife Mooney", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Deirdre Leavy", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Katie Ridge", - "author_inst": "Department of Immunology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Jamie Sugrue", - "author_inst": "School of Biochemistry and Immunology, Trinity College Dublin, Ireland" - }, - { - "author_name": "Mubarak Aldoseri", - "author_inst": "Department of Intensive Care Medicine, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Jo Hannah Kelliher", - "author_inst": "Department of Intensive Care Medicine, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Martina Hennessy", - "author_inst": "Clinical Research Facility, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Declan G Byrne", - "author_inst": "Department of Clinical Medicine, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Paul Browne", - "author_inst": "Department of Haematology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Christopher L Bacon", - "author_inst": "Department of Haematology, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Caitriona Doyle", - "author_inst": "Department of Infectious Diseases, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Ruth O'Riordan", - "author_inst": "Department of Infectious Diseases, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Anne Marie McLaughlin", - "author_inst": "Department of Respiratory Medicine, St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Ciaran Bannan", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Ignacio Martin-Loeches", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Arthur White", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Rachel M McLoughlin", - "author_inst": "Trinity College Dublin, Ireland" - }, - { - "author_name": "Colm Bergin", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Nollaig Bourke", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Cliona O'Farrelly", - "author_inst": "Trinity Biomedical Sciences Institute, Trinity College Dublin" - }, - { - "author_name": "Niall Conlon", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Cliona Ni Cheallaigh", - "author_inst": "St James's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.01.21262913", "rel_title": "Sars-Cov-2 antibody titer 3 months post-vaccination is affected by age, gender, smoking and vitamin D.", @@ -617059,6 +619513,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.30.21262341", + "rel_title": "Modelling the potential role of super spreaders on COVID-19 transmission dynamics", + "rel_date": "2021-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262341", + "rel_abs": "Superspreading phenomenon has been observed in many infectious diseases and contributes significantly to public health burden in many countries. Superspreading events have recently been reported in the transmission of the COVID-19 pandemic. The present study uses a set of nine ordinary differential equations to investigate the impact of superspreading on COVID-19 dynamics. The model developed in this study addresses the heterogeineity in infectiousness by taking into account two forms of transmission rate functions for superspreaders based on clinical (infectivity level) and social or environmental (contact level). The basic reproduction number has been derived and the contribution of each infectious compartment towards the generation of new COVID-19 cases is ascertained. Data fitting was performed and parameter values were estimated within plausible ranges. Numerical simulations performed suggest that control measures that decrease the effective contact radius and increase the transmission rate exponent will be greatly beneficial in the control of COVID-19 in the presence of superspreading phenomena.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Josiah Mushanyu", + "author_inst": "University of zimbabwe" + }, + { + "author_name": "Williams Chukwu", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Farai Nyabadza", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Gift Muchatibaya", + "author_inst": "university of Zimbabwe" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.01.458644", "rel_title": "Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets", @@ -617891,37 +620376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.31.21262923", - "rel_title": "Health impact and cost of COVID-19 prophylaxis with monoclonal antibodies", - "rel_date": "2021-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262923", - "rel_abs": "BackgroundThe COVID-19 pandemic has led to over 600,000 deaths in the United States and continues to disrupt lives even as effective vaccines are available. We aimed to estimate the impact and health system cost of implementing post-exposure prophylaxis against household exposure to COVID-19 with monoclonal antibodies.\n\nMethodsWe developed a decision-analytical model analysis of results from a recent randomized controlled trial with complementary data on household demographic structure, vaccine coverage, and COVID-19 confirmed case counts for the representative month of May, 2021. The model population includes individuals of all ages in the United States by sex and race/ethnicity.\n\nResultsIn a month of similar intensity to May, 2021, in the USA, a monoclonal antibody post-exposure prophylaxis program reaching 50% of exposed unvaccinated household members aged 50+, would avert 1,813 (1,171 - 2,456) symptomatic infections, 526 (343 - 716) hospitalizations, and 83 (56 - 116) deaths. Assuming the unit cost of administering the intervention was US$ 1,264, this program would save the health system US$ 3,055,202 (-14,034,632 - 18,787,692).\n\nConclusionsCurrently in the United States, health system and public health actors have an opportunity to improve health and reduce costs through COVID-19 post-exposure prophylaxis with monoclonal antibodies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Abraham D. Flaxman", - "author_inst": "University of Washington" - }, - { - "author_name": "Rodal Issema", - "author_inst": "University of Washington" - }, - { - "author_name": "Ruanne V. Barnabas", - "author_inst": "University of Washington" - }, - { - "author_name": "Jennifer M. Ross", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.31.21262909", "rel_title": "PERCOVID: A Model to Describe COVID Percolation on a Network of Social Relationships", @@ -619025,6 +621479,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.24.21262245", + "rel_title": "Symptomatology associated with the diffusion of the SARS-CoV-2 Lambda variant in Peru: An infodemiologic analysis", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262245", + "rel_abs": "The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) Lambda variant rapidly diffused across Peru following its identification in December 2020, and had now spread worldwide. In this study, we investigated infodemiologic trends in symptomatology associated with the Coronavirus Disease 2019 (COVID-19) following the spread of SARS-CoV-2 Lambda variant in Peru, enabling infodemiologic surveillance of SARS-CoV-2 in regions with high circulation of this new variant. Weekly Google Trends scores were obtained for key symptom keywords between March 1st, 2020 and July 4th, 2021, whilst case count data were obtained from Peruvian Ministry of Health. Multiple time series linear regression was used to assess trends in each score series, using the week of December 27th as cutoff for emergence of the Lambda variant. The significance of such trends was tested for each time period, before and after the cutoff date. A total 2,075,484 confirmed SARS-CoV-2 infections in Peru in relation to Google Trends data were analyzed. After Lambda variant emergence, searches for \"diarrhea\" demonstrated a change from a negative to positive correlation with weekly case counts and anticipated dynamic changes in case counts by 1-5 weeks. Searches for \"shortness of breath\" and \"headache\" remained consistently positively correlated to weekly case counts before and after Lambda emergence. No changes in searches for other common cold symptoms were observed, while no specific trends were observed for \"taste loss\" or \"smell loss\". Diarrhea, headache, and shortness of breath appear to be the most important symptoms for infodemiologic tracking the current outbreak in Peru and other regions with high circulation of SARS-CoV-2 Lambda variant.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Brandon Michael Henry", + "author_inst": "Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children Hospital Medical Center, Cincinnati, OH, USA" + }, + { + "author_name": "Maria Helena Santos de Oliveira", + "author_inst": "Department of Biostatistics, State University of Maringa, Maringa, Brazil" + }, + { + "author_name": "Thais Barbosa de Oliveira", + "author_inst": "Department of Biostatistics, State University of Maringa, Maringa, Brazil" + }, + { + "author_name": "Kin Israel Notarte", + "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila 1008, Philippines" + }, + { + "author_name": "Giuseppe Lippi", + "author_inst": "Section of Clinical Biochemistry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.23.21262413", "rel_title": "Towards the global equilibrium of COVID-19: statistical analysis of country-level data", @@ -619841,65 +622330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.27.21262679", - "rel_title": "BNT162b2 vaccine booster dose protection: A nationwide study from Israel", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.27.21262679", - "rel_abs": "BackgroundOn July 30, 2021, a third (booster) dose of the Pfizer BNT162b2 vaccine was approved in Israel for individuals 60 years or older who had been fully vaccinated (i.e., received two doses) at least five months previously. Here, we estimate the reduction in relative risk for confirmed infection and severe COVID-19 provided by the booster dose.\n\nMethods1,144,690 individuals aged 60y and older who were eligible for a booster dose were followed between July 30 and August 22, 2021. We defined dynamic cohorts where individuals initially belong to the non-booster cohort, leave it when receiving the booster dose and join the booster cohort 12 days later. Rates of infection and severe COVID-19 outcomes per person-days at risk were compared between the cohorts using Poisson regression, adjusting for possible confounding factors.\n\nResultsTwelve days or more after the booster dose we found an 11.4-fold (95% CI: [10.0, 12.9]) decrease in the relative risk of confirmed infection, and a >10-fold decrease in the relative risk of severe illness. Under a conservative sensitivity analysis, we find {approx}5-fold protection against confirmed infection.\n\nConclusionsIn conjunction with safety reports, this study demonstrates the effectiveness of a third vaccine dose in both reducing transmission and severe disease and indicates the great potential of curtailing the Delta variant resurgence by administering booster shots.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yinon M. Bar-On", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yair Goldberg", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Micha Mandel", - "author_inst": "he Hebrew University of Jerusalem" - }, - { - "author_name": "Omri Bodenheimer", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Laurence Freedman", - "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" - }, - { - "author_name": "Nir Kalkstein", - "author_inst": "KI Research Institute" - }, - { - "author_name": "Barak Mizrahi", - "author_inst": "KI Research Institute" - }, - { - "author_name": "Sharon Alroy-Preis", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Nachman Ash", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Ron Milo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Amit Huppert", - "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.29.21262512", "rel_title": "Correlation between times to SARS-CoV-2 symptom onset and secondary transmission undermines epidemic control efforts", @@ -621175,6 +623605,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.20.21261687", + "rel_title": "Randomized trials on non-pharmaceutical interventions for COVID-19 as of August 2021: a meta-epidemiological analysis", + "rel_date": "2021-08-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21261687", + "rel_abs": "BackgroundNumerous non-pharmaceutical interventions (NPIs) were taken worldwide to contain the spread of the COVID-19 pandemic. We aimed at providing an overview of randomized trials assessing NPIs to prevent COVID-19.\n\nMethodsWe included all randomized trials assessing NPIs to prevent COVID-19 in any country and setting registered in ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform using the COVID-evidence platform (until 17 August 2021). We searched for corresponding publications in MEDLINE/PubMed, Google Scholar, the Living Overview of Evidence platform (L-OVE), and the Cochrane COVID-19 registry as well as for results posted in registries.\n\nResultsWe identified 41 randomized trials. Of them, 11 were completed (26.8%) including 7 with published results. The 41 trials planned to recruit a median of 1,700 participants (IQR, 588 to 9,500, range 30 to 35,256,399) with a median planned duration of 8 months (IQR, 3 to 14, range 1 to 24). Most came from the United States (n=11, 26.8%). The trials mostly assessed protective equipment (n=11, 26.8%), COVID-19-related information and education programs (n=9, 22.0%), access to mass events under specific safety measures (n=5, 12.2%), testing and screening strategies (n=5, 12.2%), and hygiene management (n=5, 12.2%).\n\nConclusionsWorldwide, 41 randomized trials assessing NPIs have been initiated with published results available to inform policy decisions for only 7 of them. A long-term research agenda including behavioral, environmental, social, and systems level interventions is urgently needed to guide policies and practices in the current and future public health emergencies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Julian Hirt", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + }, + { + "author_name": "Perrine Janiaud", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + }, + { + "author_name": "Lars G. Hemkens", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.29.458083", "rel_title": "Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble", @@ -621771,141 +624228,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.26.21262705", - "rel_title": "The effectiveness of SARS-CoV-2 vaccination in preventing severe illness and death- real-world data from a cohort of patients hospitalized with COVID-19.", - "rel_date": "2021-08-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262705", - "rel_abs": "BackgroundDue to the unprecedented speed of SARS-CoV-2 vaccine development, their efficacy trials and issuance of emergency use approvals and marketing authorizations, additional scientific questions remain that need to be answered regarding vaccine effectiveness, vaccination regimens and the need for booster doses. While long-term studies on the correlates of protection, vaccine effectiveness, and enhanced surveillance are awaited, studies on breakthrough infections help us understand the nature and course of this illness among vaccinated individuals and guide in public health preparedness.\n\nMethodsThis observational cohort study aimed at comparing the differences in clinical, biochemical parameters and the hospitalization outcomes of 53 fully vaccinated individuals with those of unvaccinated (1,464) and partially vaccinated (231) individuals, among a cohort of 2,080 individuals hospitalized with SARS-CoV-2 infection.\n\nResultsCompleting the course of vaccination protected individuals from developing severe COVID-19 as evidence by lower proportions of those with hypoxia, abnormal levels of inflammatory markers, requiring ventilatory support and death compared to unvaccinated and partially vaccinated individuals. There were no differences in these outcomes among patients who received either vaccine type approved in India.\n\nConclusionWith a current rate of only 9.5% of the Indian population being fully vaccinated, efforts should be made to improve the vaccination rates as a timely measure to prepare for the upcoming waves of this highly transmissible pandemic. Vaccination rates of the communities may also guide in the planning of the health needs and appropriate use of medical resources.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe Government of India started vaccinating its citizens from the 16th of January 2021, after emergency use authorization had been received for the use of two vaccines, BBV152, a COVID-19 vaccine based on the whole-virion SARS-CoV-2 vaccine strain NIV-2020-770, (Covaxin) and the recombinant replication-deficient chimpanzee adenovirus vector encoding the spike protein ChAdOx1 nCoV-19 Corona Virus Vaccine (Covishield). These have been approved by the Indian regulatory authority based on randomized controlled studies. In these studies, was found that the vaccines led to more than 90% reduction in symptomatic COVID-19 disease. However, there is scarce evidence of the efficacy of these vaccines in real-world scenarios. A few studies have looked at vaccinated cohorts such as health care workers in whom the vaccines had an efficacy similar to the RCTs. In a study of patients with SARS-CoV-2 infection admitted to a tertiary care hospital in New Delhi, it was found that mortality in fully vaccinated patients was 12.5% as compared to 31.5% in the unvaccinated cohort.\n\nAdded-value of this studyThis cohort of hospitalized patients with SARS-CoV-2 infection was studied during the peak of the second wave of COVID-19 in India during which the delta variant of concern was the predominant infecting strain and had 26% patients who were partially vaccinated and 71.4% who were unvaccinated. Only 3% of the patients were fully vaccinated and developed a breakthrough infection. At the time of presentation, 13% of the individuals with breakthrough infection and 48{middle dot}5% in the non-vaccinated group were hypoxic. Inflammatory markers were significantly lower in the completely vaccinated patients with breakthrough infection. The need for use of steroids and anti-viral agents such as remdesivir was also significantly low in the breakthrough infection group. A significantly less proportion of the individuals with breakthrough infection required oxygen supplementation or ventilatory support. Very few deteriorated or progressed to critical illness during their hospital stay. Only 3 individuals (5.7%) out of the 53 who developed breakthrough infection succumbed to illness while case fatality rates were significantly higher in the unvaccinated (22.8%) and partially vaccinated (19.5%) groups. Propensity score weighted multivariate logistic regression analysis revealed lower odds of developing hypoxia, critical illness or death in those who were completely vaccinated.\n\nImplications of all the available evidenceThe real-world effectiveness of the vaccines against SARS-CoV-2 seems to be similar to the randomized controlled trials. The vaccines are very effective in reducing the incidence of severe COVID-19, hypoxia, critical illness and death. The reduced need for oxygen supplementation, mechanical ventilation and the requirement of corticosteroids or other expensive medications such as anti-viral drugs could go a long way in redistributing scarce health care resources. All nations must move forward and vaccinate the citizens, as the current evidence suggests that prevention is better than cure.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Hari Krishna Raju Sagiraju", - "author_inst": "Department of Preventive Oncology, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Arunmozhimaran Elavarasi", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Nishkarsh Gupta", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Rohit Kumar", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Saurav Sekhar Paul", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Saurabh Vig", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Prashant Sirohiya", - "author_inst": "National Cancer Institute, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Brajesh Ratre", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Rakesh Garg", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Anuja Pandit", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Ram Nalwa", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Balbir Kumar", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Ved Prakash Meena", - "author_inst": "Department of Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Naveet Wig", - "author_inst": "Department of Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Saurabh Mittal", - "author_inst": "Department of Pulmonary medicine, critical care and Sleep disorders, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Sourabh Pahuja", - "author_inst": "Department of Pulmonary medicine, critical care and Sleep disorders, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Karan Madan", - "author_inst": "Department of Pulmonary medicine, critical care and Sleep disorders, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Nupur Das", - "author_inst": "Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Tanima Dwivedi", - "author_inst": "Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Ritu Gupta", - "author_inst": "Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Laxmitej Wundavalli", - "author_inst": "Department of Hospital Administration, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Angel R Singh", - "author_inst": "Department of Hospital Administration, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Sheetal Singh", - "author_inst": "Department of Hospital Administration, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Abhinav Mishra", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Karanvir Singh Matharoo", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Manisha", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Sunil Kumar", - "author_inst": "Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Anant Mohan", - "author_inst": "Department of Pulmonary medicine, critical care and Sleep disorders, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Randeep Guleria", - "author_inst": "Department of Pulmonary medicine, critical care and Sleep disorders, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Sushma Bhatnagar", - "author_inst": "Department of Onco-anesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.23.21262464", "rel_title": "Opaganib in COVID-19 pneumonia: Results of a randomized, placebo-controlled Phase 2a trial", @@ -622881,6 +625203,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.25.21262636", + "rel_title": "Impact of Covid-19 Pandemic on Racial/Ethnic Differences in Mortality by Cause of Death", + "rel_date": "2021-08-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262636", + "rel_abs": "ObjectivesTo quantify changes in all-cause and cause-specific mortality by race and ethnicity between 2019 and 2020.\n\nMethodsUsing 2019 and 2020 provisional death counts from the National Center for Health Statistics and population estimates from the US Census Bureau, we estimate age-standardized death rates by race/ethnicity and attribute changes in mortality to various causes of death. We also examine how patterns of change across racial/ethnic groups vary by age and sex.\n\nResultsCovid-19 death rates in 2020 were highest in the Hispanic community whereas Black individuals had the largest increase in all-cause mortality between 2019 and 2020. Increases in mortality from heart disease, diabetes, and external causes of death accounted for the adverse trend in all-cause mortality within the Black population. Percentage increases in all-cause mortality were similar for men and women and for ages 25-64 and 65+ for Black and White populations, but increases were greatest for working-aged men among the Hispanic population.\n\nConclusionsExamining increases in non-Covid-19 causes of death is essential for fully capturing both the direct and indirect impact of the Covid-19 pandemic on racial/ethnic mortality disparities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anneliese N. Luck", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Samuel H. Preston", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Irma T. Elo", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Andrew C. Stokes", + "author_inst": "Department of Global Health, Boston University School of Public Health, Boston, MA, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.25.21262614", "rel_title": "Democratic governance and excess mortality during the COVID-19 pandemic", @@ -623665,317 +626018,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.25.21262404", - "rel_title": "Profile of Mucormycosis Cases from a Network of Hospitals in North India Amidst COVID-19 Pandemic", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262404", - "rel_abs": "Incidence of mucormycosis suddenly surged in India after the second wave of COVID-19. This is a crippling disease and needs to be studied in detail to understand the disease, its course, and the outcomes.\n\nBetween 1st March and 15th July 2021, our network of hospitals in North India received a total of 155 cases of COVID-associated mucormycosis cases as all of them reported affliction by COVID-19 earlier or concurrent. Their records were retrieved from the Electronic Health Records system of the hospitals and their demographics, clinical features, treatments, and outcomes were studied. More than 80% (125 cases) had proven disease and the remaining 30 were categorized as possible mucormycosis as per the EORTC criteria.\n\nMore than two-thirds (69.0%) of the cases were males and the mean age was 53 years for either sex. Nearly two-thirds (64.5%) had symptoms of nose and jaws and 42.6% had eye involvement. Some had multiple symptoms. As many as 78.7% had diabetes and 91.6% gave history of use of steroids during COVID-19 treatment. The primary surgery was functional endoscopic sinus surgery (FESS) (83.9%). Overall mortality was 16.8%, which is one-and-a-half times the mortality in hospitalized COVID-19 patients in the corresponding population. Occurrence of mucormycosis was associated with diabetes and use of steroids, but mortality was not associated with either of them. Cases undergoing surgery and on antifungal had steeply lower mortality (11.9% vs. 50.0%, P < 0.001) than those who were exclusively on antifungal drugs. Treatment by different drugs did not make much of a difference in mortality.", - "rel_num_authors": 74, - "rel_authors": [ - { - "author_name": "Sandeep Budhiraja", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Mona Aggarwal", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Monica Mahajan", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Abhaya Indrayan", - "author_inst": "Department of Clinical Directorate, Max Healthcare, New-Delhi, India" - }, - { - "author_name": "Vinitaa Jha", - "author_inst": "Department of Clinical Directorate, Max Healthcare, New-Delhi, India" - }, - { - "author_name": "Ambrish Mithal", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Sanjay Sachdeva", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Sumit Mrig", - "author_inst": "Max Smart Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Anurag Jain", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Ravinder Gera", - "author_inst": "Max Hospital, Gurgaon, Haryana" - }, - { - "author_name": "Rahul Aggarwal", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Suven Kalra", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "WVPS Ramalingam", - "author_inst": "BLK-Max Super Speciality Hospital, New Delhi, India" - }, - { - "author_name": "Anupal Deka", - "author_inst": "Max Super Speciality Hospital, Dehradun, Uttarakhand, India" - }, - { - "author_name": "Arjun Dass", - "author_inst": "Max Super Speciality Hospital, Mohali, Punjab, India" - }, - { - "author_name": "D Jijina", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Ajit ManSingh", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Anuj Singhal", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Rajashekhar Reddi", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Puneet Aggarwal", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Mukesh Kumar", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "J D Mukherji", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Vivek Nangia", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Ajay Lall", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Omender Singh", - "author_inst": "Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Arun Dewan", - "author_inst": "Max Smart Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Ajay Jain", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Gita G Shrivastava", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Mala Bhattacharjee", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Meena Nihalani", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Manoj Kumar", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Meenakshi Jain", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Mukesh Mehra", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Vijay Arora", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Viresh Prashant Mehta", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Dilip Bhalla", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Amit Batra", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Rajesh Gupta", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Vivek Kumar", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Sanjeev Dua", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Praveen Pandey", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Y P Singh", - "author_inst": "Max Super Speciality Hospital, Patparganj, New Delhi, India" - }, - { - "author_name": "Mohit Mathur", - "author_inst": "Max Hospital, Gurgaon, Haryana" - }, - { - "author_name": "Ashok Singh", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Sanjeev Arora", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Ajay Kumar Gupta", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Pankaj Nand Choudhary", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Manoj Singh", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Namita Kaul", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Sitla Prasad Pathak", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Sharad Joshi", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Manish Gupta", - "author_inst": "Max Super Speciality Hospital, Vaishali, U.P. India" - }, - { - "author_name": "Rajesh Mishra", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Alok Joshi", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Manoj Aggarwal", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Rajiv Gupta", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Vandana Boobna", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Yogesh Kumar Chhabra", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Inder Mohan Chugh", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Sandeep Garg", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Vikas Mittal", - "author_inst": "Max Super Speciality Hospital, Shalimar Bagh, New Delhi, India" - }, - { - "author_name": "Neha Sood", - "author_inst": "BLK-Max Super Speciality Hospital, New Delhi, India" - }, - { - "author_name": "Anil Kumar", - "author_inst": "BLK-Max Super Speciality Hospital, New Delhi, India" - }, - { - "author_name": "Rajesh Kumar Pande", - "author_inst": "BLK-Max Super Speciality Hospital, New Delhi, India" - }, - { - "author_name": "V P Singh", - "author_inst": "Max Super Speciality Hospital, Dehradun, Uttarakhand, India" - }, - { - "author_name": "Iram Khan", - "author_inst": "Max Super Speciality Hospital, Dehradun, Uttarakhand, India" - }, - { - "author_name": "Nitin Garg", - "author_inst": "Max Super Speciality Hospital, Dehradun, Uttarakhand, India" - }, - { - "author_name": "Shantanu Belwal", - "author_inst": "Max Super Speciality Hospital, Dehradun, Uttarakhand, India" - }, - { - "author_name": "Puneet Tyagi", - "author_inst": "Max Super Speciality Hospital, Dehradun, Uttarakhand, India" - }, - { - "author_name": "Anup Kumar Roy", - "author_inst": "Max Super Speciality Hospital, Mohali, Punjab, India" - }, - { - "author_name": "Deepak Bhasin", - "author_inst": "Max Super Speciality Hospital, Mohali, Punjab, India" - }, - { - "author_name": "Sachin Pandove", - "author_inst": "Max Super Speciality Hospital, Mohali, Punjab, India" - }, - { - "author_name": "Ravikant Bahl", - "author_inst": "Max Super Speciality Hospital, Mohali, Punjab, India" - }, - { - "author_name": "Prateek Soni", - "author_inst": "Max Super Speciality Hospital, Mohali, Punjab, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.25.21262529", "rel_title": "Effectiveness of vaccination against symptomatic and asymptomatic SARS-CoV-2 infection: a systematic review and meta-analysis", @@ -625123,6 +627165,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.23.21262477", + "rel_title": "Low risk of SARS-CoV-2 transmission via fomite, even in cold-chain", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262477", + "rel_abs": "BackgroundCountries continue to debate the need for decontamination of cold-chain food packaging to reduce possible SARS-CoV-2 fomite transmission among workers. While laboratory-based studies demonstrate persistence of SARS-CoV-2 on surfaces, the likelihood of fomite-mediated transmission under real-life conditions is uncertain.\n\nMethodsUsing a quantitative risk assessment model, we simulated in a frozen food packaging facility 1) SARS-CoV-2 fomite-mediated infection risks following worker exposure to contaminated plastic packaging; and 2) reductions in these risks attributed to masking, handwashing, and vaccination.\n\nFindingsIn a representative facility with no specific interventions, SARS-CoV-2 infection risk to a susceptible worker from contact with contaminated packaging was 2{middle dot}8 x 10-3 per 1h-period (95%CI: 6{middle dot}9 x 10-6, 2{middle dot}4 x 10-2). Implementation of standard infection control measures, handwashing and masks (9{middle dot}4 x 10-6 risk per 1h-period, 95%CI: 2{middle dot}3 x 10-8, 8{middle dot}1 x 10-5), substantially reduced risk (99{middle dot}7%). Vaccination of the susceptible worker (two doses Pfizer/Moderna, vaccine effectiveness: 86-99%) combined with handwashing and masking reduced risk to less than 1{middle dot}0 x 10-6. Simulating increased infectiousness/transmissibility of new variants (2-, 10-fold viral shedding) among a fully vaccinated workforce, handwashing and masks continued to mitigate risk (2{middle dot}0 x 10-6 -1{middle dot}1 x 10-5 risk per 1h-period). Decontamination of packaging in addition to these interventions reduced infection risks to below the 1{middle dot}0 x 10-6 risk threshold.\n\nInterpretationFomite-mediated SARS-CoV-2 infection risks were very low under cold-chain conditions. Handwashing and masking provide significant protection to workers, especially when paired with vaccination.\n\nFundingU.S. Department of Agriculture", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Julia S. Sobolik", + "author_inst": "Emory University" + }, + { + "author_name": "Elizabeth T. Sajewski", + "author_inst": "Emory University" + }, + { + "author_name": "Lee-Ann Jaykus", + "author_inst": "North Carolina State University" + }, + { + "author_name": "D. Kane Cooper", + "author_inst": "Emory University" + }, + { + "author_name": "Ben A. Lopman", + "author_inst": "Emory University" + }, + { + "author_name": "Alicia NM. Kraay", + "author_inst": "Emory University" + }, + { + "author_name": "P. Barry Ryan", + "author_inst": "Emory University" + }, + { + "author_name": "Jodie L. Guest", + "author_inst": "Emory University" + }, + { + "author_name": "Amy Webb-Girard", + "author_inst": "Emory University" + }, + { + "author_name": "Juan S. Leon", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.23.21262499", "rel_title": "Comparative analyses of all FDA EUA-approved rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation", @@ -625835,37 +627932,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.23.21262184", - "rel_title": "COMORBIDITY ANALYSIS: OVERLAPPING SEMICIRCLES WITH WIGNER LAW AND RANDOM MATRIX THEORY", - "rel_date": "2021-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262184", - "rel_abs": "In December 2019 COVID-19 appeared as a new pandemic that has claimed the lives of millions of people around the world. This article presents a regional analysis of COVID-19 in Mexico. Due to the comorbidities of Mexican society, the new pandemic implies a higher risk for the population. The study period runs from April 12 to October 5, 2020 (761 665 Patients). In this proposal we apply a unique methodology of random matrix theory in the moments of a probability measure that appears as the limit of the empirical spectral distribution by the Wigner semicircle law. The graphical presentation of the results is done with Machine Learning methods in the SuperHeat maps. With this is possible to analyze the behavior of patients who tested positive for COVID-19 and their comorbidities. We conclude that the most sensitive comorbidities in hospitalized patients are the following three: COPD, Other Diseases and Renal Diseases.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Oralia Nolasco", - "author_inst": "Tecana American University" - }, - { - "author_name": "Luis Alberto QuezadaTellez", - "author_inst": "Universidad Iberoamericana" - }, - { - "author_name": "Yuri Salazar Flores", - "author_inst": "Facultad de Ciencias, UNAM" - }, - { - "author_name": "Adan Diaz Hernandez", - "author_inst": "Facultad de Economia y Negocios, UniversidadAnahuac" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.08.23.21262454", "rel_title": "Evaluation of GENECUBE(R) HQ SARS-CoV-2 for anterior nasal samples and saliva samples with a new rapid examination protocol", @@ -627213,6 +629279,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.19.21262139", + "rel_title": "Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California", + "rel_date": "2021-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262139", + "rel_abs": "Associations between vaccine breakthrough cases and infection by SARS coronavirus 2 (SARS-CoV-2) variants have remained largely unexplored. Here we analyzed SARS-CoV-2 whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from February 1 to June 30, 2021, of which 125 (9.1%) were vaccine breakthrough infections. Fully vaccinated were more likely than unvaccinated persons to be infected by variants carrying mutations associated with decreased antibody neutralization (L452R, L452Q, E484K, and/or F490S) (78% versus 48%, p = 1.96e-08), but not by those associated with increased infectivity only (N501Y) (85% versus 77%, p = 0.092). Differences in viral loads were non-significant between unvaccinated and fully vaccinated persons overall (p = 0.99) and according to lineage (p = 0.09 - 0.78). Viral loads were significantly higher in symptomatic as compared to asymptomatic vaccine breakthrough cases (p < 0.0001), and symptomatic vaccine breakthrough infections had similar viral loads to unvaccinated infections (p = 0.64). In 5 cases with available longitudinal samples for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results suggest that vaccine breakthrough infecions are overrepresnted by circulating antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may potentially transmit COVID-19 as efficiently as unvaccinated infections, regardless of the infecting lineage.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Venice Servellita", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Amelia Gliwa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Erika Torres", + "author_inst": "Color Genomics" + }, + { + "author_name": "Noah Brazer", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Zhou", + "author_inst": "Color Genomics" + }, + { + "author_name": "Katherine Hernandez", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Madeline Sankaran", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Baolin Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Daniel Wong", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Candace Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yueyuan Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin Reyes", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Dustin Glasner", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Wayne Deng", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steve Miller", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Edwin Frias", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "John Hackett", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "Susan Philip", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Scott Topper", + "author_inst": "Color Genomics" + }, + { + "author_name": "Darpun Sachdev", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.24.21262415", "rel_title": "Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections", @@ -627877,61 +630050,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.25.457627", - "rel_title": "Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization", - "rel_date": "2021-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.25.457627", - "rel_abs": "SARS-CoV-2 is a zoonotic agent capable of infecting humans and a wide range of animal species. Over the duration of the pandemic, mutations in the SARS-CoV-2 Spike protein (S) have arisen in circulating viral populations, culminating in the spread of several variants of concern (VOC) with varying degrees of altered virulence, transmissibility, and neutralizing antibody escape. In this study, we employed lentivirus-based pseudotyped viruses that express specific SARS-CoV-2 S protein substitutions and cell lines that stably express ACE2 from nine different animal species to gain insights into the effects of VOC mutations on viral entry and antibody neutralization capability. All animal ACE2 receptors tested, except mink, support viral cell entry for pseudoviruses expressing the parental (prototype Wuhan-1) S at levels comparable to human ACE2. Most single S substitutions (e.g., 452R, 478K, 501Y) did not significantly change virus entry, although 614G and 484K resulted in a decreased efficiency in viral entry. Conversely, combinatorial VOC substitutions in the S protein were associated with significantly increased entry capacity of pseudotyped viruses compared to that of the parental Wuhan-1 pseudotyped virus. Similarly, infection studies using live ancestral (USA-WA1/2020), Alpha, and Beta SARS-CoV-2 viruses in hamsters revealed a higher replication potential for the Beta variant compared to the ancestral prototype virus. Moreover, neutralizing titers in sera from various animal species, including humans, were significantly reduced by single substitutions of 484K or 452R, double substitutions of 501Y-484K, 452R-484K and 452R-478K and the triple substitution of 501Y-484K-417N, suggesting that 484K and 452R are particularly important for evading neutralizing antibodies in human, cat, and rabbit sera. Cumulatively, this study reveals important insights into the host range of SARS-CoV-2 and the effect of recently emergent S protein substitutions on viral entry, virus replication and antibody-mediated viral neutralization.\n\nAuthor summaryCells stably expressing ACE2 from various animals and a lentivirus-based SARS-CoV-2 pseudotyped virus assay were established to study SARS-CoV-2 cell entry. The results demonstrated that ACE2 from a wide range of animal species facilitate S-mediated virus entry into cells, which is supported by in silico data as well as natural and experimental infection studies. Pseudotyped viruses containing mutations in the RBD of S representative of the Alpha, Gamma, and especially Beta, variants of concern demonstrated that certain mutations are associated with increased viral entry compared to the parental S. The Beta variant was also observed to have a replicative advantage in vitro and in vivo compared to the prototype virus. Pseudotyped viruses containing combinatorial substitutions of 501Y-484K-417K, 614G-501Y-484K and 614G-501Y-484K-417N increased viral entry via ACE2 across multiple species. The 501Y or 478K single substitution did not significantly affect neutralizing capacity of immune sera compared to the prototype strain, but the addition of 484K or 452R substitutions significantly reduced the neutralizing titers.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yunjeong Kim", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Natasha N Gaudreault", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "David A Meekins", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Krishani D Perera", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Dashzeveg Bold", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Jessie D Trujillo", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Igor Morozov", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Chester D McDowell", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Kyeong-Ok Chang", - "author_inst": "Kansas State University College of Veterinary Medicine" - }, - { - "author_name": "Juergen A. Richt", - "author_inst": "Kansas State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.25.457699", "rel_title": "Directing an mRNA-LNP vaccine toward lymph nodes improves humoral and cellular immunity against SARS-CoV-2", @@ -628966,6 +631084,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.16.21262150", + "rel_title": "The IHME vs Me: Modeling USA CoVID-19 Spread, Early Data to the Fifth Wave", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262150", + "rel_abs": "Epidemiologists have never had such high-quality real-time pandemic data. Modeling CoVID-19 pandemic data became a predictive tool in-stead of an afterwards analysis. How early CoVID-19 model predictions impacted US Government policies and practices is first reviewed here as an important part of the pandemic history. It spurred independent modeling efforts, such as this, to help develop a better understanding of CoVID-19 spread, and to provide a substitute for the IHME (Institute for Health Metrics & Evaluation, U. Washington) 4-month predictions for the expected pandemic evolution, which they had to revise every couple of weeks. Our alternative model, which was developed over the course of several earlier medrxiv.org preprints, is shown here to provide a good description for the entire USA CoVID-19 pandemic to date, covering: (1) the original CoVID-19 wave [3/21/20-6/07/20], (2) the Summer 2020 Resurgence [6/07/20-9/25/20], (3) the large Winter 2020 Resurgence [9/25/20-3/19/21], (4) a small Spring 2021 \"Fourth Wave\", [3/19/21-6/07/21], and (5) the present-day Summer 2021 \"Fifth Wave\" [6/07/21-present], which the USA is now in the midst of. Our analysis of the initial \"Fifth Wave\" data shows that this wave presently has the capacity to infect virtually all susceptible non-vaccinated persons who practice NO Mask-Wearing and minimal Social Distancing.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Genghmun Eng", + "author_inst": "Retired Scientist" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.18.21262061", "rel_title": "Closed Doors: Predictors of Stress, Anxiety, Depression, and PTSD During the Onset of COVID-19 Pandemic in Brazil", @@ -629818,33 +631955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.08.20.21262375", - "rel_title": "The impact on the mental health and well-being of unpaid carers affected by social distancing, self-isolation and shielding during the COVID 19 pandemic in England - a systematic review", - "rel_date": "2021-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21262375", - "rel_abs": "ObjectiveThis study explores the impact of the COVID 19 lockdown measures on the mental health and well-being of unpaid carers, who make up the largest number of the carer population in England.\n\nStudy designA systematic review research protocol was designed and used to conduct the review along with the Enhancing Transparency in Reporting the synthesis of Qualitative Research - ENTREQ statement [43]. Pre-determined inclusion and exclusion criteria were used. EndNote X9 reference management was used and the search process was represented using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flow diagram [76]. Appraisal of the included research was carried out using the Critical Appraisal Skills Programme (CASP) [57]. Line by line coding was done using inductive thematic synthesis and EPPI Reviewer 4 software [60].\n\nResultsFour themes emerged; immediate worries or fears, adapting to change, post pandemic fears and use of technology.\n\nConclusionThe measures put in place during the first lockdown period have had detrimental impacts on unpaid carers, putting them at greater risk of burnout. However, use of digital platforms could have a positive impact on well-being. Recommendations for further research are provided.\n\nWhat is new?O_ST_ABSKey findings?C_ST_ABSO_LIDiscontinued or reduced access to activities and services during the first lockdown during the pandemic has had a negative impact on both people who require care and their carers.\nC_LIO_LICarers prioritise the mental health and wellbeing needs of the people they care for over their own.\nC_LIO_LIFurther qualitative research from different groups of carers would be useful to gain a deeper understanding of the impact of the COVID 19 pandemic measures on unpaid carers.\nC_LIO_LIUse of digital technology and digital platforms may be useful tools for carers both during the pandemic and after.\nC_LI\n\nWhat this adds to what is known?O_LIThere have been very few qualitative studies on the impact of the COVID 19 pandemic on the mental health and wellbeing of unpaid carers, this review has synthesised their findings and will contribute to future research.\nC_LIO_LIUnpaid carers are known to be at risk of poor mental health and wellbeing outcomes, this review demonstrates that they are even more at risk due to the increased reliance on them during the pandemic.\nC_LI\n\nWhat is this implication and what should change?O_LIThere is limited qualitative data available from a range of different groups of carers for example, spouse carers, parent carers, carers of people who have specific needs or conditions. Therefore, purposeful sample research to determine the needs of groups of carers during the COVID 19 pandemic could be valuable.\nC_LIO_LIUnpaid carers who do not have appropriate support are more at risk of poor mental health and wellbeing outcomes. During the pandemic services have had to adapt to the various rules implemented. Digital adaptations to the provision of support to both carers and the people they care for could be beneficial both during and after the pandemic.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tabo Akafekwa", - "author_inst": "University of Manchester" - }, - { - "author_name": "Elizabeth Dalgarno", - "author_inst": "University of Manchester" - }, - { - "author_name": "Arpana Verma", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.20.21262389", "rel_title": "Model-based assessment of SARS-CoV-2 Delta variant transmission dynamics within partially vaccinated K-12 school populations", @@ -631048,6 +633158,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.23.457408", + "rel_title": "Deep immune profiling of the maternal-fetal interface with mild SARS-CoV-2 infection", + "rel_date": "2021-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457408", + "rel_abs": "Pregnant women are an at-risk group for severe COVID-19, though the majority experience mild/asymptomatic disease. Although severe COVID-19 has been shown to be associated with immune activation at the maternal-fetal interface even in the absence of active viral replication, the immune response to asymptomatic/mild COVID-19 remains unknown. Here, we assessed immunological adaptations in both blood and term decidua from 9 SARS-exposed pregnant women with asymptomatic/mild disease and 15 pregnant SARS-naive women. In addition to selective loss of tissue-resident decidual macrophages, we report attenuation of antigen presentation and type I IFN signaling but upregulation of inflammatory cytokines and chemokines in blood monocyte derived decidual macrophages. On the other hand, infection was associated with remodeling of the T cell compartment with increased frequencies of activated CD69+ tissue-resident T cells and decreased abundance of Tregs. Interestingly, frequencies of cytotoxic CD4 and CD8 T cells increased only in the blood, while CD8 effector memory T cells were expanded in the decidua. In contrast to decidual macrophages, signatures of type I IFN signaling were increased in decidual T cells. Finally, T cell receptor diversity was significantly reduced with infection in both compartments, albeit to a much greater extent in the blood. The resulting aberrant immune activation in the placenta, even with asymptomatic disease may alter the exquisitely sensitive developing fetal immune system, leading to long-term adverse outcomes for offspring.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Suhas Sureshchandra", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Michael Z. Zulu", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Brianna Doratt", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Allen Jankeel", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Delia Tifrea", + "author_inst": "University of California,Irvine" + }, + { + "author_name": "Robert A Edwards", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Monica Rincon", + "author_inst": "Oregon Health and Sciences University" + }, + { + "author_name": "Nicole E. Marshall", + "author_inst": "Oregon Health and Science University" + }, + { + "author_name": "Ilhem Messaoudi", + "author_inst": "University of California Irvine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.23.457328", "rel_title": "Presence and Stability of SARS-CoV-2 on Environmental Currency and Money Cards", @@ -631972,85 +634133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.18.21262214", - "rel_title": "Studies on the level of neutralizing antibodies produced by inactivated COVID-19 vaccines in the real world", - "rel_date": "2021-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.18.21262214", - "rel_abs": "BackgroundAlthough effective vaccines have been developed against COVID-19, the level of neutralizing antibodies (Nabs) induced after vaccination in the real world is still unknown. To evaluate the level and persistence of NAbs induced by two inactivated COVID-19 vaccines in China.\n\nMethods and findingsSerum samples were collected from 1,335 people aged 18 and over who were vaccinated with COVID-19 inactivated vaccine in Peking University Peoples Hospital from January 19 to June 23, 2021, for detection of COVID-19 antibodies. The WHO standard of SARS-CoV-2 NAbs was detected. The coefficients of variation between the detection results and the true values of the NAbs detected by the WHO standard were all lower than the WHO international standard 3% after the dilution of the original and the dilution of the theoretical concentrations of 500 IU/mL, 250 IU/mL, 125 IU/mL, 72.5 IU/mL, 36.25 IU/mL and 18.125 IU/mL. On day 11-70, the positive rate of NAbs against COVID-19 was 82% to 100%; From day 71 to 332, the positive rate of NAbs decreased to 27%. The level of NAbs was significantly higher at 3-8 Weeks than at 0-3 Weeks. There was a high linear correlation between NAbs and IgG antibodies in 1335 vaccinated patients. NAbs levels were decreased in 31 of 38 people (81.6%) at two time points after the second dose of vaccine. There was no significant difference in age between the group with increased and decreased neutralizing antibody levels ({chi}2 =-0.034, P>0.05). The positive rate of NAbs in the two-dose vaccine group (77.3%) was significantly higher than that in the one-dose group (18.1%), with statistical difference ({chi}2=312.590, P<0.001). A total of 206 people who were 11-70 days after receiving the second dose were tested and divided into three groups: 18-40 years old, 41-60 years old and >60 years old. The positive rates of NAbs in three groups (18-40 years old, 41-60 years old and >60 years old) were 95.14%, 78.43% and 81.8%, respectively. The positive rate of NAbs was significantly higher in 18-40 years old than in 41-60 years old ({chi}2=12.547, P <0.01). The titer of NAbs in 18-40 years old group was significantly higher than that in 41-60 years old group (t=-0.222, P <0.01). The positive rate of NAbs in male group (89.32%) was lower than in female (91.26%), but there was no significant difference ({chi}2=0.222, P >0.05).\n\nConclusionsThe positive rate of NAbs was the highest from 10 to 70 days after the second dose of vaccine, and the positive rate gradually decreased as time went by. There was a high linear correlation between COVID-19 NAbs and IgM/IgG antibodies in vaccinators, suggesting that in cases where NAbs cannot be detected, IgM/IgG antibodies can be detected instead. The level of NAbs produced after vaccination was affected by age, but not by gender. The highest levels of NAbs were produced between shots 21 to 56 days apart, suggesting that 21 to 56 days between shots is suitable for vaccination.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LIAt present, the inactivated vaccines that have been approved to market in China have passed clinical trials to prove their effectiveness and safety. But the level of neutralizing antibodies induced by vaccination in the real world remains unclear.\nC_LIO_LISerological testing for neutralizing antibodies against COVID-19 is important for assessing vaccine and treatment responses and comparing multiple drug candidates. We assessed the levels of neutralizing antibodies produced in populations receiving inactivated vaccines and assessed the persistence of these vaccines in producing COVID-19 neutralizing antibodies in healthy adults.\nC_LI\n\nWhat did the researchers do and find?O_LIWe collected serum samples from 1,335 people aged 18 and above who had received COVID-19 vaccine in Peking University Peoples Hospital, and divided them into two groups according to one dose of inactivated vaccine and two doses of inactivated vaccine.\nC_LIO_LIOur study found that the positive rate of NAbs was 66.2% in adults who received one or two doses of inactivated vaccine and 77.3% in adults who received two doses of inactivated vaccine in the real world.\nC_LIO_LIFrom 11 to 70 days after the second dose of vaccine, the positive rate of neutralizing antibodies against COVID-19 was 82-100%; On days 71-332, the positive rate of neutralizing antibodies decreased to 27%.\nC_LIO_LIThe titer and the positive rate of NAbs in 18-40 years old group were significantly higher than that in 41-60 years old group.\nC_LI\n\nWhat do these findings mean?O_LIWhat is novel is we observed that in the real world, the positive rate of neutralization antibody was the highest at 10 to 70 days after the second vaccination, and with the extension of the vaccination time, the positive rate of antibody gradually decreased. Therefore, we recommend that the third dose of vaccine be administered at day 61 to day 70 for COVID-19 neutralizing antibodies levels.\nC_LIO_LIWe observed that there was a high linear correlation between COVID-19 neutralization antibodies and COVID-19 IgM/IgG antibodies in vaccinators, suggesting that in cases where NAbs cannot be detected, COVID-19 IgM/IgG antibodies can be detected instead.\nC_LIO_LIIn our manuscript, we found that the titer and positive rate of neutralizing antibodies in 18-40 years old group were higher than those in 41-60 years old group. The level of neutralizing antibodies produced after vaccination was affected by age, but not by gender.\nC_LIO_LIWe also observed that the highest levels of NAbs were produced between shots 21 to 35 days apart, suggesting that 21 to 35 days between shots is suitable for vaccination.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Haiying Zhang", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Yuyuan Jia", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Ying Ji", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Xu Cong", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Yan Liu", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Ruining Yang", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Xiangsha Kong", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Yin Shi", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Ling Zhu", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Zhenyu Wang", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Wei Wang", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Ran Fei", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Feng Liu", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Fengmin Lu", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Hongsong Chen", - "author_inst": "Peking University Hepatology Institute" - }, - { - "author_name": "Haying Rao", - "author_inst": "Peking University Hepatology Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.18.21262227", "rel_title": "Modeling SARS-CoV-2 transmission at a winter destination resort region with high outside visitation", @@ -632830,6 +634912,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.14.21262042", + "rel_title": "Longitudinal monitoring of SARS-CoV-2-specific immune responses", + "rel_date": "2021-08-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.14.21262042", + "rel_abs": "The Lower Austrian Wachau region was an early COVID-19 hotspot of infection. As previously reported, in June 2020, after the first peak of infections, we determined that 8.5% and 9.0% of the participants in Wei{beta}enkirchen and surrounding communities in the Wachau region were positive for SARS-CoV-2-specific immunoglobulin G (IgG) and immunoglobulin A (IgA) antibodies, respectively. Here, we present novel data obtained eight months later (February 2021) from Wei{beta}enkirchen, after the second peak of infection, with 25.0% (138/552) and 23.6% (130/552) of participants that are positive for IgG and IgA, respectively. In participants with previous IgG/IgA positivity (June 2020), we observed a 24% reduction in IgG levels, whereas the IgA levels remained stable in February 2021. This subgroup was further analyzed for SARS-CoV-2-induced T cell activities. Although 76% (34/45) and 76% (34/45) of IgG positive and IgA positive participants, respectively, showed specific T cell activities, those were not significantly correlated with the levels of IgG or IgA. Thus, the analyses of antibodies cannot surrogate the measurement of T cell activities. For a comprehensive view on SARS-CoV-2-triggered immune responses, the measurement of different classes of antibodies should be complemented with the determination of T cell activities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Heike Rebholz", + "author_inst": "Danube Private University" + }, + { + "author_name": "Ralf J. Braun", + "author_inst": "Danube Private University" + }, + { + "author_name": "Titas Saha", + "author_inst": "Danube Private University" + }, + { + "author_name": "Oliver Harzer", + "author_inst": "Danube Private University" + }, + { + "author_name": "Miriam Schneider", + "author_inst": "Danube Private University" + }, + { + "author_name": "Dennis Ladage", + "author_inst": "Danube Private University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21262087", "rel_title": "The impact of ongoing COVID-19 lockdown on family finances and mental health", @@ -633514,61 +635635,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.20.457128", - "rel_title": "High-Spatiotemporal-Resolution Nanopore Sequencing of SARS-CoV-2 and Host Cell RNAs", - "rel_date": "2021-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.20.457128", - "rel_abs": "Recent studies have disclosed the genome, transcriptome and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for non-canonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (MOI=0.1) applied for the infection. In this study, we used direct cDNA and direct RNA nanopore sequencings for the generation of high-coverage, high-temporal-resolution transcriptomic datasets on SARS-CoV-2 and on primate host cells infected with a high virus titer (MOI=5). Sixteen sampling time points ranging from 1 to 96h with a varying time resolution and three biological replicates were used in the experiment for both the infected and the non-infected cells.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Dora Tombacz", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Akos Dormo", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Gabor Gulyas", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Zsolt Csabai", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Istvan Prazsak", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Balazs Kakuk", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Akos Harangozo", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - }, - { - "author_name": "Istvan Jankovics", - "author_inst": "Complex Medical Center" - }, - { - "author_name": "Bela Denes", - "author_inst": "Veterinary Diagnostic Directorate, National Food Chain Safety Office" - }, - { - "author_name": "Zsolt Boldogkoi", - "author_inst": "Department of Medical Biology, Albert Szent-Gyorgyi Medical School, University of Szeged" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.08.19.457020", "rel_title": "Platelet proteome analysis reveals an early hyperactive phenotype in SARS-CoV-2-infected humanized ACE2 mice", @@ -634688,6 +636754,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.13.21262039", + "rel_title": "A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21262039", + "rel_abs": "Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jade Daigle", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kathleen Racher", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Justin Hazenberg", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Allan Yeoman", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Heather Hannah", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Diep Duong", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Umar Mohammed", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Dave Spreitzer", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Branden S. J. Gregorchuk", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Breanne M. Head", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Adrienne F. A. Meyers", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Paul A. Sandstrom", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Anil Nichani", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "James I. Brooks", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael R. Mulvey", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Chand S. Mangat", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael G. Becker", + "author_inst": "Public Health Agency of Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.14.21261996", "rel_title": "Association between interruption to medical care and sickness presenteeism during the COVID-19 pandemic: a cross-sectional study in Japan", @@ -635320,89 +637469,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.17.21262164", - "rel_title": "Non-pharmaceutical interventions, vaccination and the Delta variant: epidemiological insights from modelling England's COVID-19 roadmap out of lockdown", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21262164", - "rel_abs": "BackgroundEnglands COVID-19 \"roadmap out of lockdown\" set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued. Here we assess the roadmap, the impact of the Delta variant, and potential future epidemic trajectories.\n\nMethodsWe extended a model of SARS-CoV-2 transmission to incorporate vaccination and multi-strain dynamics to explicitly capture the emergence of the Delta variant. We calibrated the model to English surveillance data using a Bayesian evidence synthesis framework, then modelled the potential trajectory of the epidemic for a range of different schedules for relaxing NPIs.\n\nFindingsThe roadmap was successful in offsetting the increased transmission resulting from lifting NPIs with increasing population immunity through vaccination. However due to the emergence of Delta, with an estimated transmission advantage of 73% (95%CrI: 68-79) over Alpha, fully lifting NPIs on 21 June 2021 as originally planned may have led to 3,400 (95%CrI: 1,300-4,400) peak daily hospital admissions under our central parameter scenario. Delaying until 19 July reduced peak hospitalisations by three-fold to 1,400 (95%CrI: 700-1,500) per day. There was substantial uncertainty in the epidemic trajectory, with particular sensitivity to estimates of vaccine effectiveness and the intrinsic transmissibility of Delta.\n\nInterpretationOur findings show that the risk of a large wave of COVID hospitalisations resulting from lifting NPIs can be substantially mitigated if the timing of NPI relaxation is carefully balanced against vaccination coverage. However, with Delta, it may not be possible to fully lift NPIs without a third wave of hospitalisations and deaths, even if vaccination coverage is high. Variants of concern, their transmissibility, vaccine uptake, and vaccine effectiveness must be carefully monitored as countries relax pandemic control measures.\n\nFundingNational Institute for Health Research, UK Medical Research Council, Wellcome Trust, UK Foreign, Commonwealth & Development Office.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed up to 23 July 2021 with no language restrictions using the search terms: (COVID-19 or SARS-CoV-2 or 2019-nCoV or \"novel coronavirus\") AND (vaccine or vaccination) AND (\"non pharmaceutical interventions\" OR \"non-pharmaceutical interventions) AND (model*). We found nine studies that analysed the relaxation of controls with vaccination roll-out. However, none explicitly analysed real-world evidence balancing lifting of interventions, vaccination, and emergence of the Delta variant.\n\nAdded value of this studyOur data synthesis approach combines real-world evidence from multiple data sources to retrospectively evaluate how relaxation of COVID-19 measures have been balanced with vaccination roll-out. We explicitly capture the emergence of the Delta variant, its transmissibility over Alpha, and quantify its impact on the roadmap. We show the benefits of maintaining NPIs whilst vaccine coverage continues to increase and capture key uncertainties in the epidemic trajectory after NPIs are lifted.\n\nImplications of all the available evidenceOur study shows that lifting interventions must be balanced carefully and cautiously with vaccine roll-out. In the presence of a new, highly transmissible variant, vaccination alone may not be enough to control COVID-19. Careful monitoring of vaccine uptake, effectiveness, variants, and changes in contact patterns as restrictions are lifted will be critical in any exit strategy.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Raphael Sonabend", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lilith K Whittles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Natsuko Imai", - "author_inst": "Imperial College London" - }, - { - "author_name": "Pablo N Perez-Guzman", - "author_inst": "Imperial College London" - }, - { - "author_name": "Edward S Knock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Thomas Rawson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katy AM Gaythorpe", - "author_inst": "Imperial College London" - }, - { - "author_name": "Bimandra A Djaafara", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wes Hinsley", - "author_inst": "Imperial College London" - }, - { - "author_name": "Richard G FitzJohn", - "author_inst": "Imperial College London" - }, - { - "author_name": "John A Lees", - "author_inst": "Imperial College London" - }, - { - "author_name": "Divya Thekke Kanapram", - "author_inst": "Imperial College London" - }, - { - "author_name": "Erik M Volz", - "author_inst": "Imperial College London" - }, - { - "author_name": "Azra C Ghani", - "author_inst": "Imperial College London" - }, - { - "author_name": "Neil M Ferguson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marc Baguelin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anne Cori", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.17.21260846", "rel_title": "COVID-19 infection, hospitalisation and death Amongst People with Rare Autoimmune Rheumatic Disease in England. Results from the RECORDER Project.", @@ -636262,6 +638328,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.10.21261836", + "rel_title": "Efficacy and Safety of Ayurveda Intervention AYUSH 64 as add-on therapy for patients with COVID 19 infections: An open labelled, Parallel Group, Randomized controlled clinical trial", + "rel_date": "2021-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261836", + "rel_abs": "The authors have withdrawn this manuscript because they found a serious issue in data-analysis which leads to wrong interpretation of the results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Pankaj Bhardwaj", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Pawan Kumar Godatwar", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Jaykaran Charan", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Sanjeev Sharma", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Shazia Shafi", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Nishant Chauhan", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Pratibha Vyas", + "author_inst": "NIIR NCD Jodhpur" + }, + { + "author_name": "Naveen Dutt", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Naresh Midha", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Ramniwas Jalandra", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Meenakshi Sharma", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Vijaya Lakshmi Nag", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Suman Sharma", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Sarvesh Kumar Singh", + "author_inst": "National Institute of Ayurveda Jaipur" + }, + { + "author_name": "Praveen Sharma", + "author_inst": "All India Institute of Medical Sciences Jodhpur" + }, + { + "author_name": "Sanjeev Misra", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21262000", "rel_title": "Seasonal betacoronavirus antibodies expansion post BNT161b2 vaccination associates with reduced SARS-CoV-2 VoCs neutralization", @@ -637138,49 +639283,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.08.13.456326", - "rel_title": "Antiviral face mask functionalized with solidified hand soap: low-cost infection prevention clothing against enveloped viruses such as SARS-CoV-2", - "rel_date": "2021-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.456326", - "rel_abs": "Infection prevention clothing is becoming an essential protective tool in the current pandemic, especially because now we know that SARS-CoV-2 can easily infect humans in poorly ventilated indoor spaces. However, commercial infection prevention clothing is made of fabrics that are not capable of inactivating the virus. Therefore, viral infections of symptomatic and asymptomatic individuals wearing protective clothing such as masks can occur through aerosol transmission or by contact with the contaminated surfaces of the masks, which are suspected as an increasing source of highly infectious biological waste. Herein, we report an easy fabrication method of a novel antiviral non-woven fabric containing polymer filaments that were coated with solidified hand soap. This extra protective fabric is capable of inactivating enveloped viruses such as SARS-CoV-2 and phi 6 in one minute of contact. In this study, this antiviral fabric was used to fabricate an antiviral face mask and did not show any cytotoxic effect in human keratinocyte HaCaT cells. Furthermore, this antiviral non-woven fabric could be used for the fabrication of other infection prevention clothing such as caps, scrubs, shirts, trousers, disposable gowns, overalls, hoods, aprons, and shoe covers. Therefore, this low-cost technology could provide a wide range of infection protective tools to combat COVID-19 and future pandemics in developed and underdeveloped countries.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alba Cano-Vicent", - "author_inst": "Universidad Catolica de Valencia San Vicente Martir" - }, - { - "author_name": "Alberto Tunon-Molina", - "author_inst": "Universidad Catolica de Valencia San Vicente Martir" - }, - { - "author_name": "Miguel Marti", - "author_inst": "Universidad Catolica de Valencia San Vicente Martir" - }, - { - "author_name": "Yukiko Muramoto", - "author_inst": "Kyoto University" - }, - { - "author_name": "Takeshi Noda", - "author_inst": "Kyoto University" - }, - { - "author_name": "Kazuo Takayama", - "author_inst": "Kyoto University" - }, - { - "author_name": "Angel Serrano-Aroca", - "author_inst": "Universidad Catolica de Valencia San Vicente Martir" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.08.15.456422", "rel_title": "Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms", @@ -638008,6 +640110,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.08.11.21261946", + "rel_title": "A Novel Convolutional Neural Network for COVID-19 detection and classification using Chest X-Ray images", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261946", + "rel_abs": "The early and rapid diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the main cause of fatal pandemic coronavirus disease 2019 (COVID-19), with the analysis of patients chest X-ray (CXR) images has life-saving importance for both patients and medical professionals. In this research a very simple novel and robust deep-learning convolutional neural network (CNN) model with less number of trainable-parameters is proposed to assist the radiologists and physicians in the early detection of COVID-19 patients. It also helps to classify patients into COVID-19, pneumonia and normal on the bases of analysis of augmented X-ray images. This augmented dataset contains 4803 COVID-19 from 686 publicly available chest X-ray images along with 5000 normal and 5000 pneumonia samples. These images are divided into 80% training and 20 % validation. The proposed CNN model is trained on training dataset and then tested on validation dataset. This model has a promising performance with a mean accuracy of 92.29%, precision of 99.96%, Specificity of 99.85% along with Sensitivity value of 85.92%. The result can further be improved if more data of expert radiologist is publically available.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Muhammad Talha Nafees", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Irshad ullah", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Rizwan", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Maaz ullah", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Irfanullah Khan", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Farhan", + "author_inst": "University of Engineering and Technology Peshawar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.08.11.21261793", "rel_title": "Development and use analysis of 'gestioemocional.cat', a web app for promoting emotional self-care and access to professional mental health resources during the covid-19 pandemic", @@ -638836,61 +640977,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.11.21261932", - "rel_title": "Mathematical modeling of vaccination rollout and NPIs lifting on COVID-19 transmission with VOC: a case study in Toronto, Canada", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261932", - "rel_abs": "BackgroundSince December 2020, public health agencies have implemented a variety of vaccination strategies to curb the spread of SARS-CoV-2, along with pre-existing Nonpharmaceutical Interventions (NPIs). Initial strategy focused on vaccinating the elderly to prevent hospitalizations and deaths. With vaccines becoming available to the broader population, we aimed to determine the optimal strategy to enable the safe lifting of NPIs while avoiding virus resurgence.\n\nMethodsWe developed a compartmental deterministic SEIR model to simulate the lifting of NPIs under different vaccination rollout scenarios. Using case and vaccination data from Toronto, Canada between December 28, 2020 and May 19, 2021, we estimated transmission throughout past stages of NPI escalation/relaxation to compare the impact of lifting NPIs on different dates on cases, hospitalizations, and deaths, given varying degrees of vaccine coverages by 20-year age groups, accounting for waning immunity.\n\nResultsWe found that, once coverage among the elderly is high enough (80% with at least one dose), the main age groups to target are 20-39 and 40-59 years, whereby first-dose coverage of at least 70% by mid-June 2021 is needed to minimize the possibility of resurgence if NPIs are to be lifted in the summer. While a resurgence was observed for every scenario of NPI lifting, we also found that under an optimistic vaccination coverage (70% by mid-June, postponing reopening from August 2021 to September 2021can reduce case counts and severe outcomes by roughly 80% by December 31, 2021.\n\nConclusionsOur results suggest that focusing the vaccination strategy on the working-age population can curb the spread of SARS-CoV-2. However, even with high vaccination coverage in adults, lifting NPIs to pre-pandemic levels is not advisable since a resurgence is expected to occur, especially with earlier reopening.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elena Aruffo", - "author_inst": "York University" - }, - { - "author_name": "Pei Yuan", - "author_inst": "York University" - }, - { - "author_name": "Yi Tan", - "author_inst": "York University" - }, - { - "author_name": "Evgenia Gatov", - "author_inst": "Toronto Public Health" - }, - { - "author_name": "Iain Moyles", - "author_inst": "York University" - }, - { - "author_name": "Jacques Belair", - "author_inst": "University of Montreal" - }, - { - "author_name": "James Watmough", - "author_inst": "University of New Brunswick" - }, - { - "author_name": "Sarah Collier", - "author_inst": "Toronto Public Health" - }, - { - "author_name": "Julien Arino", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Huaiping Zhu", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.11.21261917", "rel_title": "Epidemiological Study of COVID-19 Infections: Case of Ga East Municipal Hospital Treatment Centre - Kwabenya-Ghana.", @@ -639902,6 +641988,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.12.456168", + "rel_title": "SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact", + "rel_date": "2021-08-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.12.456168", + "rel_abs": "The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomers receptor binding domain (RBD) switching from a \"down\" (closed) to an \"up\" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 {micro}s of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibodys epitope is continuously exposed, explaining its high efficacy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yui Tik Pang", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Atanu Acharya", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Diane Lynch", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anna Pavlova", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "James Gumbart", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.08.13.456066", "rel_title": "SARS-CoV-2 Neutralization in Commercial Lots of Plasma-derived Immunoglobulin", @@ -640826,73 +642947,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.10.21261841", - "rel_title": "Specificity of SARS-CoV-2 antibody-detection assays against S and N protein among pre-COVID-19 sera from patients with protozoan and helminth parasitic infections", - "rel_date": "2021-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261841", - "rel_abs": "BackgroundWe aimed to assess the specificity of SARS-CoV-2 antibody detection assays among people with known tissue-borne parasitic infections.\n\nMethodsWe tested three SARS-CoV-2 antibody-detection assays (cPass SARS-CoV-2 Neutralization Antibody Detection Kit, Abbott SARS-CoV-2 IgG assay, and STANDARD Q COVID-19 IgM/IgG Combo Rapid Test) among 559 pre-COVID-19 sera.\n\nResultsThe specificity of assays was 95-98% overall. However, lower specificity was observed among sera from patients with protozoan infections of the reticuloendothelial system, such as human African trypanosomiasis (Abbott Architect; 88% [95%CI 75-95]), visceral leishmaniasis (SD RDT IgG; 80% [95%CI 30-99]), and from patients with recent malaria from a holoendemic area of Senegal (ranging from 91% for Abbott Architect and SD RDT IgM to 98-99% for cPass and SD RDT IgG). For specimens from patients with evidence of past or present helminth infection overall, test specificity estimates were all [≥] 96%. Sera collected from patients clinically suspected of parasitic infections that tested negative for these infections yielded a specificity of 98-100%. The majority (>85%) of false-positive results were positive by only one assay.\n\nConclusionsThe specificity of SARS-CoV-2 serological assays among sera from patients with tissue-borne parasitic infections was below the threshold required for decisions about individual patient care. Specificity is markedly increased by the use of confirmatory testing with a second assay. Finally, the SD RDT IgG proved similarly specific to laboratory-based assays and provides an option in low-resource settings when detection of anti-SARS-CoV-2 IgG is indicated.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Cedric P Yansouni", - "author_inst": "Division of Infectious Diseases and Department of Medical Microbiology, McGill University Health Centre" - }, - { - "author_name": "Jesse Papenburg", - "author_inst": "Montreal Children's Hospital" - }, - { - "author_name": "Matthew P Cheng", - "author_inst": "McGill University" - }, - { - "author_name": "Rachel Corsini", - "author_inst": "McGill Interdisciplinary Initiative in Infection and Immunity" - }, - { - "author_name": "Chelsea Caya", - "author_inst": "McGill University Health Centre - Research Institute" - }, - { - "author_name": "Fabio Vasquez Camargo", - "author_inst": "National Reference Centre for Parasitology" - }, - { - "author_name": "Luke B Harrison", - "author_inst": "McGill University Health Centre" - }, - { - "author_name": "Gerasimos Zaharatos", - "author_inst": "Optilab Montreal - McGill University Health Centre" - }, - { - "author_name": "Philippe Buscher", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Babacar Faye", - "author_inst": "University Cheikh Anta Diop" - }, - { - "author_name": "Magatte Ndiaye", - "author_inst": "University Cheikh Anta Diop" - }, - { - "author_name": "Greg Matlashewski", - "author_inst": "McGill University" - }, - { - "author_name": "Momar Ndao", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.11.21261930", "rel_title": "Geospatial Variability in Excess Death Rates during the COVID-19 Pandemic in Mexico: Examining Socio Demographic and Population Health Characteristics", @@ -642188,6 +644242,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.10.21261847", + "rel_title": "Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021", + "rel_date": "2021-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261847", + "rel_abs": "BackgroundThe COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just twenty six SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation.\n\nMethodsNine hundred and five SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, gender, nationality and age.\n\nResultsAlthough sixteen PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97% of samples. In the following two months, all samples contained the Alpha variant. However, this had changed dramatically by June and July, when all samples belonged to the Delta variant.\n\nDiscussionThis study provides a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the countrys largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under six weeks.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Georgi Merhi", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + }, + { + "author_name": "Alexander J Trotter", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Leonardo de Oliveira Martins", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Jad Koweyes", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + }, + { + "author_name": "Thanh Le-Viet", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Hala Abou Naja", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Mona Al Buaini", + "author_inst": "National Influenza Centre Research Laboratory, Rafic Hariri University Hospital, Beirut, Lebanon" + }, + { + "author_name": "Sophie J Prosolek", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Nabil-Fareed Alikhan", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Martin Lott", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Tatiana Tohmeh", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Bassam Badran", + "author_inst": "Laboratory of Molecular Biology and Cancer Immunology, Faculty of Sciences, Lebanese University" + }, + { + "author_name": "Orla J Jupp", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Sarah Gardner", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Matthew W Felgate", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Kate A Makin", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Janine M Wilkinson", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Rachael Stanley", + "author_inst": "Norfolk and Norwich University Hospital, Norwich, Norfolk, UK" + }, + { + "author_name": "Abdul K Sesay", + "author_inst": "MRC Unit The Gambia at LHSTM, Fajara, Gambia" + }, + { + "author_name": "Mark A Webber", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Rose K Davidson", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Nada Ghosn", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Mark Pallen", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Hamad Hasan", + "author_inst": "Ministry of Public Health, Beirut, Lebanon" + }, + { + "author_name": "Andrew J Page", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Sima Tokajian", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.10.21261860", "rel_title": "Heterogeneity in COVID-19 Pandemic-Induced Lifestyle Stressors Predicts Mental Health in Adults and Children in the US and UK", @@ -643000,20 +645173,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.08.11.455921", - "rel_title": "SARS-CoV-2 Spike S1 glycoprotein is a TLR4 agonist, upregulates ACE2 expression and induces pro-inflammatory M1 macrophage polarisation.", - "rel_date": "2021-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.11.455921", - "rel_abs": "Background and aimsTLR4 is an important innate immune receptor that recognizes bacterial LPS, viral proteins and other pathogen associated molecular patterns (PAMPs). It is expressed on tissue-resident and immune cells. We previously proposed a model whereby SARS-CoV-2 activation of TLR4 via its spike glycoprotein S1 domain increases ACE2 expression, viral loads and hyperinflammation with COVID-19 disease [1]. Here we test this hypothesis in vitro and demonstrate that the SARS-CoV-2 spike S1 domain is a TLR4 agonist in rat and human cells and induces a pro-inflammatory M1 macrophage phenotype in human THP-1 monocyte-derived macrophages.\n\nMethodsAdult rat cardiac tissue resident macrophage-derived fibrocytes (rcTMFs) were treated with either bacterial LPS or recombinant SARS-CoV-2 spike S1 glycoprotein. The expression of ACE2 and other inflammatory and fibrosis markers were assessed by immunoblotting. S1/TLR4 co-localisation/binding was assessed by immunocytochemistry and proximity ligation assays on rcTMFs and human HEK-293 HA-TLR4-expressing cells. THP-1 monocytes were differentiated into M1 or M2 macrophages with LPS/IFN{gamma}, S1/IFN{gamma} or IL-4 and RNA was extracted for RT-qPCR of M1/M2 markers and ACE2.\n\nResultsTLR4 activation by spike S1 or LPS resulted in the upregulation of ACE2 in rcTMFs as shown by immunoblotting. Likewise, spike S1 caused TLR4-mediated induction of the inflammatory/wound healing marker COX-2 and concomitant downregulation of the fibrosis markers CTGF and Col3a1, similar to LPS. The specific TLR4 TIR domain signalling inhibitor CLI-095 (Resatorvid(R)), blocked the effects of spike S1 and LPS, confirming that spike S1 is a TLR4 agonist and viral PAMP (VAMP). ACE2 expression was also inhibited by the dynamin inhibitor Dynasore(R), suggesting ACE2 expression is mediated by the alternative endosomal/{beta}-interferon pathway. Confocal immunofluorescence microscopy confirmed 1:1 stoichiometric spike S1 co-localisation with TLR4 in rat and human cells. Furthermore, proximity ligation assays confirmed spike S1 and TLR4 binding in human and rat cells. Spike S1/IFN-{gamma} treatment of THP-1-derived macrophages induced pro-inflammatory M1 polarisation as shown by an increase in IL-1{beta} and IL-6 mRNA.\n\nConclusionsThese results confirm that TLR4 is activated by the SARS-CoV-2 spike protein S1 domain and therefore TLR4 may be a receptor/accessory factor for the virus. By binding to and activating TLR4, spike S1 caused upregulation of ACE2, which may facilitate viral entry into cells. In addition, pro-inflammatory M1 macrophage polarisation via TLR4 activation, links TLR4 activation by spike S1 to inflammation. The clinical trial testing of CLI-095 (Resatorvid(R)) and other TLR4 antagonists in severe COVID-19, to reduce both viral entry into cells and hyperinflammation, is warranted. Our findings likely represent an important development in COVID-19 pathophysiology and treatment, particularly regarding cardiac complications and the role of macrophages.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.08.11.455899", "rel_title": "Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: a pan India study", @@ -644029,6 +646188,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.09.21261555", + "rel_title": "Mixed invasive molds among COVID-19 patients", + "rel_date": "2021-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261555", + "rel_abs": "PurposeDue to surge in COVID cases during the second wave of the COVID pandemic, the healthcare system collapsed in India with shortage of hospital beds, injudicious use of steroids and other immunomodulators, and poor glycaemic monitoring among a population with pre-existing risk of diabetes. Fungal epidemic was announced amid COVID pandemic with several cases of COVID-associated mucormycosis and aspergillosis being reported. But, there is no data regarding mixed fungal infections in COVID patients.\n\nMaterials and MethodsThe study presented a series of ten consecutive cases with dual invasive molds in patients infected with SARS-CoV-2. Among patients hospitalized with the diagnosis of COVID in May 2021 at a tertiary care center in North India, ten microbiologically confirmed dual/mixed COVID-associated mucor-aspergillosis (CAMA) were evaluated.\n\nResultsAll patients were diabetics with the majority having severe COVID pneumonia (6/10, 60%) either on admission or in the past one month, whilst two were each of moderate (20%) and mild (20%) categories of COVID. The patients were managed with amphotericin-B along with surgical intervention. In this case series, 70% of all CAMA (Rhizopus arrhizus with Aspergillus flavus in seven and Aspergillus fumigatus in three patients) patients survived, connoting the critical importance of a high index of clinical suspicion and accurate microbiological diagnosis for managing invasive molds.\n\nConclusionsMixed fungal infections i.e. CAMA during COVID and post-COVID periods may be an emerging disease. This outbreak is seen particularly in such patients with uncontrolled diabetes, on steroids, or cocktail therapy, or living in unhygienic environments.We believe that our findings would help gain a better insight into the risk and progression of invasive fungal mixed infections among COVID patients and thus play a pivotal role in diagnosing, classifying, and implementing an effective management strategy for treating similar cases in the future.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Vanya Singh", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Amber Prasad", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Manjunath Totaganti", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Amit Tyagi", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Abhinav Thaduri", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Shalini Rao", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Mukesh Bairwa", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Ashok K Singh", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.05.21261562", "rel_title": "Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward", @@ -644629,113 +646839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.08.21261510", - "rel_title": "COVID-19 in Brazilian children and adolescents: findings from 21 hospitals", - "rel_date": "2021-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.08.21261510", - "rel_abs": "IntroductionChildren and adolescents with Covid-19 have been shown lower mortality less intense symptoms when compared to adults, but studies in Brazil have been based on the compulsory notifying system only.\n\nObjectiveTo analyse clinical, laboratory, radiological characteristics and outcomes of hospitalized patients under 20 years with Covid-19.\n\nMethodsCases series of hospitalized patients with confirmed Covid-19 under 20 years, obtained from a cohort study in 37 hospitals from five states of Brazil.\n\nResultsFrom 36 patients, 20 (55.5%) were adolescentes, 20 (55.5%) were male, 18 (50.0%) had comorbidities, 2 were pregnant and in 7 (19.4%), initial symptoms occurred during hospitalization for other causes, of whom 3 were possibly infected in the hospital. Fever (61.1%), dyspnea (33.3%) and neurological symptoms (33.0%) were the most common complaints. C-reactive protein was higher than 50mg/L in 16.7% and D-dimer was above the reference limit in 22.2%. Chest X-rays were performed in 20 (55.5%) patients, 9 had abnormalities, and chest tomography in 5. Hospital length of stay ranged from 1-40 days (median 5 [interquartile range 3-10]), 16 (44.4%) needed intensive therapy, 6 (16.7%) required mechanical ventilation and one patient (2.8%) died.\n\nConclusionIn case series patients under 20 years from hospitals from 5 states of Brazil, comorbidities were frequent, and most common symptoms were fever, dyspnea and neurological symptoms. Forty-four percent required intensive therapy, showing that the disease was not as mild as it was expected, and one patient died.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Priscila Menezes Ferri Liu", - "author_inst": "Departamento de Pediatria da UFMG, Faculdade de Medicina, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Maria do Carmo Barros de Melo", - "author_inst": "Departamento de Pediatria, Faculdade de Medicina, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Lilian Martins Oliveira Diniz", - "author_inst": "Departamento de Pediatria da UFMG, Faculdade de Medicina, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Cristiane dos Santos Dias", - "author_inst": "Departamento de Pediatria, Faculdade de Medicina, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Andre Soares de Moura Costa", - "author_inst": "Hospitais da Rede Mater Dei" - }, - { - "author_name": "Barbara Lopes Farace", - "author_inst": "Hospital Risoleta Tolentino Neves" - }, - { - "author_name": "Carla Thais Candida Alves da Silva", - "author_inst": "Hospital Santo Antonio" - }, - { - "author_name": "Fernando Anschau", - "author_inst": "Hospital Nossa Senhora da Conceicao" - }, - { - "author_name": "Fernando Graca Aranha", - "author_inst": "Hospital SOS Cardio" - }, - { - "author_name": "Guilherme Fagundes Nascimento", - "author_inst": "Hospital Unimed BH" - }, - { - "author_name": "Helena Duani", - "author_inst": "Departamento de Clinica Medica. Faculdade de Medicina e Hospital das Clinicas da Universidade Federal de Minas Gerais" - }, - { - "author_name": "Jamille Hemetrio Salles Martins Costa", - "author_inst": "Hospital Marcio Cunha" - }, - { - "author_name": "Karen Brasil Ruschel", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Matheus Carvalho Alves Nogueira", - "author_inst": "Rede Mater Dei de Saude" - }, - { - "author_name": "Neimy Ramos de Oliveira", - "author_inst": "Hospital Eduardo de Menezes" - }, - { - "author_name": "Roberta Pozza", - "author_inst": "Hospital Tacchini" - }, - { - "author_name": "Saionara Cristina Francisco", - "author_inst": "Hospital Metropolitano Doutor Celio de Castro" - }, - { - "author_name": "Thalita Martins Lage", - "author_inst": "Hospital Marcio Cunha" - }, - { - "author_name": "Yuri Carlotto Ramires", - "author_inst": "Hospital Bruno Born" - }, - { - "author_name": "Daniella Nunes Pereira", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Zilma Silveira Nogueira Reis", - "author_inst": "Departamento de Ginecologia e Obstetricia, Faculdade de Medicina, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Jose Miguel Chatkin", - "author_inst": "Departamento de Pneumologia, Faculdade de Medicina, Universidade Catolica do Rio Grande do Sul" - }, - { - "author_name": "Milena Soriano Marcolino", - "author_inst": "Departamento de Clinica Medica, Faculdade de Medicina, Universidade Federal de Minas Gerais" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.08.21261763", "rel_title": "Neuro-COVID long-haulers exhibit broad dysfunction in T cell memory generation and responses to vaccination", @@ -645899,6 +648002,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.09.455656", + "rel_title": "Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection", + "rel_date": "2021-08-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.09.455656", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an unprecedented worldwide health problem. Although the primary site of infection is the lung, growing evidence points towards a crucial role of the intestinal epithelium. Yet, the exact effects of viral infection and the role of intestinal epithelial-immune cell interactions in mediating the inflammatory response are not known. In this work, we apply network biology approaches to single-cell RNA-seq data from SARS-CoV-2 infected human ileal and colonic organoids to investigate how altered intracellular pathways upon infection in intestinal enterocytes leads to modified epithelial-immune crosstalk. We point out specific epithelial-immune interactions which could help SARS-CoV-2 evade the immune response. By integrating our data with existing experimental data, we provide a set of epithelial ligands likely to drive the inflammatory response upon infection. Our integrated analysis of intra- and inter-cellular molecular networks contribute to finding potential drug targets, and suggest using existing anti-inflammatory therapies in the gut as promising drug repurposing strategies against COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Martina Poletti", + "author_inst": "Earlham Institute / Quadram Institute" + }, + { + "author_name": "Agatha Treveil", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Leila Gul", + "author_inst": "Earlham Institute, Norwich UK" + }, + { + "author_name": "Dezso Modos", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Matthew Madgwick", + "author_inst": "Earlham Institute" + }, + { + "author_name": "Marton Olbei", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Balazs Bohar", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Alberto Valdeolivas", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Denes Turei", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Bram Verstockt", + "author_inst": "KU Leuven, Leuven, Belgium" + }, + { + "author_name": "Sergio Triana", + "author_inst": "European Molecular Biology Laboratory, Heidelberg, Germany" + }, + { + "author_name": "Theodore Alexandrov", + "author_inst": "University of California San Diego, La Jolla, CA, USA" + }, + { + "author_name": "Julio Saez-Rodriguez", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Megan L Stanifer", + "author_inst": "Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Steeve Boulant", + "author_inst": "Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Tamas Korcsmaros", + "author_inst": "Earlham Institute / Quadram Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.08.08.455468", "rel_title": "A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions", @@ -646911,69 +649093,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.07.21261749", - "rel_title": "Machine learning detects SARS-CoV-2 and variants rapidly on DNA aptamer metasurfaces", - "rel_date": "2021-08-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.07.21261749", - "rel_abs": "COVID-19 is detected using reverse transcription polymerase chain reaction (RT-PCR) of nasal swabs. A very sensitive and rapid detection technique using easily-collected fluids like saliva must be developed for safe and precise mass testing. Here, we introduce a metasurface platform for direct sensing of COVID-19 from unprocessed saliva. We computationally screen gold metasurfaces out of a pattern space of 2100 combinations for strongly-enhanced light-virus interaction with machine learning and use it to investigate the presence and concentration of the SARS-CoV-2. We use machine learning to identify the virus from Raman spectra with 95.2% sensitivity and specificity on 36 PCR positive and 33 negative clinical samples and to distinguish wild-type, alpha, and beta variants. Our results could pave the way for effective, safe and quantitative preventive screening and identification of variants.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Hulya Torun", - "author_inst": "Koc University" - }, - { - "author_name": "Buse Bilgin", - "author_inst": "Koc University" - }, - { - "author_name": "Muslum Ilgu", - "author_inst": "Middle East Technical University; Aptalogic Inc." - }, - { - "author_name": "Cenk Yanik", - "author_inst": "SUNUM, Sabanci University Nanotechnology Research and Application Center" - }, - { - "author_name": "Sukru Numan Batur", - "author_inst": "Koc University" - }, - { - "author_name": "Suleyman Celik", - "author_inst": "SUNUM, Sabanci University Nanotechnology Research and Application Center" - }, - { - "author_name": "Meric Ozturk", - "author_inst": "Middle East Technical University" - }, - { - "author_name": "Ozlem Dogan", - "author_inst": "Koc University" - }, - { - "author_name": "Onder Ergonul", - "author_inst": "Koc University" - }, - { - "author_name": "Ihsan Solaroglu", - "author_inst": "Koc University" - }, - { - "author_name": "Fusun Can", - "author_inst": "Koc University" - }, - { - "author_name": "Mehmet Cengiz Onbasli", - "author_inst": "Koc University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.07.21261740", "rel_title": "'I can't cope with multiple inputs': Qualitative study of the lived experiences of 'brain fog' after Covid-19", @@ -648001,6 +650120,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.05.21261627", + "rel_title": "Systematic review protocol exploring the impact of the COVID-19 pandemic on the wellbeing of general practitioners", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261627", + "rel_abs": "BackgroundOver recent years chronic stress and burnout have been reported by doctors working in general practice in the UK NHS and internationally. The COVID-19 pandemic has changed general practitioners working lives - adding potential pressures from avoiding infection and addressing pent-up demand for care, but also changing processes such as rapidly taking up remote consultations. To date, there has been a focus on exploring the impact of the pandemic on the wellbeing of hospital clinicians. No registered systematic reviews currently focus on exploring the impact of the pandemic on the mental health and wellbeing of general practitioners.\n\nAims and objectivesTo synthesise the current international evidence base exploring the impact of COVID-19 on the mental health and wellbeing of general practitioners, and which factors are associated with their reported mental health and wellbeing during the pandemic.\n\nMethodsIn this paper we report a systematic review protocol, following PRISMA guidance. In our search strategy we will identify primary research studies or systematic reviews exploring the mental health and wellbeing of general practitioners during the COVID-19 pandemic in four databases (MEDLINE, Embase, PsychInfo and Medrxiv) and Google Scholar. We will hand-search reference lists and grey literature.\n\nTwo reviewers will undertake all stages including study selection, data extraction and quality assessment, with arbitration by a third reviewer where necessary. We will use standardised quality assessment tools to ensure transparency and reduce bias in quality assessment. Depending on the quality of included studies, we may undertake a sensitivity analysis by excluding studies from narrative synthesis that are rated as low quality using the checklists.\n\nWe will describe the findings across studies using narrative thematic data synthesis, and if sufficiently homogenous data are identified, we will pool quantitative findings through meta-analysis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Laura Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Su Golder", + "author_inst": "University of York" + }, + { + "author_name": "Veronica Dale", + "author_inst": "University of York" + }, + { + "author_name": "Holly Essex", + "author_inst": "University of York" + }, + { + "author_name": "Elizabeth McHugh", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.08.04.21261576", "rel_title": "When do elementary students need masks in school? Model-estimated risk of in-school SARS-CoV-2 transmission and related infections among household members before and after student vaccination", @@ -648541,41 +650699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.05.21261634", - "rel_title": "Long COVID in hospitalized and non-hospitalized patients in a large cohort in Northwest Spain, a prospective cohort study", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261634", - "rel_abs": "BackgroundSurvivors to COVID-19 have described long-term symptoms after acute disease. These signs constitute a heterogeneous group named long COVID or persistent COVID.\n\nObjectiveThe aim of this study is to describe persisting symptoms six months after COVID-19 diagnosis in a prospective cohort in the Northwest Spain\n\nDesignThis is a prospective cohort study performed in the COVID-19 Cohort of Galicia Sur Health Institute (COHVID-GS).\n\nParticipantsThis cohort includes patients in clinical follow-up in a health area of 569,534 inhabitants after SARS-CoV-2/COVID-19 diagnosis. Clinical and epidemiological characteristics were collected during the follow up.\n\nMain measures and key resultsA total of 284 patients completed 6 months follow-up, 176 (69.4%) required hospitalization and 29 (10.2%) of them needed critical care. At six months, 119 (48.0%) patients described one or more persisting symptoms. The most prevalent were: extra-thoracic symptoms (39.1%), chest symptoms (27%), dyspnoea (20.6%), and fatigue (16.1%). These symptoms were more common in hospitalized patients (52.3% vs 38.2%) and in women (59.0% vs 40.5%). The multivariate analysis identified Chronic Obstructive Pulmonary Disease (COPD), female gender and tobacco consumption as risk factors for long COVID.\n\nConclusionsPersisting symptoms are common after COVID-19 especially in hospitalized patients compared to outpatients (52.3% vs. 38.2%). Based on these findings, special attention and clinical follow-up after acute SARS-CoV-2 infection should be provided for hospitalized patients with previous lung diseases, tobacco consumption, and females.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alexandre Perez Gonzalez", - "author_inst": "Galicia Sur Health Research Institute (IIS Galicia Sur)" - }, - { - "author_name": "Alejandro Araujo-Ameijeiras", - "author_inst": "Galicia Sur Health Research Institute (IIS Galicia Sur)" - }, - { - "author_name": "Alberto Fernandez-Villar", - "author_inst": "Pneumology Service, Galicia Sur Health Research Instituto (IIS Galicia Sur), SERGAS-UVigo, Vigo, Spain" - }, - { - "author_name": "Manuel Crespo", - "author_inst": "Infectious Diseases Department. Hospital Universitari de Bellvitge, IDIBEL. Barcelona (Spain)" - }, - { - "author_name": "Eva Poveda", - "author_inst": "Group of Virology and Pathogenesis; Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo; SERGAS-UVigo; Vigo, Sp" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.05.21261677", "rel_title": "Phenotyping of acute and persistent COVID-19 features in the outpatient setting: exploratory analysis of an international cross-sectional online survey", @@ -649911,6 +652034,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.06.455424", + "rel_title": "Small-molecule ligands can inhibit -1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses", + "rel_date": "2021-08-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455424", + "rel_abs": "Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs--the most likely source of future zoonoses--as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed -1 PRF significantly in several of them, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sneha Munshi", + "author_inst": "University of Alberta" + }, + { + "author_name": "Krishna Neupane", + "author_inst": "University of Alberta" + }, + { + "author_name": "Sandaru M Ileperuma", + "author_inst": "University of Alberta" + }, + { + "author_name": "Matthew TJ Halma", + "author_inst": "University of Alberta" + }, + { + "author_name": "Jamie A Kelly", + "author_inst": "University of Maryland" + }, + { + "author_name": "Clarissa F Halpern", + "author_inst": "University of Maryland" + }, + { + "author_name": "Jonathan D. Dinman", + "author_inst": "University of Maryland" + }, + { + "author_name": "Sarah Loerch", + "author_inst": "University of California Santa Cruz" + }, + { + "author_name": "Michael T Woodside", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.08.06.455384", "rel_title": "The Inherent Flexibility of Receptor Binding Domains in SARS-CoV-2 Spike Protein", @@ -650503,93 +652677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.04.21261592", - "rel_title": "Estimated pediatric SARS-CoV-2 seroprevalence in Arkansas over the first year of the COVID-19 pandemic", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261592", - "rel_abs": "BackgroundSARS-CoV-2 seroprevalence studies have largely focused on adults but little is known about spread in children. We determined SARS-CoV-2 seroprevalence in children and adolescents from Arkansas over the first year of the COVID-19 pandemic.\n\nMethodsWe tested remnant serum samples from children from 1-18 years who visited Arkansas hospitals or clinics for non-COVID19-related reasons from April, 2020 through April, 2021 for SARS-CoV-2 antibodies. We used univariable and multivariable regression models to determine association between seropositivity and participant characteristics.\n\nResultsAmong 2400 participants, seroprevalence rose from 7.9% in April/May 2020 (95% CI, 4.9-10.9%) to 25.8% in April 2021 (95% CI, 22.2-29.3%). Hispanic and black children had a significantly higher association with antibody positivity than white children in multiple sampling periods.\n\nConclusionsBy spring 2021, most children in Arkansas had not been infected with SARS-CoV-2. With the emergence of SARS-CoV-2 variants, recognition of long-term effects of COVID-19, and the lack of an authorized pediatric SARS-CoV-2 vaccine, these results highlight the importance of including children in SARS-CoV-2 public health, clinical care, and research strategies. These findings are important for state and local officials as they consider measures to limit SARS-CoV-2 spread in schools and daycares for the 2021-2022 school year.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Karl William Boehme", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Joshua L Kennedy", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Jessica Snowden", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Shana M Owens", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Marianne Kouassi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ryan L Mann", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Amairani Paredes", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Claire Putt", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Laura James", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Jing Jin", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ruofei Du", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Catherine R Kirkpatrick", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Zeel Modi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Katherine Caid", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Namvar Zohoori", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Atul Kothari", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Bobby Boyanton Jr.", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "James Craig Forrest", - "author_inst": "University of Arkansas for Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.03.21260614", "rel_title": "Survival of health workers infected by SARS-CoV-2 in the context of vaccination against COVID-19 in Peru", @@ -652105,6 +654192,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.04.21261538", + "rel_title": "Association between obesity and hospitalization in mild COVID-19 young adult outpatients in Brazil: a prospective cohort study", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261538", + "rel_abs": "Background/ObjectivesThe aim of this study was to evaluate the association between obesity and hospitalization in mild COVID-19 adult outpatients in Brazil.\n\nSubjects/MethodsAdults with signs and symptoms suggestive of acute SARS-CoV-2 infection who sought two hospitals (one public and one private) emergency department (ED) were prospectively enrolled. Patients with confirmed COVID-19 at inclusion were followed by phone calls at day (D) D7, D14 and D28. Multivariable logistic regression models were employed to explore the association between obesity and other potential predictors for hospitalization.\n\nResultsA total of 1,050 participants were screened, 310 were diagnosed with COVID-19 by RT-PCR. Median age was 37.4 (IQR 29.8-45.0) years, and 186 (60.0%) were female. Duration of symptoms was 3.0 (IQR 2.0-5.0) days, and 10.0 (IQR 8.0-12.0) was the median number of symptoms at inclusion. A total of 98 (31.6%) were obese, and 243 (78.4%) had no previous medical conditions. Twenty three participants (23/310, 7.4%) required hospitalization during the period. After adjusting, obesity (BMI[≥]30.0 kg/m2) (OR=2.69, 95%CI 1.63-4.83, P<0.001) and older age (OR=1.05, 95%CI 1.01-1.09, P<0.001), were significantly associated with higher risks of hospitalization.\n\nConclusionsObesity, followed by aging, was the main factor associated with hospital admission for COVID-19 in a young population in a low-middle income country. Our findings highlighted the need for actions to promote additional protection for obese population, such as vaccination, and to encourage lifestyle changes.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Caroline Nespolo David", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Heiden Telo", + "author_inst": "School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Luciane Beatriz Kern", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Marcia Polese-Bonatto", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thais Raupp Azevedo", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Amanda Paz Santos", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Walquiria Aparecida Ferreira Almeida", + "author_inst": "General Coordination, National Immunization Program, Brazilian Ministry of Health, Brasilia, Brazil" + }, + { + "author_name": "Victor Bertollo Gomes Porto", + "author_inst": "General Coordination, National Immunization Program, Brazilian Ministry of Health, Brasilia, Brazil" + }, + { + "author_name": "Fernanda Hammes Varela", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "Regis Goulart Rosa", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Renato T Stein", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "- COVIDa study group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.05.455290", "rel_title": "SARS-CoV-2 variants of concern have acquired mutations associated with an increased spike cleavage", @@ -652853,37 +655019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.02.21261459", - "rel_title": "Dynamics of COVID-19 pandemic in India and Pakistan: A metapopulation modelling approach", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261459", - "rel_abs": "India has been the latest global epicenter for COVID-19, a novel coronavirus disease that emerged in China in late 2019. We present a base mathematical model for the transmission dynamics of COVID-19 in India and its neighbour, Pakistan. The base model, which takes the form of a deterministic system of nonlinear differential equations, is parameterized using cumulative COVID-19 mortality data from each of the two countries. The model was used to assess the population-level impact of the control and mitigation strategies implemented in the two countries (notably community lockdowns, use of face masks, and social-distancing). Numerical simulations of the basic model indicate that, based on the current baseline levels of the control and mitigation strategies implemented, the pandemic trajectory in India is on a downward trend (as characterized by the reproduction number of the disease dynamics in India below, but close to, unity). This downward trend will be reversed, and India will be recording mild outbreaks (i.e., pandemic waves), if the control and mitigation strategies are relaxed from their current levels (e.g., relaxed to the extent that the associated community transmission parameters are increased by 20% or 40% from their current baseline values). Our simulations suggest that India could record up to 460,000 cumulative deaths by early September 2021 under the baseline levels of the control strategies implemented (up to 25,000 of the projected deaths could be averted if the control and mitigation measures are strengthened to the extent that the associated community transmission parameters are reduced by 20% from their baseline values). Our simulations show that the pandemic in Pakistan is much milder, with an estimated projected cumulative mortality of about 24,000 by early September 2021 under the baseline scenario. The basic model was extended to assess the impact of back-and-forth mobility between the two countries. Simulations of the resulting metapopulation model show that the burden of the COVID-19 pandemic in Pakistan increases with increasing values of the average time residents of India spend in Pakistan. In particular, it is shown that the India- to-Pakistan mobility pattern may trigger a fourth wave of the pandemic in Pakistan (under certain mobility scenarios), with daily mortality peaking in mid-August to mid-September of 2021. Under the respective baseline control scenarios, our simulations show that the back-and-forth mobility between India and Pakistan could delay the time-to-elimination of the COVID-19 pandemic in the two countries by three to five months (specifically, under the respective baseline scenarios, elimination could be delayed in India and Pakistan to November 2022 and July 2022, respectively).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Samantha J. Brozak", - "author_inst": "Arizona State University" - }, - { - "author_name": "Binod Pant", - "author_inst": "Arizona State University" - }, - { - "author_name": "Salman Safdar", - "author_inst": "Arizona State University" - }, - { - "author_name": "Abba B. Gumel", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.05.455212", "rel_title": "Vaccination with B.1.1.7, B.1.351 and P.1 variants protects mice from challenge with wild type SARS-CoV-2", @@ -653735,6 +655870,177 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.08.02.21261379", + "rel_title": "An adaptive randomized controlled trial of non-invasive respiratory strategies in acute respiratory failure patients with COVID-19", + "rel_date": "2021-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261379", + "rel_abs": "BackgroundBoth continuous positive airway pressure (CPAP) and high-flow nasal oxygenation (HFNO) have been recommended for acute respiratory failure in COVID-19. However, uncertainty exists regarding effectiveness and safety.\n\nMethodsIn the Recovery-Respiratory Support multi-center, three-arm, open-label, adaptive, randomized controlled trial, adult hospitalized patients with acute respiratory failure due to COVID-19, deemed suitable for treatment escalation, were randomly assigned to receive CPAP, HFNO, or conventional oxygen therapy. Comparisons were made between each intervention and conventional oxygen therapy. The primary outcome was a composite of tracheal intubation or mortality within 30-days.\n\nResultsOver 13-months, 1272 participants were randomized and included in the analysis (380 (29.9%) CPAP; 417 (32.8%) HFNO; 475 (37.3%) conventional oxygen therapy). The need for tracheal intubation or mortality within 30-days was lower in the CPAP group (CPAP 137 of 377 participants (36.3%) vs conventional oxygen therapy 158 of 356 participants (44.4%); unadjusted odds ratio 0.72; 95% CI 0.53 to 0.96, P=0.03). There was no difference between HFNO and conventional oxygen therapy (HFNO 184 of 414 participants (44.4%) vs conventional oxygen therapy 166 of 368 participants (45.1%); unadjusted odds ratio 0.97; 95% CI 0.73 to 1.29, P=0.85).\n\nConclusionsCPAP, compared with conventional oxygen therapy, reduced the composite outcome of intubation or death within 30 days of randomisation in hospitalized adults with acute respiratory failure due to COVID-19. There was no effect observed, compared with conventional oxygen therapy, with the use of HFNO.\n\n(Funded by the UK National Institute for Health Research; ISRCTN 16912075).", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Gavin D Perkins", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Chen Ji", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Bronwen A Connolly", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK; Lane Fox Cli" + }, + { + "author_name": "Keith Couper", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Ranjit Lall", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Midlothian, UK; MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edin" + }, + { + "author_name": "Judy M Bradley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK" + }, + { + "author_name": "Paul Dark", + "author_inst": "NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, UK; Salford Royal Hospital, Northern Care Alliance NHS Group, Manchester, UK" + }, + { + "author_name": "Chirag Dave", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anthony De Soyza", + "author_inst": "Population and Health Science Institute, NIHR Biomedical Research Centre, Newcastle, University, Newcastle Upon Tyne, UK; Newcastle-Upon-Tyne Hospitals NHS Foun" + }, + { + "author_name": "Anna V Dennis", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anne Devrell", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; Research Champion Team, West Midlands Clinical Research Network, Wolv" + }, + { + "author_name": "Sara Fairbairn", + "author_inst": "Grange University Hospital, Aneurin Bevan University Health Board, Cwmbran, UK" + }, + { + "author_name": "Hakim Ghani", + "author_inst": "Watford General Hospital, West Hertfordshire Hospitals NHS Trust, Watford, UK" + }, + { + "author_name": "Ellen A Gorman", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK" + }, + { + "author_name": "Christopher A Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Nicholas Hart", + "author_inst": "Lane Fox Clinical Respiratory Physiology Research Centre, Guys and St.Thomas NHS Foundation Trust, London, UK; Centre for Human and Applied Physiological Scienc" + }, + { + "author_name": "Siew Wan Hee", + "author_inst": "Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Zoe Kimbley", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Shyam Madathil", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Nicola McGowan", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Benjamin Messer", + "author_inst": "Newcastle-Upon-Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK" + }, + { + "author_name": "Jay Naisbitt", + "author_inst": "Fairfield General Hospital, Pennine Acute Hospitals NHS Trust, Northern Care Alliance NHS Group, Bury, UK" + }, + { + "author_name": "Chloe Norman", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, School of Medical and Dental Sciences, University of" + }, + { + "author_name": "Emma M Parkin", + "author_inst": "Fairfield General Hospital, Pennine Acute Hospitals NHS Trust, Northern Care Alliance NHS Group, Bury, UK" + }, + { + "author_name": "Jaimin Patel", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, School of Medical and Dental Sciences, University of" + }, + { + "author_name": "Scott E Regan", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Clare Ross", + "author_inst": "Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Anthony J Rostron", + "author_inst": "Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK; Translational and Clinical Research Institute, Newcastle Universi" + }, + { + "author_name": "Mohammad Saim", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anita K Simonds", + "author_inst": "Royal Brompton and Harefield Hospital, Guys and St Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Emma Skilton", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Nigel Stallard", + "author_inst": "Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Michael Steiner", + "author_inst": "Institute for Lung Health, NIHR BRC Respiratory Medicine, Department of Respiratory Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Rama Vancheeswaran", + "author_inst": "Watford General Hospital, West Hertfordshire Hospitals NHS Trust, Watford, UK" + }, + { + "author_name": "Joyce Yeung", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Daniel F McAuley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK; Royal Victor" + }, + { + "author_name": "- Recovery- RS collaborators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.08.02.21261504", "rel_title": "SARS-CoV-2 antibody binding and neutralization in dried blood spot eluates and paired plasma", @@ -654595,29 +656901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.08.02.454730", - "rel_title": "The timing of natural killer cell response in coronavirus infection: a concise model perspective", - "rel_date": "2021-08-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.02.454730", - "rel_abs": "Coronaviruses, including SARS-CoV, MERS-CoV, and SARS-CoV-2 cause respiratory diseases with remarkably heterogeneous progression. This in part reflects the viral ability to influence the cytokine secretion and thereby the innate immune system. Especially the viral interference of IFN-I signaling and the subsequent deficiency of innate immune response in the early phase have been associated with rapid virus replication and later excessive immune responses. We propose a mathematical framework to analyze IFN-I signaling and its impact on the interaction motif between virus, NK cells and macrophages. The model recapture divergent dynamics of coronavirus infections including the possibility for elevated secretion of IL-6 and IFN-{gamma} as a consequence of exacerbated macrophage activation. Dysfunction of NK cells recruitment increase disease severity by leading to a higher viral load peak, the possibility for excessive macrophage activation, and an elevated risk of the cytokine storm. Thus the model predicts that delayed IFN-I signaling could lead to pathogenicity in the latter stage of an infection. Reversely, in case of strong NK recruitment from infected cells we predict a possible chronic disease state with moderate and potentially oscillating virus/cytokine levels.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Xiaochan Xu", - "author_inst": "Kobenhavns Universitet Niels Bohr Instituttet" - }, - { - "author_name": "Kim Sneppen", - "author_inst": "University of Copenhagen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.03.454858", "rel_title": "Protective mucosal immunity against SARS-CoV-2 after heterologous systemic RNA-mucosal adenoviral vector immunization", @@ -655761,6 +658044,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.30.21261383", + "rel_title": "COVID-19 Vaccine Uptake among U.S. Child Care Providers", + "rel_date": "2021-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261383", + "rel_abs": "STRUCUTRED ABSTRACTO_ST_ABSObjectivesC_ST_ABSEnsuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown.\n\nMethodsTo characterize the vaccine uptake among U.S. child care providers, we conducted a cross-sectional survey of the child care workforce. Providers were identified through various national databases and state registries. A link to the survey was sent via email between May 26 and June 23, 2021. Out of 44,771 potential respondents, 21,663 responded (48.4%).\n\nResultsOverall COVID-19 vaccine uptake among U.S. child care providers (78.1%, 95% CI [77.3% to 78.9%]) was higher than that of the U.S. adult population (65%). Vaccination rates varied from 53.5% to 89.4% between states. Vaccine uptake differed significantly (p < .01) based on respondent age (70.0% for ages 25-34, 91.5% for ages 75-84), race (70.0% for Black or African Americans, 92.5% for Asian-Americans), annual household income (70.7% for <$35,000, 85.0% for>$75,000), and childcare setting (72.9% for home-based, 79.7% for center-based).\n\nConclusionsCOVID-19 vaccine uptake among U.S. child care providers was higher than that of the general U.S. adult population. Those who were younger, lower income, Black or African American, resided in states either in the Mountain West or the South, and/or worked in home-based childcare programs reported the lowest rates of vaccination; state public health leaders and lawmakers should prioritize these subgroups for placement on the policy agenda to realize the largest gains in vaccine uptake among providers.\n\nTables of Contents SummaryThis article describes the results of a national survey of childcare providers to determine the overall COVID-19 vaccine uptake and the gaps in vaccine coverage.\n\nWhats Known on This SubjectEnsuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown.\n\nWhat This Study AddsWhile the vaccine uptake among U.S. child care providers was higher than that of U.S. adults, certain subgroups continue to warrant focused attention for outreach and/or placement on the policy agenda.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kavin Patel", + "author_inst": "Yale University" + }, + { + "author_name": "Amyn A. Malik", + "author_inst": "Yale University" + }, + { + "author_name": "Aiden Lee", + "author_inst": "Yale University" + }, + { + "author_name": "Madeline Klotz", + "author_inst": "Yale University" + }, + { + "author_name": "John Eric Humphries", + "author_inst": "Yale University" + }, + { + "author_name": "Thomas Murray", + "author_inst": "Yale University" + }, + { + "author_name": "David Wilkinson", + "author_inst": "Yale University" + }, + { + "author_name": "Mehr Shafiq", + "author_inst": "Yale University" + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Yale University" + }, + { + "author_name": "Jad Elharake", + "author_inst": "Yale University" + }, + { + "author_name": "Rachel Diaz", + "author_inst": "Yale University" + }, + { + "author_name": "Chin Reyes", + "author_inst": "Yale University" + }, + { + "author_name": "Saad Omer", + "author_inst": "Yale University" + }, + { + "author_name": "Walter Gilliam", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.29.21261312", "rel_title": "COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters", @@ -656577,129 +658931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.07.31.21261326", - "rel_title": "COVID-19 vaccine response in people with multiple sclerosis", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.31.21261326", - "rel_abs": "ObjectiveTo investigate the effect of disease modifying therapies on serological response to SARS-CoV2 vaccines in people with multiple sclerosis\n\nMethods473 people with multiple sclerosis from 5 centres provided one or more dried blood spot samples and questionnaires about COVID-19. Information about disease and drug history was extracted from their medical records. Dried blood spots were eluted and tested for antibodies to SARS-CoV2 receptor binding domain. Seropositivity was expressed according to validated cut-off indices. Antibody titers were partitioned into tertiles using data from people on no disease modifying therapy as a reference. We calculated the odds ratio of seroconversion (Univariate logistic regression) and compared quantitative vaccine response (Kruskal Wallis) following SARS-CoV2 vaccine according to disease modifying therapy. We used regression modelling to explore the effect of factors including vaccine timing, treatment duration, age, vaccine type and lymphocyte count on vaccine response.\n\nResultsCompared to no disease modifying therapy, the use of anti-CD20 monoclonal antibodies (odds ratio 0.03; 95% confidence interval 0.01-0.06, p<0.001) and fingolimod (odds ratio 0.41; 95% confidence interval 0.01-0.12) were associated with lower seroconversion following SARS-CoV2 vaccine. All other drug groups did not differ significantly from the untreated cohort. Time since last anti-CD20 treatment and total time on treatment were significantly related with response to vaccination. Vaccine type significantly predicted seroconversion, but not in those on anti-CD20 medications.\n\nInterpretationSome disease modifying therapies carry a risk of attenuated response to SARS-CoV2 vaccination in people with MS. We provide recommendations for the practical management of this patient group.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Emma C Tallantyre", - "author_inst": "Cardiff University" - }, - { - "author_name": "Nicola Vickaryous", - "author_inst": "Preventive Neurology Unit, Queen Mary University London" - }, - { - "author_name": "Valerie Anderson", - "author_inst": "Department of Neurology, Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, UK" - }, - { - "author_name": "Aliye Nazli Asardag", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "David Baker", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Jonathan P Bestwick", - "author_inst": "Preventive Neurology Unit, Queen Mary University London" - }, - { - "author_name": "Kathryn Bramhall", - "author_inst": "Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, UK" - }, - { - "author_name": "Randy Chance", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Nikos Evangelou", - "author_inst": "Department of Clinical Neurology, University of Nottingham" - }, - { - "author_name": "Katila George", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Gavin Giovannoni", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Leanne Grant", - "author_inst": "Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, UK" - }, - { - "author_name": "Katharine E Harding", - "author_inst": "Department of Neurology, Royal Gwent Hopsital, Newport, UK" - }, - { - "author_name": "Aimee Hibbert", - "author_inst": "Nottingham University Hospitals" - }, - { - "author_name": "Gillian Ingram", - "author_inst": "Department of Neurology, Morriston Hospital, Swansea" - }, - { - "author_name": "Meleri Jones", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Angray S Kang", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Samantha Loveless", - "author_inst": "Department of Neurology, Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, UK" - }, - { - "author_name": "Stuart Moat", - "author_inst": "Wales Newborn Screening Laboratory, Department of Medical Biochemistry, Immunology and Toxicology, University Hospital of Wales, Cardiff, Wales, UK" - }, - { - "author_name": "Neil P Robertson", - "author_inst": "Department of Neurology, Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, UK" - }, - { - "author_name": "Klaus Schmierer", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - }, - { - "author_name": "Sitash Navin Shah", - "author_inst": "Preventive Neurology Unit, Queen Mary University London" - }, - { - "author_name": "Jessica Simmons", - "author_inst": "Preventive Neurology Unit, Queen Mary University London" - }, - { - "author_name": "Matthew Upcott", - "author_inst": "School of Medicine, Cardiff University, UK" - }, - { - "author_name": "Mark D Willis", - "author_inst": "Department of Neurology, Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, UK" - }, - { - "author_name": "Stephen Jolles", - "author_inst": "Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, UK" - }, - { - "author_name": "Ruth Dobson", - "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.07.29.21261325", "rel_title": "Specialized interferon ligand action in COVID19", @@ -657847,6 +660078,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.28.21261138", + "rel_title": "Estimates of Single Dose and Full Dose BNT162b2 Vaccine Effectiveness among USAF Academy cadets, 1 Mar - 1 May 2021", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261138", + "rel_abs": "Beginning in early March 2021 and continuing through May 2021, the USAF Academy began vaccinating cadets for protection against the SARS-CoV-2 virus with the BNT162b2 (Pfizer-BioNTech) mRNA vaccine. During this period, vaccination of the almost 4200 cadet population increased from 3% to 85% and prevalence of COVID-19 in the cadet population was constant at approximately 0.4% as indicated by weekly surveillance testing. In this study, vaccine effectiveness at preventing infection is estimated by comparing infection risk as a function of time since vaccination. A statistically significant four-fold reduction in infection risk was observed 14 days after the first vaccine dose and an eleven-fold reduction in infection risk was observed in fully vaccinated cadets. Overall, the Pfizer-BioNTech vaccine was 91% (95% confidence interval = 55-99%) effective at preventing infection in healthy young adults (17-26 years of age) in a university setting and military training environment.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Douglas P Wickert", + "author_inst": "USAF Academy" + }, + { + "author_name": "Erin Almand", + "author_inst": "US Air Force Academy" + }, + { + "author_name": "Christopher A Cullenbine", + "author_inst": "USAF Academy" + }, + { + "author_name": "Odaro J Huckstep", + "author_inst": "USAF Academy" + }, + { + "author_name": "Joseph Rohrer", + "author_inst": "USAF Academy" + }, + { + "author_name": "John C Sitko", + "author_inst": "USAF Academy" + }, + { + "author_name": "James Jordan Steel", + "author_inst": "USAF Academy" + }, + { + "author_name": "Steven Hasstedt", + "author_inst": "USAF Academy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.21261286", "rel_title": "Variations in Non-Pharmaceutical Interventions by State Correlate with COVID-19 Disease Outcomes", @@ -658799,57 +661077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.29.21261306", - "rel_title": "Gender differences in housework and childcare among Japanese workers during the COVID-19 pandemic.", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261306", - "rel_abs": "ObjectivesAlthough gender stereotypes regarding paid work and unpaid work are changing, most wives are responsible for taking care of the family and home in Japan. It is unclear how time spent on housework and childcare has changed between working men and women during the COVID-19 pandemic in Japan. The purpose of this study is to investigate how working men and womens responsibilities for housework and childcare changed during the COVID-19 pandemic in Japan depending on occupation, job type, and the number of employees in the workplace.\n\nMethodsA cross-sectional analysis (N=14,454) was conducted using data from an internet monitoring study (CORoNa Work Project), which was conducted in December 2020. A multilevel logistic model with nested prefectures of residence was conducted to estimate the odds ratio (OR) for change in time devoted to housework and childcare among men and women adjusting for age, household income, frequency of telecommuting, presence of spouse who work, occupation, job type, the number of employees in the workplace, and the incidence rate of COVID-19 by prefecture.\n\nResultsRegardless of occupation related factors, more women than men reported increased time spent on housework and childcare. Furthermore, women were significantly more likely to experience an increase in time spent on those activities than men (housework: OR 1.97, 95% CI [1.75, 2.21], p < 0.001; childcare: OR 1.66, 95% CI [1.37, 2.02], p < 0.001).\n\nConclusionsThe time spent by women on housework and childcare increased significantly compared to men during the COVID-19 pandemic in Japan.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sakuragi Toshihide", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Rie Tanaka", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Masako Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.07.29.21261260", "rel_title": "Development of a Post-Acute Sequelae of COVID-19 (PASC) Symptom Lexicon Using Electronic Health Record Clinical Notes", @@ -659733,6 +661960,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.27.21261221", + "rel_title": "Changes in household food security, access to health services, and income in northern Lao PDR during the COVID-19 pandemic", + "rel_date": "2021-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261221", + "rel_abs": "BackgroundThe COVID-19 pandemic is expected to exacerbate food insecurity in low- and middle-income countries, through loss of income and disrupted food supply chains. Lao PDR has among the highest rates of malnutrition in Southeast Asia. We assessed the relative difficulty in meeting food needs during the COVID-19 pandemic in rural districts of Luang Prabang Province, Lao PDR compared to before; determined associations between pandemic-associated difficulties in food access and household, maternal and child food security; and identified resiliency-promoting strategies.\n\nMethodsIn November 2020, households (N = 1,122) with children under five years were interviewed. Respondents reported the relative ease of access of food and health care as well as changes in income and expenditures compared to before March 2020. We used generalized linear models with cluster robust standard errors to assess univariate and multivariate associations.\n\nResultsNearly four-fifths (78.5%) found it harder to meet household food needs during the pandemic. The most common reasons were increased food prices (51.2%), loss of income (45.3%), and decreased food availability (36.6%). Adjusting for demographics, households with increased difficulty meeting food needs had lower food consumption scores and child dietary diversity. Over 85% of households lost income during the pandemic. Decreased expenditures was associated with reliance on more extreme coping strategies to meet food needs. The households who experienced no change in meeting food needs produced a greater percentage of their food from homegrown methods (4.22% more, 95% CI: 1.28, 7.15), than households who found it more difficult. We estimated that decreases in child bodyweight by 0.5 - 1% would increase wasting in this population by 1.7 - 2.1 percentage points.\n\nConclusionsPandemic-associated shocks may have large effects on malnutrition prevalence. Action is needed to mitigate consequences of the pandemic on nutrition. Local food production and safety net programs that offset income losses may help.\n\nSummary BoxO_ST_ABSWhat is already known?C_ST_ABSThe COVID-19 pandemic has disrupted food supply chains and livelihoods, causing concerns that a global nutrition crisis is imminent and prompting leaders from United Nations agencies to issue an immediate call to action to direct funds towards prevention of child malnutrition. While documented COVID-19 transmission in Lao PDR was lower than that of surrounding counties, malnutrition rates are high, particularly in the northern province of Luang Prabang, which is heavily reliant on tourism for livelihoods.\n\nWhat are the new findings?Nearly four-fifths of those interviewed in Luang Prabang Province, Lao PDR reported that it was harder to meet their households food needs, compared to before the pandemic, with 51% attributing the reason to increased food prices. Over 85% of households reported losing income. Lower expenditures and increased difficulty obtaining food were both associated with lower household food consumption scores and higher household coping strategies, in adjusted analyses. Households who obtained a greater proportion of their foods through home production appeared more resilient than households who obtained a greater proportion of their foods through purchasing.\n\nWhat do the new findings imply?The pandemic may deeply exacerbate food insecurity in Lao PDR, potentially leading to increases in child wasting. Increased local food production and establishment of safety net programs that offset income losses may be two strategies that address this problem among this population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jennifer R Head", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Phetsavanh Chanthavilay", + "author_inst": "University of Health Sciences, Vientiane, Lao PDR" + }, + { + "author_name": "Helen Catton", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Ammaline Vongsitthi", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Kelley Khamphouxay", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Niphone Simphaly", + "author_inst": "Luang Prabang Provincial Health Department, Lao PDR" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.21261212", "rel_title": "An investigation of spatial-temporal patterns and predictions of the COVID-19 pandemic in Colombia, 2020-2021", @@ -660349,53 +662615,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.07.29.454323", - "rel_title": "SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1", - "rel_date": "2021-07-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.29.454323", - "rel_abs": "BackgroundGenomic surveillance of SARS-CoV-2 is paramount for understanding viral dynamics, contributing to disease control. This study analyzed SARS-CoV-2 genomic diversity in Rio Grande do Sul (RS), Brazil, including the first case of each Regional Health Coordination and cases from three epidemic peaks.\n\nMethodsNinety SARS-CoV-2 genomes from RS were sequenced and analyzed against SARS-CoV-2 datasets available in GISAID for phylogenetic inference and mutation analysis.\n\nResultsSARS-CoV-2 lineages among the first cases in RS were B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), evidencing SARS-CoV-2 introduction by both international origin and community-driven transmission. We found predominance of B.1.1.33 (50.0%) and B.1.1.28 (35.0%) during the first epidemic peak (July-August, 2020), emergence of P.2 (55.6%) in the second peak (November-December, 2020), and massive spread of P.1 and related sequences (78.4%), such as P.1-like-II, P.1.1 and P.1.2 in the third peak (February-April, 2021). Eighteen novel mutation combinations were found among P.1 genomes, and 22 different spike mutations and/or deletions among P.1 and related sequences.\n\nConclusionsThis study shows the dispersion of SARS-CoV-2 lineages in Southern Brazil, and describes SARS-CoV-2 diversity during three epidemic peaks, highlighting the spread of P.1 and the high genetic diversity of currently circulating lineages. Genomic monitoring of SARS-CoV-2 is essential to guide health authorities decisions to control COVID-19 in Brazil.\n\nSummaryNinety SARS-CoV-2 genomes from Rio Grande do Sul, Brazil, were sequenced, including the first cases from 15 State Health Coordination regions and samples from three epidemic peaks. Phylogenomic inferences showed SARS-CoV-2 lineages spread, revealing its genomic diversity.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ana Paula Muterle Varela", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Janira Prichula", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Fabiana Quoos Meyer", - "author_inst": "IPVDF" - }, - { - "author_name": "Richard Salvato", - "author_inst": "LACEN/CEVS/SES/RS" - }, - { - "author_name": "Tatiana Schaffer Gregianini", - "author_inst": "LACEN/CEVS/SES/RS" - }, - { - "author_name": "Leticia Garay Martins", - "author_inst": "CEVS/SES/RS" - }, - { - "author_name": "Adriana Seixas", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Ana Beatriz Gorini da Veiga", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.07.29.454261", "rel_title": "COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters", @@ -661515,6 +663734,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.25.21260838", + "rel_title": "Doxycycline is a safe alternative to Hydroxychloroquine + Azithromycin to prevent clinical worsening and hospitalization in mild COVID-19 patients: An open label randomized clinical trial (DOXYCOV)", + "rel_date": "2021-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.25.21260838", + "rel_abs": "ObjectiveWe aimed to compare the safety and efficacy of a doxycycline-based regimen against the national standard guidelines (Hydroxychloroquine plus Azithromycin) for the treatment of mild symptomatic COVID-19.\n\nMethodsWe conducted an open-label, randomized, non-inferiority trial, in Cameroon comparing Doxycycline 100mg, twice daily for 7 days versus Hydroxychloroquine, 400 mg daily for 5 days and Azithromycin 500mg at day 1 and 250mg from day 2 through 5, in mild COVID-19 patients. Clinical improvement, biological parameters and adverse events were assessed. The primary outcome was the proportion of clinical cure at day 3, 10 and 30. Non-inferiority was determined by the clinical cure rate between protocols with a 20 percentage points margin.\n\nResults194 participants underwent randomization and were treated with Doxycycline (n=97) or Hydroxychloroquine-Azithromycin (n=97). At day 3, 74/92 (80.4%) participants on Doxycycline versus 77/95 (81.1%) on Hydroxychloroquine-Azithromycin -based protocols were asymptomatic (p=0.91). At day 10, 88/92 (95.7%) participants on Doxycycline versus 93/95 (97.9%) on Hydroxychloroquine-Azithromycin were asymptomatic (p=0.44). At day 30 all participants were asymptomatic. SARS-CoV2 PCR was negative at Day 10 in 60/92 (65.2%) participants allocated to Doxycycline and 63/95 (66.3%) participants allocated to Hydroxychloroquine-Azithromycin. None of the participants were admitted for worsening of the disease after treatment initiation.\n\nConclusionDoxycycline 100 mg twice daily for 7 days is as effective and safe as Hydroxychloroquine-Azithromycin, for preventing clinical worsening of mild symptomatic or asymptomatic COVID-19, and achieving virological suppression.\n\nStrengths and Limitations[tpltrtarr] This study is one of the first randomized trial, assessing the efficacy and tolerance of Doxycycline to treat COVID-19\n[tpltrtarr]It is one of the first to evaluate disease progression and need to hospitalization in mild or asymptomatic COVID-19\n[tpltrtarr]Patients will not receive identical treatments\n[tpltrtarr]Doxycycline has advantages in terms of availability, safety and cost compared to Hydroxychloroquine and Azytromycin\n[tpltrtarr]Though this study has encounter 7 lost to follow-up, this does not have a major influence on our results\n[tpltrtarr]These data will assist clinicians in their daily practice, and provide a new tool for the fight against COVID-19", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Eugene Sobngwi", + "author_inst": "University of Yaounde 1" + }, + { + "author_name": "Sylvain Zemsi", + "author_inst": "RSD Institute" + }, + { + "author_name": "Magellan Guewo-Fokeng", + "author_inst": "RSD Institute" + }, + { + "author_name": "Jean Claude Katte", + "author_inst": "RSD Institute" + }, + { + "author_name": "Charles Kouanfack", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Liliane Mfeukeu-Kuate", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Armel Zemsi", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Yves Wasnyo", + "author_inst": "RSD Institute" + }, + { + "author_name": "Antoinette Assiga-Ntsama", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Jean Arnaud Ndi-Manga", + "author_inst": "RSD Institute" + }, + { + "author_name": "Joelle S Tambekou", + "author_inst": "RSD Institute" + }, + { + "author_name": "William Ngatchou", + "author_inst": "University of Douala, Faculty of Medicine and Pharmaceutical Sciences" + }, + { + "author_name": "Charlotte Moussi-Omgba", + "author_inst": "Ministry of Public Health Cameroon" + }, + { + "author_name": "Jean-Claude Mbanya", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Pierre Ongolo-Zogo", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Pierre-Joseph Fouda", + "author_inst": "Yaounde Central Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2021.07.25.21260967", "rel_title": "Influence of Novel Coronavirus COVID-19 and HIV: A Scoping Review of Hospital Course and Symptomatology", @@ -662615,93 +664913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.26.21261140", - "rel_title": "Higher serological responses and increased vaccine effectiveness demonstrate the value of extended vaccine schedules in combatting COVID-19 in England", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261140", - "rel_abs": "IntroductionIn January 2021, the UK decided to prioritise the delivery of the first dose of BNT162b2 (Pfizer/BioNTech) and AZD1222 (AstraZeneca) vaccines by extending the interval until the second dose up to 12 weeks.\n\nMethodsSerological responses were compared after BNT162b2 and AZD1222 vaccination with varying intervals in uninfected and previously-infected adults aged 50-89 years. These findings are evaluated against real-world national vaccine effectiveness (VE) estimates against COVID-19 in England.\n\nResultsWe recruited 750 participants aged 50-89 years, including 126 (16.8%) with evidence of previous infection; 421 received BNT162b2 and 329 and AZD1222. For both vaccines, over 95% had seroconverted 35-55 days after dose one, and 100% seroconverted 7+ days after dose 2. Following a 65-84 day interval between two doses, geometric mean titres (GMTs) at 14-34 days were 6-fold higher for BNT162b2 (6703; 95%CI, 5887-7633) than AZD1222 (1093; 806-1483), which in turn were higher than those receiving BNT162b2 19-29 days apart (694; 540 - 893). For both vaccines, VE was higher across all age-groups from 14 days after dose two compared to one dose, but the magnitude varied with interval between doses. Higher two-dose VE was observed with >6 week intervals between BNT162b2 doses compared to the authorised 3-week schedule, including [≥]80 year-olds.\n\nConclusionOur findings support the UK approach of prioritising the first dose of COVID-19 vaccines, with evidence of higher protection following extended schedules. Given global vaccine constraints, these results are relevant to policymakers, especially with highly transmissible variants and rising incidence in many countries.\n\nFundingPublic Health England", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Public Health England" - }, - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "Public Health England" - }, - { - "author_name": "Nick J Andrews", - "author_inst": "Public Health England" - }, - { - "author_name": "Heather Whitaker", - "author_inst": "Public Health England" - }, - { - "author_name": "Charlotte Gower", - "author_inst": "Public Health England" - }, - { - "author_name": "Julia Stowe", - "author_inst": "Public Health England" - }, - { - "author_name": "Elise Tessier", - "author_inst": "Public Health England" - }, - { - "author_name": "Sathyavani Subbarao", - "author_inst": "Public Health England" - }, - { - "author_name": "Georgina Ireland", - "author_inst": "Public Health England" - }, - { - "author_name": "Frances Baawuah", - "author_inst": "Public Health England" - }, - { - "author_name": "Ezra Linley", - "author_inst": "Public Health England" - }, - { - "author_name": "Lenesha Warrener", - "author_inst": "Public Health England" - }, - { - "author_name": "Michelle O'Brien", - "author_inst": "Brondesbury Medical Centre" - }, - { - "author_name": "Corinne Whillock", - "author_inst": "Public Health England" - }, - { - "author_name": "Paul Moss", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Shamez N Ladhani", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin E Brown", - "author_inst": "Public Health England" - }, - { - "author_name": "Mary E Ramsay", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.28.21260870", "rel_title": "Monitoring and forecasting the SARS-Covid-19 pandemic in France", @@ -663593,6 +665804,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.27.453843", + "rel_title": "Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses", + "rel_date": "2021-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.27.453843", + "rel_abs": "Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Nobuaki Fukuma", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Michelle L Hulke", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Michael I Brener", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Stephanie Golob", + "author_inst": "Department of Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Robert Zilinyi", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Zhipeng Zhou", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Christos Tzimas", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Ilaria Russo", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Claire McGroder", + "author_inst": "Division of Pulmonary, Allergy & Critical Care Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Ryan Pfeiffer", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Alexander Chong", + "author_inst": "Division of Infectious Diseases, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Geping Zhang", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Daniel Burkhoff", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Martin B Leon", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Mathew Maurer", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Jeffrey W Moses", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Anne-Catrin Uhlemann", + "author_inst": "Division of Infectious Diseases, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Hanina Hibshoosh", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Nil Uriel", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Matthias J Szabolcs", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Bj\u00f6rn Redfors", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Charles C Marboe", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Matthew R Baldwin", + "author_inst": "Division of Pulmonary, Allergy & Critical Care Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Nathan R Tucker", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Emily J Tsai", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.07.27.453973", "rel_title": "Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments", @@ -664413,113 +666739,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.07.25.21261093", - "rel_title": "Protection afforded by the BNT162b2 and mRNA-1273 COVID-19 vaccines in fully vaccinated cohorts with and without prior infection", - "rel_date": "2021-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.25.21261093", - "rel_abs": "Effect of prior SARS-CoV-2 infection on vaccine protection remains poorly understood. Here, we investigated whether persons vaccinated after a prior infection have better protection against future infection than those vaccinated without prior infection. Effect of prior infection was assessed in Qatars population, where the Alpha (B.1.1.7) and Beta (B.1.351) variants dominate incidence, using two national retrospective, matched-cohort studies, one for the BNT162b2 (Pfizer-BioNTech) vaccine, and one for the mRNA-1273 (Moderna) vaccine. Incidence rates of infection among BNT162b2-vaccinated persons, with and without prior infection, were estimated, respectively, at 1.66 (95% CI: 1.26-2.18) and 11.02 (95% CI: 9.90-12.26) per 10,000 person-weeks. The incidence rate ratio was 0.15 (95% CI: 0.11-0.20). Analogous incidence rates among mRNA-1273-vaccinated persons were estimated at 1.55 (95% CI: 0.86-2.80) and 1.83 (95% CI: 1.07-3.16) per 10,000 person-weeks. The incidence rate ratio was 0.85 (95% CI: 0.34-2.05). Prior infection enhanced protection of those BNT162b2-vaccinated, but not those mRNA-1273-vaccinated. These findings may have implications for dosing, interval between doses, and potential need for booster vaccination.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Houssein H. Ayoub", - "author_inst": "Qatar University" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Fatiha Benslimane", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. Al Khatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Patrick Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mohammad Rubayet Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Zaina Al Kanaani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Einas Al Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Riyazuddin Mohammad Shaik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hanan F. Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Mohamed Ghaith Al Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad Eid Al Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohamed H. Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.24.453631", "rel_title": "SARS-CoV-2 Delta variant pathogenesis and host response in Syrian hamsters", @@ -665607,6 +667826,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.07.22.21260878", + "rel_title": "Mental Health of HBCU College Students during the COVID-19 Pandemic", + "rel_date": "2021-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260878", + "rel_abs": "ObjectiveThis study investigated rates and predictors of mental health issues (e.g., depression and anxiety) in a sample of college students currently attending a historically Black college/university (HBCU) during the COVID-19 pandemic.\n\nParticipants/Methods98 undergraduate students (81 female and 17 male) completed an online survey containing questions about demographics, socioeconomic status, academic characteristics, and pandemic-related concerns. The survey also included PHQ-9 and GAD-7 questionnaires to evaluate depression and anxiety, respectively.\n\nResults49% of students met the clinical cutoff for depression, 39% for anxiety, and 52% for depression and/or anxiety. Significant predictors of meeting the cutoffs included parental job loss/hour reduction, being a senior, and feeling that the pandemic negatively impacted daily life, among other factors. Demographic variables (age, gender, etc.) had no effect.\n\nConclusionHBCU students show high rates of depression and anxiety during the COVID-19 pandemic, which may be predicted based on the students academic, socioeconomic, and pandemic-related concerns.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sharron Xuanren Wang", + "author_inst": "Delaware State University" + }, + { + "author_name": "Jarid Goodman", + "author_inst": "Delaware State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.07.22.21260793", "rel_title": "A spatio-temporal study of state-wide case-fatality risks during the first wave of the COVID-19 pandemic in Mexico", @@ -666487,37 +668729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.21.21260944", - "rel_title": "Severity of SARS-CoV-2 reinfections in second wave determines likelihood of mild endemicity", - "rel_date": "2021-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260944", - "rel_abs": "Immunity to SARS-CoV-2 is building up globally, but will this be sufficient to prevent future COVID-19 epidemics in the face of variants and waning immunity? Manaus, Brazil offers a concerning glimpse of what may come: six months after the majority of the citys population experienced primary infection, a second wave with a new strain resulted in more deaths than the first wave. Current hypotheses for this surge rely on prior immunity waning due to time and antigenic distance. Here we show this hypothesis predicts a severe endemic state. We propose an alternative hypothesis in which individuals infected in the first wave lose protection against transmission but retain immunity against severe disease and show this hypothesis is equally compatible with existing data. In this scenario, the increased number of deaths is due to an increased infection fatality ratio (IFR) for primary infections with the new variant. This alternative predicts a mild endemic state will be reached within decades. Collecting data on the severity of reinfections and infections post-vaccination as a function of time and antigenic distance from the original exposure is crucial for optimizing control strategies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jennie S Lavine", - "author_inst": "Emory" - }, - { - "author_name": "Ottar N Bjornstad", - "author_inst": "Penn State University" - }, - { - "author_name": "Daniel Coombs", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Rustom Antia", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.21.21260810", "rel_title": "Off-season RSV epidemics in Australia after easing of COVID-19 restrictions", @@ -667589,6 +669800,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.19.21260721", + "rel_title": "Present knowledge, attitude, practice, and fear level of Bangladeshi people towards covid-19 after one year of the pandemic situation: a web-based cross-sectional study.", + "rel_date": "2021-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260721", + "rel_abs": "In the earlier phase of the pandemic situation, the governments of Bangladesh badly suffered to adhere their people to preventive measures probably due to less knowledge and attitude towards covid-19. To tackle the second wave of coronavirus, the governments again enforced an array of preventive measures, but still encountering the same problem after a year of the pandemic situation. In an attempt to find out the reasons behind this, our study aimed to assess the present knowledge, attitude, practice, and fear level of the people. A cross-sectional study was conducted from 15th to 25th April 2021. A total of 402 participants met all the inclusion criteria and were considered for performing all statistical analyses (Descriptive statistics, Mann-Whitney U test, Kruskal-Wallis H test, Multiple logistic regression, Spearman rank-order correlation). Out of 402 participants, more than 90% participants were students and all were adults aged 16 to 30. 84.6%, 65.7%, 54%, and 21.6% participants had more adequate knowledge, more positive attitude, more frequent practice, and moderate to high fear towards covid-19, respectively. Knowledge, attitude, practice, and fear were interrelated directly or indirectly. It was found knowledgeable participants were more likely to have more positive attitude (OR = 2.12, 95% CI = 1.14-3.95, P < 0.05) and very less fear (OR = 1.98, 95% CI = 1.02-3.82, P < 0.05). More positive attitude was found as a good predictor of more frequent practice (OR = 4.33, 95% CI = 2.66-7.04, P < 0.001), and very less fear had same negative impact on both attitude (OR = 0.48, 95% CI = 0.25-0.91, P < 0.05) and practice (OR = 0.48, 95% CI = 0.27-0.85, P < 0.05). Our findings reflect that knowledge level has elevated but attitude level subsided, and practice level stayed same as was in the earlier phase of pandemic and people are no longer panicked.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tahsin Ahmed Rupok", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + }, + { + "author_name": "Sunandan Dey", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + }, + { + "author_name": "Rashni Agarwala", + "author_inst": "Department of Pharmacy, Islamic University, Kushtia-7003, Bangladesh." + }, + { + "author_name": "Md. Nurnobi Islam", + "author_inst": "Department of Chemistry, Shahjalal University of Science & Technology, Sylhet-3114, Bangladesh." + }, + { + "author_name": "Bayezid Bostami", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.21.21260624", "rel_title": "New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations", @@ -669577,29 +671823,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.20.21260875", - "rel_title": "NO INCREASE IN RELATIVE MORTALITY RATES FOR THOSE WITHOUT A COLLEGE DEGREE DURING COVID-19: AN ANOMALY", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260875", - "rel_abs": "American mortality rates have diverged in recent years between those with and without a four-year college degree, and there are many reasons to expect the education-mortality gradient to have steepened during the pandemic. Those without a BA are more likely to work in frontline occupations, to rely on public transportation, and to live in crowded quarters, all of which are associated with an increase in infection risk, a risk that was zero prior to the pandemic. We use publicly available data from the National Center for Health Statistics on deaths by age, sex, education and race/ethnicity to assess the protective effect of a BA in 2020 compared to 2019. While the BA was strongly protective during 2020, the ratio of mortality rates between those with and without a degree was little changed relative to pre-pandemic years. Among 60 groups (gender by race/ethnicity by age) that are available in the data, the relative risk reduction associated with a BA fell for more than half the groups between 2019 and 2020, and increased by more than 5 percentage points for only five groups. Our main finding is not that the BA was protective against death in 2020, which has long been the case, but that the protective effect was little different than in 2019 and earlier years, in spite of the change in the pattern of risk by occupation and income. The virus maintained the mortality-education gradient that existed pre-pandemic, at least through the end of 2020. Our results suggest that changes in the risk of infection were less important in structuring mortality than changes in the risk of death conditional on infection.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Anne Case", - "author_inst": "Princeton University" - }, - { - "author_name": "Angus Deaton", - "author_inst": "Princeton University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.23.21261013", "rel_title": "Herd immunity induced by COVID-19 vaccination programs to suppress epidemics caused by SARS-CoV-2 wild type and variants in China", @@ -670463,6 +672686,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.20.21260558", + "rel_title": "Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260558", + "rel_abs": "Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK.\n\nOverall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically.\n\nOf those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed.\n\nIntentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Rebecca Wilson", + "author_inst": "Cardiff University" + }, + { + "author_name": "Harriet Quinn-Scoggins", + "author_inst": "Cardiff University" + }, + { + "author_name": "Yvonne Moriarty", + "author_inst": "Cardiff University" + }, + { + "author_name": "Jacqueline Hughes", + "author_inst": "Cardiff University" + }, + { + "author_name": "Mark Goddard", + "author_inst": "Cardiff University" + }, + { + "author_name": "Rebecca Cannings-John", + "author_inst": "Cardiff University" + }, + { + "author_name": "Victoria Whitelock", + "author_inst": "Cancer Research UK" + }, + { + "author_name": "Katriina L Whitaker", + "author_inst": "University of Surrey" + }, + { + "author_name": "Detelina Grozeva", + "author_inst": "Cardiff University" + }, + { + "author_name": "Julia Townson", + "author_inst": "Cardiff University" + }, + { + "author_name": "Kirstie Osborne", + "author_inst": "Cancer Research UK" + }, + { + "author_name": "Stephanie Smits", + "author_inst": "Cardiff University" + }, + { + "author_name": "Michael Robling", + "author_inst": "Cardiff University" + }, + { + "author_name": "Julie Hepburn", + "author_inst": "Public Involvement Community, Health and Care Research Wales" + }, + { + "author_name": "Graham Moore", + "author_inst": "Cardiff University" + }, + { + "author_name": "Ardiana Gjini", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Kate Brain", + "author_inst": "Cardiff University" + }, + { + "author_name": "Jo Waller", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.07.19.21260139", "rel_title": "Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19", @@ -671431,49 +673741,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.07.17.21260123", - "rel_title": "Virlaza Inhibits Sars-COV-2-induced Inflammatory Response of Bronchial Epithelial Cells and Pulmonary Fibroblast", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.17.21260123", - "rel_abs": "Coronavirus disease 2019 (COVID-19), which is currently a global public health emergency and beyond vaccines as a prophylactic treatment, no specific and effective therapeutical treatments are available. COVID-19 induces a massive release of proinflammatory cytokines, which drives COVID-19 progression, severity, and mortality. In addition, bronchial epithelial cells are the first pulmonary cells activated by coronavirus-2 (SARS-Cov-2) leading to massive cytokine release, which can hyperactivate lung fibroblasts, resulting in pulmonary fibrosis, a phenomenon observed even in moderate COVID-19 survivors. This in vitro study tested the hypothesis that Virlaza, a herbal medicine, could inhibit the hyperactivation of human bronchial epithelial cells (BEAS-2B) and pulmonary fibroblasts (MRC-5) induced by SARS-Cov-2. BEAS-2B (5x104/mL/well) and MRC-5 (5x104/mL/well) cells were co-cultivated with 1ml of blood of a Sars-Cov-2 infected patient for 4 hours and Virlaza (1ug/mL) was added in the first minute of the co-culture. After 4 hours, the cells were recovered and used for analysis of cytotoxicity by MTT and for mRNA expression of P2X7 receptor E iNOS. The supernatant was used to measure ATP and cytokines. Sars-Cov-2 incubation resulted in increased release of ATP, IL-1beta, IL-6, IL-8, and TNF-alpha by BEAS-2B and MRC-5 cells (p<0.001). Treatment with Virlaza resulted in reduction of ATP, IL-1beta, IL-6, IL-8, and TNF-alpha release (p<0.001). In addition, Sars-Cov-2 incubation resulted in increased expression of P2X7 receptor and iNOS (p<0.001), which has been reversed by Virlaza (p<0.001). In conclusion, Virlaza presents important anti-inflammatory effects in the context of Sars-Cov-2 infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Maysa A R Brandao-Rangel", - "author_inst": "Federal University of Sao Paulo" - }, - { - "author_name": "Dobroslav Melamed", - "author_inst": "Libipharm" - }, - { - "author_name": "Anamei Silva-Reis", - "author_inst": "Federal University of Sao Paulo" - }, - { - "author_name": "Boris Brill", - "author_inst": "Libipharm" - }, - { - "author_name": "Lucas dos Santos Zamarioli", - "author_inst": "Federal University of Sao Paulo" - }, - { - "author_name": "Carlos R Oliveira", - "author_inst": "Federal University of Sao Paulo" - }, - { - "author_name": "Rodolfo P Vieira", - "author_inst": "Federal University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.07.18.21260732", "rel_title": "Immunogenicity of mRNA-1273, BNT162b2 and Ad26.COV2.S COVID-19 vaccines", @@ -672489,6 +674756,425 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.19.21260779", + "rel_title": "Surveillance of SARS-CoV-2 variants in Argentina: detection of Alpha, Gamma, Lambda, Epsilon and Zeta in locally transmitted and imported cases", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260779", + "rel_abs": "Molecular surveillance of SARS-CoV-2 variants was performed on a total of 2,406 samples from the capital city and nine provinces of Argentina, during 30 epidemiological weeks (EW) that covered the end of the first wave and the beginning of the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 20/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the simultaneous identification of signature mutations associated with worldwide circulating variants. In addition, whole SARS-CoV-2 genome sequences were obtained from 456 samples. The main variants found were Gamma, Lambda and Alpha, and to a lesser extent, Zeta and Epsilon. Whereas Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires (MABA), although showing a heterogeneous distribution along this region. This cost-effective surveillance protocol allowed for a rapid response in a limited access to resources scenario, added information on the expansion of the Lambda variant in South America and contributed to the implementation of public health measures to control the disease spread in Argentina.", + "rel_num_authors": 101, + "rel_authors": [ + { + "author_name": "Carolina Torres", + "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Buenos Aires, Arge" + }, + { + "author_name": "Laura Mojsiejczuk", + "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Buenos Aires, Arge" + }, + { + "author_name": "Dolores Acuna", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos" + }, + { + "author_name": "Sofia Alexay", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Ariel Amadio", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones C" + }, + { + "author_name": "Paula Aulicino", + "author_inst": "Laboratorio de Biologia Celular y Retrovirus. Hospital de Pediatria Prof. Juan P. Garrahan, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y T" + }, + { + "author_name": "Humberto Debat", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Franco Fernandez", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Stephanie Goya", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Guido Konig", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Mercedes Nabaes Jodar", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos" + }, + { + "author_name": "Luis Pianciola", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Sofia Bengoa", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Marco Cacciahue", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Cecilia Camussone", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina" + }, + { + "author_name": "Maria Jose Dus Santos", + "author_inst": "Instituto de Virologia e Innovaciones Tecnologicas (INTA-CONICET), Hurlingham, Buenos Aires, Argentina; Laboratorio de Diagnostico-UNIDAD COVID- Universidad Nac" + }, + { + "author_name": "Maria Florencia Eberhardt", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones C" + }, + { + "author_name": "Ailen Fernandez", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Maria Ines Gismondi", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina; Universidad Nacional de Luja" + }, + { + "author_name": "Matias Irazoqui", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones " + }, + { + "author_name": "Silvina Lusso", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Nathalie Marquez", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Marianne Munoz", + "author_inst": "Unidad de Genomica del Instituto de Biotecnologia/Instituto de Agrobiotecnologia y biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Monica Natale", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Belen Pisano", + "author_inst": "Instituto de Virologia Dr. J. M. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba; Consejo Nacional de Investigaciones Cientificas y Tecni" + }, + { + "author_name": "Andrea Puebla", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Re", + "author_inst": "Instituto de Virologia Dr. J. M. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba; Consejo Nacional de Investigaciones Cientificas y Tecni" + }, + { + "author_name": "Ezequiel Sosa", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Jonathan Zaiat", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Sebastian Zunino", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina; Universidad Nacional de Lujan, Departamento de C" + }, + { + "author_name": "Dario Do porto", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Maria Elina Acevedo", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Cristina Alvarez Lopez", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria Laura Alvarez", + "author_inst": "Laboratorio del Hospital Zonal Dr. Ramon Carrillo, San Carlos De Bariloche, provincia de Rio Negro, Argentina" + }, + { + "author_name": "Patricia Angeleri", + "author_inst": "Comite Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Andres Angelletti", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina; Laboratorio de Virologia, HIEAyC San Juan de D" + }, + { + "author_name": "Manuel Arca", + "author_inst": "Laboratorio de Virologia del Hospital JJ Urquiza, Concepcion del Uruguay, provincia de Entre Rios, Argentina" + }, + { + "author_name": "Gabriela Barbas", + "author_inst": "Secretaria de Prevencion y Promocion, Ministerio de Salud de la provincia de Cordoba, Argentina." + }, + { + "author_name": "Ana Bertone", + "author_inst": "Laboratorio de la Direccion de Epidemiologia, Santa Rosa, provincia de La Pampa, Argentina." + }, + { + "author_name": "Agustina Bonnet", + "author_inst": "Laboratorio de Virologia del Hospital JJ Urquiza, Concepcion del Uruguay, provincia de Entre Rios, Argentina" + }, + { + "author_name": "Ignacio Bourlot", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Alejandro Castello", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Gonzalo Castro", + "author_inst": "Laboratorio Central de la Provincia de Cordoba, Ministerio de Salud la provincia de Cordoba, Argentina." + }, + { + "author_name": "Carolina Ceriani", + "author_inst": "Laboratorio de Virologia de la Facultad de Veterinaria de la Universidad Nacional del Centro de la provincia de Buenos Aires (UNCPBA), Tandil, provincia de Buen" + }, + { + "author_name": "Carlos Cimino", + "author_inst": "Instituto Nacional de Epidemiologia Dr. Jara (Mar del Plata, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Julian Cipelli", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria Colmeiro", + "author_inst": "Laboratorio de Virologia, HIEAyC \"San Juan de Dios\", La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Andres Cordero", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Carolina Cristina", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Sofia Di Bella", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Regina Ercole", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Yesica Espasandin", + "author_inst": "Laboratorio del Hospital Zonal Dr. Ramon Carrillo, San Carlos De Bariloche, provincia de Rio Negro, Argentina" + }, + { + "author_name": "Carlos Espul", + "author_inst": "Direccion de epidemiologia y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza, Argentina." + }, + { + "author_name": "Andrea Falaschi", + "author_inst": "Direccion de epidemiologia y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza, Argentina." + }, + { + "author_name": "Facundo Fernandez Moll", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Andrea Gatelli", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Sandra Goni", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Maria E Jofre", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Jose Jaramillo", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Natalia Labarta", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria A Lacaze", + "author_inst": "Programa Laboratorio de Salud Publica Dr Dalmiro Perez Laborda, Ministerio de Salud de la provincia de San Luis, Argentina." + }, + { + "author_name": "Rocio Larreche", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Leiva", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Gustavo Levin", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Erica Luczak", + "author_inst": "Laboratorio del Hospital Interzonal General de Agudos Evita, Lanus, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Marcelo Mandile", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Carla Massone", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Melina Mazzeo", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Carla Medina", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Belen Monaco", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Luciana Montoto", + "author_inst": "Laboratorio de Biologia Molecular Hospital Pedro de Elizalde, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Mugna", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Alejandra Musto", + "author_inst": "Laboratorio del Hospital Interzonal General de Agudos Evita, Lanus, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Guillermo Ojeda", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Carolina Pintos", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina." + }, + { + "author_name": "Marcia Pozzati", + "author_inst": "Laboratorio de Biologia Molecular, Hospital Cosme Argerich, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Marilina Rahhal", + "author_inst": "Laboratorio de Hospital El Cruce Dr. Nestor C. Kirchner, CEMET, Florencio Varela, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Claudia Rechimont", + "author_inst": "Laboratorio de la Direccion de Epidemiologia, Santa Rosa, provincia de La Pampa, Argentina." + }, + { + "author_name": "Federico Remes Lenicov", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sida, CONICET-UBA, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Gabriela Rompato", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Vanesa Seery", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sida, CONICET-UBA, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Leticia Siri", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Julieta Spina", + "author_inst": "Laboratorio de Biologia Molecular. Hospital Dr. Hector Cura, Olavarria, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Cintia Streitenberger", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Ariel Suarez", + "author_inst": "Departamento de Biologia y genetica molecular; IACA Laboratorios, Bahia Blanca, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Jorgelina Suarez", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Paula Sujanski", + "author_inst": "Comite Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Juan M Talia", + "author_inst": "Programa Laboratorio de Salud Publica Dr Dalmiro Perez Laborda, Ministerio de Salud de la provincia de San Luis, Argentina." + }, + { + "author_name": "Clara Theaux", + "author_inst": "Laboratorio de Biologia molecular del Hospital General de Agudos Dr. Carlos G. Durand, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Guillermo Thomas", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Marina Ticeira", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Estefania Tittarelli", + "author_inst": "Departamento de Biologia y genetica molecular; IACA Laboratorios, Bahia Blanca, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Rosana Toro", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Osvaldo Uez", + "author_inst": "Instituto Nacional de Epidemiologia Dr. Jara (Mar del Plata, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Maria B Zaffanella", + "author_inst": "Laboratorio de Biologia Molecular. Hospital Dr. Hector Cura, Olavarria, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Cecilia Ziehm", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina." + }, + { + "author_name": "Martin Zubieta", + "author_inst": "Laboratorio de Hospital El Cruce Dr. Nestor C. Kirchner, CEMET, Florencio Varela, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "- PAIS Consortium", + "author_inst": "-" + }, + { + "author_name": "Alicia Mistchenko", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Comision de Investigaciones Cientificas de la provincia de Buenos Aires, Arg" + }, + { + "author_name": "Laura Valinotto", + "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez" + }, + { + "author_name": "Mariana Viegas", + "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.21260759", "rel_title": "Development and validation of a prognostic model for COVID-19: a population-based cohort study in Iceland", @@ -673273,29 +675959,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.20.21260858", - "rel_title": "Monday effect on confirmed cases of COVID-19 in Japan", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260858", - "rel_abs": "We examined the phenomenon of fewer new confirmed cases of COVID-19 on Mondays in Japan, which we refer to as the Monday effect, and reveal the details of this effect. Specifically, we estimated the difference between the number of new positive cases that decreased over the weekend and the number of new confirmed cases that decreased at the beginning of the week. In Japan, prefectures aggregate and announce the number of confirmed daily cases. This analysis allows us to examine whether there is a Monday effect in each prefecture. We show that the Monday effect is due to the decreased number of inspections on the weekend appearing at the beginning of the week due to a time lag. Our results indicate that the administrative system causes delays in some prefectures, and that some prefectures are less likely to conduct screenings on holidays. Our results also suggest that delays generally occur in prefectures with a population of over 2 million. Congestion, Reporting delay, Public health, COVID-19", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kuninori Nakagawa", - "author_inst": "Shizuoka University" - }, - { - "author_name": "Taro Kanatani", - "author_inst": "Shiga University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.07.20.21260278", "rel_title": "Seroprevalence and Dynamics of anti-SARS-CoV-2 antibody among healthcare workers following ChAdOx1 nCoV-19 vaccination", @@ -674311,6 +676974,65 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.07.22.453287", + "rel_title": "Competent immune responses to SARS-CoV-2 variants in older adults following mRNA vaccination", + "rel_date": "2021-07-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.22.453287", + "rel_abs": "Aging is associated with a reduced magnitude of primary immune responses to vaccination and constriction of immune receptor repertoire diversity. Clinical trials demonstrated high efficacy of mRNA based SARS-CoV-2 vaccines in older adults but concerns about virus variant escape have not been well addressed. We have conducted an in-depth analysis of humoral and cellular immunity against an early-pandemic viral isolate and compared that to the P.1. (Gamma) and B.1.617.2 (Delta) variants in <50 and >55 age cohorts of mRNA vaccine recipients. We have further measured neutralizing antibody titers for B.1.617.1 (Kappa) and B.1.595; a SARS-CoV-2 isolate bearing Spike mutation E484Q. As reported, robust immunity required the second dose of vaccine. Older vaccinees manifested robust cellular immunity against early-pandemic SARS-CoV-2 and more recent variants, which remained statistically comparable to the adult group. The older cohort had lower neutralizing capacity at the first time point following the second dose, but at later time points immunity was indistinguishable between them. While the duration of these immune responses remains to be determined over longer periods of time, these results provide reasons for optimism regarding vaccine protection of older adults against SARS-CoV-2 variants and inform thinking about boost vaccination with variant vaccines.\n\neTOC summaryVaccine responses are often diminished with aging, but we found strong responses to SARS-CoV-2 in older adults following mRNA vaccination. T cell responses were not diminished when confronted by SARS-CoV-2 variants. Neutralizing Ab were reduced but not more than those in adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC=\"FIGDIR/small/453287v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@1091655org.highwire.dtl.DTLVardef@1996173org.highwire.dtl.DTLVardef@ccf2f9org.highwire.dtl.DTLVardef@163ed22_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mladen Jergovi\u0107", + "author_inst": "University of Arizona" + }, + { + "author_name": "Jennifer L. Uhrlaub", + "author_inst": "University of Arizona" + }, + { + "author_name": "Makiko Watanabe", + "author_inst": "University of Arizona" + }, + { + "author_name": "Christine M. Bradshaw", + "author_inst": "University of Arizona" + }, + { + "author_name": "Lisa M. White", + "author_inst": "University of Arizona" + }, + { + "author_name": "Bonnie J. LaFleur", + "author_inst": "University of Arizona" + }, + { + "author_name": "Taylor Edwards", + "author_inst": "University of Arizona" + }, + { + "author_name": "Ryan Sprissler", + "author_inst": "University of Arizona" + }, + { + "author_name": "Michael Worobey", + "author_inst": "University of Arizona" + }, + { + "author_name": "Deepta Bhattacharya", + "author_inst": "University of Arizona" + }, + { + "author_name": "Janko Nikolich-\u017dugich", + "author_inst": "University of Arizona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.20.21260892", "rel_title": "Variation in SARS-CoV-2 bioaerosol production in exhaled breath", @@ -674835,85 +677557,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2021.07.21.21260103", - "rel_title": "Seroprevalence of the SARS-CoV-2 antibody in healthcare workers: a multicenter cross-sectional study in ten Colombian cities.", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260103", - "rel_abs": "Background: SARS-CoV-2 affects mainly occupational health populations. Healthcare workers are at constant risk of infection. The objective of this study was to determine the seroprevalence of SARS-CoV-2 in healthcare workers in Colombia. Methods: This study is a cross-sectional study focused on estimating the seroprevalence of SARS-CoV-2 antibodies in healthcare workers from 65 hospitals in 10 cities of Colombia during the second semester of 2020. The seroprevalence was determined using an automated immunoassay (Abbott SARS-CoV-2 CLIA IgG). The study included a survey to establish the sociodemographic variables and the risk of infection. Results: The global seroprevalence of antibodies against SARS-CoV-2 was 35% (95% Bayesian Confidence Interval 33%-37%). All the personnel reported the use of protective equipment. General services personnel and nurses presented the highest rates of seroprevalence among the healthcare workers. Low socioeconomic strata have shown a strong association with seropositivity. Conclusion: This study shows the occupational risk for SARS-CoV-2 infection among healthcare workers. Even though, all the personnel reported the use of protective equipment, the seroprevalence in the general services personnel and nurses was high. Also, it was observed a significant difference by city. The results could be used to perform prevention and control in this exposed population. However, further investigation of these is required to inform sources of infection to improve the control and occupational health practices.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jeadran N. Malagon-Rojas", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Marcela Mercado-Reyes", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Yesith Guillermo Toloza-Perez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Eliana Lizeth Parra", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Ruth Marien Palma", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Esperanza Munoz", - "author_inst": "Universidad Nacional de Colombia" - }, - { - "author_name": "Ronald Lopez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Julia Edith Almentero-Correa", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Vivian Vanesa Rubio", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Edgar Antonio Ibanez-Pinilla", - "author_inst": "Universidad El Bosque" - }, - { - "author_name": "Eliana Milena Tellez-Avila", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Gabriela Delgado", - "author_inst": "Universidad Nacional de Colombia" - }, - { - "author_name": "Claudia Patricia Jimenez-Forero", - "author_inst": "Universidad Abierta y A Distancia" - }, - { - "author_name": "Diego Viasus", - "author_inst": "Universidad del Norte de Barranquilla" - }, - { - "author_name": "Marisol Galindo", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Luisa Fernanda Lagos", - "author_inst": "Instituto Nacional de Salud" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.07.19.21260373", "rel_title": "Sociodemographic differences in patient experience with virtual care during COVID-19", @@ -675997,6 +678640,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.20.453118", + "rel_title": "Integrin activation is an essential component of SARS-CoV-2 infection", + "rel_date": "2021-07-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.453118", + "rel_abs": "Cellular entry of coronaviruses depends on binding of the viral spike (S) protein to a specific cellular receptor, the angiotensin-converting enzyme 2 (ACE2). Furthermore, the viral spike protein expresses an RGD motif, suggesting that cell surface integrins may be attachment co-receptors. However, using infectious SARS-CoV-2 requires a biosafety level 3 laboratory (BSL-3), which limits the techniques that can be used to study the mechanism of cell entry. Here, we UV-inactivated SARS-CoV-2 and fluorescently labeled the envelope membrane with octadecyl rhodamine B (R18) to explore the role of integrin activation in mediating both cell entry and productive infection. We used flow cytometry and confocal fluorescence microscopy to show that fluorescently labeled SARS-CoV-2R18 particles engage basal-state integrins. Furthermore, we demonstrate that Mn2+, which activates integrins and induces integrin extension, enhances cell binding and entry of SARS-CoV-2R18 in proportion to the fraction of integrins activated. We also show that one class of integrin antagonist, which binds to the I MIDAS site and stabilizes the inactive, closed conformation, selectively inhibits the engagement of SARS-CoV-2R18 with basal state integrins, but is ineffective against Mn2+-activated integrins. At the same time, RGD-integrin antagonists inhibited SARS-CoV-2R18 binding regardless of integrin activity state. Integrins transmit signals bidirectionally: inside-out signaling primes the ligand binding function of integrins via a talin dependent mechanism and outside-in signaling occurs downstream of integrin binding to macromolecular ligands. Outside-in signaling is mediated by G13 and induces cell spreading, retraction, migration, and proliferation. Using cell-permeable peptide inhibitors of talin, and G13 binding to the cytoplasmic tail of an integrins {beta} subunit, we further demonstrate that talin-mediated signaling is essential for productive infection by SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Peter Simons", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Derek Rinaldi", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Virginie Bondu", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Alison Kell", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Steven Bradfute", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Diane Lidke", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Tione Buranda", + "author_inst": "University of New Mexico School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.07.20.453054", "rel_title": "Discovery of nanobodies against SARS-CoV-2 and an uncommon neutralizing mechanism", @@ -676873,85 +679559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.16.21260367", - "rel_title": "Association between the COVID-19 pandemic and pertussis in France using multiple nationwide data sources", - "rel_date": "2021-07-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260367", - "rel_abs": "BackgroundInterventions to mitigate coronavirus disease 19 (COVID-19) pandemic may impact other respiratory diseases such as pertussis. We aimed to study the course of pertussis in France over an 8-year period and its association with COVID-19 mitigation strategies, using multiple nationwide data sources.\n\nMethodsWe analyzed the number of French pertussis cases between 2013 and 2020, using the PCR test results from nationwide outpatient laboratories (Source 1) and the pediatric network of 41 hospitals (Source 2), and using the reports of an office-based pediatric national network (Source 3). We conducted a quasi-experimental interrupted time-series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles, and secular trend, and included a binary variable for the first national lockdown (ordered on March 16, 2021).\n\nResultsWe identified 19,039 cases of pertussis from the three data sources during the study period. There was a significant decrease of pertussis cases following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.102 (95% CI 0.040-0.256) and 0.216 (95% CI 0.071-0.656) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 (median of 1 [IQR 0-2] vs. 0 [IQR 0-0] pertussis cases per month before and after lockdown, respectively, p=0.0048).\n\nConclusionThe drastic reduction of outpatient and hospitalized cases of pertussis strongly suggests an impact of COVID-19 mitigation measures and their consequences on pertussis epidemiology. Pertussis vaccination recommendations should be carefully followed, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.\n\nFundingThere was no specific funding for the study.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Soraya Matczak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Corinne Levy", - "author_inst": "ACTIV" - }, - { - "author_name": "Camille Fortas", - "author_inst": "The Frenche Public Health Agency" - }, - { - "author_name": "Jeremie F. Cohen", - "author_inst": "Necker-Enfants Malades Hospital" - }, - { - "author_name": "Stephane Bechet", - "author_inst": "ACTIV" - }, - { - "author_name": "Fatima Belghiti", - "author_inst": "The French Public Health Agency" - }, - { - "author_name": "Sophie Guillot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sabine Trombert", - "author_inst": "Laboratoire CERBA" - }, - { - "author_name": "Veronique Jacomo", - "author_inst": "Laboratoire Eurofins Biomnis" - }, - { - "author_name": "Yann Savitch", - "author_inst": "The French Public Health Agency" - }, - { - "author_name": "Juliette Paireau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvain Brisse", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Nicole Guiso", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Daniel Levy Bruhl", - "author_inst": "The French Public Health Agency" - }, - { - "author_name": "Robert Cohen", - "author_inst": "ACTIV" - }, - { - "author_name": "Julie Toubiana", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.17.21260655", "rel_title": "Post-COVID Syndrome. A Case Series and Comprehensive Review", @@ -677847,6 +680454,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.07.15.21260543", + "rel_title": "Understanding Adverse Population Sentiment Towards the Spread of COVID-19 in the United States", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260543", + "rel_abs": "BackgroundDuring the ongoing COVID-19 pandemic, the immediate threat of illness and mortality is not the only concern. In the United States, COVID-19 is not only causing physical suffering to patients, but also great levels of adverse sentiment (e.g., fear, panic, anxiety) among the public. Such secondary threats can be anticipated and explained through sentiment analysis of social media, such as Twitter.\n\nMethodsWe obtained a dataset of geotagged tweets on the topic of COVID-19 in the contiguous United States during the period of 11/1/2019 - 9/15/2020. We classified each tweet into \"adverse\" and \"non-adverse\" using the NRC Emotion Lexicon and tallied up the counts for each category per county per day. We utilized the space-time scan statistic to find clusters and a three-stage regression approach to identify socioeconomic and demographic correlates of adverse sentiment.\n\nResultsWe identified substantial spatiotemporal variation in adverse sentiment in our study area/period. After an initial period of low-level adverse sentiment (11/1/2019 - 1/15/2020), we observed a steep increase and subsequent fluctuation at a higher level (1/16/2020 - 9/15/2020). The number of daily tweets was low initially (11/1/2019 - 1/22/2020), followed by spikes and subsequent decreases until the end of the study period. The space-time scan statistic identified 12 clusters of adverse sentiment of varying size, location, and strength. Clusters were generally active during the time period of late March to May/June 2020. Increased adverse sentiment was associated with decreased racial/ethnic heterogeneity, decreased rurality, higher vulnerability in terms of minority status and language, and housing type and transportation.\n\nConclusionsWe utilized a dataset of geotagged tweets to identify the spatiotemporal patterns and the spatial correlates of adverse population sentiment during the first two waves of the COVID-19 pandemic in the United States. The characteristics of areas with high adverse sentiment may be relevant for communication of containment measures. The combination of spatial clustering and regression can be beneficial for understanding of the ramifications of COVID-19, as well as disease outbreaks in general.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alexander Hohl", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Moongi Choi", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Richard Medina", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Neng Wan", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Ming Wen", + "author_inst": "Department of Sociology, University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.15.21260346", "rel_title": "Elderly acceptance of telemedicine use in Hong Kong during and after the COVID-19 pandemic: a cross-sectional cohort survey", @@ -678703,61 +681345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.15.21260265", - "rel_title": "The incidence and in-hospital mortality of COVID-19 patients post-vaccination in eastern India", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260265", - "rel_abs": "ObjectivesThe comparable effectiveness of Covishield and Covaxin vaccines has not been studied. We compared the effectiveness of Covishield and Covaxin vaccines against moderate to severe COVID-19.\n\nMethodsIn this retrospective observational study, we collected data of patients who were admitted with moderate to severe COVID-19. The vaccination status and comorbidities of the patients were documented. The incidence and in-hospital mortality of COVID-19 patients was assessed. Univariate analysis was performed to determine the risk factors of in-hospital mortality.\n\nResultsOf 294 patients, 5.1% (n=15) received Covaxin and 26.5% (n=78) received Covishield; 68.4% (n=201) patients were unvaccinated. Of patients who were vaccinated and contracted COVID-19, 24.8% (n=73) had taken the first dose and 6.8% (n=20) had taken the second dose of either vaccine. The in-hospital mortality rate was 13.6% (n=40). 24/40 (60%) people who had hospital mortality were unvaccinated.3/40(7.5%) had succumbed to death after receiving double dose of Covishield, 11/40 (27.5%) had succumbed to death after receiving single dose of Covishield, 2/40(5%) had succumbed to death after receiving single dose of Covaxin, none had reported infection after receiving second dose of Covaxin. No significant association was found with the type of vaccine and the in-hospital mortality (p=0.23). Significant associations with in-hospital mortality were found with the interval before COVID-19 disease and vaccination (OR, 3.02; p=0.01); and the presence of diabetes mellitus (OR, 2.13; p=0.02), cardiovascular diseases (OR, 2.11; p<0.001), and malignancy (OR: 2.33; p=0.0325).\n\nConclusionThere was no significant difference in the effectiveness of Covaxin and Covishield in terms of the incidence of COVID-19 and in-hospital mortality. Diabetes mellitus, cardiovascular diseases, and malignancies had a significant association with in-hospital mortality in patients with moderate to severe COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Abhraneel Parames Guha", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "Aritra Chakrabarti", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "Subhrojyoti Bhowmick", - "author_inst": "KPC Medical College,kolkata" - }, - { - "author_name": "Saibal Das", - "author_inst": "Independent Clinical Pharmacology Consultant" - }, - { - "author_name": "Rahul Khandelwal", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "Aditya Kumar", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "AjoyKrishna Sarkar", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "Anupam Das", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "Krishnangshu Ray", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - }, - { - "author_name": "Sujit KarPurkayastha", - "author_inst": "Peerless Hospital and B.K.Roy Research Centre,kolkata" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.15.21260621", "rel_title": "Antibody and T cell responses to Sinopharm/BBIBP-CorV in naive and previously infected individuals in Sri Lanka", @@ -679853,6 +682440,49 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.07.17.452576", + "rel_title": "Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2 and Implications for Immune Evasion", + "rel_date": "2021-07-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.17.452576", + "rel_abs": "While the vaccination efforts against SARS-CoV-2 infections are ongoing worldwide, new genetic variants of the virus are emerging and spreading. Following the initial surges of the Alpha (B.1.1.7) and the Beta (B.1.351) variants, a more infectious Delta variant (B.1.617.2) is now surging, further deepening the health crises caused by the pandemic. The sharp rise in cases attributed to the Delta variant has made it especially disturbing and is a variant of concern. Fortunately, current vaccines offer protection against known variants of concern, including the Delta variant. However, the Delta variant has exhibited some ability to dodge the immune system as it is found that neutralizing antibodies from prior infections or vaccines are less receptive to binding with the Delta spike protein. Here, we investigated the structural changes caused by the mutations in the Delta variants receptor-binding interface and explored the effects on binding with the ACE2 receptor as well as with neutralizing antibodies. We find that the receptor-binding {beta}-loop-{beta} motif adopts an altered but stable conformation causing separation in some of the antibody binding epitopes. Our study shows reduced binding of neutralizing antibodies and provides a possible mechanism for the immune evasion exhibited by the Delta variant.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Prabin Baral", + "author_inst": "Florida International University" + }, + { + "author_name": "Nisha Bhattarai", + "author_inst": "Florida International University" + }, + { + "author_name": "Md Lokman Hossen", + "author_inst": "Florida International University" + }, + { + "author_name": "Vitalii Stebliankin", + "author_inst": "Florida International University" + }, + { + "author_name": "Bernard Gerstman", + "author_inst": "Florida International University" + }, + { + "author_name": "Giri Narasimhan", + "author_inst": "Florida International University" + }, + { + "author_name": "Prem P Chapagain", + "author_inst": "Florida International University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.16.452733", "rel_title": "One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects non-human primates from SARS-CoV-2", @@ -680581,57 +683211,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.13.21260431", - "rel_title": "Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report", - "rel_date": "2021-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260431", - "rel_abs": "We present an unofficial SARS-CoV-2 genomic surveillance report from Slovakia based on approximately 3500 samples sequenced between March 2020 and May 2021. Early samples show multiple independent imports of SARS-CoV-2 from other countries. In Fall 2020, three virus variants (B.1.160, B.1.1.170, B.1.258) dominated as the number of cases increased. In November 2020, B.1.1.7 (alpha) variant was introduced in Slovakia and quickly became the most prevalent variant in the country (> 75% of new cases by early February 2021 and > 95% in mid-March).", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Brona Brejova", - "author_inst": "Comenius University in Bratislava" - }, - { - "author_name": "Viktoria Hodorova", - "author_inst": "Comenius University in Bratislava" - }, - { - "author_name": "Kristina Borsova", - "author_inst": "Bioimedical Research Center of the Slovak Academy of Sciences" - }, - { - "author_name": "Viktoria Cabanova", - "author_inst": "Biomedical Research Center of the Slovak Academy of Sciences" - }, - { - "author_name": "Tomas Szemes", - "author_inst": "Comenius University Science Park" - }, - { - "author_name": "Matej Misik", - "author_inst": "Institute of Health Analyses, Ministry of Health, Slovakia" - }, - { - "author_name": "Boris Klempa", - "author_inst": "Biomedical Research Center of the Slovak Academy of Sciences" - }, - { - "author_name": "Jozef Nosek", - "author_inst": "Comenius University in Bratislava" - }, - { - "author_name": "Tomas Vinar", - "author_inst": "Comenius University in Bratislava" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.14.21260471", "rel_title": "Validation of a Novel Molecular Assay to the Diagnostic of COVID-19 Based on Real Time PCR with High Resolution Melting", @@ -681879,6 +684458,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.11.21260318", + "rel_title": "Harnessing the Wisdom of the Crowd to Forecast Incident and Cumulative COVID-19 Mortality in the United States", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260318", + "rel_abs": "BackgroundForecasting models have played a pivotal role in health policy decision making during the coronavirus disease-2019 (COVID-19) pandemic. A combined forecast from multiple models will be typically more accurate than an individual forecast, but there are few examples of studies of combined forecasts of COVID-19 data, focusing mainly on simple mean and median ensembles and involving short forecast evaluation periods. We aimed to investigate the accuracy of different ways of combining probabilistic forecasts of weekly COVID-19 mortality data, including two weighted methods that we developed previously, on an extended dataset and new dataset, and evaluate over a period of 52 weeks.\n\nMethodsWe considered 95% interval and point forecasts of weekly incident and cumulative COVID-19 mortalities between 16 May 2020 and 8 May 2021 in multiple locations in the United States. We compared the accuracy of simple and more complex combining methods, as well as individual models.\n\nResultsThe average of the forecasts from the individual models was consistently more accurate than the average performance of these models (the mean combination), which provides a fundamental motivation for combining. Weighted combining performed well for both incident and cumulative mortalities, and for both interval and point forecasting. Our inverse score with tuning method was the most accurate overall. The median combination was a leading method in the last quarter for both mortalities, and it was consistently more accurate than the mean combination for point forecasting. For interval forecasts of cumulative mortality, the mean performed better than the median. The best performance of the leading individual model was in point forecasting.\n\nConclusionsCombining forecasts can improve the contribution of probabilistic forecasting to health policy decision making during epidemics, and, when there are sufficient historical data on forecast accuracy, weighted combining provides the most accurate method.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kathryn S Taylor", + "author_inst": "University of Oxford" + }, + { + "author_name": "James W Taylor", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.12.21258827", "rel_title": "Olfactory detection of human odorant signatures in Covid patients by trained dogs", @@ -682591,45 +685193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.12.21260394", - "rel_title": "Patterns of SARS-CoV-2 exposure and mortality suggest endemic infections, in addition to space and population factors, shape dynamics across countries", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260394", - "rel_abs": "Some countries have been crippled by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic while others have emerged with few infections and fatalities; the factors underscoring this macro-epidemiological variation is one of the mysteries of this global catastrophe. Variation in immune responses influence SARS-CoV-2 transmission and mortality, and factors shaping this variation at the country level, in addition to other socio-ecological drivers, may be important. Here, we construct spatially explicit Bayesian models that combine data on prevalence of endemic diseases and other socio-ecological characteristics to quantify patterns of confirmed deaths and cases across the globe before mass vaccination. We find that the prevalence of parasitic worms, human immunodeficiency virus and malaria play a surprisingly important role in predicting country-level SARS-CoV-2 patterns. When combined with factors such as population density, our models predict 63% (56-67) and 76% (69-81) of confirmed cases and deaths among countries, respectively. While our findings at this macro-scale are necessarily associative, they highlight a need for studies to consider factors, such as infection by other pathogens, on global SARS-CoV-2 dynamics. These relationships are vital for developing countries that already have the highest burden of endemic disease and are becoming the most affected by the SARS-CoV-2 pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nicholas M Fountain-Jones", - "author_inst": "University of Tasmania" - }, - { - "author_name": "Luke Yates", - "author_inst": "University of Tasmania" - }, - { - "author_name": "Emily Flies", - "author_inst": "University of Tasmania" - }, - { - "author_name": "Andrew Flies", - "author_inst": "University of Tasmania" - }, - { - "author_name": "Scott Carver", - "author_inst": "University of Tasmania" - }, - { - "author_name": "Michael Charleston", - "author_inst": "University of Tasmania" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.15.21260006", "rel_title": "Social risk factors for SARS-CoV-2 acquisition in University students: cross sectional survey", @@ -683469,6 +686032,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.07.12.21260345", + "rel_title": "Factors associated with transmission in COVID-19 outbreaks in long-term care facilities", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260345", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a disproportionate impact on residents in long-term care facilities (LTCFs). Through our experience and data from managing COVID-19 exposures and outbreaks in LTCFs in the Fraser Health region in British Columbia, Canada, we identified risk factors associated with outbreak severity to inform current outbreak management strategies and future pandemic preparedness planning efforts.\n\nMethodsWe used a retrospective cohort study design to evaluate the association between non-modifiable factors (facility building, organization level, and resident population characteristics), modifiable factors (assessments for infection prevention and control (IPC) and public health measures), and severity of COVID-19 outbreaks (attack rate) in LTCFs. We modelled the COVID-19 attack rates in LTCF outbreaks using negative binomial regression models.\n\nResultsFrom March 1, 2020 to January 10, 2021, a total of 145 exposures to at least one confirmed case of COVID-19 in 82 LTCFs occurred. For every item not met in the assessment tool, a 22% increase in the attack rate was observed (rate ratio 1.2 [95% CI 1.1 - 1.4]) after adjusting for other risk factors such as age of the facility, index case type (resident vs. staff) and proportion of single bed rooms.\n\nConclusionOur findings highlight the importance of assessing IPC and public health measures for outbreak management. They also demonstrate the important modifiable and non-modifiable risk factors associated with COVID-19 outbreaks in our jurisdiction. We hope these findings will inform ongoing outbreak management and future pandemic planning efforts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rohit Vijh", + "author_inst": "School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Carmen H Ng", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + }, + { + "author_name": "Mehdi Shirmaleki", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + }, + { + "author_name": "Aamir Bharmal", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21260358", "rel_title": "Increase in SARS-CoV-2 seroprevalence in healthy blood donors after the second wave of COVID-19 pandemic in South-Eastern Italy: evidence for asymptomatic young individuals as potential virus spreaders", @@ -684309,33 +686903,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.07.14.21260514", - "rel_title": "Estimating the basic reproduction number at the beginning of an outbreak under incomplete data", - "rel_date": "2021-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21260514", - "rel_abs": "We compare different methods of estimating the basic reproduction number, R0, focusing on the early stages of an epidemic, and considering weekly reports of new infecteds. We study three standard epidemiological models: SIR, SEIR, and SEAIR and examine the sensitivity of the estimators to the model structure. As some methods are developed assuming specific epidemiological models, our work adds a study of their performance in both the well- and miss-specified settings. We focus on parameters matching various types of respiratory viruses, although the general approach is easily extendable to other scenarios.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sawitree Boonpatcharanon", - "author_inst": "Chulalongkorn University" - }, - { - "author_name": "Jane M Heffernan", - "author_inst": "York University" - }, - { - "author_name": "Hanna Jankowski", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.13.21260459", "rel_title": "The age-stratified analytical model for the spread of the COVID-19 epidemic", @@ -685550,6 +688117,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.10.21260293", + "rel_title": "Plasma P-selectin is an early marker of thromboembolism in COVID-19", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.10.21260293", + "rel_abs": "Coagulopathy and thromboembolism are known complications of SARS-CoV-2 infection. The mechanisms of COVID-19-associated hematologic complications involve endothelial cell and platelet dysfunction and have been intensively studied. We leveraged a prospectively collected acute COVID-19 biorepository to study the association of plasma levels of a comprehensive list of coagulation proteins with the occurrence of venous thromboembolic events (VTE). We included in our analysis 305 subjects with confirmed SARS-CoV-2 infection who presented to an urban Emergency Department with acute respiratory distress during the first COVID-19 surge in 2020; 13 (4.2%) were subsequently diagnosed with venous thromboembolism during hospitalization. Serial samples were obtained and assays were performed on two highly-multiplexed proteomic platforms. Nine coagulation proteins were differentially expressed in patients with thromboembolic events. P-selectin, a cell adhesion molecule on the surface of activated endothelial cells, displayed the strongest association with the diagnosis of VTE, independent of disease severity (p=0.0025). This supports the importance of endothelial activation in the mechanistic pathway of venous thromboembolism in COVID-19. P-selectin together with D-dimer upon hospital presentation provided better discriminative ability for VTE diagnosis than D-dimer alone.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bank Gabor Fenyves", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA, Department of Emergency Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Arnav Mehta", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "- MGH COVID-19 Collection & Processing Team", + "author_inst": "-" + }, + { + "author_name": "Kyle Kays", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Marcia Goldberg", + "author_inst": "Department of Medicine, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Nir Hacohen", + "author_inst": "Broad Institute and Massachusetts General Hospital" + }, + { + "author_name": "Michael Filbin", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.07.11.21260148", "rel_title": "ONLINE QUERIES AS A CRITERION FOR EVALUATION OF THE EPIDEMIOLOGICAL STATUS AND EFFECTIVENESS OF COVID-19 EPIDEMIC CONTROL MEASURES", @@ -686226,157 +688836,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.13.452251", - "rel_title": "A modular protein subunit vaccine candidate produced in yeast confers protection against SARS-CoV-2 in non-human primates", - "rel_date": "2021-07-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.13.452251", - "rel_abs": "Vaccines against SARS-CoV-2 have been distributed at massive scale in developed countries, and have been effective at preventing COVID-19. Access to vaccines is limited, however, in low- and middle-income countries (LMICs) due to insufficient supply, high costs, and cold storage requirements. New vaccines that can be produced in existing manufacturing facilities in LMICs, can be manufactured at low cost, and use widely available, proven, safe adjuvants like alum, would improve global immunity against SARS-CoV-2. One such protein subunit vaccine is produced by the Serum Institute of India Pvt. Ltd. and is currently in clinical testing. Two protein components, the SARS-CoV-2 receptor binding domain (RBD) and hepatitis B surface antigen virus-like particles (VLPs), are each produced in yeast, which would enable a low-cost, high-volume manufacturing process. Here, we describe the design and preclinical testing of the RBD-VLP vaccine in cynomolgus macaques. We observed titers of neutralizing antibodies (>104) above the range of protection for other licensed vaccines in non-human primates. Interestingly, addition of a second adjuvant (CpG1018) appeared to improve the cellular response while reducing the humoral response. We challenged animals with SARS-CoV-2, and observed a ~3.4 and ~2.9 log10 reduction in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, compared to sham controls. These results inform the design and formulation of current clinical COVID-19 vaccine candidates like the one described here, and future designs of RBD-based vaccines against variants of SARS-CoV-2 or other betacoronaviruses.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Neil C Dalvie", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Lisa H Tostanoski", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Sergio A Rodriguez-Aponte", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Kawaljit Kaur", - "author_inst": "University of Kansas" - }, - { - "author_name": "Sakshi Bajoria", - "author_inst": "University of Kansas" - }, - { - "author_name": "Ozan Kumru", - "author_inst": "University of Kansas" - }, - { - "author_name": "Amanda J Martinot", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Abishek Chandrashekar", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Katherine McMahan", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Noe B Mercado", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jingyou Yu", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Aiquan Chang", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Victoria M Giffin", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Felix Nampanya", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Shivani Patel", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Lesley Bowman", - "author_inst": "SpyBiotech Limited" - }, - { - "author_name": "Christopher A Naranjo", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Dongsoo Yun", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Zach Flinchbaugh", - "author_inst": "Bioqual" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual" - }, - { - "author_name": "Renita Brown", - "author_inst": "Bioqual" - }, - { - "author_name": "Jason Velasco", - "author_inst": "Bioqual" - }, - { - "author_name": "Elyse Teow", - "author_inst": "Bioqual" - }, - { - "author_name": "Anthony Cook", - "author_inst": "Bioqual" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual" - }, - { - "author_name": "Mark G Lewis", - "author_inst": "Bioqual" - }, - { - "author_name": "Danielle L Camp", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Judith Maxwell Silverman", - "author_inst": "Gates Medical Research Institute" - }, - { - "author_name": "Harry Kleanthous", - "author_inst": "Bill & Melinda Gates Foundation" - }, - { - "author_name": "Sangeeta B Joshi", - "author_inst": "University of Kansas" - }, - { - "author_name": "David B Volkin", - "author_inst": "University of Kansas" - }, - { - "author_name": "Sumi Biswas", - "author_inst": "SpyBiotech Limited" - }, - { - "author_name": "J Christopher Love", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Dan H Barouch", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.13.452259", "rel_title": "Xeno-nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding", @@ -687328,6 +689787,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.09.21260247", + "rel_title": "Spatiotemporal droplet dispersion measurements demonstrate face masks reduce risks from singing: results from the COvid aNd FacEmaSkS Study (CONFESS)", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260247", + "rel_abs": "BackgroundCOVID-19 has restricted singing in communal worship. We sought to understand variations in droplet transmission and the impact of wearing face masks.\n\nMethodsUsing rapid laser planar imaging, we measured droplets while participants exhaled, said hello or snake, sang a note or Happy Birthday, with and without surgical face masks. We measured mean velocity magnitude (MVM), time averaged droplet number (TADN) and maximum droplet number (MDN). Multilevel regression models were used.\n\nResultsIn 20 participants, sound intensity was 71 Decibels (dB) for speaking and 85 dB for singing (p<0.001). MVM was similar for all tasks with no clear hierarchy between vocal tasks or people and >85% reduction wearing face masks. Droplet transmission varied widely, particularly for singing. Masks decreased TADN by 99% (p<0.001) and MDN by 98% (p<0.001) for singing and 86-97% for other tasks. Masks reduced variance by up to 48%. When wearing a mask, neither singing task transmitted more droplets than exhaling.\n\nConclusionsWide variation exists for droplet production. This significantly reduced when wearing face masks. Singing during religious worship wearing a face mask appears as safe as exhaling or talking. This has implications for UK public health guidance during the COVID-19 pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Kai Man Alexander Ho", + "author_inst": "University College London" + }, + { + "author_name": "Hywel Davies", + "author_inst": "University College London" + }, + { + "author_name": "Ruth Epstein", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Paul Bassett", + "author_inst": "Statsconsultancy Ltd" + }, + { + "author_name": "Aine Hogan", + "author_inst": "University College London" + }, + { + "author_name": "Yusuf Kabir", + "author_inst": "University College London" + }, + { + "author_name": "John Rubin", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Gee Yen Shin", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Jonathan Reid", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ryo Torii", + "author_inst": "University College London" + }, + { + "author_name": "Manish Tiwari", + "author_inst": "University College London" + }, + { + "author_name": "Ramanarayanan Balachandran", + "author_inst": "University College London" + }, + { + "author_name": "Laurence Lovat", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21259864", "rel_title": "Evidence of SARS-Cov-2-specific memory B cells six months after vaccination with BNT162b2 mRNA vaccine", @@ -688056,45 +690582,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.12.452099", - "rel_title": "Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication", - "rel_date": "2021-07-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.12.452099", - "rel_abs": "Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with the viral genome replication. In this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can bind comparatively stabilized to the viral RdRp active site, as it primarily forms base stacking with the template Uracil nucleotide (at +1), which is under freely fluctuations and supports a low free energy barrier of the RDV-TP insertion ([~] 1.5 kcal/mol). In comparison, the barrier ([~] 2.6 kcal/mol), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be particularly stabilized by motif B-N691, S682, and motif F-K500 with the sugar, base, and the template backbone, respectively. Although the RDV-TP insertion can be hindered by motif-F R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif-A D623, respectively.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Moises Ernesto Romero", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Chunhong Long", - "author_inst": "Chongqing University of Posts and Telecommunications" - }, - { - "author_name": "Daniel La Rocco", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Anusha Mysore Keerthi", - "author_inst": "R.V College of Engineering" - }, - { - "author_name": "Dajun Xu", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jin Yu", - "author_inst": "University of California, Irvine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.07.13.452175", "rel_title": "Development Of The Inactivated QazCovid-In Vaccine: Protective Efficacy Of The Vaccine In Syrian Hamsters", @@ -689202,6 +691689,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.11.451855", + "rel_title": "The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes", + "rel_date": "2021-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.11.451855", + "rel_abs": "Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen deuterium exchange mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-EM, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation--an open trimer-- contains easily accessible RBDs. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.\n\nOne Sentence SummaryAn alternative conformation of SARS-CoV-2 spike ectodomain modulated by temperature, binding, and sequence variants.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shawn M Costello", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Sophie R Shoemaker", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Helen T Hobbs", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Annalee W Nguyen", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Ching-Lin Hsieh", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jennifer A Maynard", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jason S McLellan", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "John E Pak", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Susan Marqusee", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.08.21259912", "rel_title": "Efficacy and safety of Andrographis paniculata extract in patients with mild COVID-19: A randomized controlled trial", @@ -689826,53 +692364,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.08.21260186", - "rel_title": "Direct detection of humoral marker corelates of COVID-19, glycated HSA and hyperglycosylated IgG3, by MALDI-ToF mass spectrometry.", - "rel_date": "2021-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260186", - "rel_abs": "The prefusion Spike protein of SARS-CoV2 binds advanced glycation end product (AGE) glycated human serum albumin (HSA) and a higher mass, hyperglycosylated/glycated, IgG3, as determined by matrix assisted laser desorption mass spectrometry (MALDI-ToF MS). We set out to investigate if the total blood plasma of patients who had recovered from acute respiratory distress as a result of COVID-19, contained more glycated HSA and higher mass (glycosylated/glycated) IgG3 than those with only clinically mild or asymptomatic infections. A direct dilution and disulphide bond reduction method was development and applied to plasma samples from SARS-CoV2 seronegative (N = 30) and seropositive (N = 31) healthcare workers and 38 convalescent plasma samples from patients who had been admitted with acute respiratory distress syndrome (ARDS) associated with COVID-19.\n\nPatients recovering from COVID-19 ARDS had significantly higher mass, AGE-glycated HSA and higher mass IgG3 levels. This would indicate that increased levels and/or ratios of hyper-glycosylation (probably terminal sialic acid) IgG3 and AGE glycated HSA may be predisposition markers for development of ARDS as a result of COVID-19 infection. Furthermore, rapid direct analysis of plasma samples by MALDI-ToF MS for such humoral immune correlates of COVID-19 presents a feasible screening technology for the most at risk; regardless of age or known health conditions.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC=\"FIGDIR/small/21260186v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@12bfa69org.highwire.dtl.DTLVardef@45344forg.highwire.dtl.DTLVardef@16d4f7forg.highwire.dtl.DTLVardef@17e5c34_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Raymond Kruse Iles", - "author_inst": "MAP Sciences" - }, - { - "author_name": "Jason Kruse Iles", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Raminta Zmuidinaite", - "author_inst": "MAPSciences" - }, - { - "author_name": "Anna Gardiner", - "author_inst": "MAPSciences" - }, - { - "author_name": "Jonathan Lacey", - "author_inst": "MAPSciences" - }, - { - "author_name": "Stephen Harding", - "author_inst": "The Binding Site Group Ltd" - }, - { - "author_name": "Jonathan Luke Heeney", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Dr HE Baxendale", - "author_inst": "Royal Papworth Hospital NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.08.21260162", "rel_title": "Immunogenicity of Oxford-AstraZeneca COVID-19 vaccine in Vietnamese healthcare workers", @@ -690888,6 +693379,33 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2021.07.06.21260112", + "rel_title": "COVID-19 Due to Wild-Type SARS-CoV-2 More Prevalent in Adolescents and Youth than in Older Adults Based on 19 US States in Fall 2020 Prior to Vaccine Availability", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260112", + "rel_abs": "PURPOSEIn a prior study, we examined data from six US states during Summer 2020, and found that prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p<.00001) as was a prevalence-related measure: Number of cases observed / Number of cases expected (p<.005). We now extended our study to more states in Fall 2020 to confirm the prevalence relationships we found previously. Vaccines were still not available as of Fall 2020. Presumably, the SARS-CoV-2 strain circulating at the time was the wild-type lineage since no variants were reported in the US until the end of December 2020.\n\nMETHODSWe examined data from 19 U.S. states experiencing surges in cases to determine prevalence of COVID-19, and a prevalence-related measure: [Number of cases observed in a given age group] / [Number of cases expected in the age group based on population demographics].\n\nRESULTSIn 16 of the 19 states, we found that: (1) prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p-values ranged from p<0.00001 to p = 0.0175; (2) the ratio of cases observed to cases expected was significantly greater in adolescents and youth than in older adults (p-values ranging from p< 0.00001 to p = 0.004).\n\nCONCLUSIONSOur results are consistent with our previous study in Summer 2020. The finding of lower prevalence in older adults cannot be attributed to access to vaccination since our data are from Fall 2020 when vaccinations were not yet available. Our findings with the SARS-CoV-2 wild-type strain are consistent with the findings currently being reported in the UK for the delta variant. In both studies, prevalence in adolescents and youth exceeded that in older adults. The UK findings are more pronounced perhaps because that study transpired following months of vaccinations of older adults whereas ours occurred before vaccinations were available.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Barbara T Rumain", + "author_inst": "New York Medical College" + }, + { + "author_name": "Moshe Schneiderman", + "author_inst": "SUNY Downstate College of Medicine" + }, + { + "author_name": "Allan Geliebter", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.30.21259763", "rel_title": "Which children and young people are at higher risk of severe disease and death after SARS-CoV-2 infection: a systematic review and individual patient meta-analysis", @@ -691776,77 +694294,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.08.451426", - "rel_title": "Antibody and T cell memory immune response after two doses of the BNT162b2 mRNA vaccine in older adults with and without prior SARS-CoV-2 infection", - "rel_date": "2021-07-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.08.451426", - "rel_abs": "We quantified S1-specific IgG, neutralizing antibody titers, specific IFN{gamma} secreting T cells and functionality of specific CD4+ and CD8+ T cells in 130 young adults (median age 44.0 years) and 106 older residents living in a long-term care facility (86.5 years) after 2 doses of BNT162b2. Three months after the first injection, humoral and cellular memory responses were dramatically impaired in the 54 COVID-19-naive older compared to the 121 COVID-19-naive younger adults. Notably, older participants neutralizing antibodies, detected in 76.5% (versus 100% in young adults, P < 0.0001), were ten times lower than the youngers antibody titers (P < 0.0001). Antibody and T cell responses were greater among the 52 COVID-19-recovered than among the 54 COVID-19-naive older adults (P < 0.0001). Our study shows that 2 doses of BNT162b2 does not guarantee long-term protection against SARS-CoV-2 in the older. An additional dose should be considered to boost their specific memory response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Benedicte Corroyer-Simovic", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement de Geriatrie, Hopital geriatrique Les Bateliers" - }, - { - "author_name": "Enagnon Kazali Alidjinou", - "author_inst": "Universite de Lille, CHU de Lille" - }, - { - "author_name": "Sophie Miczek", - "author_inst": "Centre Hospitalier Universitaire de Lille, Medecine et sante du travail" - }, - { - "author_name": "Fanny Vuotto", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement des maladies infectieuses" - }, - { - "author_name": "Dominique Huvent-Grelle", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement de Geriatrie, Hopital geriatrique Les Bateliers" - }, - { - "author_name": "Juliette Podvin", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement de Geriatrie, Hopital geriatrique Les Bateliers" - }, - { - "author_name": "Daniel Dreuil", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement de Geriatrie, Hopital geriatrique Les Bateliers" - }, - { - "author_name": "Karine Faure", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement des maladies infectieuses" - }, - { - "author_name": "Dominique Deplanque", - "author_inst": "Centre Hospitalier Universitaire de Lille, Clinical Investigation Center 1403" - }, - { - "author_name": "Laurence Bocket", - "author_inst": "Centre Hospitalier Universitaire de Lille, Faculte de medecine, Laboratoire de virologie ULR3610" - }, - { - "author_name": "Alain Duhamel", - "author_inst": "Centre Hospitalier Universitaire de Lille, EA 2694 - Sante publique: epidemiologie et qualite du soin" - }, - { - "author_name": "Julien Labreuche", - "author_inst": "Centre Hospitalier Universitaire de Lille, EA 2694 - Sante publique: epidemiologie et qualite du soin" - }, - { - "author_name": "Annie Sobaszek", - "author_inst": "Centre Hospitalier Universitaire de Lille, Medecine et sante du travail" - }, - { - "author_name": "Francois Puisieux", - "author_inst": "Centre Hospitalier Universitaire de Lille, Departement de Geriatrie, Hopital geriatrique Les Bateliers" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.07.451538", "rel_title": "Atomistic Simulations and Deep Mutational Scanning of Protein Stability and Binding Interactions in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms", @@ -692778,6 +695225,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.06.21259473", + "rel_title": "Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259473", + "rel_abs": "As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Soa Fy Andriamandimby", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Cara E. Brook", + "author_inst": "Cara Brook" + }, + { + "author_name": "Norosoa H Razanajatovo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Jean-Marius Rakotondramanga", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Fidisoa Rasambainarivo", + "author_inst": "Princeton University" + }, + { + "author_name": "Vaomalala Raharimanga", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Iony M. Razanajatovo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Reziky Mangahasimbola", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Richter L Razafindratsimandresy", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Santatra Randrianarisoa", + "author_inst": "University of Antananarivo" + }, + { + "author_name": "Barivola Bernardson", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Joelinotahina H Rabarison", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Mirella Randrianarisoa", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Frederick S Nasolo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Roger M Rabetombosoa", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Rindra V Randremanana", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Jean-Michel Heraud", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Philippe G Dussart", + "author_inst": "Institut Pasteur de Madagascar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.08.21259776", "rel_title": "Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States", @@ -693714,73 +696248,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.07.06.451270", - "rel_title": "Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451270", - "rel_abs": "A year after the World Health Organisation (WHO) declared COVID-19 as a pandemic, much has been learned regarding SARS-CoV-2 epidemiology, vaccine production, and disease treatment. Whole-genome sequencing (WGS) has played a significant role in contributing to our understanding of the epidemiology and biology of this virus. In this paper, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asia and the impact of technological development, access to resources, and demography of individual countries on its uptake. Using Oxford Nanopore Technology (ONT), Nottingham-Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in Research Centre for Biotechnology, Indonesian Institute of Sciences (Lembaga Ilmu Pengetahuan Indonesia/LIPI) to carry out a small number of SARS-CoV-2 WGS in Indonesia. The ONT offers sequencing advantages that fit within the Indonesian context. Analyses of SARS-CoV-2 genomes deposited on GISAID from Southeast and East Asian countries reveal the importance of collecting clinical and demographic metadata and the importance of open access and data sharing. Lineage and phylogenetic analyses per 1 June 2021 found that: 1) B.1.466.2 variants were the most predominant in Indonesia, with mutations in the spike protein including D614G at 100%, N439K at 99.1%, and P681R at 69.7% frequency, 2) The variants of concern (VoCs) B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta) were first detected in Indonesia in January 2021, 3) B.1.470 was first detected in Indonesia and spread to the neighbouring regions, and 4) The highest rate of virus transmissions between Indonesia and the rest of the world appears to be through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Inswasti Cahyani", - "author_inst": "School of Life Sciences, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Eko W Putro", - "author_inst": "Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia), Bogor, Indonesia" - }, - { - "author_name": "Asep M Ridwanuloh", - "author_inst": "Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia), Bogor, Indonesia" - }, - { - "author_name": "Satrio Wibowo", - "author_inst": "PT. PathGen Diagnostik Teknologi, Cibinong, Bogor, Indonesia; Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan" - }, - { - "author_name": "Hariyatun Hariyatun", - "author_inst": "Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia), Bogor, Indonesia" - }, - { - "author_name": "Gita Syahputra", - "author_inst": "Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia), Bogor, Indonesia" - }, - { - "author_name": "Gilang Akbariani", - "author_inst": "PT. PathGen Diagnostik Teknologi, Cibinong, Bogor, Indonesia; Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan" - }, - { - "author_name": "Ahmad R Utomo", - "author_inst": "Biomedical Postgraduate Program, Universitas Yarsi, Jakarta, Indonesia" - }, - { - "author_name": "Mohammad Ilyas", - "author_inst": "Molecular Pathology Research Group, School of Medicine, University of Nottingham, United Kingdom" - }, - { - "author_name": "Matthew W Loose", - "author_inst": "School of Life Sciences, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Wien Kusharyoto", - "author_inst": "Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia), Bogor, Indonesia; Indonesian SARS-CoV-2 Genomics " - }, - { - "author_name": "- Indonesian SARS-CoV-2 Genomics Surveillance Network", - "author_inst": "-" - }, - { - "author_name": "Susanti Susanti", - "author_inst": "Molecular Pathology Research Group, School of Medicine, University of Nottingham, UK; PT. PathGen Diagnostik Teknologi, Cibinong, Bogor, Indonesia; Dept. Pharma" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.07.06.451329", "rel_title": "Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions", @@ -694792,6 +697259,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259953", + "rel_title": "High resolution linear epitope mapping of the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 mRNA vaccine recipients.", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259953", + "rel_abs": "The prompt rollout of the coronavirus disease (COVID-19) messenger RNA (mRNA) vaccine is facilitating population immunity, which shall become more dominant than natural infection-induced immunity. At the beginning of the vaccine era, understanding the epitope profiles of vaccine-elicited antibodies will be the first step in assessing functionality of vaccine-induced immunity. In this study, the high-resolution linear epitope profiles of Pfizer-BioNTech COVID-19 mRNA vaccine recipients and COVID-19 patients were delineated by using microarrays mapped with overlapping peptides of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. The vaccine-induced antibodies targeting RBD had broader distribution across the RBD than that induced by the natural infection. Thus, relatively lower neutralizability was observed when a half-maximal neutralization titer measured in vitro by live virus neutralization assays was normalized to a total anti-RBD IgG titer. However, mutation panel assays targeting the SARS-CoV-2 variants of concern have shown that the vaccine-induced epitope variety, rich in breadth, may grant resistance against future viral evolutionary escapes, serving as an advantage of vaccine-induced immunity.\n\nImportanceEstablishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of messenger RNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable. The next debate is regarding the coverage of SARS-CoV-2 variants. At the beginning of this vaccine era, it is of importance to describe the similarities and differences between the immune responses of COVID-19 vaccine recipients and naturally infected individuals. In this study, we demonstrated that the antibody profiles of vaccine recipients are richer in variety, targeting a key protein of the invading virus, than those of naturally infected individuals. Yet vaccine-elicited antibodies included more non-neutralizing antibodies than infection-elicited, their breadth in antibody variations suggested possible resilience against future SARS-CoV-2 variants. The antibody profile achieved by vaccinations in naive individuals pose important insight into the first step towards vaccine-based population immunity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yuko Nitahara", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yu Nakagama", + "author_inst": "Osaka City University" + }, + { + "author_name": "Natsuko Kaku", + "author_inst": "Osaka City University" + }, + { + "author_name": "Katherine Candray", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yu Michimuko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Evariste Tshibangu-Kabamba", + "author_inst": "Osaka City University" + }, + { + "author_name": "Akira Kaneko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Hiromasa Yamamoto", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yasumitsu Mizobata", + "author_inst": "Osaka City University" + }, + { + "author_name": "Hiroshi Kakeya", + "author_inst": "Osaka City University" + }, + { + "author_name": "Mayo Yasugi", + "author_inst": "Osaka Prefecture University" + }, + { + "author_name": "Yasutoshi Kido", + "author_inst": "Osaka City University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21254541", "rel_title": "Anticoagulants and Antiplatelets in COVID-19: Impact on Survival and Thromboembolism Development", @@ -695388,65 +697918,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2021.07.07.21259772", - "rel_title": "Sensitivity of SARS-CoV-2 antibody tests with late convalescent sera", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21259772", - "rel_abs": "SARS-CoV-2-specific IgM antibodies wane during the first three months after infection and IgG antibody levels decline. This may limit the ability of antibody tests to identify previous SARS CoV-2 infection at later time points. To examine if the sensitivity of antibody tests falls off, we compared the sensitivity of two nucleoprotein-based antibody tests, the Roche Elecsis II Anti-SARS-CoV-2 and the Abbott SARS-CoV-2 IgG assay and three glycoprotein-based tests, the Abbott SARS-CoV-2 IgG II Quant, Siemens Atellica IM COV2T and Euroimmun SARS-CoV-2 assay with 56 sera obtained 6-8 months after SARS-CoV-2 infection. The sensitivity of the Roche, Abbott SARS-CoV-2 IgG II Quant and Siemens antibody assays was 94.6 % (95% confidence interval (CI) 85.1-98.9 %), 98.2 % (95% CI: 90.4-99.9 %) and 100 % (95% CI: 93.6-100 %). The sensitivity of the N-based Abbott SARS-CoV-2 IgG and the glycoprotein-based Euroimmun ELISA was 48.2 % (95% CI: 34.7-62.0 %) and 83.9 % (95% CI: 71.7-92.4 %). The nucleoprotein-based Roche and the glycoprotein-based Abbott RBD and Siemens tests were more sensitive than the N-based Abbott and the Euroimmun antibody tests (p=0.0001 to p=0.039). The N-based Abbott antibody test was less sensitive 6-8 months than 4-10 weeks after SARS-CoV-2 infection (p = 0.0002). The findings show that most SARS CoV-2 antibody assays correctly identified previous infection 6-8 months after infection. The sensitivity of pan-Ig antibody tests was not reduced at 6-8 months when IgM antibodies have usually disappeared. However, one of the nucleoprotein-based antibody tests significantly lost sensitivity over time.\n\nHighlightsO_LIMost antibody tests correctly identified SARS CoV-2 infection 6-8 months after infection\nC_LIO_LIThe sensitivity of the antibody tests was 48.2-100 %\nC_LIO_LIThe three tests with the highest sensitivity (94.6-100 %) were the N-based Roche and the RBD-based Abbott and Siemens assays\nC_LIO_LIThe N-based Abbott IgG CMIA was significantly less sensitive 6-8 months than 4-10 weeks after infection (p = 0.0002)\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Judith Kannenberg", - "author_inst": "Institute for Medical Microbiology and Virology, Leipzig University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Carolin Schnurra", - "author_inst": "Institute for Medical Microbiology and Virology, Leipzig University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Nina Reiners", - "author_inst": "Institute for Medical Microbiology and Virology, Leipzig University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Reinhard Henschler", - "author_inst": "Institute of Transfusion Medicine, University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Raymund Buhmann", - "author_inst": "Institute of Transfusion Medicine, University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Thorsten Kaiser", - "author_inst": "Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Ronald Biemann", - "author_inst": "Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Mario Hoenemann", - "author_inst": "Institute for Medical Microbiology and Virology, Leipzig University Hospital and Medical Faculty, University of Leipzig" - }, - { - "author_name": "Grit Ackermann", - "author_inst": "Labor AlphaOmega, Leipzig" - }, - { - "author_name": "Henning Trawinski", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, Leipzig, Germany" - }, - { - "author_name": "Christian Jassoy", - "author_inst": "Institute for Medical Microbiology and Virology, Leipzig University Hospital and Medical Faculty, University of Leipzig" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.06.21259792", "rel_title": "Characteristics of children and antigen test performance at a SARS-CoV-2 community testing site", @@ -696482,6 +698953,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.05.21260050", + "rel_title": "Progressive Increase in Virulence of Novel SARS-CoV-2 Variants in Ontario, Canada, February to June, 2021", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260050", + "rel_abs": "BackgroundThe period from February to June 2021 was one during which initial wild-type SARS-CoV-2 strains were supplanted in Ontario, Canada, first by variants of concern (VOC) with the N501Y mutation (Alpha/B1.1.17, Beta/B.1.351 and Gamma/P.1 variants), and then by the Delta/B.1.617 variant. The increased transmissibility of these VOCs has been documented but data for increased virulence is limited. We used Ontarios COVID-19 case data to evaluate the virulence of these VOCs compared to non-VOC SARS-CoV-2 infections, as measured by risk of hospitalization, intensive care unit (ICU) admission, and death.\n\nMethodsWe created a retrospective cohort of people in Ontario testing positive for SARS-CoV-2 and screened for VOCs, with dates of test report between February 7 and June 27, 2021 (n=212,332). We constructed mixed effects logistic regression models with hospitalization, ICU admission, and death as outcome variables. Models were adjusted for age, sex, time, vaccination status, comorbidities, and pregnancy status. Health units were included as random intercepts.\n\nResultsCompared to non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (43-62%) for hospitalization; 89% (67-116%) for ICU admission; and 51% (30-74%) for death. Increases with Delta variant were more pronounced: 108% (80-138%) for hospitalization; 234% (164-331%) for ICU admission; and 132% (47-230%) for death.\n\nInterpretationThe progressive increase in transmissibility and virulence of SARS-CoV-2 VOCs will result in a significantly larger, and more deadly, pandemic than would have occurred in the absence of VOC emergence.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "David Fisman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Ashleigh Tuite", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21260055", "rel_title": "Critical timing for triggering public health interventions to prevent COVID-19 resurgence: a mathematical modelling study", @@ -697462,41 +699956,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2021.07.04.451027", - "rel_title": "Increased frequency of recurrent in-frame deletions in new expanding lineages of SARS CoV-2 reflects immune selective pressure", - "rel_date": "2021-07-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.04.451027", - "rel_abs": "Most of the attention in the surveillance of evolution of SARS-CoV-2 has been centered on single nucleotide substitutions in the spike glycoprotein. We show that in-frame deletions (IFDs) also play a significant role in the evolution of viral genome. The percentage of genomes and lineages with IFDs is growing rapidly and they co-occur independently in multiple lineages, including emerging variants of concerns. IFDs distribution is correlated with spike mutations associated with immune escape and concentrated in proteins involved in interactions with the host immune system. Structural analysis suggests that IFDs remodel viral proteins surfaces at common epitopes and interaction interfaces, affecting the virus interactions with the immune system. We hypothesize that the increased frequency of IFDs is an adaptive response to elevated global population immunity.\n\nSummaryMonitoring of SARS-CoV-2 genome evolution uncovers increased frequency and non-random distribution of in-frame deletions in recently emerged lineages.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Arghavan Alisoltani", - "author_inst": "University of California Riverside School of Medicine, Biosciences Division, Riverside, California" - }, - { - "author_name": "Lukasz Jaroszewski", - "author_inst": "University of California Riverside School of Medicine, Biosciences Division, Riverside, California" - }, - { - "author_name": "Mallika Iyer", - "author_inst": "Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Adam Godzik", - "author_inst": "University of California Riverside School of Medicine, Biosciences Division, Riverside, California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.06.30.21259816", "rel_title": "Impacts of school closure due to COVID-19 on the mobility trend of Japanese citizens", @@ -698576,6 +701035,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.05.21260021", + "rel_title": "Knowledge, attitude, and practice related to the COVID-19 pandemic among undergraduate medical students in Indonesia: a nationwide cross-sectional study", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260021", + "rel_abs": "IntroductionThe potential role of medical students in raising awareness during public health emergencies has been acknowledged. To further explore their potentials as public educators and role models for the communities during the coronavirus disease 2019 (COVID-19) pandemic, a study is conducted to assess the knowledge, attitude, and practice of these students toward COVID-19.\n\nMethodsAn online cross-sectional survey was conducted among undergraduate medical students in Indonesia. Socio-demographical characteristics, social interaction history, information-seeking behavior, as well as knowledge, attitude, and practice toward COVID-19 were collected through a self-reported questionnaire. A p-value of <0.05 indicated statistical significance.\n\nResultsOut of 4870 respondents, 64.9% and 51.5% had positive attitude and practice toward COVID-19 while only 29.8% had adequate knowledge. Knowledge was slightly positively correlated with attitude and practice ({rho}=0.074 and {rho}=0.054, respectively; both p<0.001), while attitude was weakly correlated with practice ({rho}=0.234, p<0.001). Several factors including age, sex, place of residence, institution type, academic level, family income, history of chronic illness, prior volunteering experience, and perceptual awareness on COVID-19 were significantly associated with either knowledge, attitude, and/or practice toward COVID-19. Furthermore, health institutions and the governments press releases, as well as health expert opinions were deemed as the most reliable sources of COVID-19-related information - yet trivially none of these sources were associated with knowledge, attitude, and practice in the study population.\n\nConclusionMany undergraduate medical students in Indonesia had positive attitude and practice against COVID-19, yet only a few had adequate knowledge. This warrants further interventions to keep them updated with COVID-19 evidence to maximize their potentials in raising public awareness on COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Imam Adli", + "author_inst": "Facullty of Medicine Universitas Indonesia" + }, + { + "author_name": "Indah Suci Widyahening", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Gilbert Lazarus", + "author_inst": "Faculty of Medicine, Universitas Indonesia" + }, + { + "author_name": "Jason Phowira", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Lyanna Azzahra", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Bagas Ariffandi", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Aziz Muhammad Putera", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "David Nugraha", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Nico Gamalliel", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Ardi Findyartini", + "author_inst": "Faculty of Medicine Universitas Indonesia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2021.07.04.21259985", "rel_title": "Covid-19 Vaccination in Pregnancy: A Systematic Review", @@ -699152,41 +701666,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.07.02.21259910", - "rel_title": "COVID-19 and regional differences in the timeliness of hip-fracture surgery: an interrupted time-series analysis", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21259910", - "rel_abs": "BackgroundIt is of great importance to examine the impact of the healthcare reorganization adopted to confront the COVID-19 pandemic on the quality of care provided by healthcare systems to non-COVID-19 patients. The aim of this study is to assess the impact of the COVID-19 national lockdown (March 9, 2020) on the quality of care provided to patients with hip fracture (HF) in Piedmont and Emilia-Romagna, 2 large regions of northern Italy severely hit by the pandemic.\n\nMethodsWe calculated the percentage of HF patients undergoing surgery within 2 days of hospital admission. An interrupted time-series analysis was performed on weekly data from December 11, 2019 to June 9, 2020 ({approx}6 months), interrupting the series in the 2nd week of March. The same data observed the year before were included as a control time series with no \"intervention\" (lockdown) in the middle of the observation period.\n\nResultsBefore the lockdown, 2-day surgery was 69.9% in Piedmont and 79.2% in Emilia-Romagna; after the lockdown, these proportions were equal to 69.8% (-0.1%) and 69.3% (- 9.9%), respectively. While Piedmont did not experience any drop in the amount of surgery, Emilia-Romagna exhibited a significantly decline at a weekly rate of -1.29% (95% CI = -1.71 to -0.88).\n\nDivergent trend patterns in the 2 study regions reflect local differences in pandemic timing as well as in healthcare services capacity, management, and emergency preparedness.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Davide Golinelli", - "author_inst": "University of Bologna" - }, - { - "author_name": "Jacopo Lenzi", - "author_inst": "University of Bologna" - }, - { - "author_name": "Emanuele Adorno", - "author_inst": "University of Bologna" - }, - { - "author_name": "Maria Michela Gianino", - "author_inst": "University of Turin" - }, - { - "author_name": "Maria Pia Fantini", - "author_inst": "University of Bologna" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.07.05.21260005", "rel_title": "Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction", @@ -700210,6 +702689,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.06.21259749", + "rel_title": "Application of nasal spray containing dimethyl sulfoxide (DSMO) and ethanol during the COVID-19 pandemic may protect healthcare workers: A randomized controlled trials", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259749", + "rel_abs": "BackgroundCoronavirus pandemic has affected a large population worldwide. Currently, the standard care for individuals who are exposed is supportive care, symptomatic management, and isolation. The aim of our study was to evaluate effects of combined use of ethanol and DMSO as a nasal spray in preventing COVID-19.\n\nMethodsWe conducted a randomized controlled trial on volunteer healthcare workers of medical centers that were at the forefront of the fight against COVID-19 in Shahroud, Iran. Two hundred and thirty-two participants were randomly assigned to intervention and control groups to receive DMSO/ethanol or routine care, respectively. The subjects were followed for 4 weeks to determine the incidence of COVID-19 infection in each group based on the RT-qPCR test. Finally, absolute risk difference and relative risk were calculated to evaluate the effect of DMSO in prevent COVID-19.\n\nResultsThe results showed that the incidence of COVID-19 in the control group and intervention group were 0.07 and 0.008, respectively. The relative risk (RR) was 0.12 (0.9-0.02) according to the incidence rate in the two groups.\n\nConclusioncombined application of DMSO and ethanol in healthcare providers can considerably prevent COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ali Hosseinzadeh", + "author_inst": "Shahroud University of medical sciences" + }, + { + "author_name": "Abbas Tavakkolian", + "author_inst": "Islamic Azad University, Shahroud Branch, Shahroud, Iran." + }, + { + "author_name": "Vahid Kia", + "author_inst": "Shahroud University of Medical Sciences" + }, + { + "author_name": "Hossein Ebrahimi", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Hossein Sheibani", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Ehsan Binesh", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Reza Jafari", + "author_inst": "Shahroud University of Medical Sciences" + }, + { + "author_name": "Seyed Mohammad Mirrezaie", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Moslem Jafarisani", + "author_inst": "Shahroud University of medical Sciences" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Shahroud University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.05.451222", "rel_title": "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques", @@ -700958,89 +703492,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.04.21259945", - "rel_title": "SARS-CoV-2 environmental contamination from hospitalised COVID-19 patients receiving aerosol generating procedures", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259945", - "rel_abs": "BackgroundContinuous positive airways pressure (CPAP) and high-flow nasal oxygen (HFNO) are considered aerosol-generating procedures (AGPs) in the treatment of COVID-19. We aimed to measure air and surface environmental contamination of SARS-CoV-2 virus when CPAP and HFNO were used, compared with supplemental oxygen, to investigate the potential risks of viral transmission to healthcare workers and patients.\n\nMethods30 hospitalised patients with COVID-19 requiring supplemental oxygen, with a fraction of inspired oxygen [≥]0.4 to maintain oxygen saturations [≥]94%, were prospectively enrolled into an observational environmental sampling study. Participants received either supplemental oxygen, CPAP or HFNO (n=10 in each group). A nasopharyngeal swab, three air and three surface samples were collected from each participant and the clinical environment. RT qPCR analyses were performed for viral and human RNA, and positive/suspected-positive samples were cultured for the presence of biologically viable virus.\n\nResultsOverall 21/30 (70%) of participants tested positive for SARS-CoV-2 RNA in the nasopharynx. In contrast, only 4/90 (4%) and 6/90 (7%) of all air and surface samples tested positive (positive for E and ORF1a) for viral RNA respectively, although there were an additional 10 suspected-positive samples in both air and surfaces samples (positive for E or ORF1a). CPAP/HFNO use or coughing was not associated with significantly more environmental contamination. Only one nasopharyngeal sample was culture positive.\n\nConclusionsThe use of CPAP and HFNO to treat moderate/severe COVID-19 was not associated with significantly higher levels of air or surface viral contamination in the immediate care environment.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Rebecca Winslow", - "author_inst": "Department of Infectious Diseases & Tropical Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham Heartlands Hospital, Bordesley Green Eas" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Department of Infectious Diseases, Imperial College London, London, W2 1NY, United Kingdom" - }, - { - "author_name": "E F Windle", - "author_inst": "College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom." - }, - { - "author_name": "I X Nur", - "author_inst": "College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom." - }, - { - "author_name": "Ranjit Lall", - "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom" - }, - { - "author_name": "Chen Ji", - "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom" - }, - { - "author_name": "Jonathan E Millar", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Paul M Dark", - "author_inst": "NIHR Manchester Biomedical Research Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Man" - }, - { - "author_name": "Jay Naisbitt", - "author_inst": "Critical Care Unit, Northern Care Alliance NHS Group, Salford Royal Hospital, Greater Manchester, M6 8HD, United Kingdom" - }, - { - "author_name": "Anita Simonds", - "author_inst": "Lung Division, Royal Brompton & Harefield Hospitals NHS Foundation Trust, Sydney Street, London, SW3 6NP, United Kingdom" - }, - { - "author_name": "Jake Dunning", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wendy Barclay", - "author_inst": "Department of Infectious Diseases, Imperial College London, London, W2 1NY, United Kingdom" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh" - }, - { - "author_name": "Gavin D Perkins", - "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK" - }, - { - "author_name": "Malcolm Gracie Semple", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Danny F McAuley", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "C A Green", - "author_inst": "Department of Infectious Diseases & Tropical Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham Heartlands Hospital, Bordesley Green Eas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.07.03.451025", "rel_title": "A cGAMP-containing hydrogel for prolonged SARS-CoV-2 RBD subunit vaccine exposure induces a broad and potent humoral response", @@ -701856,6 +704307,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259959", + "rel_title": "Efficacy and safety of cyclosporine in the management of coronavirus disease 2019: A protocol for systematic review and meta-analysis", + "rel_date": "2021-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259959", + "rel_abs": "IntroductionCyclosporine may improve the clinical course and outcomes of Coronavirus disease 2019 (COVID-19) due to its antiviral and anti-cytokine effects as shown in vitro. A few ongoing trials are exploring the benefit of adding it to the standard of care (SOC) of COVID-19 patients.\n\nObjectivesThe primary objective is to evaluate the severity of COVID-19, determined by oxygen saturation, intensive care unit (ICU) admission, or the World Health Organization COVID-19 clinical severity scale in patients treated with oral or intravenous cyclosporine added to SOC compared SOC alone or placebo. Secondary objectives include mortality, length of hospitalization, length of ICU stay, and laboratory measurements as well as the safety outcomes of cyclosporine.\n\nMethodologyA systematic review and meta-analysis of randomized clinical trials and observational studies that compared cyclosporine to placebo or SOC in COVID-19 patients will be conducted. PubMed, EMBASE, Web of Science, Cochrane Central Register of Controlled Trials, Google Scholar, and ClinicalTrials.gov will be explored for studies that satisfy pre-specified inclusion criteria. Quality assessment of all included studies will be performed. Meta-analyses will be done utilizing random effect models to estimate the effect of cyclosporine on the severity of COVID-19. Heterogeneity will be assessed utilizing Q statistics. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines will be followed.\n\nResultsThe result of this synthesis will inform potential changes in the management of COVID-19 patients, especially regarding the role of calcineurin inhibitors. Additionally, it will serve as hypothesis generating for potential future prospective studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ibtihal Abdallah", + "author_inst": "Clinical Pharmacy Department, Hamad General Hospital, Hamad Medical Corporation" + }, + { + "author_name": "Mohamed Aabdien", + "author_inst": "Community Medicine Training Program, Medical Education, Hamad Medical Corporation" + }, + { + "author_name": "Mohammed Danjuma", + "author_inst": "Division of General Internal Medicine, Weill Cornell affliated-Hamad General Hospital, Hamad Medical Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.02.21259665", "rel_title": "Assessment and Modeling of COVID-19 Outcomes in a Longitudinal Cohort of Hospitalized Adults", @@ -702552,49 +705030,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.01.21259860", - "rel_title": "Placental vascular remodeling in pregnant women with COVID-19", - "rel_date": "2021-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259860", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 has been causing the pandemic of coronavirus disease 2019 (COVID-19) that has so far resulted in over 180 million infections and nearly 4 million deaths. This respiratory virus uses angiotensin-converting enzyme 2 as a receptor to enter host cells, exhibiting a unique feature that affects various tissues in addition to the lungs. The present study reports that the placental arteries from women who gave birth to live full-term newborns while developing of COVID-19 during pregnancy exhibit severe vascular wall thickening and the occlusion of the vascular lumen. A morphometric analysis of the placental arteries stained with hematoxylin and eosin suggest a 2-fold increase in wall thickness and a 5-fold decrease in the lumen area. Immunohistochemistry with -smooth muscle actin and Massons trichrome staining showed that such placental vascular remodeling in COVID-19 is associated with smooth muscle proliferation and fibrosis. Placental vascular remodeling may represent a mechanism of the clinical problems associated with childbirth in COVID-19 patients.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sergiy G. Gychka", - "author_inst": "Bogomolets National Medical University" - }, - { - "author_name": "Iurii L. Kuchyn", - "author_inst": "Bogomolets National Medical University" - }, - { - "author_name": "Tetyana V. Savchuk", - "author_inst": "Bogomolets National Medical University" - }, - { - "author_name": "Sofia I. Nikolaienko", - "author_inst": "Bogomolets National Medical University" - }, - { - "author_name": "Volodymyr M. Zhezhera", - "author_inst": "OKHMADYT, National Children's Specialized Hospital" - }, - { - "author_name": "Ihor I. Chermak", - "author_inst": "Kyiv City Medical Center" - }, - { - "author_name": "Yuichiro J. Suzuki", - "author_inst": "Georgetown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2021.06.29.21259494", "rel_title": "The drop in reported invasive pneumococcal disease among adults during the first COVID-19 wave in the Netherlands explained.", @@ -703586,6 +706021,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.29.21259605", + "rel_title": "The SARS-CoV-2 receptor-binding domain expressed in Pichia pastoris as a candidate vaccine antigen", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259605", + "rel_abs": "1.The effort to develop vaccines based on economically accessible technological platforms available by developing countries vaccine manufacturers is essential to extend the immunization to the whole world population and to achieve the desired herd immunity, necessary to end the COVID-19 pandemic. Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed in yeast Pichia pastoris. The RBD was modified with addition of flexible N- and C-terminal amino acid extensions aimed to modulate the protein/protein interactions and facilitate protein purification. Fermentation with yeast extract culture medium yielded 30-40 mg/L. After purification by immobilized metal ion affinity chromatography and hydrophobic interaction chromatography, the RBD protein was characterized by mass-spectrometry, circular dichroism, and binding affinity to angiotensin-converting enzyme 2 (ACE2) receptor. The recombinant protein shows high antigenicity with convalescent human sera and also with sera from individuals vaccinated with the Pfizer-BioNTech mRNA or Sputnik V adenoviral-based vaccines. The RBD protein stimulates IFN{gamma}, IL-2, IL-6, IL-4, and TNF in mice secreting splenocytes from PBMC and lung CD3+ enriched cells. Immunogenicity studies with 50 {micro}g of the recombinant RBD formulated with alum, induce high levels of binding antibodies in mice and non-human primates, assessed by ELISA plates covered with RBD protein expressed in HEK293T cells. The mouse sera inhibited the RBD binding to ACE2 receptor in an in-vitro test and show neutralization of SARS-CoV-2 infection of Vero E6 cells. These data suggest that the RBD recombinant protein expressed in yeast P. pastoris is suitable as a vaccine candidate against COVID-19.\n\nHighlightsO_LIThe RBD protein (C-RBD-H6 PP) is expressed with high purity in P. pastoris.\nC_LIO_LIPhysico-chemical characterization confirms the right folding of the protein.\nC_LIO_LIThe recombinant protein shows high antigenicity with sera from convalescents.\nC_LIO_LIThe sera from animals inhibit the RBD-ACE2 binding and neutralize the virus.\nC_LIO_LIThe C-RBD-H6 protein stimulates IFN{gamma}, IL-2, IL-6, IL-4, and TNF in mice.\nC_LI", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Miladys Limonta-Fernandez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba" + }, + { + "author_name": "Glay Chinea-Santiago", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Alejandro Miguel Martin-Dunn", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Diamile Gonzalez-Roche", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Monica Bequet-Romero", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gabriel Marquez-Perera", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Isabel Gonzalez-Moya", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Camila Canaan-Haden-Ayala", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Ania Cabrales-Rico", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Luis Ariel Espinosa-Rodriguez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Yassel Ramos-Gomez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Ivan Andujar-Martinez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Luis Javier Gonzalez-Lopez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Mariela Perez de la Iglesia", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Jesus Zamora-Sanchez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Otto Cruz-Sui", + "author_inst": "Civilian Defense Scientific Research Center, Carretera de Jamaica y Autopista Nacional, San Jose de las Lajas, Mayabeque, Cuba" + }, + { + "author_name": "Gilda Lemos-Perez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gleysin Cabrera-Herrera", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Jorge Valdes-Hernandez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Eduardo Martinez-Diaz", + "author_inst": "Biotechnology and Pharmaceutical Industries Group, BioCubaFarma, Ave. Independencia 8126, esq. a Calle 100. Boyeros. La Habana, Cuba." + }, + { + "author_name": "Eulogio Pimentel-Vazquez", + "author_inst": "Biotechnology and Pharmaceutical Industries Group, BioCubaFarma, Ave. Independencia 8126, esq. a Calle 100. Boyeros. La Habana, Cuba." + }, + { + "author_name": "Marta Ayala-Avila", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gerardo Guillen-Nieto", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.28.21259452", "rel_title": "Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people", @@ -704466,29 +707008,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.28.21259039", - "rel_title": "COVID-19 vaccines and evidence-based medicine", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259039", - "rel_abs": "OBJECTIVETo clarify efficacy, effectiveness, and harm of available vaccines for COVID-19, using measures in evidence-based medicine (EBM) that, in addition to relative risk reduction, consider absolute risk reduction and variations in baseline risks.\n\nDESIGNSystematic review of studies that have considered impacts of vaccines in relation to baseline risks. Calculation of risk reduction and harms from published data in two random controlled trials and one population-based implementation study. Analysis of risk reductions in geographical areas with varying baseline risks. Comparison of results concerning COVID-19 vaccine and selected prior vaccines.\n\nSETTINGRandom controlled trials of Pfizer and Moderna vaccines in multiple countries; population-based study using Pfizer vaccine in Israel. Counties with varying baseline risks in the United States; states with varying baseline risks in India.\n\nPARTICIPANTS43,448 and 30,420 subjects in the random controlled trials; 1,198,236 subjects in the population-based study.\n\nINTERVENTIONSMulti-site random controlled trials of vaccine efficacy; population-based administration of vaccine with determination of effectiveness by comparison of vaccinated and unvaccinated subjects.\n\nMAIN OUTCOME MEASURESRelative risk reduction (RRR), absolute risk reduction (ARR), number needed to be vaccinated to prevent one symptomatic infection (NNV), absolute risk of the intervention (ARI), and number needed to harm (NNH).\n\nRESULTSA systematic review of literature in medicine and public health showed very few reports regarding ARR, NNV, ARI, and NNH; use of these indicators to compare benefits versus harms; or analysis of these EBM indicators in the context of varying baseline risks. From data in the two random controlled trials and one population-based study, calculated ARR was approximately 1 percent (as compared to RRR of 50 to 95 percent), and NNV was in the range of 100 to 500. In comparisons of ARR and NNV versus ARI and NNH, benefits and harms were not markedly different. From a sensitivity analysis of ARR and NNV in population groups with varying baseline risks, the effectiveness of vaccines as measured by ARR and NNV was substantially higher in regions with high as compared to low baseline risks. The ARR for COVID-19 vaccines was somewhat smaller and the NNV somewhat larger than achieved by some vaccines to prevent influenza and smallpox.\n\nCONCLUSIONThe efficacy and effectiveness of major COVID-19 vaccines, as measured by RRR, are impressive. As measured by ARR and NNV, which take into account variation in baseline risks, the effectiveness of the vaccines is substantially higher in areas with higher baseline risks. This finding can contribute to educational efforts, informed consent procedures, and policy making about priorities for vaccine distribution, especially under conditions of access barriers linked to poverty and inequality.\n\nWHAT IS ALREADY KNOWN ON THIS TOPICMajor COVID-19 vaccines so far have shown impressive efficacy in random controlled trials and effectiveness in population-based studies. To determine efficacy and effectiveness, these studies have used relative risk reduction (RRR), which shows the difference in event rate between those receiving and not receiving a vaccine. Reports of efficacy and effectiveness have not yet clarified other key indicators from evidence-based medicine (EBM) that consider variations baseline risks. Such indicators include measures of benefits such as absolute risk reduction (ARR) and number needed to be vaccinated (NNV), as well as measures of harm such as absolute risk of the intervention (ARI) and number needed to harm (NNH).\n\nWHAT THIS STUDY ADDSFor COVID-19 vaccines, calculated ARR is somewhat lower and NNV somewhat higher than for certain prior vaccines such as those for influenza and smallpox. Indicators of harm for COVID-19 vaccines, as measured by ARI and NNH, appear to be in the same order of magnitude as indicators of benefit such as ARR and NNV. The effectiveness of COVID-19 vaccines, as measured by ARR and NNV, is substantially higher in geographical areas with high baseline risk, compared to areas with low baseline risk.\n\nThese findings can assist in informed consent procedures, educational efforts, and priority setting in policies about distribution of vaccines, especially in the context of access barriers related to poverty and inequality.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andrew Larkin", - "author_inst": "Allende Program in Social Medicine" - }, - { - "author_name": "Howard Waitzkin", - "author_inst": "University of New Mexico, Allende Program in Social Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.28.21259672", "rel_title": "The health impacts of a 4-month long community-wide COVID-19 lockdown: Findings from a prospective longitudinal study in the state of Victoria, Australia.", @@ -705632,6 +708151,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.28.21259384", + "rel_title": "Comparison of Mental Health Symptom Changes from pre-COVID-19 to COVID-19 by Sex or Gender: A Systematic Review and Meta-analysis", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259384", + "rel_abs": "ImportanceWomen and gender-diverse individuals have faced disproportionate socioeconomic burden during COVID-19. There have been reports that this has translated into greater negative changes in mental health, but this has been based on cross-sectional research that has not accounted for pre-COVID-19 differences.\n\nObjectiveTo compare mental health symptom changes since pre-COVID-19 by sex or gender.\n\nData SourcesMEDLINE, PsycINFO, CINAHL, EMBASE, Web of Science, China National Knowledge Infrastructure, Wanfang, medRxiv, and Open Science Framework (December 31, 2019 to August 30, 2021).\n\nStudy SelectionEligible studies compared mental health symptom changes from pre-COVID-19 to COVID-19 by sex or gender.\n\nData Extraction and SynthesisData was extracted by a single reviewer with validation by a second reviewer. Adequacy of study methods and reporting was assessed using an adapted version of the Joanna Briggs Institute Checklist for Prevalence Studies. A restricted maximum-likelihood random-effects meta-analyses was conducted.\n\nMain Outcomes and MeasuresAnxiety symptoms, depression symptoms, general mental health, and stress measured continuously or dichotomously.\n\nResults12 studies (10 unique cohorts) were included. All compared females or women to males or men; none included gender-diverse individuals. Continuous symptom change differences were not statistically significant for depression (standardized mean difference [SMD]= 0.12, 95% CI -0.09 to 0.33; 4 studies, 4,475 participants; I2=69.0%) and stress (SMD= - 0.10, 95% CI -0.21 to 0.01; 4 studies, 1,533 participants; I2=0.0%), but anxiety (SMD= 0.15, 95% CI 0.07 to 0.22; 4 studies, 4,344 participants; I2=3.0%) and general mental health (SMD= 0.15, 95% CI 0.12 to 0.18; 3 studies, 15,692 participants; I2=0.0%) worsened more among females or women than males or men during COVID-19. There were no significant differences in changes in proportion above a cut-off: anxiety (difference= -0.05, 95% CI -0.20 to 0.11; 1 study, 217 participants), depression (difference= 0.12, 95% CI -0.03 to 0.28; 1 study, 217 participants), general mental health (difference= -0.03, 95% CI -0.09 to 0.04; 3 studies, 18,985 participants; I2=94.0%), stress (difference= 0.04, 95% CI -0.10 to 0.17; 1 study, 217 participants).\n\nConclusion and RelevanceMental health outcomes did not differ or were worse by amounts below thresholds for clinical significance for women compared to men.\n\nRegistrationPROSPERO (CRD42020179703).\n\nKEY MESSAGESO_ST_ABSQuestionC_ST_ABSDid mental health symptoms worsen more for females or women than males or men in COVID-19?\n\nFindingsWe reviewed almost 65,000 citations and identified 12 studies that provided data to directly compare mental health symptom changes from pre-COVID-19 to during COVID-19 for females or women versus males or men. Statistically significant, but small, sex- or gender-based differences were found in 2 of 8 mental health outcomes.\n\nMeaningMental health changes among females or women were not significantly different from males or men for most outcomes, and differences that were identified were small and less than minimally important difference thresholds.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Tiffany Dal Santo", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ying Sun", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yin Wu", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Chen He", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yutong Wang", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Xiaowen Jiang", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Kexin Li", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Olivia Bonardi", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ankur Krishnan", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Jill T. Boruff", + "author_inst": "Schulich Library of Physical Sciences, Life Sciences, and Engineering, McGill University" + }, + { + "author_name": "Danielle B. Rice", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Sarah Markham", + "author_inst": "Department of Biostatistics and Health Informatics, King's College London" + }, + { + "author_name": "Brooke Levis", + "author_inst": "Centre for Prognosis Research, School of Medicine, Keele University" + }, + { + "author_name": "Marleine Azar", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Dipika Neupane", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Amina Tasleem", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Anneke Yao", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ian Thombs-Vite", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Branka Agic", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Christine Fahim", + "author_inst": "Li Ka Shing Knowledge Institute, Unity Health Toronto" + }, + { + "author_name": "Michael S. Martin", + "author_inst": "School of Epidemiology and Public Health, University of Ottawa" + }, + { + "author_name": "Sanjeev Sockalingam", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Gustavo Turecki", + "author_inst": "Department of Psychology, McGill University" + }, + { + "author_name": "Andrea Benedetti", + "author_inst": "Department of Epidemiology, Biostatistics and Occupational Health, McGill University" + }, + { + "author_name": "Brett B Thombs", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.06.27.21259131", "rel_title": "Face mask use and associated factors among students in rural Eastern Uganda amidst the COVID-19 pandemic", @@ -706352,41 +708986,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.02.450915", - "rel_title": "Qualification of ELISA and neutralization methodologies to measure SARS-CoV-2 humoral immunity using human clinical samples", - "rel_date": "2021-07-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.02.450915", - "rel_abs": "In response to the SARS-CoV-2 pandemic many vaccines have been developed and evaluated in human clinical trials. The humoral immune response magnitude, composition and efficacy of neutralizing SARS-CoV-2 are essential endpoints for these trials. Robust assays that are reproducibly precise, linear, and specific for SARS-CoV-2 antigens would be beneficial for the vaccine pipeline. In this work we describe the methodologies and clinical qualification of three SARS-CoV-2 endpoint assays. We developed and qualified Endpoint titer ELISAs for total IgG, IgG1, IgG3, IgG4, IgM and IgA to evaluate the magnitude of specific responses to the trimeric spike (S) antigen and total IgG specific to the spike receptor binding domain (RBD) of SARS-CoV-2. We also qualified a pseudovirus neutralization assay which evaluates functional antibody titers capable of inhibiting the entry and replication of a lentivirus containing the Spike antigen of SARS-CoV-2. To complete the suite of assays we qualified a plaque reduction neutralization test (PRNT) methodology using the 2019-nCoV/USA-WA1/2020 isolate of SARS-CoV-2 to assess neutralizing titers of antibodies in plasma from normal healthy donors and convalescent COVID-19 individuals.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lauren Carter", - "author_inst": "Institute for Protein Design, University of Washington" - }, - { - "author_name": "Samuel Wren", - "author_inst": "Institute for Protein Design, University of Washington" - }, - { - "author_name": "Elizabeth Kepl", - "author_inst": "Institute for Protein Design, University of Washington" - }, - { - "author_name": "Claire Sydeman", - "author_inst": "Institute for Protein Design, University of Washington" - }, - { - "author_name": "Neil P King", - "author_inst": "Institute for Protein Design, University of Washington" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.23.21259321", "rel_title": "The IDentif.AI 2.0 Pandemic Readiness Platform: Rapid Prioritization of Optimized COVID-19 Combination Therapy Regimens", @@ -707830,6 +710429,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.28.21259628", + "rel_title": "Rotation-based schedules in elementary schools to prevent COVID-19 spread: A simulation study", + "rel_date": "2021-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259628", + "rel_abs": "BackgroundRotations of schoolchildren on a weekly basis is one of the nonpharmaceutical interventions often considered in the covid-19 pandemic. This study aims to investigate the impact of different types of rotations in various testing contexts.\n\nMethodsWe built an agent-based model of interactions among pupils and teachers based on an online survey in an elementary school in Prague, Czechia. This model contains 624 schoolchildren and 55 teachers (679 nodes) and about 27 thousands social contacts (edges) in 10 layers. The layers reflect different types of contacts (in classroom, cafeteria etc.) as described in the survey. On this multi-graph structure we run a modified SEIR model of the covid-19 dynamics. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in the period March to June 2020.\n\nFindingsThere are three main findings in our paper.\n\nO_LIWeekly rotations of in-class and distance learning reduce the spread of covid-19 by 75-81% and thus represent an effective preventative measure in school setting.\nC_LIO_LIRegular antigen testing twice a week, or weekly PCR testing, significantly reduces infections even when using tests with a lower sensitivity: tests with a 40% sensitivity reduce infections by more than 50 percent.\nC_LIO_LIThe density of revealed contact graphs for older pupils is 1.5 times higher than the younger pupils graph, the teachers network is yet an order of magnitude denser. Consequently, the infection transmission between teachers is highly overproportional in our school. Moreover, teachers act as bridges connecting clusters of classes, especially in the secondary grade where they are responsible for 14-18% of infections, in comparison to 8-11% in primary grade.\nC_LI\n\nInterpretationWeekly rotations with regular testing are a highly effective non-pharmaceutical intervention for the prevention of covid-19 spread in schools and a way to keep schools open during an epidemic or to reopen them as the epidemiological situation improves.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Cyril Brom", + "author_inst": "Faculty of Mathematics and Physics, Charles University" + }, + { + "author_name": "Tomas Diviak", + "author_inst": "School of Social Sciences, University of Manchester" + }, + { + "author_name": "Jakub Drbohlav", + "author_inst": "Ministry of Education, Youth and Sports of the Czech Republic" + }, + { + "author_name": "Vaclav Korbel", + "author_inst": "CERGE-EI" + }, + { + "author_name": "Rene Levinsky", + "author_inst": "CERGE-EI" + }, + { + "author_name": "Roman Neruda", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + }, + { + "author_name": "Gabriela Suchoparova", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + }, + { + "author_name": "Josef Slerka", + "author_inst": "Faculty of Arts, Charles University" + }, + { + "author_name": "Martin Smid", + "author_inst": "The Czech Academy of Sciences, Institute of Information Theory and Automation" + }, + { + "author_name": "Jan Trnka", + "author_inst": "Third Faculty of Medicine, Charles University" + }, + { + "author_name": "Petra Vidnerova", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.28.21259620", "rel_title": "The Evolution of Young People's Mental Health during COVID-19: Evidence from four Low-and-Middle-Income-Countries", @@ -708670,53 +711328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.28.21259613", - "rel_title": "The COVID-19 Yorkshire Rehabilitation Scale (C19-YRS): application and psychometric analysis in a post-COVID-19 syndrome cohort", - "rel_date": "2021-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259613", - "rel_abs": "BackgroundAs our understanding of the nature and prevalence of Post-COVID-19 syndrome (PCS) is increasing, a measure of the impact of COVID-19 could provide valuable insights into patients perceptions in clinical trials and epidemiological studies, as well as routine clinical practice.\n\nObjectiveTo evaluate the clinical usefulness and psychometric properties of the COVID-19 Yorkshire Rehabilitation Scale (C19-YRS) in patients with PCS.\n\nDesignA prospective, observational study of 187 consecutive patients attending a post-COVID-19 rehabilitation clinic. The C19-YRS was used to record patients symptoms, functioning and disability. A global health question was used to measure the overall impact of PCS on health. Classical psychometric methods (data quality, scaling assumptions, targeting, reliability and validity) were used to assess the C19-YRS.\n\nResultsFor the overall scale, missing data were low, scaling and targeting assumptions were satisfied, and internal consistency was high (Cronbachs alpha = 0.891). Relationships between perception of health and patients reports of symptoms, functioning and disability demonstrated good concordance.\n\nConclusionsThis is the first study to examine the psychometric properties of an outcome measure in patients with PCS. In this sample of patients, the C19-YRS was clinically useful and satisfied standard psychometric criteria, providing preliminary evidence of its suitability as a measure of PCS.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nick J Preston", - "author_inst": "1.\tAcademic Department of Rehabilitation Medicine, Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK" - }, - { - "author_name": "Amy Parkin", - "author_inst": "Leeds Community Healthcare NHS Trust, Leeds, UK" - }, - { - "author_name": "Sophie Makower", - "author_inst": "Leeds Community Healthcare NHS Trust, Leeds, UK" - }, - { - "author_name": "Denise H Ross", - "author_inst": "National Demonstration Centre for Rehabilitation, Leeds Teaching Hospitals NHS Trust, Leeds, UK" - }, - { - "author_name": "Jeremy Gee", - "author_inst": "Airedale Foundation NHS Trust" - }, - { - "author_name": "Stephen J Halpin", - "author_inst": "National Demonstration Centre for Rehabilitation, Leeds Teaching Hospitals NHS Trust, Leeds, UK" - }, - { - "author_name": "Mike C Horton", - "author_inst": "1.\tAcademic Department of Rehabilitation Medicine, Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK" - }, - { - "author_name": "Manoj Sivan", - "author_inst": "National Demonstration Centre for Rehabilitation, Leeds Teaching Hospitals NHS Trust, Leeds, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2021.06.23.21259389", "rel_title": "Altered cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy.", @@ -709540,6 +712151,81 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.06.30.450617", + "rel_title": "Detection of potential new SARS-CoV-2 Gamma-related lineage in Tocantins shows the spread and ongoing evolution of P.1 in Brazil", + "rel_date": "2021-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.30.450617", + "rel_abs": "After more than a year of the pandemic situation of COVID-19, the United Kingdom (UK), South Africa, and Brazil became the epicenter of new lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Variants of Concern (VOCs) were identified through a continuous genomic surveillance global effort, the B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) harboring a constellation set of mutations. This research aims to: (i) report the predominance of the Gamma (P.1) lineage presenting the epidemiological situation of the SARS-CoV-2 genomic surveillance at the state of Tocantins, and (ii) describe the emergence of possible new mutations and viral variants with the potential new lineage (P1-related) represented by 8 genomes from the Tocantins harboring the mutation L106F in ORF3a. At the moment, 6,687 SARS-CoV-2 genomes from GISAID carry this mutation. The whole-genome sequencing has an important role in understanding the evolution and genomic diversity of SARS-CoV-2, thus, the continuous monitoring will help in the control measures and restrictions imposed by the secretary of health of the state to prevent the spread of variants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ueric Jose Borges de Souza", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil." + }, + { + "author_name": "Raissa Nunes dos Santos", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil." + }, + { + "author_name": "Fernando Lucas Melo", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil." + }, + { + "author_name": "Aline Belmok", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil." + }, + { + "author_name": "Jucimaria Dantas Galvao", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Sirlene Borges Damasceno", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Tereza Cristina Vieira de Rezende", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Miguel de Souza Andrade", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil" + }, + { + "author_name": "Bergmann Morais Ribeiro", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil" + }, + { + "author_name": "Jose Carlos Ribeiro Junior", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Rogerio Fernandes Carvalho", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Monike da Silva Oliveira", + "author_inst": "Postgraduate Program in Tropical Medicine and Public Health, Federal University of Goias, Goiania, Goias, 74690-900, Brazil." + }, + { + "author_name": "Isac Gabriel Cunha dos Santos", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Fernando Rosado Spilki", + "author_inst": "One Health Laboratory, Feevale Techpark, Feevale University, Campo Bom, Rio Grande do Sul, 93700-000, Brazil and Molecular Microbiology Laboratory, Feevale Univ" + }, + { + "author_name": "Fabricio Souza Campos", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.06.30.450547", "rel_title": "Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2", @@ -710544,53 +713230,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.28.450274", - "rel_title": "Natural isolate and recombinant SARS-CoV-2 rapidly evolve in vitro to higher infectivity through more efficient binding to heparan sulfate and reduced S1/S2 cleavage", - "rel_date": "2021-06-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.450274", - "rel_abs": "One of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virulence factors is the ability to interact with high affinity to the ACE2 receptor, which mediates viral entry into cells. The results of our study demonstrate that within a few passages in cell culture, both the natural isolate of SARS-CoV-2 and the recombinant, cDNA-derived variant acquire an additional ability to bind to heparan sulfate (HS). This promotes a primary attachment of viral particles to cells before their further interactions with the ACE2. Interaction with HS is acquired through multiple mechanisms. These include i) accumulation of point mutations in the N-terminal domain (NTD) of the S protein, which increase the positive charge of the surface of this domain, ii) insertions into NTD of heterologous peptides, containing positively charged amino acids, and iii) mutation of the first amino acid downstream of the furin cleavage site. This last mutation affects S protein processing, transforms the unprocessed furin cleavage site into the heparin-binding peptide and makes viruses less capable of syncytia formation. These viral adaptations result in higher affinity of viral particles to heparin sepharose, dramatic increase in plaque sizes, more efficient viral spread, higher infectious titers and two orders of magnitude lower GE:PFU ratios. The detected adaptations also suggest an active role of NTD in virus attachment and entry. As in the case of other RNA+ viruses, evolution to HS binding may result in virus attenuation in vivo.\n\nIMPORTANCEThe spike protein of SARS-CoV-2 is a major determinant of viral pathogenesis. It mediates binding to ACE2 receptor and later, fusion of viral envelope and cellular membranes. The results of our study demonstrate that SARS-CoV-2 rapidly evolves during propagation in cultured cells. Its spike protein acquires mutations in the N-terminal domain (NTD) and in P1 position of the furin cleavage site (FCS). The amino acid substitutions or insertions of short peptides in NTD are closely located on the protein surface and increase its positive charge. They strongly increase affinity of the virus to heparan sulfate, make it dramatically more infectious for the cultured cells and decrease GE:PFU ratio by orders of magnitude. The S686G mutation also transforms the FCS into the heparin-binding peptide. Thus, the evolved SARS-CoV-2 variants efficiently use glycosaminoglycans on the cell surface for primary attachment before the high affinity interaction of the spikes with the ACE2 receptor.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nikita Shiliaev", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Tetyana Lukash", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Oksana Palchevska", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "David K Crossman", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Todd J. Green", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Michael Crowley", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Elena I. Frolova", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Ilya Frolov", - "author_inst": "University of Alabama at Birmingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.29.450133", "rel_title": "Absolute quantitation of individual SARS-CoV-2 RNA molecules: a new paradigm for infection dynamics and variant differences", @@ -711758,6 +714397,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.06.24.21259087", + "rel_title": "Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children", + "rel_date": "2021-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259087", + "rel_abs": "Children are consistently reported to have reduced SARS-CoV-2 infection rates and a substantially lower risk for developing severe COVID-19. However, the molecular mechanisms underlying protection against COVID-19 in younger age groups remain widely unknown. Here, we systematically characterized the single-cell transcriptional landscape in the upper airways in SARS-CoV-2 negative and age-matched SARS-CoV-2 positive children (n=42) and corresponding samples from adults (n=44), covering an age range of four weeks to 77 years. Children displayed higher basal expression of the relevant pattern recognition receptor (PRR) pathways in upper airway epithelial cells, macrophages, and dendritic cells, resulting in stronger innate antiviral responses upon SARS-CoV-2 infection compared to adults. We further detected distinct immune cell subpopulations with an overall dominance of neutrophils and a population of cytotoxic T cells occurring predominantly in children. Our study provides evidence that the airway epithelial and mucosal immune cells of children are pre-activated and primed for virus sensing, resulting in a stronger early innate antiviral responses to SARS-CoV-2 infection compared to adults.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Jennifer Loske", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Jobst R\u00f6hmel", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Soeren Lukassen", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Sebastian Stricker", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Vladimir Gon\u00e7alves Magalh\u00e3es", + "author_inst": "Research group Dynamics of Early Viral Infection and the Innate Antiviral Response, division F170, German Cancer Research Center (DKFZ)" + }, + { + "author_name": "Johannes Liebig", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Robert Lorenz Chua", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Loreen Th\u00fcrmann", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Marey Messingschlager", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Anke Seegebarth", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Bernd Timmermann", + "author_inst": "Max Planck Institute for Molecular Genetics, Berlin" + }, + { + "author_name": "Sven Klages", + "author_inst": "Max Planck Institute for Molecular Genetics, Berlin" + }, + { + "author_name": "Markus Ralser", + "author_inst": "Institute of Biochemistry, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Birgit Sawitzki", + "author_inst": "Institute of Medical Immunology, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Victor M Corman", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Christian Conrad", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Sven Laudi", + "author_inst": "Department of Anesthesiology and Intensive Care, University Hospital Leipzig" + }, + { + "author_name": "Marco Binder", + "author_inst": "Research group Dynamics of Early Viral Infection and the Innate Antiviral Response, division F170, German Cancer Research Center (DKFZ)," + }, + { + "author_name": "Saskia Trump", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin Center for Digital Health, Berlin Institute of Health at Charite" + }, + { + "author_name": "Roland Eils", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Marcus Mall", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Irina Lehmann", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin Center for Digital Health, Berlin Institute of Health at Charite" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.23.21259394", "rel_title": "Macro-Level Drivers of SARS-CoV-2 Transmission: A Data-Driven Analysis of Factors Contributing to Epidemic Growth During the First Wave of outbreaks in the United States", @@ -712950,169 +715696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.06.28.450190", - "rel_title": "Enhanced fitness of SARS-CoV-2 variant of concern B.1.1.7, but not B.1.351, in animal models", - "rel_date": "2021-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.450190", - "rel_abs": "Emerging variants of concern (VOCs) drive the SARS-CoV-2 pandemic. We assessed VOC B.1.1.7, now prevalent in several countries, and VOC B.1.351, representing the greatest threat to populations with immunity to the early SARS-CoV-2 progenitors. B.1.1.7 showed a clear fitness advantage over the progenitor variant (wt-S614G) in ferrets and two mouse models, where the substitutions in the spike glycoprotein were major drivers for fitness advantage. In the \"superspreader\" hamster model, B.1.1.7 and wt-S614G had comparable fitness, whereas B.1.351 was outcompeted. The VOCs had similar replication kinetics as compared to wt-S614G in human airway epithelial cultures. Our study highlights the importance of using multiple models for complete fitness characterization of VOCs and demonstrates adaptation of B.1.1.7 towards increased upper respiratory tract replication and enhanced transmission in vivo.\n\nSummary sentenceB.1.1.7 VOC outcompetes progenitor SARS-CoV-2 in upper respiratory tract replication competition in vivo.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Lorenz Ulrich", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Nico Joel Halwe", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Adriano Taddeo", - "author_inst": "Institute of Virology and Immunology, Mittelhaeusern, Switzerland" - }, - { - "author_name": "Nadine Ebert", - "author_inst": "Institute of Virology and Immunology, Bern, Switzerland" - }, - { - "author_name": "Jacob Sch\u00f6n", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Christelle Devisme", - "author_inst": "Institute of Virology and Immunology, Mittelhaeusern, Switzerland" - }, - { - "author_name": "Bettina Salome Tr\u00fceb", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Bernd Hoffmann", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Manon Wider", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Meriem Bekliz", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Switzerland" - }, - { - "author_name": "Manel Essaidi-Laziosi", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Switzerland" - }, - { - "author_name": "Marie Luisa Schmidt", - "author_inst": "Charite, Universitaetsmedizin Berlin, Institute of Virology, Berlin, Germany" - }, - { - "author_name": "Daniela Niemeyer", - "author_inst": "Charite, Universitaetsmedizin Berlin, Institute of Virology, Berlin, Germany" - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charite, Universitaetsmedizin Berlin, Institute of Virology, Berlin, Germany" - }, - { - "author_name": "Anna Kraft", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Aur\u00e9lie Godel", - "author_inst": "Institute of Virology and Immunology, Mittelhaeusern, Switzerland" - }, - { - "author_name": "Laura Laloli", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Jenna Nicole Kelly", - "author_inst": "Institute of Virology and Immunology, Bern, Switzerland" - }, - { - "author_name": "Angele Breithaupt", - "author_inst": "Department of Experimental Animal Facilities and Biorisk Management, Friedrich Loeffler Institut; Greifswald Insel Riems, Germany" - }, - { - "author_name": "Claudia Wylezich", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "In\u00eas Margarida Berenguer Veiga", - "author_inst": "Institute of Virology and Immunology, Bern, Switzerland" - }, - { - "author_name": "Mitra Gultom", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Kenneth Adea", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Switzerland" - }, - { - "author_name": "Benjamin Meyer", - "author_inst": "Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Christiane Eberhardt", - "author_inst": "Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Lisa Thomann", - "author_inst": "Institute of Virology and Immunology, Bern, Switzerland" - }, - { - "author_name": "Monika Gsell-Albert", - "author_inst": "Institute for Infectious Diseases, University of Bern; Bern, Switzerland" - }, - { - "author_name": "Fabien Labroussaa", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern; Bern, Switzerland" - }, - { - "author_name": "J\u00f6rg Jores", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Artur Summerfield", - "author_inst": "Institute of Virology and Immunology, Mittelhaeusern, Switzerland" - }, - { - "author_name": "Christian Drosten", - "author_inst": "German Centre for Infection Research, partner site Charite, Berlin, Germany" - }, - { - "author_name": "Isabella Anne Eckerle", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Switzerland" - }, - { - "author_name": "Ronald Dijkman", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Donata Hoffmann", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Volker Thiel", - "author_inst": "Institute of Virology and Immunology, Bern, Switzerland" - }, - { - "author_name": "Martin Beer", - "author_inst": "Institute of Diagnostic Virology, Friedrich Loeffler Institut, Federal Research Institute of Animal Health, Greifswald Insel Riems, Germany" - }, - { - "author_name": "Charaf Benarafa", - "author_inst": "Institute of Virology and Immunology, Mittelhaeusern, Switzerland" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.28.450214", "rel_title": "A bifluorescent-based assay for the identification of neutralizing antibodies against SARS-CoV-2 variants of concern in vitro and in vivo", @@ -714524,6 +717107,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.24.21259444", + "rel_title": "Early warning signals predict emergence of COVID-19 waves", + "rel_date": "2021-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259444", + "rel_abs": "Early warning signals (EWSs) aim to predict changes in complex systems from phenomenological signals in time series data. These signals have recently been shown to precede the initial emergence of disease outbreaks, offering hope that policy makers can make predictive rather than reactive management decisions. Here, using daily COVID-19 case data in combination with a novel, sequential analysis, we show that composite EWSs consisting of variance, autocorrelation, and return rate not only pre-empt the initial emergence of COVID-19 in the UK by 14 to 29 days, but also the following wave six months later. We also predict there is a high likelihood of a third wave as of the data available on 9th June 2021. Our work suggests that in highly monitored disease time series such as COVID-19, EWSs offer the opportunity for policy makers to improve the accuracy of time critical decisions based solely upon surveillance data.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Duncan A O'Brien", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christopher F Clements", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.24.21259469", "rel_title": "Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner", @@ -715132,69 +717738,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.17.21258275", - "rel_title": "Integrating PCR-free amplification and synergistic sensing for ultrasensitive and rapid CRISPR/Cas12a-based SARS-CoV-2 antigen detection", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21258275", - "rel_abs": "Antigen detection provides particularly valuable information for medical diagnoses; however, the current detection methods are less sensitive and accurate than nucleic acid analysis. The combination of CRISPR/Cas12a and aptamers provides a new detection paradigm, but sensitive sensing and stable amplification in antigen detection remain challenging. Here, we present a PCR-free multiple trigger dsDNA tandem-based signal amplification strategy and a de novo designed dual aptamer synergistic sensing strategy. Integration of these two strategies endowed the CRISPR/Cas12a and aptamer-based method with ultra-sensitive, fast, and stable antigen detection. In a demonstration of this method, the limit of detection was at the single virus level (0.17 fM, approximately two copies/L) in SARS-CoV-2 antigen nucleocapsid protein analysis of saliva or serum samples. The entire procedure required only 20 minutes. Given our systems simplicity and modular setup, we believe that it could be adapted reasonably easily for general applications in CRISPR/Cas12a-aptamer-based detection.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xiangxiang Zhao", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - }, - { - "author_name": "Zhengduo Wang", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - }, - { - "author_name": "Bowen Yang", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - }, - { - "author_name": "Zilong Li", - "author_inst": "State Key Laboratory of Microbial Resources and Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" - }, - { - "author_name": "Yaojun Tong", - "author_inst": "State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University." - }, - { - "author_name": "Yuhai Bi", - "author_inst": "State Key Laboratory of Microbial Resources and Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" - }, - { - "author_name": "Zhenghong Li", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - }, - { - "author_name": "Xuekui Xia", - "author_inst": "Key Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)." - }, - { - "author_name": "Xiangyin Chen", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - }, - { - "author_name": "Weishan Wang", - "author_inst": "State Key Laboratory of Microbial Resources and Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" - }, - { - "author_name": "Gao-Yi Tan", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - }, - { - "author_name": "Lixin Zhang", - "author_inst": "State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST)." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.23.21258626", "rel_title": "Report on Three Round COVID-19 Risk Blind Tests by Screening Eye-region Manifestations", @@ -716182,6 +718725,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.24.21259218", + "rel_title": "Long-term course of humoral and cellular immune responses in outpatients after SARS-CoV-2 infection", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259218", + "rel_abs": "Characterisation of the naturally acquired B and T cell immune responses to SARS-CoV-2 is important for the development of public health and vaccination strategies to manage the burden of COVID-19 disease. We conducted a prospective, longitudinal analysis in COVID-19 recovered patients at various time points over a 10-month period in order to determine how circulating antibody levels and interferon-gamma (IFN-{gamma}) release by peripheral blood cells change over time following natural infection.\n\nFrom March 2020 till January 2021, we enrolled 412 adults mostly with mild or moderate disease course. At each study visit, subjects donated peripheral blood for testing of anti-SARS-CoV-2 IgG antibodies and IFN-{gamma} release after SARS-CoV-2 S-protein stimulation. Anti-SARS-CoV-2 IgG antibodies were identified in 316/412 (76.7%) of the patients and 215/412 (52.2%) had positive neutralizing antibody levels. Likewise, in 274/412 (66.5 %) positive IFN-{gamma} release and IgG antibodies were detected. With respect to time after infection, both IgG antibody levels and IFN-{gamma} concentrations decreased by about half within three hundred days. Statistically, IgG and IFN-{gamma} production were closely associated, but on an individual basis we observed patients with high antibody titres but low IFN-{gamma} levels and vice versa.\n\nOur data suggest that immunological reaction is acquired in most individuals after infection with SARS-CoV-2 and is sustained in the majority of patients for at least 10 months after infection. Since no robust marker for protection against COVID-19 exists so far, we recommend utilizing both, IgG and IFN-{gamma} release for an individual assessment of immunity status.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julia Schiffner", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany" + }, + { + "author_name": "Insa Backhaus", + "author_inst": "Institute of Medical Sociology, Centre for Health and Society, Medical Faculty and University Hospital, Heinrich-Heine-University, Duesseldorf, Germany" + }, + { + "author_name": "Jens Rimmele", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Soeren Schulz", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Till Moehlenkamp", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Julia Maria Klemens", + "author_inst": "Institute for Experimental Immunology, affiliated to EUROIMMUN Medizinische Labordiagnostika AG, Luebeck, Germany" + }, + { + "author_name": "Dorinja Zapf", + "author_inst": "Institute for Experimental Immunology, affiliated to EUROIMMUN Medizinische Labordiagnostika AG, Luebeck, Germany" + }, + { + "author_name": "Werner Solbach", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.22.21259316", "rel_title": "Investigating phenotypes of pulmonary COVID-19 recovery: a longitudinal observational prospective multicenter trial", @@ -716858,33 +719452,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.06.21.21259258", - "rel_title": "Digital contact tracing contributes little to COVID-19 outbreak containment", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259258", - "rel_abs": "Digital contact tracing applications have been introduced in many countries to aid in the containment of COVID-19 outbreaks. Initially, enthusiasm was high regarding their implementation as a non-pharmaceutical intervention (NPI). Yet, no country was able to prevent larger outbreaks without falling back to harsher NPIs, and the total effect of digital contact tracing remains elusive. Based on the results of empirical studies and modeling efforts, we show that digital contact tracing apps might have prevented cases on the order of single-digit percentages up until now, at best. We show that this poor impact can be attributed to a combination of low participation rates, a non-flexible reliance on symptom-based testing, low engagement of participants, and delays between testing and test result upload. We find that contact tracing does not change the epidemic threshold and exclusively prevents more cases during the supercritical phase of an epidemic, making it unfit as a tool to prevent outbreaks. Locally clustered contact structures may increase the interventions efficacy, but only if the number of contacts per individual is homogeneously distributed, a condition usually not found in contact networks. Our results suggest that policy makers cannot rely on digital contact tracing to contain outbreaks of COVID-19 or similar diseases.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Angelique Burdinski", - "author_inst": "Institute for Theoretical Biology and Integrated Research Institute for the Life-Sciences, Humboldt University of Berlin, Germany" - }, - { - "author_name": "Dirk Brockmann", - "author_inst": "Institute for Theoretical Biology and Integrated Research Institute for the Life-Sciences, Humboldt University of Berlin, Germany" - }, - { - "author_name": "Benjamin F Maier", - "author_inst": "Institute for Theoretical Biology and Integrated Research Institute for the Life-Sciences, Humboldt University of Berlin, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.21.21258990", "rel_title": "SARS-CoV-2 Breakthrough Infections in Fully Vaccinated Individuals", @@ -717976,6 +720543,25 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.06.23.449627", + "rel_title": "E484K and N501Y SARS-CoV 2 Spike Mutants Increase ACE2 Recognition but Reduce Affinity for Neutralizing Antibody", + "rel_date": "2021-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449627", + "rel_abs": "SARS-CoV2 mutants emerge as variants of concern (VOC) due to altered selection pressure and rapid replication kinetics. Among them, lineages B.1.1.7, B.1.351, and P.1 contain a key mutation N501Y. B.1.135 and P.1 lineages have another mutation, E484K. Here, we decode the effect of these two mutations on the host receptor, ACE2, and neutralizing antibody (B38) recognition. The gain in binding affinity for the N501Y RBD mutant to the ACE2 is attributed to improved {pi}-{pi} stacking and {pi}-cation interactions. The enhanced receptor affinity of the E484K mutant is caused due to the formation of a specific hydrogen bond and salt-bridge interaction with Glu75 of ACE2. Notably, both the mutations reduce the binding affinity for B38 due to the loss of several hydrogen-bonding interactions. The insights obtained from the study are crucial to interpret the increased transmissibility and reduction in the neutralization efficacy of rapidly emerging SARS-CoV2 VOCs.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sandipan Chakraborty", + "author_inst": "Amity University, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.06.23.449535", "rel_title": "Integrative COVID-19 Biological Network Inference with Probabilistic Core Decomposition", @@ -718616,73 +721202,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.15.21258924", - "rel_title": "Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of 2020 excess mortality data", - "rel_date": "2021-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258924", - "rel_abs": "IntroductionIn countries with weak surveillance systems confirmed COVID-19 deaths are likely to underestimate the death toll of the pandemic. Many countries also have incomplete vital registration systems, hampering excess mortality estimation. Here, we fitted a dynamic transmission model to satellite imagery data on burial patterns in Mogadishu, Somalia during 2020 to estimate the date of introduction, transmissibility and other epidemiologic characteristics of SARS-CoV-2 in this low-income, crisis-affected setting.\n\nMethodsWe performed Markov chain Monte Carlo (MCMC) fitting with an age-structured compartmental COVID-19 model to provide median estimates and credible intervals for the date of introduction, the basic reproduction number (R0) and the effect of non-pharmaceutical interventions in Mogadishu up to September 2020.\n\nResultsUnder the assumption that excess deaths in Mogadishu February-September 2020 were directly attributable to SARS-CoV-2 infection we arrived at median estimates of October-November 2019 for the date of introduction and low R0 estimates (1.3-1.5) stemming from the early and slow rise of excess deaths. The effect of control measures on transmissibility appeared small.\n\nConclusionSubject to study assumptions, a very early SARS-CoV-2 introduction event may have occurred in Somalia. Estimated transmissibility in the first epidemic wave was lower than observed in European settings.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mihaly Koltai", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Abdihamid Warsame", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Farah Bashiir", - "author_inst": "Somali Disaster Resilience Institute" - }, - { - "author_name": "Terri Freemantle", - "author_inst": "Satellite Applications Catapult" - }, - { - "author_name": "Chris Williams", - "author_inst": "Satellite Applications Catapult" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "LSHTM" - }, - { - "author_name": "Nicholas G Davies", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Ahmed Aweis", - "author_inst": "Somali Disaster Resilience Institute" - }, - { - "author_name": "Mohamed Ahmed", - "author_inst": "Somali Disaster Resilience Institute" - }, - { - "author_name": "Abdirisak Dalmar", - "author_inst": "Somali Disaster Resilience Institute" - }, - { - "author_name": "Francesco Checchi", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.18.21259157", "rel_title": "Clinical profiles at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period using a machine learning approach", @@ -719682,6 +722201,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.23.449583", + "rel_title": "The Influence of Public Health Faculty on College and University Plans during the COVID-19 Pandemic", + "rel_date": "2021-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449583", + "rel_abs": "The purpose of this study was to determine whether the institutional presence of public health faculty within colleges and universities influenced operational plans for the fall semester of 2020. Using cross-sectional data collected by the College Crisis Initiative of Davidson College, six levels of instructional modalities (ranked from least to most restrictive) were compared between Council on Education of Public Health (CEPH)-accredited and non-CEPH-accredited 4-year institutions. Institutions with CEPH-accredited schools and programs were more likely to select some restrictive teaching modalities: 63.8% more likely to use hybrid/hyflex or more restrictive and 66.9% more likely to be primarily online (with some in person) or more restrictive. However, having CEPH-accredited programs did not push institutions to the most restrictive modalities. COVID-19 cases in county, enrollment, and political affiliation of the state governor were also found to influence instructional modality selection. While any ecological study has certain limitations, this study demonstrates that college and university fall plans appear to have been influenced by the presence of CEPH-accredited schools and programs of public health, and/or the input of their faculty. The influence of relevant faculty expertise on institutional decision-making can help inform college and university responses to future crises.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "David A Johnson", + "author_inst": "University of Louisville, School of Public Heath and Information Sciences" + }, + { + "author_name": "Meredith Cahill", + "author_inst": "University of Louisville, School of Public Health and Information Sciences" + }, + { + "author_name": "Sara Choate", + "author_inst": "University of Louisville, School of Public Health and Information Sciences" + }, + { + "author_name": "Dave Roelfs", + "author_inst": "University of Louisville, College of Arts and Sciences, Department of Sociology" + }, + { + "author_name": "Sarah E Walsh", + "author_inst": "Eastern Michigan University, School of Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.06.18.21258477", "rel_title": "The polarity and specificity of SARS-CoV2 -specific T lymphocyte responses determine disease susceptibility", @@ -720390,37 +722944,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.16.21258869", - "rel_title": "Testing & Opening in Augustusburg A Success Story?", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21258869", - "rel_abs": "The city of Augustusburg allowed for opening of, inter alia, restaurants and hotels joint with large-scale testing. We evaluate this testing & opening (T&O) experiment by comparing the evolution of case rates in Augustusburg with the evolution in other communities of Saxony. We have access to small-scale SARS-CoV-2 infection data at the community level (\" Gemeinde\") instead of the county level (\" Landkreis\") usually used for disease surveillance. Despite data challenges, we conclude that T&O did not lead to any increase in case rates in Augustusburg compared to its control county. When we measure the effect of T&O on cumulative cases, we find a small increase in Augustusburg. This difference almost completely disappears when we control for the effect of higher case rates due to more testing. Generally speaking, T&O worked much better than in comparable projects elsewhere.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Marc Diederichs", - "author_inst": "Johannes Gutenberg University" - }, - { - "author_name": "Timo Friedel Mitze", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Felix Schulz", - "author_inst": "Johannes Gutenberg University" - }, - { - "author_name": "Klaus Waelde", - "author_inst": "Johannes Gutenberg University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.19.21259173", "rel_title": "Did social factors buffer against the effect of adversities on self-harm during the COVID-19 pandemic? A longitudinal analysis of 49,227 UK adults", @@ -721020,6 +723543,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.19.21258892", + "rel_title": "Breastfeeding mother-child clinical outcomes after COVID-19 vaccination", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21258892", + "rel_abs": "This is a prospective cohort study of 88 lactating women in Singapore who received two doses of BNT162b2 vaccination (Pfizer/BioNTech), whereby outcomes of mother-child dyads within 28 days after the second vaccine dose were determined through a structured questionnaire. Minimal effects related to breastfeeding were reported in this cohort; 3 of 88 (3.4%) women had mastitis with 1 of 88 (1.1%) women experiencing breast engorgement. We report an incidence of lymphadenopathy in our cohort at 5 of 88 (5.7%). Reassuringly, there was no change in reported breastmilk supply after vaccination. The most common side effect was pain/redness/swelling at the injection site, which was experienced by 57 of 88 (64.8%) women. There were no serious adverse events of anaphylaxis and hospital admissions. No adverse symptoms were reported in 67 of 88 (76.1%) breastfed children.\n\nWhats known on this subjectTwo studies reported no serious adverse effects in both mother-child dyads after mRNA COVID-19 vaccination in mothers. Up to 61.9-67% lactating women experienced minor side effects.\n\nWhat this study addsWe report an incidence of lymphadenopathy in our cohort at 5.7% as opposed to 0.3% from the Pfizer-BioNTech COVID-19 trial. Reassuringly, there was no change in reported milk supply after vaccination. Minimal effects related to breastfeeding were reported in this cohort; 3 (3.4%) women had mastitis with 1 person experiencing breast engorgement. The most common side effect was pain/redness/swelling at the injection site at 64.8%, which was experienced by 57 of 88 (65%) women. No adverse symptoms were reported in the breastfed children.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jia Ming Low", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Le Ye Lee", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Yvonne Peng Mei Ng", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Youjia Zhong", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Zubair Amin", + "author_inst": "National University Hospital of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.06.21.449352", "rel_title": "Cytoplasmic tail truncation of SARS-CoV-2 Spike protein enhances titer of pseudotyped vectors but masks the effect of the D614G mutation", @@ -721624,61 +724182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.16.21259035", - "rel_title": "Endonuclease-based genotyping of the RBM, a first-line method for the surveillance of emergence or evolution of SARS-CoV-2 Variants.", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21259035", - "rel_abs": "Since the beginning of the Covid-19 pandemics, variants have emerged. Whereas most of them have no to limited selective advantage, some display increased transmissibility and/or resistance to immune response. To date, most of the mutations involved in the functional adaptation are found in the Receptor Binding Module (RBM), close to the interface with the human receptor ACE2. In this study, we thus developed and validated a fast and simple molecular assay allowing the detection and partial identification of the mutations in the RBM coding sequence. After the amplification of the region of interest, the amplicon is heat-denatured and hybridized with an amplicon of reference. The presence of a mutation in the heteroduplex can be cleaved by a mismatch-specific endonuclease and the cleavage pattern is analysed by capillary electrophoresis. The approach was first validated on viral RNA purified different SARS-CoV-2 variants produced in the lab before being implemented for clinical samples. The results highlighted the performance of the assay for the detection of mutations in the RBM from clinical samples. The procedure can be easily set up for high throughput identification of the presence of mutations and serve as a first-line screening to select the samples for full genome sequencing.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eva Lopez", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Margot Barthelemy", - "author_inst": "Aix Marseille University" - }, - { - "author_name": "Cecile Baronti", - "author_inst": "Institut de Recherche pour le Developpement" - }, - { - "author_name": "Shirley Masse", - "author_inst": "Universite de Corse" - }, - { - "author_name": "Alessandra Falchi", - "author_inst": "EA7310 BIOSCOPE, Laboratoire de Virologie, Universite de Corse-Inserm, 20250 Corte, France" - }, - { - "author_name": "Fabien Durbesson", - "author_inst": "Aix Marseille University" - }, - { - "author_name": "Renaud Vincentelli", - "author_inst": "AFMB" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Aix Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health & IHU Mediterranee Infection, APHM Public Hospi" - }, - { - "author_name": "Remi N Charrel", - "author_inst": "Aix Marseille University" - }, - { - "author_name": "Bruno Coutard", - "author_inst": "Aix Marseille University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.15.21251794", "rel_title": "Neutrophil Lymphocyte Ratio as a Predictor of Glucocorticoid Effectiveness in Covid-19 Treatment", @@ -722770,6 +725273,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.15.21258529", + "rel_title": "The impact of temperature on the transmission potential and virulence of COVID-19 in Tokyo, Japan", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258529", + "rel_abs": "BackgroundAssessing the impact of temperature on COVID-19 epidemiology is critical for implementing non-pharmaceutical interventions. However, few studies have accounted for the nature of contagious diseases, i.e., their dependent happenings.\n\nAimWe aimed to quantify the impact of temperature on the transmissibility and virulence of COVID-19 in Tokyo, Japan. We employed two epidemiological measurements of transmissibility and severity: the effective reproduction number (Rt) and case fatality risk (CFR).\n\nMethodsWe used empirical surveillance data and meteorological data in Tokyo to estimate the Rt and time-delay adjusted CFR and to subsequently assess the nonlinear and delay effect of temperature on Rt and time-delay adjusted CFR.\n\nResultsFor Rt at low temperatures, the cumulative relative risk (RR) at first temperature percentile (3.3{degrees}C) was 1.3 (95% confidence interval (CI): 1.1-1.7). As for the virulence to humans, moderate cold temperatures were associated with higher CFR, and CFR also increased as the temperature rose. The cumulative RR at the 10th and 99th percentiles of temperature (5.8{degrees}C and 30.8{degrees}C) for CFR were 3.5 (95%CI: 1.3-10) and 6.4 (95%CI: 4.1-10.1).\n\nConclusionsThis study provided information on the effects of temperature on the COVID-19 epidemiology using Rt and time-delay adjusted CFR. Our results suggest the importance to take precautions to avoid infection in both cold and warm seasons to avoid severe cases of COVID-19. The results and proposed framework will also help in assessing possible seasonal course of COVID-19 in the future.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lisa Yamasaki", + "author_inst": "Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Hiroaki Murayama", + "author_inst": "International University of Health and Welfare" + }, + { + "author_name": "Masahiro Hashizume", + "author_inst": "Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.18.21258649", "rel_title": "Large-scale screening of asymptomatic for SARS-CoV-2 variants of concern and rapid P.1 takeover, Curitiba, Brazil", @@ -723590,20 +726120,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.21.449320", - "rel_title": "The green tea catechin EGCG provides proof-of-concept for a pan-coronavirus entry inhibitor", - "rel_date": "2021-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449320", - "rel_abs": "The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has emphasized the serious threat to human health posed by emerging coronaviruses. Effective antiviral countermeasures are urgently needed as vaccine development and deployment against an emerging coronavirus takes time, even in the best-case scenario. The green tea catechin, epigallocatechin gallate (EGCG), has broad spectrum antiviral activity. We demonstrate here that EGCG prevents murine and human coronavirus infection and blocks the entry of lentiviral particles pseudotyped with spike proteins from highly pathogenic coronaviruses, as well as a bat coronavirus poised to emerge into humans. We show that EGCG treatment reduces coronavirus attachment to target cell surfaces. Our results demonstrate the potential for the development of pan-coronavirus attachment inhibitors to protect against current and future emerging coronaviruses.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.21.449205", "rel_title": "One viral sequence for each host? - The neglected within-host diversity as the main stage of SARS-CoV-2 evolution", @@ -725051,6 +727567,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.17.448816", + "rel_title": "Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with Pol \u03b1 - Primase", + "rel_date": "2021-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448816", + "rel_abs": "The molecular mechanisms that drive the infection by the SARS-CoV-2 coronavirus - the causative agent of the COVID-19 (Coronavirus disease-2019) pandemic - are under intense current scrutiny, to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated.\n\nRecent cell-based analyses of SARS-CoV-2 protein - protein interactions have mapped the human proteins targeted by the virus. The DNA polymerase - primase complex or primosome - responsible for initiating DNA synthesis in genomic duplication - was identified as a target of nsp1 (non structural protein 1), a major virulence factor in the SARS-CoV-2 infection.\n\nHere, we report the biochemical characterisation of the interaction between nsp1 and the primosome and the cryoEM structure of the primosome - nsp1 complex. Our data provide a structural basis for the reported interaction between the primosome and nsp1. They suggest that Pol - primase plays a part in the immune response to the viral infection, and that its targeting by SARS-CoV-2 aims to interfere with such function.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mairi L Kilkenny", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Charlotte E Veale", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Amir Guppy", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Steven W Hardwick", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Dimitri Y Chirgadze", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Neil J Rzechorzek", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Joseph D Maman", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Luca Pellegrini", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.06.18.449086", "rel_title": "Differences in IgG antibody responses following BNT162b2 and mRNA-1273 Vaccines", @@ -725615,121 +728178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.18.21258689", - "rel_title": "Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258689", - "rel_abs": "We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern, but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of two months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7s set of mutations.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Ben Jackson", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Maciej F Boni", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Matthew J Bull", - "author_inst": "Public Health Wales NHS Trust" - }, - { - "author_name": "Amy Colleran", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Rachel M Colquhoun", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Alistair Darby", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Sam Haldenby", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Verity Hill", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Anita Lucaci", - "author_inst": "University of Liverpool" - }, - { - "author_name": "John T McCrone", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Samuel Nicholls", - "author_inst": "University of Birmingham" - }, - { - "author_name": "\u00c1ine O'Toole", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Nicole Pacchiarini", - "author_inst": "Public Health Wales NHS Trust" - }, - { - "author_name": "Radoslaw Poplawski", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Emily Scher", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Flora Todd", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Hermione Webster", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Mark Whitehead", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Claudia Wierzbicki", - "author_inst": "University of Liverpool" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "" - }, - { - "author_name": "Nicholas J Loman", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Thomas R Connor", - "author_inst": "Cardiff University" - }, - { - "author_name": "David L Robertson", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Oliver L Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.17.448891", "rel_title": "A Robust High-throughput Fluorescent Polarization Assay for the Evaluation and Screening of SARS-CoV-2 Fusion Inhibitors", @@ -726829,6 +729277,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.15.21258928", + "rel_title": "Benefits of Surveillance Testing and Quarantine in a SARS-CoV-2 Vaccinated Population of Students on a University Campus", + "rel_date": "2021-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258928", + "rel_abs": "Surveillance testing and quarantine have been effective measures for limiting SARS-CoV-2 transmission on university campuses. However, the importance of these measures needs to be re-evaluated in the context of a complex and rapidly changing environment that includes vaccines, variants, and waning immunity. Also, recent guidelines from the CDC suggest that vaccinated students do not need to participate in surveillance testing. We used an agent-based SEIR model to evaluate the utility of surveillance testing and quarantine in a fully vaccinated student population where vaccine effectiveness may be impacted by the type of vaccination, the presence of variants, and the loss of vaccine-induced or natural immunity over time. We found that weekly surveillance testing at 90% vaccine effectiveness only marginally reduces viral transmission as compared to no testing. However, at 50%-75% effectiveness, surveillance testing can provide over 10-fold reduction in the number of infections on campus over the course of the semester. We also show that a 10-day quarantine protocol for exposures has limited effect on infections until vaccine effectiveness drops to 50%, and that increased surveillance testing for exposures is at least as effective as quarantine at limiting infections. Together these findings provide a foundation for universities to design appropriate mitigation protocols for the 2021-2022 academic year.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Francis C. Motta", + "author_inst": "Department of Mathematical Sciences, Florida Atlantic University" + }, + { + "author_name": "Kevin A. McGoff", + "author_inst": "Department of Mathematics and Statistics, University of North Carolina, Charlotte" + }, + { + "author_name": "Anastasia Deckard", + "author_inst": "Office of Information Technology, Duke University" + }, + { + "author_name": "Cameron R. Wolfe", + "author_inst": "Department of Medicine, Duke University School of Medicine" + }, + { + "author_name": "M. Anthony Moody", + "author_inst": "Department of Pediatrics, Duke University School of Medicine" + }, + { + "author_name": "Kyle Cavanaugh", + "author_inst": "Department of Family Medicine, Duke University School of Medicine" + }, + { + "author_name": "Thomas N. Denny", + "author_inst": "Duke Human Vaccine Institute & Department of Medicine, Duke University School of Medicine" + }, + { + "author_name": "John Harer", + "author_inst": "Department of Mathematics, Duke University" + }, + { + "author_name": "Steven B. Haase", + "author_inst": "Department of Biology, Duke University & Department of Medicine, Duke University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.16.21258981", "rel_title": "Remdesivir to treat COVID-19: can dosing be optimized?", @@ -727593,29 +730092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.17.448868", - "rel_title": "Quantitative Analysis of Genomic Sequences of Virus RNAs Using a Metric-Based Algorithm", - "rel_date": "2021-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448868", - "rel_abs": "This work aims to study the virus RNAs using a novel algorithm for accelerated exploring any-length genomic fragments in sequences using Hamming distance between the binary-expressed characters of an RNA and query patterns. The found repetitive genomic sub-sequences of different lengths were placed on one plot as genomic trajectories (walks) to increase the effectiveness of geometrical multi-scale genomic studies. Primary attention was paid to the building and analysis of the atg-triplet walks composing the schemes or skeletons of the viral RNAs. The 1-D distributions of these codon-starting atg-triplets were built with the single-symbol walks for full-scale analyses. The visual examination was followed by calculating statistical parameters of genomic sequences, including the estimation of geometry deviation and fractal properties of inter-atg distances. This approach was applied to the SARS CoV-2, MERS CoV, Dengue and Ebola viruses, whose complete genomic sequences are taken from GenBank and GISAID databases. The relative stability of these distributions for SARS CoV-2 and MERS CoV viruses was found, unlike the Dengue and Ebola distributions that showed an increased deviation of their geometrical and fractal characteristics of atg-distributions. The results of this work can found in classification of the virus families and in the study of their mutation.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alex Belinsky", - "author_inst": "MAchH-3DP Inc." - }, - { - "author_name": "Guennadi Kouzaev", - "author_inst": "Norwegian University of Science and Technology-NTNU" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.06.10.21258709", "rel_title": "Effectiveness and Safety of Niclosamaide as Add-on Therapy to the Standard of Care Measures in COVID-19 Management: Randomized controlled clinical trial", @@ -729199,6 +731675,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.448611", + "rel_title": "SARS-CoV-2 Viral Replication in a High Throughput Human Primary Epithelial Airway Organ Model", + "rel_date": "2021-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.15.448611", + "rel_abs": "COVID-19 emerged as a worldwide pandemic early in 2020, and at this writing has caused over 170 million cases and 3.7 million deaths worldwide, and almost 600,000 deaths in the United States. The rapid development of several safe and highly efficacious vaccines stands as one of the most extraordinary achievements in modern medicine, but the identification and administration of efficacious therapeutics to treat patients suffering from COVID-19 has been far less successful. A major factor limiting progress in the development of effective treatments has been a lack of suitable preclinical models for the disease, currently reliant upon various animal models and in vitro culture of immortalized cell lines. Here we report the first successful demonstration of SARS-CoV-2 infection and viral replication in a human primary cell-based organ-on-chip, leveraging a recently developed tissue culture platform known as PREDICT96. This successful demonstration of SARS-CoV-2 infection in human primary airway epithelial cells derived from a living donor represents a powerful new pathway for disease modeling and an avenue for screening therapeutic candidates in a high throughput platform.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Christine R Fisher", + "author_inst": "Draper" + }, + { + "author_name": "Felix Mba Medie", + "author_inst": "Draper" + }, + { + "author_name": "Rebeccah J Luu", + "author_inst": "Draper" + }, + { + "author_name": "Rob Gaibler", + "author_inst": "Draper" + }, + { + "author_name": "Caitlin R Miller", + "author_inst": "Draper" + }, + { + "author_name": "Thomas J Mulhern", + "author_inst": "Draper" + }, + { + "author_name": "Vidhya Vijayakumar", + "author_inst": "Draper" + }, + { + "author_name": "Elizabeth Marr", + "author_inst": "Draper" + }, + { + "author_name": "Jehan Alladina", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Benjamin Medoff", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey T Borenstein", + "author_inst": "Draper" + }, + { + "author_name": "Ashley L Gard", + "author_inst": "Draper" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.06.12.21258829", "rel_title": "The Spectre of SARS-CoV-2 in the Ambient Urban Natural Water in Ahmedabad and Guwahati: A Tale of Two Cities", @@ -730130,29 +732669,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.06.14.448413", - "rel_title": "Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses", - "rel_date": "2021-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.448413", - "rel_abs": "The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for propagation of coronaviruses. A combination of genomic features that make up PFE--the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements--puts severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess evolutionary dynamics of PFE in great detail. Here we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well defined phylogenetic specificity. We further examined sequencing data from over 350,000 complete genomes and 55,000 raw read datasets to demonstrate exceptional conservation of the PFE region.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Han Mei", - "author_inst": "Penn State" - }, - { - "author_name": "Anton Nekrutenko", - "author_inst": "Penn State" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.06.14.448421", "rel_title": "MMMVI: Detecting SARS-CoV-2 Variants of Concern in Metagenomic Samples", @@ -731056,6 +733572,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.21258346", + "rel_title": "Antibody response after a single dose of ChAdOx1-nCOV (Covishield) vaccine in subjects with prior SARS-CoV2 infection: Is a single dose sufficient?", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258346", + "rel_abs": "It is crucial to know whether a single dose of vaccine against SARS-CoV-2 is sufficient to elicit immune response in previously infected people in India. A total of 121 participants (baseline seropositive 46 and seronegative 75) were included to study the immune response to ChAdOx1-nCOV (Covishield) vaccine in previously infected or uninfected people. IgG antibodies were estimated at three different time intervals, i.e. pre-vaccination, 25-35 days post 1st vaccination and 25-35 days post 2nd vaccination. The IgG antibody titre was significantly high among previous seropositive subjects with single dose of vaccine compared to seronegative group with both doses of vaccine respectively (4.59{+/-}1.04 vs 3.08{+/-}1.22, p-value: <0.0001).\n\nIn conclusion, a single dose of Covishield(R) vaccine might be sufficient to induce an effective immune responsein subjects with prior SARS-CoV2 infection. Stratifying vacinees based on their SARS-CoV2 IgG antibody titre before vaccination would help in meeting the increasing vaccine demand and could be effective to circumvent further wave of the pandemic in India.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Biswajyoti Borkakoty", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Mandakini Das Sarmah", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Chandra Kanta Bhattacharjee", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Nargis Bali", + "author_inst": "Sher-i- Kasmir Institute of Medical Science, Jammu and Kasmir, India" + }, + { + "author_name": "Gayatri Gogoi", + "author_inst": "Assam Medical College and Hospital, Dibrugarh, Assam, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.14.21258871", "rel_title": "SARS-CoV-2 Spike protein binding of glycated serum albumin - its potential role in the pathogenesis of the COVID-19 clinical syndromes and bias towards individuals with pre-diabetes/type 2 diabetes & metabolic diseases.", @@ -731508,37 +734059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.14.21257728", - "rel_title": "Moral injury and wellbeing in essential workers during the Covid-19 pandemic: Local survey findings", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21257728", - "rel_abs": "Essential workers have faced many difficult situations working during in the pandemic. Staff may feel that they, or other people, have acted wrongly and be distressed by this. This represents moral injury, which has been linked with significant mental ill health.\n\nThis survey asked essential workers in County Durham and Darlington about their experiences during the first wave of the pandemic and anything they felt would help. Wellbeing and moral injury were rated using sliders.\n\nThere were 566 responses. A majority of respondents reported feeling troubled by other peoples actions they felt were wrong (60% scored over 40, where 0 is \"not at all troubled\" and 100 \"very troubled\", median score=52.5). Respondents were generally less troubled by their own actions (median score=3). Wellbeing and moral injury scores varied by employment sector (e.g. NHS staff were more troubled by the actions of others than non-NHS staff).\n\nStaff suggestions included regular supervisor check-ins, ensuring kindness from everyone, fair rules and enforcement and improving communication and processes. Respondents offered simple, practical actions that could be taken by leaders at team, organisation, societal and government policy levels to tackle moral injury and the underlying causes of moral injurious environments.\n\nUsing these findings to develop a strategy to address moral injury is important, not only for staff wellbeing, but staff retention and continued delivery of vital services in these challenging times. Working together, we can seek to reduce and mitigate \"moral injury\" the same way we do for other physical \"injuries\" in the workplace.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Catherine Anne Guy", - "author_inst": "Tees, Esk and Wear Valleys NHS Foundation Trust" - }, - { - "author_name": "Edward Kunonga", - "author_inst": "Tees, Esk and Wear Valleys NHS Foundation Trust" - }, - { - "author_name": "Angela Kennedy", - "author_inst": "Cumbria, Northumberland, Tyne and Wear NHS Foundation Trust" - }, - { - "author_name": "Paras Patel", - "author_inst": "Tees, Esk and Wear Valleys NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.13.21258654", "rel_title": "Analysis of Social Combinations of Coronavirus Vaccination: Evidence from a Conjoint Analysis", @@ -732311,6 +734831,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.11.21258564", + "rel_title": "Chronic fatigue and post-exertional malaise in people living with long COVID", + "rel_date": "2021-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258564", + "rel_abs": "PurposePeople living with long COVID describe a high symptom burden, and a more detailed assessment of chronic fatigue and post-exertional malaise (PEM) may inform the development of rehabilitation recommendations. The aims of this study were to use validated questionnaires to measure the severity of fatigue and compare this with normative data and thresholds for clinical relevance in other diseases; measure and describe the impact of PEM; and assess symptoms of dysfunctional breathing, self-reported physical activity/sitting time, and health-related quality of life.\n\nMethodsThis was an observational study involving an online survey for adults living with long COVID (data collection from February-April, 2021) following a confirmed or suspected SARS-CoV-2 infection. Questionnaires included the Functional Assessment of Chronic Illness Therapy-Fatigue Scale (FACIT-F) and DePaul Symptom Questionnaire-Post-Exertional Malaise.\n\nResultsAfter data cleaning, n=213 participants were included in the analysis. Participants primarily identified as women (85.5%), aged 40-59 (78.4%), who had been experiencing long COVID symptoms for [≥]6 months (72.3%). The total FACIT-F score was 18{+/-}10 (where the score can range from 0-52, and a lower score indicates more severe fatigue), and 71.4% were experiencing chronic fatigue. Post-exertional symptom exacerbation affected most participants, and 58.7% met the scoring thresholds used in people living with myalgic encephalomyelitis/chronic fatigue syndrome. PEM occurred alongside a reduced capacity to work, be physically active, and function both physically and socially.\n\nConclusionLong COVID is characterized by chronic fatigue that is clinically relevant and is at least as severe as fatigue in several other clinical conditions, including cancer. PEM appears to be a common and significant challenge for the majority of this patient group. Patients, researchers, and allied health professionals are seeking information on safe rehabilitation for people living with long COVID, particularly regarding exercise. Fatigue and post-exertional symptom exacerbation must be monitored and reported in studies involving interventions for people with long COVID.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rosie Twomey", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jessica DeMars", + "author_inst": "Breath Well Physio" + }, + { + "author_name": "Kelli Franklin", + "author_inst": "Patient Partner" + }, + { + "author_name": "S. Nicole Culos-Reed", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jason Weatherald", + "author_inst": "University of Calgary" + }, + { + "author_name": "James G Wrightson", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.11.21258445", "rel_title": "Estimating the Burden of SARS-CoV-2 among the Rohingya Refugees", @@ -733107,25 +735666,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.06.10.21258589", - "rel_title": "Early evidence for the safety of certain COVID-19 vaccines using empirical Bayesian modeling from VAERS", - "rel_date": "2021-06-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258589", - "rel_abs": "The advent of vaccines against SARS-CoV-2 ushered in an unprecedented global response to COVID-19, with the largest and most ambitious mass vaccination campaign in human history. The scale of this effort means that safety signals suggesting adverse effects may only be detectable using passive reporting. This paper examines reports to the CDC/FDAs VAERS system in the first six months of 2021, using an empirical Bayesian model with a gamma Poisson shrinker to identify potential safety signals from COVID-19 vaccines currently on the U.S. market. Based on this preliminary data, it is concluded that the COVID-19 vaccines safety significantly exceeds that of previously marketed vaccines, and other than a known risk of thrombotic events, no safety signals of concern emerge.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Chris von Csefalvay", - "author_inst": "Starschema" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.09.21258668", "rel_title": "Modeling and reviewing analysis of the COVID-19 epidemic in Algeria with diagnostic shadow", @@ -734133,6 +736673,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.06.08.21258533", + "rel_title": "The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258533", + "rel_abs": "BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data.\n\nMethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality.\n\nResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive.\n\nConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.\n\nSummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Aleksandra Kovacevic", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Matthieu Domenech de Cell\u00e8s", + "author_inst": "Max Planck Institute for Infection Biology" + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Univ Versailles Saint Quentin / Institut Pasteur / Inserm" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.10.21254528", "rel_title": "NEWS-2 score assessment of inpatient referral during the COVID 19 epidemic", @@ -734705,53 +737280,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.06.08.21258002", - "rel_title": "Rising Through the Pandemic: A scoping review of quality improvement in public health during the COVID-19 pandemic", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258002", - "rel_abs": "BackgroundThe COVID-19 pandemic generated a growing interest in and need for evidence-based tools to facilitate the implementation of emergency management strategies within public health practice. Quality improvement (QI) has been identified as a key framework and philosophy to guide organizational emergency response efforts; however, the nature and extent to which it has been used in public health settings during the COVID-19 pandemic remains unclear.\n\nMethodsWe conducted a scoping review of literature published January 2020 - February 2021 and focused on the topic of QI at public health agencies during the COVID-19 pandemic. The search was conducted on four bibliographic databases, in addition to a supplementary grey literature search using custom Google search engines and targeted website search methods. Of the 1,878 peer-reviewed articles assessed, 15 records met the inclusion criteria. An additional 11 relevant records were identified during the grey literature search, for a total of 26 records included in the scoping review.\n\nResultsRecords were organized into five topics: 1) collaborative problem solving and analysis with stakeholders; 2) supporting learning and capacity building in QI; 3) learning from past emergencies; 4) implementing QI methods during COVID-19; and 5) evaluating performance using frameworks/indicators.\n\nConclusionsThe literature indicates that QI-oriented activities are occurring at the organizational and program levels to enhance COVID-19 response. To optimize the benefits that QI approaches and methodologies may offer, it is important for public health agencies to focus on both widespread integration of QI as part of an organizations management philosophy and culture, as well as project level activities at all stages of the emergency management cycle.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Xinjie Cindy Yin", - "author_inst": "Ontario Agency for Health Promotion and Protection (Public Health Ontario)" - }, - { - "author_name": "Michelle Pang", - "author_inst": "Ontario Agency for Health Promotion and Protection (Public Health Ontario)" - }, - { - "author_name": "Madelyn Law", - "author_inst": "Brock University, Department of Health Sciences" - }, - { - "author_name": "Fiona Guerra", - "author_inst": "Ontario Agency for Health Promotion and Protection (Public Health Ontario)" - }, - { - "author_name": "Tracey O'Sullivan", - "author_inst": "University of Ottawa, Faculty of Health Sciences. LIFE Research Institute, University of Ottawa." - }, - { - "author_name": "Rachel E. Laxer", - "author_inst": "Ontario Agency for Health Promotion and Protection (Public Health Ontario)" - }, - { - "author_name": "Brian Schwartz", - "author_inst": "Ontario Agency for Health Promotion and Protection (Public Health Ontario)" - }, - { - "author_name": "Yasmin Khan", - "author_inst": "Ontario Agency for Health Promotion and Protection (Public Health Ontario). University of Toronto, Dalla Lana School of Public Health. University of Toronto, Di" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.06.05.21258311", "rel_title": "Antibody Responses after SARS-CoV-2 Vaccination in Lymphoma", @@ -735907,6 +738435,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.11.448011", + "rel_title": "B.1.1.7 and B.1.351 SARS-CoV-2 variants display enhanced Spike-mediated fusion", + "rel_date": "2021-06-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.11.448011", + "rel_abs": "Severe COVID-19 is characterized by lung abnormalities, including the presence of syncytial pneumocytes. Syncytia form when SARS-CoV-2 spike protein expressed on the surface of infected cells interacts with the ACE2 receptor on neighbouring cells. The syncytia forming potential of spike variant proteins remain poorly characterized. Here, we first assessed Alpha and Beta spread and fusion in cell cultures. Alpha and Beta replicated similarly to D614G reference strain in Vero, Caco-2, Calu-3 and primary airway cells. However, Alpha and Beta formed larger and more numerous syncytia. Alpha, Beta and D614G fusion was similarly inhibited by interferon induced transmembrane proteins (IFITMs). Individual mutations present in Alpha and Beta spikes differentially modified fusogenicity, binding to ACE2 and recognition by monoclonal antibodies. We further show that Delta spike also triggers faster fusion relative to D614G. Thus, SARS-CoV-2 emerging variants display enhanced syncytia formation.\n\nSynopsisThe Spike protein of the novel SARS-CoV-2 variants are comparative more fusogenic than the earlier strains. The mutations in the variant spike protein differential modulate syncytia formation, ACE2 binding, and antibody escape.\n\nO_LIThe spike protein of Alpha, Beta and Delta, in the absence of other viral proteins, induce more syncytia than D614G\nC_LIO_LIThe ACE2 affinity of the variant spike proteins correlates to their fusogenicity\nC_LIO_LIVariant associated mutations P681H, D1118H, and D215G augment cell-cell fusion, while antibody escape mutation E484K, K417N and {Delta}242-244 hamper it.\nC_LIO_LIVariant spike-mediated syncytia formation is effectively restricted by IFITMs\nC_LI", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Maaran Michael Rajah", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Mathieu Hubert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Elodie Bishop", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nell Saunders", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "R\u00e9my Robinot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ludivine Grzelak", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jeremy Dufloo", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Stacy Gellenoncourt", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Alice Bongers", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marija Zivaljic", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fran\u00e7oise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Lisa Chakrabarti", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.10.447999", "rel_title": "A combination of RBD and NTD neutralizing antibodies limits the generation of SARS-CoV-2 spike neutralization-escape mutants", @@ -736659,85 +739274,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.08.21258518", - "rel_title": "Immunity to SARS-CoV-2 persists 9 months post-symptoms with an altered T cell phenotype compared to influenza A virus-specific memory", - "rel_date": "2021-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258518", - "rel_abs": "SARS-CoV-2 induces T cell, B cell and antibody responses that are detected for several months in recovered individuals. Whether this response resembles a typical respiratory viral infection is a matter of debate. Here we followed T cell and antibody responses in 24 mainly non-hospitalized SARS-CoV-2 recovered subjects at two time points (median of 45- and 145-days post-symptom onset). Antibody responses were detected in 95% of subjects, with a strong correlation between plasma and salivary anti-S and anti-RBD IgG, as well as a correlation between circulating T follicular helper cells and the SARS-CoV-2-specific IgG response. Based on intracellular cytokine production or proliferation, CD4+ T cell responses to SARS-CoV-2 were detected in all subjects, decaying with a half-life of 5-6 months for S-specific IL-2-producing cells. CD4+ responses were largely of the T helper 1 phenotype, but with a lower ratio of IFN-{gamma}: IL-2 producing cells and a lower frequency of CD8+: CD4+ T cells compared to influenza A virus-(IAV)-specific memory responses within the same subjects. Analysis of secreted molecules also revealed a lower ratio of IFN-{gamma}: IL-2 and IFN-{gamma}: IL-6 and an altered cytotoxic profile for S- and N-specific compared to IAV-specific responses. These data suggest that the memory T-cell phenotype after a single infection with SARS-CoV-2 persists over time, with an altered cytokine and cytotoxic profile compared to long term memory to IAV within the same subjects.\n\nOne Sentence SummaryImmunity to SARS-CoV-2 in a cohort of patients, mainly with mild COVID-19 disease, persists to 9 months with an altered T cell cytokine and cytotoxicity profile compared to influenza A virus-specific memory T cells from the same subjects.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jaclyn C Law", - "author_inst": "University of Toronto" - }, - { - "author_name": "Melanie Girard", - "author_inst": "University of Toronto" - }, - { - "author_name": "Gary Y.C. Chao", - "author_inst": "University of Toronto" - }, - { - "author_name": "Lesley A Ward", - "author_inst": "University of Toronto" - }, - { - "author_name": "Baweleta Isho", - "author_inst": "University of Toronto" - }, - { - "author_name": "Bhavisha Rathod", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System" - }, - { - "author_name": "Karen Colwill", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System" - }, - { - "author_name": "Zhijie Li", - "author_inst": "University of Toronto" - }, - { - "author_name": "James M Rini", - "author_inst": "University of Toronto" - }, - { - "author_name": "Feng Yun Yue", - "author_inst": "University of Toronto" - }, - { - "author_name": "Samira Mubareka", - "author_inst": "Sunnybrook Research Institute and University of Toronto" - }, - { - "author_name": "Allison J McGeer", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mt. Sinai Hospital, Sinai Health System and University of Toronto" - }, - { - "author_name": "Mario A Ostrowski", - "author_inst": "University of Toronto and Keenan research centre of St. Michaels hospital" - }, - { - "author_name": "Jennifer L Gommerman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Anne-Claude Gingras", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital; Sinai Health System" - }, - { - "author_name": "Tania H Watts", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.06.10.21257749", "rel_title": "Inferring global-scale temporal latent topics from news reports to predict public health interventions for COVID-19", @@ -737837,6 +740373,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.06.21258425", + "rel_title": "Functional dependence of COVID-19 growth rate on lockdown conditions and rate of vaccination.", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258425", + "rel_abs": "It is shown that derived from the solution of differential equations analytical model adequately describes development epidemics with changes in both lockdown conditions and the effective rate of mass vaccination of the population. As in previous studies, the control calculations are in good agreement with observations at all stages of epidemic growth. One of the two model coefficients is uniquely related to the lockdown efficiency parameter. We obtained an approximate correlation between this parameter and the main conditions of lockdown, in particular, physical distancing, reduction in social contacts and strictness of the mask regime.\n\nThe calculation of the incident over a seven-day period using the proposed model is in good agreement with the observational data. Analysis of both curves shows that a better agreement can be obtained by taking into account the lag time of the epidemic response of about 10 days.\n\nFrom the reverse calculation a time-varying curve of the infection rate associated with the \"new\" virus strain under mutation conditions is obtained, which is qualitatively confirmed by the sequencing data.\n\nBased on these studies, it is possible to conclude that the ASILV analytical model developed here can be used to reliably and promptly predict epidemic development under conditions of lockdown and mass vaccination without the use of numerical methods.\n\nThe functional relationships identified allow us to conduct a rapid analysis of the impact of each of the model parameters on the overall process of the epidemic.\n\nIn contrast to previous studies, the calculations of the proposed model were performed using EXCEL, rather than a standard calculator. This is due to the need to account for multiple changes in lockdown conditions and vaccination rates.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Felix Mairanowski", + "author_inst": "Husmann Rus" + }, + { + "author_name": "Denis Below", + "author_inst": "Potsdam Universitet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.09.21258609", "rel_title": "Depressive and anxiety symptoms and COVID-19-related factors among men and women in Nigeria", @@ -738729,25 +741288,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.06.06.21258428", - "rel_title": "g-CXR-Net: A Graphic Application for the Rapid Recognition of SARS-CoV-2 from Chest X-Rays", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258428", - "rel_abs": "g-CXR-Net is a graphic application for the rapid recognition of SARS-CoV-2 from Antero/Posterior chest X-rays. It employs the Artificial Intelligence engine of CXR-Net (arXiv:2103.00087) to generate masks of the lungs overlapping the heart and large vasa, probabilities for Covid vs. non-Covid assignment, and high resolution heat maps that identify the SARS associated lung regions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Domenico L Gatti", - "author_inst": "Wayne State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.06.06.21258430", "rel_title": "WHAT ABOUT USING SNIFFIN STICKS 12 SCREENING TEST TO IDENTIFY POST-COVID-19 OLFACTORY DISORDERS?", @@ -739891,6 +742431,153 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.09.447527", + "rel_title": "Second Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern", + "rel_date": "2021-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.09.447527", + "rel_abs": "Recently emerged SARS-CoV-2 variants show resistance to some antibodies that were authorized for emergency use. We employed hybridoma technology combined with authentic virus assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize new variants of SARS-CoV-2. AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 and B.1.351. Finally, the combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. The neutralizing properties were fully reproduced in chimeric mouse-human versions, which may represent a promising tool for COVID-19 therapy.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Branislav Kovacech", + "author_inst": "AXON COVIDAX a. s., Slovakia" + }, + { + "author_name": "Lubica Fialova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Peter Filipcik", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Monika Zilkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Rostislav Skrabana", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Natalia Paulenka-Ivanovova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Andrej Kovac", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Denisa Palova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Gabriela Paulikova Rolkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Katarina Tomkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Natalia Turic Csokova", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Karina Markova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michaela Skrabanova", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Kristina Sinska", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Neha Basheer", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Petra Majerova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Jozef Hanes", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Vojtech Parrak", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Prcina", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Ondrej Cehlar", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Martin Cente", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Juraj Piestansky", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Fresser", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Novak", + "author_inst": "Axon Neuroscience SE, Cyprus" + }, + { + "author_name": "Monika Slavikova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Kristina Borsova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Microbiology and Virology, Faculty of Natural" + }, + { + "author_name": "Viktoria Cabanova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Bronislava Brejova", + "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Tomas Vinar", + "author_inst": "Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Jozef Nosek", + "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Boris Klempa", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Norbert Zilka", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Eva Kontsekova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.09.21258553", "rel_title": "Analysis of cell-mediated immunity in people with long Covid.", @@ -740623,85 +743310,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.06.08.447491", - "rel_title": "ROS/RNS balancing, aerobic fermentation regulation and cell cycle control a complex early trait ('CoV-MAC-TED') for combating SARS-CoV-2-induced cell reprogramming", - "rel_date": "2021-06-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.08.447491", - "rel_abs": "In a perspective entitled From plant survival under severe stress to anti-viral human defense we raised and justified the hypothesis that transcript level profiles of justified target genes established from in vitro somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named ReprogVirus was proposed for in vitro-scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the ReprogVirus platform was initiated. This initiative aims to identify in a common effort across scientific boundaries critical virus footprints from diverse virus origins and variants as a basis for anti-viral strategy design. This approach is open for validation and extension.\n\nIn the present study, we initiated validation by experimental transcriptome data available in public domain combined with advancing plant wet lab research. We compared plant-adapted transcriptomes according to RegroVirus complemented by alternative oxidase (AOX) genes during de novo programming under SE-inducing conditions with in vitro corona virus-induced transcriptome profiles. This approach enabled identifying a major complex trait for early de novo programming during SARS-CoV-2 infection, called CoV-MAC-TED. It consists of unbalanced ROS/RNS levels, which are connected to increased aerobic fermentation that links to alpha-tubulin-based cell restructuration and progression of cell cycle.\n\nWe conclude that anti-viral/anti-SARS-CoV-2 strategies need to rigorously target CoV-MAC-TED in primary infected nose and mouth cells through prophylactic and very early therapeutic strategies. We also discuss potential strategies in the view of the beneficial role of AOX for resilient behavior in plants.\n\nFurthermore, following the general observation that ROS/RNS equilibration/redox homeostasis is of utmost importance at the very beginning of viral infection, we highlight that de-stressing disease and social handling should be seen as essential part of anti-viral/anti-SARS-CoV-2 strategies.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jose Helio Costa", - "author_inst": "1.\tFunctional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil" - }, - { - "author_name": "Gunasekharan Mohanapriya", - "author_inst": "Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India" - }, - { - "author_name": "Bharadwaj Revuru", - "author_inst": "Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India" - }, - { - "author_name": "Carlos Noceda", - "author_inst": "Cell and Molecular Biotechnology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universi" - }, - { - "author_name": "Karine Leitao Lima Thiers", - "author_inst": "Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil" - }, - { - "author_name": "Shahid Aziz", - "author_inst": "1.\tFunctional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil" - }, - { - "author_name": "Shivani Srivatsava", - "author_inst": "Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources, Institute (TERI), TERI Gram, Gual Pahari, Gurugram, India" - }, - { - "author_name": "Manuela Oliveira", - "author_inst": "Department of Mathematics and CIMA - Center for Research on Mathematics and its Applications, Universidade de Evora, Evora, Portugal" - }, - { - "author_name": "Kapuganti Jagadis Gupta", - "author_inst": "National Institute of Plant Genome Research, Aruna Asaf Marg, New Delhi, India" - }, - { - "author_name": "Aparajita Kumari", - "author_inst": "National Institute of Plant Genome Research, Aruna Asaf Marg, New Delhi, India" - }, - { - "author_name": "Debabrata Sircar", - "author_inst": "Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand, India" - }, - { - "author_name": "Sarma Rajeev Kumar", - "author_inst": "Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India" - }, - { - "author_name": "Arvind Achra", - "author_inst": "Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi, India." - }, - { - "author_name": "Ramalingam Sathishkumar", - "author_inst": "Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India" - }, - { - "author_name": "Alok Adhloeya", - "author_inst": "Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources, Institute (TERI), TERI Gram, Gual Pahari, Gurugram, India." - }, - { - "author_name": "Birgit Arnholdt-Schmitt", - "author_inst": "1.\tFunctional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.06.08.447530", "rel_title": "Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro", @@ -741837,6 +744445,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.06.05.21258407", + "rel_title": "Prediction of severe COVID-19 cases requiring intensive care in Osaka, Japan", + "rel_date": "2021-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.05.21258407", + "rel_abs": "BackgroundTo avoid exhaustion of medical resources by COVID-19 care, policy-makers must predict care needs, specifically estimating the proportion of severe cases likely to require intensive care. In Osaka prefecture, Japan, the number of these severe cases exceeded the capacity of ICU units prepared for COVID-19 from mid-April, 2021.\n\nObjectiveThis study used a statistical model to elucidate dynamics of severe cases in Osaka and validated the model through prospective testing.\n\nMethodsThe study extended from April 3, 2020 through April 26, 2021 in Osaka prefecture, Japan prefecture. We regressed the number of severe cases on the number of severe cases the day prior and the newly onset patients of more than 21 days prior.\n\nResultsWe selected the number of severe cases the day prior and the number of newly onset patients on 21 and 28 days prior as explanatory variables for explaining the number of severe cases based on the adjusted determinant coefficient. The adjusted coefficient of determination was greater than 0.995 and indicated good fit. Prospective out of sample three-week prediction forecast the peak date precisely, but the level was not t.\n\nDiscussion and ConclusionA reason for the gap in the prospective prediction might be the emergence of variant strains.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.04.21257951", "rel_title": "Early Epidemiological Evidence of Public Health Value of WA Notify, a Smartphone-based Exposure Notification Tool: Modeling COVID-19 Cases Averted in Washington State", @@ -742593,45 +745228,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.07.447338", - "rel_title": "In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR", - "rel_date": "2021-06-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.07.447338", - "rel_abs": "A number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases - as seen with the B.1.1.7 variant - can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charite RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values observed with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fee Zimmermann", - "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" - }, - { - "author_name": "Maria Urban", - "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" - }, - { - "author_name": "Christian Krueger", - "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" - }, - { - "author_name": "Mathias Walter", - "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" - }, - { - "author_name": "Roman Woelfel", - "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" - }, - { - "author_name": "Katrin Zwirglmaier", - "author_inst": "Bundeswehr Institute of Microbiology, Munich, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.06.07.447334", "rel_title": "Dynamics and self-assembly of the SARS-CoV-2 spike transmembrane domain", @@ -743447,6 +746043,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.03.21258307", + "rel_title": "Loss of recognition of SARS-CoV-2 B.1.351 variant spike epitopes but overall preservation of T cell immunity", + "rel_date": "2021-06-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258307", + "rel_abs": "SARS-CoV-2 variants have emerged that escape neutralization and potentially impact vaccine efficacy. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is poorly studied. We assessed both neutralizing antibody and T cell responses in 44 South African COVID-19 patients infected either with B.1.351, now dominant in South Africa, or infected prior to its emergence ( first wave), to provide an overall measure of immune evasion. We show for the first time that robust spike-specific CD4 and CD8 T cell responses were detectable in B.1.351-infected patients, similar to first wave patients. Using peptides spanning only the B.1.351 mutated regions, we identified CD4 T cell responses targeting the wild type peptides in 12/22 (54.5%) first wave patients, all of whom failed to recognize corresponding B.1.351-mutated peptides (p=0.0005). However, responses to the mutated regions formed only a small proportion (15.7%) of the overall CD4 response, and few patients (3/44) mounted CD8 responses that targeted the mutated regions. First wave patients showed a 12.7 fold reduction in plasma neutralization of B.1.351. This study shows that despite loss of recognition of immunodominant CD4 epitope(s), overall CD4 and CD8 T cell responses to B.1.351 are preserved. These observations may explain why, despite substantial loss of neutralizing antibody activity against B.1.351, several vaccines have retained the ability to protect against severe COVID-19 disease.\n\nOne Sentence SummaryT cell immunity to SARS-CoV-2 B.1.351 is preserved despite some loss of variant epitope recognition by CD4 T cells.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Roanne Keeton", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Thandeka Moyo-Gwete", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Tandile Hermanus", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Prudence Kgagudi", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Richard Baguma", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Houriiyah Tegally", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)" + }, + { + "author_name": "Deelan Doolabh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Arash Iranzadeh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Lynn Tyers", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Hygon Mutavhatsindi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marius Tincho", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ntombi Benede", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Gert Marais", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Lionel Chinhoyi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Mathilda Mennen", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sango Skelem", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elsa Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "- SA-CIN", + "author_inst": "" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)" + }, + { + "author_name": "Carolyn Williamson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Penny Moore", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Robert Wilkinson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ntobeko Ntusi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Wendy Burgers", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.04.447160", "rel_title": "Drug Repurposing for the SARS-CoV-2 Papain-Like Protease", @@ -744103,41 +746818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.02.21258231", - "rel_title": "Effectiveness of mRNA COVID-19 Vaccines among Employees in an American Healthcare System", - "rel_date": "2021-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258231", - "rel_abs": "BackgroundThe mRNA SARS-CoV-2 vaccines have shown great promise in clinical trials. The purpose of this study was to evaluate the effectiveness of these vaccines under real-world conditions in the USA.\n\nMethodsEmployees of the Cleveland Clinic Health System, previously not infected with SARS-CoV-2, and working in Ohio on Dec 16, 2020, the day COVID-19 vaccination began, were included. The cumulative incidence of SARS-CoV-2 infection, over the next 5 months, was compared among those who received the vaccine and those who did not, by modeling vaccination as a time-dependent covariate in Cox proportional hazards regression analyses adjusted for the slope of the epidemic curve as a continuous time-dependent covariate.\n\nResultsOf the 46866 included employees, 28223 (60%) were vaccinated by the end of the study period. The cumulative incidence of SARS-CoV-2 infection was much higher among those not vaccinated than those vaccinated. Only 15 (0.7%) of the 2154 SARS-CoV-2 infections during the study occurred among those vaccinated. After adjusting for the slope of the epidemic curve, age, and job type, vaccination was associated with a significantly reduced risk of SARS-CoV-2 infection (HR 0.03, 95% C.I. 0.02 - 0.06, p < 0.001), corresponding to a vaccine effectiveness rate of 97.1% (95% CI 94.3 - 98.5). Vaccine effectiveness was 89.2% at 7 days and 95.0% at 14 days after the first vaccine dose.\n\nConclusionsThe mRNA SARS-CoV-2 vaccines are over 97% protective against COVID-19 in the working-age population, with substantial protection possibly apparent within a few days of the first dose.\n\nSummaryThe effectiveness of mRNA SARS-CoV-2 vaccines was evaluated among 46866 employees in an American healthcare system. After adjusting for age, job type, and the phase of the epidemic, vaccination was 97.1% effective in preventing COVID-19 among the fully vaccinated, and 89.2% protective within 7 days of the first dose.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nabin K. Shrestha", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Amy S Nowacki", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Patrick C Burke", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Paul Terpeluk", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Steven M Gordon", - "author_inst": "Cleveland Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.03.21258258", "rel_title": "Group Testing Large Populations for SARS-CoV-2", @@ -745105,6 +747785,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.03.446942", + "rel_title": "Visualization of SARS-CoV-2 infection dynamic", + "rel_date": "2021-06-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.03.446942", + "rel_abs": "Replication-competent recombinant viruses expressing reporter genes provide valuable tools to investigate viral infection. Low levels of reporter gene expressed from previous reporter-expressing rSARS-CoV-2 have jeopardized their use to monitor the dynamics of SARS-CoV-2 infection in vitro or in vivo. Here, we report an alternative strategy where reporter genes were placed upstream of the viral nucleocapsid gene followed by a 2A cleavage peptide. The higher levels of reporter expression using this strategy resulted in efficient visualization of rSARS-CoV-2 in infected cultured cells and K18 hACE2 transgenic mice. Importantly, real-time viral infection was readily tracked using a non-invasive in vivo imaging system and allowed us to rapidly identify antibodies which are able to neutralize SARS-CoV-2 infection in vivo. Notably, these reporter-expressing rSARS-CoV-2 retained wild-type virus like pathogenicity in vivo, supporting their use to investigate viral infection, dissemination, pathogenesis and therapeutic interventions for the treatment of SARS-CoV-2 in vivo.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jesus Silvas", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Juan C de la Torre", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.04.447114", "rel_title": "Sub-Picomolar Detection of SARS-CoV-2 RBD via Computationally-Optimized Peptide Beacons", @@ -745617,101 +748352,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.02.21258097", - "rel_title": "Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment LC-MS/MS Analysis", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258097", - "rel_abs": "Reliable, robust, large-scale molecular testing for SARS-CoV-2 is essential for monitoring the ongoing Covid-19 pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immunoaffinity enrichment combined with liquid chromatography - mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in PBS swab media from combined throat/nasopharynx/saliva samples.\n\nThe results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their corresponding RT-PCR readout (r=0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative readout of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct [≤]30). These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Andreas Hober", - "author_inst": "The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm. Sweden" - }, - { - "author_name": "Tran-Minh Khue Hua", - "author_inst": "The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm. Sweden" - }, - { - "author_name": "Dominic Foley", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Thomas McDonald", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Johannes P.C. Vissers", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Rebecca Pattison", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Samantha Ferries", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Sigurd Hermansson", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Ingvar Betner", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Mathias Uhlen", - "author_inst": "The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm. Sweden" - }, - { - "author_name": "Morteza Razavi", - "author_inst": "SISCAPA Assay Technologies, Inc., Washington DC; Victoria BC Canada" - }, - { - "author_name": "Richard Yip", - "author_inst": "SISCAPA Assay Technologies, Inc., Washington DC; Victoria BC Canada" - }, - { - "author_name": "Matthew E Pope", - "author_inst": "SISCAPA Assay Technologies, Inc., Washington DC; Victoria BC Canada" - }, - { - "author_name": "Terry W Pearson", - "author_inst": "SISCAPA Assay Technologies, Inc., Washington DC; Victoria BC Canada" - }, - { - "author_name": "N. Leigh Anderson", - "author_inst": "SISCAPA Assay Technologies, Inc., Washington DC; Victoria BC Canada" - }, - { - "author_name": "Amy Bartlett", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Lisa Calton", - "author_inst": "Waters Corporation, Wilmslow, UK; Milford, MA; Stockholm, Sweden" - }, - { - "author_name": "Jessica J. Alm", - "author_inst": "Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Lars Engstrand", - "author_inst": "Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Fredrik Edfors", - "author_inst": "The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm. Sweden" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.01.21258188", "rel_title": "Antibody responses to BNT162b2 mRNA COVID-19 vaccine in 2,015 healthcare workers in a single tertiary referral hospital in Japan", @@ -747039,6 +749679,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.06.01.21258172", + "rel_title": "Humoral and cellular immune response against SARS-CoV-2 variants following heterologous and homologous ChAdOx1 nCoV-19/BNT162b2 vaccination.", + "rel_date": "2021-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258172", + "rel_abs": "Cerebral venous thrombosis was reported as a rare but serious adverse event in young and middle-aged vaccinees following immunization with AstraZenecas ChAdOx1-nCov-19 vaccine. As a consequence, several European governments recommended using this vaccine only in individuals older than 60 years leaving millions of ChAd primed individuals with the decision to either receive a second shot of ChAd or a heterologous boost with mRNA-based vaccines. However, such combinations have not been tested so far. We used Hannover Medical Schools COVID-19 Contact (CoCo) Study cohort of health care professionals (HCP) to monitor ChAd primed immune responses before and three weeks after booster with ChAd or BioNTech/Pfizers BNT162b2. Whilst both vaccines boosted prime-induced immunity, BNT induced significantly higher frequencies of Spike-specific CD4 and CD8 T cells and, in particular, high titers of neutralizing antibodies against the B.1.1.7, B.1.351 and the P.1 variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2).", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Joana Barros-Martins", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Swantje Hammerschmidt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Ivan Odak", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Metodi V Stankov", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Gema Morillas Ramos", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Alexandra Jablonka", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Annika Heidemann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christiane Ritter", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Michaela Friedrichsen", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christian R Schultze-Florey", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Inga Ravens", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Willenzon Stefanie", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anja Bubke", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Jasmin Ristenpart", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anika Janssen", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "George Ssebyatika", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Guenter Bernhardt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Jan R Muench", + "author_inst": "Ulm University" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Stefan Poehlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Thomas Krey", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Berislav Bosnjak", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Reinhold Foerster", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Georg MN Behrens", + "author_inst": "Hannover Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.01.21258150", "rel_title": "Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort", @@ -747659,109 +750414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.03.446968", - "rel_title": "Enteric coronavirus infection and treatment modeled with an immunocompetent human intestine-on-a-chip", - "rel_date": "2021-06-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.03.446968", - "rel_abs": "Many patients infected with coronaviruses, such as SARS-CoV-2 and NL63 that use ACE2 receptors to infect cells, exhibit gastrointestinal symptoms and viral proteins are found in the human gastrointestinal tract, yet little is known about the inflammatory and pathological effects of coronavirus infection on the human intestine. Here, we used a human intestine-on-a-chip (Intestine Chip) microfluidic culture device lined by patient organoid-derived intestinal epithelium interfaced with human vascular endothelium to study host cellular and inflammatory responses to infection with NL63 coronavirus. These organoid-derived intestinal epithelial cells dramatically increased their ACE2 protein levels when cultured under flow in the presence of peristalsis-like mechanical deformations in the Intestine Chips compared to when cultured statically as organoids or in Transwell inserts. Infection of the intestinal epithelium with NL63 on-chip led to inflammation of the endothelium as demonstrated by loss of barrier function, increased cytokine production, and recruitment of circulating peripheral blood mononuclear cells (PMBCs). Treatment of NL63 infected chips with the approved protease inhibitor drug, nafamostat, inhibited viral entry and resulted in a reduction in both viral load and cytokine secretion, whereas remdesivir, one of the few drugs approved for COVID19 patients, was not found to be effective and it also was toxic to the endothelium. This model of intestinal infection was also used to test the effects of other drugs that have been proposed for potential repurposing against SARS-CoV-2. Taken together, these data suggest that the human Intestine Chip might be useful as a human preclinical model for studying coronavirus related pathology as well as for testing of potential anti-viral or anti-inflammatory therapeutics.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Amir Bein", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Seongmin Kim", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Girija Goyal", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Wuji Cao", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Cicely Fadel", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Arash Naziripour", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Sanjay Sharma", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Ben Swenor", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Nina LoGrande", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Atiq Nurani", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Vincent N Miao", - "author_inst": "MIT" - }, - { - "author_name": "Andrew W Navia", - "author_inst": "MIT" - }, - { - "author_name": "Carly GK Ziegler", - "author_inst": "MIT" - }, - { - "author_name": "Jose Ordovas-Montanes", - "author_inst": "MIT" - }, - { - "author_name": "Pranav Prabhala", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Min Sun Kim", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Rachelle Prantil-Baun", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Melissa Rodas", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Amanda Jiang", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Gladness Tillya", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - }, - { - "author_name": "Alex K Shalek", - "author_inst": "MIT" - }, - { - "author_name": "Donald E Ingber", - "author_inst": "Wyss Institute for Biologically Inspired Engineering at Harvard University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.05.30.21258071", "rel_title": "Implementing Mandatory Testing and a Public Health Commitment to Control COVID-19 on a College Campus", @@ -748949,6 +751601,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.05.29.21258010", + "rel_title": "Rapid and sustained decline in CXCL-10 (IP-10) annotates clinical outcomes following TNF-\u03b1 antagonist therapy in hospitalized patients with severe and critical COVID-19 respiratory failure", + "rel_date": "2021-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.29.21258010", + "rel_abs": "BackgroundA feed-forward pathological signaling loop generated by TNF and IFN-{gamma} in inflamed lung tissue, driving CXCL-10 (IP-10) and CXCL-9 chemokine-mediated activated T-cell and monocyte/macrophage tissue recruitment, may define, sustain and amplify the inflammatory biology of lethal COVID-19 respiratory failure.\n\nMethodsTo assess TNF-antagonist therapy, 18 hospitalized adults with hypoxic respiratory failure and COVID-19 pneumonia received single-dose infliximab-abda therapy 5mg/kg intravenously between April and December 2020. The primary endpoint was time to increase in oxygen saturation to fraction of inspired oxygen ratio (SpO2/FiO2) by [≥] 50 compared to baseline and sustained for 48 hours. Secondary endpoints included 28-day mortality, dynamic cytokine profiles (Human Cytokine 48-Plex Discovery Assay, Eve Technologies), secondary infections, duration of supplemental oxygen support and hospitalization.\n\nFindingsPatients were predominantly in critical respiratory failure (15/18, 83%), male (14/18, 78%), above 60 years (median 63 yrs, range 31-80), race-ethnic minorities (13/18, 72%), lymphopenic (13/18, 72%), steroid-treated (17/18, 94%), with a median ferritin of 1953ng/ml. Sixteen patients (89%) met the primary endpoint within a median of 4 days, 15/18 (83%) recovered from respiratory failure, and 14/18 (78%) were discharged in a median of 8 days and were alive at 28-day follow-up. Deaths among three patients [≥] 65yrs age with pre-existing lung disease or multiple comorbidities were attributed to secondary lung infection. Mean plasma IP-10 levels declined sharply from 9183 pg/ml to 483 pg/ml at Day 3 and further to 146 pg/ml at Day 14/discharge. Significant declines in IFN-{gamma}, TNF, IL-27, CRP and ferritin were specifically observed at Day 3 whereas other cytokines were unmodified. IL-6 levels declined sharply among patients with baseline levels >10 pg/ml. Among 13 lymphopenic patients, six (46%) had resolution of lymphopenia by day 3, and 11 by day 14. CXCR3-ligand (IP-10 and CXCL-9) declines were strongly correlated among patients with lymphopenia reversal (Day 3, Pearson r: 0.98, p-value: 0.0006).\n\nInterpretationConsistent with a pathophysiological role of TNF, the clinical and cytokine data indicate that infliximab-abda may rapidly abrogate pathological inflammatory signaling to facilitate clinical recovery in severe and critical COVID-19. Randomized studies are required to formally assess mortality outcomes. Funding: National Center for Advancing Translational Sciences", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hilal Hachem", + "author_inst": "Tufts Medical Center, Boston MA (current affiliation: Northern Light Cancer Institute,Bangor ME)" + }, + { + "author_name": "Amandeep Godara", + "author_inst": "Tufts Medical Center, Boston MA (current affiliation: University of Utah, Salt Lake City, UT)" + }, + { + "author_name": "Courtney Schroeder", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Daniel Fein", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Hashim Mann", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Christian Lawlor", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Jill Marshall", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Andreas Klein", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Deborah Poutsiaka", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Janis L Breeze", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Raghav Joshi", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Paul Mathew", + "author_inst": "Tufts Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257820", "rel_title": "The Female Predominant Persistent Immune Dysregulation of the Post COVID Syndrome: A Cohort Study", @@ -749697,25 +752412,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.06.01.446677", - "rel_title": "Immune dynamics in a time of covid", - "rel_date": "2021-06-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446677", - "rel_abs": "Motivated by curiosities of disease progression seen in the coronavirus pandemic, we analyze a minimalist predator-prey model for the immune system (predator) competing against a pathogen (prey). We find that the mathematical model alone accounts for numerous paradoxical behaviors observed in this and other infections. These include why an exponentially growing pathogen requires an exposure threshold to take hold, how chronic and recurrent infections can arise, and what can allow very sick patients to recover, while healthier patients succumb. We also examine the distinct dynamical roles that specific, \"innate,\" and nonspecific, \"adaptive,\" immunity play, and we describe mathematical effects of infection history on prognosis. Finally, we briefly discuss predictions for some of the effects of timing and strengths of antibiotics or immunomodulatory agents.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Troy Shinbrot", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.01.446639", "rel_title": "Effects of the COVID-19 pandemic on publication landscape in chimeric antigen receptor-modified immune cell research", @@ -750723,6 +753419,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.28.21258008", + "rel_title": "College Students' COVID-19 Vaccine Beliefs and Intentions: Implications for interventions", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258008", + "rel_abs": "On college campuses, effective management of vaccine-preventable transmissible pathogens requires understanding student vaccination intentions. This is necessary for developing and tailoring health messaging to maximize uptake of health information and vaccines. The current study explored students beliefs and attitudes about vaccines in general, and the new COVID-19 vaccines specifically. This study provides insights into effective health messaging needed to rapidly increase COVID-19 vaccination on college campuses--information that will continue to be informative in future academic years across a broad scope of pathogens. Data were collected via an online cohort survey of college students aged 18 years and older residing on or near the campus of a large public university during fall 2020. Overall, we found COVID-19 vaccine hesitancy in college students correlated strongly with some concerns about vaccines in general as well as with concerns specific to COVID-19 vaccines. Taken together, these results provide further insight for message development and delivery, and can inform more effective interventions to advance critical public health outcomes on college campuses beyond the current pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Meg L Small", + "author_inst": "Penn State University" + }, + { + "author_name": "Robert Lennon", + "author_inst": "Penn State University" + }, + { + "author_name": "John Dziak", + "author_inst": "Penn State University" + }, + { + "author_name": "Rachel A Smith", + "author_inst": "Penn State University" + }, + { + "author_name": "Gillian Sommerville", + "author_inst": "Penn State University" + }, + { + "author_name": "Nita Bharti", + "author_inst": "Penn State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.31.21257656", "rel_title": "Acute kidney injury in hospitalized patients due to COVID-19", @@ -751367,33 +754102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.01.446591", - "rel_title": "Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies", - "rel_date": "2021-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446591", - "rel_abs": "The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly-conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Qiaozhen Ye", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Shan Lu", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Kevin D Corbett", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.01.446623", "rel_title": "Synergistic inhibition of two host factors that facilitate entry of Severe Acute Respiratory Syndrome Coronavirus 2", @@ -752177,6 +754885,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.05.28.21257993", + "rel_title": "The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia", + "rel_date": "2021-05-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21257993", + "rel_abs": "Loss of sense of smell is a characteristic symptom of infection with SARS-CoV-2. However, specific mechanisms linking infection with loss of smell are poorly understood. Using self-reported symptom data from the 23andMe COVID-19 study, we describe the demographic patterns associated with COVID-19 related anosmia, and find the symptom is more often reported in women and younger respondents, and less often by those of East Asian and African American ancestry compared to those of European ancestry. We ran a trans-ethnic genome-wide association study (GWAS) comparing loss of smell or taste (n=47,298) with no loss of smell or taste (n=22,543) among those with a positive SARS-CoV-2 test result. We identified an association (rs7688383) in the vicinity of the UGT2A1 and UGT2A2 genes (OR=1.115, p-value=4x10-15), which have been linked to olfactory function. These results may shed light on the biological mechanisms underlying COVID-19 related anosmia.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Janie F. Shelton", + "author_inst": "23andMe" + }, + { + "author_name": "Anjali J. Shastri", + "author_inst": "23andMe" + }, + { + "author_name": "- The 23andMe COVID-19 Team", + "author_inst": "" + }, + { + "author_name": "Stella Aslibekyan", + "author_inst": "23andMe" + }, + { + "author_name": "Adam Auton", + "author_inst": "23andMe" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.05.28.21258007", "rel_title": "Temporal stability and detection sensitivity of the dry swab-based diagnosis of SARS-CoV-2", @@ -752808,73 +755551,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.31.445871", - "rel_title": "Correlation of vaccine-elicited antibody levels and neutralizing activities against SARS-CoV-2 and its variants", - "rel_date": "2021-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.445871", - "rel_abs": "Both Pfizer-BNT162b2 and Moderna-mRNA-1273 vaccines can elicit an effective immune response against SARS-CoV-2 infection. However, the elicited serum antibody levels vary substantially and longitudinally decrease after vaccination. We examined the correlation of vaccination-induced IgG levels and neutralization titers against newly emerged variants remains and demonstrate a significant reduction of neutralization activities against the variants (B.1.1.7, B.1.525, and B.1.351) in Pfizer or Moderna vaccined sera. There was a significant and positive correlation between serum IgG levels and ID50 titers for not only SARS-CoV-2 WT but also the variants. These findings indicate that a high level of anti-spike IgG may offer better protection against infection from SARS-CoV-2 and its variants. Therefore, it is necessary to longitudinally monitor specific serum IgG level for evaluating the protective efficacy of the vaccines against SARS-CoV-2 and its new variants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jinbiao Liu", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Brittany H Bodnar", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19141, USA; Center for Metabolic Disease Rese" - }, - { - "author_name": "Xu Wang", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Peng Wang", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Fengzhen Meng", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Adil I Khan", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "A Sami Saribas", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19141, USA; Center for Metabolic Disease Rese" - }, - { - "author_name": "Nigam H Padhiar", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Elizabeth McCluskey", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Sahil Shah", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19141, USA; Center for Metabolic Disease Rese" - }, - { - "author_name": "Jin Jun Luo", - "author_inst": "Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - }, - { - "author_name": "Wenhui Hu", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19141, USA; Center for Metabolic Disease Rese" - }, - { - "author_name": "Wen-Zhe Ho", - "author_inst": "Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.31.445667", "rel_title": "Revealing the host antiviral protein ZAP-S as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting", @@ -753798,6 +756474,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.26.21257854", + "rel_title": "Corowa-kun: Impact of a COVID-19 vaccine information chatbot on vaccine hesitancy, Japan 2021", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257854", + "rel_abs": "BackgroundFew studies have assessed how mobile messenger apps affect COVID-19 vaccine hesitancy. We created a COVID-19 vaccine information chatbot in a popular messenger app in Japan to answer commonly asked questions.\n\nMethodsLINE is the most popular messenger app in Japan. Corowa-kun, a free chatbot, was created in LINE on February 6, 2021. Corowa-kun provides instant, automated answers to frequently asked COVID-19 vaccine questions. In addition, a cross-sectional survey assessing COVID-19 vaccine hesitancy was conducted via Corowa-kun during April 5-12, 2021.\n\nResultsA total of 59,676 persons used Corowa-kun during February-April 2021. Of them, 10,192 users (17%) participated in the survey. Median age was 55 years (range 16-97), and most were female (74%). Intention to receive a COVID-19 vaccine increased from 59% to 80% after using Corowa-kun (p < 0.01). Overall, 20% remained hesitant: 16% (1,675) were unsure, and 4% (364) did not intend to be vaccinated. Factors associated with vaccine hesitancy were: age 16 to 34 (odds ratio [OR] = 3.7, 95% confidential interval [CI]: 3.0-4.6, compared to age [≥]65), female sex (OR = 2.4, Cl: 2.1-2.8), and history of a previous vaccine side-effect (OR = 2.5, Cl: 2.2-2.9). Being a physician (OR = 0.2, Cl: 0.1-0.4) and having received a flu vaccine the prior season (OR = 0.4, Cl: 0.3-0.4) were protective.\n\nConclusionsCorowa-kun reduced vaccine hesitancy by providing COVID-19 vaccine information in a messenger app. Mobile messenger apps could be leveraged to increase COVID-19 vaccine acceptance.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Takaaki Kobayashi", + "author_inst": "University of Iowa Hospitals and Clinics" + }, + { + "author_name": "Yuka Nishina", + "author_inst": "Juntendo University Faculty of Medicine" + }, + { + "author_name": "Hana Tomoi", + "author_inst": "MSc Public Health (Cand.), Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ko Harada", + "author_inst": "Okayama University Graduate School of Medicine" + }, + { + "author_name": "Kyuto Tanaka", + "author_inst": "Kawasaki Municipal Hospital" + }, + { + "author_name": "Eiyu Matsumoto", + "author_inst": "University of Iowa Hospitals & Clinics" + }, + { + "author_name": "Kenta Horimukai", + "author_inst": "Jikei University Katsushika Medical Center" + }, + { + "author_name": "Jun Ishihara", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shugo Sasaki", + "author_inst": "Saitama Medical University Hospital" + }, + { + "author_name": "Kanako Inaba", + "author_inst": "Kanto Central Hospital" + }, + { + "author_name": "Kyosuke Seguchi", + "author_inst": "Kameda Medical Center" + }, + { + "author_name": "Hiromizu Takahashi", + "author_inst": "Juntendo University Faculty of Medicine" + }, + { + "author_name": "Jorge Salinas", + "author_inst": "University of Iowa Hospitals & Clinics" + }, + { + "author_name": "Yuji Yamada", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.29.443900", "rel_title": "Broadening a SARS-CoV-1 neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution", @@ -754430,53 +757177,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.27.21257713", - "rel_title": "Emergency department admissions during COVID-19: explainable machine learning to characterise data drift and detect emergent health risks", - "rel_date": "2021-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257713", - "rel_abs": "Supervised machine learning algorithms deployed in acute healthcare settings use data describing historical episodes to predict clinical outcomes. Clinical settings are dynamic environments and the underlying data distributions characterising episodes can change with time (a phenomenon known as data drift), and so can the relationship between episode characteristics and associated clinical outcomes (so-called, concept drift). We demonstrate how explainable machine learning can be used to monitor data drift in a predictive model deployed within a hospital emergency department. We use the COVID-19 pandemic as an exemplar cause of data drift, which has brought a severe change in operational circumstances. We present a machine learning classifier trained using (pre-COVID-19) data, to identify patients at high risk of admission to hospital during an emergency department attendance. We evaluate our models performance on attendances occurring pre-pandemic (AUROC 0.856 95%CI [0.852, 0.859]) and during the COVID-19 pandemic (AUROC 0.826 95%CI [0.814, 0.837]). We demonstrate two benefits of explainable machine learning (SHAP) for models deployed in healthcare settings: (1) By tracking the variation in a features SHAP value relative to its global importance, a complimentary measure of data drift is found which highlights the need to retrain a predictive model. (2) By observing the relative changes in feature importance emergent health risks can be identified.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Christopher Duckworth", - "author_inst": "University of Southampton" - }, - { - "author_name": "Francis P Chmiel", - "author_inst": "University of Southampton" - }, - { - "author_name": "Dan K. Burns", - "author_inst": "University of Southampton" - }, - { - "author_name": "Zlatko D Zlatev", - "author_inst": "University of Southampton" - }, - { - "author_name": "Neil M White", - "author_inst": "University of Southampton" - }, - { - "author_name": "Michael Kiuber", - "author_inst": "University Hospital Southampton" - }, - { - "author_name": "Thomas W. V. Daniels", - "author_inst": "University Hospitals Southampton" - }, - { - "author_name": "Michael Boniface", - "author_inst": "University of Southampton" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.05.27.21257916", "rel_title": "Modeling of the COVID-19 Cases in Gulf Cooperation Council (GCC) countries using ARIMA and MA-ARIMA models.", @@ -755532,6 +758232,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.28.446159", + "rel_title": "SARS-CoV-2 transmission via apical syncytia release from primary bronchial epithelia and infectivity restriction in children epithelia", + "rel_date": "2021-05-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446159", + "rel_abs": "The beta-coronavirus SARS-CoV-2 is at the origin of a persistent worldwide pandemic. SARS-CoV-2 infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract eventually causing acute severe respiratory syndrome with a high degree of mortality in the elderly. Here we use reconstituted primary bronchial epithelia from adult and children donors to follow the infection dynamic following infection with SARS-CoV-2. We show that in bronchial epithelia derived from adult donors, infections initiate in multi-ciliated cells. Then, infection rapidly spread within 24-48h throughout the whole epithelia. Within 3-4 days, large apical syncytia form between multi-ciliated cells and basal cells, which dissipate into the apical lumen. We show that these syncytia are a significant source of the released infectious dose. In stark contrast to these findings, bronchial epithelia reconstituted from children donors are intrinsically more resistant to virus infection and show active restriction of virus spread. This restriction is paired with accelerated release of IFN compared to adult donors. Taken together our findings reveal apical syncytia formation as an underappreciated source of infectious virus for either local dissemination or release into the environment. Furthermore, we provide direct evidence that children bronchial epithelia are more resistant to infection with SARS-CoV-2 providing experimental support for epidemiological observations that SARS-CoV-2 cases fatality is linked to age.\n\nSignificance StatementBronchial epithelia are the primary target for SARS-CoV-2 infections. Our work uses reconstituted bronchial epithelia from adults and children. We show that infection of adult epithelia with SARS-CoV-2 is rapid and results in the synchronized release of large clusters of infected cells and syncytia into the apical lumen contributing to the released infectious virus dose. Infection of children derived bronchial epithelia revealed an intrinsic resistance to infection and virus spread, probably as a result of a faster onset of interferon secretion. Thus, our data provide direct evidence for the epidemiological observation that children are less susceptible to SARS-CoV-2.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Guillaume Beucher", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Marie-Lise Blondot", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Alexis Celle", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Noemie Pied", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Patricia Recordon-Pinson", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Pauline Esteves", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Muriel Faure", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Mathieu Metifiot", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Sabrina Lacomme", + "author_inst": "University of Bordeaux, CNRS, Institute of Neurodegenerative Diseases, IINS, UMR 5293, Bordeaux, France, University of Bordeaux, CNRS, INSERM, Bordeaux Imaging " + }, + { + "author_name": "Denis Dacheaux", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Derrick Roy Robinson", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Gernot Laengst", + "author_inst": "Universitaet Regensburg" + }, + { + "author_name": "Fabien Beaufils", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Marie-Edith Lafon", + "author_inst": "CHU de Bordeaux, Laboratoire de Virologie, 33000 Bordeaux, France" + }, + { + "author_name": "Patrick Berger", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France." + }, + { + "author_name": "Marc Landry", + "author_inst": "University of Bordeaux, CNRS, Institute of Neurodegenerative Diseases, IINS, UMR 5293, Bordeaux, France, University of Bordeaux, CNRS, INSERM, Bordeaux Imaging " + }, + { + "author_name": "Jean-Marie Denis Malvy", + "author_inst": "Department for infectious and tropical d ideales, University Hospital center Pellegrin, Bordeaux, & Inserm 1219, University of Bordeaux, Bordeaux, France" + }, + { + "author_name": "Thomas Trian", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France." + }, + { + "author_name": "Marie-Line Andreola", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Harald Wodrich", + "author_inst": "Universite de Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.28.446020", "rel_title": "Evaluating the risk of SARS-CoV-2 transmission to bats using a decision analytical framework", @@ -756011,41 +758806,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.25.21257434", - "rel_title": "Geographical and temporal distribution of SARS-CoV-2 globally: An attempt to correlate case fatality rate with the circulating dominant SARS-CoV-2 clades", - "rel_date": "2021-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257434", - "rel_abs": "Uncontrolled high transmission is driving the continuous evolution of SARS-CoV-2, leading to the nonstop emergence of the new variants with varying sensitivity to the neutralizing antibodies and vaccines.Wehave analysed of 8,82,740 SARS-CoV-2 genome sequences, collected and sequenced during late December 2019 to 25 March 2021 from all across the world. The findings revealed differences in temporal and spatial distribution,and predominance of various clades/variants among six different continents.We found no clear association between the pathogenic potential of the various clades by comparing the case fatality rate (CFR) of 170 countries with the predominant SARS-CoV-2 clades in those countries, demonstrating the insignificance of the clade specific mutations on case fatality. Overall, relying on a large-scale dataset,this study illustratedthe time-basedevolution andprevalence of various clades/variantsamong different geographic regions.The study may help in designing continent specific vaccines in the future.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rakesh Sarkar", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Mamta Chawla-Sarkar", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Swagata Majumdar", - "author_inst": "Institute of Post Graduate Medical Education and Research, Kolkata" - }, - { - "author_name": "Mahadeb Lo", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Shiladitya Chattopadhyay", - "author_inst": "Technion Israel Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.25.21257501", "rel_title": "Multiplexed Detection of COVID-19 with Single-Molecule Technology", @@ -757041,6 +759801,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.25.21257811", + "rel_title": "Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257811", + "rel_abs": "Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire class of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Zachary R Stromberg", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Brian T Foley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ad\u00e1n Myers y Guti\u00e9rrez", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Attelia Hollander", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Samantha J Courtney", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Alina Deshpande", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ebany J Martinez-Finley", + "author_inst": "Presbyterian Healthcare Services" + }, + { + "author_name": "Jason Mitchell", + "author_inst": "Presbyterian Healthcare Services" + }, + { + "author_name": "Harshini Mukundan", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Karina Yusim", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Jessica Z Kubicek-Sutherland", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257828", "rel_title": "Correlation of the commercial anti-SARS-CoV-2 receptor binding domain antibody test with the chemiluminescent reduction neutralizing test and possible detection of antibodies to emerging variants", @@ -758061,81 +760884,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.05.24.21256813", - "rel_title": "Cohort profile: Actionable Register of Geneva Outpatients with SARS-CoV-2 (ARGOS)", - "rel_date": "2021-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21256813", - "rel_abs": "PurposeThe Actionable Register of Geneva Out- and inpatients with SARS-CoV-2 (ARGOS) is an ongoing prospective cohort created by the Geneva Directorate of Health (GDH). It consists of an operational database compiling all SARS-CoV-2 test results conducted in the Geneva area since late February 2020. This article aims at presenting this comprehensive cohort, in light of some of the varying public health measures in Geneva, Switzerland, since March 2020.\n\nParticipantsAs of June 1st, 2021, the database included 356868 patients, among which 65475 had at least one positive test result for SARS-CoV-2. Among all positive patients, 37.6% were contacted only once, 10.6 % had one follow-up call, 8.5% had two, and 27.7% had 3 or more follow-up calls. Participation rate among positive patients is 94%. Data collection is ongoing.\n\nFindings to dateARGOS data illustrates the magnitude of COVID-19 pandemic in Geneva, Switzerland, and details a variety of population factors and outcomes. The content of the cohort includes demographic data, comorbidities and risk factors for poor clinical outcome, self-reported COVID-19 symptoms, environmental and socio-economic factors, prospective and retrospective contact tracing data, travel quarantine data, and deaths. The registry has already been used in several publications focusing on symptoms and long COVID, infection fatality rate, and re-infection.\n\nFuture plansThe data of this large real-world registry provides a valuable resource for various types of research, such as clinical research, epidemiological research or policy assessment as it illustrates the impact of public health policies and overall disease burden of COVID-19.\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDYO_LIARGOS main strength consists of its large number of cases, representative of all diagnosed cases on a regional level with the primary aim of assessing all cases.\nC_LIO_LIARGOS involves every individual who performed a SARS-CoV-2 test (PCR or antigenic) and is not limited to hospitalized patients, thus providing a valuable resource to assess the overall disease burden of COVID-19 in a geographically defined population.\nC_LIO_LITo mitigate confounding effects and improve data analysis and interpretation, we present the data according to four policy periods.\nC_LIO_LIThis cohort is multicentric as it includes all tests performed in Genevas hospitals (both public and private), private practices and medical centers.\nC_LIO_LIDue to operational needs, symptoms and comorbidities are self-reported, which may lead to measurement error or misclassification.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Camille Genecand", - "author_inst": "Division of General Surgeon, Geneva Directorate of Health, Geneva, Switzerland" - }, - { - "author_name": "Denis Mongin", - "author_inst": "Division of General Surgeon, Geneva Directorate of Health, Geneva, Switzerland" - }, - { - "author_name": "Flora Koegler", - "author_inst": "Division of General Internal Medicine, Department of Internal Medicine, Geneva University Hospital, Geneva, Switzerland" - }, - { - "author_name": "Dan Lebowitz", - "author_inst": "Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Simon Regard", - "author_inst": "1Division of General Surgeon, Geneva Directorate of Health, Geneva, Switzerland" - }, - { - "author_name": "Mayssam Nehme", - "author_inst": "Division of Primary Care Medicine, Department of Community Medicine and Primary Care and Emergency Medicine, Geneva University Hospital, Geneva, Switzerland" - }, - { - "author_name": "Olivia Braillard", - "author_inst": "Division of Primary Care Medicine, Department of Community Medicine and Primary Care and Emergency Medicine, Geneva University Hospital, Geneva, Switzerland" - }, - { - "author_name": "Marwene Grira", - "author_inst": "Division of Primary Care Medicine, Department of Community Medicine and Primary Care and Emergency Medicine, Geneva University Hospital, Geneva, Switzerland" - }, - { - "author_name": "Dominique Joubert", - "author_inst": "Quality of Care Service, University Hospital of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Pierre Chopard", - "author_inst": "Quality of Care Service, University Hospital of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Elisabeth Delaporte", - "author_inst": "Division of General Surgeon, Geneva Directorate of Health, Geneva, Switzerland" - }, - { - "author_name": "Jerome Stirnemann", - "author_inst": "Division of General Internal Medicine, Department of Internal Medicine, Geneva University Hospital, Geneva, Switzerland" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Division of Primary Care Medicine, Department of Community Medicine and Primary Care and Emergency Medicine, Geneva University Hospital, Geneva, Switzerland" - }, - { - "author_name": "Aglae Tardin", - "author_inst": "Division of General Surgeon, Geneva Directorate of Health, Geneva, Switzerland" - }, - { - "author_name": "Delphine Sophie Courvoisier", - "author_inst": "Quality of Care Service, University Hospital of Geneva, Geneva, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.24.21257729", "rel_title": "Standardised, quantitative neutralisation responses to SARS-CoV-2 Variants of Concern by convalescent anti-sera from first wave infections of UK Health Care Workers and Patients", @@ -759215,6 +761963,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.24.21257465", + "rel_title": "Psychological factors underpinning vaccine willingness in Israel, Japan and Hungary", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257465", + "rel_abs": "The rapid international spread of the SARS-CoV-2 virus 19 led to unprecedented attempts to develop and administer an effective vaccine. However, there is considerable vaccine hesitancy in some countries. We investigated willingness to vaccinate in three nations with historically different levels of vaccine willingness and attitudes: Israel, Japan and Hungary. Employing an ecological-systems approach we analysed associations between demographic factors and health status, individual cognitions, normative pressures, trust in government, belief in COVID-19 myths and willingness to be vaccinated, using data from three nationally representative samples (Israel, N=1011 (Jan 2021); Japan, N= 997 (Feb 2021); Hungary, N=1131 (Apr 2021)). In Israel 74% indicated a willingness to vaccinate, but only 51% in Japan and 31% in Hungary. Multigroup regression analyses indicated greater vaccine willingness amongst those who perceived benefits to vaccination, anticipated regret if not vaccinated and trusted the government. Multi-group latent class analysis of ten COVID-19 (mis)beliefs identified three classes of myths, with concerns about the alteration of DNA (Israel), allergies (Hungary) and catching COVID-19 from the vaccine (Japan) specific to vaccine willingness for each culture. Intervention campaigns should focus on increasing trust and addressing culturally specific myths while emphasising the individual and social group benefits of vaccination.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Robin Goodwin", + "author_inst": "University of Warwick" + }, + { + "author_name": "Menachem Ben-Ezra", + "author_inst": "Ariel University" + }, + { + "author_name": "Masahito Takahashi", + "author_inst": "Yamaguchi University Japan" + }, + { + "author_name": "Lan Anh Nguyen Luu", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Krisztina Borsfay", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Monika Kovacs", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Wai Kai Hou", + "author_inst": "Education University Hong Kong" + }, + { + "author_name": "Yaira Hamama-Raz", + "author_inst": "Ariel University" + }, + { + "author_name": "Yafit Levin", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.21.21257612", "rel_title": "COVID-19 vaccination hesitancy model: The impact of vaccine education on controlling the outbreak in the United States", @@ -759707,33 +762506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.23.21257689", - "rel_title": "A random forest model for forecasting regional COVID-19 cases utilizing reproduction number estimates and demographic data", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.23.21257689", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWDuring the COVID-19 pandemic, predicting case spikes at the local level is important for a precise, targeted public health response and is generally done with compartmental models. The performance of compartmental models is highly dependent on the accuracy of their assumptions about disease dynamics within a population; thus, such models are susceptible to human error, unexpected events, or unknown characteristics of a novel infectious agent like COVID-19. We present a relatively non-parametric random forest model that forecasts the number of COVID-19 cases at the U.S. county level. Its most prioritized training features are derived from easily accessible, standard epidemiological data (i.e., regional test positivity rate) and the effective reproduction number (Rt) from compartmental models. A novel input training feature is case projections generated by aligning estimated effective reproduction number (pre-computed by COVIDActNow.org) with real time testing data until maximally correlated, helping our model fit better to the epidemics trajectory as ascertained by traditional models. Poor reliability of Rt is partially mitigated with dynamic population mobility and prevalence and mortality of non-COVID-19 diseases to gauge population disease susceptibility. The model was used to generate forecasts for 1, 2, 3, and 4 weeks into the future for each reference week within 11/01/2020 - 01/10/2021 for 3068 counties. Over this time period, it maintained a mean absolute error (MAE) of less than 300 weekly cases/100,000 and consistently outperformed or performed comparably with gold-standard compartmental models. Furthermore, it holds great potential in ensemble modeling due to its potential for a more expansive training feature set while maintaining good performance and limited resource utilization.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Joseph Galasso", - "author_inst": "University of Dallas" - }, - { - "author_name": "Duy M. Cao", - "author_inst": "University of Dallas" - }, - { - "author_name": "Robert Hochberg", - "author_inst": "University of Dallas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.22.21257643", "rel_title": "A statistical model of COVID-19 testing in populations: effects of sampling bias and testing errors", @@ -760945,6 +763717,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.25.445601", + "rel_title": "Genomic Surveillance of COVID-19 Variants with Language Models and Machine Learning", + "rel_date": "2021-05-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.25.445601", + "rel_abs": "The global efforts to control COVID-19 are threatened by the rapid emergence of novel SARS-CoV-2 variants that may display undesirable characteristics such as immune escape, increased transmissibility or pathogenicity. Early prediction for emergence of new strains with these features is critical for pandemic preparedness. We present Strainflow, a supervised and causally predictive model using unsupervised latent space features of SARS-CoV-2 genome sequences. Strainflow was trained and validated on 0.9 million sequences for the period December, 2019 to June, 2021 and the frozen model was prospectively validated from July, 2021 to December, 2021. Strainflow captured the rise in cases two months ahead of the Delta and Omicron surges in most countries including the prediction of a surge in India as early as beginning of November, 2021. Entropy analysis of Strainflow unsupervised embeddings clearly reveals the explore-exploit cycles in genomic feature-space, thus adding interpretability to the deep learning based model. We also conducted codon-level analysis of our model for interpretability and biological validity of our unsupervised features. Strainflow application is openly available as an interactive web-application for prospective genomic surveillance of COVID-19 across the globe.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sargun Nagpal", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ridam Pal", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ashima", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ananya Tyagi", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Sadhana Tripathi", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Aditya Nagori", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Saad Ahmad", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Hara Prasad Mishra", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Rintu Kutum", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Tavpritesh Sethi", + "author_inst": "Indraprastha Institute of Information Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.05.24.445517", "rel_title": "Evolutionary Inference Predicts Novel ACE2 Protein Interactions Relevant to COVID-19 Pathologies", @@ -761577,225 +764404,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.05.21.445189", - "rel_title": "Evaluation of mRNA-1273 against SARS-CoV-2 B.1.351 Infection in Nonhuman Primates", - "rel_date": "2021-05-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445189", - "rel_abs": "BackgroundVaccine efficacy against the B.1.351 variant following mRNA-1273 vaccination in humans has not been determined. Nonhuman primates (NHP) are a useful model for demonstrating whether mRNA-1273 mediates protection against B.1.351.\n\nMethodsNonhuman primates received 30 or 100 {micro}g of mRNA-1273 as a prime-boost vaccine at 0 and 4 weeks, a single immunization of 30 {micro}g at week 0, or no vaccine. Antibody and T cell responses were assessed in blood, bronchioalveolar lavages (BAL), and nasal washes. Viral replication in BAL and nasal swabs were determined by qRT-PCR for sgRNA, and histopathology and viral antigen quantification were performed on lung tissue post-challenge.\n\nResultsEight weeks post-boost, 100 {micro}g x2 of mRNA-1273 induced reciprocal ID50 neutralizing geometric mean titers against live SARS-CoV-2 D614G and B.1.351 of 3300 and 240, respectively, and 430 and 84 for the 30 {micro}g x2 group. There were no detectable neutralizing antibodies against B.1351 after the single immunization of 30 {micro}g. On day 2 following B.1.351 challenge, sgRNA in BAL was undetectable in 6 of 8 NHP that received 100 {micro}g x2 of mRNA-1273, and there was a [~]2-log reduction in sgRNA in NHP that received two doses of 30 {micro}g compared to controls. In nasal swabs, there was a 1-log10 reduction observed in the 100 {micro}g x2 group. There was limited inflammation or viral antigen in lungs of vaccinated NHP post-challenge.\n\nConclusionsImmunization with two doses of mRNA-1273 achieves effective immunity that rapidly controls lower and upper airway viral replication against the B.1.351 variant in NHP.", - "rel_num_authors": 51, - "rel_authors": [ - { - "author_name": "Kizzmekia S. Corbett", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Anne Werner", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Matthew Gagne", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Juan Moliva", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Barbara Flynn", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Angela Choi", - "author_inst": "Moderna Inc." - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna Inc." - }, - { - "author_name": "Kathryn E. Foulds", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Shayne Andrew", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Dillon Flebbe", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Evan Lamb", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Saule T. Nurmukhambetova", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Samantha Provost", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Kevin W. Bock", - "author_inst": "Infectious Disease Pathogenesis Section; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda" - }, - { - "author_name": "Mahnaz Minai", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Bianca M. Nagata", - "author_inst": "Infectious Disease Pathogenesis Section; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda" - }, - { - "author_name": "Alex Van Ry", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Zackery Flinchbaugh", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Timothy S. Johnston", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Elham Bayat Mokhtari", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Prakriti Mudvari", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Amy R. Henry", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Farida Laboune", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Becky Chang", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Maciel Porto", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Jaclyn Wear", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Gabriela S. Alvarado", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Seyhan Boyoglu-Barnum", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "John-Paul Todd", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Bridget Bart", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Anthony Cook", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Alan Dodson", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Katelyn Steingrebe", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Sayda Elbashir", - "author_inst": "Moderna Inc." - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Kai Wu", - "author_inst": "Moderna Inc." - }, - { - "author_name": "Darin K. Edwards", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Swagata Kar", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual, Inc." - }, - { - "author_name": "Eli Boritz", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Ian Moore", - "author_inst": "Infectious Disease Pathogenesis Section; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna Inc." - }, - { - "author_name": "Mehul Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Adrian McDermott", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Mario Roederer", - "author_inst": "Vaccine Research Center" - }, - { - "author_name": "Martha C. Nason", - "author_inst": "Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Nancy J. Sullivan", - "author_inst": "VRC, NIH" - }, - { - "author_name": "Daniel C. Douek", - "author_inst": "NIH Vaccine Research Center" - }, - { - "author_name": "Barney S. Graham", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Robert A. Seder", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.21.445201", "rel_title": "Evidence for Deleterious Original Antigenic Sin in SARS-CoV-2 Immune Response", @@ -762691,6 +765299,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.20.21257542", + "rel_title": "The maladaptive vascular response in COVID-19 acute respiratory distress syndrome and recovery", + "rel_date": "2021-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257542", + "rel_abs": "Vascular injury is a menacing element of acute respiratory distress syndrome (ARDS) pathogenesis. To better understand the role of vascular injury in COVID-19 ARDS, we used lung autopsy immunohistochemistry and blood proteomics from COVID-19 subjects at distinct timepoints in disease pathogenesis, including a hospitalized cohort at risk of ARDS development (\"at risk\", N=59), an intensive care unit cohort with ARDS (\"ARDS\", N=31), and a cohort recovering from ARDS (\"recovery\", N=12). COVID-19 ARDS lung autopsy tissue revealed an association between vascular injury and platelet-rich microthrombi. This link guided the derivation of a protein signature in the at risk cohort characterized by lower expression of vascular proteins in subjects who died, an early signal of vascular limitation termed the maladaptive vascular response. These findings were replicated in COVID-19 ARDS subjects, as well as when bacterial and influenza ARDS patients (N=29) were considered, hinting at a common final pathway of vascular injury that is more disease (ARDS) then cause (COVID-19) specific, and may be related to vascular cell death. Among recovery subjects, our vascular signature identified patients with good functional recovery one year later. This vascular injury signature could be used to identify ARDS patients most likely to benefit from vascular targeted therapies.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "David R Price", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Elisa Benedetti", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Katherine Hoffman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Luis Gomez-Escobar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Sergio Alvarez-Mulett", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Allyson Capili", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hina Sarwath", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Christopher N. Parkhurst", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Elyse LaFond", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Karissa Weidman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Arjun Ravishankar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jin Gyu Cheong", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Richa Batra", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Mustafa Buyukozkan", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Kelsey Chetnik", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Imaani Easthausen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Edward J. Schenck", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Alexandra C. Racanelli", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hasina Outtz Reed", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jeffrey C. Laurence", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Steven Zvi Josefowicz", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lindsay Lief", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Mary E. Choi", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Shahin Rafii", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Frank Schmidt", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Alain C. Borczuk", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jan Krumsiek", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Augustine M. K. Choi", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.05.20.21256954", "rel_title": "Efficacy and safety of novel probiotic formulation in adult Covid19 outpatients: a randomized, placebo-controlled clinical trial", @@ -763623,93 +766358,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.20.21257552", - "rel_title": "Identification and trajectory of growth of concerning SARS-CoV-2 variants in Houston, Texas, January through April 2021 based on 11,568 genome sequences", - "rel_date": "2021-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257552", - "rel_abs": "Genetic variants of the SARS-CoV-2 virus are of substantial concern because they can detrimentally alter the pandemic course and disease features in individual patients. Here we report SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist healthcare system diagnosed from January 1, 2021 through May 31, 2021. The SARS-CoV-2 variant designated U.K. B.1.1.7 increased rapidly and caused 63%-90% of all new cases in the Houston area in the latter half of May. Eleven of the 3,276 B.1.1.7 genomes had an E484K change in spike protein. Compared with non-B.1.1.7 patients, individuals with B.1.1.7 had a significantly lower cycle threshold value (a proxy for higher virus load) and significantly higher rate of hospitalization. Other variants (e.g., B.1.429, B.1.427, P.1, P.2, and R.1) also increased rapidly, although the magnitude was less than for B.1.1.7. We identified 22 patients infected with B.1.617 \"India\" variants; these patients had a high rate of hospitalization. Vaccine breakthrough cases (n=207) were caused by a heterogeneous array of virus genotypes, including many that are not variants of interest or concern. In the aggregate, our study delineates the trajectory of concerning SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, and heralds the arrival and spread of B.1.617 variants in the metroplex.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Randall James Olsen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Paul Christensen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Scott Wesley Long", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Sishir Subedi", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Parsa Hodjat", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Robert Olson", - "author_inst": "University of Chicago" - }, - { - "author_name": "Marcus Nguyen", - "author_inst": "University of Chicago" - }, - { - "author_name": "James Davis", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "Prasanti Yerramilli", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Matthew Ojeda-Saavedra", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Layne Pruitt", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Kristina Reppond", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Madison Shyer", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Jessica Cambric", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Ryan Gadd", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Ilya Finkelstein", - "author_inst": "University of Texas" - }, - { - "author_name": "Jimmy Gollihar", - "author_inst": "University of Texas" - }, - { - "author_name": "James Musser", - "author_inst": "Houston Methodist Hosptial" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.05.21.21257211", "rel_title": "Clinical, immunological and genomic characterization of asymptomatic and symptomatic cases with SARS-CoV-2 infection, India", @@ -764725,6 +767373,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.20.21256969", + "rel_title": "Implementation of a qPCR assay coupled with genomic surveillance for real-time monitoring of SARS-CoV-2 variants of concern.", + "rel_date": "2021-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21256969", + "rel_abs": "We developed a genomic surveillance program for real-time monitoring of SARS-CoV-2 variants of concern in Uruguay. Here, we present the first results, including the proposed qPCR-VOC method, the general workflow and the report of the introduction and community transmission of the VOC P.1 in Uruguay in multiple independent events.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Natalia Rego", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo." + }, + { + "author_name": "Alicia Costabile", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Centro de Innovacion en Vigilancia Epidemiologica, Institut Pasteur Montevideo" + }, + { + "author_name": "Mercedes Paz", + "author_inst": "Centro de Innovacion en Vigilancia Epidemiologica, Institut Pasteur Montevideo" + }, + { + "author_name": "Cecilia Salazar", + "author_inst": "Laboratorio de Genomica Microbiana, Institut Pasteur Montevideo" + }, + { + "author_name": "Paula Perbolianachis", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR" + }, + { + "author_name": "Lucia Spangemberg", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Ignacio Ferres", + "author_inst": "Laboratorio de Genomica Microbiana, Institut Pasteur Montevideo" + }, + { + "author_name": "Rodrigo Arce", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR; Laboratorio Biol" + }, + { + "author_name": "Alvaro Fajardo", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR" + }, + { + "author_name": "Mailen Arleo", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Tania Possi", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Ines Bellini", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Lucia Bilbao", + "author_inst": "Departamento de Genomica, Instituto de Investigaciones Biologicas Clemente Estable. Laboratorio de Biologia Molecular, Sanatorio Americano" + }, + { + "author_name": "Natalia Reyes", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Maria Noel Bentancor", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Andres Lizosain", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Maria Jose Benitez", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Matias Castells", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Matias Victoria", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Leticia Maya", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Viviana Bortagaray", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Ana Moller", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Gonzalo Bello", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Ighor Arantes", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Mariana Brandes", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Pablo Smircich", + "author_inst": "Departamento de Genomica, Instituto de Investigaciones Biologicas Clemente Estable. Laboratorio de Interacciones Moleculares, Facultad de Ciencias, UdelaR." + }, + { + "author_name": "Odhille Chappos", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Melissa Duquia", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Belen Gonzalez", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Luciana Griffero", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Mauricio Mendez", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Maria Pia Techera", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Juan Zanetti", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Bernardina Rivera", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Matias Maidana", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Martina Alonso", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Cecilia Alonso", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Julio Medina", + "author_inst": "Ministerio de Salud Publica (Uruguay) / Catedra de Enfermedades Infecciosas, Fac. de Medicina, UdelaR." + }, + { + "author_name": "Henry Albornoz", + "author_inst": "Ministerio de Salud Publica (Uruguay)" + }, + { + "author_name": "Rodney Colina", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Veronica Noya", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Gregorio Iraola", + "author_inst": "Institut Pasteur de Montevideo" + }, + { + "author_name": "Tamara Fernandez-Calero", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Gonzalo Andres Moratorio", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pilar Moreno", + "author_inst": "Universidad de la Republica. Insitut Pasteur de Montevideo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.19.21257439", "rel_title": "Rapid And high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351", @@ -765473,57 +768316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.19.21257489", - "rel_title": "Demographic disparities in clinical outcomes of COVID-19: data from a statewide cohort in South Carolina", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257489", - "rel_abs": "BackgroundCurrent literature examining the clinical characteristics of COVID-19 patients under-represent COVID-19 cases who were either asymptomatic or had a mild illness.\n\nObjectiveTo generate a state-level description and examine the demographic disparities of clinical outcomes of COVID-19.\n\nDesignStatewide population-based cohort study\n\nSettingCOVID-19 surveillance facilities in South Carolina\n\nPatientsAdults COVID-19 cases reported to the SC DHEC by Case Report Form during March 04-December 31, 2020\n\nMeasurementsThe primary predictors were socio-demographic characteristics. The outcomes were COVID-19 disease severity, hospitalization, and mortality, which collected from the standardized CRF.\n\nResultsAmong a total of 280,177 COVID-19 cases, 5.2% (14,451) were hospitalized and 1.9% (5,308) died. Individuals who were older, male gender, Blacks, Hispanic or Latino, and residing in small towns had higher odds for hospitalization and death from COVID-19 (Ps<0.0001). Regarding disease severity, 144,157 (51.5%) were asymptomatic, while 34.4% and 14.2% had mild and moderate/severe symptoms, respectively. Older individuals (OR: 1.14, 95%CI: 1.11, 1.18), Hispanic or Latino (OR: 2.07; 95%CI: 1.96, 2.18), and people residing in small towns (OR: 1.15; 95%CI: 1.08, 1.23) had higher odds of experiencing moderate/severe symptoms, while male and Asian (vs Whites) patients had lower odds of experiencing moderate/severe symptoms.\n\nLimitationsPotential misclassification of outcomes due to missing data; other variables were not evaluated, such as comorbidities.\n\nConclusionAs the first statewide population-based study using data from multiple healthcare systems with a long follow-up period in the US, we provide a more generalizable picture of COVID-19 symptoms and clinical outcomes. The findings from this study reinforce the fact that rural residence, racial and ethnic social determinants of health, unfortunately, remain predictors of poor health outcomes for COVID-19 patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xueying YANG", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Jiajia Zhang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shujie Chen", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Larisa Bruner", - "author_inst": "South Carolina Department of Health and Environmental Control" - }, - { - "author_name": "Abdoulaye Diedhiou", - "author_inst": "South Carolina Department of Health and Environmental Control" - }, - { - "author_name": "Cheryl Scott", - "author_inst": "South Carolina Department of Health and Environmental Control" - }, - { - "author_name": "Ali Mansaray", - "author_inst": "South Carolina Department of Health and Environmental Control" - }, - { - "author_name": "Sharon Weissman", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.19.21257429", "rel_title": "Efficacy of Sofosbuvir plus Ledipasvir in Egyptian patients with COVID-19 compared to standard treatment: Randomized controlled trial", @@ -766491,6 +769283,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.21.445152", + "rel_title": "The Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase", + "rel_date": "2021-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445152", + "rel_abs": "The COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics to treat coronavirus infections. Numerous antiviral targets are being investigated, but non-structural protein 13 (nsp13) stands out as a highly conserved and yet under studied target. Nsp13 is a superfamily 1 (SF1) helicase that translocates along and unwinds viral RNA in an ATP dependent manner. Currently, there are no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP or RNA bound presenting a significant hurdle to the rational design of therapeutics. To address this knowledge gap, we have built models of SARS-CoV-2 nsp13 in Apo, ATP, ssRNA and ssRNA+ATP substrate states. Using 30 s of Gaussian accelerated molecular dynamics simulation (at least 6 s per substrate state), these models were confirmed to maintain substrate binding poses that are similar to other SF1 helicases. A gaussian mixture model and linear discriminant analysis structural clustering protocol was used to identify key aspects of the ATP-dependent RNA translocation mechanism. Namely, four RNA-nsp13 structures are identified that exhibit ATP-dependent populations and support the inch-worm mechanism for translocation. These four states are characterized by different RNA-binding poses for motifs Ia, IV and V and suggest a powerstroke-like motion of domain 2A relative to domain 1A. This structural and mechanistic insight of nsp13 RNA translocation presents novel targets for the further development of antivirals.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ryan Weber", + "author_inst": "Colorado State University" + }, + { + "author_name": "Martin McCullagh", + "author_inst": "Oklahoma State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.05.21.445090", "rel_title": "Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution", @@ -767059,41 +769874,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.05.18.21252341", - "rel_title": "A model framework for projecting the prevalence and impact of Long-COVID in the UK", - "rel_date": "2021-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21252341", - "rel_abs": "BackgroundThe objective of this paper is to model lost Quality Adjusted Life Years (QALYs) from symptoms arising from COVID-19 in the UK population, including symptoms of long-COVID. The scope includes QALYs lost to symptoms, but not deaths, due to acute COVID-19 and long COVID.\n\nMethodsThe prevalence of symptomatic COVID-19, encompassing acute symptoms and long-COVID symptoms, was modelled using a decay function. Permanent injury as a result of COVID-19 infection, was modelled as a fixed prevalence. Both parts are combined to calculate QALY loss due to COVID-19 symptoms.\n\nResultsAssuming a 60% final attack rate for SARS-CoV-2 infection in the population, we modelled 299,719 QALYs lost within 1 year of infection (90% due to symptomatic COVID-19 and 10% permanent injury) and 557,754 QALYs lost within 10 years of infection (49% due to symptomatic COVID-19 and 51% due to permanent injury). The UK Government willingness-to-pay to avoid these QALY losses would be {pound}17.9 billion and {pound}32.2 billion, respectively. Additionally, 90,143 people were subject to permanent injury from COVID-19 (0.14% of the population).\n\nConclusionGiven the ongoing development in information in this area, we present a model framework for calculating the health economic impacts of symptoms following SARS-CoV-2 infection. This model framework can aid in quantifying the adverse health impact of COVID-19, long COVID and permanent injury following COVID-19 in society and assist the proactive management of risk posed to health. Further research is needed using standardised measures of patient reported outcomes relevant to long COVID and applied at a population level.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christopher John Martin", - "author_inst": "Crystallise Ltd" - }, - { - "author_name": "Stuart McDonald", - "author_inst": "Lloyds Banking Group" - }, - { - "author_name": "Michiel Luteijn", - "author_inst": "Hannover Re UK Life Branch" - }, - { - "author_name": "Josephine Robertson", - "author_inst": "University of Edinburgh, Usher Institute" - }, - { - "author_name": "William Letton", - "author_inst": "Crystallise Ltd" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.18.21257423", "rel_title": "Telecommuting intensity among Japanese workers according to regional cumulative COVID-19 incidence: a cross-sectional study", @@ -768433,6 +771213,177 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.05.14.21257058", + "rel_title": "Multicenter cohort study of multisystem inflammatory syndrome in children (MIS-C)", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257058", + "rel_abs": "BACKGROUNDSARS-CoV-2 infection can lead to multisystem inflammatory syndrome in children (MIS-C). We investigated risk factors for severe disease and explored changes in severity over time.\n\nMETHODSChildren up to 17 years of age admitted March 1, 2020 through March 7th, 2021 to 15 hospitals in Canada, Iran and Costa Rica with confirmed or probable MIS-C were included. Descriptive analysis and comparison by diagnostic criteria, country, and admission date was performed. Adjusted absolute average risks (AR) and risk differences (RD) were estimated for characteristics associated with ICU admission or cardiac involvement.\n\nRESULTSOf 232 cases (106 confirmed) with median age 5.8 years, 56% were male, and 22% had comorbidities. ICU admission occurred in 73 (31%) but none died. Median length of stay was 6 days (inter-quartile range 4-9). Children 6 to 12 years old had the highest AR for ICU admission (44%; 95% confidence interval [CI] 34-53). Initial ferritin greater than 500 mcg/L was associated with ICU admission. When comparing cases admitted up to October 31, 2020 to those admitted later, the AR for ICU admission increased from 25% (CI 17-33) to 37% (CI 29-46) and for cardiac involvement from 44% (CI 35-53) to 75% (CI 66-84). Risk estimates for ICU admission in the Canadian cohort demonstrated a higher risk in December 2020-March 2021 compared to March-May 2020 (RD 25%; 95%CI 7-44).\n\nINTERPRETATIONMIS-C occurred primarily in previously well children. Illness severity appeared to increase over time. Despite a high ICU admission incidence, most children were discharged within one week.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Joanna Merckx", + "author_inst": "Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal" + }, + { + "author_name": "Suzette Cooke", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Tala El Tal", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Ronald M. Laxer", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Ari Bitnun", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Shaun K Morris", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "E Ann Yeh", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Carmen Yea", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Peter Gill", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Jesse Papenburg", + "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" + }, + { + "author_name": "Marie-Astrid Lefebvre", + "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" + }, + { + "author_name": "Rolando Ulloa-Gutierrez", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Helena Brenes-Chacon", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Adriana Yock-Corrales", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Gabriela Ivankovich-Escoto", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Alejandra Soriano-Fallas", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Marcela Hernandez-de Mezerville", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Tammie Dewan", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Lea Restivo", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Alireza Nateghian", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Behzad Haghighi Aski", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Ali Manafi", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Rachel Dwilow", + "author_inst": "Department of Pediatrics, University of Manitoba, Winnipeg, Manitoba" + }, + { + "author_name": "Jared Bullard", + "author_inst": "Department of Pediatrics, University of Manitoba, Winnipeg, Manitoba" + }, + { + "author_name": "Alison Lopez", + "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "Department of Pediatrics, University of British Columbia; Vaccine Evaluation Center, BC Childrens Hospital Research Institute, Vancouver, BC" + }, + { + "author_name": "Ashley Roberts", + "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC" + }, + { + "author_name": "Michelle Barton", + "author_inst": "Department of Pediatrics, Western University, London, Ontario" + }, + { + "author_name": "Dara Petel", + "author_inst": "Department of Pediatrics, Western University, London, Ontario" + }, + { + "author_name": "Nicole Le Saux", + "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario" + }, + { + "author_name": "Jennifer Bowes", + "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario" + }, + { + "author_name": "Rupeena Purewal", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Janell Lautermilch", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Sarah Tehseen", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Ann Bayliss", + "author_inst": "Department of Pediatrics, Trillium Health Partners, Mississauga, Ontario" + }, + { + "author_name": "Jacqueline K. Wong", + "author_inst": "Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada" + }, + { + "author_name": "Kirk Leifso", + "author_inst": "Department of Pediatrics, Queens University, Kingston, Ontario" + }, + { + "author_name": "Cheryl Foo", + "author_inst": "Department of Pediatrics, Memorial University, St Johns, Newfoundland and Labrador" + }, + { + "author_name": "Joan Robinson", + "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, Alberta" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.05.13.21257067", "rel_title": "Contact tracing indicators for COVID-19: rapid scoping review and conceptual framework", @@ -769081,49 +772032,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.18.21256802", - "rel_title": "The impact of leadership on the nursing workforce during the COVID-19 pandemic", - "rel_date": "2021-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21256802", - "rel_abs": "AimsTo determine how the learning about protective factors from previous pandemics were implemented and the impact of this on nurses experience.\n\nBackgroundThe COVID-19 pandemic led to systemic change within healthcare settings and demands placed on frontline nurses has been overwhelming. Lessons learned from previous pandemics indicate that clear communication and strong visible leadership can mitigate the impact stressful events may have on nurses. Conversely, a lack of clear leadership and regulatory protocols in times of crisis can lead to an increase in psychological distress for nurses.\n\nDesignSecondary analysis of semi-structured interview transcripts.\n\nMethodsSecondary data analysis was conducted on data collected during a hospital-wide evaluation of barriers and facilitators to changes implemented to support the surge of COVID-19 related admissions in wave one of the pandemic. Participants represented three-levels of leadership: whole trust (n=17), division (n=7), ward/department-level (n=8), and individual nurses (n=16). Data were collected through semi-structured video interviews between May and July 2020. Interviews were analysed using Framework analysis.\n\nResultsKey changes that were implemented in wave one reported at whole trust level included: a new acute staffing level, redeploying nurses, increasing the visibility of nursing leadership, new staff wellbeing initiatives, new roles created to support families and various training initiatives. Two main themes emerged from the interviews at division, ward/department and individual nurse level: impact of leadership, and impact on the delivery of nursing care.\n\nConclusionsLeadership through a crisis is essential for the protective effect of nurses emotional wellbeing. While nursing leadership was made more visible during wave one of the pandemic and processes were in place to increase communication, system-level challenges resulting in negative experiences existed. By identifying these challenges, it has been possible to overcome them during wave two by employing different leadership styles, to support nurse wellbeing", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Natasha Phillips", - "author_inst": "NHSX" - }, - { - "author_name": "Luke Hughes", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Cecilia Vindrola-Padros", - "author_inst": "University College London" - }, - { - "author_name": "Anika Petrella", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lorna A Fern", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Flo Panel-Coates", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Rachel M Taylor", - "author_inst": "University College London Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2021.05.19.444774", "rel_title": "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution", @@ -769943,6 +772851,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.14.21257224", + "rel_title": "Surveillance of COVID-19 vaccination in US nursing homes, December 2020-April 2021", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257224", + "rel_abs": "Unstructured AbstractMonitoring COVID-19 vaccination coverage among nursing home (NH) residents and staff is important to ensure high coverage and guide patient-safety policies. With the termination of the federal Pharmacy Partnership for Long-Term Care Program, another source of facility-based vaccination data is needed. We compared numbers of COVID-19 vaccinations administered to NH residents and staff reported by pharmacies participating in the temporary federal Pharmacy Partnership for Long-Term Care Program with those reported by NHs participating in new COVID-19 vaccination modules of CDCs National Healthcare Safety Network (NHSN). Pearson correlation coefficients comparing the number vaccinated between the two approaches were 0.89, 0.96, and 0.97 for residents and 0.74, 0.90, and 0.90 for staff, in the weeks ending January 3, 10, and 17, respectively. Based on subsequent NHSN reporting, vaccination coverage with [≥]1 vaccine dose reached 77% for residents and 50% for staff the week ending January 31 and plateaued through April 2021.\n\nThree-question summary boxO_LIWhat is the current understanding of the subject?\nBecause of high risk of disease, nursing home residents and staff were prioritized for COVID-19 vaccination when doses were limited.\nC_LIO_LIWhat does this report add to the literature?\nNational monitoring of nursing home residents and staff vaccination coverage through the CDC National Healthcare Safety Network (NHSN) correlated with vaccination administration reports from the federal Pharmacy Partnership for Long-Term Care Program in January 2021. NHSN-reported vaccination coverage rates plateaued from February through April 2021.\nC_LIO_LIWhat are the implications for public health practice?\nNHSN can track COVID-19 vaccination in nursing homes and help guide efforts to increase vaccine uptake in residents and staff.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrew I Geller", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Daniel S Budnitz", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Heather Dubendris", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Radhika Gharpure", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Minn Minn Soe", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hsiu Wu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Elizabeth J Kalayil", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Andrea L Benin", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Suchita A Patel", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Megan C Lindley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Ruth Link-Gelles", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.13.21257164", "rel_title": "KL-MOB Automated Covid-19 Recognition Using a Novel Approach Based on Image Enhancement and a Modified MobileNet CNN", @@ -772355,97 +775322,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.14.21257229", - "rel_title": "Symptom profiles and accuracy of clinical definitions for COVID-19 in the community. Results of the Virus Watch community cohort.", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257229", - "rel_abs": "BackgroundUnderstanding the symptomatology and accuracy of clinical case definitions for COVID-19 in the community is important for the initiation of Test, Trace and Isolate (TTI) and may, in future, be important for early prescription of antivirals.\n\nMethodsVirus Watch is a large community cohort with prospective daily recording of a wide range of symptoms and self-reporting of swab results (mainly undertaken through the UK TTI system). We compared frequency, severity, timing, and duration of symptoms in test positive and test negative cases. We compared the test performance of the current UK case definition used by TTI (any one of: new continuous cough, high temperature, or loss of or altered sense of smell or taste) with a wider definition that also included muscle aches, chills, headache, or loss of appetite.\n\nFindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition.\n\nInterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ellen Fragaszy", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; Department of Infectious Disease Epidemiology, London School " - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London" - }, - { - "author_name": "Cyril Geismar", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College" - }, - { - "author_name": "Anna Aryee", - "author_inst": "Institute of Health Informatics, University College London" - }, - { - "author_name": "Sarah Beale", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College" - }, - { - "author_name": "Isobel Braithwaite", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London" - }, - { - "author_name": "Thomas Byrne", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London" - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London" - }, - { - "author_name": "Jo Gibbs", - "author_inst": "Institute for Global Health, University College London" - }, - { - "author_name": "Pia Hardelid", - "author_inst": "Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Jana Kovar", - "author_inst": "Institute of Epidemiology and Health Care, University College London" - }, - { - "author_name": "Vasileios Edward Lampos", - "author_inst": "Department of Computer Science, University College London" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Francis Crick Institute, London, UK" - }, - { - "author_name": "Annalan Mathew Dwight Navaratnam", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; . Institute of Epidemiology and Health Care, University Colle" - }, - { - "author_name": "Vincent Grigori Nguyen", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College" - }, - { - "author_name": "Parth Patel", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "Institute of Epidemiology and Health Care, University College London" - }, - { - "author_name": "- Virus Watch Collaborative", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.14.21257218", "rel_title": "Effectiveness of BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector vaccine on mortality following COVID-19", @@ -773177,6 +776053,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.18.21257267", + "rel_title": "Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257267", + "rel_abs": "BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions.\n\nMethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47).\n\nInterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Peter W Horby", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res" + }, + { + "author_name": "Mark Campbell", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King" + }, + { + "author_name": "Enti Spata", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Jonathan R Emberson", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Natalie Staplin", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Guilherme Pessoa-Amorim", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Leon Peto", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat" + }, + { + "author_name": "Martin Wiselka", + "author_inst": "Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom" + }, + { + "author_name": "Laura Wiffen", + "author_inst": "Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom" + }, + { + "author_name": "Simon Tiberi", + "author_inst": "Department of Infection, Barts Health NHS Trust, London, United Kingdom" + }, + { + "author_name": "Ben Caplin", + "author_inst": "Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom" + }, + { + "author_name": "Caroline Wroe", + "author_inst": "James Cook University Hospital, Middlesbrough, United Kingdom" + }, + { + "author_name": "Christopher Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom" + }, + { + "author_name": "Paul Hine", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom" + }, + { + "author_name": "Benjamin Prudon", + "author_inst": "North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom" + }, + { + "author_name": "Tina George", + "author_inst": "Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom" + }, + { + "author_name": "Andrew Wight", + "author_inst": "Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" + }, + { + "author_name": "Buddha Basnyat", + "author_inst": "Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal" + }, + { + "author_name": "Maya H Buch", + "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom" + }, + { + "author_name": "Lucy C Chappell", + "author_inst": "School of Life Course Sciences, King?s College London, London, United Kingdom" + }, + { + "author_name": "Jeremy N Day", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, " + }, + { + "author_name": "Raph L Hamers", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine " + }, + { + "author_name": "Thomas Jaki", + "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United" + }, + { + "author_name": "Edmund Juszczak", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting" + }, + { + "author_name": "Alan Montgomery", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Andrew Mumford", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom" + }, + { + "author_name": "Kathryn Rowan", + "author_inst": "Intensive Care National Audit & Research Centre, London, United Kingdom" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer" + }, + { + "author_name": "Marion Mafham", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Richard Haynes", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King" + }, + { + "author_name": "Martin J Landray", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.16.21257283", "rel_title": "Early Anakinra Treatment for COVID-19 Guided by Urokinase Plasminogen Receptor", @@ -774085,41 +777116,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.05.16.21257300", - "rel_title": "Will there be a third COVID-19 wave? A SVEIRD model based study of Indian situation.", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.16.21257300", - "rel_abs": "Since first patient detected in India in late February, 2020, SARS-CoV-II virus is playing havoc on India. After the first wave, India is now riding the 2nd wave. As was in the case of European countries like Italy and UK, the 2nd wave is more contagious and at the time of writing this paper, the per day infection is as high as 400,000. The alarming thing is it is not uncommon that people is getting infected multiple time. On the other hand, mass vaccination has started step by step. There is also growing danger of potential 3rd wave is unavoidable, which can even infect kids and minors.\n\nIn this situation, an estimation of the dynamics of SARS-CoV-2 is absolutely necessary to combat the pandemic. We have used a modified SEIRD model, that includes vaccination and repeat infection as well. We have studied India and 8 Indian states with varying SARS-CoV-2 infection. We have shown that, Covid-19 wave will be repeated time to time, but the intensity will slow down with time. In most possible situation, our calculation shows COVID-19 will remain as endemic for foreseeable future, unless we are able to increase our vaccination rate manifold.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dwarakesh Kannan", - "author_inst": "Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, TamilNadu, India, 603203" - }, - { - "author_name": "Gurusriram R", - "author_inst": "Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, TamilNadu, India, 603203" - }, - { - "author_name": "Rudra Banerjee", - "author_inst": "Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, TamilNadu, India, 603203" - }, - { - "author_name": "Srijit Bhattacharjee", - "author_inst": "Indian Institute of Information Technology (IIIT), Allahabad, Deoghat, Jhalwa, Uttar Pradesh, India, 211015" - }, - { - "author_name": "Pritish Kumar Varadwaj", - "author_inst": "Indian Institute of Information Technology Allahabad" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.17.21257092", "rel_title": "Public attitudes to COVID-19 vaccines: A qualitative study", @@ -775147,6 +778143,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.15.21256976", + "rel_title": "Excess mortality during the COVID-19 pandemic: a geospatial and statistical analysis in Mogadishu, Somalia", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.15.21256976", + "rel_abs": "BackgroundWhile the impact of the COVID-19 pandemic has been well documented in high-income countries, much less is known about its impact in Somalia where health systems are weak and vital registration is under developed.\n\nMethodsWe used remote sensing and geospatial analysis to quantify the number of burials from January 2017 to September 2020 in Mogadishu. We imputed missing grave counts using surface area data. Simple interpolation and a generalised additive mixed growth model were used to predict both actual and counterfactual burial rates by cemetery and across Mogadishu during the most likely period of COVID-19 excess mortality and to compute excess burials. We also undertook a qualitative survey of key informants to determine the drivers of COVID-19 excess mortality.\n\nResultsBurial rates increased during the pandemic period with a ratio to pre-pandemic levels averaging 1.5-fold and peaking at 2.2-fold. When scaled to plausible range of baseline Crude Death Rates (CDR), excess death toll between January and September 2020 ranged between 3,200 and 11,800. When compared to burial records of the Barakaat Cemetery Committee our estimates were found to be lower.\n\nConclusionsOur study points to considerable under estimation of COVID-19 impact in Banadir and an overburdened public health system struggling to deal with the increasing severity of the epidemic in 2020.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Abdihamid Warsame", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Farah Bashiir", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Terri Freemantle", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Chris Williams", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Yolanda Vazquez", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Chris Reeve", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Ahmed Aweis", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Mohamed Ahmed", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Francesco Checchi", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Abdirisak Dalmar", + "author_inst": "Somali Disaster Resilience Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.12.21257123", "rel_title": "Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults", @@ -775815,105 +778866,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.16.444369", - "rel_title": "Broad neutralization against SARS-CoV-2 variants induced by a modified B.1.351 protein-based COVID-19 vaccine candidate", - "rel_date": "2021-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.16.444369", - "rel_abs": "Beginning in late 2020, the emergence and spread of multiple variant SARS-CoV-2 strains harboring mutations which may enable immune escape necessitates the rapid evaluation of second generation COVID-19 vaccines, with the goal of inducing optimized immune responses that are broadly protective. Here we demonstrate in a mouse immunogenicity study that two doses of a modified B.1.351 spike (S)-Trimer vaccine (B.1.351 S-Trimer) candidate can induce strong humoral immune responses that can broadly neutralize both the original SARS-CoV-2 strain (Wuhan-Hu-1) and Variants of Concern (VOCs), including the UK variant (B.1.1.7), South African variant (B.1.351) and Brazil variant (P.1). Furthermore, while immunization with two doses (prime-boost) of Prototype S-Trimer vaccine (based on the original SARS-CoV-2 strain) induced lower levels of cross-reactive neutralization against the B.1.351 variant, a third dose (booster) administered with either Prototype S-Trimer or B.1.351 S-Trimer was able to increase neutralizing antibody titers against B.1.351 to levels comparable to neutralizing antibody titers against the original strain elicited by two doses of Prototype S-Trimer.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Danmei Su", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Xinglin Li", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Cui He", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Xueqin Huang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Meilin Chen", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Qiang Wang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Wenchang Qin", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Ying Liang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Rong Xu", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Jinhua Wu", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Peiwen Luo", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Xiaofang Yang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Yilan Zeng", - "author_inst": "Public Health Clinical Center of Chengdu, Chengdu, China" - }, - { - "author_name": "Mei Luo", - "author_inst": "Public Health Clinical Center of Chengdu, Chengdu, China" - }, - { - "author_name": "Dongxia Luo", - "author_inst": "Public Health Clinical Center of Chengdu, Chengdu, China" - }, - { - "author_name": "David M Salisbury", - "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Donna Ambrosino", - "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "George Siber", - "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Ralf Clemens", - "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Peng Liang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Joshua G. Liang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.17.444467", "rel_title": "Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 cells but not in human primary airway epithelium cells", @@ -777088,6 +780040,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.13.444010", + "rel_title": "Durability of mRNA-1273-induced antibodies against SARS-CoV-2 variants", + "rel_date": "2021-05-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.13.444010", + "rel_abs": "SARS-CoV-2 mutations may diminish vaccine-induced protective immune responses, and the durability of such responses has not been previously reported. Here, we present a comprehensive assessment of the impact of variants B.1.1.7, B.1.351, P.1, B.1.429, and B.1.526 on binding, neutralizing, and ACE2-blocking antibodies elicited by the vaccine mRNA-1273 over seven months. Cross-reactive neutralizing responses were rare after a single dose of mRNA-1273. At the peak of response to the second dose, all subjects had robust responses to all variants. Binding and functional antibodies against variants persisted in most subjects, albeit at low levels, for 6 months after the primary series of mRNA-1273. Across all assays, B.1.351 had the greatest impact on antibody recognition, and B.1.1.7 the least. These data complement ongoing studies of clinical protection to inform the potential need for additional boost vaccinations.\n\nOne-Sentence SummaryMost mRNA-1273 vaccinated individuals maintained binding and functional antibodies against SARS-CoV-2 variants for 6 months.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Amarendra Pegu", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Stephen D. Schmidt", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Chloe A. Talana", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Jim Albert", + "author_inst": "Emmes Company, Rockville, MD, USA." + }, + { + "author_name": "Evan Anderson", + "author_inst": "Department of Medicine, Center for Childhood Infections and Vaccines (CCIV) of Childrens Healthcare of Atlanta and Emory University Department of Pediatrics, At" + }, + { + "author_name": "Hamilton Bennett", + "author_inst": "Moderna, Inc., Cambridge, MA, USA." + }, + { + "author_name": "Kizzmekia Corbett", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Britta Flach", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Lisa Jackson", + "author_inst": "Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA." + }, + { + "author_name": "Brett Leav", + "author_inst": "Moderna, Inc., Cambridge, MA, USA." + }, + { + "author_name": "Julie E. Ledgerwood", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Catherine J. Luke", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Mat Makowski", + "author_inst": "Emmes Company, Rockville, MD, USA." + }, + { + "author_name": "Paul C. Roberts", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Mario Roederer", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Paulina Alejandra Rebolledo", + "author_inst": "Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur, GA, USA." + }, + { + "author_name": "Christina A. Rostad", + "author_inst": "Department of Medicine, Center for Childhood Infections and Vaccines (CCIV) of Childrens Healthcare of Atlanta and Emory University Department of Pediatrics, At" + }, + { + "author_name": "Nadine G. Rouphael", + "author_inst": "Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur, GA, USA." + }, + { + "author_name": "Lingshu Wang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Eun Sung Yang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "John H. Beigel", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Barney S. Graham", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Adrian McDermott", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Nicole A Doria-Rose", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.14.444076", "rel_title": "The Spike Proteins of SARS-CoV-2 B.1.617 and B.1.618 Variants Identified in India Provide Partial Resistance to Vaccine-elicited and Therapeutic Monoclonal Antibodies.", @@ -777988,81 +781055,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.12.21257116", - "rel_title": "Determinants of COVID-19 vaccine hesitancy and vaccine uptake in a national cohort of U.S. adults", - "rel_date": "2021-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257116", - "rel_abs": "We estimated the trends and correlates of vaccine hesitancy, and its association with subsequent vaccine uptake among 5,458 adults in the United States. Participants belonged to the CHASING COVID Cohort, a national longitudinal study. Trends and correlates of vaccine hesitancy were examined longitudinally in eight interview rounds from October 2020 to July 2021. We also estimated the association between willingness to vaccinate and subsequent vaccine uptake through July 2021. Vaccine delay and refusal decreased from 51% and 8% in October 2020 to 8% and 6% in July 2021, respectively. Compared to Non-Hispanic (NH) White participants, NH Black and Hispanic participants had higher adjusted odds ratios (aOR) for both vaccine delay (aOR: 2.0 [95% CI: 1.5, 2.7] for NH Black and 1.3 [95% CI: 1.0, 1.7] for Hispanic) and vaccine refusal (aOR: 2.5 [95% CI: 1.8, 3.6] for NH Black and 1.4 [95% CI: 1.0, 2.0] for Hispanic) in June 2021. COVID-19 vaccine hesitancy was associated with lower odds of subsequent vaccine uptake (aOR: 0.15, 95% CI: 0.13, 0.18 for vaccine-delayers and aOR: 0.02; 95% CI: 0.01, 0.03 for vaccine-refusers compared to vaccine-willing participants), adjusted for sociodemographic factors and COVID-19 history. Vaccination awareness and distribution efforts should focus on vaccine delayers.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Madhura S Rane", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Shivani Kochhar", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Emily Poehlein", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "William You", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "McKaylee M Robertson", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Rebecca Zimba", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Drew A. Westmoreland", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Matthew L Romo", - "author_inst": "Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York (CUNY); New York City, New York US" - }, - { - "author_name": "Sarah G. Kulkarni", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Mindy Chang", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Amanda Berry", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Angela M. Parcesepe", - "author_inst": "Department of Maternal and Child Health, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA" - }, - { - "author_name": "Andrew R. Maroko", - "author_inst": "Department of Environmental, Occupational, and Geospatial Health Sciences, Graduate School of Public Health and Health Policy, City University of New York (CUNY" - }, - { - "author_name": "Christian Grov", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Denis Nash", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.12.21257126", "rel_title": "Bayesian Model Averaging to Account for Model Uncertainty in Estimates of a Vaccine's Effectiveness", @@ -779242,6 +782234,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.13.21256639", + "rel_title": "Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.1.7 Variant", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21256639", + "rel_abs": "BackgroundCovid-19 vaccines are urgently needed, especially against emerging variants. NVX-CoV2373 is a recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 rS) nanoparticle vaccine containing trimeric full-length SARS-CoV-2 spike glycoprotein and Matrix-M adjuvant.\n\nMethodsA phase 3, randomized, observer-blinded, placebo-controlled trial was conducted in adults 18-84 years old who received two intramuscular 5-{micro}g doses, 21 days apart, of NVX-CoV2373 or placebo (1:1) across 33 sites in the United Kingdom. The primary efficacy endpoint was virologically confirmed symptomatic Covid-19 with onset 7 days after second vaccination in serologically negative participants.\n\nResultsA total of 15,187 participants were randomized, of whom 7569 received NVX-CoV2373 and 7570 received placebo; 27.2% were 65 years or older, 44.7% had comorbidities and 4.2% had baseline serological evidence of SARS-CoV-2. There were 10 cases of Covid-19 among NVX-CoV2373 recipients and 96 cases among placebo recipients, with symptom onset at least 7 days after second vaccination; NVX-CoV2373 was 89.7% (95% confidence interval, 80.2 to 94.6) effective in preventing Covid-19, with no hospitalizations or deaths reported. There were five cases of severe Covid-19, all in the placebo group. Post hoc analysis revealed efficacies of 96.4% (73.8 to 99.5) and 86.3% (71.3 to 93.5) against the prototype strain and B.1.1.7 variant, respectively. Vaccine efficacy was similar across subgroups, including participants with comorbidities and those [≥]65 years old. Reactogenicity was generally mild and transient. The incidence of serious adverse events was low and similar in the two groups.\n\nConclusionA two-dose regimen of NVX-CoV2373 conferred 89.7% protection against a blend of prototype and variant Covid-19, demonstrated high efficacy against the B.1.1.7 variant, and had a reassuring safety profile.\n\n(Funded by Novavax, Inc. EudraCT number, 2020-004123-16).", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Seth Toback", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Paul T. Heath", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Eva P. Galiza", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "David Baxter", + "author_inst": "Stockport NHS Foundation Trust, Stepping Hill Hospital" + }, + { + "author_name": "Marta Boffito", + "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust and Imperial College London" + }, + { + "author_name": "Duncan Browne", + "author_inst": "Royal Cornwall Hospital NHS Trust" + }, + { + "author_name": "Fiona Burns", + "author_inst": "Institute for Global Health, University College London and Royal Free London NHS Foundation Trust" + }, + { + "author_name": "David R. Chadwick", + "author_inst": "Centre for Clinical Infection, South Tees Hospitals NHS Foundation Trust, James Cook University Hospital" + }, + { + "author_name": "Rebecca Clark", + "author_inst": "Layton Medical Centre" + }, + { + "author_name": "Catherine Cosgrove", + "author_inst": "Vaccine Institute, St. Georges, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "James Galloway", + "author_inst": "Centre for Rheumatic Disease, Kings College London" + }, + { + "author_name": "Anna L. Goodman", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, University College London" + }, + { + "author_name": "Amardeep Heer", + "author_inst": "Lakeside Healthcare Research, Lakeside Surgeries Corby" + }, + { + "author_name": "Andrew Higham", + "author_inst": "University Hospitals of Morecambe Bay NHS Foundation Trust" + }, + { + "author_name": "Shalini Iyengar", + "author_inst": "Accelerated Enrollment Solutions, Synexus Hexham, Hexham General Hospital" + }, + { + "author_name": "Arham Jamal", + "author_inst": "Accelerated Enrollment Solutions, Synexus Thames Valley" + }, + { + "author_name": "Christopher Jeanes", + "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust" + }, + { + "author_name": "Philip A. Kalra", + "author_inst": "Salford Royal NHS Foundation Trust, Northern Care Alliance" + }, + { + "author_name": "Christina Kyriakidou", + "author_inst": "Accelerated Enrolment Solutions, Synexus Midlands" + }, + { + "author_name": "Daniel F. McAuley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, Queen's University of Belfast & Royal Victoria Hospital" + }, + { + "author_name": "Agnieszka Meyrick", + "author_inst": "Accelerated Enrolment Solutions, Synexus Merseyside" + }, + { + "author_name": "Angela M. Minassian", + "author_inst": "Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford" + }, + { + "author_name": "Jane Minton", + "author_inst": "St James's University Hospital, Leeds Teaching Hospitals NHS Trust" + }, + { + "author_name": "Patrick Moore", + "author_inst": "The Adam Practice, University Hospital Southampton NHS Foundation Trust" + }, + { + "author_name": "Imrozia Munsoor", + "author_inst": "Accelerated Enrolment Solutions, Synexus Glasgow" + }, + { + "author_name": "Helen Nicholls", + "author_inst": "Accelerated Enrolment Solutions, Synexus Wales" + }, + { + "author_name": "Orod Osanlou", + "author_inst": "Bangor University and Betsi Cadwaladr University" + }, + { + "author_name": "Jonathan Packham", + "author_inst": "University of Nottingham and Haywood Hospital, Midlands Partnership NHS Foundation Trust" + }, + { + "author_name": "Carol Pretswell", + "author_inst": "Accelerated Enrolment Solutions, Synexus Lancashire" + }, + { + "author_name": "Alberto San Francisco Ramos", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Dinesh Saralaya", + "author_inst": "National Institute for Health Research and Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Ray P. Sheridan", + "author_inst": "Royal Devon & Exeter Hospital" + }, + { + "author_name": "Richard Smith", + "author_inst": "East Suffolk and North Essex NHS Foundation Trust and University of Essex" + }, + { + "author_name": "Roy L. Soiza", + "author_inst": "Aberdeen Royal Infirmary, NHS Grampian & Ageing Clinical and Experimental Research (ACER) Group, University of Aberdeen" + }, + { + "author_name": "Pauline A. Swift", + "author_inst": "Epsom and St Helier University Hospitals NHS Trust" + }, + { + "author_name": "Emma C Thomson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jeremy Turner", + "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust" + }, + { + "author_name": "Marianne Elizabeth Viljoen", + "author_inst": "Accelerated Enrolment Solutions, Synexus Manchester" + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Iksung Cho", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Joy Rivers", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Kathy Smith", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.06.21256757", "rel_title": "COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study", @@ -779886,25 +783073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.07.21256798", - "rel_title": "Longer incubation periods of SARS-CoV-2 infection in infants", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256798", - "rel_abs": "ObjectiveA large body of research has described the incubation period of SARS-CoV-2 infection, an important metric for assessing the risk of developing a disease as well as surveillance. While longer incubation periods for elderly have been found, it remains elusive whether this also holds true for infants and children, partly due to the lack of data. The present work clarified the incubation periods of COVID-19 for infants and children.\n\nMethodsUsing the data released by the Chinese health authorities and municipal offices, statistical comparisons of clinical features were made between infants (aged below 1 year) and children (aged between 1 and 17 years). An age-varying incubation period distribution period was modeled using maximum likelihood estimation modified for interval censored exposure time and age.\n\nDiscussionReported in 56 web pages, a total of 65 cases from 20 provinces dated between January and June 2020, including 18 infants and 47 children, were eligible for inclusion. Infants appeared to bear more severe clinical courses, as demonstrated by the higher prevalence of breathing difficulty as well as nasal congestion. In contrast, fever was less prominent in infants than in children. The incubation period was found to decrease with age, with infants appearing to have longer incubation periods.\n\nConclusionFever remained to be one of the most commonly seen symptoms in infants and children with SARS-CoV-2 infection and have continued to determine the time of symptom onset. While shorter incubation periods should be seen in patients with weaker immune system due to weaker antiviral response that is beneficial for viral growth, the longer incubation period in infants may be due to their weaker febrile response to the virus, leading to prolonged symptom onset.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Char Leung", - "author_inst": "Deakin University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.10.21256816", "rel_title": "Cost-effectiveness of whole area testing of asymptomatic SARS-CoV-2 infections in Merthyr Tydfil, 2020: A Modelling and economic analysis", @@ -781748,6 +784916,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.06.21256738", + "rel_title": "The evaluation of a novel digital immunochromatographic assay with silver amplification to detect SARS-CoV-2", + "rel_date": "2021-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256738", + "rel_abs": "IntroductionRapid antigen tests are convenient for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, they have lower sensitivities than nucleic acid amplification tests. In this study, we evaluated the diagnostic performance of Quick Chaser(R) Auto SARS-CoV-2, a novel digital immunochromatographic assay that is expected to have higher sensitivity than conventional antigen tests.\n\nMethodsA prospective observational study was conducted between February 8 and March 24, 2021. We simultaneously obtained two nasopharyngeal samples, one for evaluation with the QuickChaser(R) Auto SARS-CoV-2 antigen test and the other for assessment with reverse transcription PCR (RT-PCR), considered the gold-standard reference test. The limit of detection (LOD) of the new antigen test was compared with those of four other commercially available rapid antigen tests.\n\nResultsA total of 1401 samples were analyzed. SARS-CoV-2 was detected by reference RT-PCR in 83 (5.9%) samples, of which 36 (43.4%) were collected from symptomatic patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 74.7% (95% confidence interval (CI): 64.0-83.6%), 99.8% (95% CI: 99.5-100%), 96.9% (95% CI: 89.2-99.6%), and 98.4% (95% CI: 97.6-99.0%), respectively. When limited to samples with a cycle threshold (Ct) <30 or those from symptomatic patients, the sensitivity increased to 98.3% and 88.9%, respectively. The QuickChaser(R) Auto SARS-CoV-2 detected 34-120 copies/test, which indicated greater sensitivity than the other rapid antigen tests.\n\nConclusionsQuickChaser(R) Auto SARS-CoV-2 showed sufficient sensitivity and specificity in clinical samples of symptomatic patients. The sensitivity was comparable to RT-PCR in samples with Ct<30.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yoko Kurihara", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Yoshihiko Kiyasu", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Yusaku Akashi", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Yuto Takeuchi", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Kenji Narahara", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Sunao Mori", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Tomonori Takeshige", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Shigeyuki Notake", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Atsuo Ueda", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Koji Nakamura", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiroichi Ishikawa", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiromichi Suzuki", + "author_inst": "University of Tsukuba" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.12.21256693", "rel_title": "Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols", @@ -782476,57 +785707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.07.21256852", - "rel_title": "Clinical outcomes and cost-effectiveness of COVID-19 vaccination in South Africa", - "rel_date": "2021-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256852", - "rel_abs": "Low- and middle-income countries are implementing COVID-19 vaccination strategies in light of varying vaccine efficacies and costs, supply shortages, and resource constraints. Here, we use a microsimulation model to evaluate clinical outcomes and cost-effectiveness of a COVID-19 vaccination program in South Africa. We varied vaccination coverage, pace, acceptance, effectiveness, and cost as well as epidemic dynamics. Providing vaccines to at least 40% of the population and prioritizing vaccine rollout prevented >9 million infections and >73,000 deaths and reduced costs due to fewer hospitalizations. Model results were most sensitive to assumptions about epidemic growth and prevalence of prior immunity to SARS-CoV-2, though the vaccination program still provided high value and decreased both deaths and health care costs across a wide range of assumptions. Vaccination program implementation factors, including prompt procurement, distribution, and rollout, are likely more influential than characteristics of the vaccine itself in maximizing public health benefits and economic efficiency.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Krishna P Reddy", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kieran P Fitzmaurice", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Justine A Scott", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Guy Harling", - "author_inst": "University College London" - }, - { - "author_name": "Richard J Lessells", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Christopher Panella", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Fatma M Shebl", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kenneth A Freedberg", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Mark J Siedner", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.08.21256891", "rel_title": "Homebrew reagents for low cost RT-LAMP", @@ -783482,6 +786662,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.05.11.21257016", + "rel_title": "Comparative sensitivity evaluation for 122 CE-marked SARS-CoV-2 antigen rapid tests", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257016", + "rel_abs": "ObjectiveIndependent evaluation of the sensitivity of CE-marked SARS-CoV-2 antigen rapid diagnostic tests (Ag RDT) offered in Germany.\n\nMethodThe sensitivity of 122 Ag RDT was adressed using a common evaluation panel. Minimum sensitivity of 75% for panel members with CT<25 was used for differentiation of devices eligible for reimbursement in in the German healthcare system.\n\nResultsThe sensitivity of different SARS-CoV-2 Ag RDT varied over a wide range. The sensitivity limit of 75% for panel members with CT <25 was met by 96 of the 122 tests evaluated; 26 tests exhibited lower sensitivity, few of which were completely failing. Some devices exhibited high sensitivity, e.g. 100% for CT<30.\n\nConclusionThis comparative evaluation succeeded to distinguish less sensitive from better performing Ag RDT. Most of the Ag RDT evaluated appear to be suitable for fast identification of acute infections associated with high viral loads. Market access of SARS-CoV-2 Ag RDT should be based on minimal requirements for sensitivity and specificity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Heinrich Scheiblauer", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Angela Filomena", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Andreas Nitsche", + "author_inst": "Robert Koch-Institute, Seestrasse 10, D-13353 Berlin" + }, + { + "author_name": "Andreas Puyskens", + "author_inst": "Robert Koch-Institute, Seestrasse 10, D-13353 Berlin" + }, + { + "author_name": "Victor Corman", + "author_inst": "Institute of Virology, Charite, Chariteplatz 1, D-10117 Berlin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charite, Chariteplatz 1, D-10117 Berlin" + }, + { + "author_name": "Katrin Zwirglmaier", + "author_inst": "Bundeswehr Institute of Microbiology, Neuherbergstr 11, D-80937 Munich" + }, + { + "author_name": "Constanze Lange", + "author_inst": "LADR GmbH, Lauenburger Str. 67, D-21502 Geesthacht" + }, + { + "author_name": "Petra Emmerich", + "author_inst": "Bernhard-Nocht Institute, Dep.Virology, Bernhard-Nocht Str. 74, D-20359 Hamburg" + }, + { + "author_name": "Michael Mueller", + "author_inst": "MVZ Labor 28 GmbH, Mecklenburgische Str. 2, D-14197 Berlin" + }, + { + "author_name": "Olivia Knauer", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Micha Nuebling", + "author_inst": "Paul-Ehrlich-Institut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.10.21256996", "rel_title": "Quantifying the potential for dominant spread of SARS-CoV-2 variant B.1.351 in the United States", @@ -784458,37 +787701,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.11.443708", - "rel_title": "Energy Landscape of the SARS-CoV-2 Reveals Extensive Conformational Heterogeneity", - "rel_date": "2021-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443708", - "rel_abs": "Cryo-electron microscopy (cryo-EM) has produced a number of structural models of the SARS-CoV-2 spike, already prompting biomedical outcomes. However, these reported models and their associated electrostatic potential maps represent an unknown admixture of conformations stemming from the underlying energy landscape of the spike protein. As for any protein, some of the spikes conformational motions are expected to be biophysically relevant, but cannot be interpreted only by static models. Using experimental cryo-EM images, we present the energy landscape of the spike protein conformations, and identify molecular rearrangements along the most-likely conformational path in the vicinity of the open (so called 1RBD-up) state. The resulting global and local atomic refinements reveal larger movements than those expected by comparing the reported 1RBD-up and 1RBD-down cryo-EM models. Here we report greater degrees of \"openness\" in global conformations of the 1RBD-up state, not revealed in the single-model interpretations of the density maps, together with conformations that overlap with the reported models. We discover how the glycan shield contributes to the stability of these conformations along the minimum free-energy pathway. A local analysis of seven key binding pockets reveals that six out them, including those for engaging ACE2, therapeutic mini-proteins, linoleic acid, two different kinds of antibodies, and protein-glycan interaction sites, switch conformations between their known apo- and holo-conformations, even when the global spike conformation is 1RBD-up. This is reminiscent of a conformational pre-equilibrium. We found only one binding pocket, namely antibody AB-C135 to remain closed along the entire minimum free energy path, suggesting an induced fit mechanism for this enzyme.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ghoncheh Mashayekhi", - "author_inst": "Univ. of Wisconsin Milwaukee" - }, - { - "author_name": "John Vant", - "author_inst": "Arizona State University" - }, - { - "author_name": "Abhishek Singharoy", - "author_inst": "Arizona State University" - }, - { - "author_name": "Abbas Ourmazd", - "author_inst": "Univ. of Wisconsin Milwaukee" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.05.12.443888", "rel_title": "mRNA vaccine-induced SARS-CoV-2-specific T cells recognize B.1.1.7 and B.1.351 variants but differ in longevity and homing properties depending on prior infection status", @@ -785624,6 +788836,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.11.21256479", + "rel_title": "Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence", + "rel_date": "2021-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256479", + "rel_abs": "ObjectivesTo describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence.\n\nDesignCase control analysis with cases stratified by HIV-1 and tuberculosis status.\n\nSettingA single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis.\n\nParticipants104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9%) were male and 31 (29.8%) HIV-1 co-infected. 40 adults (35.7% male, 30.9% HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis.\n\nResultsTwo or more co-morbidities were present in 57.7% of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48%), type 2 diabetes mellitus (39%), obesity (31%) but also HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p < 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis.\n\nConclusionsIn this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high.\n\nWhat is already known on this topic?It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection.\n\nWhat this study addsTwo or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30%) and active tuberculosis (14%). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29% of all COVID-19 patients and in 40% of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Elsa du Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town and Imperial College London" + }, + { + "author_name": "Remy Daroowala", + "author_inst": "Imperial College London and University of Cape Town" + }, + { + "author_name": "Qonita Said-Hartley", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marvin Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rene Tina Goliath", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Fatima Abrahams", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Amanda Jackson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sean Wasserman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Brian Allwood", + "author_inst": "University of Stellenbosch" + }, + { + "author_name": "Angharad G Davis", + "author_inst": "University College London, Francis Crick Institute, and University of Cape Town" + }, + { + "author_name": "Rachel Lai", + "author_inst": "Imperial College London and Francis Crick Institute" + }, + { + "author_name": "Anna Kathleen Coussens", + "author_inst": "Walter and Eliza Hall Institute and University of Cape Town" + }, + { + "author_name": "Katalin Andrea Wilkinson", + "author_inst": "The Francis Crick Institute and University of Cape Town" + }, + { + "author_name": "Jantina De Vries", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Nicki Tiffin", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Maddalena Cerrone", + "author_inst": "Imperial College London and Francis Crick Institute" + }, + { + "author_name": "Ntobeko Ntusi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Robert J Wilkinson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "- HIATUS investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.05.11.21256877", "rel_title": "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity", @@ -787052,105 +790363,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.10.21256912", - "rel_title": "Household overcrowding and risk of SARS-CoV-2: analysis of the Virus Watch prospective community cohort study in England and Wales", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256912", - "rel_abs": "BackgroundHousehold overcrowding is associated with increased risk of infectious diseases across contexts and countries. Limited data exist linking household overcrowding and risk of COVID-19. We used data collected from the Virus Watch cohort to examine the association between overcrowded households and SARS-CoV-2.\n\nMethodsThe Virus Watch study is a household community cohort of acute respiratory infections in England & Wales that began recruitment in June 2020. We calculated the persons per room for each household and classified accommodation as overcrowded when the number of rooms{square}was fewer than the number of people. We considered two primary outcomes - PCR-confirmed positive SARS-CoV-2 antigen tests and laboratory confirmed SARS-CoV-2 antibodies (Roche Elecsys anti-N total immunoglobulin assay). We used mixed effects logistic regression models that accounted for household structure to estimate the association between household overcrowding and SARS-CoV-2 infection.\n\nResultsThe proportion of participants with a positive SARS-CoV-2 PCR result was highest in the overcrowded group (6.6%; 73/1,102) and lowest in the under-occupied group (2.9%; 682/23,219). In a mixed effects logistic regression model that included age, sex, ethnicity, household income and geographical region, we found strong evidence of an increased odds of having a positive PCR SARS-CoV-2 antigen result (Odds Ratio 3.72; 95% CI: 1.92, 7.13; p-value < 0.001) and increased odds of having a positive SARS-CoV-2 antibody result in individuals living in overcrowded houses (2.96; 95% CI: 1.13, 7.74; p-value =0.027) compared to people living in under-occupied houses. The proportion of variation at the household level was 9.91% and 9.97% in the PCR and antibody models respectively.\n\nDiscussionPublic health interventions to prevent and stop the spread of SARS-CoV-2 should consider the much greater risk of infection for people living in overcrowded households and pay greater attention to reducing household transmission. There is an urgent need to better recognise housing as a leading determinant of health in the context of a pandemic and beyond.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Robert W Aldridge", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Helen Pineo", - "author_inst": "Institute for Environmental Design and Engineering, Bartlett School of Environment, Energy and Resources, University College London, London, UK." - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col" - }, - { - "author_name": "Max Eyre", - "author_inst": "Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK" - }, - { - "author_name": "Jana Kovar", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" - }, - { - "author_name": "Vincent Nguyen", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Sarah Beale", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col" - }, - { - "author_name": "Thomas Byrne", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Anna Aryee", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Colette Smith", - "author_inst": "Institute for Global Health, University College London, London, UK." - }, - { - "author_name": "Delanjathan Devakumar", - "author_inst": "Institute for Global Health, University College London, London, UK." - }, - { - "author_name": "Jonathon Taylor", - "author_inst": "Department of Civil Engineering, Tampere University, Finland." - }, - { - "author_name": "Vittal Katikireddi", - "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow Institute of Health and Wellbeing, Glasgow, UK." - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Cyril Geismar", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col" - }, - { - "author_name": "Parth Patel", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Isobel Braithwaite", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK." - }, - { - "author_name": "Annalan M D Navaratnam", - "author_inst": "Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col" - }, - { - "author_name": "Anne M Johnson", - "author_inst": "Institute for Global Health, University College London, London, UK." - }, - { - "author_name": "Andrew Hayward", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.11.443659", "rel_title": "SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes", @@ -788286,6 +791498,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.07.21256743", + "rel_title": "Effect of using personal protective equipment during the COVID-19 pandemic on the quality indicators of screening colonoscopies.", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256743", + "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) has affected many facets of the practice of medicine including screening colonoscopies.\n\nAimsOur study looks to observe if there has been an effect on the quality of colonoscopies, as indicated by quality measures such as cecal intubation rate (CIR), cecal intubation time (CIT), scope withdrawal time (SWT) and adenoma detection rate (ADR) with the adoption of standard COVID-19 precautions.\n\nMethodsWe conducted a retrospective chart review to analyze the effects of the COVID-19 pandemic on screening colonoscopies. The study utilized data on CIR, CIT, SWT and ADR from outpatient, non-emergent procedures conducted at 3 endoscopy suites of St Lukes University Health Network. All inpatient and emergent procedures were excluded.\n\nResultsOur study demonstrated that the total number of screening colonoscopies was decreased between 2019 to 2020 (318 in 2019 vs 157 in 2020, p= 0.005). CIT (320{+/-}105 seconds in 2019 vs 392{+/-}107 seconds in 2020, p=0.001) and SWT (706{+/-}232 seconds in 2019 vs 830{+/-}241 seconds in 2020, p=0.001) were increased while CIR (98.2% in 2019 vs 96.6% in 2020, p=0.04) was decreased between 2019 and 2020 likely due to PPE introduction. ADR was similar between the two groups (38.23 (12.50-66.66) in 2019 vs 38.18(16.66-66.00) in 2020, p=0.8).\n\nConclusionOur study showed that quality indices for screening colonoscopies like CIR, CIT, and SWT were negatively impacted during the COVID-19 time period. ADR, however, were similar. Thus, the efficiency of the procedures was affected by the use of PPE but it did not affect the colonoscopys clinical benefit.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Subin G Chirayath", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Janak Bahirwani", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Parampreet Kaur", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Noel Martins", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Ronak Modi", + "author_inst": "St. Luke's University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.05.08.21256792", "rel_title": "Yet another lockdown? A large-scale study on people's unwillingness to be confined during the first 5 months of the COVID-19 pandemic in Spain", @@ -789222,33 +792469,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.10.21256955", - "rel_title": "SARS-CoV-2 Heterogeneity by Ethnicity in Los Angeles", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256955", - "rel_abs": "Recent studies have identified notable disparities in SARS-CoV-2 infection risk among ethnic minorities. We evaluated SARS-CoV-2 test results from individuals presenting for testing in Los Angeles between June-December, 2020. We calculated prevalence ratios for various employment categories. Among 518,914 test results, of which 295,295 (56.9%) were from individuals reporting Hispanic ethnicity, SARS-CoV-2 positivity was 16.5% among Hispanic individuals compared to 5.0% among non-Hispanic individuals (p-value<0.01). The prevalence ratios comparing Hispanic and non- Hispanic individuals was highest for members of the media (PR=6.7; 95% CI 4.3-10.4), government employees (PR=4.0; 95% CI 3.3-4.9), and agricultural workers (PR=4.0; 95% CI 3.2-5.0). Such heterogeneity warrants further investigation in order to develop targeted public health interventions towards specific drivers of SARS-CoV-2 transmission.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lao-Tzu Allan-Blitz", - "author_inst": "Brigham and Women's Hospital Division of Cardiovascular Medicine" - }, - { - "author_name": "Fred Hertlein", - "author_inst": "Curative Inc." - }, - { - "author_name": "Jeffrey D. Klausner", - "author_inst": "Keck School of Medicine, University of Southern California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.07.21256826", "rel_title": "A quantitative risk-benefit analysis of ChAdOx1 nCoV-19 vaccine among people under 60 in Italy", @@ -790540,6 +793760,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.05.21256668", + "rel_title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "rel_date": "2021-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "rel_abs": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sofia de la Fuente Garcia", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Fasih Haider", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Saturnino Luz", + "author_inst": "The University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.05.05.21256677", "rel_title": "SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 epidemic in Lombardy, Italy (March - June 2020)", @@ -791688,85 +794935,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.08.443244", - "rel_title": "The K18-hACE2 Transgenic Mouse Model Recapitulates Non-Severe and Severe COVID-19 in Response to Infectious Dose of SARS-CoV-2 Virus", - "rel_date": "2021-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.08.443244", - "rel_abs": "A comprehensive analysis and characterization of a SARS-CoV-2 infection model that mimics non-severe and severe COVID-19 in humans is warranted for understating the virus and developing preventive and therapeutic agents. Here, we characterized the K18-hACE2 mouse model expressing human (h)ACE2 in mice, controlled by the human keratin 18 (K18) promoter, in epithelia, including airway epithelial cells where SARS-CoV-2 infections typically start. We found that intranasal inoculation with higher viral doses (2x103 and 2x104 PFU) of SARS-CoV-2 caused lethality of all mice and severe damage of various organs, including lungs, liver, and kidney, while lower doses (2x101 and 2x102 PFU) led to less severe tissue damage and some mice recovered from the infection. In this humanized hACE2 mouse model, SARS-CoV-2 infection damaged multiple tissues, with a dose-dependent effect in most tissues. Similar damage was observed in biopsy samples from COVID-19 patients. Finally, the mice that recovered after infection with a low dose of virus also survived rechallenge with a high dose of virus. Compared to other existing models, the K18-hACE2 model seems to be the most sensitive COVID-19 model reported to date. Our work expands the information available about this model to include analysis of multiple infectious doses and various tissues with comparison to human biopsy samples from COVID-19 patients. In conclusion, the K18-hACE2 mouse model recapitulates both severe and non-severe COVID-19 in humans and can provide insight into disease progression and the efficacy of therapeutics for preventing or treating COVID-19.\n\nImportanceThe pandemic of COVID-19 has reached 112,589,814 cases and caused 2,493,795 deaths worldwide as of February 23, 2021, has raised an urgent need for development of novel drugs and therapeutics to prevent the spread and pathogenesis of SARS-CoV-2. To achieve this goal, an animal model that recapitulates the features of human COVID-19 disease progress and pathogenesis is greatly needed. In this study, we have comprehensively characterized a mouse model of SARS-CoV-2 infection using K18-hACE2 transgenic mice. We infected the mice with low and high doses of SARS-CoV-2 virus to study the pathogenesis and survival in response to different infection patterns. Moreover, we compared the pathogenesis of the K18-hACE2 transgenic mice with that of the COVID-19 patients to show that this model could be a useful tool for the development of anti-viral drugs and therapeutics.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jianhua Yu", - "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center" - }, - { - "author_name": "Wenjuan Dong", - "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center" - }, - { - "author_name": "Aimin Li", - "author_inst": "Pathology Shared Resource Core, Beckman Research Institute, City of Hope National Medical Center" - }, - { - "author_name": "Jianying Zhang", - "author_inst": "Department of Computational and Quantitative Medicine, City of Hope National Medical Center" - }, - { - "author_name": "Michael Caligiuri", - "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center" - }, - { - "author_name": "Sierra Jaramillo", - "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University" - }, - { - "author_name": "Heather L. Mead", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Nathan Eric Stone", - "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University" - }, - { - "author_name": "Ashley Jones", - "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University" - }, - { - "author_name": "Daniel R Kollath", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Vanessa K Coyne", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Martha Yearsley", - "author_inst": "Department of Pathology, The Ohio State University" - }, - { - "author_name": "Li-Shu Wang", - "author_inst": "Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin" - }, - { - "author_name": "Bridget M. Barker", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Paul Keim", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Tasha Barr", - "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.08.443207", "rel_title": "Suppression of Global Protein Translation in SARS-CoV-2 Infection", @@ -792690,6 +795858,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.04.21256655", + "rel_title": "COVID-19 cases from the first local outbreak of SARS-CoV-2 B.1.1.7 variant in China presented more serious clinical features: a prospective, comparative cohort study", + "rel_date": "2021-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256655", + "rel_abs": "BackgroundThe SARS-CoV-2 B.1.1.7 variant which was first identified in the United Kingdom (U.K.) has increased sharply in numbers worldwide and was reported to be more contagious. On January 17, 2021, a COVID-19 clustered outbreak caused by B.1.1.7 variant occurred in a community in Daxing District, Beijing, China. Three weeks prior, another non-variant (lineage B.1.470) COVID-19 outbreak occurred in Shunyi District, Beijing. This study aimed to investigate the clinical features of B.1.1.7 variant infection.\n\nMethodsA prospective cohort study was conducted on COVID-19 cases admitted to Ditan hospital since January 2020. Data of 74 COVID-19 cases from two independent COVID-19 outbreaks in Beijing were extracted as study subjects from a Cloud Database established in Ditan hospital, which included 41 Shunyi cases (Shunyi B.1.470 group) and 33 Daxing cases (Daxing B.1.1.7 group) that have been hospitalized since December 25, 2020 and January 17, 2021, respectively. We conducted a comparison of the clinical characteristics, RT-qPCR results and genomic features between the two groups.\n\nFindingsCases from Daxing B.1.1.7 group (15 [45.5%] male; median age, 39 years [range, 30.5, 62.5]) and cases from Shunyi B.1.470 group (25 [61.0%] male; median age, 31 years [range, 27.5, 41.0]) had a statistically significant difference in median age (P =0.014). Seven clinical indicators of Daxing B.1.1.7 group were significantly higher than Shunyi B.1.470 group including patients having fever over 38{degrees}C (14/33 [46.43%] in Daxing B.1.1.7 group vs. 9/41 (21.95%) in Shunyi B.1.470 group [P = 0 .015]), C-reactive protein ([CRP, mg/L], 4.30 [2.45, 12.1] vs. 1.80, [0.85, 4.95], [P = 0.005]), Serum amyloid A ([SAA, mg/L], 21.50 [12.50, 50.70] vs. 12.00 [5.20, 26.95], [P = 0.003]), Creatine Kinase ([CK, U/L]), 110.50 [53.15,152.40] vs. 70.40 [54.35,103.05], [P = 0.040]), D-dimer ([DD, mg/L], 0.31 [0.20, 0.48] vs. 0.24 [0.17,0.31], [P = 0.038]), CD4+ T lymphocyte ([CD4+ T, mg/L], [P = 0.003]), and Ground-glass opacity (GGO) in lung (15/33 [45.45%] vs. 5/41 [12.20%], [P =0.001]). After adjusting for the age factor, B.1.1.7 variant infection was the risk factor for CRP (P = 0.045, Odds ratio [OR] 2.791, CI [1.025, 0.8610]), SAA (0.011, 5.031, [1.459, 17.354]), CK (0.034, 4.34, [0.05, 0.91]), CD4+ T (0.029, 3.31, [1.13, 9.71]), and GGO (0.005, 5.418, [1.656, 17.729]) of patients. The median Ct value of RT-qPCR tests of the N-gene target in the Daxing B.1.1.7 group was significantly lower than the Shunyi B.1.470 group (P=0.036). The phylogenetic analysis showed that only 2 amino acid mutations in spike protein were detected in B.1.470 strains while B.1.1.7 strains had 3 deletions and 7 mutations.\n\nInterpretationClinical features including a more serious inflammatory response, pneumonia and a possible higher viral load were detected in the cases infected with B.1.1.7 SARS-CoV-2 variant. It could therefore be inferred that the B.1.1.7 variant may have increased pathogenicity.\n\nFundingThe study was funded by the National Key Research and Development Program (grant nos.2020YFC0846200 and 2020YFC0848300) and National Natural Science Foundation of China (grant no. 82072295).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yang Song M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Ziruo Ge M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Shuping Cui M.Sc.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China and Peking University, Ditan Teaching Hospital, Beijing, Ch" + }, + { + "author_name": "Di Tian M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Gang Wan M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Shuangli Zhu B.Sc.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Xianbo Wang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yu Wang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Xiang Zhao M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Pan Xiang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yanli Xu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Tingyu Zhang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Long Liu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Gang Liu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yanhai Wang M.Sc.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Jianbo Tan M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Wei Zhang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Wenbo Xu M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Zhihai Chen M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.04.21256635", "rel_title": "Visual Exploratory Analysis of COVID-19 Pandemic: One Year After the Outbreak", @@ -793258,57 +796517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.06.21256544", - "rel_title": "Longitudinal Evaluation of mRNA Vaccinated Subjects using a Quidel Multianalyte Point-of-Care SARS-CoV-2 IgG Immunoassay", - "rel_date": "2021-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256544", - "rel_abs": "Infection from SARS-CoV-2 elicits an immune response to the nucleocapsid (N) and spike proteins (subunits S1 and S2). In this study, we set out to understand the utility of the multiplexed Quidel Sofia 2 SARS-CoV-2 IgG Antibody Fluorescent Immuno-Assay (FIA) that measures IgG antibodies against these three primary SARS-CoV-2 antigens from a single sample in 15 minutes. Using this assay with samples that were collected prior to the COVID-19 pandemic (n=816) and diseased state samples (n=99), the specificities for the three antigens were 98.4-99.9% and 98.0-100.0%, respectively. A longitudinal study was designed to collect weekly fingerstick, venous whole blood, serum and plasma samples from subjects vaccinated with the Moderna or Pfizer/BioNtech mRNA vaccines. The majority of these enrolled subjects had no known prior infection while a subset was known to have had prior COVID-19 infection. We found that the fingerstick whole blood samples performed as effectively as serum, plasma, and venous whole blood samples with a 95.8-99.5% agreement allowing physicians in a near-patient setting to rapidly provide results to their patients. Additionally, as this assay measures an IgG response against three viral proteins, S1, S2 and N, we were able to characterize immune response between i) naturally infected subjects, ii) vaccinated subjects with no prior infection, iii) vaccinated subjects with known prior infection, and iv) vaccinated subjects with prior asymptomatic exposure/infection. The Quidel Sofia 2 SARS-CoV-2 IgG FIA will aid in providing insights to the protective humoral responses as an increasing number of the world population is vaccinated against SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xi Chen", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Sarika Agarwal", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Stewart Hoelscher", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Richard Egan", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Dipesh Jaiswal", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Adonis Stassinopoulos", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Robert Reed", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Jason McClure", - "author_inst": "Quidel Corp" - }, - { - "author_name": "Werner Kroll", - "author_inst": "Quidel Corp" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.04.21256472", "rel_title": "Multicentric Evaluation of a Novel Point of Care Electrochemical ELISA Platform for SARS-CoV-2 Specific IgG and IgM Antibody Assay", @@ -794744,6 +797952,57 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.05.01.21256182", + "rel_title": "Modelling upper respiratory viral load dynamics of SARS-CoV-2", + "rel_date": "2021-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256182", + "rel_abs": "Relationships between viral load, severity of illness, and transmissibility of virus, are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response, and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with control of viral load. Neutralizing antibody correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralizing antibody. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joseph D Challenger", + "author_inst": "Imperial College London" + }, + { + "author_name": "Cher Y Foo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Yue Wu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ada WC Yan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mahdi Moradi Marjaneh", + "author_inst": "Imperial College London" + }, + { + "author_name": "Felicity Liew", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ryan S Thwaites", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lucy C Okell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aubrey J Cunnington", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.03.21256520", "rel_title": "The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses", @@ -795720,117 +798979,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.06.442916", - "rel_title": "Identification of DAXX As A Restriction Factor Of SARS-CoV-2 Through A CRISPR/Cas9 Screen", - "rel_date": "2021-05-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.06.442916", - "rel_abs": "Interferon restricts SARS-CoV-2 replication in cell culture, but only a handful of Interferon Stimulated Genes with antiviral activity against SARS-CoV-2 have been identified. Here, we describe a functional CRISPR/Cas9 screen aiming at identifying SARS-CoV-2 restriction factors. We identified DAXX, a scaffold protein residing in PML nuclear bodies known to limit the replication of DNA viruses and retroviruses, as a potent inhibitor of SARS-CoV-2 and SARS-CoV replication in human cells. Basal expression of DAXX was sufficient to limit the replication of SARS-CoV-2, and DAXX over-expression further restricted infection. In contrast with most of its previously described antiviral activities, DAXX-mediated restriction of SARS-CoV-2 was independent of the SUMOylation pathway. SARS-CoV-2 infection triggered the re-localization of DAXX to cytoplasmic sites and promoted its degradation. Mechanistically, this process was mediated by the viral papain-like protease (PLpro) and the proteasome. Together, these results demonstrate that DAXX restricts SARS-CoV-2, which in turn has evolved a mechanism to counteract its action.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Alice Mac Kain", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ghizlane Maarifi", - "author_inst": "Institut de Recherche en Infectiologie de Montpellier (IRIM)" - }, - { - "author_name": "Sophie-Marie Aicher", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Nathalie Arhel", - "author_inst": "Institut de Recherche en Infectiologie de Montpellier (IRIM)" - }, - { - "author_name": "Artem Baidaliuk", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sandie Munier", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Thomas Vallet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Quang Dinh Tran", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Alexandra Hardy", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Maxime Chazal", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fran\u00e7oise Porrot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Molly Ohainle", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jared Carlson-Stevermer", - "author_inst": "Synthego Corporation" - }, - { - "author_name": "Jennifer Oki", - "author_inst": "Synthego Corporation" - }, - { - "author_name": "Kevin Holden", - "author_inst": "Synthego Corporation" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Timoth\u00e9e Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Nolwenn Jouvenet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "S\u00e9bastien Nisole", - "author_inst": "Institut de Recherche en Infectiologie de Montpellier (IRIM)" - }, - { - "author_name": "Marco Vignuzzi", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ferdinand Roesch", - "author_inst": "INRAE" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.05.442875", "rel_title": "The Effect of Minnelide against SARS-CoV-2 in a Murine Model", @@ -796797,6 +799945,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.05.442782", + "rel_title": "Combination Respiratory Vaccine Containing Recombinant SARS-CoV-2 Spike and QuadrivalentSeasonal Influenza Hemagglutinin Nanoparticles with Matrix-M Adjuvant", + "rel_date": "2021-05-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442782", + "rel_abs": "The 2019 outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, has spread globally with high morbidity and mortality. Co-circulating seasonal influenza has greatly diminished recently, but expected to return with novel strains emerging, thus requiring annual strain adjustments. We have developed a recombinant hemagglutinin (HA) quadrivalent nanoparticle influenza vaccine (qNIV) produced using an established recombinant insect cell expression system to produce nanoparticles. Influenza qNIV adjuvanted with Matrix-M was well-tolerated and induced robust antibody and cellular responses, notably against both homologous and drifted A/H3N2 viruses in Phase 1, 2, and 3 trials. We also developed a full-length SARS-CoV-2 spike protein vaccine which is stable in the prefusion conformation (NVX-CoV2373) using the same platform technology. In phase 3 clinical trials, NVX-CoV2373 is highly immunogenic and protective against the prototype strain and B.1.1.7 variant. Here we describe the immunogenicity and efficacy of a combination quadrivalent seasonal flu and COVID-19 vaccine (qNIV/CoV2373) in ferret and hamster models. The combination qNIV/CoV2373 vaccine produces high titer influenza hemagglutination inhibiting (HAI) and neutralizing antibodies against influenza A and B strains. The combination vaccine also elicited antibodies that block SARS-CoV-2 spike protein binding to the human angiotensin converting enzyme-2 (hACE2) receptor. Significantly, hamsters immunized with qNIV/CoV2373 vaccine and challenged with SARS-CoV-2 were protected against weight loss and were free of replicating SARS-CoV-2 in the upper and lower respiratory tract with no evidence of viral pneumonia. This study supports evaluation of qNIV/CoV2373 combination vaccine as a preventive measure for seasonal influenza and CoVID-19.\n\nHighlightsO_LICombination qNIV/CoV2373 vaccine induced protective hemagglutination inhibition (HAI) responses to seasonal influenza A and B unchanged when formulated with recombinant spike.\nC_LIO_LICombination qNIV/CoV2373 vaccine maintained clinical and virologic protection against experimental challenge with SARS-CoV-2.\nC_LIO_LICombination qNIV/CoV2373 vaccine showed no clinical or histological sign of enhanced disease following experimental challenge with SARS-CoV-2.\nC_LIO_LICombination qNIV/CoV2373 vaccine induced antibodies against SARS-CoV-2 neutralizing epitopes common between US-WA and B.1.352 variant.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Micheal J Massare", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Rhonda Flores", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Mimi Guebre-Xabier", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Jing-Hui Tian", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Alyse D Portnoff", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Louis Fries", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Vivek Shinde", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Larry R Ellingsworth", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.04.442701", "rel_title": "SARS-CoV-2 cell-to-cell infection is resistant to neutralizing antibodies", @@ -797425,33 +800640,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.01.21256469", - "rel_title": "Smart Testing with Vaccination: A Bandit Algorithm for Active Sampling for Managing COVID-19", - "rel_date": "2021-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256469", - "rel_abs": "This paper presents methods to choose individuals to test for infection during a pandemic such as COVID-19, characterized by high contagion and presence of asymptomatic carriers. The smart-testing ideas presented here are motivated by active learning and multi-armed bandit techniques in machine learning. Our active sampling method works in conjunction with vaccination and quarantine policies and is adaptive to changes in real-time data. Using a data-driven agent-based model simulating New York City we show that the algorithm samples individuals to test in a manner that rapidly traces infected individuals. The results show that smart-testing is effective in significantly reducing infection and death rates as compared to current policies, with or without vaccination.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yingfei Wang", - "author_inst": "University of Washington" - }, - { - "author_name": "Inbal Yahav", - "author_inst": "Coller School of Management, Tel Aviv University" - }, - { - "author_name": "Balaji Padmanabhan", - "author_inst": "Muma College of Business, University of South Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.01.21256428", "rel_title": "Prevalence use of nonsteroidal anti-inflammatory drugs in the general population with COVID-19 and associated COVID-19 risk, hospitalization, severity, death, and safety outcomes: A systematic review and meta-analysis", @@ -798735,6 +801923,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.30.21256377", + "rel_title": "Disordered eating and self-harm as risk factors for poorer mental health during the COVID-19 pandemic: A population-based cohort study", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256377", + "rel_abs": "BackgroundYoung adults and especially those with pre-existing mental health conditions, such as disordered eating and self-harm, appear to be at greater risk of developing metal health problems during the COVID-19 pandemic. However, it is unclear whether this increased risk is affected by any changes in lockdown restrictions, and whether any lifestyle changes could moderate this increased risk.\n\nMethodsIn a longitudinal UK-based birth cohort (The Avon Longitudinal Study of Parents and Children, ALSPAC) we assessed the relationship between pre-pandemic measures of disordered eating and self-harm and mental health during the COVID-19 pandemic in 2,657 young adults. Regression models examined the relationship between self-reported disordered eating, self-harm, and both disordered eating and self-harm at age 25 years and depressive symptoms, anxiety symptoms and mental wellbeing during a period of eased restrictions in the COVID-19 pandemic (May-July 2020) when participants were aged 27-29 years. Analyses were adjusted for sex, questionnaire completion date, pre-pandemic socioeconomic disadvantage and pre-pandemic mental health and wellbeing. We also examined whether lifestyle changes (sleep, exercise, alcohol, visiting green space, eating, talking with family/friends, hobbies, relaxation) in the initial UK lockdown (April-May 2020) moderated these associations.\n\nResultsPre-existing disordered eating, self-harm and comorbid disordered eating and self-harm were all associated with the reporting of a higher frequency of depressive symptoms and anxiety symptoms, and poorer mental wellbeing during the pandemic compared to individuals without disordered eating and self-harm. Associations remained when adjusting for pre-pandemic mental health measures. There was little evidence that interactions between disordered eating and self-harm exposures and lifestyle change moderators affected pandemic mental health and wellbeing.\n\nConclusionsYoung adults with pre-pandemic disordered eating, self-harm and comorbid disordered eating and self-harm were at increased risk for developing symptoms of depression, anxiety and poor mental wellbeing during the COVID-19 pandemic, even when accounting for pre-pandemic mental health. Lifestyle changes during the pandemic do not appear to alter this risk. A greater focus on rapid and responsive service provision is essential to reduce the impact of the pandemic on the mental health of these already vulnerable individuals.\n\nPlain English summaryThe aim of this project was to explore the mental health of young adults with disordered eating behaviours (such as fasting, vomiting/taking laxatives, binge-eating and excessive exercise) and self-harm during the COVID-19 pandemic. We analysed data from an established study that has followed children from birth (in 1991 and 1992) up to present day, including during the pandemic when participants were 28 years old. We looked at the relationship between disordered eating and/or self-harm behaviours from before the pandemic and mental health problems (symptoms of depression and anxiety) and mental wellbeing during the pandemic. We also explored whether there were any lifestyle changes (such as changes in sleep, exercise, visiting green space) that might be linked to better mental health and wellbeing in young adults with disordered eating and self-harm. We found that young adults with prior disordered eating and/or self-harm had more symptoms of depression and anxiety, and worse mental wellbeing than individuals without prior disordered eating or self-harm. However, lifestyle changes did not appear to affect mental health and wellbeing in these young adults. Our findings suggest that people with a history of disordered eating and/or self-harm were at high risk for developing mental health problems during the pandemic, and they will need help from mental health services.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Naomi Warne", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jon Heron", + "author_inst": "University of Bristol" + }, + { + "author_name": "Becky Mars", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Francesca Solmi", + "author_inst": "UCL" + }, + { + "author_name": "Rebecca Pearson", + "author_inst": "Univeristy of Bristol" + }, + { + "author_name": "Paul Moran", + "author_inst": "University of Bristol" + }, + { + "author_name": "Helen Bould", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.04.442648", "rel_title": "Immunolocalization studies of vimentin and ACE2 on the surface of cells exposed to SARS-CoV-2 Spike proteins", @@ -799395,29 +802630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.01.21256447", - "rel_title": "Forecasting COVID-19 Spreading in Canada using Deep Learning", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256447", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe novel coronavirus disease 2019 (COVID-19) is disrupting all aspects of our lives as the global spread of the virus continues. In this difficult period, various research projects are taking place to study and analyse the dynamics of the pandemic. In the present work, we firstly present a deep overview of the main forecasting models to predict the new cases of COVID-19. In this context, we focus on univariate time series models in order to analyze the dynamic change of this pandemic through time. We secondly shed light on multivariate time series forecasting models using weather and daily tests data, to study the impact of exogenous features on the progression of COVID-19. In the final stage of this paper, we present our proposed approach based on LSTM and GRU ensemble learning model and evaluate the results using the MAE, RMSE and MAPE for the prediction of new cases. The results of our experiments using the Canadian dataset show that the ensemble model performs well in comparison to other models. In addition, this research provides us with a new outcome regarding the dynamic correlation between temperature, humidity and daily test data and its impact on the new contaminated cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Fadoua Khennou", - "author_inst": "Universit\u00e9 de Moncton" - }, - { - "author_name": "Moulay A. Akhloufi", - "author_inst": "Universit\u00e9 de Moncton" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.01.21256458", "rel_title": "COVID-19 monitoring in rural communities: First comparison of lagoon and pumping station samples for wastewater-based epidemiology", @@ -800305,6 +803517,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.04.21256298", + "rel_title": "Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256298", + "rel_abs": "Inflammatory responses rapidly detect pathogen invasion and mount a regulated reaction. However, dysregulated anti-pathogen immune responses can provoke life-threatening inflammatory pathologies collectively known as cytokine release syndrome (CRS), exemplified by key clinical phenotypes unearthed during the SARS-Cov-2 pandemic. The underlying pathophysiology of CRS remains elusive. We found that FLIP, a protein that controls caspase-8 death pathways, was highly expressed in myeloid cells of COVID-19 lungs. FLIP controlled CRS by fueling a STAT3-dependent inflammatory program. Indeed, constitutive expression of a viral FLIP homologue in myeloid cells triggered a STAT3-linked, progressive and fatal inflammatory syndrome in mice, characterized by elevated cytokine output, lymphopenia, lung injury and multiple organ dysfunctions that mimicked human CRS. As STAT3-targeting approaches relieved inflammation, immune disorders, and organ failures in these mice, targeted intervention towards this pathway could suppress the lethal CRS inflammatory state.\n\nOne sentence summaryFLIP-expressing myeloid cells are key drivers of CRS through aberrant overexpression of STAT3 pathway. STAT3-targeting is effective in mitigating CRS like severe COVID-19.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.05.04.21256489", "rel_title": "COVID-19 VACCINE PERCEPTIONS AND DIFFERENCES BY SEX, AGE, AND EDUCATION: FINDINGS FROM A CROSS-SECTIONAL ASSESSMENT OF 1367 COMMUNITY ADULTS IN ONTARIO", @@ -800716,37 +803942,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.03.21255735", - "rel_title": "Preventing disproportionate mortality in ICU overload situations: Empirical evidence from the first COVID-19 wave in Europe", - "rel_date": "2021-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21255735", - "rel_abs": "Avoiding overloading the healthcare system remains a central issue during the COVID-19 pandemic. The logic of preventing such overload situations is intuitive since the level and quality of critical care is a function of the available capacity to provide it. Where this capacity is no longer available due to a surge in admissions, patient outcomes will invariably deteriorate in the long run - ultimately leading to disproportionate mortality. In this paper, we study the three worst affected regions in Italy, the Netherlands, and Germany during the first COVID-19 wave in the spring of 2020. We report on quantitative analyses that show how mortality rises non-linearly as the proportion of COVID-19 patients in the ICU increases. We identify changes to the patient-staff ratio, increasing exhaustion and infection levels amongst staff, as well as equipment shortages, as likely causes driving this rise in mortality. We explore these findings further with interviews of key stakeholders in the respective healthcare systems. Our results demonstrate that the common approach of managing COVID-19 surges by stretching ICU capacity in hotspot regions may be detrimental to patient outcomes. Instead, we posit that transferring patients proactively out of developing hotspots to less affected regions, well before high ICU workload situations emerge, will improve overall patient outcomes.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paul Buijs", - "author_inst": "University of Groningen" - }, - { - "author_name": "Rodolfo Catena", - "author_inst": "University of Oxford" - }, - { - "author_name": "Matthias Holweg", - "author_inst": "University of Oxford" - }, - { - "author_name": "Taco van der Vaart", - "author_inst": "University of Groningen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.04.29.21251164", "rel_title": "Uncovering the compounding effects of COVID-19 and racism on mental health disparities among biomedical PhD and MD students", @@ -801870,6 +805065,165 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.01.442279", + "rel_title": "Signaling through Fc\u03b3RIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19", + "rel_date": "2021-05-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.01.442279", + "rel_abs": "Patients with COVID-19 present with a wide variety of clinical manifestations. Thromboembolic events constitute a significant cause of morbidity and mortality in patients infected with SARS-CoV-2. Severe COVID-19 has been associated with hyperinflammation and pre-existing cardiovascular disease. Platelets are important mediators and sensors of inflammation and are directly affected by cardiovascular stressors. In this report, we found that platelets from severely ill, hospitalized COVID-19 patients exhibit higher basal levels of activation measured by P-selectin surface expression, and have a poor functional reserve upon in vitro stimulation. Correlating clinical features to the ability of plasma from COVID-19 patients to stimulate control platelets identified ferritin as a pivotal clinical marker associated with platelet hyperactivation. The COVID-19 plasma-mediated effect on control platelets was highest for patients that subsequently developed inpatient thrombotic events. Proteomic analysis of plasma from COVID-19 patients identified key mediators of inflammation and cardiovascular disease that positively correlated with in vitro platelet activation. Mechanistically, blocking the signaling of the Fc{gamma}RIIa-Syk and C5a-C5aR pathways on platelets, using antibody-mediated neutralization, IgG depletion or the Syk inhibitor fostamatinib, reversed this hyperactivity driven by COVID-19 plasma and prevented platelet aggregation in endothelial microfluidic chamber conditions, thus identifying these potentially actionable pathways as central for platelet activation and/or vascular complications in COVID-19 patients. In conclusion, we reveal a key role of platelet-mediated immunothrombosis in COVID-19 and identify distinct, clinically relevant, targetable signaling pathways that mediate this effect. These studies have implications for the role of platelet hyperactivation in complications associated with SARS-CoV-2 infection.\n\nCover illustration O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY\n\nOne-sentence summaryThe Fc{gamma}RIIA and C5a-C5aR pathways mediate platelet hyperactivation in COVID-19", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Sokratis A. Apostolidis", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amrita Sarkar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Heather M. Giannini", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Rishi R. Goel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Divij Mathew", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Aae Suzuki", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amy E. Baxter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Allison R. Greenplate", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Cecile Alanio", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mohamed Abdel-Hakeem", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Derek A. Oldridge", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Josephine R. Giles", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jennifer E. Wu", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zeyu Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yinghui Jane Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ajinkya Pattekar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sasikanth Manne", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Oliva Kuthuru", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jeanette Dougherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Brittany Weiderhold", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ariel R. Weisman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Caroline A.G. Ittner", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Debora Dunbar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ian Frank", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alexander C. Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Laura A. Vella", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "- The UPenn COVID Processing Unit", + "author_inst": "-" + }, + { + "author_name": "John P. Reilly", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Lubica Rauova", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Liang Zhao", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Nuala J. Meyer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mortimer Poncz", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Charles S. Abrams", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "E John Wherry", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.03.441080", "rel_title": "Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7", @@ -802686,61 +806040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.29.21256333", - "rel_title": "Quantifying COVID-19 vaccination hesitancy during early vaccination rollout in Canada", - "rel_date": "2021-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256333", - "rel_abs": "BackgroundUnderstanding vaccination hesitancy during early vaccination rollout in Canada can help the governments vaccination efforts in education and outreach, which may help eventually achieving herd immunity. This study uses an online survey to assess vaccination hesitancy in population subgroups in Canada.\n\nMethodPanel members from the nationally representative Angus Reid Forum were randomly invited to complete an online survey on their experiencing with COVID-19 symptoms and testing, as well as intention to vaccination against COVID-19. Respondents were asked \"when a vaccine against the coronavirus becomes available to you, will you get vaccinated or not?\" Vaccination hesitancy was defined as choosing \"No - I will not get a coronavirus vaccination\" as a response.\n\nResults14,621 panel members (46% male and 53% female) completed the survey. Although the respondents overrepresent age 60+ and higher levels of education, other demographics, the prevalences of smoking, obesity, diabetes and hypertension were comparable to the Canadian national census and health surveys. COVID-19 vaccination hesitancy is relatively low overall (9%). Being a resident of Alberta (predicted probability = 15%), aged 40-59 (OR = 0.87, 0.78 - 0.97, predicted probability = 12%), identifying as a visible minority (OR = 0.56, 0.37 - 0.84, predicted probability = 15%), having some college level education or lower (predicted probability = 14%), or living in households of at least 5 are related to greater vaccination hesitancy (OR = 0.82, 0.76 - 0.88, predicted probability = 13%).\n\nConclusionOur study enhances the understanding of COVID-19 vaccination hesitancy and identifies key population groups with higher vaccination hesitancy. As the Canadian COVID-19 vaccination effort continues, policymakers may focus outreach, education, and other efforts on these groups, which also represent groups with higher risks for contracting and dying from COVID-19. Furthermore, Canada would need to vaccinate virtually the entire population to reach herd immunity due to its relatively low infection level, and a high vaccination hesitancy would be a major hurdle to achieving that.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xuyang Tang", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Hellen Gelband", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Nico Nagelkerke", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Isaac Bogoch", - "author_inst": "University Health Network" - }, - { - "author_name": "Patrick E Brown", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Ed Morawski", - "author_inst": "Angus Reid Forum" - }, - { - "author_name": "Teresa Lam", - "author_inst": "Angus Reid Forum" - }, - { - "author_name": "Angus Reid", - "author_inst": "Angus Reid Forum" - }, - { - "author_name": "Prabhat Jha", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "- Action to beat coronavirus/Action pour battre le coronavirus (Ab-C) Study Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.29.21256317", "rel_title": "The comparison of vaccine hesitancy of COVID-19 vaccination in China and the United States", @@ -803644,6 +806943,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.28.21256146", + "rel_title": "The causal effects of chronic air pollution on the intensity of COVID-19 disease: Some answers are blowing in the wind", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21256146", + "rel_abs": "The threats posed by COVID-19 have catalyzed a search by researchers across multiple disciplines for policy-relevant findings about critical risk factors. We contribute to this effort by providing causal estimates of the link between increased chronic ambient pollutant concentrations and the intensity of COVID-19 disease, as measured by deaths and hospitalizations in New York City from March through August, 2020. Given concerns about unobservable characteristics that contribute to both ambient air pollutant concentrations and the impacts of COVID-19 disease, we instrument for pollutant concentrations using the time spent downwind of nearby highways and estimate key causal relationships using two-stage least squares models. The causal links between increases in concentrations of our traffic-related air pollutants (PM2.5, NO2, and NO) and COVID-19 deaths are much larger than the correlations presented in recent observational studies. We find that a 0.16 g/m3 increase in average ambient PM2.5 concentration leads to an approximate 30% increase in COVID-19 deaths. This is the change in concentration associated with being downwind of a nearby highway. We see that this effect is mostly driven by residents with at least 75 years of age. In addition to emphasizing the importance of searching for causal relationships, our analysis highlights the value of increasing the density of pollution-monitoring networks and suggests potential benefits of further tightening of Clean Air Act amendments, as our estimated effects occur at concentrations well below thresholds set by the National Ambient Air Quality Standards.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marc N Conte", + "author_inst": "Fordham University" + }, + { + "author_name": "Matthew Gordon", + "author_inst": "Yale University" + }, + { + "author_name": "Nicole Swartwood", + "author_inst": "Harvard T.H. Chan School" + }, + { + "author_name": "Rachel Wilwerding", + "author_inst": "Fordham University" + }, + { + "author_name": "Chu A. (Alex) Yu", + "author_inst": "Wake Forest University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.27.21256210", "rel_title": "U.S. Regional Differences in Physical Distancing: Evaluating Racial and Socioeconomic Divides During the COVID-19 Pandemic", @@ -804232,45 +807566,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.04.27.21256215", - "rel_title": "Racial and ethnic disparities for SARS-CoV-2 positivity in the United States: a generalizing pandemic", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256215", - "rel_abs": "The coronavirus pandemic has disproportionally impacted racial and ethnic minority communities in the United States. These disparities may be changing over time as outbreaks occur in different communities. Using electronic health record data from the Department of Veterans Affairs, we estimated odds ratios, stratified by region and time period, for testing positive for SARS-CoV-2 among 951,408 individuals tested for SARS-CoV-2 between February 12, 2020 and February 12, 2021. Our study found racial and ethnic disparities for testing positive were most pronounced at the beginning of the pandemic and decreased over time. A key finding was that the disparity among Hispanic individuals attenuated but remained elevated over the entire study period. We identified variation in racial and ethnic disparities in SARS-CoV-2 positivity by time and region independent of underlying health status and other key factors in a nationwide cohort, which provides important insight for strategies to contain and prevent further outbreaks.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jacqueline M Ferguson", - "author_inst": "US Department of Veterans Affairs, Stanford University School of Medicine" - }, - { - "author_name": "Amy C Justice", - "author_inst": "US Department of Veterans Affairs, Yale School of Public Health, Yale School of Medicine" - }, - { - "author_name": "Thomas F Osborne", - "author_inst": "US Department of Veterans Affairs, Stanford University" - }, - { - "author_name": "Hoda S Abdel Magid", - "author_inst": "US Department of Veterans Affairs, Stanford University, Santa Clara University" - }, - { - "author_name": "Amanda L Purnell", - "author_inst": "US Department of Veterans Affairs" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "US Department of Veterans Affairs, London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.29.21256260", "rel_title": "COMPARISON OF PERFORMANCE CHARACTERISTICS BETWEEN LATERAL FLOW, ELISA AND ELECTROCHEMILUMINESCENCE IMMUNOASSAYS FOR THE DETECTION OF SARS-COV-2 ANTIBODIES AMONG HEALTHCARE WORKERS", @@ -805240,6 +808535,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.04.28.21255760", + "rel_title": "SARS-CoV-2 infections in nasal epithelial cells from smokers versus non-smokers", + "rel_date": "2021-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21255760", + "rel_abs": "Whether smoking exacerbates Coronavirus disease 2019 is still debated. Ex-vivo Infection of reconstituted epithelial tissues from smoker versus non-smoker donors suggested comparable susceptibility to SARS-CoV-2 in epithelia from both groups.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Manel Essaidi-Laziosi", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Giulia Torriani", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Catia Alvarez", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "University Hospitals of Geneva" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.27.21255023", "rel_title": "Large university with high COVID-19 incidence did not increase risk to non-student population", @@ -806096,73 +809426,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.29.442010", - "rel_title": "The natural stilbenoid (-)-hopeaphenol inhibits cellular entry of SARS-CoV-2 USA-WA1/2020, B.1.1.7 and B.1.351 variants", - "rel_date": "2021-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.29.442010", - "rel_abs": "Antivirals are urgently needed to combat the global SARS-CoV-2/COVID-19 pandemic, supplement existing vaccine efforts, and target emerging SARS-CoV-2 variants of concern. Small molecules that interfere with binding of the viral spike receptor binding domain (RBD) to the host ACE2 receptor may be effective inhibitors of SARS-CoV-2 cell entry. Here we screened 512 pure compounds derived from natural products using a high-throughput RBD/ACE2 binding assay and identified (-)-hopeaphenol, a resveratrol tetramer, in addition to vatalbinoside A and vaticanol B, as potent and selective inhibitors of RBD/ACE2 binding and viral entry. For example, (-)-hopeaphenol disrupted RBD/ACE2 binding with a 50% inhibitory concentration (IC50) of 0.11 M in contrast to an IC50 of 28.3 M against the unrelated host ligand/receptor binding pair PD-1/PD-L1 (selectivity index = 257.3). When assessed against the USA-WA1/2020 variant, (-)-hopeaphenol also inhibited entry of a VSV{Delta}G-GFP reporter pseudovirus expressing SARS-CoV-2 spike into ACE2-expressing Vero-E6 cells and in vitro replication of infectious virus in cytopathic effect assays (IC50 = 10.2 M) without cytotoxicity. Notably, (-)- hopeaphenol also inhibited two emerging variants of concern originating from the United Kingdom (B.1.1.7) and South Africa (B.1.351) in both cytopathic effect and spike-containing pseudovirus assays with similar (B.1.1.7) or improved (B.1.351) efficacies over the USA- WA1/2020 variant. These results identify (-)-hopeaphenol and related stilbenoid analogues as potent and selective inhibitors of viral entry across multiple SARS-CoV-2 variants including those with increased infectivity and/or reduced susceptibility to existing vaccines.\n\nImportanceSARS-CoV-2 antivirals are needed to supplement existing vaccine efforts and target emerging viral variants with increased infectivity or reduced susceptibility to existing vaccines. Here we show that (-)-hopeaphenol, a naturally-occurring stilbenoid compound, in addition to its analogues vatalbinoside A and vaticanol B, inhibit SARS-CoV-2 by blocking the interaction of the viral spike protein with the cellular ACE2 entry receptor. Importantly, in addition to inhibiting the early USA-WA1/2020 SARS-CoV-2 variant, hopeaphenol also inhibits emerging variants of concern including B.1.1.7 (\"United Kingdom variant\") and B.1.351 (\"South Africa variant\"), with improved efficacy against B.1.351. (-)-Hopeaphenol therefore represents a new antiviral lead against infection from multiple SARS-CoV-2 variants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ian Tietjen", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Joel Cassel", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Emery T Register", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Xiang Yang Zhou", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Troy E Messick", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Frederick Keeney", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Lily D Lu", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Karren D Beattie", - "author_inst": "Griffith Institute for Drug Discovery, Griffith University" - }, - { - "author_name": "Topul Rali", - "author_inst": "The University of Papua New Guinea" - }, - { - "author_name": "Hildegund CJ Ertl", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Joseph M Salvino", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Rohan A Davis", - "author_inst": "Griffith Institute for Drug Discovery, Griffith University" - }, - { - "author_name": "Luis J Montaner", - "author_inst": "The Wistar Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.29.442018", "rel_title": "Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2", @@ -807226,6 +810489,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.04.26.21255732", + "rel_title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "rel_date": "2021-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "rel_abs": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sarah Beale", + "author_inst": "University College London" + }, + { + "author_name": "Isobel Braithwaite", + "author_inst": "University College London" + }, + { + "author_name": "Annalan MD Navaratnam", + "author_inst": "University College London" + }, + { + "author_name": "Pia Hardelid", + "author_inst": "University College London" + }, + { + "author_name": "Alison Rodger", + "author_inst": "University College London; Royal Free London NHS Foundation Trust," + }, + { + "author_name": "Anna Aryee", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Edward Byrne", + "author_inst": "University College London" + }, + { + "author_name": "Wing Lam Erica Fong", + "author_inst": "University College London" + }, + { + "author_name": "Ellen Fragaszy", + "author_inst": "University College London" + }, + { + "author_name": "Cyril Geismar", + "author_inst": "University College London" + }, + { + "author_name": "Jana Kovar", + "author_inst": "University College London" + }, + { + "author_name": "Vincent Nguyen", + "author_inst": "University College London" + }, + { + "author_name": "Parth Patel", + "author_inst": "University College London" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "University College London" + }, + { + "author_name": "Robert W Aldridge", + "author_inst": "University College London" + }, + { + "author_name": "Andrew C Hayward", + "author_inst": "University College London" + }, + { + "author_name": "- Virus Watch Collaborative", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.25.21256067", "rel_title": "Trends of SARS-CoV-2 antibody prevalence in selected regions across Ghana", @@ -807834,117 +811180,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.26.21255788", - "rel_title": "Ethnic differences in SARS-CoV-2 vaccine hesitancy in United Kingdom healthcare workers: Results from the UK-REACH prospective nationwide cohort study", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255788", - "rel_abs": "BackgroundIn most countries, healthcare workers (HCWs) represent a priority group for vaccination against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) due to their elevated risk of COVID-19 and potential contribution to nosocomial SARS-CoV-2 transmission. Concerns have been raised that HCWs from ethnic minority groups are more likely to be vaccine hesitant (defined by the World Health Organisation as refusing or delaying a vaccination) than those of White ethnicity, but there are limited data on SARS-CoV-2 vaccine hesitancy and its predictors in UK HCWs.\n\nMethodsNationwide prospective cohort study and qualitative study in a multi-ethnic cohort of clinical and non-clinical UK HCWs. We analysed ethnic differences in SARS-CoV-2 vaccine hesitancy adjusting for demographics, vaccine trust, and perceived risk of COVID-19. We explored reasons for hesitancy in qualitative data using a framework analysis.\n\nFindings11,584 HCWs were included in the cohort analysis. 23% (2704) reported vaccine hesitancy. Compared to White British HCWs (21.3% hesitant), HCWs from Black Caribbean (54.2%), Mixed White and Black Caribbean (38.1%), Black African (34.4%), Chinese (33.1%), Pakistani (30.4%), and White Other (28.7%) ethnic groups were significantly more likely to be hesitant. In adjusted analysis, Black Caribbean (aOR 3.37, 95% CI 2.11 - 5.37), Black African (aOR 2.05, 95% CI 1.49 - 2.82), White Other ethnic groups (aOR 1.48, 95% CI 1.19 - 1.84) were significantly more likely to be hesitant. Other independent predictors of hesitancy were younger age, female sex, higher score on a COVID-19 conspiracy beliefs scale, lower trust in employer, lack of influenza vaccine uptake in the previous season, previous COVID-19, and pregnancy. Qualitative data from 99 participants identified the following contributors to hesitancy: lack of trust in government and employers, safety concerns due to the speed of vaccine development, lack of ethnic diversity in vaccine studies, and confusing and conflicting information. Participants felt uptake in ethnic minority communities might be improved through inclusive communication, involving HCWs in the vaccine rollout, and promoting vaccination through trusted networks.\n\nInterpretationDespite increased risk of COVID-19, HCWs from some ethnic minority groups are more likely to be vaccine hesitant than their White British colleagues. Strategies to build trust and dispel myths surrounding the COVID-19 vaccine in these communities are urgently required. Public health communications should be inclusive, non-stigmatising and utilise trusted networks.\n\nFundingMRC-UK Research and Innovation (MR/V027549/1), the Department of Health and Social Care through the National Institute for Health Research (NIHR), and NIHR Biomedical Research Centres and NIHR Applied Research Collaboration East Midlands.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched Pubmed using the following search terms ((COVID-19).ti,ab OR (SARS-CoV-2).ti,ab) AND ((vaccine).ti,ab OR (vaccination).ti,ab OR (immunisation).ti,ab)) AND ((healthcare worker).ti,ab OR (health worker).ti,ab OR (doctor).ti,ab OR (nurse).ti,ab OR (healthcare professional).ti,ab)) AND ((hesitancy).ti,ab OR (refusal).ti,ab OR (uptake).ti,ab)). The search returned 60 results, of which 38 were excluded after title and abstract screening, 11 studies were not conducted in a population of healthcare workers, 20 did not present data on vaccine intention or uptake, 5 were related to vaccines other than the SARS-CoV-2 vaccine, 1 was unrelated to vaccination and 1 had been withdrawn. The 22 remaining articles were survey studies focussed on SARS-CoV-2 vaccine intention in healthcare workers. Estimates of SARS-CoV-2 vaccine acceptance varied widely from 27{middle dot}7% - 94{middle dot}5% depending on the country in which the study was performed, and the occupational group studied. Only 2 studies (both conducted in the USA) had a sample size greater than 10,000. Most studies found females, non-medical healthcare staff and those refusing influenza vaccine to be more likely to be hesitant. There was conflicting evidence about the effects of age and previous COVID-19 on hesitancy. Only 3 studies (all from the USA), presented data disaggregated by ethnicity, all finding Black ethnic HCWs were most likely to be hesitant. Common themes amongst studies that investigated reasons for vaccine hesitancy were concerns about safety of vaccines, fear of side effects and short development timeframes. We did not find any studies on SARS-CoV-2 vaccine hesitancy in UK healthcare workers in the published literature.\n\nAdded value of this studyThis study is amongst the largest SARS-CoV-2 vaccine hesitancy studies in the literature. It is the largest study outside the USA and is the only study in UK HCWs. Our work focusses on the association of ethnicity with vaccine hesitancy, and we are the first study outside the USA to present results by ethnic group. The large number of ethnic minority HCWs in our study allows for examination of the outcome by more granular ethnicity categories than have previously been studied, allowing us to detect important differences in vaccine hesitancy levels within the broad White and Asian ethnic groupings. Our large sample size and the richness of our cohort study dataset allows us to control for many potential confounders in our multivariable analysis, and provide novel data on important potential drivers of hesitancy including discrimination, COVID-19 conspiracy beliefs, religion/religiosity and personality traits. Additionally, we combine quantitative with qualitative data providing a deeper understanding of the drivers of hesitancy and potential strategies to improve vaccine uptake in HCWs from ethnic minority communities.\n\nImplications of all the available evidenceAround a quarter of UK healthcare workers reported SARS-CoV-2 vaccine hesitancy. In accordance with previous studies in other countries, we determined that female sex and lack of influenza vaccine in the previous season were important predictors of SARS-CoV-2 vaccine hesitancy in UK HCWs, although in contrast to most studies in the published literature, after adjustment we do not demonstrate differences in hesitancy levels by occupational role. Importantly, previous literature provides conflicting evidence of the effects of age and previous SARS-CoV-2 infection on vaccine hesitancy. In our study, younger HCWs and those with evidence of previous COVID-19 were more likely to be hesitant. This study provides novel data on increased hesitancy levels within Black Caribbean, Mixed White and Black Caribbean, Black African, Chinese, Pakistani and White Other ethnic groups. Mistrust (of vaccines in general, in SARS-CoV-2 vaccines specifically, in healthcare systems and research) and misinformation appear to be important drivers of hesitancy within HCWS in the UK. Our data indicate that despite facing an increased risk of COVID-19 compared to their White colleagues, UK HCWs from some ethnic minority groups continue to exhibit greater levels of SARS-CoV-2 vaccine hesitancy. This study provides policy makers with evidence to inform strategies to improve uptake.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Katherine Woolf", - "author_inst": "UCL" - }, - { - "author_name": "Ian Christopher McManus", - "author_inst": "University College London" - }, - { - "author_name": "Christopher A Martin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Laura B Nellums", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Anna Louise Guyatt", - "author_inst": "University of Leicester" - }, - { - "author_name": "Carl Melbourne", - "author_inst": "University of Leicester" - }, - { - "author_name": "Luke Bryant", - "author_inst": "University of Leicester" - }, - { - "author_name": "Mayuri Gogoi", - "author_inst": "University of Leicester" - }, - { - "author_name": "Fatimah Wobi", - "author_inst": "University of Leicester" - }, - { - "author_name": "Amani Al-Oraibi", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Osama B Hassan", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Amit Gupta", - "author_inst": "Oxford University Hospitals NHS Trust" - }, - { - "author_name": "Catherine John", - "author_inst": "University of Leicester" - }, - { - "author_name": "Martin D Tobin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Susan Carr", - "author_inst": "General Medical Council" - }, - { - "author_name": "Sandra Simpson", - "author_inst": "Nottinghamshire Healthcare Foundation Trust" - }, - { - "author_name": "Bindu Gregary", - "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Avinash Aujayeb", - "author_inst": "Northumbria Healthcare NHS Foundation Trust" - }, - { - "author_name": "Stephen Zingwe", - "author_inst": "Berkshire Healthcare NHS Foundation Trust" - }, - { - "author_name": "Rubina Reza", - "author_inst": "Derbyshire Healthcare NHS Foundation Trust" - }, - { - "author_name": "Laura J Gray", - "author_inst": "University of Leicester" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - }, - { - "author_name": "- UK-REACH Study Collaborative Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.27.441655", "rel_title": "A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice", @@ -809124,6 +812359,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.19.21255709", + "rel_title": "Perceived public health threat a key factor for willingness to get the COVID-19 vaccine in Australia", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255709", + "rel_abs": "BackgroundVaccination rollout against COVID-19 has begun across multiple countries worldwide. Although the vaccine is free, rollout might still be compromised by hesitancy or concerns about COVID-19 vaccines.\n\nMethodsWe conducted two online surveys of Australian adults in April (during national lockdown; convenience cross-sectional sample) and November (virtually no cases of COVID-19; nationally representative sample) 2020, prior to vaccine rollout. We asked about intentions to have a potential COVID-19 vaccine (If a COVID-19 vaccine becomes available, I will get it) and free-text responses (November only).\n\nResultsAfter adjustment for differences in sample demographics, the estimated proportion agreeing to a COVID-19 vaccine if it became available in April (n=1146) was 76.2%. In November (n=2034) this was estimated at 71.4% of the sample; additional analyses identified that the variation was driven by differences in perceived public health threat between April and November. Across both surveys, female gender, being younger, having inadequate health literacy and lower education were associated with reluctance to be vaccinated against COVID-19. Lower perceived susceptibility to COVID-19, belief that data on the efficacy of vaccines is largely made up, having lower confidence in government, and lower perception of COVID-19 as a public health threat, were also associated with reluctance to be vaccinated against COVID-19. The top three reasons for agreeing to vaccinate (November only) were to protect myself and others, moral responsibility, and having no reason not to get it. For those who were indifferent or disagreeing to vaccinate, safety concerns were the top reason, followed by indecision and lack of trust in the vaccine respectively.\n\nCONCLUSIONSThese findings highlight some factors related to willingness to accept a COVID-19 vaccine prior to one being available in Australia. Now that the vaccine is being offered, this study identifies key issues that can inform public health messaging to address vaccine hesitancy.\n\nHIGHLIGHTSO_LIPerceived public health threat is associated with intentions to vaccinate\nC_LIO_LIThose believing the efficacy of vaccines is made up were less willing to get vaccinated\nC_LIO_LITo protect myself and others was the top reason for getting the vaccine\nC_LIO_LISafety concerns was the top reason against getting the vaccine\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rachael H Dodd", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kristen Pickles", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Erin Cvejic", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Samuel Cornell", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Jennifer MJ Isautier", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Tessa Copp", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Brooke Nickel", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Carissa Bonner", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Carys Batcup", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Danielle M Muscat", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Julie Ayre", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kirsten J McCaffery", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.19.21255714", "rel_title": "Antibody response after COVID-19 mRNA vaccination in relation to age, sex, and side effects", @@ -809756,109 +813054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.21.21255807", - "rel_title": "A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255807", - "rel_abs": "BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19.\n\nMethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed.\n\nFindings298 participants were enrolled from 3rd June 2020 to 29th January 2021. The primary outcome was assessed in 292 participants. The primary endpoint was not significantly different between the azithromycin and control groups (Adjusted OR 0{middle dot}91 [95% CI 0{middle dot}43-1{middle dot}92], p=0{middle dot}80). Rates of respiratory failure, progression to pneumonia, all-cause mortality, and adverse events, including serious cardiovascular events, were not significantly different between groups.\n\nInterpretationIn patients with mild-moderate COVID-19 managed without hospital admission, adding azithromycin to standard care treatment did not reduce the risk of subsequent hospitalisation or death. Our findings do not support the use of azithromycin in patients with mild-moderate COVID-19.\n\nFundingNIHR Oxford BRC, University of Oxford and Pfizer Inc.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE and the Cochrane Central register of Controlled Trials (CENTRAL) with the terms (\"azithromycin\") AND (\"COVID\" OR \"COVID-19\") AND (\"clinical trials\"), until March 25, 2021, with no language restrictions. We identified 42 studies, among which there were four completed randomised trials of azithromycin (with or without hydroxychloroquine) in hospitalised patients with severe disease, and three completed randomised trials of azithromycin in mild COVID-19 in primary care. The four trials in hospitalised patients randomised 8,988 participants to azithromycin or standard care or hydroxychloroquine and found no evidence of a difference in mortality, duration of hospital stay or peak disease severity. Of the three trials in primary care, these randomised participants with early disease to 3 or 5 days of therapy, of which only one assessed azithromycin as standalone therapy. This large, adaptive platform trial in the UK randomised 540 participants in primary care to 3 days treatment with azithromycin versus 875 to standard care alone and found no meaningful difference in time to first reported recovery, or of rates of hospitalisation (3% versus 3%) and there were no deaths. We did not identify any randomised trials in patients with COVID-19 managed in ambulatory care.\n\nAdded value of this studyThe ATOMIC2 trial was uniquely-designed to assess azithromycin as a standalone therapy in those with mild-moderately COVID-19 presenting to emergency care, but assessed as appropriate for initial ambulatory management without hospital admission. ATOMIC2 also uniquely assessed high-dose, long-duration treatment to investigate the efficacy of putative anti-inflammatory effects. We found that azithromycin 500 mg daily for 14 days did not reduce the proportion of participants who died or required hospital admission from any cause over the 28 days from randomisation.\n\nImplications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Timothy SC Hinks", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lucy Cureton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ruth Knight", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ariel Wang", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jennifer L Cane", - "author_inst": "University of Oxford" - }, - { - "author_name": "Vicki S Barber", - "author_inst": "University of Oxford" - }, - { - "author_name": "Joanna Black", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susan J Dutton", - "author_inst": "University of Oxford" - }, - { - "author_name": "James Melhorn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Maisha Jabeen", - "author_inst": "University of Oxford" - }, - { - "author_name": "Phil Moss", - "author_inst": "St George's Hospital, London" - }, - { - "author_name": "Rajendar Garlapati", - "author_inst": "East Lancashire NHS Hospitals" - }, - { - "author_name": "Tanya Baron", - "author_inst": "Oxford University Hospitals NHS Trust" - }, - { - "author_name": "Graham Johnson", - "author_inst": "Royal Derby Hospital" - }, - { - "author_name": "Fleur Cantle", - "author_inst": "Kings College Hospital, London" - }, - { - "author_name": "David Clarke", - "author_inst": "Royal Berkshire Hospital" - }, - { - "author_name": "Samer Elkhodair", - "author_inst": "University College London Hospital" - }, - { - "author_name": "Jonathan Underwood", - "author_inst": "Cardiff University" - }, - { - "author_name": "Daniel Lasserson", - "author_inst": "Oxford University Hospitals NHS Trust" - }, - { - "author_name": "Ian D Pavord", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sophie B Morgan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Duncan Richards", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.21.21255889", "rel_title": "Evaluation of Different Types of Face Masks to Limit the Spread of SARS CoV 2, A Modeling Study", @@ -810761,6 +813956,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.24.21256054", + "rel_title": "High proportion of post-acute sequelae of SARS-CoV-2 infection in individuals 1-6 months after illness and association with disease severity in an outpatient telemedicine population", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.24.21256054", + "rel_abs": "BackgroundIndividuals with coronavirus disease 2019 (COVID-19) may have persistent symptoms following their acute illness. The prevalence and predictors of these symptoms, termed post-acute sequelae of SARS-CoV-2 (PASC), are not fully described.\n\nMethodsParticipants discharged from an outpatient telemedicine program for COVID-19 were emailed a survey (1-6 months after discharge) about ongoing symptoms, acute illness severity, and quality of life. Standardized telemedicine notes from acute illness were used for covariates (comorbidities and provider-assessed symptom severity). Bivariate and multivariable analyses were performed to assess predictors of persistent symptoms.\n\nResultsTwo hundred and ninety patients completed the survey, of whom 115 (39.7%) reported persistent symptoms including fatigue (n= 59, 20.3%), dyspnea on exertion (n=41, 14.1%), and mental fog (n=39, 13.5%) among others. Proportion of persistent symptoms did not differ based on duration since illness (<90 days: n=32, 37.2% versus >90 days: n=80, 40.4%, p = 0.61). Predictors of persistent symptoms included provider-assessed moderate-severe illness (aOR 3.24, 95% CI 1.75, 6.02), female sex (aOR 1.99 95% 0.98, 4.04; >90 days out: aOR 2.24 95% CI 1.01, 4.95), and middle age (aOR 2.08 95% CI 1.07, 4.03). Common symptoms associated with reports of worse physical health included weakness, fatigue, myalgias, and mental fog.\n\nConclusionsSymptoms following acute COVID-19 are common and may be predicted by factors during the acute phase of illness. Fatigue and neuropsychiatric symptoms figured prominently. Select symptoms seem to be particularly associated with perceptions of physical health following COVID-19 and warrant specific attention on future studies of PASC.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "James B O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "H. Caroline Minton", + "author_inst": "Rollins School of Public Health, Emory University" + }, + { + "author_name": "Mary Morrow", + "author_inst": "Emory Healthcare" + }, + { + "author_name": "Colin Johnson", + "author_inst": "Emory Healthcare" + }, + { + "author_name": "Miranda A Moore", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ghazala A. D. O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Karima Benameur", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jason Higdon", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jessica K. Fairley", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.26.21256131", "rel_title": "SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples", @@ -811357,37 +814603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.25.21254890", - "rel_title": "Estimating the false positive rate of highly automated SARS-CoV-2 nucleic acid amplification testing", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.25.21254890", - "rel_abs": "Molecular testing for infectious diseases is generally both very sensitive and specific. Well-designed PCR primers rarely cross-react with other analytes, and specificities seen during test validation are often 100%. However, analytical specificities measured during validation may not reflect real-world performance across the entire testing process. Here, we use the unique environment of SARS-CoV-2 screening among otherwise well individuals to examine the false positivity rate of high throughput so-called \"sample-to-answer\" nucleic acid amplification testing (NAAT) on three commercial assays: the Hologic Panther Fusion(R), Hologic Aptima(R) transcription mediated amplification (TMA), and Roche cobas(R) 6800. We used repetitive sampling of the same person as the gold standard to determine test specificity rather than retesting of the same sample. We examined 451 people repetitively sampled over 7 months via nasal swab, comprising 7,242 results. During the study period there were twelve positive tests (0.17%) from 9 people. Eight positive tests (0.11%, five individuals) were considered bona fide true positives based on repeat positives or outside testing and epidemiological data. One positive test had no follow-up testing or metadata and could not be adjudicated. Three positive tests (three individuals) did not repeat as positive on a subsequent collection, nor did the original positive specimen test positive on an orthogonal platform. We consider these three tests false positives and estimate the overall false positive rate of high-throughput automated, sample-to-answer NAAT testing to be approximately 0.041% (3/7242). These data help laboratorians, epidemiologists, and regulators understand specificity and positive predictive value associated with high-throughput NAAT testing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Christopher M Chandler", - "author_inst": "University of Washington" - }, - { - "author_name": "Lori Bourassa", - "author_inst": "University of Washington" - }, - { - "author_name": "Patrick C Mathias", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "University of Washington Medical Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.18.21255682", "rel_title": "Effective vaccine allocation strategies, balancing economy with infection control against COVID-19 in Japan", @@ -812571,6 +815786,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.23.21255995", + "rel_title": "Regional opening strategies with commuter testing and containment of new SARS-CoV-2 variants", + "rel_date": "2021-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255995", + "rel_abs": "BackgroundDespite the vaccination process in Germany, a large share of the population is still susceptible to SARS-CoV-2. In addition, we face the spread of novel variants. Until we overcome the pandemic, reasonable mitigation and opening strategies are crucial to balance public health and economic interests.\n\nMethodsWe model the spread of SARS-CoV-2 over the German counties by a graph-SIR-type, metapopulation model with particular focus on commuter testing. We account for political interventions by varying contact reduction values in private and public locations such as homes, schools, workplaces, and other. We consider different levels of lockdown strictness, commuter testing strategies, or the delay of intervention implementation. We conduct numerical simulations to assess the effectiveness of the different intervention strategies after one month. The virus dynamics in the regions (German counties) are initialized randomly with incidences between 75-150 weekly new cases per 100,000 inhabitants (red zones) or below (green zones) and consider 25 different initial scenarios of randomly distributed red zones (between 2 and 20 % of all counties). To account for uncertainty, we consider an ensemble set of 500 Monte Carlo runs for each scenario.\n\nResultsWe find that the strength of the lockdown in regions with out of control virus dynamics is most important to avoid the spread into neighboring regions. With very strict lockdowns in red zones, commuter testing rates of twice a week can substantially contribute to the safety of adjacent regions. In contrast, the negative effect of less strict interventions can be overcome by high commuter testing rates. A further key contributor is the potential delay of the intervention implementation. In order to keep the spread of the virus under control, strict regional lockdowns with minimum delay and commuter testing of at least twice a week are advisable. If less strict interventions are in favor, substantially increased testing rates are needed to avoid overall higher infection dynamics.\n\nConclusionsOur results indicate that local containment of outbreaks and maintenance of low overall incidence is possible even in densely populated and highly connected regions such as Germany or Western Europe. While we demonstrate this on data from Germany, similar patterns of mobility likely exist in many countries and our results are, hence, generalizable to a certain extent.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Martin J Kuehn", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Daniel Abele", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Sebastian Binder", + "author_inst": "Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany" + }, + { + "author_name": "Kathrin Rack", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Margrit Klitz", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Jan Kleinert", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Jonas Gilg", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Luca Spataro", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Wadim Koslow", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Martin Siggel", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Michael Meyer-Hermann", + "author_inst": "Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany." + }, + { + "author_name": "Achim Basermann", + "author_inst": "German Aerospace Center, Institute for Software Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.22.21255941", "rel_title": "Predicting the end of Covid-19 infection for various countries using a stochastic agent-based model taking into account vaccination rates and the new mutant", @@ -813215,65 +816493,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.25.441316", - "rel_title": "Analysis of viral RNA-host protein interactomes enables rapid antiviral drug discovery", - "rel_date": "2021-04-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.25.441316", - "rel_abs": "RNA viruses including SARS-CoV-2, Ebola virus (EBOV), and Zika virus (ZIKV) constitute a major threat to global public health and society. The interactions between viral genomes and host proteins are essential in the life cycle of RNA viruses and thus provide targets for drug development. However, viral RNA-host protein interactions have remained poorly characterized. Here we applied ChIRP-MS to profile the interactomes of human proteins and the RNA genomes of SARS-CoV-2, EBOV, and ZIKV in infected cells. Integrated interactome analyses revealed interaction patterns that reflect both common and virus-specific host responses, and enabled rapid drug screening to target the vulnerable host factors. We identified Enasidenib as a SARS-CoV-2 specific antiviral agent, and Trifluoperazine and Cepharanthine as broad spectrum antivirals against all three RNA viruses.\n\nOne Sentence SummaryInteractome analyses of host proteins and the SARS-CoV-2, EBOV, and ZIKV RNA genomes unveil viral biology and drug targets.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Shaojun Zhang", - "author_inst": "MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for " - }, - { - "author_name": "Wenze Huang", - "author_inst": "MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for " - }, - { - "author_name": "Lili Ren", - "author_inst": "Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Xiaohui Ju", - "author_inst": "Center for Infectious Disease Research, School of Medicine, Tsinghua University" - }, - { - "author_name": "Mingli Gong", - "author_inst": "Center for Infectious Disease Research, School of Medicine, Tsinghua University" - }, - { - "author_name": "Jian Rao", - "author_inst": "Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Lei Sun", - "author_inst": "MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for " - }, - { - "author_name": "Pan Li", - "author_inst": "MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for " - }, - { - "author_name": "Qiang Ding", - "author_inst": "Center for Infectious Disease Research, School of Medicine, Tsinghua University" - }, - { - "author_name": "Jianwei Wang", - "author_inst": "Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Qiangfeng Cliff Zhang", - "author_inst": "MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for " - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.23.441209", "rel_title": "Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern", @@ -814169,6 +817388,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.21.21255874", + "rel_title": "Evaluation of the sensitivity, accuracy and currency of the Cochrane COVID-19 Study Register for supporting rapid evidence synthesis production", + "rel_date": "2021-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255874", + "rel_abs": "IntroductionThe Cochrane COVID-19 Study Register (CCSR) is a public, continually updated, curated database of COVID-19 study references. The aim of this study-based register is to support rapid and living evidence synthesis, including a project to build an evidence ecosystem of COVID-19 research (CEOsys). In November and December 2020 we conducted an evaluation of the CCSR for CEOsys, measured its performance and identified areas for improvement.\n\nMethodsFor the evaluation we generated a purposive sample of 286 studies from 20 reviews to calculate the CCSRs sensitivity (comprehensiveness), accuracy (correctly classified and linked studies) and currency (time to publish and process references).\n\nResultsThe CCSR had an overall sensitivity of 77.2%, with the highest sensitivity for interventional studies (94.4%) and lowest sensitivity for modelling studies (63.6%). The study register had 100% sensitivity for trial registry records, 86.5% for journal articles and 52.4% for preprints. 98.3% of references were correctly classified with regard to study type, and 93.4% with regard to study aim. 89% of studies were correctly linked. 81.4% of references were published to the register in under 30 days, with 0.5 day (median) for trial registry records, 2 days for journal articles and 56 days for preprints.\n\nConclusionThe CCSR had high sensitivity, accurate study classifications and short publishing times for journal articles and trial registry records. We identified that the CCSRs coverage and publishing times for preprints needed improvement. Finally, the evaluation illustrated the value of a study-based register for identifying additional study references for analysis in evidence synthesis.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Maria-Inti Metzendorf", + "author_inst": "Cochrane Metabolic and Endocrine Disorders Group, Institute of General Practice, Medical Faculty of the Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Robin M Featherstone", + "author_inst": "Cochrane, Editorial and Methods Department, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255631", "rel_title": "Risk Profile of Thanksgiving Gatherers and Subsequent SARS-CoV2 Testing and Diagnosis", @@ -814785,49 +818027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.04.24.21255892", - "rel_title": "Safety and efficacy of Pulmonary physiotherapy in hospitalized patients with severe COVID-19 pneumonia (PPTCOVID): A prospective, randomised, single-blind, controlled trial", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.24.21255892", - "rel_abs": "BackgroundPulmonary physiotherapy (PPT) is an important treatment in the management of patients with different types of pulmonary disorders. We aimed to evaluate safety and efficacy of PPT in hospitalized patients with severe COVID-19 pneumonia.\n\nMethodsIn this randomised, single-blind, controlled trial, we enrolled hospitalized, non-intubated patients (18 to 75 years with oxygen saturation (Spo2) in free-air breathing [≤]90%) with COVID-19 pneumonia at a referral hospital. Participants were randomly assigned (1:1) to receive PPT (six sessions PPT with breathing exercises and airway clearance techniques) or basic care. The primary outcomes were venous blood O2 (pO2) and CO2 (pCO2) pressures, Spo2, and three-minute walking test (3MWT) that were assessed before and end of sixth session. Secondary outcomes included level of dyspnea, venous blood PH, one-month mortality, three-month mortality and short form-36 (SF-36) after one and three months. The assessor was blinded to the assignment. This trial is registered with ClinicalTrials.gov (NCT04357340).\n\nFindingsIn April-May 2020, 40 participants were randomly assigned to PPT or basic care groups. While at the end of intervention, pO2 (adjusted mean difference to baseline measure (AMD) 6.43 mmHg [95%CI 2.8, 10.07], P<0.01), Spo2 (AMD 4.43% [95%CI 2.04, 6.83], P=0.0011), and 3MTW (AMD 91.44 m [95%CI 68.88, 113.99], P<0.01) were higher in PPT group and basic care group, pCO2 was not improved (AMD -2.1 mmHg [95%CI-6.36, 2.21], P=0.33). Mortality rate was 20% (OR adjusted to baseline Spo2 .19 [95%CI .03, 1.30], P=.09) and 25% (OR adjusted to baseline Spo2 .16 [95%CI .26, 1.05], P=.056) lower in the PPT group at three-month at one-month and three-month, respectively. There were no significant differences in most SF-36 domains scores after one and three months. No serious adverse event was observed during PPT sessions.\n\nConclusionEarly PPT can be considered a safe and effective therapeutic choice for patients with severe COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mohammad Javaherian", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Azadeh Shadmehr", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Abbasali Keshtkar", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Mohammad Taghi Beigmohammadi", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Narges Dabbaghipour", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Aabis Syed", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Behrouz Attarbashi Moghaddam", - "author_inst": "Tehran University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2021.04.22.440932", "rel_title": "Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India", @@ -815699,6 +818898,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.22.21255952", + "rel_title": "COVID-19 pandemic: Analyzing of different pandemic control strategies using saturation models", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255952", + "rel_abs": "Since December 2019, the world is confronted with the outbreak of the respiratory disease COVID-19. At the beginning of 2020, the COVID-19 epidemic evolved into a pandemic, which continues to this day. Within many countries, several control strategies or combinations of them, like restrictions (e.g. lockdown actions), medical care (e.g. development of vaccine or medicaments) and medical prevention (e.g. hygiene concept), were established with the goal to control the pandemic. Depending on the chosen control strategy, the COVID-19 spreading behavior slowed down or approximately stopped for a defined time range. This phenomenon is called saturation effect and can be described by saturation models: E.g. a fundamental approach is Verhulst (1838). The model parameter allows the interpretation of the spreading speed (growth) and the saturation effect in a sound way. This paper shows results of a research study of the COVID-19 spreading behavior and saturation effects depending on different pandemic control strategies in different countries and time phases based on Johns Hopkins University data base (2020). The study contains the analyzing of saturation effects related to short time periods, e.g. possible caused by lockdown strategies, geographical influences and medical prevention activities. The research study is focusing on reference countries like Germany, Japan, Denmark, Iceland, Ireland and Israel.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Stefan Bracke", + "author_inst": "University of Wuppertal, Germany" + }, + { + "author_name": "Lars Grams", + "author_inst": "University of Wuppertal, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255953", "rel_title": "COVID-19 pandemic: Analyzing of spreading behavior, the impact of restrictions and prevention measures in Germany and Japan.", @@ -816691,49 +819913,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.04.22.441045", - "rel_title": "Inactivation of SARS-CoV-2 by \u03b2-propiolactone Causes Aggregation of Viral Particles and Loss of Antigenic Potential", - "rel_date": "2021-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.22.441045", - "rel_abs": "Inactivated viral preparations are important resources in vaccine and antisera industry. Of the many vaccines that are being developed against COVID-19, inactivated whole-virus vaccines are also considered effective. {beta}-propiolactone (BPL) is a widely used chemical inactivator of several viruses. Here, we analyze various concentrations of BPL to effectively inactivate SARS-CoV-2 and their effects on the biochemical properties of the virion particles. BPL at 1:2000 (v/v) concentrations effectively inactivated SARS-CoV-2. However, higher BPL concentrations resulted in the loss of both protein content as well as the antigenic integrity of the structural proteins. Higher concentrations also caused substantial aggregation of the virion particles possibly causing undesirable outcomes including a potential immune escape by infectious virions, and a loss in antigenic potential. We also identify that the viral RNA content in the culture supernatants can be a direct indicator of their antigenic content. Our findings may have important implications in the vaccine and antisera industry during COVID-19 pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Divya Gupta Ms", - "author_inst": "Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Haripriya Parthasarathy Ms", - "author_inst": "Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Vishal Sah Mr", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Dixit Tandel Mr", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Dhiviya Vedagiri Ms", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Shashikala Reddy Dr", - "author_inst": "Osmania Medical College" - }, - { - "author_name": "Krishnan Harinivas Harshan Dr", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.20.21255810", "rel_title": "A Multicenter Evaluation of Blood Purification with Seraph 100 Microbind Affinity Blood Filter for the Treatment of Severe COVID-19: A Preliminary Report", @@ -817649,6 +820828,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.19.21255727", + "rel_title": "Prolonged activation of nasal immune cell populations and development of tissue-resident SARS-CoV-2 specific CD8 T cell responses following COVID-19", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255727", + "rel_abs": "The immune system plays a major role in Coronavirus Disease 2019 (COVID-19) pathogenesis, viral clearance and protection against re-infection. Immune cell dynamics during COVID-19 have been extensively documented in peripheral blood, but remain elusive in the respiratory tract. We performed minimally-invasive nasal curettage and mass cytometry to characterize nasal immune cells of COVID-19 patients during and 5-6 weeks after hospitalization. Contrary to observations in blood, no general T cell depletion at the nasal mucosa could be detected. Instead, we observed increased numbers of nasal granulocytes, monocytes, CD11c+ NK cells and exhausted CD4+ T effector memory cells during acute COVID-19 compared to age-matched healthy controls. These pro-inflammatory responses were found associated with viral load, while neutrophils also negatively correlated with oxygen saturation levels. Cell numbers mostly normalized following convalescence, except for persisting CD127+ granulocytes and activated T cells, including CD38+ CD8+ tissue-resident memory T cells. Moreover, we identified SARS-CoV-2 specific CD8+ T cells in the nasal mucosa in convalescent patients. Thus, COVID-19 has both transient and long-term effects on the immune system in the upper airway.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Anna H.E. Roukens", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Marion Konig", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tim Dalebout", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tamar Tak", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Shohreh Azimi", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Yvonne Kruize", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Cilia R. Pothast", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Renate S. Hagedoorn", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Sesmu M. Arbous", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jaimie L.H. Zhang", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Maaike Verheij", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Corine Prins", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Anne M. Does van der", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Pieter S. Hiemstra", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jutte J.C. Vries de", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jacqueline J. Janse", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Meta Roestenberg", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Sebenzile K. Myeni", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Marjolein Kikkert", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Mirjam H.M. Heemskerk", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Maria Yazdanbakhsh", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Hermelijn H. Smits", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Simon P. Jochems", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "- BEAT-COVID group", + "author_inst": "" + }, + { + "author_name": "- COVID-19 LUMC group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.19.21255723", "rel_title": "B and T cell immune responses elicited by the BNT162b2 (Pfizer BioNTech) COVID-19 vaccine in nursing home residents", @@ -818353,49 +821647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2021.04.14.21255261", - "rel_title": "COVID-19 risk assessment for the Tokyo Olympic Games", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255261", - "rel_abs": "ObjectivesTo explore effective prevention and control measures for Coronavirus Disease 2019 (COVID-19) in large international events through simulations of different interventions according to risk assessment.\n\nMethodsWe used random model to calculate the number of initial infected patients. And Poisson distribution was used to determine the number of initial infected patients based on the number of countries involved. Further, to simulate the COVID-19 transmission, the susceptible-exposed-symptomatic-asymptomatic-recovered-hospitalized (SEIARH) model was established based on susceptible-exposed-infectious-recovered (SEIR) mathematical model of epidemic diseases. According to risk assessment indicators produced by different scenarios of the simulated interventions, the risk of COVID-19 transmission in Tokyo Olympic Games was assessed.\n\nResultsThe large-scale vaccination will effectively control the spread of COVID-19. If the effective rate of vaccine is 100%, and the vaccination rate of athletes reaches 80%, an epidemic prevention barrier can be established.\n\nConclusionsThe current COVID-19 prevention measures proposed by the Japan Olympic Committee were needed to be enhanced. For the vaccination intervention had the best control effect, a mass vaccination serves was an effective way to control COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Wenhui Zhu", - "author_inst": "Department of Epidemiology and Health Statistics, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu 610041, Sichuan" - }, - { - "author_name": "Jie Feng", - "author_inst": "Department of Epidemiology and Health Statistics, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu 610041, Sichuan" - }, - { - "author_name": "Cheng Li", - "author_inst": "Department of Epidemiology and Health Statistics, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu 610041, Sichuan" - }, - { - "author_name": "Huimin Wang", - "author_inst": "Department of Epidemiology and Health Statistics, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu 610041, Sichuan" - }, - { - "author_name": "Yang Zhong", - "author_inst": "Department of Epidemiology and Health Statistics, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu 610041, Sichuan" - }, - { - "author_name": "Xingyu Zhang", - "author_inst": "Thomas E.Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh 15213, Pennsylvania, USA" - }, - { - "author_name": "Tao Zhang", - "author_inst": "Department of Epidemiology and Health Statistics, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu 610041, Sichuan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.17.21255440", "rel_title": "Understanding the barriers to pooled SARS-CoV-2 testing in the United States", @@ -819582,6 +822833,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.20.21255350", + "rel_title": "When can we safely return to normal? A novel method for identifying safe levels of NPIs in the context of COVID-19 vaccinations", + "rel_date": "2021-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255350", + "rel_abs": "Over the course of the COVID-19 pandemic, governing bodies and individuals have relied on a variety of non-pharmaceutical interventions (NPIs) to control the transmission of SARS-CoV-2, which posed an acute threat to individuals well-being and consistently impacted economic activities in many countries worldwide. NPIs have been implemented at varying levels of severity and in response to widely-divergent perspectives of risk tolerance. Now, concurrently with the introduction of multiple SARS-CoV-2 vaccines, the world looks optimistically to a \"return to normality\". In this work, we propose a multi-disciplinary approach, combining transmission modeling with control and optimization theory, to examine how risk tolerance and vaccination rates will impact the safe return to normal behavior over the next few months. To this end, we consider a version of the Susceptible-Exposed-Infected-Recovered transmission model that accounts for hospitalizations, vaccinations, and loss of immunity. We then propose a novel control approach to calibrate the necessary level of NPIs at various geographical levels to guarantee that the number of hospitalizations does not exceed a given risk tolerance (i.e., a maximum allowable threshold). Our model and control objectives are calibrated and tailored for the state of Colorado, USA. Our results suggest that: (i) increasing risk tolerance can decrease the number of days required to discontinue all NPIs; (ii) increasing risk tolerance inherently increases COVID-19 deaths even in the context of vaccination; (iii) if the vaccination uptake in the population is 70% or less, then return to normal behavior within the next year may newly stress the healthcare system. Furthermore, by using a multi-region model accounting for travel, our simulations predict that: (iv) relaxation should take into account regional heterogeneity in transmission and travel; and (v) premature relaxation of NPIs, even if restricted only to low-density regions, will lead to exceeding hospitalization limits even when highly-populated regions implement full-closures. Although the simulations are performed for the state of Colorado, the proposed model of transmission and control methods are applicable to any area worldwide and can be utilized at any geographical granularity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gianluca Bianchin", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Emiliano Dall'Anese", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Jorge Ivan Poveda", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Andrea Buchwald", + "author_inst": "University of Colorado Anschutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.21.440801", "rel_title": "Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania", @@ -820294,53 +823576,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.04.20.440588", - "rel_title": "MARCH8 targets cytoplasmic lysine residues of various viral envelope glycoproteins", - "rel_date": "2021-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440588", - "rel_abs": "The host transmembrane protein MARCH8 is a RING finger E3 ubiquitin ligase that downregulates various host transmembrane proteins, such as MHC-II. We have recently reported that MARCH8 expression in virus-producing cells impairs viral infectivity by reducing virion incorporation of not only HIV-1 envelope glycoproteins but also vesicular stomatitis virus G-glycoprotein through two different pathways. However, the MARCH8 inhibition spectrum remains largely unknown. Here, we investigate the antiviral spectrum of MARCH8 using HIV-1 pseudotyped with a variety of viral envelope glycoproteins. Pseudotyping experiments revealed that viral envelopes derived from the rhabdovirus, arenavirus, coronavirus, and togavirus (alphavirus) families were sensitive to MARCH8-mediated inhibition. Lysine mutations at the cytoplasmic tails of rabies virus-G, lymphocytic choriomeningitis virus glycoproteins, SARS-CoV and SARS-CoV-2 spike proteins, and Chikungunya virus and Ross River virus E2 proteins conferred resistance to MARCH8. Immunofluorescence showed impaired downregulation of the mutants of these viral envelopes by MARCH8, followed by lysosomal degradation, suggesting that MARCH8-mediated ubiquitination leads to intracellular degradation of these envelopes. Indeed, rabies virus-G and Chikungunya virus E2 proteins proved to be clearly ubiquitinated. We conclude that MARCH8 has inhibitory activity on a variety of viral envelope glycoproteins whose cytoplasmic lysine residues are targeted by this antiviral factor.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yanzhao Zhang", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Seiya Ozono", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takuya Tada", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Minoru Tobiume", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masanori Kameoka", - "author_inst": "Kobe University Graduate School of Health Sciences" - }, - { - "author_name": "Satoshi Kishigami", - "author_inst": "University of Yamanashi" - }, - { - "author_name": "Hideaki Fujita", - "author_inst": "Nagasaki International University" - }, - { - "author_name": "Kenzo Tokunaga", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.13.21255447", "rel_title": "Genetic risk prediction of COVID-19 susceptibility and severity in the Indian population", @@ -821332,6 +824567,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.14.21255448", + "rel_title": "Gender Differences in Health Protective Behaviors During the COVID-19 Pandemic in Taiwan: An Empirical Study", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255448", + "rel_abs": "IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection produces more severe symptoms and a higher mortality in men than in women. The role of biological sex in the immune response to SARS-CoV-2 is believed to explain this sex disparity. However, the contribution of gender factors that influence health protective behaviors and therefore health outcomes, remains poorly explored.\n\nMethodsWe assessed the contributions of gender in attitudes towards the COVID-19 pandemic, using a hypothetical influenza pandemic data from the 2014 Taiwan Social Change Survey. Participants were selected through a stratified, three-stage probability proportional-to-size sampling from across the nation, to fill in questionnaires that asked about their perception of the hypothetical pandemic, and intention to adopt health protective behaviors.\n\nResultsA total of 1,990 participants (median age 45.92 years, 49% women) were included. Significant gender disparities (p<0.001) were observed. The risk perception of pandemic (OR=1.28, 95% CI=1.21-1.35, p<0.001), older age (1.06, 95%=1.05-1.07, p<0.001), female gender (OR = 1.18, 95% CI = 1.09{square}1.27, p<0.001), higher education (OR=1.10, 95% CI=1.06-1.13, p<0.001), and larger family size (OR=1.09, 95% CI=1.06-1.15, p<0.001) were positively associated with health protective behaviors. The risk perception of pandemic (OR=1.25, 95% CI=1.15-1.36), higher education (OR=1.07, 95% CI=1.02-1.13, p<0.05), being married (OR=1.17, 95% CI=1.01-1.36, p<0.05), and larger family size (OR=1.33, 95% CI=1.25-1.42, p<0.001), were positively associated with intention to receive a vaccine. However, female gender was negatively associated with intention to receive a vaccine (OR=0.85, 95% CI=0.75-0.90, p<0.01) and to comply with contact-tracing (OR=0.95, 95% CI=0.90-1.00, p<0.05) compared to men. Living with children was also negatively associated with intention to receive vaccines (OR=0.77, 95% CI=0.66-0.90, p<0.001).\n\nConclusionThis study unveils gender differences in risk perception, health protective behaviors, vaccine hesitancy, and compliance with contact-tracing using a hypothetical viral pandemic. Gender-specific health education raising awareness of health protective behaviors may be beneficial to prevent future pandemics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jasmine Tan", + "author_inst": "School of Medicine, National Taiwan University, Taipei, Taiwan" + }, + { + "author_name": "Yilin Yoshida", + "author_inst": "Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA" + }, + { + "author_name": "Kevin Sheng-Kai Ma", + "author_inst": "Department of Life Science, National Taiwan University, Taipei, Taiwan" + }, + { + "author_name": "Franck Mauvais-Jarvis", + "author_inst": "Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.14.21255490", "rel_title": "Expectant parents' perceptions of healthcare and support during COVID-19 in the UK: A thematic analysis.", @@ -822116,69 +825382,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.15.21255560", - "rel_title": "COVID-19 transmission in a theme-park", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255560", - "rel_abs": "BackgroundAs COVID-19 vaccination coverage increases, public health and industries are contemplating re-opening measures of public spaces, including theme-parks. To re-open, theme-parks must provide public health mitigation plans. Questions on implementation of public health mitigation strategies such as park cleaning, COVID-19 testing, and enforcement of social distancing and the wearing of personal protective equipment (PPE) in the park remain.\n\nMethodsWe have developed a mathematical model of COVID-19 transmission in a theme-park that considers direct human-human and indirect environment-human transmission of the virus. The model thus tracks the changing infection/disease landscape of all visitors, workers, and environmental reservoirs in a theme park setting.\n\nFindingsModels results show that theme-park public health mitigation must include mechanisms that reduce virus contamination of the environment to ensure that workers and visitors are protected from COVID-19 transmission in the park. Thus, cleaning rates and mitigation of human-environment contact increases in importance.\n\nConclusionOur findings have important practical implications in terms of public health as policy- and decision-makers are equipped with a mathematical tool that can guide theme-parks in developing public health mitigation strategies for a safe re-opening.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Elena Aruffo", - "author_inst": "York University" - }, - { - "author_name": "Safia Athar", - "author_inst": "York University" - }, - { - "author_name": "Angie Raad", - "author_inst": "York University" - }, - { - "author_name": "Md Afsar Ali", - "author_inst": "York University" - }, - { - "author_name": "Mohammed Althubyani", - "author_inst": "York University" - }, - { - "author_name": "Christopher Chow", - "author_inst": "York University" - }, - { - "author_name": "Mahmuda Ruma", - "author_inst": "York University" - }, - { - "author_name": "Chao Liu", - "author_inst": "Northeastern University" - }, - { - "author_name": "Jianhong Wu", - "author_inst": "York University" - }, - { - "author_name": "Ali Asgary", - "author_inst": "York University" - }, - { - "author_name": "Jude Dzevela Kong", - "author_inst": "York University" - }, - { - "author_name": "Jane M. Heffernan", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.15.21255577", "rel_title": "Diagnostic accuracy of SARS-CoV-2 rapid antigen detection testing in symptomatic and asymptomatic children in the clinical setting", @@ -823066,6 +826269,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.14.21255512", + "rel_title": "Assessing the Mortality Impact of the COVID-19 Pandemic in Florida State Prisons", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255512", + "rel_abs": "BackgroundThe increased risk of COVID-19 infection among incarcerated individuals due to environmental hazards is well known and recent studies have highlighted the higher rates of infection and mortality prisoners in the United States face due to COVID-19. However, the impact of COVID-19 on all-cause mortality rates in incarcerated populations has not been studied.\n\nMethodsUsing data reported by the Florida Department of Corrections on prison populations and mortality events we conducted a retrospective cohort study of all individuals incarcerated in Florida state prisons between 2015 and 2020. We calculated excess deaths by estimating age-specific expected deaths from mortality trends in 2015 through 2019 and taking the difference between observed and expected deaths during the pandemic period. We calculated life table measures using standard demographic techniques and assessed significant yearly changes using bootstrapping.\n\nFindingsThe Florida Department of Corrections reported 510 total deaths from March 1, 2020 to December 31, 2020 among the state prison population. This was 42% higher (rate ratio 1.42, 95% CI 1.15 to 1.89) than the expected number of deaths in light of mortality rates for previous years. Reported COVID-19 deaths in a month were positively correlated with estimated excess deaths (80.4%, p <.01). Using age-specific mortality estimates, we found that life expectancy at age 20 declined by 4 years (95% CI 2.06-6.57) between 2019 and 2020 for the Florida prison population.\n\nInterpretationThe Florida prison population saw a significant increase in all-cause mortality during the COVID-19 pandemic period, leading to a decrease in life expectancy of more than four years. Life years lost by the Florida prison population were likely far greater than those lost by the general United States population, as reported by other studies. This difference in years lost highlights the need for increased interventions to protect vulnerable incarcerated populations during pandemics.\n\nFundingVital Projects Fund, Arnold Ventures, US Centers for Disease Control, Eunice Kennedy Shriver National Institute of Child Health and Human Development", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Neal Marquez", + "author_inst": "University of Washington" + }, + { + "author_name": "Aaron Littman", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Victoria Rossi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Michael Everett", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Erika Tyagi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Hope Johnson", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Sharon Dolovich", + "author_inst": "University of California Los Angeles" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.14.21255476", "rel_title": "Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020", @@ -823946,53 +827192,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.20.21255743", - "rel_title": "Simulation of aerosol and droplet spread during upper airway and gastrointestinal endoscopy", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255743", - "rel_abs": "ObjectiveAerosols and droplets are the main vectors in transmission of highly contagious SARS-Cov-2. Invasive diagnostic procedures like upper airway and gastrointestinal endoscopy have been declared as aerosol generating procedures. Protection of health care workers is crucial in times of COVID-19 pandemic.\n\nMethodsWe simulated aerosol and droplet spread during upper airway and gastrointestinal endoscopy with and without physico-mechanical barriers using a simulation model.\n\nResultsA clear plastic drape as used for central venous access markedly reduced visualized aerosol and droplet spread during endoscopy.\n\nConclusionA simple and cheap drape has the potential to reduce aerosol and droplet spread during endoscopy. In terms of health care worker protection, this may be important particularly in low- or moderate-income countries.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Johannes Heymer", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Florian Dengler", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Alexander Krohn", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Christina Jaki", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Tobias Schilling", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Martina Mueller-Schilling", - "author_inst": "University Hospital Regensburg" - }, - { - "author_name": "Arne Kandulski", - "author_inst": "University Hospital Regensburg" - }, - { - "author_name": "Matthias Ott", - "author_inst": "Klinikum Stuttgart" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.04.18.21255700", "rel_title": "Study Pre-protocol for 'BronchStart - The Impact of the COVID-19 Pandemic on the Timing, Age and Severity of Respiratory Syncytial Virus (RSV) Emergency Presentations; a Multi-Centre Prospective Observational Cohort Study'", @@ -825396,6 +828595,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255396", + "rel_title": "Ultra-fast, high throughput and inexpensive detection of SARS-CoV-2 seroconversion", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255396", + "rel_abs": "A technique allowing high throughput, fast and low-cost quantitative analysis of human IgG antibodies reacting to SARS-CoV-2 antigens will be required to understand the levels of protecting antibodies in the population raised in response to infections and/or to immunization. We described previously a fast, simple, and inexpensive Ni2+ magnetic bead immunoassay which allowed detection of human antibodies reacting against the SARS-CoV-2 nucleocapsid protein using a minimal amount of serum or blood. A major drawback of the previously described system was that it only processed 12 samples simultaneously. Here we describe a manually operating inexpensive 96 well plate magnetic extraction / homogenization process which allows high throughput analysis delivering results of 96 samples in chromogenic format in 12 minutes or in fluorescent ultrafast format which takes only 7 minutes. We also show that His tag antigen purification can be performed on the fly while loading antigens to the Ni2+ magnetic beads in a process which takes only 12 min reducing the pre analytical time and cost. Finally, we show that the magnetic bead immunoassay is antigen flexible and can be performed using either Nucleocapsid, Spike or Spike RBD. The method performed with low inter and intra assay variability using different antigens and detection modes and was able to deliver >99.5% specificity and >95% sensitivity for a cohort of 203 pre pandemic and 63 COVID-19 positive samples.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Marcelo S Conzentino Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Tatiele P.C. Santos Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Khaled Selim", + "author_inst": "Tubingen University" + }, + { + "author_name": "Berenike Wagner", + "author_inst": "Tubingen University" + }, + { + "author_name": "Janette T Alford", + "author_inst": "Tubingen University" + }, + { + "author_name": "Nelli Deobald", + "author_inst": "Tubingen University" + }, + { + "author_name": "Nigella M Paula", + "author_inst": "UFPR" + }, + { + "author_name": "Fabiane G.M Rego Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Dalila L Zanette", + "author_inst": "Fiocruz" + }, + { + "author_name": "Mateus N Aoki", + "author_inst": "Fiocruz" + }, + { + "author_name": "Jeanine M Nardin", + "author_inst": "Hospital Erasto Gaerthener" + }, + { + "author_name": "Maria C.C Huergo", + "author_inst": "Prefeitura Municipal de Guaratuba" + }, + { + "author_name": "Rodrigo A Reis", + "author_inst": "UFPR" + }, + { + "author_name": "Luciano Huergo Sr.", + "author_inst": "UFPR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.12.21255330", "rel_title": "Identification of natural SARS-CoV-2 infection in seroprevalence studies among vaccinated populations", @@ -826184,77 +829454,6 @@ "type": "confirmatory results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.19.440435", - "rel_title": "SARS-CoV-2 20I/501Y.V1 variant in the hamster model", - "rel_date": "2021-04-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.19.440435", - "rel_abs": "Late 2020, SARS-CoV-2 Alpha variant from lineage B.1.1.7 emerged in United Kingdom and gradually replaced the G614 strains initially involved in the global spread of the pandemic. In this study, we used a Syrian hamster model to compare a clinical strain of Alpha variant with an ancestral G614 strain. The Alpha variant succeeded to infect animals and to induce a pathology that mimics COVID-19. However, both strains replicated to almost the same level and induced a comparable disease and immune response. A slight fitness advantage was noted for the G614 strain during competition and transmission experiments. These data do not corroborate the epidemiological situation observed during the first half of 2021 in humans nor reports that showed a more rapid replication of Alpha variant in human reconstituted bronchial epithelium.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Maxime Cochin", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "L\u00e9a Luciani", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Franck Touret", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Jean S\u00e9lim Driouich", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Paul-R\u00e9mi Petit", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Gr\u00e9gory Moureau", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "C\u00e9cile Baronti", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Caroline Laprie", - "author_inst": "Laboratoire Vet-Histo, Marseille, France" - }, - { - "author_name": "Laurence Thirion", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Piet Maes", - "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Robbert Boudewijns", - "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - }, - { - "author_name": "Antoine Nougair\u00e8de", - "author_inst": "Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.19.440414", "rel_title": "Low dose inocula of SARS-CoV-2 B.1.1.7 variant initiate more robust infections in the upper respiratory tract of hamsters than earlier D614G variants", @@ -827214,6 +830413,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.13.21255384", + "rel_title": "Outcomes of COVID-19 infection in patients treated with Clozapine.", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255384", + "rel_abs": "BackgroundClozapine, an antipsychotic, is associated with increased susceptibility to infection with COVID-19, compared to other antipsychotics.\n\nAimsTo investigate associations between clozapine treatment and increased risk of adverse outcomes of COVID-19, namely COVID-related hospitalisation and intensive care treatment, and death, among patients taking antipsychotics with schizophrenia-spectrum disorders.\n\nMethodUsing data from South London and Maudsley NHS Foundation Trust (SLAM) clinical records, via the Clinical Record Interactive Search system, we identified 157 individuals who had an ICD-10 diagnosis of schizophrenia-spectrum disorders, were taking antipsychotics at the time of the COVID-19 pandemic in the UK, and had a laboratory-confirmed COVID-19 infection. The following health outcomes were measured: COVID-related hospitalisation, COVID-related intensive care treatment death. We tested associations between clozapine treatment and each outcome using logistic regression models, adjusting for gender, age, ethnicity, neighbourhood deprivation, obesity, smoking status, diabetes, asthma, bronchitis and hypertension using propensity scores.\n\nResultsIn the 157 individuals who developed COVID while on antipsychotics, there were 44 COVID-related hospitalisations, 13 COVID-related intensive care treatments and 13 deaths of any cause during the follow-up period. In the unadjusted analysis, there was no significant association between clozapine and any of the outcomes and there remained no associations following adjusting for the confounding variables.\n\nConclusionsIn our sample of patients with COVID-19 and schizophrenia-spectrum disorders, we found no evidence that clozapine treatment puts patients at increased risk of hospitalisation, intensive care treatment or death, compared to any other antipsychotic treatment. However, further research should be considered in larger samples to confirm this.\n\nConflict of interestRDH has received research funding from Roche, Pfizer, Janssen, and Lundbeck. DFF has received research funding from Janssen and Lundbeck. JHM has received research funding from Lundbeck. JTT has received research funding from Bristol-Meyers-Squibb. RS declares research support in the last 36 months from Janssen, GSK and Takeda.\n\nEthics statementThe research was conducted under ethical approval reference 18/SC/0372 from Oxfordshire Research Ethics Committee C.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Risha Govind", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Daniela Fonseca de Freitas", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Megan Pritchard", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Mizanur Khondoker", + "author_inst": "Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, UK." + }, + { + "author_name": "James T Teo", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Robert Stewart", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Richard D. Hayes", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "James H. MacCabe", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.13.21255413", "rel_title": "The impact of population mobility on COVID-19 incidence and socioeconomic disparities at the sub-city level in 314 Latin American cities", @@ -827994,101 +831240,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.16.440083", - "rel_title": "Antibody Cocktail Exhibits Broad Neutralization against SARS-CoV-2 and SARS-CoV-2 variants", - "rel_date": "2021-04-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.16.440083", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446 -S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, F61 and H121 exhibited efficient neutralizing activity against variants B.1.1.7 and B.1.351, those showed immune escape. Efficient neutralization of F61 and H121 against multiple mutations within RBD revealed a broad neutralizing activity against SARS-CoV-2 variants, which mitigated the risk of viral escape. Our findings defined the basis of therapeutic cocktails of F61 and H121 with broad neutralization and delivered a guideline for the current and future vaccine design, therapeutic antibody development, and antigen diagnosis of SARS-CoV-2 and its novel variants.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Yuanyuan Qu", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Xueyan Zhang", - "author_inst": "Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China;University of Chinese Academy of S" - }, - { - "author_name": "Meiyu Wang", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" - }, - { - "author_name": "Lina Sun", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430065, China" - }, - { - "author_name": "Cheng Li", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China;" - }, - { - "author_name": "Wei Wu", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Zhen Chen", - "author_inst": "Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China" - }, - { - "author_name": "Qiangling Yin", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Xiaolin Jiang", - "author_inst": "Shandong Center for Disease Control and Prevention, Jinan 250014, China" - }, - { - "author_name": "Yang Liu", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Chuan Li", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Jiandong Li", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Tianlei Ying", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China;" - }, - { - "author_name": "Dexin Li", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Faxian Zhan", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430065, China" - }, - { - "author_name": "Youchun Wang", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Wuxiang Guan", - "author_inst": "Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China;" - }, - { - "author_name": "Shiwen Wang", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - }, - { - "author_name": "Mifang Liang", - "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, Chi" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.16.21255614", "rel_title": "Evaluating Vaccine Efficacy Against SARS-CoV-2 Infection", @@ -828976,6 +832127,129 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.04.13.21255139", + "rel_title": "Strong anti-viral responses in pediatric COVID-19 patients in South Brazil", + "rel_date": "2021-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255139", + "rel_abs": "Epidemiological evidence that COVID-19 manifests as a milder disease in children compared to adults has been reported by numerous studies, but the mechanisms underlying this phenomenon have not been characterized. It is still unclear how frequently children get infected, and/or generate immune responses to SARS-CoV-2. We have performed immune profiling of pediatric and adult COVID-19 patients in Brazil, producing over 38 thousand data points, asking if cellular or humoral immune responses could help explain milder disease in children. In this study, pediatric COVID-19 patients presented high viral titers. Though their non-specific immune profile was dominated by naive, non-activated lymphocytes, their dendritic cells expressed high levels of HLA-DR and were low in CX3CR1, indicating competence to generate immune responses that are not targeted to inflamed tissue. Finally, children formed strong specific antibody and T cell responses for viral structural proteins. Childrens T cell responses differed from adults in that their CD8+ TNF+ T cell responses were low for S peptide but significantly higher against N and M peptide pools. Altogether, our data support a scenario in which SARS-CoV-2 infected children may contribute to transmission, though generating strong and differential responses to the virus that might associate with protection in pediatric COVID-19 presentation.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Tiago Fazolo", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Karina Lima", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Julia C. Fontoura", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Priscila Oliveira de Souza", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Gabriel Hilario", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Renata Zorzetto", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Luiz Rodrigues Jr.", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Veridiane Maria Pscheidt", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Jayme Ferreira Neto", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Alisson F. Haubert", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Izza Gambin", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Aline C. Oliveira", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Raissa S. Mello", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Matheus Gutierrez", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Rodrigo Benedetti Gassen", + "author_inst": "Center for Transplantation Sciences, Department of Surgery, Massachusetts" + }, + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Fernanda Hammes Varela", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "M\u00e1rcia Polese-Bonatto", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thiago J. Borges", + "author_inst": "Center for Transplantation Sciences, Department of Surgery, Massachusetts" + }, + { + "author_name": "Sidia Maria Callegari-Jacques", + "author_inst": "Departamento de Estat\u00edstica, Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Marcela Santos Correa da Costa", + "author_inst": "Coordena\u00e7\u00e3o-Geral do Programa Nacional de Imuniza\u00e7\u00f5es - Departamento de Imuniza\u00e7\u00f5es e Doen\u00e7as Transmiss\u00edveis - Secretaria de Vigil\u00e2ncia em Sa\u00fade - Minist\u00e9rio da" + }, + { + "author_name": "Jaqueline de Araujo Schwartz", + "author_inst": "Coordena\u00e7\u00e3o-Geral do Programa Nacional de Imuniza\u00e7\u00f5es - Departamento de Imuniza\u00e7\u00f5es e Doen\u00e7as Transmiss\u00edveis - Secretaria de Vigil\u00e2ncia em Sa\u00fade - Minist\u00e9rio da" + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Renato T. Stein", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Cristina Bonorino", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.04.10.21254878", "rel_title": "Preparations of Dutch emergency departments for the COVID-19 pandemic: a questionnaire-based study", @@ -829704,61 +832978,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.15.21255591", - "rel_title": "The impact of the COVID-19 pandemic on influenza, respiratory syncytial virus, and other seasonal respiratory virus circulation in Canada", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255591", - "rel_abs": "BackgroundThe ongoing coronavirus disease 2019 (COVID-19) pandemic has resulted in implementation of public health measures worldwide to mitigate disease spread, including; travel restrictions, lockdowns, messaging on handwashing, use of face coverings and physical distancing. As the pandemic progresses, exceptional decreases in seasonal respiratory viruses are increasingly reported. We aimed to evaluate the impact of the pandemic on circulation of influenza, respiratory syncytial virus and other seasonal respiratory viruses in Canada.\n\nMethodsEpidemiologic data were obtained from the Canadian Respiratory Virus Detection Surveillance System. Weekly data from the week ending 30th August 2014 until the week ending the 13th February 2021 were analysed. We compared trends in laboratory detection and test volumes during the 2020/2021 influenza season with baseline pre-pandemic seasons from 2014 to 2019.\n\nFindingsWe observed a dramatically lower percentage of tests positive for all seasonal respiratory viruses during 2020-2021 compared to baseline. For influenza A and B the percent positive decreased to 0{middle dot}0017 and 0{middle dot}0061 times that of baseline respectively and for RSV, the percent positive dropped to 0{middle dot}0145 times that of baseline. Ongoing detection of enterovirus/rhinovirus occurred, with regional variation in the epidemic patterns and intensity.\n\nInterpretationWe report an effective absence of the annual seasonal epidemic of most seasonal respiratory viruses in 2020/2021. This dramatic decrease is likely related to implementation of multi-layered public health measures during the pandemic. The impact of such measures may have relevance for public health practice in mitigating seasonal respiratory virus epidemics and for informing responses to future respiratory virus pandemics.\n\nFundingNo additional funding source was required for this study.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, preprint servers and country-specific public health rapid communications to identify surveillance and epidemiological studies on influenza, respiratory syncytial virus and other seasonal respiratory virus detection during the COVID-19 pandemic. A number of regional and national studies were identified worldwide. The majority of these studies focus on influenza epidemiology and all studies show consistent decreases in circulation of seasonal non-SARS-CoV-2 respiratory viruses. One previous study on the impact of non-pharmaceutical interventions on laboratory detections of influenza A and B in Canada included data for the 2019/2020 influenza season. Another recent study examined the effect of seasonal respiratory virus transmission on COVID-19 syndromic surveillance in the province of Ontario, Canada. No previous Canada-wide study has described the epidemiology of influenza, respiratory syncytial virus and other seasonal respiratory virus detection during the 2020/2021 influenza season.\n\nAdded value of this studyThe Canadian Respiratory Virus Detection Surveillance System provides weekly respiratory virus detection reports from sentinel laboratories across Canada for influenza, respiratory syncytial virus, parainfluenza viruses, adenovirus, human metapneumovirus, enterovirus/rhinovirus and seasonal coronaviruses. Data have been collected continuously since 2004. Analysis of this dataset provides a comprehensive assessment of the impact of the COVID-19 pandemic on circulation of seasonal respiratory viruses in Canada and analysis of data from the Canadian Public Health Infobase on COVID-19 allowed comparison of SARS-CoV-2 epidemiology. This is the first country-wide study in the Northern hemisphere to describe the concurrent epidemiology of all major seasonal respiratory viruses and SARS-CoV-2 during the 2020/2021 influenza season.\n\nImplications of all the available evidenceThe effective absence of the annual seasonal epidemic for most non-SARS-CoV-2 respiratory viruses in 2020/2021 has important public health implications for informing ongoing and future responses to respiratory virus epidemics and pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Helen E Groves", - "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada" - }, - { - "author_name": "Pierre-Philippe Piche-Renaud", - "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada" - }, - { - "author_name": "Adriana Peci", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Daniel Farrar", - "author_inst": "Centre for Global Child Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada" - }, - { - "author_name": "Steven Buckrell", - "author_inst": "Public Health Agency of Canada, Ottawa, Ontario, Canada" - }, - { - "author_name": "Christina Bancej", - "author_inst": "Public Health Agency of Canada, Ottawa, Ontario, Canada" - }, - { - "author_name": "Claire Sevenhuysen", - "author_inst": "Public Health Agency of Canada, Ottawa, Ontario, Canada" - }, - { - "author_name": "Aaron Campigotto", - "author_inst": "Division of Microbiology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada" - }, - { - "author_name": "Jonathan Gubbay", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Shaun Morris", - "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.11.21255273", "rel_title": "SARS-CoV-2 Immunogenicity in individuals infected before and after COVID-19 vaccination: Israel, January-March 2021: Implications for vaccination policy", @@ -830666,6 +833885,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.08.21255118", + "rel_title": "The association between loneliness during the COVID-19 pandemic and psychological distress", + "rel_date": "2021-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255118", + "rel_abs": "The purpose of this study was to examine the association between loneliness and psychological distress during the COVID-19 pandemic in Japan. We conducted a cross-sectional, online study from 22 to 26 December 2020. A total of 27,036 participants, all employed at the time of the survey, were included in the analysis. Participants were asked if they felt loneliness in a single-item question. The Kessler 6 (K6) was used to assess psychological distress defined as K6 scores of 5 or higher, and 13 or higher. The odds ratios (ORs) of psychological distress associated with loneliness were estimated using a multilevel logistic model nested in the prefecture of residence, with adjustment for age, sex, marital status, equivalent income, educational level, smoking, alcohol consumption, job type, number of workplace employees, and cumulative incidence rate of COVID-19 in the prefecture. Communication with friends, acquaintances, and family was strongly associated with psychological distress, so we adjusted for these factors and eating meals alone. Results showed a significant association between loneliness and psychological distress (OR = 36.62, 95%CI = 32.95-40.69). Lack of friends to talk to, lack of acquaintances to ask for help, and lack of people to communicate with through social networking sites were all strongly associated with psychological distress, as were family time and solitary eating. Even after adjusting for these factors, loneliness was still strongly associated with psychological distress (OR = 29.36, 95%CI = 26.44-32.98). The association between loneliness during the COVID-19 pandemic and psychological distress indicates the need for intervention.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yusuke Konno", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" + }, + { + "author_name": "Ayako Hino", + "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japa" + }, + { + "author_name": "Reiji Yoshimura", + "author_inst": "Department of Psychiatry, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.09.21255215", "rel_title": "Impacts of COVID-19 on sick leave", @@ -831218,97 +834488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.04.13.21255409", - "rel_title": "Efficacy of a nasal spray containing Iota-Carrageenan in the prophylaxis of COVID-19 in hospital personnel dedicated to patients care with COVID-19 disease. A pragmatic multicenter, randomized, double-blind, placebo-controlled trial (CARR-COV-02)", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255409", - "rel_abs": "BackgroundIota-Carrageenan (I-C) is a sulfate polysaccharide synthesized by red algae, with demonstrated antiviral activity and clinical efficacy as nasal spray in the treatment of common cold. In vitro, I-C inhibits SARS-CoV-2 infection in cell culture.\n\nMethodsThis is a pragmatic multicenter, randomized, double-blind, placebo-controlled trial assessing the use of a nasal spray containing I-C in the prophylaxis of COVID-19 in hospital personnel dedicated to care of COVID-19 patients.\n\nClinically healthy physicians, nurses, kinesiologists and others medical providers were assigned in a 1:1 ratio to receive four daily doses of I-C spray or placebo for 21 days.\n\nThe primary end point was clinical COVID-19, as confirmed by reverse-transcriptase-polymerase-chain-reaction testing, over a period of 21 days. The trial is registered at ClinicalTrials.gov (NCT04521322).\n\nFindingsA total of 394 individuals were randomly assigned to receive I-C or placebo. Both treatment groups had similar baseline characteristics.\n\nThe incidence of COVID19 was significantly lower in the I-C group compared to placebo (1{middle dot}0% vs 5{middle dot}0%) (Odds Ratio 0{middle dot}19 (95% confidence interval 0{middle dot}05 to 0{middle dot}77; p= 0{middle dot}03). Workday loss in placebo group compared to I-Cc were 1.6% days / person (95% ci, 1.0 to 2.2); p <0.0001\n\nThere were no differences in the incidence of adverse events across the two groups (17{middle dot}3% in the I-C group and 15{middle dot}2% in the placebo group, p= 0{middle dot}5).\n\nInterpretationI-C showed significant efficacy in preventing SARS-Cov-2 infection in hospital personnel dedicated to care patients with COVID-19 disease.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for research articles published up to February 14, 2021, with no language restrictions, using the terms \"SARS-CoV-2\" or \"COVID-19\", \"prevention\", \"clinical trial\", and \"prophylaxis\". Except for studies on vaccines we only found three peer-reviewed publications available on the efficacy of Hydroxycholoquine to prevent COVID-19 disease in individuals at risk of exposure. Hydroxychloroquine did not prevent COVID-19 used as pre or postexposure prophylaxis. We also did not find results from clinical trials on the efficacy of carrageenan in the prevention or treatment of cOVID-19.\n\nAdded value of this studyWe report the clinical efficacy of a nasal spray with Iota-Carrageenan for the prevention of COVID-19 disease in a randomised, double-blind, placebo-controlled, multicentre study in Republica Argentina, including 394 participants.\n\nImplications of all the available evidenceA simple intervention such as the administration of a nasal spray with Iota-Carrageenan, in addition to hand hygiene, use of personal protective equipment and social distancing, could provide additional protection until vaccines can be administered to the majority of the population.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Juan Manuel Figueroa", - "author_inst": "ICT Milstein-CONICET-Fundacion Pablo Cassara" - }, - { - "author_name": "Monica Lombardo", - "author_inst": "2.\tHospital Universitario CEMIC (Ciudad Autonoma de Buenos Aires, Argentina)" - }, - { - "author_name": "Ariel Dogliotti", - "author_inst": "Instituto Cardiovascular de Rosario (Provincia de Santa Fe, Argentina)" - }, - { - "author_name": "Luis Flynn", - "author_inst": "Sanatorio de Ninos de Rosario (Provincia de Santa Fe, Argentina)" - }, - { - "author_name": "Robert P. Giugliano", - "author_inst": "Brigham and Womens Hospital-Harvard Medical School. Boston, MA, USA" - }, - { - "author_name": "Guido Simonelli", - "author_inst": "Departement de Medecine, Universite de Montreal and Centre d etudes avancees en medecine du sommeil, Hopital du Sacre Coeur de Montreal. Quebec, Canada." - }, - { - "author_name": "Ricardo Valentini", - "author_inst": "Hospital Universitario CEMIC. Ciudad Autonoma de Buenos Aires, Argentina" - }, - { - "author_name": "Agnel Ramos", - "author_inst": "Sanatorio Parque de Rosario. Provincia de Santa Fe, Argentina" - }, - { - "author_name": "Pablo Romano", - "author_inst": "Clinica y Maternidad Santa Isabel. Ciudad Autonoma de Buenos Aires, Argentina" - }, - { - "author_name": "Marcelo Marcote", - "author_inst": "Hospital Interzonal de Agudos Pte. Peron. Provincia de Buenos Aires, Argentina" - }, - { - "author_name": "Alicia Michelini", - "author_inst": "Hospital Pediatrico Avelino Castelan. Provincia de Chaco, Argentina" - }, - { - "author_name": "Alejandro Salvado", - "author_inst": "Hospital Britanico de Buenos Aires. Ciudad Autonoma de Buenos Aires, Argentina" - }, - { - "author_name": "Emilio Sykora", - "author_inst": "Clinica Monte Grande. Provincia de Buenos Aires, Argentina" - }, - { - "author_name": "Cecilia Kniz", - "author_inst": "Hospital 4 de Junio Dr Ramon Carrillo. Provincia de Chaco, Argentina" - }, - { - "author_name": "Marcelo Kobelinsky", - "author_inst": "Clinica Modelo de Moron. Provincia de Buenos Aires, Argentina" - }, - { - "author_name": "David Salzberg", - "author_inst": "Hospital Gral. de Agudos Dr. Teodoro Alvarez. Ciudad Autonoma de Buenos Aires, Argentina" - }, - { - "author_name": "Diana Jerusalinsky", - "author_inst": "Instituto de Biologia Celular y Neurociencia IBCN. Universidad de Buenos Aires. CONICET. Ciudad Autonoma de Buenos Aires, Argentina" - }, - { - "author_name": "Osvaldo Uchitel", - "author_inst": "17.\t Instituto de Fisiologia, Biologia Molecular y Neurociencias. Universidad de Buenos Aires. CONICET. Ciudad Autonoma de Buenos Aires, Argentina" - }, - { - "author_name": "- CARR-COV2 Trial Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.13.21255342", "rel_title": "Protocol for the COG-UK hospital onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in United Kingdom NHS hospitals", @@ -832472,6 +835651,109 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.04.13.439641", + "rel_title": "Spike Protein Targeting \"Nano-Glue\" that Captures and Promotes SARS-CoV-2 Elimination", + "rel_date": "2021-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439641", + "rel_abs": "The global emergency caused by the SARS-CoV-2 pandemics can only be solved with adequate preventive and therapeutic strategies, both currently missing. The electropositive Receptor Binding Domain (RBD) of SARS-CoV-2 spike protein with abundant {beta}-sheet structure serves as target for COVID-19 therapeutic drug design. Here, we discovered that ultrathin 2D CuInP2S6 (CIPS) nanosheets as a new agent against SARS-CoV-2 infection, which also able to promote viral host elimination. CIPS exhibits extremely high and selective binding capacity with the RBD of SARS-CoV-2 spike protein, with consequent inhibition of virus entry and infection in ACE2-bearing cells and human airway epithelial organoids. CIPS displays nano-viscous properties in selectively binding with spike protein (KD < 1 pM) with negligible toxicity in vitro and in vivo. Further, the CIPS-bound SARS-CoV-2 was quickly phagocytosed and eliminated by macrophages, suggesting CIPS could be successfully used to capture and facilitate the virus host elimination with possibility of triggering anti-viral immunization. Thus, we propose CIPS as a promising nanodrug for future safe and effective anti-SARS-CoV-2 therapy, as well as for use as disinfection agent and surface coating material to constrain the SARS-CoV-2 spreading.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Guofang Zhang", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Yalin Cong", + "author_inst": "University of Chinese Academy of Science" + }, + { + "author_name": "Guoli Cao", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Liang Li", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Peng Yu", + "author_inst": "School of Materials Science and Engineering, Sun Yat-sen University" + }, + { + "author_name": "Qingle Song", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Ke Liu", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing Qu", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing Wang", + "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University" + }, + { + "author_name": "Wei Xu", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Shumin Liao", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yunping Fan", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yufeng Li", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Guocheng Wang", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Lijing Fang", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Yanzhong Chang", + "author_inst": "College of Life Science, Hebei Normal University" + }, + { + "author_name": "Yuliang Zhao", + "author_inst": "Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Diana Boraschi", + "author_inst": "The Institute of Biochemistry and Cell Biology, National Research Council" + }, + { + "author_name": "Hongchang Li", + "author_inst": "Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences" + }, + { + "author_name": "Chunying Chen", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Liming Wang", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Yang Li", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.14.439793", "rel_title": "Neuropilin-1 Mediates SARS-CoV-2 Infection in Bone Marrow-derived Macrophages", @@ -833152,53 +836434,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.12.21255084", - "rel_title": "Reliability of Spike Gene Target Failure for ascertaining SARS-CoV-2 lineage B.1.1.7 prevalence in a hospital setting", - "rel_date": "2021-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255084", - "rel_abs": "The appearance of the SARS-CoV-2 lineage B.1.1.7 in the UK in late 2020, associated with faster transmission, sparked the need to find effective ways to monitor its spread. The set of mutations that characterise this lineage include a deletion in position 69 and 70 of the spike protein, which is known to be associated with Spike Gene Target Failure (SGTF) in a commonly used three gene diagnostic qPCR assay. The lower cost and faster turnaround times compared to whole genome sequencing make the use of qPCR for monitoring of the variant spread an attractive proposition. However, there are several potential issues with this approach. Here we use 826 SARS-CoV-2 samples collected in a hospital setting as part of the Hospital Onset COVID Infection (HOCI) study where qPCR was used for viral detection, followed by whole genome sequencing (WGS), to identify the factors to consider when using SGTF to infer lineage B.1.1.7 prevalence in a hospital setting, with potential implications for locations where this variant has recently been introduced.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jose Afonso Guerra-Assuncao", - "author_inst": "University College London" - }, - { - "author_name": "Paul A Randell", - "author_inst": "North West London Pathology" - }, - { - "author_name": "Florencia A.T. Boshier", - "author_inst": "University College London" - }, - { - "author_name": "Michael Andrew Crone", - "author_inst": "Imperial College London" - }, - { - "author_name": "Juanita Pang", - "author_inst": "University College London" - }, - { - "author_name": "Tabitha W. Mahungu", - "author_inst": "Royal Free London NHS Foundation Trust" - }, - { - "author_name": "Paul Freemont", - "author_inst": "Imperial College London" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.09.21255166", "rel_title": "Two Distinct Dynamic Process Models of COVID-19 Spread with Divergent Vaccination Outcomes", @@ -834070,6 +837305,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.11.21253563", + "rel_title": "Impact of COVID -19 on Depression and Anxiety among Healthcare Professionals in Abu Dhabi", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21253563", + "rel_abs": "COVID-19 have affected Healthcare workers is many ways. One of the important areas is the psychological impact. The aim of this study is to examine the effects of the COVID-19 outbreak on the mental health of healthcare Professionals (HCP). A cross-sectional study was conducted between April 11th, and July 23rd, 2020, to assess depression and anxiety of healthcare workers, during the COVID-19 pandemic. An online, self-administered, anonymous questionnaire evaluated 1,268 HCP. More than half of the participants reported symptoms of anxiety (51.5%). Mild anxiety was reported in 28.8% of participating HCP, and 12.68 % of the participants registered moderate anxiety scores, while 9.95 % reported severe anxiety. Depression symptoms were revealed in 38.3 % of participating providers. Among all participates, 4.3 % and 2.7 % reported moderately severe and severe depression, accordingly, while 22.5%, and 8.8 % of the participating health care providers documented mild and moderate depression. The high prevalence of anxiety and depression recorded among HCP during the pandemic suggests that mental health intervention and support are necessary to ensure the psychological well-being of HCP.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Amal Alzarooni", + "author_inst": "Ambulatory health care,Abu Dhabi Health Services Company, UAE" + }, + { + "author_name": "Aljazia Alghfeli", + "author_inst": "Ambulatory health care, Abu Dhabi Health Services Company, AE" + }, + { + "author_name": "Hamda Alremeithi", + "author_inst": "Ambulatory health care,Abu Dhabi Health Services Company , UAE" + }, + { + "author_name": "Roqayah Al Madhaani,", + "author_inst": "Ambulatory Healthcare Services,Abu Dhabi Health Services Company, UAE" + }, + { + "author_name": "Latifa Al Ketbi,", + "author_inst": "Ambulatory Healthcare Services, Abu Dhabi Health Services Company, UAE" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.09.21255179", "rel_title": "SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan", @@ -834802,169 +838072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.10.21255202", - "rel_title": "GRAd-COV2, a gorilla adenovirus based candidate vaccine against COVID-19, is safe and immunogenic in young and older adults", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.10.21255202", - "rel_abs": "Safe and effective vaccines against coronavirus disease 2019 (COVID-19) are urgently needed to control the ongoing pandemic. Although impressive progress has been made with several COVID-19 vaccines already approved, it is clear that those developed so far cannot meet the global vaccine demand. We have developed a COVID-19 vaccine based on a replication-defective gorilla adenovirus expressing the stabilized pre-fusion SARS-CoV-2 Spike protein, named GRAd-COV2. We aimed to assess the safety and immunogenicity of a single-dose regimen of this vaccine in healthy younger and older adults to select the appropriate dose for each age group. To this purpose, a phase 1, dose-escalation, open-label trial was conducted including 90 healthy subjects, (45 aged 18-55 years and 45 aged 65-85 years), who received a single intramuscular administration of GRAd-CoV2 at three escalating doses. Local and systemic adverse reactions were mostly mild or moderate and of short duration, and no serious AE was reported. Four weeks after vaccination, seroconversion to Spike/RBD was achieved in 43/44 young volunteers and in 45/45 older subjects. Consistently, neutralizing antibodies were detected in 42/44 younger age and 45/45 older age volunteers. In addition, GRAd-COV2 induced a robust and Th1-skewed T cell response against the S antigen in 89/90 subjects from both age groups. Overall, the safety and immunogenicity data from the phase 1 trial support further development of this vaccine.\n\nOne Sentence SummaryGRAd-COV2, a candidate vaccine for COVID-19 based on a novel gorilla adenovirus, is safe and immunogenic in younger and older adults", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Simone Lanini", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Stefania Capone", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Andrea Antinori", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Stefano Milleri", - "author_inst": "Centro Ricerche Cliniche di Verona srl P.le Scuro, 10 37134 Verona" - }, - { - "author_name": "Emanuele Nicastri", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Roberto Camerini", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Chiara Agrati", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Concetta Castilletti", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Federica Mori", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Alessandra Sacchi", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Roberta Gagliardini", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Virginia Ammendola", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Eleonora Cimini", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Fabiana Grazioli", - "author_inst": "ReiThera Srl. Via di Castel Roman100. 00128 Rome. Italy" - }, - { - "author_name": "Laura Scorzolini", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Federico Napolitano", - "author_inst": "ReiThera Srl. Via di Castel Roman100. 00128 Rome. Italy" - }, - { - "author_name": "Maria Maddalena Plazzi", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Marco Soriani", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Aldo De Luca", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Simone Battella", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Andrea Sommella", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Alessandra Maria Contino", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Federica Barra", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Michela Gentile", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Angelo Raggioli", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Youfang Shi", - "author_inst": "First Affiliated Hospital of Soochow University, No. 188 Shizi Str. Suzhou, Jiangsu, China and Shanghai Institute of Nutrition and Health, Shanghai Institutes f" - }, - { - "author_name": "Enrico Girardi", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Markus Maeurer", - "author_inst": "Division of Immunotherapy,ImmunoSurgery,Champalimaud Foundation Avenida Brasilia1400038 Lisboa Portugal Lisboa and I Medical Clinic, University of Mainz Paul Eh" - }, - { - "author_name": "Maria Rosaria Capobianchi", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Francesco Vaia", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - }, - { - "author_name": "Mauro Piacentini", - "author_inst": "Department of Biology, University of Rome \"Tor Vergata Via Cracovia, 50, 00133 Rome Italy" - }, - { - "author_name": "Guido Kroemer", - "author_inst": "Sorbonne Universite ,Institut Universitaire de France ,France and Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif,and Pole de Biolog" - }, - { - "author_name": "Alessandra Vitelli", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Stefano Colloca", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Antonella Folgori", - "author_inst": "ReiThera Srl. Via di Castel Romano 100. 00128 Rome. Italy" - }, - { - "author_name": "Giuseppe Ippolito", - "author_inst": "Istituto Nazionale per Le Malattie Infettive Lazzaro Spallanzani IRCCS, Via Portuense 292 Rome Italy" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.09.21255219", "rel_title": "Early Experience With Neutralizing Monoclonal Antibody Therapy For COVID-19", @@ -836052,6 +839159,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.09.21255161", + "rel_title": "The PUPPY Study - Protocol for a Longitudinal Mixed Methods Study Exploring Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255161", + "rel_abs": "BackgroundThe COVID-19 pandemic significantly disrupted primary care in Canada, with many walk-in clinics and family practices initially closing or being perceived as inaccessible, pharmacies remaining open with restrictions on patient interactions, rapid uptake of virtual care, and reduced referrals for lab tests, diagnostics, and specialist care. The PUPPY Study (Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year) seeks to understand the impact of COVID-19 across the quadruple aim of primary care, with particular focus on the impacts on patients without attachment to a regular provider and those with chronic health conditions.\n\nObjectiveThe PUPPY Study objective is to understand the impact of COVID-19 across the quadruple aim of primary care.\n\nMethodsThe PUPPY study builds on an existing research program exploring patients access and attachment to primary care, pivoted to adapt to the emerging COVID-19 context. We will undertake a longitudinal mixed methods study to understand critical gaps in primary care access and coordination, comparing data pre- and post-pandemic in three Canadian provinces (Quebec, Ontario, and Nova Scotia). Multiple data sources will be used including: a policy review; qualitative interviews with primary care policymakers, providers (i.e., family physicians, nurse practitioners, and pharmacists), and patients (N=120); and medication prescribing and healthcare billings. The findings will inform the strengthening of primary care during and beyond the COVID-19 pandemic.\n\nResultsFunding was provided by the Canadian Institutes of Health Research COVID-19 Rapid Funding Opportunity Grant. Ethical approval to conduct this study was granted in Ontario (Queens Health Sciences & Affiliated Teaching Hospitals Research Ethics Board, file number 6028052; Western University Health Sciences Research Ethics Board, project 116591; University of Toronto Health Sciences Research Ethics Board, protocol number 40335), Quebec (Centre integre universitaire de sante et de services sociaux de lEstrie, project number 2020-3446) and Nova Scotia (Nova Scotia Health Research Ethics Board, file number 1024979).\n\nConclusionsThis is the first study of its kind exploring the impacts of COVID-19 on primary care systems, with particular focus on the issues of patients attachment and access to primary care. Through a multi-stakeholder, cross-jurisdictional approach, the PUPPY Study will generate findings and implications for future policy and practice.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Emily Gard Marshall", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Mylaine Breton", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Benoit Cossette", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Jennifer Isenor", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Maria Mathews", + "author_inst": "Western University" + }, + { + "author_name": "Caitlyn Ayn", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Melanie Ann Smithman", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "David Stock", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Eliot Frymire", + "author_inst": "Queen's University" + }, + { + "author_name": "Lynn Edwards", + "author_inst": "Nova Scotia Health" + }, + { + "author_name": "Michael Green", + "author_inst": "Queen's University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2021.04.08.21255046", "rel_title": "COVID-19 and mortality risk in patients with psychiatric disorders", @@ -836708,69 +839874,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.04.11.439347", - "rel_title": "An AI-guided invariant signature places MIS-C with Kawasaki disease in a continuum of host immune responses", - "rel_date": "2021-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.11.439347", - "rel_abs": "A significant surge in cases of multisystem inflammatory syndrome in children (MIS-C, also called Pediatric Inflammatory Multisystem Syndrome - PIMS) has been observed amidst the COVID-19 pandemic. MIS-C shares many clinical features with Kawasaki disease (KD), although clinical course and outcomes are divergent. We analyzed whole blood RNA sequences, serum cytokines, and formalin fixed heart tissues from these patients using a computational toolbox of two gene signatures, i.e., the 166-gene viral pandemic (ViP) signature, and its 20-gene severe (s)ViP subset that were developed in the context of SARS-CoV-2 infection and a 13-transcript signature previously demonstrated to be diagnostic for KD. Our analyses revealed that KD and MIS-C are on the same continuum of the host immune response as COVID-19. While both the pediatric syndromes converge upon an IL15/IL15RA-centric cytokine storm, suggestive of shared proximal pathways of immunopathogenesis, they diverge in other laboratory parameters and cardiac phenotypes. The ViP signatures also revealed unique targetable cytokine pathways in MIS-C, place MIS-C farther along in the spectrum in severity compared to KD and pinpoint key clinical (reduced cardiac function) and laboratory (thrombocytopenia and eosinopenia) parameters that can be useful to monitor severity.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Debashis Sahoo", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Gajanan Dattatray", - "author_inst": "UCSD" - }, - { - "author_name": "Chisato Shimizu", - "author_inst": "UCSD" - }, - { - "author_name": "Jihoon Kim", - "author_inst": "UCSD" - }, - { - "author_name": "Soni Khandelwal", - "author_inst": "UCSD" - }, - { - "author_name": "Adriana H. Tremoulet", - "author_inst": "UCSD" - }, - { - "author_name": "John Kanegaye", - "author_inst": "UCSD" - }, - { - "author_name": "- Pediatric Emergency Medicine Kawasaki Disease Research Group", - "author_inst": "" - }, - { - "author_name": "Joseph Bocchini", - "author_inst": "UCSD" - }, - { - "author_name": "Soumita Das", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Jane C. Burns", - "author_inst": "UCSD" - }, - { - "author_name": "Pradipta Ghosh", - "author_inst": "UCSD" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.12.439201", "rel_title": "Impairment of SARS-CoV-2 spike glycoprotein maturation and fusion activity by the broad-spectrum anti-infective drug nitazoxanide", @@ -837830,6 +840933,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.09.439260", + "rel_title": "Nosocomial Pseudomonas aeruginosaregulates alginate biosynthesis and Type VI secretion system during adaptive and convergent evolution for coinfection in critically ill COVID-19 patients", + "rel_date": "2021-04-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439260", + "rel_abs": "COVID-19 pandemic has caused millions of death globally and caused huge impact on the health of infected patients. Shift in the lung microbial ecology upon such viral infection often worsens the disease and increases host susceptibility to secondary infections. Recent studies have indicated that bacterial coinfection is an unignorable factor contributing to the aggravation of COVID-19 and posing great challenge to clinical treatments. However, there is still a lack of in-depth investigation on the coinfecting bacteria in COVID-19 patients for better treatment of bacterial coinfection. With the knowledge that Pseudomonas aeruginosa is one of the top coinfecting pathogens, we analyzed the adaptation and convergent evolution of nosocomial P. aeruginosa isolated from two critical COVID-19 patients in this study. We sequenced and compared the genomes and transcriptomes of P. aeruginosa isolates longitudinally and parallelly for its evolutionary traits. P. aeruginosa overexpressed alginate and attenuated Type VI secretion system (T6SS) during coinfection for excessive biofilm formation and suppressed virulence. Results of bacterial competition assay and macrophage cytotoxicity test indicated that P. aeruginosa reduced its virulence towards both prokaryotic competitors and eukaryotic host through inhibiting its T6SS during evolution. P. aeuginosa T6SS is thus one of the reasons for its advantage to cause coinfection in COVID-19 patients while the attenuation of T6SS could cause a shift in the microecological composition in the lung. Our study will contribute to the development of therapeutic measures and the discovery of novel drug target to eliminate P. aeruginosa coinfection in COVID-19 patient.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zhao Cai", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Xiangke Duan", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Han Zhang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Shuhong Han", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China" + }, + { + "author_name": "Kaiwei Yu", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Yingdan Zhang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Yang Liu", + "author_inst": "Medical Research Center, Southern University of Science and Technology Hospital" + }, + { + "author_name": "Liang Yang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.10.439275", "rel_title": "CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity", @@ -838518,29 +841668,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.09.439051", - "rel_title": "Large fluctuations of the fusion intermediate help SARS-CoV-2 capture host cell membranes", - "rel_date": "2021-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439051", - "rel_abs": "Cell entry by SARS-CoV-2 is accomplished by the S2 subunit of the spike S protein on the virion surface by capture of the host cell membrane and fusion with the viral envelope. Capture and fusion require the prefusion S2 to transit to its potent, fusogenic form, the fusion intermediate (FI). However, the FI structure is unknown, detailed computational models of the FI are unavailable, and the mechanisms and timing of membrane capture and fusion are not established. Here, we constructed a full-length model of the CoV-2 FI by extrapolating from known CoV-2 pre- and postfusion structures. In atomistic and coarse-grained molecular dynamics simulations the FI was remarkably flexible and executed large bending and extensional fluctuations due to three hinges in the C-terminal base. Simulations suggested a host cell membrane capture time of [~] 2 ms. Isolated fusion peptide simulations identified an N-terminal helix that directed and maintained binding to the membrane but grossly underestimated the binding time, showing that the fusion peptide environment is radically altered when attached to its host fusion protein. The large configurational fluctuations of the FI generated a substantial exploration volume that aided capture of the target membrane, and may set the waiting time for fluctuation-triggered refolding of the FI that draws the viral envelope and host cell membrane together for fusion. These results describe the FI as a machinery designed for efficient membrane capture and suggest novel potential drug targets.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC=\"FIGDIR/small/439051v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@1374b59org.highwire.dtl.DTLVardef@133d21forg.highwire.dtl.DTLVardef@127f2ddorg.highwire.dtl.DTLVardef@1b9ab8f_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rui Su", - "author_inst": "Columbia University" - }, - { - "author_name": "Jin Zeng", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.04.09.439166", "rel_title": "Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques", @@ -839608,6 +842735,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.04.05.21254834", + "rel_title": "Performance of Repeat BinaxNOW SARS-CoV-2 Antigen Testing in a Community Setting, Wisconsin, November-December 2020", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254834", + "rel_abs": "Repeating the BinaxNOW antigen test for SARS-CoV-2 by two groups of readers within 30 minutes resulted in high concordance (98.9%) in 2,110 encounters. BinaxNOW test sensitivity was 77.2% (258/334) compared to real-time reverse transcription-polymerase chain reaction. Repeating antigen testing on the same day did not significantly improve test sensitivity while specificity remained high.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Melisa M. Shah", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Phillip P. Salvatore", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Laura Ford", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emiko Kamitani", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melissa J. Whaley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kaitlin Mitchell", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Dustin W. Currie", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Clint N. Morgan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah E. Segaloff", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Shirley Lecher", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Tarah Somers", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Miriam E. Van Dyke", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John Paul Bigouette", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Augustina Delaney", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Juliana DaSilva", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michelle O'Hegarty", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Lauren Boyle-Estheimer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Fatima Abdirizak", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sandor E. Karpathy", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer Meece", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Lynn Ivanic", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Kimberly Goffard", + "author_inst": "Winnebago County Health Department" + }, + { + "author_name": "Doug Gieryn", + "author_inst": "Winnebago County Health Department" + }, + { + "author_name": "Alana Sterkel", + "author_inst": "Wisconsin State Laboratory of Hygiene" + }, + { + "author_name": "Allen Bateman", + "author_inst": "Wisconsin State Laboratory of Hygiene" + }, + { + "author_name": "Juliana Kahrs", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Kimberly Langolf", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Tara Zochert", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Nancy W. Knight", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Christopher H. Hsu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah L. Kirking", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jacqueline E. Tate", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.04.21254881", "rel_title": "Neutralization of SARS-CoV-2 variants by convalescent and vaccinated serum", @@ -840200,45 +843470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.07.21254917", - "rel_title": "Statistical Design and Analysis of PCR Tests for Fast Mutating Viruses", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21254917", - "rel_abs": "As the SARS-CoV-2 virus mutates, mutations harboured in patients become increasingly diverse. Patients classified into two strains may have overlapping non-variant-defining mutations.\n\nMutation calling by sequencing is relative to a reference genome. As SARS-CoV-2 mutates, tracking emerging mutant strains may become increasingly problematic if the reference genome remains Wuhan-Hu-1, because the comparison then becomes indirect: current dominant strain relative to Wuhan-Hu-1 versus emerging strain relative to Wuhan-Hu-1.\n\nThe original Thermo Fishers TaqPath PCR test, on which the UK has standardized national testing of SARS-CoV-2 primarily, targets Wuhan-Hu-1. PCR targets appear readily updated, as TaqPath 2.0 now targets both currently known and future SARS-CoV-2 mutations, probing the N gene and ORF1ab but not the S gene, with 8 probes instead of the original 3 probes. Going forward, our statistical method can more directly compare current wildtype versus emerging mutants, since our new method can use any pair of probes updated to probe the current wildtype and anticipated mutations.\n\nThe fact that patients harbour mixtures of mutations allows our statistical methods to potentially catch emerging mutants. Given a PCR test which targets the current dominant strain (current wildtype), our statistical method can potentially directly differentiate the current wildtype from an emerging strain.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yang Han", - "author_inst": "University of Manchester" - }, - { - "author_name": "Yujia Sun", - "author_inst": "University of Manchester" - }, - { - "author_name": "Jason C Hsu", - "author_inst": "Ohio State University" - }, - { - "author_name": "Thomas House", - "author_inst": "University of Manchester" - }, - { - "author_name": "Nick Gent", - "author_inst": "Public Health England" - }, - { - "author_name": "Ian Hall", - "author_inst": "University of Manchester; Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.07.21255024", "rel_title": "Improved diagnosis of SARS-CoV-2 by using Nucleoprotein and Spike protein fragment 2 in quantitative dual ELISA tests", @@ -841174,6 +844405,205 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.06.438709", + "rel_title": "Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape", + "rel_date": "2021-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438709", + "rel_abs": "An ideal anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse SARS-related coronaviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD), including S3094, the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 in vitro neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Tyler N Starr", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "Nadine Czudnochowski", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Fabrizia Zatta", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Zhuoming Liu", + "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA" + }, + { + "author_name": "Amin Addetia", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "Dora Pinto", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Martina Beltramello", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Patrick Hernandez", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Allison J Greaney", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98" + }, + { + "author_name": "Roberta Marzi", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "William G Glass", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA" + }, + { + "author_name": "Ivy Zhang", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Pro" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "John E Bowen", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Jason A Wojcechowskyj", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Laura E Rosen", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Jiayi Zhou", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Martin Montiel-Ruiz", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Hannah Kaiser", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Heather Tucker", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Michael P. Housley", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Julia Di Iulio", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Gloria Lombardo", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Maria Agostini", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Nicole Sprugasci", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Katja Culap", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Stefano Jaconi", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Marcel Meury", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Exequiel Dellota", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Elisabetta Cameroni", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Tristan I Croll", + "author_inst": "Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK" + }, + { + "author_name": "Jay C Nix", + "author_inst": "Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "Colin Havenar-Daughton", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Florian A Lempp", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Matteo Samuele Pizzuto", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "John D Chodera", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA" + }, + { + "author_name": "Christy M Hebner", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Sean PJ Whelan", + "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA" + }, + { + "author_name": "Herbert W Virgin", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; D" + }, + { + "author_name": "David Veesler", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98" + }, + { + "author_name": "Gyorgy Snell", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.07.438806", "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease", @@ -842282,93 +845712,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.07.21253850", - "rel_title": "Immunogenicity and Safety of a SARS-CoV-2 Inactivated Vaccine (KCONVAC) in Healthy Adults: Two Randomized, Double-blind, and Placebo-controlled Phase 1/2 Clinical Trials", - "rel_date": "2021-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21253850", - "rel_abs": "BackgroundThe significant morbidity and mortality resulted from the infection of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for urgent development of effective and safe vaccines. We report the immunogenicity and safety of a SARS-CoV-2 inactivated vaccine, KCONVAC, in healthy adults.\n\nMethodsTwo phase 1 and phase 2 randomized, double-blind, and placebo-controlled trials of KCONVAC were conducted in Chinese healthy adults aged 18 through 59 years. The phase 1 trial was conducted in a manner of dosage escalation. The first 30 participants were randomized in a ratio of 4:1 to receive two doses of either KCONVAC at 5 g per dose or placebo on Day 0 and Day 14, and the second 30 participants were randomized to receive either KCONVAC at 10 g per dose or placebo following the same procedures. The participants in the phase 2 trial were randomized in a ratio of 2:2:1 to receive either KCONVAC at 5 g or 10 g per dose, or placebo on Day 0 and Day 14, or Day 0 and Day 28. In the phase 1 trial, the primary safety endpoint was the proportion of participants experiencing adverse reactions/events within 28 days following each vaccination. Antibody response and cellular response were assayed in the phase 1 trial. In the phase 2 trial, the primary immunogenicity endpoint was the seroconversion and titre of neutralization antibody, and the seroconversion of receptor binding domain (RBD)-IgG 28 days after the second dose.\n\nFindingsIn the phase 1 trial, 60 participants were enrolled and received at least one dose of 5-g vaccine (N=24), 10-g vaccine (N=24), or placebo (N=12). In the phase 2 trial, 500 participants were enrolled and received at least one dose of 5-g vaccine (N=100 for 0/14 or 0/28 regimens), 10-g vaccine (N=100 for each regimen), or placebo (N=50 for each regimen). In the phase 1 trial, 13 (54%), 11(46%), and 7 (58%) participants reported at least one adverse event (AE), of whom 10 (42%), 6 (25%), and 6 (50%) participants reported at least one vaccination-related AE after receiving 5-g vaccine, 10-g vaccine, or placebo, respectively. In the phase 2 trial, 16 (16%), 19 (19%), and 9 (18%) participants reported at least one AE, of whom 13 (13%), 17 (17%), and 6 (12%) participants reported at least one vaccination-related AE after receiving 5-g vaccine, 10-g vaccine, or placebo at the regimen of Day 0/14, respectively. Similar results were observed in the three treatment groups of Day 0/28 regimen. All the AEs were grade 1 or 2 in intensity. No AE of grade 3 or more was reported. One SAE (foot fracture) was reported in the phase 1 trial. KCONVAC induced significant antibody response. 87{middle dot}5% (21/24) to 100% (24/24) of participants in the phase 1 trial and 83{middle dot}0% (83/100) to 100% (99/99) of participants in the phase 2 trial seroconverted for neutralising antibody to live virus, neutralising antibody to pseudovirus, and RBD-IgG after receiving two doses. Across the treatment groups in the two trials, the geometric mean titres (GMTs) of neutralising antibody to live virus ranged from 29{middle dot}3 to 49{middle dot}1 at Day 0/14 regimen and from 100{middle dot}2 to 131{middle dot}7 at Day 0/28 regimen, neutralising antibody to pseudovirus ranged from 69{middle dot}4 to 118{middle dot}7 at Day 0/14 regimen and from 153{middle dot}6 to 276{middle dot}6 at Day 0/28 regimen, and RBD-IgG ranged from 605{middle dot}3 to 1169{middle dot}8 at Day 0/14 regimen and from 1496{middle dot}8 to 2485{middle dot}5 at Day 0/28 regimen. RBD-IgG subtyping assay showed that a significant part of RBD-IgG was IgG1. The vaccine induced obvious T-cell response with 56{middle dot}5% (13/23) and 62{middle dot}5% (15/24) of participants in 5-g and 10-g vaccine groups showed positive interferon-{gamma} enzyme-linked immunospot responses 14 days after the second dose in the phase 1 trial, respectively.\n\nInterpretationKCONVAC is well tolerated and able to induce robust antibody response and cellular response in adults aged 18 to 59 years, which warrants further evaluation with this vaccine in the upcoming phase 3 efficacy trial.\n\nFundingGuandong Emergency Program for Prevention and Control of COVID-19 (2020A1111340002) and Shenzhen Key Research Project for Prevention and Control of COVID-19.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Hong-Xing Pan", - "author_inst": "NHC Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention)" - }, - { - "author_name": "Jian-Kai Liu", - "author_inst": "Shenzhen Kangtai Biological Products Co., Ltd.," - }, - { - "author_name": "Bao-Ying Huang", - "author_inst": "NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Gui-Fan Li", - "author_inst": "Beijing Minhai Biological Technology Co., Ltd.," - }, - { - "author_name": "Xian-Yun Chang", - "author_inst": "Beijing Minhai Biological Technology Co., Ltd.," - }, - { - "author_name": "Ya-Fei Liu", - "author_inst": "Beijing Minhai Biological Technology Co., Ltd.," - }, - { - "author_name": "Wen-Ling Wang", - "author_inst": "NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Kai Chu", - "author_inst": "NHC Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention)" - }, - { - "author_name": "Jia-Lei Hu", - "author_inst": "NHC Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention)" - }, - { - "author_name": "Jing-Xin Li", - "author_inst": "NHC Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention)" - }, - { - "author_name": "Dan-Dan Zhu", - "author_inst": "Huaiyin District Center for Disease Control and Prevention" - }, - { - "author_name": "Jing-Liang Wu", - "author_inst": "Huaiyin District Center for Disease Control and Prevention" - }, - { - "author_name": "Xiao-Yu Xu", - "author_inst": "Vazyme Biotech Co., Ltd.," - }, - { - "author_name": "Li Zhang", - "author_inst": "China National Institute for Food and Drug Control" - }, - { - "author_name": "Meng Wang", - "author_inst": "China National Institute for Food and Drug Control" - }, - { - "author_name": "Wen-Jie Tan", - "author_inst": "NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" - }, - { - "author_name": "Wei-Jin Huang", - "author_inst": "China National Institute for Food and Drug Control" - }, - { - "author_name": "Feng-Cai Zhu", - "author_inst": "NHC Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.06.21254973", "rel_title": "COVID-19 vaccination acceptability in the UK at the start of the vaccination programme: a nationally representative cross-sectional survey (CoVAccS wave 2)", @@ -843548,6 +846891,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.01.21254798", + "rel_title": "Female-male differences in COVID vaccine adverse events have precedence in seasonal flu shots: a potential link to sex-associated baseline gene expression patterns", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254798", + "rel_abs": "Nearly 150 million doses of FDA-authorized COVID vaccines have been administered in the United States. Sex-based differences of adverse events remain poorly understood, mandating the need for real-world investigation from Electronic Health Records (EHRs) and broader epidemiological data sets. Based on an augmented curation of EHR clinical notes of 31,064 COVID-vaccinated individuals (19,321 females and 11,743 males) in the Mayo Clinic, we find that nausea and vomiting were documented significantly more frequently in females than males after both vaccine doses (nausea: RRDose 1 = 1.67, pDose 1 <0.001, RRDose 2 = 2.2, pDose 1 < 0.001; vomiting: RRDose 1 = 1.58, pDose 1 < 0.001, RRDose 2 = 1.88, pDose 1 = 3.4x10-2). Conversely, fever, fatigue, and lymphadenopathy were more common in males after the first dose vaccination (fever RR = 0.62; p = 8.65x10-3; fatigue RR = 0.86, p = 2.89x10-2; lymphadenopathy RR = 0.61, p = 3.45x10-3). Analysis of the Vaccine Adverse Events Reporting System (VAERS) database further confirms that nausea comprises a larger fraction of total reports among females than males (RR: 1.58; p<0.001), while fever comprises a larger fraction of total reports among males than females (RR: 0.84; p<0.001). Importantly, increased reporting of nausea and fever among females and males, respectively, is also observed for prior influenza vaccines in the VAERS database, establishing that these differences are not unique to the recently developed COVID-19 vaccines. Investigating the mechanistic basis underlying these clinical findings, an analysis of bulk RNA-sequencing data from 12,158 human blood samples (8626 female, 3532 male) reveals 85 genes that are not only significantly different in their gene expression between females and males at baseline, but also have established literature-based associations to COVID-19 as well as the vaccine-related adverse events of clinical consequence. The NLRP3 inflammasome and the NR3C1 glucocorticoid receptor emerge as particularly promising baseline links to sex-associated vaccine adverse events, warranting targeted investigation of these signaling pathways and associated cell types. From a public health standpoint, our clinical findings shall aid in educating patients on the sex-associated risks they should expect for COVID-19 vaccines and also promote better clinical management of vaccine-associated adverse events.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Praveen Kumar-M", + "author_inst": "nference" + }, + { + "author_name": "Eli Silvert", + "author_inst": "nference" + }, + { + "author_name": "Enrique Garcia-Rivera", + "author_inst": "nference" + }, + { + "author_name": "Mariola Szenk", + "author_inst": "nference" + }, + { + "author_name": "Rohit Suratekar", + "author_inst": "nference Labs" + }, + { + "author_name": "Patrick Lenehan", + "author_inst": "nference" + }, + { + "author_name": "Emily Lindemer", + "author_inst": "nference" + }, + { + "author_name": "John C OHoro", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Amy W Williams", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Abinash Virk", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Melanie D Swift", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Gregory J Gores", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.05.21254897", "rel_title": "No Evidence of Infectious SARS-CoV-2 in Human Milk: Analysis of a Cohort of 110 Lactating Women", @@ -844064,53 +847482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2021.04.05.21254819", - "rel_title": "Quantification of specific antibodies against SARS-CoV-2 in breast milk of lactating women vaccinated with an mRNA vaccine", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254819", - "rel_abs": "The recent approval of vaccines against COVID-19 has generated great concern among breastfeeding women, since these patients were excluded from vaccination clinical trials. The present study aimed to analyze the levels of specific SARS-CoV-2 antibodies in breast milk of mRNA-vaccinated women across time and their correlation with serum antibody levels.\n\nMethodsprospective study including lactating women aged over 18 who were vaccinated against SARS-CoV-2 with the Pfizer-BioNTech(R) COVID-19 vaccine (BNT162b2). Paired serum and breast milk samples were simultaneously taken from each participant at three timepoints after receiving the vaccine: 2 weeks after 1st dose, 2 weeks after 2nd dose and 4 weeks after 2nd dose (Timepoints 1, 2 and 3, respectively). Levels of IgG antibodies against the spike protein (S1 subunit) were determined for each sample (Architect, Abbott(R)).\n\nResultswe collected and analyzed 52 serum and 52 milk samples from the first 18 study participants. Median (interquartile range) IgG(S1) levels for serum - milk pairs at each timepoint were 410 (208-606) - 1.7 (0-2.9) AU/ml at Timepoint 1, 11505 (8933 - 21184) - 52.2 (34.1-113) at Timepoint 2 and 8311 (5578-17419) - 41.7 (24.8-75.3) at Timepoint 3. Pearsons correlation coefficient between breast milk and serum IgG(S1) levels was 0.71. No major adverse reactions were observed in mothers or infants.\n\nConclusionsBreast milk from women vaccinated with mRNA-based Pfizer-BioNTech(R) vaccine contains specific anti-SARS-CoV-2 IgG(S1) antibodies, with levels increasing considerably after second dose. IgG(S1) levels in breast milk are positively correlated with corresponding serum levels.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Erika Esteve-Palau", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - }, - { - "author_name": "Araceli Gonzalez-Cuevas", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - }, - { - "author_name": "M. Eugenia Guerrero", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - }, - { - "author_name": "Clara Garcia-Terol", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - }, - { - "author_name": "M. Carmen Alvarez", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - }, - { - "author_name": "Geneva Garcia-Aranda", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - }, - { - "author_name": "David Casadevall", - "author_inst": "Clinical Data Science Team, Scientific Department, Savana (Madrid, Spain)" - }, - { - "author_name": "Vicens Diaz-Brito", - "author_inst": "Parc Sanitari Sant Joan de Deu (Sant Boi, Barcelona, Spain)" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.02.21254818", "rel_title": "Covid-19 does not look like what you are looking for: clustering symptoms by nation and multi- morbidities reveal substantial differences to the classical symptom triad", @@ -845326,6 +848697,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.02.21254809", + "rel_title": "Risk factors for severity on admission and the disease progression during hospitalization in a large cohort of COVID-19 patients in Japan", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254809", + "rel_abs": "ObjectivesTo investigate the risk factors contributing to severity on admission. Additionally, risk factors on worst severity and fatality were studied. Moreover, factors were compared based on three points: early severity, worst severity, and fatality.\n\nDesignA observational cohort study utilizing data entered in a Japan nationwide COVID-19 inpatient registry, COVIREGI-JP.\n\nSettingAs of August 31, 2020, 7,546 cases from 780 facilities have been registered. Participating facilities cover a wide range of hospitals where COVID-19 patients are admitted in Japan.\n\nParticipantsParticipants who had a positive test result on any applicable SARS-CoV-2 diagnostic tests, and were admitted to participating healthcare facilities. A total of 3,829 cases were identified from January 16 to May 31, 2020, of which 3,376 cases were included in this study.\n\nPrimary and secondary outcoe measuresPrimary outcome was severe or non-severe on admission, determined by the requirement of mechanical ventilation or oxygen therapy, SpO2, or respiratory rate. Secondary outcome was the worst severity during hospitalization, judged by the requirement of oxygen and/or IMV/ECMO.\n\nResultsRisk factors for severity on admission were older age, male, cardiovascular disease, chronic respiratory disease, diabetes, obesity, and hypertension. Cerebrovascular disease, liver disease, renal disease or dialysis, solid tumor, and hyperlipidemia did not influence severity on admission; however it influenced worst severity. Fatality rates for obesity, hypertension, and hyperlipidemia were relatively lower.\n\nConclusionsThis study segregated the comorbidities driving severity and death. It is possible that risk factors for severity on admission, worst severity, and fatality are not consistent and may be propelled by different factors. Specifically, while hypertension, hyperlipidemia, and obesity had major effect on worst severity, their impact was mild on fatality in the Japanese population. Some studies contradict our results; therefore, detailed analyses, considering in-hospital treatments, are needed for validation.\n\nTrial registrationUMIN000039873. https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000045453\n\nStrengths and limitations of this studyO_LIIn this article, we studied the disease progression of COVID-19, by comparing the risk factors on three points: early severity, worst severity, and fatality.\nC_LIO_LIOur results are useful from a public health perspective, as we provide risk factors for predicting the severity on admission and disease progression from patients background factors.\nC_LIO_LIThis study pointed out the possibility that risk factors of the severity on admission, worst severity, and fatality are not consistent and may be propelled by different factors.\nC_LIO_LIOur data were collected from hundreds of healthcare facilities; thus data accuracy may be questionable.\nC_LIO_LIAlso, treatment type, dosage, duration, and combination varied immensely across the facilities and we did not consider treatments prior to and during hospitalization in the analysis.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Mari Terada", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Hiroshi Ohtsu", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Sho Saito", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kayoko Hayakawa", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Shinya Tsuzuki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yusuke Asai", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Nobuaki Matsunaga", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Satoshi Kutsuna", + "author_inst": "National Centre for Global Health and Medicine" + }, + { + "author_name": "Wataru Sugiura", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.01.21254755", "rel_title": "Rapid screening for variants of concern in routine SARS-CoV-2 PCR diagnostics", @@ -846082,33 +849508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.06.21255033", - "rel_title": "COVID-19 Time-varying Reproduction Numbers Worldwide: An Empirical Analysis of Mandatory and Voluntary Social Distancing", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21255033", - "rel_abs": "This paper estimates time-varying COVID-19 reproduction numbers worldwide solely based on the number of reported infected cases, allowing for under-reporting. Estimation is based on a moment condition that can be derived from an agent-based stochastic network model of COVID-19 transmission. The outcomes in terms of the reproduction number and the trajectory of per-capita cases through the end of 2020 are very diverse. The reproduction number depends on the transmission rate and the proportion of susceptible population, or the herd immunity effect. Changes in the transmission rate depend on changes in the behavior of the virus, re-flecting mutations and vaccinations, and changes in peoples behavior, reflecting voluntary or government mandated isolation. Over our sample period, neither mutation nor vaccination are major factors, so one can attribute variation in the transmission rate to variations in behavior. Evidence based on panel data models explaining transmission rates for nine European countries indicates that the diversity of outcomes resulted from the non-linear interaction of mandatory containment measures, voluntary precautionary isolation, and the economic incentives that gov-ernments provided to support isolation. These effects are precisely estimated and robust to various assumptions. As a result, countries with seemingly different social distancing policies achieved quite similar outcomes in terms of the reproduction number. These results imply that ignoring the voluntary component of social distancing could introduce an upward bias in the estimates of the effects of lock-downs and support policies on the transmission rates.\n\nJEL ClassificationD0, F6, C4, I120, E7", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Alexander Chudiik", - "author_inst": "Federal Reserve Bank of Dallas" - }, - { - "author_name": "M. Hashem Pesaran", - "author_inst": "University of Southern California, USA and Trinity College, Cambridge, UK" - }, - { - "author_name": "Alessandro Rebucci", - "author_inst": "Johns Hopkins Carey Business School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.06.21254800", "rel_title": "Impacts of Morally Distressing Experiences on the Mental Health of Canadian Health Care Workers During the COVID-19 Pandemic", @@ -847096,6 +850495,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.05.438465", + "rel_title": "The Up state of the SARS-COV-2 Spike homotrimer favors an increased virulence for new variants", + "rel_date": "2021-04-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.438465", + "rel_abs": "The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were released - the only scientifically verified and efficient therapeutic option thus far - a few mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged raising doubts about their efficiency. Therefore, this work aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor binding domain (RBD) and Angiotensin Converting Enzyme 2 (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state (the one in which the virus can interact with the cellular receptor ACE2) than due to alterations in the complexation RBD-ACE2, once the increased observed in the free energy values is small. Conversely, the South African variant (B.1.351), when compared with the wild type SARS-CoV-2, is much more stable in the opened state (either with one or two RBDs in the up position) than in the closed state (with the three RBDs in the down position). Such results contribute to the understanding of the natural history of disease and also to indicate possible strategies to both develop new therapeutic molecules and to adjust the vaccine doses for a higher production of B cells antibodies.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Carolina Correa Giron", + "author_inst": "Universidade Federal do Triangulo Mineiro" + }, + { + "author_name": "Aatto Laaksonen", + "author_inst": "Stockholm University" + }, + { + "author_name": "Fernando Luis Barroso da Silva", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.05.438500", "rel_title": "An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19", @@ -847876,105 +851302,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.04.05.21254707", - "rel_title": "Implementation of SARS-CoV-2 monoclonal antibody infusion sites at three medical centers in the United States: Strengths and challenges assessment to inform COVID-19 pandemic and future public health emergency use", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254707", - "rel_abs": "BackgroundThe COVID-19 pandemic caught the globe unprepared without targeted medical countermeasures, such as therapeutics, to target the emerging SARS-CoV-2 virus. However, in recent months multiple monoclonal antibody therapeutics to treat COVID-19 have been authorized by the U.S. Food and Drug Administration (FDA) under Emergency Use Authorization (EUA). Despite these authorizations and promising clinical trial efficacy results, monoclonal antibody therapies are currently underutilized as a treatment for COVID-19 across the U.S. Many barriers exist when deploying a new infused therapeutic during an ongoing pandemic with limited resources and staffing, and it is critical to better understand the process and site requirements of incorporating monoclonal antibody infusions into pandemic response activities.\n\nMethodsWe examined the monoclonal antibody infusion site process components, resources, and requirements during the COVID-19 pandemic using data from three initial infusion sites at medical centers in the U.S. supported by the National Disaster Medical System. A descriptive analysis was conducted using process assessment metrics to inform recommendations to strengthen monoclonal antibody infusion site implementation.\n\nResultsThe monoclonal antibody infusion sites varied in physical environment and staffing models due to state polices, infection control mechanisms, and underlying medical system structure, but exhibited a common process workflow. Sites operationalized an infusion process staffing model with at least two nurses per ten infusion patients. Monoclonal antibody implementation success factors included tailoring the infusion process to the patient community, strong engagement with local medical providers, batch preparing the therapy before patient arrival, placing the infusion center in proximity to emergency services, and creating procedures resilient to EUA changes. Infusion process challenges stemmed from confirming patient SARS-CoV-2 positivity, strained staff, scheduling needs, and coordination with the pharmacy for therapy preparation.\n\nConclusionsInfusion site processes are most effective when integrated into the pre-existing pandemic response ecosystems and can be implemented with limited staff and physical resources. As the pandemic and policy tools such as EUAs evolve, monoclonal antibody infusion processes must also remain adaptable, as practice changes directly affect resources, staffing, timing, and workflows. Future use may be aided by incorporating innovative emergency deployment techniques, such as vehicle and home-based therapy administration, and by developing drug delivery mechanisms that alleviate the need for observed intravenous infusions by medically-accredited staff.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Anastasia S Lambrou", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S., Johns Hopkins University A" - }, - { - "author_name": "John T Redd", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Miles A Stewart", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S., Johns Hopkins University A" - }, - { - "author_name": "Kaitlin Rainwater-Lovett", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S., Johns Hopkins University A" - }, - { - "author_name": "Jonathan K Thornhill", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S., Johns Hopkins University A" - }, - { - "author_name": "Lynn Hayes", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Gina Smith", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "George M Thorp", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Christian Tomaszewski", - "author_inst": "El Centro Regional Medical Center, El Centro, CA, U.S., UC San Diego Health, San Diego, CA, U.S." - }, - { - "author_name": "Adolphe Edward", - "author_inst": "El Centro Regional Medical Center, El Centro, CA, U.S., UC San Diego Health, San Diego, CA, U.S." - }, - { - "author_name": "Natalia Elias Calles", - "author_inst": "TMC HealthCare, Tucson, AZ, U.S." - }, - { - "author_name": "Mark Amox", - "author_inst": "Sunrise Hospital and Medical Center, Las Vegas, NV, U.S." - }, - { - "author_name": "Steven Merta", - "author_inst": "Sunrise Hospital and Medical Center, Las Vegas, NV, U.S." - }, - { - "author_name": "Tiffany Pfundt", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Victoria Callahan", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Adam Tewell", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Helga Scharf-Bell", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Samuel Imbriale", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Jeffrey D Freeman", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S., Johns Hopkins University A" - }, - { - "author_name": "Michael Anderson", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - }, - { - "author_name": "Robert P Kadlec", - "author_inst": "Office of the Assistant Secretary for Preparedness and Response, U. S. Department of Health and Human Services, Washington, DC, U.S." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.04.03.21254873", "rel_title": "DRUL for School: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2", @@ -848974,6 +852301,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.06.438634", + "rel_title": "Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis", + "rel_date": "2021-04-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438634", + "rel_abs": "The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria. The abundance of gram-negative bacteria (Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas) was higher than the gram-positive bacteria (Staphylococcus and Lactobacillus) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282{+/-}199.6 vs 838.1{+/-}91.33; p=0.0757), PGN (34.64{+/-}3.178 vs 17.53{+/-}2.12; p<0.0001), and LPS (405.5{+/-}48.37 vs 249.6{+/-}17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ram Prasad", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Michael John Patton", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jason L Floyd", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Cristiano P Vieira", + "author_inst": "Univeristy of Alabama at Birmingham" + }, + { + "author_name": "Seth D. Fortmann", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mariana DuPont", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Angie Harbour", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jeremy R Chen See", + "author_inst": "WrightLabs LLC" + }, + { + "author_name": "Justin Wright", + "author_inst": "Wright Labs LLC" + }, + { + "author_name": "Regina Lamendella", + "author_inst": "Juniata College" + }, + { + "author_name": "Bruce R. Stevens", + "author_inst": "University of Florida College of Medicine" + }, + { + "author_name": "Maria B. Grant", + "author_inst": "University of Alabama- Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.05.438537", "rel_title": "High-Potency Polypeptide-based Interference for Coronavirus Spike Glycoproteins", @@ -849794,49 +853184,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.21254502", - "rel_title": "Increased household secondary attacks rates with Variant of Concern SARS-CoV-2 index cases", - "rel_date": "2021-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254502", - "rel_abs": "IMPORTANCEHigher secondary attack rates related to variant of concern (VOC) index cases have been reported, but have not been explored within households, which continue to be an important source of coronavirus disease 2019 (COVID-19) transmission\n\nOBJECTIVETo compare secondary attack rates in households with VOC versus non-VOC index cases.\n\nDESIGNA retrospective cohort study of household index cases reported from February 7 - 27, 2021. A propensity-score matched cohort was derived to calculate adjusted estimates.\n\nSETTINGOntario, Canada.\n\nPARTICIPANTSA population-based cohort of all private households with index cases. We excluded cases in congregate settings, as well as households with one individual or with >1 case with the same earliest symptom onset date.\n\nEXPOSUREVOC status, defined as either individuals confirmed as B.1.1.7 using whole genome sequencing or those that screened positive for the N501Y mutation using real-time PCR.\n\nMAIN OUTCOME AND MEASUREHousehold secondary attack rate, defined as the number of household secondary cases that occurred 1-14 days after the index case divided by the total number of household secondary contacts.\n\nRESULTSWe included 1,259 index VOC and non-VOC cases in the propensity score-matched analysis. The secondary attack rate for VOC index cases in this matched cohort was 1.31 times higher than non-VOC index cases (RR=1.31, 95%CI 1.14-1.49), similar to the unadjusted estimate. In stratified analyses, the higher secondary attack rate for VOC compared to non-VOC index cases was accentuated for asymptomatic index cases (RR=1.91, 95% CI 0.96-3.80) and presymptomatic cases (RR=3.41, 95%CI 1.13-10.26)\n\nCONCLUSIONS AND RELEVANCEThis study provides strong evidence of increased transmissibility in households due to VOCs and suggests that asymptomatic and pre-symptomatic transmission may be of particular importance for VOCs. Our study suggests that more aggressive public health measures will be needed to control VOCs and that ongoing research is needed to understand mechanisms of VOC transmissibility to curb their associated morbidity and mortality.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Semra Tibebu", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Nick Daneman", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Michael Whelan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Thuva Vanniyasingam", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Michelle Murti", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Kevin A Brown", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.31.21254692", "rel_title": "Autoantibodies stabilize neutrophil extracellular traps in COVID-19", @@ -850960,6 +854307,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.02.438288", + "rel_title": "An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity", + "rel_date": "2021-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438288", + "rel_abs": "During the current SARS-CoV-2 pandemic that is devastating the modern societies worldwide, many variants that naturally acquire multiple mutations have emerged. Emerging mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has recently been investigated, that to human leukocyte antigen (HLA)-restricted cellular immunity remains unaddressed. Here we demonstrate that two recently emerging mutants in the receptor binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429) and Y453F (in B.1.298), can escape from the HLA-24-restricted cellular immunity. These mutations reinforce the affinity to viral receptor ACE2, and notably, the L452R mutation increases protein stability, viral infectivity, and potentially promotes viral replication. Our data suggest that the HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes, and the escape from cellular immunity can be a further threat of the SARS-CoV-2 pandemic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC=\"FIGDIR/small/438288v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@153428forg.highwire.dtl.DTLVardef@136ca5aorg.highwire.dtl.DTLVardef@1ee490org.highwire.dtl.DTLVardef@2fe478_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Chihiro Motozono", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Jiri Zahradnik", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Isaac Ngare", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Hesham Nasser", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Yusuke Kosugi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Shiho Torii", + "author_inst": "Osaka University" + }, + { + "author_name": "Akiko Yonekawa", + "author_inst": "Kyushu University" + }, + { + "author_name": "Nobuyuki Shimono", + "author_inst": "Kyushu University" + }, + { + "author_name": "Yoji Nagasaki", + "author_inst": "Kyushu Medical Center" + }, + { + "author_name": "Rumi Minami", + "author_inst": "Kyushu Medical Center" + }, + { + "author_name": "Takashi Toya", + "author_inst": "Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital" + }, + { + "author_name": "Noritaka Sekiya", + "author_inst": "Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital" + }, + { + "author_name": "Takasuke Fukuhara", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Gideon Schreiber", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) consortium", + "author_inst": "-" + }, + { + "author_name": "So Nakagawa", + "author_inst": "Tokai University School of Medicine" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.04.438420", "rel_title": "Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2", @@ -851652,129 +855114,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.02.438292", - "rel_title": "Sex differences in lung imaging and SARS-CoV-2 antibody responses in a COVID-19 golden Syrian hamster model", - "rel_date": "2021-04-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438292", - "rel_abs": "In the ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more severe outcomes are reported in males compared with females, including hospitalizations and deaths. Animal models can provide an opportunity to mechanistically interrogate causes of sex differences in the pathogenesis of SARS-CoV-2. Adult male and female golden Syrian hamsters (8-10 weeks of age) were inoculated intranasally with 105 TCID50 of SARS-CoV-2/USA-WA1/2020 and euthanized at several time points during the acute (i.e., virus actively replicating) and recovery (i.e., after the infectious virus has been cleared) phases of infection. There was no mortality, but infected male hamsters experienced greater morbidity, losing a greater percentage of body mass, developing more extensive pneumonia as noted on chest computed tomography, and recovering more slowly than females. Treatment of male hamsters with estradiol did not alter pulmonary damage. Virus titers in respiratory tissues, including nasal turbinates, trachea, and lungs, and pulmonary cytokine concentrations, including IFN{beta} and TNF, were comparable between the sexes. However, during the recovery phase of infection, females mounted two-fold greater IgM, IgG, and IgA responses against the receptor-binding domain of the spike protein (S-RBD) in both plasma and respiratory tissues. Female hamsters also had significantly greater IgG antibodies against whole inactivated SARS-CoV-2 and mutant S-RBDs, as well as virus neutralizing antibodies in plasma. The development of an animal model to study COVID-19 sex differences will allow for a greater mechanistic understanding of the SARS-CoV-2 associated sex differences seen in the human population.\n\nImportanceMen experience more severe outcomes from COVID-19 than women. Golden Syrian hamsters were used to explore sex differences in the pathogenesis of a human clinical isolate of SARS-CoV-2. After inoculation, male hamsters experienced greater sickness, developed more severe lung pathology, and recovered more slowly than females. Sex differences in disease could not be reversed by estradiol treatment in males and were not explained by either virus replication kinetics or the concentrations of inflammatory cytokines in the lungs. During the recovery period, antiviral antibody responses in the respiratory tract and plasma, including to newly emerging SARS-CoV-2 variants, were greater in females than male hamsters. Greater lung pathology during the acute phase combined with reduced antiviral antibody responses during the recovery phase of infection in males than females illustrate the utility of golden Syrian hamsters as a model to explore sex differences in the pathogenesis of SARS-CoV-2 and vaccine-induced immunity and protection.\n\nOne Sentence SummaryFollowing SARS-CoV-2 infection, male hamsters experience worse clinical disease and have lower antiviral antibody responses than females.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Santosh Dhakal", - "author_inst": "The Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Camilo A. Ruiz-Bedoya", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Ruifeng Zhou", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Patrick Creisher", - "author_inst": "The Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Jason Villano", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Kirsten Littlefield", - "author_inst": "Johns Hopkins Bloomberg School of Public Health," - }, - { - "author_name": "Jennie Castillo", - "author_inst": "Johns Hopkins Medicine" - }, - { - "author_name": "Paula Marinho", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Anne Jedlicka", - "author_inst": "Johns Hopkins School of Public Health" - }, - { - "author_name": "Alvaro Ordonez", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Natalia Majewska", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Michael Betenbaugh", - "author_inst": "John Hopkins University" - }, - { - "author_name": "Kelly Flavahan", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Alice Mueller", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Monika Looney", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Darla Quijada", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Filipa Mota", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Sarah E. Beck", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Jacqueline K Brockhurst", - "author_inst": "NIAID - NIH" - }, - { - "author_name": "Alicia Braxton", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Natalie Castell", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Kelly A. Metcalf Pate", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Petros C. Karakousis", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Joseph L. Mankowski", - "author_inst": "John Hopkins University School of Medicine" - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Sanjay K Jain", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Sabra L. Klein", - "author_inst": "The Johns Hopkins Bloomberg School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.27.21254461", "rel_title": "Determining the cutoff points of the 5C scale for assessment of COVID-19 vaccines psychological antecedents among the Arab population: A multinational study", @@ -852806,6 +856145,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.02.438155", + "rel_title": "An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2", + "rel_date": "2021-04-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438155", + "rel_abs": "The on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has infected hundreds of millions of people and killed more than two million people worldwide. Currently, there are no effective drugs available for treating SARS-CoV-2 infections; however, vaccines are now being administered worldwide to control this virus. In this study, we have studied SARS-CoV-2 helicase, Nsp13, which is critical for viral replication. We compared the Nsp13 sequences reported from India with the first reported sequence from Wuhan province, China to identify and characterize the mutations occurring in this protein. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited high antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were also analysed. Furthermore, several of these Nsp13 epitopes harbour mutations, which were further characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. Altogether, we report the candidate epitopes of Nsp13 that may help the scientific community to understand the evolution of SARS-CoV-2 variants and their probable implications.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sushant Kumar", + "author_inst": "Patna University" + }, + { + "author_name": "Gajendra Kumar Azad", + "author_inst": "Patna University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.04.02.438204", "rel_title": "Discovery and in-vitro evaluation of potent SARS-CoV-2 entry inhibitors", @@ -853690,61 +857052,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.31.437960", - "rel_title": "Coagulation factors directly cleave SARS-CoV-2 spike and enhance viral entry", - "rel_date": "2021-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437960", - "rel_abs": "Coagulopathy is a significant aspect of morbidity in COVID-19 patients. The clotting cascade is propagated by a series of proteases, including factor Xa and thrombin. While certain host proteases, including TMPRSS2 and furin, are known to be important for cleavage activation of SARS-CoV-2 spike to promote viral entry in the respiratory tract, other proteases may also contribute. Using biochemical and cell-based assays, we demonstrate that factor Xa and thrombin can also directly cleave SARS-CoV-2 spike, enhancing viral entry. A drug-repurposing screen identified a subset of protease inhibitors that promiscuously inhibited spike cleavage by both transmembrane serine proteases as well as coagulation factors. The mechanism of the protease inhibitors nafamostat and camostat may extend beyond inhibition of TMPRSS2 to coagulation-induced spike cleavage. Anticoagulation is critical in the management of COVID-19, and early intervention could provide collateral benefit by suppressing SARS-CoV-2 viral entry. We propose a model of positive feedback whereby infection-induced hypercoagulation exacerbates SARS-CoV-2 infectivity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Edward R Kastenhuber", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Javier A. Jaimes", - "author_inst": "Cornell University" - }, - { - "author_name": "Jared L. Johnson", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Marisa Mercadante", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Yiska Weisblum", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Yaron Bram", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Robert E. Schwartz", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Gary R. Whittaker", - "author_inst": "Cornell University" - }, - { - "author_name": "Lewis C. Cantley", - "author_inst": "Weill Cornell Medical College" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.01.436305", "rel_title": "An alphavirus replicon-based vaccine expressing a stabilized Spike antigen induces sterile immunity and prevents transmission of SARS-CoV-2 between cats", @@ -854960,6 +858267,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.28.21254496", + "rel_title": "SARS-CoV-2 infections in children and adolescents with rheumatic musculoskeletal diseases: data from the National Pediatric Rheumatology Database in Germany", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.28.21254496", + "rel_abs": "ObjectivesDue to their underlying disease as well as therapeutic immunosuppression, children and adolescents with rheumatic and musculoskeletal diseases (RMD) may be at higher risk for a severe course or worse outcome of COVID-19, and SARS-CoV2 infection may trigger a flare of the RMD. To address these issues, a specific SARS-CoV-2 questionnaire was implemented in the National Pediatric Rheumatology Database (NPRD) in Germany.\n\nMethodsDemographic, clinical and treatment data from juvenile patients with RMD as well as data about SARS-CoV-2 infection like test date and method, clinical characteristics, disease course, outcome and impact on the disease activity of the RMD documented on this questionnaire were analyzed.\n\nResultsFrom April 17th, 2020, to February 14th, 2021, data were collected from 79 patients (53% female) with RMD with median age of 14 years, diagnosed with juvenile idiopathic arthritis (57%), autoinflammatory (23%) and connective tissue disease (8%). Sixty-one patients (77%) received disease-modifying antirheumatic drugs (DMARDs), 43% biologic DMARDs, and 9% systemic glucocorticoids. Sixty patients (76%) developed symptoms of COVID-19. Disease severity was mild and outcome was good in the majority of patients. Two patients were hospitalized, one of whom required intensive care and died of cardiorespiratory failure. In 84% of SARS-CoV-2-positive patients, no relevant increase in disease activity of the RMD was observed.\n\nConclusionsIn our cohort, COVID-19 in juvenile patients with RMD under various medications was mild with good outcome in the majority of cases. SARS-CoV-2 infection does not appear to have a relevant impact on disease activity of the underlying condition.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Claudia Sengler", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Sascha Eulert", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Martina Niewerth", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Kirsten Minden", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Gerd Horneff", + "author_inst": "Asklepios Klinik St. Augustin, Allgemeine Kinder- und Jugendmedizin, Sankt Augustin, Germany" + }, + { + "author_name": "Jasmin B Kuemmerle-Deschner", + "author_inst": "Tuebingen University Hospital, Department of Pediatric and Adolescent Medicine, Tuebingen, Germany" + }, + { + "author_name": "Caroline Siemer", + "author_inst": "Deutsches Zentrum fuer Kinder- und Jugendrheumatologie, Garmisch-Partenkirchen, Germany" + }, + { + "author_name": "Rainer Berendes", + "author_inst": "Kinderkrankenhaus St. Marien, Landshut, Germany" + }, + { + "author_name": "Hermann Girschick", + "author_inst": "Krankenhaus im Friedrichshain, Klinik fuer Kinder- und Jugendmedizin, Berlin, Germany" + }, + { + "author_name": "Regina Huehn", + "author_inst": "Universitaetsklinikum Halle (Saale), Klinik fuer Kinder- und Jugendmedizin, Haale (Saale), Germany" + }, + { + "author_name": "Michael Borte", + "author_inst": "Klinikum St. Georg, Klinik fuer Kinder- und Jugendmedizin, Leipzig, Germany" + }, + { + "author_name": "Anton Hospach", + "author_inst": "Olgahospital and Women`s Clinic, Paediatrie 2 - Allgemeine und spezielle Paediatrie, Stuttgart, Germany" + }, + { + "author_name": "Wolfgang Emminger", + "author_inst": "Universitaetskinderklinik Wien, Wien, Austria" + }, + { + "author_name": "Jakob Peter Armann", + "author_inst": "University Hospital and Medical Faculty Carl Gustav Carus, Technische Uni" + }, + { + "author_name": "Ariane Klein", + "author_inst": "Asklepios Klinik St. Augustin, Allgemeine Kinder- und Jugendmedizin, Sankt Augustin, Germany" + }, + { + "author_name": "Tilmann Kallinich", + "author_inst": "Charite - Universitaetsmedizin Berlin, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.03.29.21254538", "rel_title": "Half year longitudinal seroprevalence of SARS-CoV-2-antibodies and rule compliance in German hospital employees", @@ -855576,45 +858962,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.03.29.21254548", - "rel_title": "The implementation of a virtual ward using digital solutions informing community clinicians in early supported discharge of patients with SARS-Cov2 respiratory symptoms from an acute hospital setting", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254548", - "rel_abs": "ObjectivesTo assess the short run successes and challenges of the implementation of a digitally supported accelerated acute hospital discharge scheme for patients admitted with Covid-19.\n\nDesignAnalysis of the safety, resource use and health outcomes within the virtual service for the first 65 patients that have been discharged from a virtual respiratory ward.\n\nSettingCommunity based intervention using digital technology and a multi-disciplinary team of specialist clinicians to monitor patients at home.\n\nParticipants65 patients discharged from hospital followed until discharge from the virtual ward.\n\nResults24.6% of 65 patients had symptoms that were coded red (urgent response required) in CliniTouch Vie in the first day after hospital discharge falling to 7.7% on their final day on the virtual ward; p=0.049. Reductions in red days decreased significantly over time, from 33.8% of patients in their first three days to 10.8% in their final three days; all patients p=0.002. Four patients were re-admitted to hospital, all for clotting disorders. There was one death within this group, which following senior clinical review was deemed to be unrelated to infection with Covid-19.\n\nThe most important gain for Glenfield hospital was in expediting the rapid discharge of patients admitted with Covid-19 into a supported environment and the freeing up of beds. On 15th January, 48% of beds were taken up with patients admitted with Covid-19 symptoms.\n\nIn November 2020, immediately prior to the launch of the virtual ward, the mean length of stay for patients who did not access high dependency care or oxygen was 5.5 (+/-1.3) days. The mean length of stay in patients discharged into the virtual ward thereafter was 3.3 (+/-0.4) days; relative reduction, 40.3% (p<0.001).\n\nThe cost of care provision in the virtual ward was 8,662 UK Pounds in total and 133.26 UK pounds per patient. The estimated overall savings were 68,052 UK Pounds and the mean saving per patient was estimated at {pound}1,047 UK Pounds.\n\nConclusionsThe virtual ward appeared to assist with earlier discharges, had a low rate of clinically necessary re-admissions, the safety of patients was not compromised and whilst cost savings were not the primary objective, it seemed to also reduce overall resource use and costs.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jim Swift", - "author_inst": "Spirit Health Group" - }, - { - "author_name": "Alex woodward", - "author_inst": "Leicestershire Partnership Trust" - }, - { - "author_name": "Zoe Harris", - "author_inst": "Leicestershire Partnership Trust" - }, - { - "author_name": "Noel I O'Kelly", - "author_inst": "Spirit Health Group" - }, - { - "author_name": "Chris Barker", - "author_inst": "Spirit Health Group" - }, - { - "author_name": "Sudip Ghosh", - "author_inst": "De Montford University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2021.03.29.21254526", "rel_title": "Longitudinal experiences and impact of the COVID-19 pandemic among people with past or current eating disorders in Sweden", @@ -856486,6 +859833,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.29.21254590", + "rel_title": "Use of portable air cleaners to reduce aerosol transmission on a hospital COVID-19 ward", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254590", + "rel_abs": "ObjectiveTo study the airflow, transmission and clearance of aerosols in the clinical spaces of a hospital ward that had been used to care for patients with COVID-19, and to examine the impact of portable air cleaners on aerosol clearance.\n\nDesignObservational study\n\nSettingA single ward of a tertiary public hospital in Melbourne Australia\n\nInterventionGlycerine-based aerosol was used as a surrogate for respiratory aerosols. The transmission of aerosols from a single patient room into corridors and a nurses station in the ward was measured. The rate of clearance of aerosols was measured over time from the patient room, nurses station and ward corridors with and without air cleaners (also called portable HEPA filters).\n\nResultsAerosols rapidly travelled from the patient room into other parts of the ward. Air cleaners were effective in increasing the clearance of aerosols from the air in clinical spaces and reducing their spread to other areas. With two small domestic air cleaners in a single patient room of a hospital ward, 99% of aerosols could be cleared within 5.5 minutes.\n\nConclusionAir cleaners may be useful in clinical spaces to help reduce the risk of healthcare acquired acquisition of respiratory viruses that are transmitted via aerosols. They are easy to deploy and are likely to be cost effective in a variety of healthcare settings", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kirsty Lee Buising", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Robyn Schofield", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Louis Irving", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Melita Keywood", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Ashley Stevens", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Nick Keogh", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Grant Skidmore", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Imogen Wadlow", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Kevin Kevin", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Behzad Rismanchi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Amanda Wheeler", + "author_inst": "Australian Catholic University" + }, + { + "author_name": "Ruhi Humphries", + "author_inst": "Commonwealth Scientific and Industrial research Organization" + }, + { + "author_name": "Marion Kainer", + "author_inst": "Western Health" + }, + { + "author_name": "Forbes McGain", + "author_inst": "Western Health" + }, + { + "author_name": "Jason Monty", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Caroline Marshall", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254509", "rel_title": "Genetic associations with severe COVID-19", @@ -857074,81 +860500,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254053", - "rel_title": "Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples", - "rel_date": "2021-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254053", - "rel_abs": "Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized, and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 20 selected sites in the Kathmandu Valley, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heat-map was created to visualize transmission activity in the community based on viral load intensity and corresponding geospatial data. Further, 41 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n=9, 2%) were novel and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. We also observed more transition than transversion on detected mutations, indicating rapid viral evolution in the host. Our study has demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Rajindra Napit", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Prajwol Manandhar", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Ashok Chaudhary", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Bishwo Shrestha", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Ajit Poudel", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Roji Raut", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Saman Pradhan", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Samita Raut", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Sujala Mathema", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Rajesh Rajbhandari", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Sameer Dixit", - "author_inst": "Center for Molecular Dynamics Nepal" - }, - { - "author_name": "Jessica S Schwind", - "author_inst": "Georgia Southern University" - }, - { - "author_name": "Christine K Johnson", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Jonna K Mazet", - "author_inst": "University of California Davis" - }, - { - "author_name": "Dibesh Karmacharya", - "author_inst": "Center for Molecular Dynamics Nepal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.29.21254151", "rel_title": "Six-month pulmonary impairment after severe COVID-19: a prospective, multicenter follow-up study", @@ -858312,6 +861663,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.27.21254480", + "rel_title": "Assessing the impact of widespread respirator use in curtailing COVID-19 transmission in the United States", + "rel_date": "2021-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21254480", + "rel_abs": "Dynamic models are used to assess the impact of three types of face masks-cloth masks, surgical/procedure masks and respirators-in controlling the COVID-19 pandemic in the United States. We showed that the pandemic would have failed to establish in the US if a nationwide mask mandate, based on using respirators with moderately-high compliance, had been implemented during the first two months of the pandemic. The other mask types would fail to prevent the pandemic from becoming established. When mask usage compliance is low to moderate, respirators are far more effective in reducing disease burden. Using data from the third wave, we showed that the epidemic could be eliminated in the US if at least 40% of the population consistently wore respirators in public. Surgical masks can also lead to elimination, but requires compliance of at least 55%. Daily COVID-19 mortality could be eliminated in the US by June or July 2021 if 95% of the population opted for either respirators or surgical masks from the beginning of the third wave. We showed that the prospect of effective control or elimination of the pandemic using mask-based strategy is greatly enhanced if combined with other nonpharmaceutical interventions (NPIs) that significantly reduce the baseline community transmission. By slightly modifying the model to include the effect of a vaccine against COVID-19 and waning vaccine-derived and natural immunity, this study shows that the waning of such immunity could trigger multiple new waves of the pandemic in the US. The number, severity and duration of the projected waves depend on the quality of mask type used and the level of increase in the baseline levels of other NPIs used in the community during the onset of the third wave of the pandemic in the US. Specifically, no severe fourth or subsequent wave of the pandemic will be recorded in the US if surgical masks or respirators are used, particularly if the mask-use strategy is combined with an increase in the baseline levels of other NPIs. This study further emphasizes the role of human behavior towards masking on COVID-19 burden, and highlights the urgent need to maintain a healthy stockpile of highly-effective respiratory protection, particularly respirators, to be made available to the general public in times of future outbreaks or pandemics of respiratory diseases that inflict severe public health and socio-economic burden on the population.\n\nAuthor summaryWe developed and used dynamic models to assess the role of highly-effective face coverings on the control and mitigation of the COVID-19 pandemic in the US. The study indicates that implementing and sustaining mask mandates is useful in containing diseases like COVID-19. Additionally, the study suggests that prioritizing the use of respirators is more effective in combating the disease than using other mask types. Specifically, the COVID-19 pandemic would have been prevented from being established in the US if four in every five Americans started wearing respirators during the first two months of the pandemic. The study further shows that COVID-19 can be eliminated in the US if a universal masking strategy that emphasizes respirators, requiring only 23% compliance, is combined with other nonpharmaceutical interventions that can reduce community transmission by 20%. Furthermore, the daily COVID-19 death rate can be completely suppressed by June 2021 if 95% of the population consistently use respirators. The elimination will extend to January 2022 if cloth masks were adopted instead. We conclude that stockpiling and distributing highly-efficient face coverings, notably respirators, will be vital in effectively curtailing future epidemics and pandemics of respiratory diseases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Calistus N Ngonghala", + "author_inst": "University of Florida" + }, + { + "author_name": "James R Knitter", + "author_inst": "The University of Arizona, College of Medicine, Tucson" + }, + { + "author_name": "Lucas Marinacci", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Matthew H Bonds", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Abba B Gumel", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.26.21254429", "rel_title": "Forecasting the Spreading Trajectory of the COVID-19 Pandemic", @@ -859084,45 +862470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.437530", - "rel_title": "Age-dependent appearance of SARS-CoV-2 entry cells in mouse chemosensory systems reflects COVID-19 anosmia and ageusia symptoms.", - "rel_date": "2021-03-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.29.437530", - "rel_abs": "COVID-19 pandemic has given rise to a collective scientific effort to study its viral causing agent SARS-CoV-2. Research is focusing in particular on its infection mechanisms and on the associated-disease symptoms. Interestingly, this environmental pathogen directly affects the human chemosensory systems leading to anosmia and ageusia. Evidence for the presence of the cellular entry sites of the virus, the ACE2/TMPRSS2 proteins, has been reported in non-chemosensory cells in the rodents nose and mouth, missing a direct correlation between the symptoms reported in patients and the observed direct viral infection in human sensory cells. Here, mapping the gene and protein expression of ACE2/TMPRSS2 in the mouse olfactory and gustatory cells, we precisely identified the virus target cells to be of basal and sensory origin and we revealed their age-dependent appearance. Our results not only clarify human viral-induced sensory symptoms but also propose new investigative perspectives based on ACE2-humanized mouse models.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Julien Brechbuhl", - "author_inst": "University of Lausanne" - }, - { - "author_name": "Dean Wood", - "author_inst": "University of Lausanne" - }, - { - "author_name": "Sofiane Bouteiller", - "author_inst": "University of Lausanne" - }, - { - "author_name": "Ana Catarina Lopes", - "author_inst": "University of Lausanne" - }, - { - "author_name": "Chantal Verdumo", - "author_inst": "University of Lausanne" - }, - { - "author_name": "Marie-Christine Broillet", - "author_inst": "University of Lausanne" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2021.03.29.437516", "rel_title": "Sexually dimorphic placental responses to maternal SARS-CoV-2 infection", @@ -860098,6 +863445,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.26.21254427", + "rel_title": "Assessment of serological assays for identifying high titer convalescent plasma", + "rel_date": "2021-03-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254427", + "rel_abs": "The COVID-19 pandemic has been accompanied by the largest mobilization of therapeutic convalescent plasma (CCP) in over a century. Initial identification of high titer units was based on dose-response data using the Ortho VITROS IgG assay. The proliferation of SARS-CoV-2 serological assays and non-uniform application has led to uncertainty about their interrelationships. The purpose of this study was to establish correlations and analogous cutoffs between commercially available serological tests (Ortho, Abbott, Roche), a spike ELISA, and a virus neutralization assay using convalescent plasma from a cohort of 79 donors from April 2020. Relationships relative to FDA-approved cutoffs under the CCP EUA were identified by linear regression and receiver operator characteristic curves. Relative to the Ortho VITROS assay, the r2 of the Abbott, Roche, the anti-Spike ELISA and the neutralizing assay were 0.58, 0.5, 0.82, and 0.44, respectively. The best correlative index for establishing high-titer units was 3.82 S/C for the Abbott, 10.89 COI for the Roche, 1:1,202 for the anti-Spike ELISA, and 1:200 by the neutralization assay. The overall agreement using derived cutoffs compared to the CCP EUA Ortho VITROS cutoff of 9.5 was 92.4% for Abbott, 84.8% for Roche, 87.3% for the anti-S ELISA and 78.5% for the neutralization assay. Assays based on antibodies against the nucleoprotein (Roche, Abbott) and neutralizing antibody tests were positively associated with the Ortho assay, although their ability to distinguish FDA high-titer specimens was imperfect. The resulting relationships help reconcile results from the large body of serological data generated during the COVID-19 pandemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Christopher W. Farnsworth", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Brett Case", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Karl Hock", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Rita E Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jane O'Halloran", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Rachel Presti", + "author_inst": "Wash U" + }, + { + "author_name": "Charles William Goss", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Adriana M Rauseo", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Ali Ellebedy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Elitza S Theel", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Michael Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jeffrey P Henderson", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.27.21254471", "rel_title": "Estimation of SARS-CoV-2 antibody prevalence through integration of serology and incidence data", @@ -860706,57 +864116,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.27.437300", - "rel_title": "Rapid Evolution of SARS-CoV-2 Challenges Human Defenses", - "rel_date": "2021-03-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.27.437300", - "rel_abs": "Evolutionary ecology theory provides an avenue to anticipate the future behavior of SARS-CoV-2. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein believed to determine infectivity. We estimate that 384 million people were infected by March 1st, 2021, producing up to 1021 copies of the virus, with one new RBD variant appearing for every 600,000 human infections, resulting in approximately three new effective RBD variants produced daily. Doubling the number of RBD variants every 71.67 days followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics.\n\nOne-Sentence SummaryAccelerating evolution of SARS-CoV-2 demands formulating universal vaccines and treatments based on big-data simulations of possible new variants.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Carlos M. Duarte", - "author_inst": "KAUST" - }, - { - "author_name": "David Ketcheson", - "author_inst": "KAUST" - }, - { - "author_name": "Victor M Eguiluz", - "author_inst": "Instituto de Fisica Interdisciplinar y Sistemas Complejos IFISC (UIB-CSIC), Palma de Mallorca, Spain" - }, - { - "author_name": "Susana R Agusti", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Juan F Gracia", - "author_inst": "Instituto de Fisica Interdisciplinar y Sistemas Complejos IFISC (UIB-CSIC), Palma de Mallorca, Spain" - }, - { - "author_name": "Tahira Jamil", - "author_inst": "Kaust" - }, - { - "author_name": "Elisa Laiolo", - "author_inst": "KAUST" - }, - { - "author_name": "Takashi Gojobori", - "author_inst": "King Abdullah University of Science and Technology" - }, - { - "author_name": "Intikhab Alam", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.03.27.437309", "rel_title": "The nucleotide addition cycle of the SARS-CoV-2 polymerase", @@ -861984,6 +865343,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.17.21253847", + "rel_title": "Femtomolar SARS-CoV-2 Antigen Detection Using the Microbubbling Digital Assay with Smartphone Readout Enables Antigen Burden Quantitation and Dynamics Tracking", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253847", + "rel_abs": "BackgroundLittle is known about the dynamics of SARS-CoV-2 antigen burden in respiratory samples in different patient populations at different stages of infection. Current rapid antigen tests cannot quantitate and track antigen dynamics with high sensitivity and specificity in respiratory samples.\n\nMethodsWe developed and validated an ultra-sensitive SARS-CoV-2 antigen assay with smartphone readout using the Microbubbling Digital Assay previously developed by our group, which is a platform that enables highly sensitive detection and quantitation of protein biomarkers. A computer vision-based algorithm was developed for microbubble smartphone image recognition and quantitation. A machine learning-based classifier was developed to classify the smartphone images based on detected microbubbles. Using this assay, we tracked antigen dynamics in serial swab samples from COVID patients hospitalized in ICU and immunocompromised COVID patients.\n\nResultsThe limit of detection (LOD) of the Microbubbling SARS-CoV-2 Antigen Assay was 0.5 pg/mL (10.6 fM) recombinant nucleocapsid (N) antigen or 4000 copies/mL inactivated SARS-CoV-2 virus in nasopharyngeal (NP) swabs, comparable to many rRT-PCR methods. The assay had high analytical specificity towards SARS-CoV-2. Compared to EUA-approved rRT-PCR methods, the Microbubbling Antigen Assay demonstrated a positive percent agreement (PPA) of 97% (95% confidence interval (CI), 92-99%) in symptomatic individuals within 7 days of symptom onset and positive SARS-CoV-2 nucleic acid results, and a negative percent agreement (NPA) of 97% (95% CI, 94-100%) in symptomatic and asymptomatic individuals with negative nucleic acid results. Antigen positivity rate in NP swabs gradually decreased as days-after-symptom-onset increased, despite persistent nucleic acid positivity of the same samples. The computer vision and machine learning-based automatic microbubble image classifier could accurately identify positives and negatives, based on microbubble counts and sizes. Total microbubble volume, a potential marker of antigen burden, correlated inversely with Ct values and days-after-symptom-onset. Antigen was detected for longer periods of time in immunocompromised patients with hematologic malignancies, compared to immunocompetent individuals. Simultaneous detectable antigens and nucleic acids may indicate the presence of replicating viruses in patients with persistent infections.\n\nConclusionsThe Microbubbling SARS-CoV-2 Antigen Assay enables sensitive and specific detection of acute infections, and quantitation and tracking of antigen dynamics in different patient populations at various stages of infection. With smartphone compatibility and automated image processing, the assay is well-positioned to be adapted for point-of-care diagnosis and to explore the clinical implications of antigen dynamics in future studies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Hui Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zhao Li", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sheng Feng", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Anni Wang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Melissa Richard-Greenblatt", + "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Emily Hutson", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Stefen Andrianus", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Laurel Glaser", + "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Kyle G Rodino", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jianing Qian", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dinesh Jayaraman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ronald Collman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Abigail L Glascock", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Frederic Bushman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jae Seung Lee", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sara Cherry", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alejandra Fausto", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Hyun Koo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Patricia M Corby", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Una ODoherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alfred L Garfall", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dan T Vogl", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Edward A Stadtmauer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ping Wang", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.21.21254061", "rel_title": "Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status", @@ -862784,49 +866258,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.23.21254092", - "rel_title": "Reconstructing the COVID-19 epidemic in Delhi, India: infection attack rate and reporting of deaths", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254092", - "rel_abs": "India reported over 10 million COVID-19 cases and 149,000 deaths in 2020. To estimate exposure and the potential for further spread, we used a SARS-CoV-2 transmission model fit to seroprevalence data from three serosurveys in Delhi and the time-series of reported deaths to reconstruct the epidemic. The cumulative proportion of the population estimated infected was 48.7% (95% CrI 22.1% - 76.8%) by end-September 2020. Using an age-adjusted overall infection fatality ratio (IFR) based on age-specific estimates from mostly high-income countries (HICs), we estimate that 15.0% (95% CrI 9.3% - 34.0%) of COVID-19 deaths were reported. This indicates either under-reporting of COVID-19 deaths and/or a lower age-specific IFR in India compared with HICs. Despite the high attack rate of SARS-CoV-2, a third wave occurred in late 2020, suggesting that herd immunity was not yet reached. Future dynamics will strongly depend on the duration of immunity and protection against new variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Margarita Pons-Salort", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jacob John", - "author_inst": "Christian Medical College, Vellore" - }, - { - "author_name": "Oliver J Watson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nicholas F Brazeau", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert Verity", - "author_inst": "Imperial College London" - }, - { - "author_name": "Gagandeep Kang", - "author_inst": "Christian Medical College, Vellore" - }, - { - "author_name": "Nicholas C Grassly", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.21254150", "rel_title": "Point-of-care lung ultrasonography for early identification of mild COVID-19: a prospective cohort of outpatients in a Swiss screening center", @@ -863958,6 +867389,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.23.21254169", + "rel_title": "COVID-19 antibody seroprevalence in Duhok, Kurdistan Region, Iraq: A population-based study", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254169", + "rel_abs": "ObjectiveThis population-based study aimed to evaluate the seroprevalence of antibodies to SARS-CoV-2 in Duhok City, Kurdistan Region of Iraq.\n\nMethodsWe analyzed the national COVID-19 database that contains data regarding COVID-19 testing, management, and clinical outcomes in Duhok. For this study, different subdistricts within each district of Duhok were considered distinct clusters. Blood samples were collected from and questionnaires were administered to eligible and consenting participants who were members of different families from the subdistricts. Immunoassays were conducted to detect antibodies against SARS-CoV-2, and the associations between certain variables were investigated.\n\nResultsThe average number cases of COVID-19 before November 2020 was 23141 {+/-} 4364, which was significantly higher than the average number of cases between November 2020 and February 2021 (3737 {+/-} 2634; P = 0.001). A total of 743 individuals agreed to participate and were enrolled in the study. Among the participants, 465/743 (62.58%) were found to have antibodies against severe acute respiratory syndrome coronavirus 2. Among the participants with antibodies, 262/465 (56.34%) denied having any history of COVID-19-related symptoms. The most common symptom was fever (81.77%), followed by myalgia (81.28%). We found that antibody levels increased steadily with age (Pearson correlation coefficient = 0.117; P = 0.012). A significant association was found between antibody levels and the presence of symptoms (P = 0.023; odds ratio = 1.0023; 95% confidence interval = 1.0002-1.0061).\n\nConclusionsA significant reduction in the number of COVID-19 cases was observed. This might be due to the high prevalence of SARS-CoV-2 antibodies in Duhok. However, infection-prevention measures should be followed as it remains unclear whether acquired immunity is protective against reinfection. It expected that the infection rates during the next wave will not be as high as the first wave due to the high infection rate in the society.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nawfal R Hussein", + "author_inst": "Department of Biomolecular Sciences, College of Medicine, University of Zakho" + }, + { + "author_name": "Amer Balatay", + "author_inst": "Department of pharmacology and clinical pharmacy, College of pharmacy, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Ibrahim A Naqid", + "author_inst": "Department of Biomedical Sciences, College of Medicine, University of Zakho, Kurdistan Region, Iraq" + }, + { + "author_name": "Shakir A Jamal", + "author_inst": "Department of Biomedical Sciences, College of Medicine, University of Zakho, Kurdistan Region, Iraq" + }, + { + "author_name": "Narin A Rasheed", + "author_inst": "Akre Technical Institute, Duhok Polytechnic University, Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Alind N Ahmed", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Reving S Salih", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Ahmed S Mahdi", + "author_inst": "Childhood Friends Hospital of Amedi, Kurdistan Region of Iraq" + }, + { + "author_name": "Sabeeha A Mansour", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Shaveen Mahdi", + "author_inst": "Duhok Maternity Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Nashwan Ibrahim", + "author_inst": "Department of Surgery, College of Medicine, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Dildar H Musa", + "author_inst": "Department of Surgery, College of Medicine, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Zana SM Saleem", + "author_inst": "Department of Medicine, College of Medicine, University of Duhok, Duhok, Kurdistan Region of Iraq" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.23.21253460", "rel_title": "Serological profiles of pan-coronavirus-specific responses in COVID-19 patients using a multiplexed electro-chemiluminescence-based testing platform", @@ -864522,109 +868020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.25.21254330", - "rel_title": "Understanding the effectiveness of government interventions in Europe's second wave of COVID-19", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254330", - "rel_abs": "As European governments face resurging waves of COVID-19, non-pharmaceutical interventions (NPIs) continue to be the primary tool for infection control. However, updated estimates of their relative effectiveness have been absent for Europes second wave, largely due to a lack of collated data that considers the increased subnational variation and diversity of NPIs. We collect the largest dataset of NPI implementation dates in Europe, spanning 114 subnational areas in 7 countries, with a systematic categorisation of interventions tailored to the second wave. Using a hierarchical Bayesian transmission model, we estimate the effectiveness of 17 NPIs from local case and death data. We manually validate the data, address limitations in modelling from previous studies, and extensively test the robustness of our estimates. The combined effect of all NPIs was smaller relative to estimates from the first half of 2020, indicating the strong influence of safety measures and individual protective behaviours--such as distancing--that persisted after the first wave. Closing specific businesses was highly effective. Gathering restrictions were highly effective but only for the strictest limits. We find smaller effects for closing educational institutions compared to the first wave, suggesting that safer operation of schools was possible with a set of stringent safety measures including testing and tracing, preventing mixing, and smaller classes. These results underscore that effectiveness estimates from the early stage of an epidemic are measured relative to pre-pandemic behaviour. Updated estimates are required to inform policy in an ongoing pandemic.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Mrinank Sharma", - "author_inst": "Department of Statistics, University of Oxford, UK" - }, - { - "author_name": "S\u00f6ren Mindermann", - "author_inst": "Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, UK" - }, - { - "author_name": "Charlie Rogers-Smith", - "author_inst": "OATML Group (work done while at OATML as an external collaborator), Department of Computer Science, University of Oxford, UK" - }, - { - "author_name": "Gavin Leech", - "author_inst": "Department of Computer Science, University of Bristol, UK" - }, - { - "author_name": "Benedict Snodin", - "author_inst": "Future of Humanity Institute, University of Oxford, UK" - }, - { - "author_name": "Janvi Ahuja", - "author_inst": "Medical Sciences Division, University of Oxford, UK" - }, - { - "author_name": "Jonas B. Sandbrink", - "author_inst": "Medical Sciences Division, University of Oxford, UK" - }, - { - "author_name": "Joshua Teperowski Monrad", - "author_inst": "Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, UK" - }, - { - "author_name": "George Altman", - "author_inst": "Manchester University NHS Foundation Trust, UK" - }, - { - "author_name": "Gurpreet Dhaliwal", - "author_inst": "The Francis Crick Institute, London, UK" - }, - { - "author_name": "Lukas Finnveden", - "author_inst": "Future of Humanity Institute, University of Oxford, UK" - }, - { - "author_name": "Alexander John Norman", - "author_inst": "Mathematical, Physical and Life Sciences (MPLS) Doctoral Training Centre, University of Oxford, UK." - }, - { - "author_name": "Sebastian B. Oehm", - "author_inst": "Medical Research Council Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Julia Fabienne Sandk\u00fchler", - "author_inst": "Independent researcher, Essen, Germany" - }, - { - "author_name": "Thomas Mellan", - "author_inst": "Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Jan Kulveit", - "author_inst": "Future of Humanity Institute, University of Oxford, UK" - }, - { - "author_name": "Leonid Chindelevitch", - "author_inst": "Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Seth Flaxman", - "author_inst": "Department of Mathematics, Imperial College London, UK" - }, - { - "author_name": "Yarin Gal", - "author_inst": "Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, UK" - }, - { - "author_name": "Swapnil Mishra", - "author_inst": "Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Jan Markus Brauner", - "author_inst": "Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, UK" - }, - { - "author_name": "Samir Bhatt", - "author_inst": "Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.25.21254231", "rel_title": "Monitoring occurrence of SARS-CoV-2 in school populations: a wastewater-based approach", @@ -865500,6 +868895,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2021.03.23.21254207", + "rel_title": "Association between the physical work environment and work functioning impairment while working from home under the COVID-19 pandemic in Japanese workers", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254207", + "rel_abs": "ObjectiveThis study examined the relationship between the physical work environment and work functioning impairment while working from home in the context of rapid changes associated with the COVID-19 pandemic.\n\nMethodsThis cross-sectional study of internet monitors was conducted between December 22 and 26, 2020. Of a total of 33,302 participants, 5,760 who worked from home at least 1 day a month, excluding those who met the exclusion criteria, were included in the analysis. A binary subjective assessment of the physical work environment while working from home was used as an exposure factor. We examined 9 items related to the physical work environment, including level of illuminance and use of suitable desks and chairs, traditionally recommended for health and safety management when working at a desk. The number of non-conformities to 7 items was also used as an exposure factor. The presence of severe work functioning impairment was measured using the Work Functioning impairment Scale (WFun), a self-reported outcome measure of the degree of work functioning impairment. Odds ratios of severe work functioning impairment were estimated using mixed-effects logistic regression analysis with the prefecture of residence as a random effect.\n\nResultsMultivariate analysis showed that the odds ratio of severe work functioning impairment was significantly higher among those who indicated \"No\" to all recommended items except for \"I work at a desk/chair for office use.\" The highest odds ratio of work functioning impairment was associated with a \"No\" response to \"There is enough light to do my work\" (aOR: 2.02, 95%CI: 1.73-2.35, p<0.01). Our results also suggest the presence of a dose-response relationship between the number of non-conformities to recommendations for work environments while working from home and work functioning impairment.\n\nConclusionsOur findings suggest that it is important for both companies and individual workers to create a work environment that prevents negative health outcomes and improves productivity while working from home.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Makoto Okawara", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohiro Ishimaru", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Ayako Hino", + "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Kazunori Ikegami", + "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.25.21254314", "rel_title": "Automatic identification of risk factors for SARS-CoV-2 positivity and severe clinical outcomes of COVID-19 using Data Mining and Natural Language Processing", @@ -866116,53 +869562,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.24.21253576", - "rel_title": "ACE gene variants rise the risk of severe COVID-19 in patients with hypertension, dyslipidemia or diabetes. A pilot study", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21253576", - "rel_abs": "Coronavirus disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to scale and threaten human health and public safety. It is essential to identify those risk factors that lead to a poor prognosis of the disease. A predisposing host genetic background could be one of these factors that explain the interindividual variability to COVID-19 severity. Thus, we have studied whether the rs4341 and rs4343 polymorphisms of the angiotensin converting enzyme (ACE) gene, key regulator of the renin-aldosterone-angiotensin system (RAAS), could explain the different outcomes of 128 COVID-19 patients with diverse degree of severity (33 asymptomatic or mildly asymptomatic, 66 hospitalized in the general ward, and 29 admitted to the ICU). We found that G allele of rs4341 and rs4343 was associated with severe COVID-19 in hypertensive patients, independently of gender (p<0.05). G-carrier genotypes of both polymorphisms were also associated with higher mortality (p< 0.05) and higher severity of COVID-19 in dyslipidemic (p<0.05) and type 2 diabetic patients (p< 0.01).\n\nIn conclusion, our preliminary study suggests that the G-containing genotypes of rs4341 and rs4343 confer an additional risk of adverse COVID-19 prognosis. Thus, rs4341 and rs4343 polymorphisms of ACE could be predictive markers of severity of COVID-19 in those patients with hypertension, dyslipidemia or diabetes. The knowledge of these genetic data could contribute to precision management of SARS-CoV-2 infected patients when admitted to hospital.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mar\u00eda \u00cd\u00f1iguez", - "author_inst": "Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Spain." - }, - { - "author_name": "Patricia P\u00e9rez-Matute", - "author_inst": "Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Spain" - }, - { - "author_name": "Pablo Villoslada-Blanco", - "author_inst": "Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Spain." - }, - { - "author_name": "Emma Recio-Fernandez", - "author_inst": "Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Spain" - }, - { - "author_name": "Diana Ezquerro-Perez", - "author_inst": "Infectious Diseases Department. Hospital Universitario San Pedro, Spain" - }, - { - "author_name": "Jorge Alba", - "author_inst": "Infectious Diseases Department. Hospital Universitario San Pedro, Spain" - }, - { - "author_name": "M.Lourdes Ferreira-Laso", - "author_inst": "Department of Anesthesiology and Postoperative Care, Hospital Universitario San Pedro, Spain" - }, - { - "author_name": "Jos\u00e9 A. Oteo", - "author_inst": "Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), Spain; Infectious Disea" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.21254238", "rel_title": "Dramatic drop of new SARS-CoV-2 infections among health care workers after the first dose of the BNT162b2 mRNA Covid-19 Vaccine", @@ -866994,6 +870393,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.24.21254046", + "rel_title": "Sudden rise in COVID-19 case fatality among young and middle-aged adults in the south of Brazil after identification of the novel B.1.1.28.1 (P.1) SARS-CoV-2 strain: analysis of data from the state of Parana", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254046", + "rel_abs": "Brazil is currently suffering a deadly surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, which has been attributed to the spread of a new strain known as P.1 (B.1.1.28.1). In this investigation, we analyzed coronavirus disease 2019 (COVID-19) public health data from Parana, the largest state in southern half of Brazil, between September 1, 2020 and March 17, 2021, to evaluate recent trends in case fatality rates in different age groups. A total of 553,518 cases of SARS-CoV-2, 8,853 currently registered as fatal, were finally included in our analysis. All age groups showed either decline or stabilization of the case fatality rates (CFRs) between September 2020 and January 2021. In February 2021, an increase in CFR for almost all age groups could be instead observed. All groups above 20 years of age showed statistically significant increases in CFR when diagnosed in February 2021 as opposed to January 2021. Patients aged 20-29 years experienced a tripling of their CFR, from 0.04% to 0.13%, while those aged 30-39, 40-49, 50-59 experienced approximate CFR doubling. Individuals between 20 and 29 years of age whose diagnosis was made in February 2021 had an over 3-fold higher risk of death compared to those diagnosed in January 2021 (Risk Ratio (RR): 3.15 [95%CI: 1.52-6.53], p<0.01), while those aged 30-39, 40-49, 50-59 years experienced 93% (1.93 [95%CI:1.31-2.85], p<0.01), 110% (RR: 2.10 [95%CI:1.62-2.72], p<0.01), and 80% (RR: 1.80 [95%CI:1.50-2.16], p<0.01) increases in risk of death, respectively. Notably, the observed CFR increase coincided with the second consecutive month of declining number of diagnosed SARS-CoV-2 cases. Taken together, these preliminary findings suggest significant increases in CFR in young and middle-aged adults after identification of a novel SARS-CoV-2 strain circulating in Brazil, and this should raise public health alarms, including the need for more aggressive local and regional public health interventions and faster vaccination.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Maria Helena Santos de Oliveira", + "author_inst": "Federal University of Parana" + }, + { + "author_name": "Giuseppe Lippi", + "author_inst": "University of Verona" + }, + { + "author_name": "Brandon Michael Henry", + "author_inst": "Cincinnati Children's Hospital Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.24.21254254", "rel_title": "Dental mitigation strategies to reduce aerosolization of SARS-CoV-2", @@ -867818,93 +871244,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.03.26.437123", - "rel_title": "Occurrence of COVID-19 symptoms during SARS-CoV-2 infection defines waning of humoral immunity", - "rel_date": "2021-03-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.26.437123", - "rel_abs": "Approximately half of the SARS-CoV-2 infections occur without apparent symptoms, raising questions regarding long-term humoral immunity in asymptomatic individuals. Plasma levels of immunoglobulin G (IgG) and M (IgM) against the viral spike or nucleoprotein were determined for 25,091 individuals enrolled in a surveillance program in Wuhan, China. We compared 405 asymptomatic individuals with 459 symptomatic COVID-19 patients. The well-defined duration of the SARS-CoV-2 endemic in Wuhan allowed a side-by-side comparison of antibody responses following symptomatic and asymptomatic infections without subsequent antigen re-exposure. IgM responses rapidly declined in both groups. However, both the prevalence and durability of IgG responses and neutralizing capacities correlated positively with symptoms. Regardless of sex, age, and body weight, asymptomatic individuals lost their SARS-CoV-2-specific IgG antibodies more often and rapidly than symptomatic patients. These findings have important implications for immunity and favour immunization programs including individuals after asymptomatic infections.\n\nOne-Sentence SummaryPrevalence and durability of SARS-CoV-2-specific IgG responses and neutralizing capacities correlate with COVID-19 symptoms.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jun Wu", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Boyun Liang", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Yaohui Fang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences; Wuhan 430071, China" - }, - { - "author_name": "Hua Wang", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Xiaoli Yang", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Shu Shen", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences; Wuhan 430071, China" - }, - { - "author_name": "Liangkai Chen", - "author_inst": "Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 4" - }, - { - "author_name": "Sumeng Li", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Sihong Lu", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Tiandan Xiang", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Jia Liu", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Vu Thuy Khanh Le-Trilling", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen; Essen 45147, Germany" - }, - { - "author_name": "Mengji Lu", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen; Essen 45147, Germany" - }, - { - "author_name": "Dongliang Yang", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - }, - { - "author_name": "Fei Deng", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences; Wuhan 430071, China" - }, - { - "author_name": "Ulf Dittmer", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen; Essen 45147, Germany" - }, - { - "author_name": "Mirko Trilling", - "author_inst": "Institute for Virology, University Hospital of Essen, University of Duisburg-Essen; Essen 45147, Germany" - }, - { - "author_name": "Xin Zheng", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan 430022, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.26.437153", "rel_title": "Comparison of SARS-CoV-2 VOC 202012/01 (UK variant) and D614G variant transmission by different routes in Syrian hamsters", @@ -869111,6 +872450,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.25.436930", + "rel_title": "Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India", + "rel_date": "2021-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.436930", + "rel_abs": "Emergence of distinct viral clades has been observed in SARS-CoV2 variants across the world and India. Identification of the genomic diversity and the phylodynamic profiles of the prevalent strains of the country are critical to understand the evolution and spread of the variants. We performed whole-genome sequencing of 54 SARS-CoV2 strains collected from COVID-19 patients in Kolkata, West Bengal during August to October 2020. Phylogeographic and phylodynamic analyses were performed using these 54 and other sequences from India and abroad available in GISAID database. Spatio-temporal evolutionary dynamics of the pathogen across various regions and states of India over three different time periods in the year 2020 were analyzed. We estimated the clade dynamics of the Indian strains and compared the clade specific mutations and the co-mutation patterns across states and union territories of India over the time course. We observed that GR, GH and G (GISAID) or 20B and 20A (Nextstrain) clades were the prevalent clades in India during middle and later half of the year 2020. However, frequent mutations and co-mutations observed within the major clades across time periods do not show much overlap, indicating emergence of newer mutations in the viral population prevailing in the country. Further, we explored the possible association of specific mutations and co-mutations with the infection outcomes manifested within the Indian patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nupur Biswas", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Priyanka Mallick", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Sujay Krishna Maity", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Debaleena Bhowmik", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Arpita Ghosh Mitra", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Soumen Saha", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Aviral Roy", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Partha Chakrabarti", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Sandip Paul", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Saikat Chakrabarti", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.03.25.437046", "rel_title": "Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring", @@ -869799,77 +873193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.17.21253076", - "rel_title": "Head-to-head performance comparison of self-collected nasal versus professional-collected nasopharyngeal swab for a WHO-listed SARS-CoV-2 antigen-detecting rapid diagnostic test", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253076", - "rel_abs": "BackgroundIn 2020, the World Health Organization (WHO) recommended two SARS-CoV-2 lateral flow antigen detecting rapid diagnostics tests (Ag-RDTs), both initially with nasopharyngeal (NP) sample collection. Independent head-to-head studies demonstrated for SARS-CoV-2 Ag-RDTs nasal sampling to be a comparable and reliable alternative for nasopharyngeal (NP) sampling.\n\nMethodsWe conducted a head-to-head comparison study of a supervised, self-collected nasal mid-turbinate (NMT) swab and a professional-collected NP swab, using the Panbio Ag-RDT (the second WHO-listed SARS-CoV-2 Ag-RDT, distributed by Abbott). We calculated positive and negative percent agreement and, compared to the reference standard reverse transcription polymerase chain reaction (RT-PCR), sensitivity and specificity for both sampling techniques.\n\nResultsA SARS-CoV-2 infection could be diagnosed by RT-PCR in 45 of 290 participants (15.5%). Comparing the NMT and NP sampling the positive percent agreement of the Ag-RDT was 88.1% (37/42 PCR positives detected; CI 75.0% - 94.8%). The negative percent agreement was 98.8% (245/248; CI 96.5% - 99.6%). The overall sensitivity of Panbio with NMT sampling was 84.4% (38/45; CI 71.2% - 92.3%) and 88.9% (40/45; CI 76.5% - 95.5%) with NP sampling. Specificity was 99.2% (243/245; CI 97.1% - 99.8%) for both, NP and NMT sampling. The sensitivity of the Panbio test in participants with high viral load (> 7 log10 SARS-CoV-2 RNA copies/mL) was 96.3% (CI 81.7% - 99.8%) for both, NMT and NP sampling.\n\nConclusionFor the Panbio Ag-RDT supervised NMT self-sampling yields to results comparable to NP sampling. This suggests that nasal self-sampling could be used for scale-up population testing.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Julian A.F. Klein", - "author_inst": "Division of Clinical Tropical Medicine, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - }, - { - "author_name": "Lisa J. Kr\u00fcger", - "author_inst": "Division of Clinical Tropical Medicine, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - }, - { - "author_name": "Frank Tobian", - "author_inst": "Division of Clinical Tropical Medicine, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - }, - { - "author_name": "Mary Gaeddert", - "author_inst": "Division of Clinical Tropical Medicine, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - }, - { - "author_name": "Federica Lainati", - "author_inst": "Division of Clinical Tropical Medicine, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - }, - { - "author_name": "Paul Schnitzler", - "author_inst": "Department of Virology, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - }, - { - "author_name": "Andreas K. Lindner", - "author_inst": "Institute of Tropical Medicine and Health, Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Institute of Tropical Medicine and Health, Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Britta Knorr", - "author_inst": "Local Health Authority of Heidelberg and Rhein-Neckar-Region, Germany" - }, - { - "author_name": "Andreas Welker", - "author_inst": "Local Health Authority of Heidelberg and Rhein-Neckar-Region, Germany" - }, - { - "author_name": "Margaretha de Vos", - "author_inst": "Foundation for Innovative New Diagnostics" - }, - { - "author_name": "Jilian A. Sacks", - "author_inst": "Foundation for Innovative New Diagnostics" - }, - { - "author_name": "Camille Escadafal", - "author_inst": "Foundation for Innovative New Diagnostics" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Division of Clinical Tropical Medicine, Centre of Infectious Diseases, Heidelberg University Hospital, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.17.21253821", "rel_title": "Increased prevalence of AB group and FY*A red blood cell antigen in Caucasian SARS-CoV-2 convalescent plasma donors", @@ -870777,6 +874100,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.22.21254134", + "rel_title": "Relationship between COVID-19 pandemic and ecological, economic, and social characteristics", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254134", + "rel_abs": "COVID-19 pandemic had huge impacts on the global world, with both a negative impact on society and economy, but a positive one on nature. But this universal effect resulted in different infection rates from country to country. We analyzed the relationship between the pandemic and ecological, economic, and social characteristics. All of these data were collected in 140 countries at 6 time points. Correlations were studied using univariate and multivariate regression models.\n\nThe world was interpreted as a single global ecosystem consisting of ecosystem units representing countries. We first studied 140 countries around the world together, and infection rates were related to per capita GDP, Ecological Footprint, median age, urban population, and Biological Capacity, globally. We then ranked 140 countries by infection rate and created 4 equal groups, each with 35 countries. In the first group, the infection rate was very high and was related to the Ecological Footprint (consumption) and GDP per capita (production). This group is dominated by developed countries and their ecological characteristics have proven to be particularly significant. In groups 2, 3, and 4, infection rates were high, moderate, and low, and were primarily associated with median age and urban population.\n\nIn the scientific discussion, we have interpreted why infection is high in developed countries. Sustainable ecosystems are balanced, unlike the ecosystems of developed countries. According to science, the resilience and health of both natural ecosystems and humans are closely linked to the world of microbial communities. Our results suggest that both the economy and society need to be in harmony with nature, creating sustainable ecosystems in developed countries as well.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Attila Muranyi", + "author_inst": "Institute for Soil Science and Agricultural Chemistry, Hungarian Academy of Sciences" + }, + { + "author_name": "Balint Varga", + "author_inst": "Department of Computer Science, Institute of Mathematics, Eotvos Lorand University, Budapest, Hungary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.20.21253892", "rel_title": "Intention of Healthcare Workers to Receive COVID-19 Vaccine: A Cross-Sectional Survey in 10 Countries in Eastern Mediterranean Region", @@ -871469,93 +874815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.03.21.21251651", - "rel_title": "Low prevalence of COVID-19 Exposure is Coincident with Self-reported Compliance with Public Health Guidelines among Essential Employees at an Institute of Higher Education", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21251651", - "rel_abs": "ImportanceDetailed analysis of infection rates paired with behavioral and employee reported risk factors are vital to understanding how COVID-19 transmission may be inflamed or mitigated in the workplace. Institutes of Higher Education are heterogeneous work units that supported continued in person employment during COVID-19, providing an excellent test site for occupational health evaluation.\n\nObjectiveTo evaluate self-reported behaviors and SARS-CoV-2 among essential in-person employees during the first six months of the COVID-19 pandemic.\n\nDesignCross-sectional, conducted from July 13-September 2, 2020.\n\nSettingInstitute of Higher Education in Fort Collins, Colorado.\n\nParticipantsEmployees identified to be an essential in-person employee during the first six months of the pandemic (1,522 invited, 1,507 qualified, 603 (40%) completed the survey). Of those completing the survey, 84.2% (508) elected to participate in blood and nasal swab sample collection to assess active SARS-CoV-2 infection via qRT-PCR, and past infection by serology (overall completion rate of 33.7%). Eligibility included > 18 years old, able to read and understand English, not currently experiencing cough, shortness of breath or difficulty breathing, fever >100.4F (38C), chills/shaking with chills, muscle pain, new or worsening headaches, sore throat or new loss of sense of taste/smell.\n\nExposureSelf-reported COVID-19 protective behaviors\n\nMain Outcome(s) and Measure(s)Current SARS-CoV-2 infection detected by qRT-PCR or previous SARS-CoV-2 infection detected by IgG SARS-CoV-2 testing platform.\n\nResultsThere were no qRT-PCR positive tests, and only 2 (0.39%) contained seroreactive IgG antibodies. Participants were 60% female, 90% non-Hispanic white, mean age 41 years (18-70 years). Handwashing and mask wearing were reported frequently both at work (98% and 94% respectively) and outside work (91% and 95% respectively) while social distancing was reported less frequently at work (79%) then outside of work (92%) [p < .001]. Participants were more highly motivated to avoid exposures out of concern for spreading to others (83%) than for personal implications (63%) [p < .001].\n\nConclusions and RelevanceThis is one of the first reports to document that complex work environments can be operated safely during the COVID-19 pandemic when employees report compliance with public health practices both at and outside work.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Tracy L Nelson", - "author_inst": "Colorado State University" - }, - { - "author_name": "Bailey Fosdick", - "author_inst": "Colorado State University" - }, - { - "author_name": "Laurie M Biela", - "author_inst": "Colorado State University" - }, - { - "author_name": "Hayden Schoenberg", - "author_inst": "Colorado State University" - }, - { - "author_name": "Sarah Mast", - "author_inst": "Colorado State University" - }, - { - "author_name": "Emma McGinnis", - "author_inst": "Colorado State University" - }, - { - "author_name": "Michael C Young", - "author_inst": "Colorado State University" - }, - { - "author_name": "Lori Lynn", - "author_inst": "Colorado State University" - }, - { - "author_name": "Scott Fahrner", - "author_inst": "Colorado State University" - }, - { - "author_name": "Laura Nolt", - "author_inst": "Colorado State University" - }, - { - "author_name": "Tina Dihle", - "author_inst": "Colorado State University" - }, - { - "author_name": "Kendra Quicke", - "author_inst": "Colorado State University" - }, - { - "author_name": "Emily Gallichotte", - "author_inst": "Colorado State University" - }, - { - "author_name": "Emily Fitzmeyer", - "author_inst": "Colorado State University" - }, - { - "author_name": "Gregory Ebel", - "author_inst": "Colorado State University" - }, - { - "author_name": "Kristy Pabilonia", - "author_inst": "Colorado State University" - }, - { - "author_name": "Nicole Ehrhart", - "author_inst": "Colorado State University" - }, - { - "author_name": "Sue VandeWoude", - "author_inst": "Colorado State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.23.21254175", "rel_title": "The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: analysis of high-throughput genetic, epigenetic, and gene expression studies", @@ -872409,6 +875668,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.14.21253532", + "rel_title": "Epicardial adipose tissue thickness is associated with increased severity and mortality related to SARS-CoV-2 infection", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.14.21253532", + "rel_abs": "BACKGROUNDIncreased adiposity and visceral obesity have been linked to adverse COVID-19 outcomes. The amount of epicardial adipose tissue (EAT) may have relevant implications given its proximity to the heart and lungs. Here, we explored the role of EAT in increasing the risk for COVID-19 adverse outcomes.\n\nMETHODSWe included 748 patients with COVID-19 attending a reference center in Mexico City. EAT thickness, sub-thoracic and extra-pericardial fat were measured using thoracic CT scans. We explored the association of each thoracic adipose tissue compartment with COVID-19 mortality and severe COVID-19 (defined as mortality and need for invasive mechanical ventilation), according to the presence or absence of obesity. Mediation analyses evaluated the role of EAT in facilitating the effect of age, body mass index and cardiac troponin levels with COVID-19 outcomes.\n\nRESULTSEAT thickness was associated with increased risk of COVID-19 mortality (HR 1.18, 95%CI 1.01-1.39) independent of age, gender, comorbid conditions and BMI. Increased EAT was associated with lower SpO2 and PaFi index and higher levels of cardiac troponins, D-dimer, fibrinogen, C-reactive protein, and 4C severity score, independent of obesity. EAT mediated 13.1% (95%CI 3.67-28.0%) and 5.1% (95%CI 0.19-14.0%) of the effect of age and 19.4% (95%CI 4.67-63.0%) and 12.8% (95%CI 0.03-46.0%) of the effect of BMI on requirement for intubation and mortality, respectively. EAT also mediated the effect of increased cardiac troponins on myocardial infarction during COVID-19.\n\nCONCLUSIONEAT is an independent risk factor for severe COVID-19 and mortality independent of obesity. EAT partly mediates the effect of age and BMI and increased cardiac troponins on adverse COVID-19 outcomes.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Roopa Mehta", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Leonardo Mancillas-Adame", + "author_inst": "Facultad de Medicina, Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Marcela Rodr\u00edguez-Flores", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Natalia Ram\u00edrez-Pedraza", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Bethsabel Rodr\u00edguez-Encinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carolina Isabel P\u00e9rez-Carri\u00f3n", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Mar\u00eda Isabel Jasso-\u00c1vila", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jorge Valladares-Garcia", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Pablo Esteban Vanegas-Cedillo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Diana Hern\u00e1ndez-Ju\u00e1rez", + "author_inst": "dianaheez@hotmail.com" + }, + { + "author_name": "Arsenio Vargas-V\u00e1zquez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Monica Chapa-Ibarguengoitia", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Paloma Almeda-Vald\t\u00e9s", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Daniel Elias-Lopez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Arturo Galindo-Fraga", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfonso Gulias-Herrero", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfredo Ponce de Leon", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jose Sifuentes-Osornio", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carlos A. Aguilar-Salinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2021.03.16.21253652", "rel_title": "Within-Day Variability of SARS-CoV-2 RNA in Municipal Wastewater Influent During Periods of Varying COVID-19 Prevalence and Positivity", @@ -872993,53 +876351,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.23.21253258", - "rel_title": "High incidence of pulmonary thromboembolism in hospitalized SARS-CoV-2 infected patients", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21253258", - "rel_abs": "IntroductionSARS-CoV-2 infected patients present thrombotic complications caused by direct endothelial cells injury of the microvessels. Pulmonary thromboembolism (PE) has been reported by Computed Tomography pulmonary angiogram (CTPA) in patients with COVID-19 pneumonia with high D-dimer levels.\n\nObjectivesWe present the characteristics of SARS-CoV-2 infected patients diagnosed of PE by CTPA in our hospital. We also present the comparison of these findings with non-infected patients with PE data.\n\nMethodsPatients 18 years of age or older with SARS-CoV2 virus infection, and patients with suspected infection at beginning of admission but with negative PCR, were studied with CTPA for suspicion of VTE, during their hospitalization.\n\nResultsDuring the study period, 52 CTPA were performed in our hospital, sixteen in SARS-CoV-2 infected patients. No significant differences in age (p=0.43) and sex (p=0.31) were found between the two groups, infected and non-infected patients. In the infected group, the patients who had PE had a much lower median age (47.8 years) than those without PE (73.3 years). No differences between infected and non-infected patients were detected in the diagnosis of PE with CTPA, 28.6% versus 27.8% (p=1.00). Overall patient mortality was 1.9%; one patient died (6.3%) in the infected group, and none in the non-infected group (p=0.31).\n\nConclusionA considerable incidence of PE diagnosed by CTPA in SARS-CoV-2 infected patients has been observed, despite thrombo-prophylaxis.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "DAVID EL-QUTOB Sr.", - "author_inst": "Unit of Allergy, Universitary Hospital of La Plana in Vila-Real, Spain." - }, - { - "author_name": "Laura Alvarez", - "author_inst": "Service of Pharmacy, Universitary Hospital of La Plana in Vila-Real, Spain." - }, - { - "author_name": "Patricia Garcia", - "author_inst": "Section of Pneumology, Universitary Hospital of La Plana in Vila-Real, Spain" - }, - { - "author_name": "Montserrat Robustillo", - "author_inst": "Unit of Rheumatology, Universitary Hospital of La Plana in Vila-Real, Spain" - }, - { - "author_name": "Ines Barreda", - "author_inst": "Section of Neurophysiology, Universitary Hospital of La Plana in Vila-Real, Spain" - }, - { - "author_name": "MARIA NIETO", - "author_inst": "Unit of Allergy, Universitary Hospital of La Plana in Vila-Real, Spain" - }, - { - "author_name": "Maria Teresa Pin", - "author_inst": "Unit of Nephrology, Universitary Hospital of La Plana in Vila-Real, Spain" - }, - { - "author_name": "Francisco Javier Carrera", - "author_inst": "Service of Pharmacy, Universitary Hospital of La Plana in Vila-Real, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.03.17.21253138", "rel_title": "Mortality during the COVID-19 pandemic: findings from the CLINIMEX exercise cohort in the year of 2020", @@ -874375,6 +877686,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.21.21254047", + "rel_title": "Factors influencing COVID-19 vaccination uptake in an elderly sample in Poland", + "rel_date": "2021-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254047", + "rel_abs": "BackgroundsThis research represents an investigation into potential predictors for the uptake of the COVID-19 vaccination in Poland, following the instigation of policies to encourage the over-seventies to be vaccinated.\n\nMethodsIndividuals participated in cross-sectional structured interviews. 1427 respondents were questioned for determining vaccination uptake, revealing attitudes regarding vaccination, where information was sourced from, health status and behavior, demographics and socio-economic profiles.\n\nResultsSelected predictors for acceptance of the vaccination were: being talked through the importance of the vaccination and potential side-effects by a medical professional; sharing living space with others; having a high ranking occupation; suffering from chronic illnesses; being able to access medical services by driving or walking rather than using public transport or relying on others. Those who opted not to be vaccinated most frequently justify their decision by saying that they were concerned about the efficacy of the vaccine or that they were worried about side-effects.\n\nConclusionsIt appears that the current nationwide campaign has successfully raised awareness regarding the vaccine, but this research indicates that a more information-based campaign, focusing on evidence of the vaccines efficacy and the non-serious nature of all side-effects, could lead to improved uptake of the COVID-19 vaccine.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Marta Malesza", + "author_inst": "University of Economics and Human Sciences in Warsaw" + }, + { + "author_name": "Magdalena Bozym", + "author_inst": "Military Academy Hospital, Warsaw, Poland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.21.21254068", "rel_title": "Determinants of COVID-19 outcomes: A systematic review.", @@ -875335,45 +878669,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.23.436593", - "rel_title": "Dry Swab Method of sample collection for SARS-CoV2 testing can be used for culturing virus", - "rel_date": "2021-03-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.23.436593", - "rel_abs": "Back groundEarlier studies suggested the use of dry swab method for SARS-CoV-2 detection as it does not need VTM and subsequent RNA extraction step making the process cheaper, safer and faster. In this study we explore whether the virus in the dry swab is viable and can be cultured and propagated.\n\nMethodSwabs were spiked with SARS-CoV-2 and stored in three different conditions: a) as dry swab (SD, eluted in 1 mL DMEM), b) in 1 mL of Viral Transport Medium (SVTM), and c) in 1 mL of Tris-EDTA buffer (STE). The sample groups were stored either at room temperature (RT, 25{degrees}C{+/-}1{degrees}C) or at 4{degrees}C for 1, 4, 8, 12, 24, 48 and 72 hours before being used as viral inoculums for the propagation studies in Vero cells.\n\nResultsThe RT-qPCR data suggests that SD incubated both at RT and 4{degrees}C harbors viral particles that are viable and culturable at par with SVTM and STE.\n\nConclusionThe dry swab method, in addition to its advantages in detection of the virus, also renders viable viral particles that can be cultured and propagated.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sushma Ram", - "author_inst": "CSIR-CCMB" - }, - { - "author_name": "M. Ghalib Enayathullah", - "author_inst": "CSIR-CCMB" - }, - { - "author_name": "Yash Parekh", - "author_inst": "CSIR-CCMB" - }, - { - "author_name": "Karthik Bharadwaj Tallapaka", - "author_inst": "CSIR-CCMB" - }, - { - "author_name": "Rakesh K Mishra", - "author_inst": "CSIR-CCMB" - }, - { - "author_name": "Bokara Kiran Kumar", - "author_inst": "CCMB" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.22.436481", "rel_title": "Neutralization of European, South African, and United States SARS-CoV-2 mutants by a human antibody and antibody domains", @@ -876473,6 +879768,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.03.19.21253425", + "rel_title": "COVID 19 Vaccine Perceptions in the New York State Intellectual and Developmental Disabilities Community", + "rel_date": "2021-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253425", + "rel_abs": "BackgroundPeople with intellectual and developmental disabilities (IDD) are at disproportionate risk for severe COVID-19 outcomes, particularly those living in congregate care settings. Yet, there is limited data on vaccine perceptions in the disability community.\n\nObjectiveTo explore COVID-19 vaccine perceptions in individuals with IDD, their family members, and those who work with them, to inform a statewide vaccine information and messaging project.\n\nMethodsA national survey, adapted for the IDD community, was distributed to a convenience sample of IDD organizations throughout New York State, in five languages. Constructs included vaccine intention, reasons for vaccine hesitancy, and trusted sources of vaccine information. Zip code data were used to map respondent location and vaccine preferences.\n\nResultsOf n= 825 respondents, approximately 75% intended to or had received the vaccine, across roles (i.e., people with disabilities, family members, direct care workers) and racial/ethnic groups. Greater vaccine hesitancy was reported in younger individuals and those making decisions on behalf of a person with IDD. Concerns included side effects and the swiftness of vaccine development. Black and Hispanic participants had heightened concerns about being an \"experiment\" for the vaccine. Trusted sources of information included healthcare providers and family members. Respondents who intended/got the vaccine were distributed throughout the state.\n\nConclusionsVaccine preferences in this New York State disability community sample align with national data. Identified concerns suggest the need for community education that addresses misperceptions. Age and race differences in perspectives highlight the need for tailored education, delivered by trusted messengers.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Suzannah Iadarola", + "author_inst": "University of Rochester Medical Center, Director, Strong Center for Developmental Disabilities" + }, + { + "author_name": "Joanne Siegel", + "author_inst": "Einstein College of Medicine-Montefiore Medical Center" + }, + { + "author_name": "Qi Gao", + "author_inst": "Einstein College of Medicine" + }, + { + "author_name": "Kathleen McGrath", + "author_inst": "Einstein College of Medicine" + }, + { + "author_name": "Karen Bonuck", + "author_inst": "Einstein College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.21.21254048", "rel_title": "Factors informing healthcare workers' willingness to work during the COVID-19 pandemic", @@ -877181,101 +880511,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.22.435960", - "rel_title": "CVnCoV protects human ACE2 transgenic mice from ancestral B BavPat1 and emerging B.1.351 SARS-CoV-2", - "rel_date": "2021-03-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.435960", - "rel_abs": "The ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic necessitates the fast development of vaccines as the primary control option. Recently, viral mutants termed \"variants of concern\" (VOC) have emerged with the potential to escape host immunity. VOC B.1.351 was first discovered in South Africa in late 2020, and causes global concern due to poor neutralization with propensity to evade preexisting immunity from ancestral strains. We tested the efficacy of a spike encoding mRNA vaccine (CVnCoV) against the ancestral strain BavPat1 and the novel VOC B.1.351 in a K18-hACE2 transgenic mouse model. Naive mice and mice immunized with formalin-inactivated SARS-CoV-2 preparation were used as controls. mRNA-immunized mice developed elevated SARS-CoV-2 RBD-specific antibody as well as neutralization titers against the ancestral strain BavPat1. Neutralization titers against VOC B.1.351 were readily detectable but significantly reduced compared to BavPat1. VOC B.1.351-infected control animals experienced a delayed course of disease, yet nearly all SARS-CoV-2 challenged naive mice succumbed with virus dissemination and high viral loads. CVnCoV vaccine completely protected the animals from disease and mortality caused by either viral strain. Moreover, SARS-CoV-2 was not detected in oral swabs, lung, or brain in these groups. Only partial protection was observed in mice receiving the formalin-inactivated virus preparation. Despite lower neutralizing antibody titers compared to the ancestral strain BavPat1, CVnCoV shows complete disease protection against the novel VOC B.1.351 in our studies.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Donata Hoffmann", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Bjoern Corleis", - "author_inst": "Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Susanne Rauch", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Nicole Roth", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Janine Muehe", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Nico Joel Halwe", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Lorenz Ulrich", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Charlie Fricke", - "author_inst": "Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Jacob Schoen", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Anna Kraft", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Angele Breithaupt", - "author_inst": "Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Kerstin Wernike", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Anna Michelitsch", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Franziska Sick", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Claudia Wylezich", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Stefan O. Mueller", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Thomas C. Mettenleiter", - "author_inst": "Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Benjamin Petsch", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Anca Dorhoi", - "author_inst": "Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Martin Beer", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.22.436375", "rel_title": "An mRNA vaccine against SARS-CoV-2: Lyophilized, liposome-based vaccine candidate EG-COVID induces high levels of virus neutralizing antibodies", @@ -878463,6 +881698,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.03.19.21253962", + "rel_title": "The effects of physical distancing and lockdown to restrain SARS-CoV-2 outbreak in the Italian Municipality of Cogne", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253962", + "rel_abs": "The outbreak of SARS-CoV-2 started in Wuhan, China, and is now a pandemic. An understanding of the prevalence and contagiousness of the disease, and of whether the strategies used to contain it to date have been successful, is important for understanding future containment strategies. One strategy for controlling the spread of SARS-CoV-2 is to adopt strong social distancing policies. The Municipality of Cogne (I), adopted strict lockdown rules from March 4, 2020 up to May 18, 2020. This first wave of the pandemic impressed by the extremely low impact of the SARS-CoV-2 on the locals, compared to the number accused on all the Italian territory. Starting from October 2020 up to the end of December, when the second wave hit Italy and Cogne territory, heavier effects were observed. In order to cast light on the effectiveness of the adopted strategy 74,5% of the local population underwent to a blood screening to detect IgM and IgG antibodies and after six months all the people tested positive were again investigated to establish the longitudinal changes in antibodies level. Moreover, within the context of this survey a rare and interesting case of secondary infection has been identified and here presented.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gianpiero Gervino", + "author_inst": "University of Torino" + }, + { + "author_name": "Fabio Truc", + "author_inst": "University of Torino" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.03.18.21253881", "rel_title": "A Prospective Study of Long-Term Outcomes Among Hospitalized COVID-19 Patients with and without Neurological Complications", @@ -879227,101 +882485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.03.16.21253752", - "rel_title": "Predicting clinical outcomes in the Machine Learning era: The Piacenza score a purely data driven approach for mortality prediction in COVID-19 Pneumonia", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253752", - "rel_abs": "BackgroundSeveral models have been developed to predict mortality in patients with COVID-19 pneumonia, but only few have demonstrated enough discriminatory capacity. Machine-learning(ML) algorithms represent a novel approach for data-driven prediction of clinical outcomes with advantages over statistical modelling. We developed the Piacenza score, a ML-based score, to predict 30-day mortality in patients with COVID-19 pneumonia.\n\nMethods852 patients (mean age 70years, 70%males) were enrolled from February to November 2020. The dataset was randomly splitted into derivation and test. The Piacenza score was obtained through the Naive Bayes classifier and externally validated on 86 patients. Using a forward-search algorithm the following six features were identified: age; mean corpuscular haemoglobin concentration; PaO2 /FiO2 ratio; temperature; previous stroke; gender. In case one or more of the features are not available for a patient, the model can be re-trained using only the provided features.\n\nWe also compared the Piacenza score with the 4C score and with a Naive Bayes algorithm with 14 variables chosen a-priori.\n\nResultsThe Piacenza score showed an AUC of 0.78(95% CI 0.74-0.84, Brier-score 0.19) in the internal validation cohort and 0.79(95% CI 0.68-0.89, Brier-score 0.16) in the external validation cohort showing a comparable accuracy respect to the 4C score and to the Naive Bayes model with a-priori chosen features, which achieved an AUC of 0.78(95% CI 0.73-0.83, Brier-score 0.26) and 0.80(95% CI 0.75-0.86, Brier-score 0.17) respectively.\n\nConclusionA personalized ML-based score with a purely data driven features selection is feasible and effective to predict mortality in patients with COVID-19 pneumonia.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "geza halasz", - "author_inst": "Cardiology department, Guglielmo Da Saliceto Hospital, Piacenza, Italy" - }, - { - "author_name": "Michela Sperti", - "author_inst": "PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy." - }, - { - "author_name": "Matteo Villani", - "author_inst": "Anesthesiology and ICU department Guglielmo da Saliceto Hospital; Piacenza, Italy." - }, - { - "author_name": "Umberto Michelucci", - "author_inst": "TOELT LLC, Birchlenstr. 25, 8600 Dubendorf, Switzerland." - }, - { - "author_name": "Piergiuseppe Agostoni", - "author_inst": "Department of Clinical Sciences and Community Health, Centro Cardiologico Monzino, IRCCS Milan, Italy." - }, - { - "author_name": "Andrea Biagi", - "author_inst": "Cardiology Department Guglielmo Da Saliceto Hospital; Piacenza, Italy." - }, - { - "author_name": "Luca Rossi", - "author_inst": "Cardiology Department Guglielmo Da Saliceto Hospital; Piacenza, Italy." - }, - { - "author_name": "Andrea Botti", - "author_inst": "Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy." - }, - { - "author_name": "Chiara Mari", - "author_inst": "Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy." - }, - { - "author_name": "Marco Maccarini", - "author_inst": "Istituto Dalle Molle di studi sulI'Intelligenza Artificiale IDSIA - USI/SUPSI, Via la Santa 1, CH-6962 Lugano-Viganello, Switzerland." - }, - { - "author_name": "Filippo Pura", - "author_inst": "Istituto Dalle Molle di studi sulI'Intelligenza Artificiale IDSIA - USI/SUPSI, Via la Santa 1, CH-6962 Lugano-Viganello, Switzerland." - }, - { - "author_name": "Loris Roveda", - "author_inst": "Istituto Dalle Molle di studi sulI'Intelligenza Artificiale IDSIA - USI/SUPSI, Via la Santa 1, CH-6962 Lugano-Viganello, Switzerland." - }, - { - "author_name": "alessia nardecchia", - "author_inst": "IIS A.Cesaris, viale Cadorna, Casalpusterlengo, Italy." - }, - { - "author_name": "Emanuele Mottola", - "author_inst": "7HC srl, Rome Italy." - }, - { - "author_name": "Massimo Nolli", - "author_inst": "Anesthesiology and ICU department Guglielmo da Saliceto Hospital; Piacenza, Italy." - }, - { - "author_name": "elisabetta salvioni", - "author_inst": "Department of Clinical Sciences and Community Health, Centro Cardiologico Monzino, IRCCS Milan, Italy." - }, - { - "author_name": "massimo mapelli", - "author_inst": "Department of Clinical Sciences and Community Health, Centro Cardiologico Monzino, IRCCS Milan, Italy." - }, - { - "author_name": "Marco Agostino deriu", - "author_inst": "PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy" - }, - { - "author_name": "Dario Piga", - "author_inst": "Istituto Dalle Molle di studi sulI'Intelligenza Artificiale IDSIA - USI/SUPSI, Via la Santa 1, CH-6962 Lugano-Viganello, Switzerland." - }, - { - "author_name": "Massimo Piepoli", - "author_inst": "Cardiology Department Guglielmo Da Saliceto Hospital; Piacenza, Italy." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.19.21253946", "rel_title": "The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein", @@ -880993,6 +884156,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.19.21253974", + "rel_title": "Data-driven estimate of SARS-CoV-2 herd immunity threshold in populations with individual contact pattern variations", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253974", + "rel_abs": "The development of efficacious vaccines has made it possible to envision mass vaccination programs aimed at suppressing SARS-CoV-2 transmission around the world. Here we use a data-driven age-structured multilayer representation of the population of 34 countries to estimate the disease induced immunity threshold, accounting for the contact variability across individuals. We show that the herd immunization threshold of random (un-prioritized) mass vaccination programs is generally larger than the disease induced immunity threshold. We use the model to test two additional vaccine prioritization strategies, transmission-focused and age-based, in which individuals are inoculated either according to their behavior (number of contacts) or infection fatality risk, respectively. Our results show that in the case of a sterilizing vaccine the behavioral strategy achieves herd-immunity at a coverage comparable to the disease-induced immunity threshold, but it appears to have inferior performance in averting deaths than the risk vaccination strategy. The presented results have potential use in defining the effects that the heterogeneity of social mixing and contact patterns has on herd immunity levels and the deployment of vaccine prioritization strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dan Lu", + "author_inst": "University of Zaragoza" + }, + { + "author_name": "Alberto Aleta", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington" + }, + { + "author_name": "Romualdo Pastor-Satorras", + "author_inst": "Universitat Politecnica de Catalunya" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Yamir Moreno", + "author_inst": "University of Zaragoza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.18.21253931", "rel_title": "A convergence based assessment of relative differences in age-stratified susceptibility and infectiousness for SARS-CoV-2 variants of B.1.1.7 lineage", @@ -881693,37 +884895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.19.21253963", - "rel_title": "Effect of information about COVID-19 vaccine effectiveness and side effects on behavioural intentions: two online experiments", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253963", - "rel_abs": "The success of mass COVID-19 vaccination campaigns rests on widespread uptake. However, although vaccinations provide good protection, they do not offer full immunity and while they likely reduce transmission of the virus to others, the extent of this remains uncertain. This produces a dilemma for communicators who wish to be transparent about benefits and harms and encourage continued caution in vaccinated individuals but not undermine confidence in an important public health measure. In two large pre-registered experimental studies on quota-sampled UK public participants we investigate the effects of providing transparent communication--including uncertainty--about vaccination effectiveness on decision-making. In Study 1 (n = 2,097) we report that detailed information about COVID-19 vaccines, including results of clinical trials, does not have a significant impact on beliefs about the efficacy of such vaccines, concerns over side effects, or intentions to receive a vaccine. Study 2 (n = 2,217) addressed concerns that highlighting the need to maintain protective behaviours (e.g. social distancing) post-vaccination may lower perceptions of vaccine efficacy and willingness to receive a vaccine. We do not find evidence of this: transparent messages did not significantly reduce perceptions of vaccine efficacy, and in some cases increased perceptions of efficacy. We again report no main effect of messages on intentions to receive a vaccine. The results of both studies suggest that transparently informing people of the limitations of vaccinations does not reduce intentions to be vaccinated but neither does it increase intentions to engage in protective behaviours post-vaccination.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "John R. Kerr", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Alexandra L.J. Freeman", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Theresa M. Marteau", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Sander van der Linden", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.16.21253736", "rel_title": "Neurological manifestations of patients with mild-to-moderate COVID-19 attending a public hospital in Lima, Peru", @@ -882535,6 +885706,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.16.21253731", + "rel_title": "The Spike-specific IgA in milk commonly-elicited after SARS-Cov-2 infection is concurrent with a robust secretory antibody response, exhibits neutralization potency strongly correlated with IgA binding, and is highly durable over time", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253731", + "rel_abs": "Approximately 10% of infants will experience COVID-19 illness requiring advanced care (1). A potential mechanism to protect this population could be provided by passive immunity through the milk of a previously infected mother. We and others have reported on the presence of SARS-CoV-2-specific antibodies in human milk (2-5). We now report the prevalence of SARS-CoV-2 IgA in the milk of 75 COVID-19-recovered participants, and find that 88% of samples are positive for Spike-specific IgA. In a subset of these samples, 95% exhibited robust IgA activity as determined by endpoint binding titer, with 50% considered high-titer. These IgA positive specimens were also positive for Spike-specific antibodies bearing the secretory component. Levels of IgA antibodies and antibodies bearing secretory component were shown to be strongly positively correlated. The secretory IgA response was dominant among the milk samples tested compared to the IgG response, which was present in 75% of samples and found to be of high-titer in only 13% of cases. Our IgA durability analysis using 28 paired samples, obtained 4-6 weeks and 4-10 months after infection, found that all samples exhibited persistently significant Spike-specific IgA, with 43% of donors exhibiting increasing IgA titers over time. Finally, COVID-19 and pre-pandemic control milk samples were tested for the presence of neutralizing antibodies; 6 of 8 COVID-19 samples exhibited neutralization of Spike-pseudotyped VSV (IC50 range, 2.39 - 89.4ug/mL) compared to 1 of 8 controls. IgA binding and neutralization capacities were found to be strongly positively correlated. These data are highly relevant to public health, not only in terms of the protective capacity of these antibodies for breastfed infants, but also for the potential use of such antibodies as a COVID-19 therapeutic, given that secretory IgA is highly stable not only in milk and the infant mouth and gut, but in all mucosa including the gastrointestinal tract, upper airway, and lungs (6).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alisa Fox", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica Marino", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kasopefoluwa Y. Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jennifer Hahn-Holbrook", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Susan Zolla-Pazner", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rebecca L Powell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.17.21252673", "rel_title": "Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece", @@ -883287,161 +886509,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.18.435972", - "rel_title": "A single BNT162b2 mRNA dose elicits antibodies with Fc-mediated effector functions and boost pre-existing humoral and T cell responses", - "rel_date": "2021-03-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.18.435972", - "rel_abs": "The standard dosing of the Pfizer/BioNTech BNT162b2 mRNA vaccine validated in clinical trials includes two doses administered three weeks apart. While the decision by some public health authorities to space the doses because of limiting supply has raised concerns about vaccine efficacy, data indicate that a single dose is up to 90% effective starting 14 days after its administration. We analyzed humoral and T cells responses three weeks after a single dose of this mRNA vaccine. Despite the proven efficacy of the vaccine at this time point, no neutralizing activity were elicited in SARS-CoV-2 naive individuals. However, we detected strong anti-receptor binding domain (RBD) and Spike antibodies with Fc-mediated effector functions and cellular responses dominated by the CD4+ T cell component. A single dose of this mRNA vaccine to individuals previously infected by SARS-CoV-2 boosted all humoral and T cell responses measured, with strong correlations between T helper and antibody immunity. Neutralizing responses were increased in both potency and breadth, with distinctive capacity to neutralize emerging variant strains. Our results highlight the importance of vaccinating uninfected and previously-infected individuals and shed new light into the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support to spacing the doses of two-vaccine regimens to vaccinate a larger pool of the population in the context of vaccine scarcity against SARS-CoV-2.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Alexandra Tauzin", - "author_inst": "CRCHUM" - }, - { - "author_name": "Manon Nayrac", - "author_inst": "CRCHUM" - }, - { - "author_name": "Mehdi Benlarbi", - "author_inst": "CRCHUM" - }, - { - "author_name": "Shang Yu Gong", - "author_inst": "CRCHUM" - }, - { - "author_name": "Romain Gasser", - "author_inst": "CRCHUM" - }, - { - "author_name": "Guillaume Beaudoin-Bussieres", - "author_inst": "CRCHUM" - }, - { - "author_name": "Nathalie Brassard", - "author_inst": "CRCHUM" - }, - { - "author_name": "Annemarie Laumaea", - "author_inst": "CRCHUM" - }, - { - "author_name": "Dani Vezina", - "author_inst": "CRCHUM" - }, - { - "author_name": "Jeremie Prevost", - "author_inst": "CRCHUM" - }, - { - "author_name": "Sai Priya Anand", - "author_inst": "CRCHUM" - }, - { - "author_name": "Catherine Bourassa", - "author_inst": "CRCHUM" - }, - { - "author_name": "Gabrielle Gendron-Lepage", - "author_inst": "CRCHUM" - }, - { - "author_name": "Halima Medjahed", - "author_inst": "CRCHUM" - }, - { - "author_name": "Guillaume Goyette", - "author_inst": "CRCHUM" - }, - { - "author_name": "Julia Niessl", - "author_inst": "CRCHUM" - }, - { - "author_name": "Olivier Tastet", - "author_inst": "CRCHUM" - }, - { - "author_name": "Laurie Gokool", - "author_inst": "CRCHUM" - }, - { - "author_name": "Chantal Morrisseau", - "author_inst": "CRCHUM" - }, - { - "author_name": "Pascale Arlotto", - "author_inst": "CRCHUM" - }, - { - "author_name": "Leonidas Stamatatos", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Andrew T McGuire", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Catherine Larochelle", - "author_inst": "CRCHUM" - }, - { - "author_name": "Pradeep Uchil", - "author_inst": "Yale" - }, - { - "author_name": "Maolin Lu", - "author_inst": "Yale" - }, - { - "author_name": "Walther Mothes", - "author_inst": "Yale" - }, - { - "author_name": "Gaston De Serres", - "author_inst": "INSPQ" - }, - { - "author_name": "Sandrine Moreira", - "author_inst": "LSPQ" - }, - { - "author_name": "Michel Roger", - "author_inst": "LSPQ" - }, - { - "author_name": "Jonathan Richard", - "author_inst": "CRCHUM" - }, - { - "author_name": "Valerie Martel-Laferriere", - "author_inst": "CRCHUM" - }, - { - "author_name": "Ralf Duerr", - "author_inst": "NYU" - }, - { - "author_name": "Cecile Tremblay", - "author_inst": "CRCHUM" - }, - { - "author_name": "Daniel E Kaufmann", - "author_inst": "CRCHUM" - }, - { - "author_name": "Andres Finzi", - "author_inst": "CRCHUM" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.18.435945", "rel_title": "Myocarditis in naturally infected pets with the British variant of COVID-19", @@ -884485,6 +887552,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.13.21253527", + "rel_title": "PD-1highCXCR5-CD4+ Peripheral Helper T (Tph) cells Promote Tissue-Homing Plasmablasts in COVID-19", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253527", + "rel_abs": "A dysregulated immune response against coronavirus-2 (SARS-CoV-2) plays a critical role in the outcome of patients with coronavirus disease 2019 (COVID-19). A significant increase in circulating plasmablasts is characteristic of COVID-19 though the underlying mechanisms and its prognostic implications are not known. Here, we demonstrate that in the acute phase of COVID-19, activated PD-1highCXCR5-CD4+ T cells, peripheral helper T cells, (Tph) are significantly increased and promote inflammatory tissue-homing plasmablasts in patients with stable but not severe COVID-19. Analysis of scRNA-seq data revealed that plasmablasts in stable patients express higher levels of tissue-homing receptors including CXCR3. The increased Tph cells exhibited \"B cell help\" signatures similar to that of circulating T follicular helper (cTfh) cells and promoted B cell differentiation in vitro. Compared with cTfh cells, Tph cells produced more IFN{gamma}, inducing tissue-homing chemokine receptors on plasmablasts. Finally, expansion of activated Tph cells was correlated with the frequency of CXCR3+ plasmablasts in the acute phase of patients with stable disease. Our results demonstrate a novel role for Tph cells in acute viral immunity by inducing ectopic, antibody secreting plasmablasts.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hiromitsu Asashima", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Subhasis Mohanty", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Michela Comi", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "William E Ruff", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kenneth B Hoehn", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Patrick Wong", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Inessa Cohen", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Sarah Coffey", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Khadir Raddassi", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Omkar Chaudhary", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Avraham Unterman", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Brinda Emu", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Steven H Kleinstein", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Ruth R Montgomery", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Charles S Dela Cruz", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Naftali Kaminski", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Albert C Shaw", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "David A Hafler", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Tomokazu S Sumida", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.15.21253619", "rel_title": "COVID-19 with early neurological and cardiac thromboembolic phenomena--timeline of incidence and clinical features", @@ -885045,49 +888207,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.15.21253608", - "rel_title": "Quantitative Comparison of SARS-CoV-2 Nucleic Acid Amplification Test and Antigen Testing Algorithms: A Decision Analysis Simulation Model", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253608", - "rel_abs": "BackgroundAntigen tests for SARS-CoV-2 offer advantages over nucleic acid amplification tests (NAATs, such as RT-PCR), including lower cost and rapid return of results, but show reduced sensitivity. Public health organizations continue to recommend different strategies for utilizing NAATs and antigen tests in various settings. There has not yet been a quantitative comparison of the expected performance of these strategies.\n\nMethodsWe utilized a decision analysis approach to simulate the expected outcomes of six algorithms for implementing NAAT and antigen testing, analogous to testing strategies recommended by public health organizations. Each algorithm was simulated 50,000 times for four SARS-CoV-2 infection prevalence levels ranging from 5% to 20% in a population of 100000 persons seeking testing. Primary outcomes were number of missed cases, number of false-positive diagnoses, and total test volumes. Outcome medians and 95% uncertainty ranges (URs) were reported.\n\nResultsAlgorithms that use NAATs to confirm all negative antigen results minimized missed cases but required high NAAT capacity: 92,200 (95% UR: 91,200-93,200) tests (in addition to 100,000 antigen tests) at 10% prevalence. Substituting repeat antigen testing in lieu of NAAT confirmation of all initial negative antigen tests resulted in 2,280 missed cases (95% UR: 1,507-3,067) at 10% prevalence. Selective use of NAATs to confirm antigen results when discordant with symptom status (e.g., symptomatic persons with negative antigen results) resulted in the most efficient use of NAATs, with 25 NAATs (95% UR: 13-57) needed to detect one additional case at 10% prevalence compared to exclusive use of antigen tests.\n\nConclusionsNo single SARS-CoV-2 testing algorithm is likely to be optimal across settings with different levels of prevalence and for all programmatic priorities; each presents a trade-off between prioritized outcomes and resource constraints. This analysis provides a framework for selecting setting-specific strategies to achieve acceptable balances and trade-offs between programmatic priorities and constraints.\n\nDisclaimerThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the U.S. Centers for Disease Control and Prevention.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Phillip P Salvatore", - "author_inst": "Centers for Disease Control and Prevention, Epidemic Intelligence Service, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - }, - { - "author_name": "Melisa M Shah", - "author_inst": "Centers for Disease Control and Prevention, Epidemic Intelligence Service, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - }, - { - "author_name": "Laura Ford", - "author_inst": "Centers for Disease Control and Prevention, Epidemic Intelligence Service, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - }, - { - "author_name": "Augustina Delaney", - "author_inst": "Centers for Disease Control and Prevention, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - }, - { - "author_name": "Christopher H Hsu", - "author_inst": "Centers for Disease Control and Prevention, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - }, - { - "author_name": "Jacqueline E Tate", - "author_inst": "Centers for Disease Control and Prevention, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - }, - { - "author_name": "Hannah L Kirking", - "author_inst": "Centers for Disease Control and Prevention, Coronavirus Disease 2019 (COVID-19) Response Team, Atlanta, Georgia, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.15.21253609", "rel_title": "Seroreactivity to SARS-CoV-2 in individuals attending a university campus in Bogota Colombia", @@ -886231,6 +889350,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.16.435705", + "rel_title": "Identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species", + "rel_date": "2021-03-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.435705", + "rel_abs": "Understanding how SARS-CoV-2 interacts with different mammalian angiotensin-converting enzyme II (ACE2) cell entry receptors elucidates determinants of virus transmission and facilitates development of vaccines for humans and animals. Yeast display-based directed evolution identified conserved ACE2 mutations that increase spike binding across multiple species. Gln42Leu increased ACE2-spike binding for human and four of four other mammalian ACE2s; Leu79Ile had a effect for human and three of three mammalian ACE2s. These residues are highly represented, 83% for Gln42 and 56% for Leu79, among mammalian ACE2s. The above findings can be important in protecting humans and animals from existing and future SARS-CoV-2 variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pete Heinzelman", + "author_inst": "UW-Madison" + }, + { + "author_name": "Jonathan Greenhalgh", + "author_inst": "University of Wisconsin--Madison" + }, + { + "author_name": "Philip A Romero", + "author_inst": "UW-Madison" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.03.16.434488", "rel_title": "SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2", @@ -887195,45 +890341,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.16.435601", - "rel_title": "Cluster Analysis of SARS-CoV-2 Gene using Deep Learning Autoencoder: Gene Profiling for Mutations and Transitions", - "rel_date": "2021-03-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.435601", - "rel_abs": "We report on a method for analyzing the variant of coronavirus genes using autoencoder. Since coronaviruses have mutated rapidly and generated a large number of genotypes, an appropriate method for understanding the entire population is required. The method using autoencoder meets this requirement and is suitable for understanding how and when the variants emarge and disappear. For the over 30,000 SARS-CoV-2 ORF1ab gene sequences sampled globally from December 2019 to February 2021, we were able to represent a summary of their characteristics in a 3D plot and show the expansion, decline, and transformation of the virus types over time and by region. Based on ORF1ab genes, the SARS-CoV-2 viruses were classified into five major types (A, B, C, D, and E in the order of appearance): the virus type that originated in China at the end of 2019 (type A) practically disappeared in June 2020; two virus types (types B and C) have emerged in the United States and Europe since February 2020, and type B has become a global phenomenon. Type C is only prevalent in the U.S. and is suspected to be associated with high mortality, but this type also disappeared at the end of June. Type D is only found in Australia. Currently, the epidemic is dominated by types B and E.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jun Miyake", - "author_inst": "Osaka University" - }, - { - "author_name": "Takaaki Sato", - "author_inst": "Department of Material and Life Science, Graduate School of Engineering, Osaka University" - }, - { - "author_name": "Shunsuke Baba", - "author_inst": "Department of Material and Life Science, Graduate School of Engineering, Osaka University" - }, - { - "author_name": "Hayato Nakamura", - "author_inst": "Department of Material and Life Science, Graduate School of Engineering, Osaka University" - }, - { - "author_name": "Hirohiko Niioka", - "author_inst": "Osaka University Institute for Datability Science" - }, - { - "author_name": "Yoshihisa Nakazawa", - "author_inst": "Hitz Research Alliance Laboratory, Graduate School of Engineering, Osaka University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.15.435496", "rel_title": "Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain", @@ -888457,6 +891564,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.11.21253404", + "rel_title": "COVID-19 Underreporting and its Impact on Vaccination Strategies", + "rel_date": "2021-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253404", + "rel_abs": "We present a novel methodology for the stable rate estimation of hospitalization and death related to the Corona Virus Disease 2019 (COVID-19) using publicly available reports from various distinct communities. These rates are then used to estimate underreported infections on the corresponding areas by making use of reported daily hospitalizations and deaths. The impact of underreporting infections on vaccination strategies is estimated under different disease-transmission scenarios using a Susceptible-Exposed-Infective-Removed-like (SEIR) epidemiological model.\n\nOne sentence SummaryUsing a novel methodology, we estimate COVID-19 underreporting from public data, quantifying its impact on vaccination.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vinicius V. L. Albani", + "author_inst": "Universidade Federal de Santa Catarina" + }, + { + "author_name": "Jennifer Loria", + "author_inst": "Instituto Nacional de Matematica Pura e Aplicada and Universidad de Costa Rica" + }, + { + "author_name": "Eduardo Massad", + "author_inst": "Fundacao Getulio Vargas" + }, + { + "author_name": "Jorge P. Zubelli", + "author_inst": "Khalifa University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253000", "rel_title": "Novel highly divergent SARS-CoV-2 lineage with the Spike substitutions L249S and E484K", @@ -889433,77 +892571,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.13.435256", - "rel_title": "Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex", - "rel_date": "2021-03-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.13.435256", - "rel_abs": "Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA-protein crosslinking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3-segment of the product-RNA generated by backtracking extrudes through the RdRp NTP-entry tunnel, that a mismatched nucleotide at the product-RNA 3-end frays and enters the NTP-entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.\n\nSignificance StatementThe COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome is replicated and transcribed by its RNA-dependent RNA polymerase (RdRp), which is the target for antivirals such as remdesivir. We use a combination of approaches to show that backtracking (backwards motion of the RdRp on the template RNA) is a feature of SARS-CoV-2 replication/transcription. Backtracking may play a critical role in proofreading, a crucial process for SARS-CoV-2 resistance against many antivirals.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Brandon Malone", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "James Chen", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Qi Wang", - "author_inst": "D. E. Shaw Research" - }, - { - "author_name": "Eiiza Llewellyn", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Young Joo Choi", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Paul Dominic B. Olinares", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Xinyun Cao", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Carolina Hernandez", - "author_inst": "New York Structural Biology Center" - }, - { - "author_name": "Edward T. Eng", - "author_inst": "New York Structural Biology Center" - }, - { - "author_name": "Brian T. Chait", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "David E. Shaw", - "author_inst": "D. E. Shaw Research" - }, - { - "author_name": "Robert Landick", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Seth A. Darst", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Elizabeth A. Campbell", - "author_inst": "The Rockefeller University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.13.435221", "rel_title": "Clomipramine suppresses ACE2-mediated SARS-CoV-2 entry", @@ -890791,6 +893858,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.12.21253484", + "rel_title": "Limits of lockdown: characterising essential contacts during strict physical distancing", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253484", + "rel_abs": "COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Amy C Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Leon Danon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hannah Christensen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Northstone", + "author_inst": "University of Bristol" + }, + { + "author_name": "Daniel Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Trickey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gibran Hemani", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Sauchelli", + "author_inst": "NIHR Bristol Biomedical Research Centre, University of Bristol" + }, + { + "author_name": "Adam Finn", + "author_inst": "University of Bristol" + }, + { + "author_name": "Nicholas J Timpson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253493", "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 among Health Care Workers in Kenya", @@ -891759,45 +894889,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.08.21253164", - "rel_title": "COVID-19 lockdowns may reduce resistance genes diversity in the human microbiome and the need for antibiotics", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253164", - "rel_abs": "2.Recently, much attention has been paid to the COVID-19 pandemic, yet bacterial resistance to antibiotics remains a serious and unsolved public health problem, which kills thousands of people annually, being an insidious and silent pandemic. In this study, we explored the idea of confinement and the tightening of the hygiene measures to contain the spreading of coronavirus, to simulate the effect that it has on lowering the spreading of pathogenic bacteria in a human network, and on the need to use antibiotics. For that, we used computational biology to generate simulations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Joao S Rebelo", - "author_inst": "cE3c - FCUL" - }, - { - "author_name": "Celia PF Domingues", - "author_inst": "cE3c - FCUL" - }, - { - "author_name": "Francisco Dionisio", - "author_inst": "cE3c - FCUL" - }, - { - "author_name": "Manuel Carmo Gomes", - "author_inst": "FCUL" - }, - { - "author_name": "Ana Botelho", - "author_inst": "INIAV" - }, - { - "author_name": "Teresa Nogueira", - "author_inst": "INIAV" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.08.21253075", "rel_title": "Evolutionary and phenotypic characterization of spike mutations in a new SARS-CoV-2 Lineage reveals two Variants of Interest", @@ -892793,6 +895884,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253260", + "rel_title": "Analytical and clinical performances of a SARS-CoV-2 S-RBD IgG assay: comparison with neutralization titers", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253260", + "rel_abs": "BackgroundSARS-CoV-2 serology presents an important role in understanding the virus epidemiology, in vaccine prioritization strategies and in convalescent plasma therapy. Immunoassays performances have to be accurately evaluated and correlated with neutralizing antibodies to be used as a surrogate measure of neutralizing activity. We investigate the analytical and clinical performance of a SARS-CoV-2 RBD IgG assay, automated on a high throughput platform, and the correlation of the antibodies (Ab) levels with the plaque reduction neutralization (PRNT50) Ab titers.\n\nMethodsA series of 546 samples were evaluated by SARS-CoV-2 RBD IgG assay (Snibe diagnostics), including 171 negative and 168 positive SARS-CoV-2 subjects and a further group of 207 subjects of the COVID-19 family clusters follow-up cohort.\n\nResultsAssay precision was acceptable at low and medium levels; linearity was excellent in all the measurement range. Considering specimens collected after 14 days post symptoms onset, overall sensitivity and specificity were 99.0% and 92.5%, respectively. A total of 281 leftover samples results of the PRNT50 test were available. An elevated correlation was obtained between the SARS-CoV-2 RBD IgG assay and the PRNT50 titer at univariate (rho = 0.689) and multivariate (rho = 0.712) analyses.\n\nConclusionsSARS-CoV-2 S-RBD IgG assay achieves elevated analytical and clinical performances, and a strong correlation with sera neutralization activity.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrea Padoan", + "author_inst": "university of padova" + }, + { + "author_name": "Francesco Bonfante", + "author_inst": "Istituto Zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Chiara Cosma", + "author_inst": "Department of Laboratory medicine, University-hospital of padova, italy" + }, + { + "author_name": "Costanza Di Chiara", + "author_inst": "Department of women's and children's health, university of padova" + }, + { + "author_name": "Laura Sciacovelli", + "author_inst": "Department of Laboratory Medicine, University-Hospital of Padova" + }, + { + "author_name": "Matteo Pagliari", + "author_inst": "Istituto zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Alessio Bortolami", + "author_inst": "Istituto zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Paola Costenaro", + "author_inst": "Department for Women's and Children's Health, University of Padova, Italy" + }, + { + "author_name": "Giulia Musso", + "author_inst": "Department of Laboratory Medicine, University-Hospital of Padova, Italy" + }, + { + "author_name": "Daniela Basso", + "author_inst": "University of Padova" + }, + { + "author_name": "Mario Plebani", + "author_inst": "University of Padova" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21252711", "rel_title": "An In-House ELISA for SARS-CoV-2 RBD uncovers elevatedimmune response at higher altitudes", @@ -893685,33 +896835,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.03.10.21253244", - "rel_title": "The impact of the UK's first COVID-19 lockdown on rates of violence and aggression on psychiatric inpatient wards", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253244", - "rel_abs": "AimsInpatient life in UK mental health hospitals was profoundly altered during the first wave of the COVID-19 pandemic. We analysed whether these changes impacted the rate of violent and aggressive incidents across acute adult wards and psychiatric intensive care units in a South London NHS Mental Health Trust during the first UK lockdown.\n\nMethodsWe used an interrupted time series analysis to assess whether the rate of violent and aggressive incidents changed during the lockdown period from 23rd March 2020 to 15th June 2020. We used a quasi-poisson general additive model to model the weekly rate of violent incidents as a function of a seasonal trend, time trend, and impact of lockdown, using data from 1st January 2017 to 27th September 2020.\n\nResultsThere was a 35% increase in the rate of incidents of violence and aggression [IR = 1.35, 95% CI: 1.15 - 1.58, p < 0.001] between March 23rd 2020 and June 15th 2020. In addition, there was strong evidence of temporal (p < 0.001) and seasonal trends (p < 0.001).\n\nConclusionsOur results suggest that restrictions to life increased the rate of violent incidents on the mental health wards studied here.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "James Payne-Gill", - "author_inst": "South London & Maudsley" - }, - { - "author_name": "Corin Whitfield", - "author_inst": "South London & Maudsley" - }, - { - "author_name": "Alison Beck", - "author_inst": "South London & Maudsley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.03.10.21253266", "rel_title": "Acceptability of contact management and care of simple cases of COVID-19 at home: a mixed-method study in Senegal", @@ -894619,6 +897742,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253322", + "rel_title": "A Dynamical Map to Describe Covid-19 Epidemics", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253322", + "rel_abs": "Nonlinear dynamics perspective is an interesting approach to describe COVID-19 epidemics, providing information to support strategic decisions. This paper proposes a dynamical map to describe COVID-19 epidemics based on the classical susceptible-exposed-infected-recovered (SEIR) differential model, incorporating vaccinated population. On this basis, the novel map represents COVID-19 discrete-time dynamics by adopting three populations: infected, cumulative infected and vaccinated. The map promotes a dynamical description based on algebraic equations with a reduced number of variables and, due to its simplicity, it is easier to perform parameter adjustments. In addition, the map description allows analytical calculations of useful information to evaluate the epidemic scenario, being important to support strategic decisions. In this regard, it should be pointed out the estimation of the number death cases, infectious rate and the herd immunization point. Numerical simulations show the model capability to describe COVID-19 dynamics, capturing the main features of the epidemic evolution. Reported data from Germany, Italy and Brazil are of concern showing the map ability to describe different scenario patterns that include multi-wave and plateaus behaviors. The effect of vaccination is analyzed considering different campaign strategies, showing its importance to control the epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Eduardo Villela M. dos Reis", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Marcelo A. Savi", + "author_inst": "Universidade Federal do Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21253259", "rel_title": "Evaluation of Measles Surveillance System amidst Covid 19 pandemic in Asutifi North District, Ahafo Region, Ghana.", @@ -895227,93 +898373,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.11.21253142", - "rel_title": "Evolution of antibodies against SARS-CoV-2 over seven months: experience of the Nationwide Seroprevalence ENE-COVID Study in Spain", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253142", - "rel_abs": "ObjectivesTo analyse temporal trends in SARS-CoV-2 anti-nucleocapsid IgG throughout the four rounds of the nationwide seroepidemiologic study ENE-COVID (April-November 2020), and to compare the fourth-round results of two immunoassays detecting antibodies against nucleocapsid and to S protein receptor-binding domain (RBD).\n\nMethodsA chemiluminescent microparticle immunoassay (CMIA) was offered to all participants in the first three rounds (Abbott; anti-nucleocapsid IgG). In the fourth round we offered this test and a chemiluminescence immunoassay (CLIA) (Beckman; anti-RBD IgG) to i) a randomly selected sub-cohort, ii) participants who were IgG-positive in any of the three first rounds; and iii) participants who were IgG-positive in the fourth round by point-of-care immunochromatography.\n\nResultsImmunoassays involving 10,153 participants (82.2% of people invited to donate samples) were performed in the fourth round. A total of 2595 participants (35.1% of participants with immunoassay results in the four rounds) were positive for anti-nucleocapsid IgG in at least one round. Anti-nucleocapsid IgG became undetectable in 43.3% of participants with positive first-round results. Pneumonia was more frequent in participants with anti-nucleocapsid IgG in all four rounds (11.2%) than those in which IgG became undetectable (2.4%).\n\nIn fourth round, anti-nucleocapsid and anti-RBD IgG were detected in 5.5% and 5.4% participants of the randomly selected sub-cohort, and in 26.6% and 25.9% participants with at least one previous positive result, respectively. Agreement between techniques was 90.3% (kappa: 0.72).\n\nConclusionsThe response of IgG to SARS-CoV-2 is heterogeneous and conditioned by infection severity. A substantial proportion of the SARS-CoV-2 infected population may have negative serologic results in the post-infection months.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Mayte Perez-Olmeda", - "author_inst": "National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain" - }, - { - "author_name": "Jose M Saugar", - "author_inst": "National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain" - }, - { - "author_name": "Aurora Fernandez-Garcia", - "author_inst": "National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. Consortium for Biomedical Research in Epidemiology and Public Healt" - }, - { - "author_name": "Beatriz Perez-Gomez", - "author_inst": "Instituto de Salud Carlos III" - }, - { - "author_name": "Marina Pollan", - "author_inst": "Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP). National Centre for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain" - }, - { - "author_name": "Ana Avellon", - "author_inst": "National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. Consortium for Biomedical Research in Epidemiology and Public Heal" - }, - { - "author_name": "Roberto Pastor-Barriuso", - "author_inst": "National Centre for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain. Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)" - }, - { - "author_name": "Nerea Fernandez-de Larrea", - "author_inst": "Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP). National Centre for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain" - }, - { - "author_name": "Mariano Martin", - "author_inst": "Deputy Directorate of Information Technologies, Ministry of Health, Madrid, Spain" - }, - { - "author_name": "Israel Cruz", - "author_inst": "National School of Public Health, Instituto de Salud Carlos III, Madrid, Spain" - }, - { - "author_name": "Jose L Sanmartin", - "author_inst": "Deputy Directorate of Information Technologies, Ministry of Health, Madrid, Spain" - }, - { - "author_name": "Giovanni Fedele", - "author_inst": "National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain." - }, - { - "author_name": "Jose Leon Paniagua", - "author_inst": "Instituto de Salud Carlos III, Madrid, Spain." - }, - { - "author_name": "Juan F Munoz-Montalvo", - "author_inst": "Deputy Directorate of Information Technologies, Ministry of Health, Madrid, Spain" - }, - { - "author_name": "Faustino Blanco", - "author_inst": "General Secretary of Health, Ministry of Health, Madrid, Spain." - }, - { - "author_name": "Raquel Yotti", - "author_inst": "Instituto de Salud Carlos III, Madrid, Spain." - }, - { - "author_name": "Jesus Oteo-Iglesias", - "author_inst": "Instituto de Salud Carlos III" - }, - { - "author_name": "- ENE-COVID Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.10.21253330", "rel_title": "Characterizing the COVID-19 illness experience to inform the study of post-acute sequalae and recovery: a qualitative study", @@ -896149,6 +899208,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.11.21253367", + "rel_title": "SARS-CoV-2 specific immune-signature in direct contacts of COVID-19 cases protect them from contracting disease: A Retrospective Study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253367", + "rel_abs": "The response to SARS-CoV-2 is largely impacted by the level of exposure and the status of immunity. The nature of protection shown by direct contacts of COVID-19 positive patients is quite intriguing to note. We aimed to study the immune differences reinforcing contact individuals in circumventing the disease. Our observation showed direct contacts of PCR positive patients developed elevated neutralizing antibody titres and cytokine levels. On the other hand, single cell data revealed differential usage of V(D)J genes and unique BCR clonotypes imparting protective immune signatures.\n\nTopicsserologic tests, immunoglobulin a, immunoglobulin g, immunoglobulin m, antibody titre; cytokine levels; virus neutralization; V(D)J sequencing; BCR clonotypes", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sunil K. Raghav", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Kaushik Sen", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Arup Ghosh", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Sudeshna Datta", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Abdul Ahad", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Atimukta Jha", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Sanchari Chatterjee", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Sandhya Suranjika", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Soumya Sengupta", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Gargee Bhattacharya", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Omprakash Shriwas", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Kiran Avula", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Jayasingh Kshatri", + "author_inst": "ICMR-Regional Medical Research Center" + }, + { + "author_name": "Punit Prasad", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Ajay K. Parida", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.09.21253218", "rel_title": "An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status", @@ -896973,33 +900107,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.11.21253431", - "rel_title": "Prediction of severe COVID-19 cases requiring a ventilator in Tokyo, Japan", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253431", - "rel_abs": "BackgroundTo avoid exhaustion of medical resources by COVID-19, policy-makers must predict care needs, specifically the proportion of severe cases likely to need ventilator care.\n\nObjectiveThis study was designed to use a statistical model to elucidate dynamics of severe cases in Tokyo and to discuss the timing of effective policy activation.\n\nMethodsThe study extended from April 27 through October 18, 2020 in Japans Tokyo Metropolitan area. Medical exhaustion was defined as use of more than half of the ventilator capacity available before the COVID-19 outbreak. We regressed the number of severe cases on the newly onset patients of more than 14 days prior. As earlier research indicated, the COVID-19 severity changed at the end of May. Therefore, we added dummy variables to reflect changing severity from June and its product with newly onset patients as the explanatory variable. Then we calculated the threshold using R(t): R(t)=0.99 for the number of patients 14 days prior was used as a threshold at which strong countermeasures should be activated to keep to avoid medical exhaustion.\n\nResultsThe critical number signaling medical exhaustion in Tokyo was defined as 655 cases. We selected 15, 30, 60 and 90 days prior as explanatory variables for explaining the number of severe cases. A coefficient of determination larger than 0.95 was inferred as indicating good fit. The threshold was estimated as more than 4500 cases for R(t)=1.1 and monotonically decreasing by R(t) to be 600 cases for R(t)=2.5.\n\nDiscussion and ConclusionResults showed that newly onset patients reported more than 14 days prior can explain the number of severe cases very well. We also confirmed the threshold number of patients 14 days prior by R(t) for which strong countermeasures should be activated to avoid medical exhaustion with R(t)=0.99. This method is expected to be useful for countermeasure activation policies for Tokyo.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junko Kurita", - "author_inst": "Tokiwa University, Ibaraki, Japan" - }, - { - "author_name": "Tamie Sugawara", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - }, - { - "author_name": "Yasushi Ohksa", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.12.21253452", "rel_title": "Google Trends as a method to predict new COVID-19 cases", @@ -897802,6 +900909,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.11.434841", + "rel_title": "Antibody responses to SARS-CoV-2 mRNA vaccines are detectable in saliva", + "rel_date": "2021-03-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.11.434841", + "rel_abs": "Vaccines are critical for curtailing the COVID-19 pandemic (1, 2). In the USA, two highly protective mRNA vaccines are available: BNT162b2 from Pfizer/BioNTech and mRNA-1273 from Moderna (3, 4). These vaccines induce antibodies to the SARS-CoV-2 S-protein, including neutralizing antibodies (NAbs) predominantly directed against the Receptor Binding Domain (RBD) (1-4). Serum NAbs are induced at modest levels within [~]1 week of the first dose, but their titers are strongly boosted by a second dose at 3 (BNT162b2) or 4 weeks (mRNA-1273) (3, 4). SARS-CoV-2 is most commonly transmitted nasally or orally and infects cells in the mucosae of the respiratory and to some extent also the gastrointestinal tract (5). Although serum NAbs may be a correlate of protection against COVID-19, mucosal antibodies might directly prevent or limit virus acquisition by the nasal, oral and conjunctival routes (5). Whether the mRNA vaccines induce mucosal immunity has not been studied. Here, we report that antibodies to the S-protein and its RBD are present in saliva samples from mRNA-vaccinated healthcare workers (HCW). Within 1-2 weeks after their second dose, 37/37 and 8/8 recipients of the Pfizer and Moderna vaccines, respectively, had S-protein IgG antibodies in their saliva, while IgA was detected in a substantial proportion. These observations may be relevant to vaccine-mediated protection from SARS-CoV-2 infection and disease.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Thomas J. Ketas", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Devidas Chaturbhuj", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Victor Cruz Portillo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Erik Francomano", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Encouse Golden", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Sharanya Chandrasekhar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Gargi Debnath", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Randy Diaz Tapia", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Anila Yasmeen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Wilhem Leconet", + "author_inst": "Genmab" + }, + { + "author_name": "Zhen Zhao", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Philip J.M. Brouwer", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Melissa M. Cushing", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Rogier Sanders", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Albert Cupo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Per Johan Klasse", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Silvia C. Formenti", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "John P. Moore", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.11.434937", "rel_title": "SARS-CoV-2 comprehensive receptor profiling: mechanistic insight to drive new therapeutic strategies", @@ -898466,49 +901660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.09.21253203", - "rel_title": "Antibody response to SARS-CoV-2 vaccination is extremely vivacious in subjects with previous SARS-CoV-2 infection", - "rel_date": "2021-03-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253203", - "rel_abs": "BackgroundThe SARS-CoV-2 pandemic calls for rapid actions, now principally oriented to a world-wide vaccination campaign.\n\nIn this study we verified if, in individuals with a previous SARS-CoV-2 infection, a single dose of mRNA vaccine would be immunologically equivalent to a full vaccine schedule in naive individuals.\n\nMethodsHealth care workers (184) with a previous SARS-CoV-2 infection were sampled soon before the second dose of vaccine and between 7 and 10 days after the second dose, the last sampling time was applied to SARS-CoV-2 naive individuals, too.\n\nAntibodies against SARS-CoV-2 were measured using Elecsys(R) Anti-SARS-CoV-2 S immunoassay.\n\nThe study was powered for non-inferiority. We used non parametric tests and Pearson correlation test to perform inferential analysis.\n\nResultsAfter a single vaccine injection, the median titer of specific antibodies in individuals with previous COVID-19 was 30,527 U/ml (IQR 19,992-39,288) and in subjects with previous SARS-CoV-2 asymptomatic infection was 19,367.5 U/ml (IQR 14,688-31,353) (P=0.032). Both results were far above the median titer in naive individuals after a full vaccination schedule: 1,974.5 U/ml (IQR 895-3,455) (P<0.0001). Adverse events after vaccine injection were more frequent after the second dose of vaccine (mean 0.95, 95%CI from 0.75 to 1.14 versus mean 1.91, 95%CI from 1.63 to 2.19)(P<0.0001) and in exposed compared to naive (mean 1.63; 95%CI from 1.28 to 1.98 versus mean 2.35; 95%CI from 1.87 to 2.82)(P=0.015).\n\nConclusionIn SARS-CoV-2 naturally infected individuals a single mRNA vaccine dose seems sufficient to reach immunity. Modifying current dosing schedules would speed-up vaccination campaigns.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Annapaola Callegaro", - "author_inst": "ASST Papa Giovanni XXIII" - }, - { - "author_name": "Daniela Borleri", - "author_inst": "ASST Papa Giovanni XXIII" - }, - { - "author_name": "Claudio Farina", - "author_inst": "ASST Papa Giovanni XXIII" - }, - { - "author_name": "Gavino Napolitano", - "author_inst": "ASST Papa Giovanni XXIII" - }, - { - "author_name": "Daniela Valenti", - "author_inst": "ASST Papa Giovanni XXIII" - }, - { - "author_name": "Marco Rizzi", - "author_inst": "ASST Papa Giovanni XXIII" - }, - { - "author_name": "Franco Maggiolo", - "author_inst": "ASST Papa Giovanni XXIII" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.10.432949", "rel_title": "Bromodomain and Extraterminal Protein Inhibitor, Apabetalone (RVX-208), Reduces ACE2 Expression and Attenuates SARS-CoV-2 Infection in vitro", @@ -899755,6 +902906,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.09.21252764", + "rel_title": "A High Rate of COVID-19 Vaccine Hesitancy Among Arabs: Results of a Large-scale Survey", + "rel_date": "2021-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21252764", + "rel_abs": "In this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns about side effects and distrust in healthcare policies, vaccine expedited production, published studies and vaccine producing companies. We also found that female participants, participants 30-59 year-old, those with no chronic diseases, those with lower-level of academic education, and those who do not know the type of vaccine authorized in their countries are more hesitant to receive COVID-19 vaccination. On the other hand, participants who regularly receive the influenza vaccine, health care workers, and those from countries with higher rates of COVID-19 infections showed more vaccination willingness. Interactive representation of our results is posted on our project website at https://mainapp.shinyapps.io/CVHAA.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eyad A. Qunaibi", + "author_inst": "Department of Pharmaceutical Sciences, Jerash Private University, Jerash, Jordan" + }, + { + "author_name": "Mohamed Helmy", + "author_inst": "Agency for Science, Research and Technology" + }, + { + "author_name": "Iman Basheti", + "author_inst": "Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan" + }, + { + "author_name": "Iyad Sultan", + "author_inst": "King Hussein Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.08.21253141", "rel_title": "COVID-19 is associated with multiple sclerosis exacerbations that are prevented by disease modifying therapies", @@ -900855,137 +904037,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.10.434840", - "rel_title": "Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike", - "rel_date": "2021-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.10.434840", - "rel_abs": "Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Pei Tong", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Avneesh Gautam", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Ian Windsor", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Meghan Travers", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Yuezhou Chen", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Nicholas Garcia", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Noah Whiteman", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Lindsay McKay", - "author_inst": "Department of Microbiology, Boston University School of Medicine, Boston, MA, USA" - }, - { - "author_name": "Felipe J.N. Lelis", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Shaghayegh Habibi", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Yongfei Cai", - "author_inst": "Laboratory of Molecular Medicine, Boston Childrens Hospital, Boston, MA, USA" - }, - { - "author_name": "Linda J. Rennick", - "author_inst": "The Center for Vaccine Research, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "W. Paul Duprex", - "author_inst": "The Center for Vaccine Research, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Kevin McCarthy", - "author_inst": "The Center for Vaccine Research, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Christy L. Lavine", - "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA" - }, - { - "author_name": "Teng Zuo", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Junrui Lin", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Adam Zuiani", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Jared Feldman", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Elizabeth A. MacDonald", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Blake M. Hauser", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Anthony Griffths", - "author_inst": "Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA" - }, - { - "author_name": "Michael S. Seaman", - "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Department of Microbiology, Cambridge, MA, USA" - }, - { - "author_name": "Bing Chen", - "author_inst": "Laboratory of Molecular Medicine, Boston Childrens Hospital, Boston, MA, USA" - }, - { - "author_name": "Donna Neuberg", - "author_inst": "Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA" - }, - { - "author_name": "Goran Bajic", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Laboratory of Molecular Medicine, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Stephen C. Harrison", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Laboratory of Molecular Medicine, Boston Childrens Hospital, Harvard Medical School, Howard Hughe" - }, - { - "author_name": "Duane R. Wesemann", - "author_inst": "Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.04.21252167", "rel_title": "Tocilizumab efficacy in COVID-19 patients is associated with respiratory severity-based stages", @@ -902213,6 +905264,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.08.21252839", + "rel_title": "Transmission of SARS-CoV-2 by children attending school. Interim report on an observational, longitudinal sampling study of infected children, contacts, and the environment", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252839", + "rel_abs": "BackgroundAssessing transmission of SARS-CoV-2 by children in schools is of critical importance to inform public health action. We assessed frequency of acquisition of SARS-CoV-2 by contacts of children with COVID-19 in schools and households, as well as the amount of virus shed into the air and onto fomites in both settings.\n\nMethodsCases of COVID-19 in children in London schools were identified via notification. Weekly sampling for 3-4 weeks and PCR testing for SARS-CoV-2 of immediate classroom contacts (the \"bubble\"), non-bubble school contacts, and household contacts was undertaken supported by genome sequencing, along with surface and air sampling in the school and home environment.\n\nResultsWithin schools, secondary transmission was not detected in 28 individual bubble contacts, representing 10 distinct bubble classes. Across 8 non-bubble classes, 3/62 pupils tested positive- all three were asymptomatic and tested positive in one setting on the same day, unrelated to the original index case. In contrast, the secondary attack rate in naive household contacts was 14.3% (5/35) rising to 19.1% (9/47) when considering all household contacts. Environmental contamination with SARS-CoV-2 was rare in schools, regardless of school type; fomite SARS-CoV-2 RNA was identified in 4/189 (2.1%) samples in bubble classrooms, 2/127 (1.6%) samples in non-bubble classrooms, and 5/130 (3.8%) samples in washrooms. This contrasted with fomites in households, where SARS-CoV-2 RNA was identified in 60/248 (24.2%) bedroom samples, 66/241 (27.4%) communal room samples, and 21/188 (11.2%) bathroom samples. Air sampling identified SARS-CoV-2 RNA in just 1/68 (1.5%) of school air samples, compared with 21/85 (24.7%) of air samples taken in homes.\n\nSummaryThe low levels of environmental contamination in schools are consistent with low transmission frequency and adequate levels of cleaning and ventilation in schools during the period of study. Secondary transmission in schools was rare. The high frequency of secondary transmission in households associated with evident viral shedding throughout the home suggests a need to improve advice to households with infection in children in order to prevent onward community spread by sibling and adult contacts. The data highlight that transmission from children is very likely to occur when precautions are reduced.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Rebecca Cordery", + "author_inst": "Public Health England" + }, + { + "author_name": "Lucy Reeves", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jie Zhou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aileen G. Rowan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patricia Watber", + "author_inst": "Imperial College London" + }, + { + "author_name": "Carolina Rosadas", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Andrew Crone", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marko Storch", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Freemont", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lucy Mosscrop", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alice Cowley", + "author_inst": "Public Health England" + }, + { + "author_name": "Gina Zelent", + "author_inst": "Public Health England" + }, + { + "author_name": "Kate Bisset", + "author_inst": "Public Health England" + }, + { + "author_name": "Holly LeBlond", + "author_inst": "Public Health England" + }, + { + "author_name": "Sadie Regmi", + "author_inst": "Public Health England" + }, + { + "author_name": "Christian Buckingham", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ramlah Junaideen", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nadia Abdulla", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joseph Eliahoo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Miranda Mindlin", + "author_inst": "Public Health England" + }, + { + "author_name": "Theresa Lamagni", + "author_inst": "Public Health England" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham P Taylor", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shiranee Sriskandan", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.08.21252200", "rel_title": "Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study", @@ -903165,105 +906327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2021.03.07.21253094", - "rel_title": "COVID-19 vaccine response in pregnant and lactating women: a cohort study", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.07.21253094", - "rel_abs": "BackgroundPregnant and lactating women were excluded from initial COVID-19 vaccine trials; thus, data to guide vaccine decision-making are lacking. We sought to evaluate the immunogenicity and reactogenicity of COVID-19 mRNA vaccination in pregnant and lactating women.\n\nMethods131 reproductive-age vaccine recipients (84 pregnant, 31 lactating, and 16 non-pregnant) were enrolled in a prospective cohort study at two academic medical centers. Titers of SARS-CoV-2 Spike and RBD IgG, IgA and IgM were quantified in participant sera (N=131), umbilical cord sera (N=10), and breastmilk (N=31) at baseline, 2nd vaccine dose, 2-6 weeks post 2nd vaccine, and delivery by Luminex, and confirmed by ELISA. Titers were compared to pregnant women 4-12 weeks from native infection (N=37). Post-vaccination symptoms were assessed. Kruskal-Wallis tests and a mixed effects model, with correction for multiple comparisons, were used to assess differences between groups.\n\nResultsVaccine-induced immune responses were equivalent in pregnant and lactating vs non-pregnant women. All titers were higher than those induced by SARS-CoV-2 infection during pregnancy. Vaccine-generated antibodies were present in all umbilical cord blood and breastmilk samples. SARS-CoV-2 specific IgG, but not IgA, increased in maternal blood and breastmilk with vaccine boost. No differences were noted in reactogenicity across the groups.\n\nConclusionsCOVID-19 mRNA vaccines generated robust humoral immunity in pregnant and lactating women, with immunogenicity and reactogenicity similar to that observed in non-pregnant women. Vaccine-induced immune responses were significantly greater than the response to natural infection. Immune transfer to neonates occurred via placental and breastmilk.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Kathryn J Gray", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Evan A Bordt", - "author_inst": "Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Caroline Atyeo", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA, PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA" - }, - { - "author_name": "Elizabeth Deriso", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Babatunde Akinwunmi", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Nicola Young", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Aranxta Medina Baez", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Lydia L Shook", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA, Vincent Center for Reproductive Biology, Massa" - }, - { - "author_name": "Dana Cvrk", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Kaitlyn James", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Rose De Guzman", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Sara Brigida", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Khady Diouf", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Ilona Goldfarb", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Lisa M Bebell", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, MGH Center for Global Health, and Harvard Medical School, Boston, MA" - }, - { - "author_name": "Lael M Yonker", - "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA" - }, - { - "author_name": "Alessio Fasano", - "author_inst": "Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA" - }, - { - "author_name": "Sayed A Rabi", - "author_inst": "Department of Cardiothoracic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Michal A Elovitz", - "author_inst": "Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Andrea G Edlow", - "author_inst": "Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massa" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.03.07.21253095", "rel_title": "Exploration of interethnic variation and repurposed drug efficacy in the treatment of SARS-CoV-2 Infection (COVID-19)", @@ -904651,6 +907714,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.06.434059", + "rel_title": "Structural Analysis of Spike Protein Mutations in an Emergent SARS-CoV-2 Variant from the Philippines", + "rel_date": "2021-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.434059", + "rel_abs": "A SARS-CoV-2 lineage designated as P.3 with multiple signature mutations in the Spike protein region was recently reported with cases from the Central Visayas Region of the Philippines. Whole genome sequencing revealed that the 33 samples under this lineage all contain the E484K, N501Y, and P681H Spike mutations previously found in variants of concern (VOC) such as the B.1.351, the P.1 and B.1.1.7 variants first reported in South Africa, Brazil, and the United Kingdom, respectively. The possible implications of the mutations found in the Spike protein of P.3 were analyzed for their potential effects on structure, stability, and molecular surface character. The analysis suggests that these mutations could significantly impact the possible interactions of the Spike protein with the ACE2 receptor and neutralizing antibodies, and warrants further clinical investigation. Some of the mutations affecting the N and C terminal domains may have effects on Spike monomer and trimer stability. This report provides insights on relevant targets for the design of future diagnostics, therapeutics and vaccines against the evolving SARS-CoV-2 variants in the Philippines.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Neil Andrew David Bascos", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Denise Mirano-Bascos", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Cynthia Palmes Saloma", + "author_inst": "University of the Philippines" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.08.434390", "rel_title": "Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses", @@ -905231,29 +908321,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.04.21252897", - "rel_title": "Predictive Capacity of COVID-19 Test Positivity Rate", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252897", - "rel_abs": "COVID-19 infections can spread silently, due to the simultaneous presence of significant numbers of both critical and asymptomatic to mild cases. While for the former reliable data are available (in the form of number of hospitalization and/or beds in intensive care units), this is not the case of the latter. Hence, analytical tools designed to generate reliable forecast and future scenarios, should be implemented to help decision makers planning ahead (e.g. medical structures and equipment). Previous work of one of the authors shows that an alternative formulation of the Test Positivity Rate (TPR), i.e. the proportion of the number of persons tested positive in a given day, exhibits a strong correlation with the number of patients admitted in hospital and intensive care units. In this paper, we investigate the lagged correlation structure between the newly defined TPR and the hospitalized people time series, exploiting a rigorous statistical model, the Seasonal Auto Regressive Moving Average (SARIMA). The rigorous analytical framework chosen, i.e. the stochastic processes theory, allowed for a reliable forecasting about 12 days ahead, of those quantities. The proposed approach would also allow decision makers to forecast the number of beds in hospitals and intensive care units needed 12 days ahead. The obtained results show that a standardized TPR index is a valuable metric to monitor the growth of the COVID-19 epidemic. The index can be computed on daily basis and it is probably one of the best forecasting tools available today for predicting hospital and intensive care units overload, being an optimal compromise between simplicity of calculation and accuracy.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Livio Fenga", - "author_inst": "Istat" - }, - { - "author_name": "Mauro Gaspari", - "author_inst": "University of Bologna" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.02.21252759", "rel_title": "Trends in SARS-CoV-2 detection during social relaxation measures over ten months of COVID-19 pandemic in the metropolitan area of Rio de Janeiro, Brazil", @@ -906209,6 +909276,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.04.21252658", + "rel_title": "SARS-CoV-2-specific T Cell Memory is Sustained in COVID-19 Convalescents for 8 Months with Successful Development of Stem Cell-like Memory T Cells", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252658", + "rel_abs": "Memory T cells contribute to rapid viral clearance during re-infection, but the longevity and differentiation of SARS-CoV-2-specific memory T cells remain unclear. We conducted direct ex vivo assays to evaluate SARS-CoV-2-specific CD4+ and CD8+ T cell responses in COVID-19 convalescents up to 254 days post-symptom onset (DPSO). Here, we report that memory T cell responses were maintained during the study period. In particular, we observed sustained polyfunctionality and proliferation capacity of SARS-CoV-2-specific T cells. Among SARS-CoV-2-specific CD4+ and CD8+ T cells detected by activation-induced markers, the proportion of stem cell-like memory T (TSCM) cells increased, peaking at approximately 120 DPSO. Development of TSCM cells was confirmed by SARS-CoV-2-specific MHC-I multimer staining. Considering the self-renewal capacity and multipotency of TSCM cells, our data suggest that SARS-CoV-2-specific T cells are long-lasting after recovery from COVID-19. The current study provides insight for establishing an effective vaccination program and epidemiological measurement.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jae Hyung Jung", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Min-Seok Rha", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Moa Sa", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Hee Kyoung Choi", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Ji Hoon Jeon", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Hyeri Seok", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Dae Won Park", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Su-Hyung Park", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Hye Won Jeong", + "author_inst": "Chungbuk National University College of Medicine" + }, + { + "author_name": "Won Suk Choi", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Eui-Cheol Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.04.21252528", "rel_title": "Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England", @@ -906909,41 +910035,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.05.21252719", - "rel_title": "COVID 19 Knowledge, Attitude, and Practice of the Healthcare Providers in United Arab Emirates", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252719", - "rel_abs": "BackgroundHealth care providers at increased risk of COVID-19 infection, inadequate knowledge and practice about COVID-19, and infection control may lead to increased risk of disease transmission. Early diagnosis and appropriate management of COVID 19 cases is important in preventing transmission and improving patient outcomes. The aim of this study was to assess the knowledge, altitude, and practice of healthcare providers in the United Arab Emirates toward COVID-19 and to examine its determinants.\n\nMethodA cross-sectional study was conducted to assess knowledge, attitudes, and practice (KAP) of Healthcare providers regarding COVID-19. The study was conducted during the COVID-19 pandemic from of April 11 to July 23, using an online anonymous self-administered questionnaire.\n\nResultsA total of 2371 healthcare providers responded to the survey. A total of 1091 worked in inpatient hospitals, 494 in primary health care, and 388 in emergency and ICU care. The overall performance score for all healthcare providers was as follows: 49.1%, poor score; 41.8 %, intermediate score; and 9.2%, good score with a mean result of 17.14. Factors leading to better overall performance scores were years of experience, pediatricians specialty, and specialists occupation. A total of 55.7% received good direct knowledge from all healthcare providers. In practice, 48% had good practices toward COVID-19. The overall attitude mean was 2.8, from a maximum score of 7, indicating a positive attitude toward COVID-19.\n\nConclusionsThe study-demonstrated gaps in specific aspects of knowledge and practice that should be focused on in future education and HCP awareness. A structured training program targeting all HCPs is needed to have good clinical knowledge and practice about COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Aljazia Khalfan Alghfeli", - "author_inst": "Ambulatory HealthCare services , SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Amal Abdul Rahim Al Zarouni", - "author_inst": "Ambulatory HealthCare services , SEHA, Abu Dhabi, United Arab Emirates" - }, - { - "author_name": "Hamda Musabbah Alremeithi", - "author_inst": "Ambulatory HealthCare services , SEHA, Abu Dhabi, United Arab Emirates," - }, - { - "author_name": "Roqayah Abdulla Almadhaani", - "author_inst": "Ambulatory HealthCare services , SEHA, Abu Dhabi, United Arab Emirates," - }, - { - "author_name": "Latifa Baynouna Alketbi", - "author_inst": "Ambulatory HealthCare services, SEHA, Abu Dhabi, United Arab Emirates," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.05.21252590", "rel_title": "First dose mRNA vaccination is sufficient to reactivate immunological memory to SARS-CoV-2 in ex COVID-19 subjects", @@ -908143,6 +911234,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.03.06.21253058", + "rel_title": "Low Dose Regimens of BNT162b2 mRNA Vaccine Exceed SARS-Cov-2 Correlate of Protection Estimates for Symptomatic Infection, in those 19-55 Years of Age", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.06.21253058", + "rel_abs": "BackgroundAn exact correlate of protection (CoP) is not yet known for symptomatic COVID-19. However, it is still possible to show a new vaccine regimen exceeds an unknown CoP, provided the regimen shows an equivalent or greater immunological response in all measured indicators relative to the immunological response elicited by a clinically proven vaccine regimen. The principle of comparing immunogenicity between regimens is what the FDA, EMA, and Access Consortium use to authorize modifications to the vaccines for VOC, without requiring clinical efficacy studies before implementation. It is logical to apply the same principle to modifying vaccine doses if the data is available to do so. A two dose 30ug regimen of BNT162b2 has strong clinical evidence of efficacy, as does a single dose 30 ug regimen. The immunological markers for these regimens have been profiled in detail in Phase 1 and 2 trial data.\n\nMethodsThe immunological profile (including binding antibodies, viral neutralization, cytokine profiles, and CD4 and 8 expansion) of the 2 dose 30ug BNT162b2 vaccine is examined, referred to as a highly conservative CoP estimate. The single dose 30 ug BNT162b2 immunological profile is also examined, a tenable CoP estimate. Data from the phase 1 and 2 trials are examined to see if alternate regimens meet or exceed the level of each immune marker measured, relative to the regimens listed above that have proven clinical efficacy.\n\nResultsFor adults aged 19-55, a 2 dose 10ug BNT162b2 regimen elicits a comparable response to the standard 30 ug dose for each immune indicator, with viral neutralization nearly an order of magnitude greater than the tenable CoP estimate. Similarly, a single dose 10ug BNT 162b2 regimen or a two dose 1ug BNT 162b2 regimen equals or exceeds the immunogenicity of a single 30 ug dose.\n\nConclusionIf it is reasonable for the FDA, EMA, and Access Consortium to approve vaccine modifications without a clinical trial based on immunogenicity data, three alternate low dose regimens were identified that meet the requirements of having comparable immunogenicity relative to a protocol that has proven clinical efficacy. Immediate implementation of these lower dose regimens should be considered as they have major implications in alleviating vaccine supply, as well as improving vaccine side effect profile, and lowering total cost of vaccination.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Graham Jurgens", + "author_inst": "Unaffiliated" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.06.21252964", "rel_title": "Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data", @@ -908835,89 +911945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.04.21252876", - "rel_title": "Multi-Omic Profiling of Plasma Identify Biomarkers and Pathogenesis of COVID-19 in Children", - "rel_date": "2021-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252876", - "rel_abs": "Although children usually develop less severe disease responding to COVID-19 than adults, little is known about the pathogenesis of COVID-19 in children. Herein, we conducted the plasma proteomic and metabolomic profiling of a cohort of COVID-19 pediatric patients with mild symptoms. Our data show that numerous proteins and metabolites involved in immune as well as anti-inflammatory processes were up-regulated on a larger scale in children than in adults. By developing a machine learning-based pipeline, we prioritized two sets of biomarker combinations, and identified 5 proteins and 5 metabolites as potential children-specific COVID-19 biomarkers. Further study showed that these identified metabolites not only inhibited the expression of pro-inflammatory factors, but also suppressed coronaviral replication, implying that these factors played key roles in protecting pediatric patients from both viral infection and infection-induced inflammation. Together, our study uncovered a protective mechanism responding to COVID-19 in children, and sheds light on potential therapies.\n\nTeaserAnti-inflammatory metabolites were highly elevated in the plasma of COVID-19 pediatric patients with mild symptoms.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Chong Wang", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Xufang Li", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Wanshan Ning", - "author_inst": "MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Li" - }, - { - "author_name": "Sitang Gong", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Fengxia Yang", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Chunxiao Fang", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Yu Gong", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Di Wu", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy Sciences, Wuhan, Hubei 430071, China" - }, - { - "author_name": "Muhan Huang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy Sciences, Wuhan, Hubei 430071, China" - }, - { - "author_name": "Yujie Gou", - "author_inst": "MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Li" - }, - { - "author_name": "Shanshan Fu", - "author_inst": "MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Li" - }, - { - "author_name": "Yujie Ren", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Ruyi Yang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy Sciences, Wuhan, Hubei 430071, China" - }, - { - "author_name": "Yang Qiu", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy Sciences, Wuhan, Hubei 430071, China" - }, - { - "author_name": "Yu Xue", - "author_inst": "MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Li" - }, - { - "author_name": "Yi Xu", - "author_inst": "Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510120, China" - }, - { - "author_name": "Xi Zhou", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy Sciences, Wuhan, Hubei 430071, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.03.21252872", "rel_title": "Longitudinal Analysis Reveals Distinct Antibody and Memory B Cell Responses in SARS-CoV2 Naive and Recovered Individuals Following mRNA Vaccination", @@ -910249,6 +913276,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.02.21252766", + "rel_title": "Self-reported symptoms, self-reported viral testing result and seroprevalence of SARS CoV-2 among a community sample in Essex County New Jersey: A brief report.", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252766", + "rel_abs": "BackgroundSARS-CoV-2, the virus that causes COVID-19, has rapidly spread globally beginning in late 2019. Early areas impacted by this pandemic in the US include Essex County, New Jersey. Beyond understanding the prevalence of active infections and deaths, it is important to understand the true burden of infection in the community, as indicated by seroprevalence of antibodies directed to the virus. Understanding the spectrum of disease is key to the effectiveness of primary prevention and control measures and the design of interventions against transmission of infection.\n\nMethodsWe utilized venue-based-sampling (VBS), implemented by a community partner, to sample members of the community in Essex County. In VBS the venues are randomized as a proxy for randomizing the attendees of the venues. We asked standard demographic questions, questions about symptoms and PCR testing and previous antibody testing. Participants provide a blood sample collected by finger stick with the Neoteryx Mitra Collection device. Samples were tested using a novel ELISA based approached developed by our team.\n\nResultsFrom September 15, 2020 to December 22, 2020, we conducted 92 randomly selected sampling events where we approached 1349 individuals for screening. Of these, 924 consented and had complete data for analysis. Only 6.5% of the sample reported any COVID-19 like symptoms while 45.9% had sought out a COVID-19 test. In total 13 (1.4%) participants received a positive SARS-CoV-2 PCR test result. While 33 participants (2.6%) sought a SARS-CoV-2 antibody test, only 0.5% of the sample reported a positive antibody result. Testing in this study identified 83 (9.0%) participants positive for SARS-CoV-2 antibodies.\n\nConclusionWe recruited a large sample of the population of Essex County, New Jersey using VBS, electronic surveys, novel sample collection and lab methods. Our findings suggest that the burden of SARS-Cov-2 is slightly more than six times than that suggested by PCR testing. This burden is higher than most estimates obtained through studies of remnant blood samples from hospitals (4.2%), samples from staff at a public-school system (2.9%), and residents of a California county recruited with targeted Facebook ads (1.5%). (9-11) Moreover, with only 6.5% of the sample reporting any COVID-19-like symptoms, our finding suggests that the number of asymptomatic persons may be close to 1.5 times greater than anyone reporting symptoms.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Henry F Raymond", + "author_inst": "School of Public Health, Rutgers University" + }, + { + "author_name": "Pratik Datta", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Rahul Ukey", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Peng Wang", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Richard J Martino", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Kristen D Krause", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Corey Rosmarin-DeStefano", + "author_inst": "North Jersey Community Research Initiative, Newark, NJ" + }, + { + "author_name": "Abraham Pinter", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Perry N Halkitis", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Maria L Gennaro", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.03.21252809", "rel_title": "Sharing positive changes made during COVID-19 national lockdown: a multi-method co-production study", @@ -910881,81 +913963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.03.21252706", - "rel_title": "Model-based evaluation of transmissibility and reinfection for the P.1 variant of the SARS-CoV-2", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252706", - "rel_abs": "O_TEXTBOXSummary boxO_ST_ABSWhat is already known about this topic?C_ST_ABSA new variant of concern of SARS-CoV-2 (P.1). emerged in the city of Manaus in November 2020. Since then, a sharp increase in COVID-19 cases in Manaus led to the collapse of the health system in early 2021.\n\nWhat is added by this report?Transmissibility and reinfection of P.1 were estimated using an epidemiological model-based fitting and public health data. The transmissibility is 2.5 times greater than the wild variant and reinfection probability is 6.4% on average.\n\nWhat are the implications for public health practice?This new variant poses a global threat due to its very high transmissibility. The results highlight the need to urgently monitor and contain its spread.\n\nC_TEXTBOX", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Renato M. Coutinho", - "author_inst": "Universidade Federal do ABC, Santo Andre, SP" - }, - { - "author_name": "Flavia Maria Darci Marquitti", - "author_inst": "Universidade Estadual de Campinas, Campinas, SP" - }, - { - "author_name": "Leonardo Souto Ferreira", - "author_inst": "Universidade Estadual Paulista, Sao Paulo, SP" - }, - { - "author_name": "Marcelo Eduardo Borges", - "author_inst": "Observatorio COVID-19 BR" - }, - { - "author_name": "Rafael Lopes Paixao da Silva", - "author_inst": "Universidade Estadual Paulista, Sao Paulo, SP" - }, - { - "author_name": "Otavio Canton", - "author_inst": "Universidade Estadual Paulista, Sao Paulo, SP" - }, - { - "author_name": "Tatiana P. Portella", - "author_inst": "Universidade de Sao Paulo, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Silas Poloni Lyra", - "author_inst": "Universidade Estadual Paulista, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Caroline Franco", - "author_inst": "Universidade Estadual Paulista, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Mateusz M. Plucinski", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Fernanda C. Lessa", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, USA" - }, - { - "author_name": "Antonio D Silva", - "author_inst": "Universidade Federal do Maranhao" - }, - { - "author_name": "Roberto A. Kraenkel", - "author_inst": "Universidade Estadual Paulista, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Maria Amelia S M Veras", - "author_inst": "Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo" - }, - { - "author_name": "Paulo Inacio Prado", - "author_inst": "Universidade de Sao Paulo, Sao Paulo, SP, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.03.21252812", "rel_title": "Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines", @@ -911983,6 +914990,77 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.05.434152", + "rel_title": "Scalable, Micro-Neutralization Assay for Qualitative Assessment of SARS-CoV-2 (COVID 19) Virus-Neutralizing Antibodies in Human Clinical Samples", + "rel_date": "2021-03-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.434152", + "rel_abs": "As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was expanding, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for a high-quality neutralization assay against SARS-CoV-2, a previously established fluorescence reduction neutralization assay (FRNA) against Middle East respiratory syndrome coronavirus (MERS-CoV) was modified and optimized. The SARS-CoV-2 FRNA provides a quantitative assessment of a large number of infected cells through use of a high-content imaging system. Because of this approach, and the fact that it does not involve subjective interpretation, this assay is more efficient and more accurate than other neutralization assays. In addition, the ability to set robust acceptance criteria for individual plates and specific test wells provided further rigor to this assay. Such agile adaptability avails use with multiple virus variants. By February 2021, the SARS-CoV-2 FRNA had been used to screen over 5,000 samples, including acute and convalescent plasma or serum samples and therapeutic antibody treatments, for SARS-CoV-2 neutralizing titers.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Michael R Holbrook", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Richard S Bennett", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Elena N Postnikova", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Janie Liang", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Robin Gross", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Dawn Gerhardt", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Shalamar Georgia-Clark", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Yingyun Cai", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Shuiqinq Yu", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Lindsay Marron", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Greg Kocher", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Steven Mazur", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Saurabh Dixit", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Vladimir V Lukin", + "author_inst": "Kearney" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.05.434119", "rel_title": "SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA", @@ -912683,65 +915761,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.03.04.433882", - "rel_title": "A novel conformational state for SARS-CoV-2 main protease", - "rel_date": "2021-03-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433882", - "rel_abs": "The SARS-CoV-2 main protease (Mpro) has a pivotal role in mediating viral genome replication and transcription of coronavirus, making it a promising target for drugs against Covid-19 pandemic. Here we present a crystal structure of Mpro disclosing new structural features of key regions of the enzyme. We show that the oxyanion loop, involved in substrate recognition and enzymatic activity, can adopt a new conformation, which is stable and significantly different from the known ones. In this new state the S1 subsite of the substrate binding region is completely reshaped and a new cavity near the S2 subsite is created. This new structural information expands the knowledge of the conformational space available to Mpro, paving the way for the design of novel classes of inhibitors specifically designed to target this unprecedented binding site conformation, thus enlarging the chemical space for urgent antiviral drugs against Covid-19 pandemic.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Emanuele Fornasier", - "author_inst": "University of Padua" - }, - { - "author_name": "Maria Ludovica Macchia", - "author_inst": "University of Padua" - }, - { - "author_name": "Gabriele Giachin", - "author_inst": "University of Padua" - }, - { - "author_name": "Alice Sosic", - "author_inst": "University of Padua" - }, - { - "author_name": "Matteo Pavan", - "author_inst": "University of Padua" - }, - { - "author_name": "Mattia Sturlese", - "author_inst": "University of Padua" - }, - { - "author_name": "Cristiano Salata", - "author_inst": "University of Padua" - }, - { - "author_name": "Stefano Moro", - "author_inst": "University of Padua" - }, - { - "author_name": "Barbara Gatto", - "author_inst": "University of Padua" - }, - { - "author_name": "Massimo Bellanda", - "author_inst": "University of Padua" - }, - { - "author_name": "Roberto Battistutta", - "author_inst": "University of Padua" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.04.433919", "rel_title": "UBXN3B Restricts Viral Pathogenesis by Maintaining Hematopoietic Homeostasis", @@ -913893,6 +916912,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.02.21252420", + "rel_title": "Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in an longitudinally sampled cohort of COVID-19 outpatients", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252420", + "rel_abs": "BackgroundSustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection.\n\nMethodsNinety-five outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models.\n\nResultsViral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI [≥] 25kg/m2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044).\n\nConclusionsWe demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Annukka A. R. Antar", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Tong Yu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Nora Pisnic", + "author_inst": "The Johns Hopkins University Bloomberg School of Medicine" + }, + { + "author_name": "Razvan Azamfirei", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jeffrey A Tornheim", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Diane M. Brown", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kate Kruczynski", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Justin P. Hardick", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Thelio Sewell", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Minyoung Jang", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Taylor Church", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Samantha N. Walch", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Carolyn Reuland", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Vismaya S. Bachu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kirsten Littlefield", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Han-Sol Park", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Rebecca L. Ursin", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Abhinaya Ganesan", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Oyinkansola Kusemiju", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Brittany Barnaba", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Curtisha Charles", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Michelle Prizzi", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jaylynn R. Johnstone", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Christine Payton", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Weiwei Dai", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joelle Fuchs", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Guido Massaccesi", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Derek T. Armstrong", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jennifer L. Townsend", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sara C. Keller", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Zoe O Demko", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Chen Hu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Mei-Cheng Wang", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Lauren M. Sauer", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba H. Mostafa", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jeanne C. Keruly", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shruti H. Mehta", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Sabra L. Klein", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Andrea L. Cox", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Christopher D. Heaney", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "David L. Thomas", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Paul W. Blair", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Yukari C. Manabe", + "author_inst": "The Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.01.21252243", "rel_title": "On the Environmental Determinants of COVID-19 Seasonality", @@ -914529,57 +917739,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.03.02.433604", - "rel_title": "Blockade of SARS-CoV-2 infection in-vitro by highly potent PI3K-\u03b1/mTOR/BRD4 inhibitor", - "rel_date": "2021-03-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.02.433604", - "rel_abs": "Pathogenic viruses like SARS-CoV-2 and HIV hijack the host molecular machinery to establish infection and survival in infected cells. This has led the scientific community to explore the molecular mechanisms by which SARS-CoV-2 infects host cells, establishes productive infection, and causes life-threatening pathophysiology. Very few targeted therapeutics for COVID-19 currently exist, such as remdesivir. Recently, a proteomic approach explored the interactions of 26 of 29 SARS-CoV-2 proteins with cellular targets in human cells and identified 67 interactions as potential targets for drug development. Two of the critical targets, the bromodomain and extra-terminal domain proteins (BETs): BRD2/BRD4 and mTOR, are inhibited by the dual inhibitory small molecule SF2523 at nanomolar potency. SF2523 is the only known mTOR PI3K-/(BRD2/BRD4) inhibitor with potential to block two orthogonal pathways necessary for SARS-CoV-2 pathogenesis in human cells. Our results demonstrate that SF2523 effectively blocks SARS-CoV-2 replication in lung bronchial epithelial cells in vitro, showing an IC50 value of 1.5 {micro}M, comparable to IC50 value of remdesivir (1.1 {micro}M). Further, we demonstrated that the combination of doses of SF2523 and remdesivir is highly synergistic: it allows for the reduction of doses of SF2523 and remdesivir by 25-fold and 4-fold, respectively, to achieve the same potency observed for a single inhibitor. Because SF2523 inhibits two SARS-CoV-2 driven pathogenesis mechanisms involving BRD2/BRD4 and mTOR signaling, our data suggest that SF2523 alone or in combination with remdesivir could be a novel and efficient therapeutic strategy to block SARS-CoV-2 infection and hence be beneficial in preventing severe COVID-19 disease evolution.\n\nOne Sentence SummaryEvidence of in silico designed chemotype (SF2523) targeting PI3K-/mTOR/BRD4 inhibits SARS-CoV-2 infection and is highly synergistic with remdesivir.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Arpan Acharya", - "author_inst": "Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center; Omaha, NE 68131, USA." - }, - { - "author_name": "Kabita Pandey", - "author_inst": "Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center; Omaha, NE 68131, USA." - }, - { - "author_name": "Michellie Thurman", - "author_inst": "Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center; Omaha, NE 68131, USA." - }, - { - "author_name": "Kishore B Challagundla", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Nebraska Medical Centre, Omaha, NE, 68131, USA" - }, - { - "author_name": "Kendra R Vann", - "author_inst": "Department of Pharmacology, University of Colorado School of Medicine; Aurora, CO 80045, USA." - }, - { - "author_name": "Tatiana G Kutateladze", - "author_inst": "Department of Pharmacology, University of Colorado School of Medicine; Aurora, CO 80045, USA" - }, - { - "author_name": "Guillermo A Morales", - "author_inst": "SignalRx Pharmaceuticals, Inc.; Cumming, GA 30041, USA." - }, - { - "author_name": "Donald L Durden", - "author_inst": "SignalRx Pharmaceuticals, Inc.; Cumming, GA 30041, USA; Division of Pediatric Hematology-Oncology, Department of Pediatrics, Moores Cancer Center, UC San Diego " - }, - { - "author_name": "Siddappa N Byrareddy", - "author_inst": "Department of Pharmacology and Experimental Neuroscience, Department of Biochemistry and Molecular Biology, Department of Genetics, Cell Biology, and Anatomy, U" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.03.02.432977", "rel_title": "Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly", @@ -916103,6 +919262,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252328", + "rel_title": "SARS-CoV-2 antibodies detected in human breast milk post-vaccination", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252328", + "rel_abs": "ImportanceThe SARS-CoV-2 pandemic has infected over a hundred million people worldwide, with almost 2.5 million deaths at the date of this publication. In the United States, Pfizer-BioNTech and Moderna vaccines were first administered to the public starting in December 2020, and no lactating women were included in the initial trials of safety/efficacy. Research on SARS-CoV-2 vaccination in lactating women and the potential transmission of passive immunity to the infant through breast milk is needed to guide patients, clinicians and policy makers during the worldwide effort to curb the spread of this virus.\n\nObjectiveTo determine whether SARS-CoV-2 specific immunoglobins are found in breast milk post-vaccination, and to characterize the time course and types of immunoglobulins present.\n\nDesignProspective cohort study\n\nSettingProvidence Portland Medical Center, Oregon, USA\n\nParticipantsSix lactating women who planned to receive both doses of the Pfizer-BioNTech or Moderna vaccine between December 2020 and January 2021. Breast milk samples were collected pre-vaccination and at 11 additional timepoints, with last sample at 14 days post 2nd dose of vaccine.\n\nExposureTwo doses of Pfizer-BioNTech or Moderna SARS-CoV-2 vaccine.\n\nMain Outcome(s) and Measure(s)Levels of SARS-CoV-2 specific IgA and IgG immunoglobulins in breast milk.\n\nResultsIn this cohort of 6 lactating women who received 2 doses of SARS-CoV-2 vaccine, we observed significantly elevated levels of SARS-CoV-2 specific IgG and IgA antibodies in breast milk beginning at Day 7 after the initial vaccine dose, with an IgG-dominant response.\n\nConclusions and RelevanceWe are the first to show that maternal vaccination results in SARS-CoV-2 specific immunoglobulins in breast milk that may be protective for infants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jill K Baird", + "author_inst": "Legacy Medical Group, Portland OR USA" + }, + { + "author_name": "Shawn M Jensen", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Walter J Urba", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Bernard A Fox", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Jason R Baird", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.26.21252555", "rel_title": "Introductions and evolutions of SARS-CoV-2 strains in Japan", @@ -916783,33 +919977,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.28.21250921", - "rel_title": "SARS-CoV-2 infection in households with and without young children: Nationwide cohort study", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21250921", - "rel_abs": "BackgroundInfections with seasonally spreading human coronaviruses (HCoVs) are common among young children during winter months in the northern hemisphere, with immunological response lasting around a year. However, it is not clear whether recent household exposure to HCoVs reduces the risk of SARS-CoV-2 infection.\n\nMethodsIn a nationwide cohort study we followed all adults in Denmark aged 18 to 60 years from February 27 to November 15, 2020. Hazard ratios of SARS-CoV-2 infection by number of young children aged ten months to five years living in the household were estimated using Cox regression adjusted for adult age, gender, and other potential confounders. In sensitivity analyses we investigated the effect of age of children in the household, number of children living outside of the household, and number of other adult household-members.\n\nResultsAmong 449,915 adults in Denmark living in households with young children, 5,761 were tested positive for SARS-CoV-2, while among 2,629,821 adults without young children in their household, 33,788 were tested positive for SARS-CoV-2 (adjusted hazard ratio, 1.05; 95% confidence interval, 1.02 to 1.09). Sensitivity analyses of age of children in the household, number of children living outside of the household, and number of additional adult household members found increasing number of children, and especially increasing number of older children, to substantially increase the risk of SARS-CoV-2 infection.\n\nConclusionsLiving in a household with young children was not associated with decreased risk of SARS-CoV-2 infection, thereby suggesting no strong preventive effect of recent exposure to HCoVs against SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anders Husby", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Giulia Corn", - "author_inst": "Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Tyra Grove Krause", - "author_inst": "Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.28.21252610", "rel_title": "Vaccine hesitancy and reasons for refusing the COVID-19 vaccination among the U.S. public: A cross-sectional survey", @@ -918109,6 +921276,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.01.21252598", + "rel_title": "Investigation of ventilation conditions associated with CO2 concentration changes in ultrasonographic exam room from the perspective of COVID-19 infection control", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252598", + "rel_abs": "ObjectivesVentilation is an important factor in preventing COVID-19 infection. To clarify the state of ventilation in ultrasonic exam rooms, as an index of ventilation rate, the carbon dioxide (CO2) concentration in our exam rooms was measured.\n\nMethodsWe measured the CO2 concentration in each exam room before the examination and 0-15 minutes after end of the exam.\n\nThe subjects were 70 cases (abdomen: 24, breast: 16, neck: 16, and musculoskeletal: 14). In infant cases, one parent accompanied the patient during the examination.\n\nResultsThe highest CO2 concentration was 2261 ppm, observed after the breast examination. In all cases, the CO2 concentration in the exam room was highest immediately after the examination or two minutes after. Almost all cases had recovered to within 120% of the pre-examination CO2 concentrations within 15 minutes after the examination. The average CO2 concentration after ultrasonography was significantly higher for breast examinations than others.\n\nConclusionsEven in a hospital with modern ventilation equipment, the CO2 concentration in the ultrasound room was high after the exam and it takes 15 minutes to recover to the pre-exam state. Care must be taken to ensure adequate ventilation in ultrasonographic facilities.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Roka Namoto Matsubayashi", + "author_inst": "National Hospital Organization Kyushu Medical Center" + }, + { + "author_name": "Shino Harada", + "author_inst": "National Hospital Organization Kyushu Medical Center" + }, + { + "author_name": "Mitsuhiro Tominaga", + "author_inst": "National Hospital Organization Kyushu Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.01.21252330", "rel_title": "Does Telemedicine Reduce health disparities? Longitudinal Evidence during the COVID-19 Pandemic in the US", @@ -918645,45 +921839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2021.02.27.21252458", - "rel_title": "Factors Associated with Serious Psychological Distress during the COVID-19 Pandemic in Japan", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252458", - "rel_abs": "ImportanceThe coronavirus disease 2019 (COVID-19) pandemic may have a negative impact on mental health of the population, leading to higher suicide rates, in many countries. However, little is known about risk factors associated with worsened mental health during the COVID-19 pandemic.\n\nObjectiveTo investigate the factors associated with serious psychological distress (SPD) during the COVID-19 pandemic in Japan.\n\nDesign, Setting, and ParticipantsA cross-sectional study using a large-scale internet survey conducted between August 25 and September 30, 2020, in Japan.\n\nExposuresDemographics (age, gender, marital status, family composition, and caregiving burden), socio-economic status (income level, employment type, educational attainment), the experience of domestic violence (DV), the state of emergency, fear of COVID-19, and stigma related to COVID-19.\n\nMain Outcomes and MeasuresPrevalence of SPD, defined as Kessler 6 scale score [≥]13.\n\nResultsAmong 25,482 individuals included in this study, 2,556 (10%) met the criteria of SPD. Overall, women (adjusted odds ratio [aOR] 1.59; 95%CI, 1.17-2.16; P=0.003), ages 15-29 (aOR compared with ages 45-59, 2.35; 95%CI, 1.64-3.38; P<0.001), low income (aOR compared with intermediate income, 1.70; 95%CI, 1.16-2.49; P=0.007), providing caregiving to family members (aOR, 5.48; 95%CI, 3.51-8.56; P<0.001), experiencing DV (aOR, 5.72; 95%CI, 3.81-8.59; P<0.001), and fear of COVID-19 (aOR, 1.96; 95%CI, 1.55-2.48; P<0.001) were associated with a higher rate of SPD. Among women aged 15-29 years, who experienced the highest rate of SPD, caregiving, DV, fear of COVID-19, and COVID-19-related stigma were associated with a higher rate of SPD; whereas economic situation (income level and employment type) and social isolation (marital status) were not associated with the prevalence of SPD.\n\nConclusions and RelevanceEconomic situation, caregiving burden, DV, and fear of COVID-19 were independently associated with SPD during the COVID-19 pandemic. Among young women--who have a higher risk of suicide during the COVID-19 pandemic in Japan--similar factors, except economic situation, were associated with a higher rate of SPD. Targeted interventions based on age and gender may be more effective in mitigating the negative impact of the COVID-19 pandemic on the populations mental health.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Takashi Yoshioka", - "author_inst": "Fukushima Medical University" - }, - { - "author_name": "Ryo Okubo", - "author_inst": "National Center of Neurology and Psychiatry" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Osaka International Cancer Institute" - }, - { - "author_name": "Satomi Odani", - "author_inst": "Osaka International Cancer Institute" - }, - { - "author_name": "Tomohiro Shinozaki", - "author_inst": "Tokyo University of Science" - }, - { - "author_name": "Yusuke Tsugawa", - "author_inst": "UCLA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.02.26.21252538", "rel_title": "Prioritizing the first doses of SARS-CoV-2 vaccine to save the elderly: the case study of Italy", @@ -919823,6 +922978,137 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.01.433314", + "rel_title": "Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains", + "rel_date": "2021-03-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433314", + "rel_abs": "We examined the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 that arose in the United Kingdom and spread globally. Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa B.1.351 variant, than of the infecting variant. The drop in cross-reactivity was more pronounced following B.1.1.7 than parental strain infection, indicating asymmetric heterotypic immunity induced by SARS-CoV-2 variants.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Nikhil Faulkner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Kevin Ng", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Mary Wu", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Saira Hussain", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Maria Greco", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "William Bolland", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Scott Warchal", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Marios Margaritis", + "author_inst": "UCL" + }, + { + "author_name": "Stavroula Paraskevopoulou", + "author_inst": "UCL" + }, + { + "author_name": "Judith Heaney", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Rickman", + "author_inst": "UCL" + }, + { + "author_name": "Catherine Houlihan", + "author_inst": "UCL" + }, + { + "author_name": "Moria Spyer", + "author_inst": "UCL" + }, + { + "author_name": "Daniel Frampton", + "author_inst": "UCL" + }, + { + "author_name": "Matthew Byott", + "author_inst": "UCL" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "University of KwaZulu-Natal,SA" + }, + { + "author_name": "Alex Sigal", + "author_inst": "University of KwaZulu-Natal,SA" + }, + { + "author_name": "Svend Kjaer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Charles Swanton", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Sonia Gandhi", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rupert Beale", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Mccauley", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rodney Daniels", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Michael Howell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "David Bauer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCL" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.27.433180", "rel_title": "Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees.", @@ -920415,53 +923701,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.23.21251934", - "rel_title": "Synthetic protein antigens for COVID-19 diagnostics", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21251934", - "rel_abs": "There is an urgent need for inexpensive, rapid and specific antigen-based assays to test for infection with SARS-CoV-2 and distinguish variants arising as the COVID-19 pandemic spreads. We have identified a small, synthetic protein (JS7), representing a region of maximum variability within the receptor binding domain (RBD), which binds antibodies in sera from nine patients with PCR-verified COVID-19 of varying severity. Antibodies binding to either JS7 or the SARS-CoV-2 recombinant RBD, as well as those that disrupt binding between a fragment of the ACE2 receptor and the RBD, are proportional to disease severity and clinical outcome. Binding to JS7 was inhibited by linear peptides from the RBD interface with ACE2. Variants of JS7, such as N501Y, can be quickly synthesized in a pure form in large quantities by automated methods. JS7 and related synthetic antigens can provide a basis for specific diagnostics for SARS-CoV-2 infections.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Catherine H Schein", - "author_inst": "UTMB" - }, - { - "author_name": "Susan F McClellan", - "author_inst": "UTMB Galveston" - }, - { - "author_name": "Corri B Levine", - "author_inst": "UTMB Galveston" - }, - { - "author_name": "Surendra S Negi", - "author_inst": "UTMB Galveston" - }, - { - "author_name": "Werner Braun", - "author_inst": "UTMB Galveston" - }, - { - "author_name": "Stephen Dreskin", - "author_inst": "University of Colorado" - }, - { - "author_name": "Elizabeth S Anaya", - "author_inst": "Los Alamos Natl Lab" - }, - { - "author_name": "Jurgen Schmidt", - "author_inst": "Los Alamos Natl. Lab" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.25.21252441", "rel_title": "Leveraging genetic data to elucidate the relationship between Covid-19 and ischemic stroke", @@ -921397,6 +924636,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.25.21252451", + "rel_title": "Muscle Strength Explains the Protective Effect of Physical Activity against COVID-19 Hospitalization among Adults aged 50 Years and Older", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252451", + "rel_abs": "ObjectivesPhysical activity has been proposed as a protective factor for COVID-19 hospitalization. However, the mechanisms underlying this association are unclear. Here, we examined the association between physical activity and COVID-19 hospitalization and whether this relationship was explained by other risk factors for severe COVID-19.\n\nMethodWe used data from adults aged 50 years and older from the Survey of Health, Ageing and Retirement in Europe. The outcome was self-reported hospitalization due to COVID-19 measured before August 2020. The main exposure was usual physical activity, self-reported between 2004 and 2017. Data were analyzed using logistic regression models.\n\nResultsAmong the 3139 participants included in the study (69.3 {+/-} 8.5 years, 1763 women), 266 were tested positive for COVID-19 and 66 were hospitalized. Results showed that individuals who engaged in physical activity more than once a week had lower odds of COVID-19 hospitalization than individuals who hardly ever or never engaged in physical activity (odds ratios = 0.41, 95% confidence interval = 0.22-0.74, p = .004). This association between physical activity and COVID-19 hospitalization was explained by muscle strength, but not by other risk factors.\n\nConclusionThese findings suggest that, after 50 years of age, engaging in physical activity more than once a week is associated with lower odds of COVID-19 hospitalization. The protective effect of physical activity on COVID-19 hospitalization is explained by muscle strength.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Silvio Maltagliati", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Stefan Sieber", + "author_inst": "University of Geneva" + }, + { + "author_name": "Philippe Sarrazin", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Stephane Cullati", + "author_inst": "University of Fribourg" + }, + { + "author_name": "Aina Chalabaev", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Gregoire P Millet", + "author_inst": "University of Lausanne" + }, + { + "author_name": "Matthieu P Boisgontier", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Boris Cheval", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.02.26.21252552", "rel_title": "The Charitable Feeding System helps Food Insecure Participants maintain Fruit and Vegetable intake during COVID-19.", @@ -921981,45 +925267,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.26.21252483", - "rel_title": "Mathematical modeling to inform vaccination strategies and testing approaches for COVID-19 in nursing homes", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252483", - "rel_abs": "BackgroundNursing home residents and staff were included in the first phase of COVID-19 vaccination in the United States. Because the primary trial endpoint was vaccine efficacy (VE) against symptomatic disease, there are limited data on the extent to which vaccines protect against SARS-CoV-2 infection and the ability to infect others (infectiousness). Assumptions about VE against infection and infectiousness have implications for possible changes to infection prevention guidance for vaccinated populations, including testing strategies.\n\nMethodsWe use a stochastic agent-based SEIR model of a nursing home to simulate SARS-CoV-2 transmission. We model three scenarios, varying VE against infection, infectiousness, and symptoms, to understand the expected impact of vaccination in nursing homes, increasing staff vaccination coverage, and different screening testing strategies under each scenario.\n\nResultsIncreasing vaccination coverage in staff decreases total symptomatic cases in each scenario. When there is low VE against infection and infectiousness, increasing staff coverage reduces symptomatic cases among residents. If vaccination only protects against symptoms, but asymptomatic cases remain infectious, increased staff coverage increases symptomatic cases among residents through exposure to asymptomatic but infected staff. High frequency testing is needed to reduce total symptomatic cases if the vaccine has low efficacy against infection and infectiousness, or only protects against symptoms.\n\nConclusionsEncouraging staff vaccination is not only important for protecting staff, but might also reduce symptomatic cases in residents if a vaccine confers at least some protection against infection or infectiousness.\n\nSummaryThe extent of efficacy of SARS-CoV-2 vaccines against infection, infectiousness, or disease, impacts strategies for vaccination and testing in nursing homes. If vaccines confer some protection against infection or infectiousness, encouraging vaccination in staff may reduce symptomatic cases in residents.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Rebecca Kahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Inga Holmdahl", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Sujan Reddy", - "author_inst": "US Centers for Disease Control and Prevention" - }, - { - "author_name": "John Jernigan", - "author_inst": "US Centers for Disease Control and Prevention" - }, - { - "author_name": "Michael J Mina", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Rachel B Slayton", - "author_inst": "US Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.26.21251868", "rel_title": "The localized rise of a B.1.526 variant containing an E484K mutation in New York State", @@ -922883,6 +926130,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252319", + "rel_title": "Control of COVID-19 transmission on an urban university campus during a second wave of the pandemic", + "rel_date": "2021-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252319", + "rel_abs": "ImportanceThe COVID-19 pandemic had a wide-ranging impact on educational institutions across the United States. Given potential financial challenges and adverse psychosocial effects of campus closure, as done in the spring of 2020 in response to the first wave, many institutions of higher education developed strategies to allow campuses to reopen and operate in the fall despite the ongoing threat of COVID-19. Many however opted to have limited campus re-opening in order to minimize potential risk of spread of SARS-CoV-2.\n\nObjectiveTo analyze how Boston University (BU) fully reopened its campus in the fall of 2020 and controlled COVID-19 transmission despite worsening transmission in the city of Boston.\n\nDesignMulti-faceted intervention case study.\n\nSettingLarge urban university campus.\n\nInterventionsThe BU response included a high-throughput SARS-CoV-2 PCR testing facility with capacity to delivery results in less than 24 hours; routine asymptomatic screening for COVID-19; daily health attestations; compliance monitoring and feedback; robust contact tracing, quarantine and isolation in on campus facilities; face mask use; enhanced hand hygiene; social distancing recommendations; de-densification of classrooms and public places; and enhancement of all building air systems.\n\nMain Outcomes and MeasuresBetween August and December 2020, BU conducted >500,000 COVID-19 tests and identified 719 individuals with COVID-19: 627 (87.2%) students, 11 (1.5%) faculty, and 212 (25.5%) staff. Overall, about 1.8% of the BU community tested positive. Infections among faculty and staff were mostly acquired off campus, while undergraduate infections were more likely acquired in non-classroom campus settings. Of 837 close contacts traced, 86 (10.3%) tested positive for COVID-19. BU contact tracers identified a source of transmission for 51.5% of cases with 55.7% identifying a source outside of BU. Among infected faculty and staff with a known source of infection, the majority reported a transmission source outside of BU (100% for faculty and 79.8% for staff).\n\nConclusions and RelevanceBU was successful in containing COVID-19 transmission on campus while minimizing off campus acquisition of COVID-19 from the greater Boston area. A coordinated strategy of testing, contact tracing, isolation and quarantine, with robust management and oversight, can control COVID-19 transmission, even in an urban university setting.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Davidson H Hamer", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Laura White", + "author_inst": "Boston University" + }, + { + "author_name": "Helen E Jenkins", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "christopher J gill", + "author_inst": "boston university school of public health" + }, + { + "author_name": "Hannah N. Landsberg", + "author_inst": "Boston University" + }, + { + "author_name": "Catherine Klapperich", + "author_inst": "Boston University" + }, + { + "author_name": "Katia Bulekova", + "author_inst": "Boston University" + }, + { + "author_name": "Judy Platt", + "author_inst": "Boston University" + }, + { + "author_name": "Linette Decarie", + "author_inst": "Boston University" + }, + { + "author_name": "Wayne Gilmore", + "author_inst": "Boston University" + }, + { + "author_name": "Megan Pilkington", + "author_inst": "Boston University" + }, + { + "author_name": "Trevor L. McDowell", + "author_inst": "Boston University" + }, + { + "author_name": "Mark A. Fari", + "author_inst": "Boston University" + }, + { + "author_name": "Douglas M. Densmore", + "author_inst": "Boston University" + }, + { + "author_name": "Lena Landaverde", + "author_inst": "Boston University" + }, + { + "author_name": "Wenrui Li", + "author_inst": "Boston University" + }, + { + "author_name": "Tom Rose", + "author_inst": "Boston University" + }, + { + "author_name": "Stephen P. Burgay", + "author_inst": "Boston University" + }, + { + "author_name": "Candice Miller", + "author_inst": "Boston University" + }, + { + "author_name": "Lynn Doucette-Stamm", + "author_inst": "Boston University" + }, + { + "author_name": "Kelly Lockard", + "author_inst": "Boston University" + }, + { + "author_name": "Kenneth Elmore", + "author_inst": "Boston University" + }, + { + "author_name": "Tracy Schroeder", + "author_inst": "Boston University" + }, + { + "author_name": "Ann M. Zaia", + "author_inst": "Boston University" + }, + { + "author_name": "Eric D. Kolaczyk", + "author_inst": "Boston University" + }, + { + "author_name": "Gloria Waters", + "author_inst": "Boston University" + }, + { + "author_name": "Robert A. Brown", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.23.21252299", "rel_title": "The Public Health Impact of Delaying a Second Dose of the BNT162b2 or mRNA-1273 COVID-19 Vaccine", @@ -923763,69 +927133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.24.21252103", - "rel_title": "COVIDReady2 Study Protocol: Cross-sectional Survey of Medical Student Volunteering and Education During the COVID-19 Pandemic in the United Kingdom", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252103", - "rel_abs": "Background and objectivesCovid-19 has led to global disruption of healthcare. Many students volunteered to provide clinical support. Volunteering to work in a clinical capacity was a unique medical education opportunity; however, it is unknown whether this was a positive learning experience or which volunteering roles were of most benefit to students.\n\nMethods and DesignThe COVIDReady2 study is a national cross-sectional study of all medical students at UK medical schools. The primary outcome is to explore the experiences of medical students who volunteered during the pandemic in comparison to those who did not. We will compare responses to determine the educational benefit and issues they faced. In addition to quantitative analysis, thematic analysis will be used to identify themes in qualitative responses.\n\nDiscussionThere is a growing body of evidence to suggest that service roles have potential to enhance medical education; yet, there is a shortage of studies able to offer practical advice for how these roles may be incorporated in future medical education. We anticipate that this study will help to identify volunteer structures that have been beneficial for students, so that similar infrastructures can be used in the future, and help inform medical education in a non-pandemic setting.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Matthew H V Byrne", - "author_inst": "Nuffield Department of Surgical Sciences, University of Oxford, UK" - }, - { - "author_name": "James Ashcroft", - "author_inst": "University of Cambridge, Department of Surgery, Addenbrookes Hospital, UK" - }, - { - "author_name": "Laith Alexander", - "author_inst": "St Thomas Hospital, London, UK" - }, - { - "author_name": "Jonathan C M Wan", - "author_inst": "St Thomas Hospital, London, UK" - }, - { - "author_name": "Anmol Arora", - "author_inst": "School of Clinical Medicine, University of Cambridge" - }, - { - "author_name": "Megan E L Brown", - "author_inst": "Health Professions Education Unit, Hull York Medical School, University of York, UK" - }, - { - "author_name": "Anna Harvey", - "author_inst": "Kings College London GKT School of Medical Education, UK" - }, - { - "author_name": "Andrew Clelland", - "author_inst": "University of Cambridge, Department of Surgery, Addenbrookes Hospital, UK" - }, - { - "author_name": "Nicholas Schindler", - "author_inst": "Norfolk and Norwich University Hospitals NHS Foundation Trust, Paediatric Department, UK" - }, - { - "author_name": "Cecilia Brassett", - "author_inst": "University of Cambridge, Department of Physiology, Development and Neuroscience, UK" - }, - { - "author_name": "Rachel Allan", - "author_inst": "Nuffield Department of Primary Care Health Sciences, Medical Sciences Division, University of Oxford, UK" - }, - { - "author_name": "- MedEd Collaborative", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.02.24.21252329", "rel_title": "Long COVID neuropsychological deficits after severe, moderate or mild infection", @@ -925009,6 +928316,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.23.21252294", + "rel_title": "Evaluation of COVID-19 as a risk factor for maternal-fetal and neonatal complications: protocol of a systematic review and meta-analysis of cohort and case-control studies.", + "rel_date": "2021-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252294", + "rel_abs": "BackgroundCOVID-19 in pregnant women has been suggested to impair maternal-fetal and neonatal outcomes. We then designed the present systematic review with meta-analysis to evaluate the repercussion of such disease over maternal fetal and neonatal mortality, need for intensive care, way of delivery, premature delivery, birth weight, Apgar score, presence of intrauterine growth restriction (IGR), and presence of amniotic fluid change.\n\nMethodsWe will conduct a computerized search through MEDLINE/PubMed, LILACS/BIREME, Web of science, Biorxiv, Medrxiv, and Embase on July 23, 2020. We will include cohort and case-control studies fully reported comparing pregnant women with COVID-19 with those not affected by the disease for maternal fetal and neonatal mortality, need for intensive care, way of delivery, premature delivery occurrence, birth weight, Apgar scores, presence of intrauterine growth restriction, and presence of amniotic fluid change. Three doubles of reviewers will perform in duplicate and independently all steps on screening, risk of bias judgments, and data extraction with ability to discuss disagreements with supervising authors. Pooled effects will be estimated by both fixed and random-effects models and presented according to qualitative and quantitative heterogeneity assessment. Sensitivity analyses will be performed as well as a priori subgroup, meta-regression and multiple meta-regression analyses. Well also evaluate the risk of selective publication by assessing funnel plot asymmetry and the quality of the evidence by the application of the GRADE recommendations.\n\nDiscussionThis systematic review with meta-analysis aims to assess the repercussion of COVID-19 in pregnant women over maternal-fetal and neonatal outcomes and to help clinicians and health systems improve such population outcomes throughout the current pandemic.\n\nSystematic review registrationThis review protocol was also submitted to PROSPERO registration on February 9, 2021.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Priscila Bezerra", + "author_inst": "Instituto de Medicina Integral professor Fernando Figueira" + }, + { + "author_name": "Fernanda Gabriella de Siqueira Barros Nogueira Sr.", + "author_inst": "Instituto de Medicina Integral Prof. Fernando Figueira (IMIP)" + }, + { + "author_name": "Alan Chaves dos Santos", + "author_inst": "Instituto de medicina integral professor Fernando Figueira" + }, + { + "author_name": "Anna Katharina Souza Lima", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "David Emanuel Ribeiro", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Elias Almeida Silva Barbosa", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Suellen Casado dos Santos", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Clistenes Cristian de Carvalho", + "author_inst": "Instituto de Medicina Integral Professor Fernando Figueira" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.02.23.21251915", "rel_title": "Clinical evaluation of the molecular-based BD SARS-CoV-2/Flu for the BD MAX\u2122 System", @@ -925889,69 +929243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.02.24.21252047", - "rel_title": "Evaluation of a surrogate virus neutralization test for high-throughput serosurveillance of SARS-CoV-2", - "rel_date": "2021-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252047", - "rel_abs": "High-throughput serological tests that can detect neutralizing antibodies against SARS-CoV-2 are desirable for serosurveillance and vaccine efficacy evaluation. Although the conventional neutralization test (cVNT) remains the gold standard to confirm the presence of neutralizing antibodies in sera, the test is too labour-intensive for massive screening programs and less reproducible as live virus and cell culture is involved. Here, we performed an independent evaluation of a commercially available surrogate virus neutralization test (sVNT, GenScript cPass) that can be done without biosafety level 3 containment in less than 2 hours. When using the cVNT and a Luminex multiplex immunoassay (MIA) as reference, the sVNT obtained a sensitivity of 94% (CI 90-96%) on a panel of 317 immune sera that were obtained from hospitalized and mild COVID-19 cases from Belgium and a sensitivity of 89% (CI 81-93%) on a panel of 184 healthcare workers from the Democratic Republic of Congo. We also found strong antibody titer correlations (rs>0.8) among the different techniques used. In conclusion, our evaluation suggests that the sVNT could be a powerful tool to monitor/detect neutralising antibodies in cohort and population studies. The technique could be especially useful for vaccine evaluation studies in sub-Saharan Africa where the basic infrastructure to perform cVNTs is lacking.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "joachim Marien", - "author_inst": "Institute of Tropical medicine Antwerp" - }, - { - "author_name": "Johan Michiels", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Leo Heyndrickx", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Antoine Nkuba-Ndaye", - "author_inst": "Institut National de Recherche Biomedicale" - }, - { - "author_name": "Ann Ceulemans", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Koen Koen Bartholomeeusen", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Joule Madinga", - "author_inst": "Institut National de Recherche Biomedicale" - }, - { - "author_name": "Placide Mbala-Kingebeni", - "author_inst": "Institut National de Recherche Biomedicale" - }, - { - "author_name": "Veerle Vanlerberghe", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Steve Ahuka-Mundeke", - "author_inst": "Institut National de Recherche Biomedicale" - }, - { - "author_name": "Linfa Wang", - "author_inst": "SingHealth Duke-NUS Global Health Institute" - }, - { - "author_name": "Kevin K. Arien", - "author_inst": "Institute of Tropical Medicine Antwerp" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.24.21252337", "rel_title": "A prospective evaluation of the analytical performance of GENECUBE(R) HQ SARS-CoV-2 and GENECUBE(R) FLU A/B", @@ -927019,6 +930310,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.22.21252254", + "rel_title": "Associations Between Google Search Trends for Symptoms and COVID-19 Confirmed and Death Cases in the United States", + "rel_date": "2021-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252254", + "rel_abs": "We utilize functional data analysis techniques to investigate patterns of COVID-19 positivity and mortality in the US and their associations with Google search trends for COVID-19 related symptoms. Specifically, we represent state-level time series data for COVID-19 and Google search trends for symptoms as smoothed functional curves. Given these functional data, we explore the modes of variation in the data using functional principal component analysis (FPCA). We also apply functional clustering analysis to identify patterns of COVID-19 confirmed case and death trajectories across the US. Moreover, we quantify the associations between Google COVID-19 search trends for symptoms and COVID-19 confirmed case and death trajectories using dynamic correlation. Finally, we examine the dynamics of correlations for the top nine Google search trends of symptoms commonly associated with COVID-19 confirmed case and death trajectories. Our results reveal and characterize distinct patterns for COVID-19 spread and mortality across the US. The dynamics of these correlations suggest the feasibility of using Google queries to forecast COVID-19 cases and mortality for up to three weeks in advance. Our results and analysis framework set the stage for the development of predictive models for forecasting COVID-19 confirmed cases and deaths using historical data and Google search trends for nine symptoms associated with both outcomes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mostafa Abbas", + "author_inst": "Geisinger" + }, + { + "author_name": "Thomas B. Morland", + "author_inst": "Geisinger" + }, + { + "author_name": "Eric S. Hall", + "author_inst": "Geisinger" + }, + { + "author_name": "Yasser El-Manzalawy", + "author_inst": "Geisinger" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.23.21252230", "rel_title": "Prior COVID-19 Infection and Antibody Response to Single Versus Double Dose mRNA SARS-CoV-2 Vaccination", @@ -927715,85 +931037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.24.432203", - "rel_title": "Discovery of a AhR flavonoid agonist that counter-regulates ACE2 expression in rodent models of inflammation and attenuates ACE2-SARS-CoV2 interaction in vitro", - "rel_date": "2021-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432203", - "rel_abs": "The severe acute respiratory syndrome (SARS)-CoV-2, a newly emerged coronavirus first identified in 2019, is the pathogenetic agent od Corona Virus Induced Disease (COVID)19. The virus enters the human cells after binding to the angiotensin converting enzyme (ACE) 2 receptor in target tissues. ACE2 expression is induced in response to inflammation. The colon expression of ACE2 is upregulated in patients with inflammatory bowel disease (IBD), highlighting a potential risk of intestinal inflammation in promoting viral entry in the human body. Because mechanisms that regulate ACE2 expression in the intestine are poorly understood and there is a need of anti-SARS-CoV2 therapies, we have settled to investigate whether natural flavonoids might regulate the expression of ACE2 in intestinal models of inflammation. The results of these studies demonstrated that pelargonidin, a natural flavonoid bind and activates the Aryl hydrocarbon Receptor (AhR) in vitro and reverses intestinal inflammation caused by chronic exposure to high fat diet or to the intestinal braking-barrier agent DSS in a AhR-dependent manner. In these two models, development of colon inflammation associated with upregulation of ACE2 mRNA expression. Colon levels of ACE2 mRNA were directly correlated with TNF mRNA levels. In contrast to ACE2 the angiotensin 1-7 receptor MAS was downregulated in the inflamed tissues. Molecular docking studies suggested that pelargonidin binds a fatty acid binding pocket on the receptor binding domain of SARS-CoV2 Spike protein. In vitro studies demonstrated that pelargonidin significantly reduces the binding of SARS-CoV2 Spike protein to ACE2 and reduces the SARS-CoV2 replication in a concentration-dependent manner. In summary, we have provided evidence that a natural flavonoid might hold potential in reducing intestinal inflammation and ACE2 induction in the inflamed colon in a AhR-dependent manner.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Michele Biagioli", - "author_inst": "University of Perugia" - }, - { - "author_name": "Silvia Marchian\u00f2", - "author_inst": "University of Perugia" - }, - { - "author_name": "Rosalinda Roselli", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Cristina Di Giorgio", - "author_inst": "University of Perugia" - }, - { - "author_name": "Rachele Bellini", - "author_inst": "University of Perugia" - }, - { - "author_name": "Martina Bordoni", - "author_inst": "University of Perugia" - }, - { - "author_name": "Anna Gidari", - "author_inst": "University of Perugia" - }, - { - "author_name": "Samuele Sabbatini", - "author_inst": "University of Perugia" - }, - { - "author_name": "Daniela Francisci", - "author_inst": "University of Perugia" - }, - { - "author_name": "Bianca Fiorillo", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Bruno Catalanotti", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Eleonora Distrutti", - "author_inst": "SC di Gastroenterologia ed Epatologia, Azienda Ospedaliera di Perugia" - }, - { - "author_name": "Adriana Carino", - "author_inst": "University of Perugia" - }, - { - "author_name": "Angela Zampella", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Gabriele Costantino", - "author_inst": "Department of Food and Drugs, University of Parma" - }, - { - "author_name": "Stefano Fiorucci", - "author_inst": "University of Perugia" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.02.24.432694", "rel_title": "Rapid adaptation and remote delivery of undergraduate research training during the COVID 19 Pandemic", @@ -928941,6 +932184,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.19.21252073", + "rel_title": "Health-related quality of life of adult COVID-19 patients following one-month illness experience since diagnosis: findings of a cross-sectional study in Bangladesh", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252073", + "rel_abs": "BackgroundThe pandemic coronavirus disease 2019 (COVID-19) stances an incredible impact on the quality of life of the patients. The disease not only denigrates the physical health of the patients but also affects their mental health. This cross-sectional study aimed to assess the health-related quality of life (HRQOL) of patients.\n\nMethodsThe study was conducted at the National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh during the period from June to November 2020. The study enrolled 1204 adult (>18 years) COVID-19 patients diagnosed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay and completed the one-month duration of illness. The patients were interviewed with the CDC HRQOL-14 questionnaire to assess their HRQOL. Data were collected by telephone-interview and reviewing medical records using a semi-structured questionnaire and checklist respectively. Informed consent was obtained from each patient before data collection.\n\nResultsThe majority of the COVID-19 patients were males (72.3%), urban residents (50.2%), and diverse service holders (49.6%). More than one-third (35.5%) of patients had comorbidity including hypertension (55.6%), diabetes mellitus (55.6%), ischaemic heart disease (16.4%), chronic lung (12.4%), kidney (2.8%), and liver (4.2%) diseases. The mean{+/-}SD duration of physical illness was 9.83({+/-}7.09) days, and it was 7.97({+/-}8.12) days for mental illness. During the one-month disease course, the general health condition was excellent/very good/good in 70.1% of the patients while it was fair/poor in 29.8% of the patients. Older age, sex, and marital status were significantly associated with at least one dimension of HRQOL. Patients having symptoms of COVID-19 and comorbidity had significantly poorer HRQOL.\n\nConclusionCOVID-19 pretenses a significant impact on the HRQOL of the patients including physical and mental illness during the clinical course. Our findings suggest more pragmatic preventive, promotive, and curative measures considering illness experiences of the COVID-19 patients to restore their quality of life.\n\nHighlightsSince COVID-19 was identified first in china in 2019, it has been transmitted globally and caused a significant impact on human health. A few studies have been carried out on HRQOL of COVID-19 patients and struggled with an accurate estimation of the severity of their physical and mental illness. Most of the studies recognized the poor quality of life of COVID-19 patients after the one-month disease course. Our study provides new insights on the HRQOL of the COVID-19 patients using the CDC HRQOL-14 questionnaire. We measured the HRQOL following one-month illness experience of the patients using three modules: the healthy days core; the activity limitations; and the healthy days symptoms. The study adds information regarding general health conditions including both the physical and mental health of COVID-19 patients. The study also complements information regarding the activity limitations of the patients. The study findings could contribute to designing an efficient clinical algorithm to alleviate the illness sufferings of the COVID-19 patients using a more pragmatic approach. The study conserves decisive policy implications to concoct effective interventions for improving the HRQOL of COVID-19 patients in the country and elsewhere in other countries world-wide.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Md. Ziaul Islam", + "author_inst": "National Institute of Preventive and Social Medicine (NIPSOM)" + }, + { + "author_name": "Baizid Khoorshid Riaz", + "author_inst": "National Institute of Preventive and Social Medicine" + }, + { + "author_name": "Syeda Sumaiya Efa", + "author_inst": "Diabetic Association of Bangladesh" + }, + { + "author_name": "Sharmin Farjana", + "author_inst": "Shaheed Suhrawardy Medical College Hospital" + }, + { + "author_name": "Fahad Mahmood", + "author_inst": "National Institute of Preventive and Social Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.20.21251855", "rel_title": "Transmission of SARS-CoV-2 Considering Shared Chairs in Outpatient Dialysis: A Real-World Case-Control Study", @@ -929613,57 +932891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.21.21252137", - "rel_title": "Evolving Infection Paradox of SARS-CoV-2: Fitness Costs Virulence?", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.21.21252137", - "rel_abs": "SARS-CoV-2 is evolved into eight fundamental clades where four (G, GH, GR, and GV) are globally prevalent in 2020. How the featured co-occurring mutations of these clades are linked with viral fitness is the main question here and we thus proposed a hypothetical model using in silico approach to explain the plausible epistatic effects of those mutations on viral replication and transmission. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p<0.0001) since more flexible RdRp (mutated)-NSP8 interaction may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein and/or RNA interactions. Another silent 5UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H constricted ion-channel through inter-transmembrane-domain interaction of cysteine(C81)-histidine(H57) and GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events featuring the fitness of SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "A. S. M. Rubayet Ul Alam", - "author_inst": "Department of Microbiology, Jashore University of Science and Technology, Jashore-7408, Bangladesh" - }, - { - "author_name": "Ovinu Kibria Islam", - "author_inst": "Department of Microbiology, Jashore University of Science and Technology, Jashore-7408, Bangladesh" - }, - { - "author_name": "Md. Shazid Hasan", - "author_inst": "Department of Microbiology, Jashore University of Science and Technology, Jashore-7408, Bangladesh" - }, - { - "author_name": "Mir Raihanul Islam", - "author_inst": "BRAC James P Grant School of Public Health, BRAC University, Bangladesh" - }, - { - "author_name": "Shafi Mahmud", - "author_inst": "Genetic Engineering and Biotechnology, University of Rajshahi, Rajshai-6205, Bangladesh" - }, - { - "author_name": "Hassan M. AlEmran", - "author_inst": "Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore-7408, Bangladesh" - }, - { - "author_name": "Iqbal K Jahid", - "author_inst": "Dept. of Microbiology, Jashore University of Science and Technology" - }, - { - "author_name": "Keith A. Crandall", - "author_inst": "Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Wa" - }, - { - "author_name": "M. Anwar Hossain", - "author_inst": "Jashore University of Science and Technology, Jashore-7408, Bangladesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.21.21252132", "rel_title": "Heterogeneity in COVID-19 severity patterns among age-gender groups: an analysis of 778 692 Mexican patients through a meta-clustering technique", @@ -930887,6 +934114,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.19.21252106", + "rel_title": "Impact of environmental temperature on Covid-19 spread: Model and analysis of measurements recorded during the second pandemic in Cyprus", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252106", + "rel_abs": "The paper investigates the effect of the environmental temperature on the spread of COVID-19. We study the daily numbers of the cases infected and deaths caused by Covid-19 during the second wave of the pandemic within 2020, and how they were affected by the daily average-high temperature for the districts of the Republic of Cyprus. Among the findings of the paper, we show that (i) the average ratio of the PCR to rapid positive tests is [~]2.57{+/-}0.25, as expected from the tests responses, indicating that PCR overestimates positivity by [~]2.5 times; (ii) the average age of deaths caused by Covid-19 increases with rate about a year of age per week; (iii) the probability of a person infected by Covid-19 to develop severe symptoms leading to death is strongly depended on the persons age, while the probability of having a death on the age of [~]67 or younger is less than 1/1000; (iv) the number of infected cases and deaths declined dramatically when the environmental temperature reaches and/or climbs above the critical temperature of TC=30.1{+/-}2.4 C0; (v) the observed negative correlation between the exponential growth rate of the infected cases and the environmental temperature can be described within the framework of chemical kinetics, with at least two competing reactions, the connection of the coronavirus towards the receptor and the dissolution of the coronavirus; the estimated activation energy difference corresponding to the competing chemical reactions, 0.212{+/-}0.25 eV, matches the known experimental value; and (vi) the infected cases will decline to zero, when the environmental temperature climbs above the critical temperature within the summery days of 2021, which is expected for the Republic of Cyprus by the 16th of May, 2021.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "George Livadiotis", + "author_inst": "Southwest Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.22.21252208", "rel_title": "Vaccination efforts in Brazil: scenarios and perspectives under a mathematical modeling approach", @@ -931763,49 +935009,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.18.21252027", - "rel_title": "Single-Particle Counting Based on Digital Plasmonic Nanobubble Detection for Rapid and Ultrasensitive Diagnostics", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21252027", - "rel_abs": "Rapid and sensitive diagnostics of infectious diseases is an urgent and unmet need as evidenced by the COVID-19 pandemic. Here we report a novel strategy, based on DIgitAl plasMONic nanobubble Detection (DIAMOND), to address these gaps. Plasmonic nanobubbles are transient vapor bubbles generated by laser heating of plasmonic nanoparticles and allow single-particle detection. Using gold nanoparticles labels and an optofluidic setup, we demonstrate that DIAMOND achieves a compartment-free digital counting and works on homogeneous assays without separation and amplification steps. When applied to the respiratory syncytial virus diagnostics, DIAMOND is 150 times more sensitive than commercial lateral flow assays and completes measurements within 2 minutes. Our method opens new possibilities to develop single-particle digital detection methods and facilitate rapid and ultrasensitive diagnostics.\n\nOne Sentence SummarySingle-particle digital plasmonic nanobubble detection allows rapid and ultrasensitive detection of viruses in a one-step homogeneous assay.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yaning Liu", - "author_inst": "University of Texas at Dallas" - }, - { - "author_name": "Haihang Ye", - "author_inst": "University of Texas at Dallas" - }, - { - "author_name": "HoangDinh Huynh", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Peiyuan Kang", - "author_inst": "University of Texas at Dallas" - }, - { - "author_name": "Chen Xie", - "author_inst": "University of Texas at Dallas" - }, - { - "author_name": "Jeffrey S Kahn", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Zhenpeng Qin", - "author_inst": "University of Texas at Dallas" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.22.21252225", "rel_title": "Neutralizing antibody responses 10 months after mild and moderately-severe SARS-CoV-2 infection", @@ -932713,6 +935916,153 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.02.20.432046", + "rel_title": "Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant", + "rel_date": "2021-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.20.432046", + "rel_abs": "The emergence of SARS-CoV-2 variants with mutations in the spike protein is raising concerns about the efficacy of infection- or vaccine-induced antibodies to neutralize these variants. We compared antibody binding and live virus neutralization of sera from naturally infected and spike mRNA vaccinated individuals against a circulating SARS-CoV-2 B.1 variant and the emerging B.1.351 variant. In acutely-infected (5-19 days post-symptom onset), convalescent COVID-19 individuals (through 8 months post-symptom onset) and mRNA-1273 vaccinated individuals (day 14 post-second dose), we observed an average 4.3-fold reduction in antibody titers to the B.1.351-derived receptor binding domain of the spike protein and an average 3.5-fold reduction in neutralizing antibody titers to the SARS-CoV-2 B.1.351 variant as compared to the B.1 variant (spike D614G). However, most acute and convalescent sera from infected and all vaccinated individuals neutralize the SARS-CoV-2 B.1.351 variant, suggesting that protective immunity is retained against COVID-19.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Venkata Viswanadh Edara", + "author_inst": "Emory University" + }, + { + "author_name": "Carson Norwood", + "author_inst": "Emory University" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University" + }, + { + "author_name": "Lilin Lai", + "author_inst": "Emory University" + }, + { + "author_name": "Meredith E Davis-Gardner", + "author_inst": "Emory University" + }, + { + "author_name": "William H Hudson", + "author_inst": "Emory University" + }, + { + "author_name": "Grace Mantus", + "author_inst": "Emory University" + }, + { + "author_name": "Lindsay E Nyhoff", + "author_inst": "Emory University" + }, + { + "author_name": "Max W Adelman", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Fineman", + "author_inst": "Emory University" + }, + { + "author_name": "Shivan Patel", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Byram", + "author_inst": "Emory University" + }, + { + "author_name": "Dumingu Nipuni Gomes", + "author_inst": "Emory University" + }, + { + "author_name": "Garett Michael", + "author_inst": "Emory University" + }, + { + "author_name": "Hayatu Abdullahi", + "author_inst": "Emory University" + }, + { + "author_name": "Nour Beydoun", + "author_inst": "Emory University" + }, + { + "author_name": "Bernadine Panganiban", + "author_inst": "Emory University" + }, + { + "author_name": "Nina McNair", + "author_inst": "Emory University" + }, + { + "author_name": "Kieffer Hellmeister", + "author_inst": "Emory University" + }, + { + "author_name": "Jamila Pitts", + "author_inst": "Emory University" + }, + { + "author_name": "Joy Winters", + "author_inst": "Emory University" + }, + { + "author_name": "Jennifer Kleinhenz", + "author_inst": "Emory University" + }, + { + "author_name": "Jacob Usher", + "author_inst": "Emory University" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University" + }, + { + "author_name": "Jesse J Waggoner", + "author_inst": "Emory University" + }, + { + "author_name": "Ahmed Babiker", + "author_inst": "Emory University" + }, + { + "author_name": "David S Stephens", + "author_inst": "Emory University" + }, + { + "author_name": "Evan J Anderson", + "author_inst": "Emory University" + }, + { + "author_name": "Srilatha Edupuganti", + "author_inst": "Emory University" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University" + }, + { + "author_name": "Rafi Ahmed", + "author_inst": "Emory University" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Emory University" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.20.432110", "rel_title": "A novel glucocorticoid and androgen receptor modulator reduces viral entry and innate immune inflammatory responses in the Syrian Hamster model of SARS-CoV-2", @@ -933273,41 +936623,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.21.432171", - "rel_title": "An Autoantigen Profile of Human A549 Lung Cells Reveals Viral and Host Etiologic Molecular Attributes of Autoimmunity in COVID-19", - "rel_date": "2021-02-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.21.432171", - "rel_abs": "We aim to establish a comprehensive COVID-19 autoantigen atlas in order to understand autoimmune diseases caused by SARS-CoV-2 infection. Based on the unique affinity between dermatan sulfate and autoantigens, we identified 348 proteins from human lung A549 cells, of which 198 are known targets of autoantibodies. Comparison with current COVID data identified 291 proteins that are altered at protein or transcript level in SARS-CoV-2 infection, with 191 being known autoantigens. These known and putative autoantigens are significantly associated with viral replication and trafficking processes, including gene expression, ribonucleoprotein biogenesis, mRNA metabolism, translation, vesicle and vesicle-mediated transport, and apoptosis. They are also associated with cytoskeleton, platelet degranulation, IL-12 signaling, and smooth muscle contraction. Host proteins that interact with and that are perturbed by viral proteins are a major source of autoantigens. Orf3 induces the largest number of protein alterations, Orf9 affects the mitochondrial ribosome, and they and E, M, N, and Nsp proteins affect protein localization to membrane, immune responses, and apoptosis. Phosphorylation and ubiquitination alterations by viral infection define major molecular changes in autoantigen origination. This study provides a large list of autoantigens as well as new targets for future investigation, e.g., UBA1, UCHL1, USP7, CDK11A, PRKDC, PLD3, PSAT1, RAB1A, SLC2A1, platelet activating factor acetylhydrolase, and mitochondrial ribosomal proteins. This study illustrates how viral infection can modify host cellular proteins extensively, yield diverse autoantigens, and trigger a myriad of autoimmune sequelae.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Julia Y. Wang", - "author_inst": "Curandis" - }, - { - "author_name": "Wei Zhang", - "author_inst": "Guizhou Medical University" - }, - { - "author_name": "Michael W. Roehrl", - "author_inst": "Curandis" - }, - { - "author_name": "Victor B. Roehrl", - "author_inst": "Curandis" - }, - { - "author_name": "Michael H. Roehrl", - "author_inst": "Memorial Sloan Kettering Cancer Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/341636", "rel_title": "The interspecific fungal hybrid Verticillium longisporum displays sub-genome-specific gene expression", @@ -934355,6 +937670,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251838", + "rel_title": "Profile of SARS-CoV-2-specific CD4 T cell response: Relationship with disease severity and impact of HIV-1 and active Mycobacterium tuberculosis co-infection", + "rel_date": "2021-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251838", + "rel_abs": "T cells are involved in control of COVID-19, but limited knowledge is available on the relationship between antigen-specific T cell response and disease severity. Here, we assessed the magnitude, function and phenotype of SARS-CoV-2-specific CD4 T cells in 95 hospitalized COVID-19 patients (38 of them being HIV-1 and/or tuberculosis (TB) co-infected) and 38 non-COVID-19 patients, using flow cytometry. We showed that SARS-CoV-2-specific CD4 T cell attributes, rather than magnitude, associates with disease severity, with severe disease being characterized by poor polyfunctional potential, reduced proliferation capacity and enhanced HLA-DR expression. Moreover, HIV-1 and TB co-infection skewed the SARS-CoV-2 T cell response. HIV-1 mediated CD4 T cell depletion associated with suboptimal T cell and humoral immune responses to SARS-CoV-2; and a decrease in the polyfunctional capacity of SARS-CoV-2-specific CD4 T cells was observed in COVID-19 patients with active TB. Our results also revealed that COVID-19 patients displayed reduced frequency of Mtb-specific CD4 T cells, with possible implications for TB disease progression. There results corroborate the important role of SARS-CoV-2-specific T cells in COVID-19 pathogenesis and support the concept of altered T cell functions in patients with severe disease.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elsa du Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Remy Daroowala", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rene T Goliath", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Fatima Abrahams", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Qonita Said-Hartley", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Brian W Allowed", + "author_inst": "Stellenbosch University and Tygerberg Hospital" + }, + { + "author_name": "Marvin Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Katalin A Wilkinson", + "author_inst": "University of Cape Town and The Francis Crick Institute" + }, + { + "author_name": "Cecilia S Lindestam Arlehamn", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Sean Wasserman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Robert J Wilkinson", + "author_inst": "University of Cape Town, Imperial College London and The Francis Crick Institute" + }, + { + "author_name": "- the HIATUS consortium", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.18.21251939", "rel_title": "Applicability of Neighborhood and Building Scale Wastewater-Based Genomic Epidemiology to Track the SARS-CoV-2 Pandemic and other Pathogens.", @@ -934867,45 +938257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.18.431684", - "rel_title": "Delivery of recombinant SARS-CoV-2 envelope protein into human cells", - "rel_date": "2021-02-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.18.431684", - "rel_abs": "SARS-CoV-2 envelope protein (S2-E) is a conserved membrane protein that is essential to coronavirus assembly and budding. Here, we describe the recombinant expression and purification of S2-E into amphipol-class amphipathic polymer solutions. The physical properties of amphipols underpin their ability to solubilize and stabilize membrane proteins without disrupting membranes. Amphipol delivery of S2-E to pre-formed planar bilayers results in spontaneous membrane integration and formation of viroporin ion channels. Amphipol delivery of the S2-E protein to human cells results in membrane integration followed by retrograde trafficking to a location adjacent to the endoplasmic reticulum-to-Golgi intermediate compartment (ERGIC) and the Golgi, which are the sites of coronavirus replication. Delivery of S2-E to cells enables both chemical biological approaches for future studies of SARS-CoV-2 pathogenesis and development of \"Trojan Horse\" anti-viral therapies. This work also establishes a paradigm for amphipol-mediated delivery of membrane proteins to cells.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "James M Hutchison", - "author_inst": "Vanderbilt University School of Medicine Basic Sciences" - }, - { - "author_name": "Ricardo Capone", - "author_inst": "Vanderbilt University School of Medicine Basic Sciences" - }, - { - "author_name": "Dustin D Luu", - "author_inst": "Arizona State University" - }, - { - "author_name": "Arina Hadziselimovic", - "author_inst": "Vanderbilt University School of Medicine Basic Sciences" - }, - { - "author_name": "Wade D Van Horn", - "author_inst": "Arizona State University" - }, - { - "author_name": "Charles R. Sanders", - "author_inst": "Vanderbilt University School of Medicine Basic Sciences" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.02.19.424337", "rel_title": "Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors", @@ -935733,6 +939084,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251625", + "rel_title": "Healthcare-associated COVID-19 in England: a national data linkage study", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251625", + "rel_abs": "ObjectivesNosocomial transmission was an important aspect of SARS-CoV-1 and MERS-CoV outbreaks. Healthcare-associated SARS-CoV-2 infection has been reported in single and multi-site hospital-based studies in England, but not nationally.\n\nMethodsAdmission records for all hospitals in England were linked to SARS-CoV-2 national test data for the period 01/03/2020 to 31/08/2020. Case definitions were: community-onset community-acquired (CO.CA), first positive test (FPT) <14 days pre-admission, up to day 2 of admission; hospital-onset indeterminate healthcare-associated (HO.iHA), FPT on day 3-7; hospital-onset probable healthcare-associated (HO.pHA), FPT on day 8-14; hospital-onset definite healthcare-associated (HO.HA), FPT from day 15 of admission until discharge; community-onset possible healthcare-associated (CO.pHA), FPT [≤]14 days post-discharge.\n\nResultsOne-third (34.4%, 100,859/293,204) of all laboratory-confirmed COVID-19 cases were linked to a hospital record. HO.pHA and HO.HA cases represented 5.3% (15,564/293,204) of all laboratory-confirmed cases and 15.4% (15,564/100,859) of laboratory-confirmed cases among hospital patients. CO.CA and CO.pHA cases represented 86.5% (253,582/293,204) and 5.1% (14,913/293,204) of all laboratory-confirmed cases, respectively.\n\nConclusionsUp to 1 in 6 SARS-CoV-2 infections among hospitalised patients with COVID-19 in England during the first 6 months of the pandemic could be attributed to nosocomial transmission, but these represent less than 1% of the estimated 3 million COVID-19 cases in this period.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Alex Bhattacharya", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon M Collin", + "author_inst": "Public Health England" + }, + { + "author_name": "James Stimson", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon Thelwall", + "author_inst": "Public Health England" + }, + { + "author_name": "Olisaeloka Nsonwu", + "author_inst": "Public Health England" + }, + { + "author_name": "Sarah Gerver", + "author_inst": "Public Health England" + }, + { + "author_name": "Julie Robotham", + "author_inst": "Public Health England" + }, + { + "author_name": "Mark Wilcox", + "author_inst": "University of Leeds" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "Public Health England" + }, + { + "author_name": "Russell Hope", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251844", "rel_title": "An exploratory study on the correlation of population SARS-CoV-2 cycle threshold values to local disease dynamics", @@ -936349,69 +939755,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.02.15.21251552", - "rel_title": "Evaluating the effect of COVID-19 on dispensing patterns: a national cohort analysis", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251552", - "rel_abs": "BackgroundMedication prescribing and dispensing often regarded as one of the most effective ways to manage and improve population health. Prescribed and dispensed medications can be monitored through data linkage for each patient. We hypothesised that changes in patient care resulting from COVID-19, changed the way patients access their prescribed medication.\n\nObjectiveTo develop an efficient approach for evaluation of the impact of COVID-19 on drug dispensing patterns.\n\nMethodsRetrospective observational study using national patient-level dispensing records in Wales-UK. Total dispensed drug items between 01-Jan-2016 and 31-Dec-2019 (counterfactual pre-COVID-19) were compared to 2020 (COVID-19 year). We compared trends of dispensed items in three main British National Formulary (BNF) sections(Cardiovascular system, Central Nervous System, Immunological & Vaccine) using European Age-Standardized rates. We developed an online tool to enable monitoring of changes in dispensing as the pandemic evolves.\n\nResultAmongst all BNF chapters, 52,357,639 items were dispensed in 2020 compared to 49,747,141 items in 2019 demonstrating a relative increase of 5.25% in 2020(95%CI[5.21,5.29]). Comparison of monthly patterns of 2020 and 2019 dispensed items showed a notable difference between the total number of dispensed drug items each month, with an average difference (D) of +290,055 and average Relative Change (RC) of +5.52%. The greatest RC was observed in a substantial March-2020 increase (D=+1,501,242 and RC=+28%), followed by second peak in June (D=+565,004, RC=+10.97%). May was characterised by lower dispensing (D=-399,244, RC=-5.9%). Cardiovascular categories were characterised, across all age groups, by dramatic March-2020 increases, at the epidemic peak, followed by months of lower than expected dispensing, and gradual recovery by September. The Central Nervous System category was similar, but with only a short decline in May, and quicker recovery. A stand-out grouping was Immunological and Vaccine, which dropped to very low levels across all age groups, and all months (including the March dispensing peak).\n\nConclusionsAberration in clinical service delivery during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Fatemeh Torabi", - "author_inst": "Population Data Science and Health Data Research UK,Swansea University" - }, - { - "author_name": "Ashley Akbari", - "author_inst": "Population Data Science and Health Data Research UK,Swansea University" - }, - { - "author_name": "Laura North", - "author_inst": "Population Data Science and Health Data Research UK,Swansea University" - }, - { - "author_name": "Daniel Harris", - "author_inst": "Population Data Science and Health Data Research UK,Swansea University" - }, - { - "author_name": "Gareth Davies", - "author_inst": "Population Data Science and Health Data Research UK,Swansea University" - }, - { - "author_name": "Mike Gravenor", - "author_inst": "Swansea University" - }, - { - "author_name": "Rowena Griffiths", - "author_inst": "Population Data Science and Health Data Research UK,Swansea University" - }, - { - "author_name": "Jane Lyons", - "author_inst": "Population Data Science and Health Data Research UK, SwanseaUniversity" - }, - { - "author_name": "Neil Jenkins", - "author_inst": "NHS Wales Shared Services Partnership" - }, - { - "author_name": "Andrew Morris", - "author_inst": "Swansea University" - }, - { - "author_name": "Julian Halcox", - "author_inst": "Population Data Science and Health Data Research UK, Swansea University" - }, - { - "author_name": "Ronan A. Lyons", - "author_inst": "Population Data Science and Health Data Research UK, Swansea University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.02.11.20233593", "rel_title": "'Trained immunity' from Mycobacterium spp. (environmental or BCG) exposure predicts protection from Coronavirus disease 2019 (COVID-19)", @@ -937371,6 +940714,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.17.21251758", + "rel_title": "Prediction of Mortality in hospitalized COVID-19 patients in a statewide health network", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251758", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSImportanceC_ST_ABSA predictive model to automatically identify the earliest determinants of both hospital discharge and mortality in hospitalized COVID-19 patients could be of great assistance to caregivers if the predictive information is generated and made available in the immediate hours following admission.\n\nObjectiveTo identify the most important predictors of hospital discharge and mortality from measurements at admission for hospitalized COVID-19 patients.\n\nDesignObservational cohort study.\n\nSettingElectronic records from hospitalized patients.\n\nParticipantsPatients admitted between March 3rd and August 24th with COVID-19 in Johns Hopkins Health System hospitals.\n\nExposures216 phenotypic variables collected within 48 hours of admission.\n\nMain OutcomesWe used age-stratified (<60 and >=60 years) random survival forests with competing risks to identify the most important predictors of death and discharge. Fine-Gray competing risk regression (FGR) models were then constructed based on the most important RSF-derived covariates.\n\nResultsOf 2212 patients, 1913 were discharged (age 57{+/-}19, time-to-discharge 9{+/-}11 days) while 279 died (age 75{+/-}14, time to death 14{+/-}15 days). Patients >= 60 years were nearly 10 times as likely to die within 60 days of admission as those <60. As the pandemic evolved, the rate of hospital discharge increased in both older and younger patients. Incident death and hospital discharge were accurately predicted by measures of respiratory distress, inflammation, infection, renal function, red cell turn over and cardiac stress. FGR models for each of hospital discharge and mortality as outcomes based on these variables performed well in the older (AUC 0.80-0.85 at 60-days) and younger populations (AUC >0.90 at 60-days).\n\nConclusions and RelevanceWe identified markers collected within 2 days of admission that predict hospital discharge and mortality in COVID-19 patients and provide prediction models that may be used to guide patient care. Our proposed model suggests that hospital discharge and mortality can be forecasted with high accuracy based on 8-10 variables at this stage of the COVID-19 pandemic. Our findings also point to several specific pathways that could be the focus of future investigations directed at reducing mortality and expediting hospital discharge among COVID-19 patients. Probability of hospital discharge increased over the course of the pandemic.\n\nKO_SCPLOWEYC_SCPLOW PO_SCPLOWOINTSC_SCPLOWO_ST_ABSQuestionC_ST_ABSCan we predict the likelihood of hospital discharge as well as mortality from data obtained in the first 48 hours from admission in hospitalized COVID-19 patients?\n\nFindingsModels based on extensive phenotyping mined directly from electronic medical records followed by variable selection, accounted for the competing events of hospital death versus discharge, predicted both death and discharge with area under the receiver operating characteristic curves of >0.80.\n\nMeaningHospital discharge and mortality can be forecasted with high accuracy based on just 8-10 variables, and the probability of hospital discharge increased over the course of the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bharath Ambale Venkatesh", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Thiago Quinaglia", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Mahsima Shabani", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Jaclyn Sesso", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Karan Kapoor", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Matthew Matheson", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Colin O Wu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Christopher Cox", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joao A Lima", + "author_inst": "Johns Hopkins Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251849", "rel_title": "Convalescent plasma for preventing critical illness in COVID-19: A phase 2 trial and immune profile", @@ -938099,45 +941493,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.02.17.21251926", - "rel_title": "SARS-CoV-2 Shedding Dynamics Across the Respiratory Tract, Sex, and Disease Severity for Adult and Pediatric COVID-19", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251926", - "rel_abs": "BackgroundSARS-CoV-2 shedding dynamics in the upper (URT) and lower respiratory tract (LRT) remain unclear.\n\nObjectiveTo analyze SARS-CoV-2 shedding dynamics across COVID-19 severity, the respiratory tract, sex and age cohorts (aged 0 to 17 years, 18 to 59 years, and 60 years or older).\n\nDesignSystematic review and pooled analyses.\n\nSettingMEDLINE, EMBASE, CENTRAL, Web of Science Core Collection, medRxiv and bioRxiv were searched up to 20 November 2020.\n\nParticipantsThe systematic dataset included 1,266 adults and 136 children with COVID-19.\n\nMeasurementsCase characteristics (COVID-19 severity, age and sex) and quantitative respiratory viral loads (rVLs).\n\nResultsIn the URT, adults with severe COVID-19 had higher rVLs at 1 DFSO than adults (P = 0.005) or children (P = 0.017) with nonsevere illness. Between 1-10 DFSO, severe adults had comparable rates of SARS-CoV-2 clearance from the URT as nonsevere adults (P = 0.479) and nonsevere children (P = 0.863). In the LRT, severe adults showed higher post-symptom-onset rVLs than nonsevere adults (P = 0.006). In the analyzed period (4-10 DFSO), severely affected adults had no significant trend in SARS-CoV-2 clearance from LRT (P = 0.105), whereas nonsevere adults showed a clear trend (P < 0.001). After stratifying for disease severity, sex and age (including child vs. adult) were not predictive of the duration of respiratory shedding.\n\nLimitationLimited data on case comorbidities and few samples in some cohorts.\n\nConclusionHigh, persistent LRT shedding of SARS-CoV-2 characterized severe COVID-19 in adults. After symptom onset, severe cases tended to have higher URT shedding than their nonsevere counterparts. Disease severity, rather than age or sex, predicted SARS-CoV-2 kinetics. LRT specimens should more accurately prognosticate COVID-19 severity than URT specimens.\n\nPrimary Funding SourceNatural Sciences and Engineering Research Council.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Paul Z Chen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Niklas Bobrovitz", - "author_inst": "University of Toronto" - }, - { - "author_name": "Zahra Premji", - "author_inst": "University of Calgary" - }, - { - "author_name": "Marion Koopmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "David N Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Frank X Gu", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.17.21251961", "rel_title": "Diagnostic Performance of Pooled RT-PCR Testing for SARS-CoV-2 Detection", @@ -939101,6 +942456,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.15.21249420", + "rel_title": "COVID-19 Associated Stroke--A Single Centre Experience", + "rel_date": "2021-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21249420", + "rel_abs": "Background and PurposeVarious neurological complications have been reported in association with COVID-19. We report our experience of COVID-19 with stroke at a single center over a period of eight months spanning 1 March to 31 October 2020.\n\nMethodsWe recruited all patients admitted to Internal Medicine with an acute stroke, who also tested positive for COVID-19 on RTPCR. We included all stroke cases in our analysis for prediction of in-hospital mortality, and separately analyzed arterial infarcts for vascular territory of ischemic strokes.\n\nResultsThere were 62 stroke cases among 3923 COVID-19 admissions (incidence 1.6%). Data was available for 58 patients {mean age 52.6 years; age range 17-91; F/M=20/38; 24% (14/58) aged [≤]40; 51% (30/58) hypertensive; 36% (21/58) diabetic; 41% (24/58) with O2 saturation <95% at admission; 32/58 (55.17 %) in-hospital mortality}. Among 58 strokes, there were 44 arterial infarcts, seven bleeds, three arterial infarcts with associated cerebral venous sinus thrombosis, two combined infarct and bleed, and two of indeterminate type. Among the total 49 infarcts, Carotid territory was the commonest affected (36/49; 73.5%), followed by vertebrobasilar (7/49; 14.3%) and both (6/49; 12.2%). Concordant arterial block was seen in 61% (19 of 31 infarcts with angiography done). Early stroke (within 48 hours of respiratory symptoms) was seen in 82.7% (48/58) patients. Patients with poor saturation at admission were older (58 vs 49 years) and had more comorbidities and higher mortality (79% vs 38%). Mortality was similar in young strokes and older patients, although the latter required more intense respiratory support. Logistic regression analysis showed that low GCS and requirement for increasing intensity of respiratory support predicted in-hospital mortality.\n\nConclusionsWe had a 1.6% incidence of COVID-19 related stroke of which the majority were carotid territory infarcts. In-hospital mortality was 55.17%, predicted by low GCS at admission.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Uma Sundar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Niteen Karnik", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Amita Mukhopadhyay", + "author_inst": "Dr Chandramma Dayananda Sagar Institute of Medical Education and Research, Kanakapura 562112, Ramanagara District, Karnataka, India" + }, + { + "author_name": "Pramod Darole", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Shaonak Kolte", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Ashank Bansal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Yojana Gokhale", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dnaneshwar Asole", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Anagha Joshi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Sangeeta Pednekar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Swati Chavan", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Trupti Trivedi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Namita Padwal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Lalana Kalekar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Charulata Londhe", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Rupal Padhiyar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dharmendra Pandey", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dhirendra Yadav", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Sonal Honrao", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Prerana Bhavsar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Priyanshu Shah", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Satish Gosavi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Aniket Wadal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Awesh Shingare", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Mayuri Trivedi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Gauri Pathak Oak", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.13.21251670", "rel_title": "Excess Mortality in Suicide caused by COVID-19 in Japan", @@ -939857,61 +943331,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.02.18.431484", - "rel_title": "A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine", - "rel_date": "2021-02-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.18.431484", - "rel_abs": "Several SARS-CoV-2 vaccines have received EUAs, but many issues remain unresolved, including duration of conferred immunity and breadth of cross-protection. Adjuvants that enhance and shape adaptive immune responses that confer broad protection against SARS-CoV-2 variants will be pivotal for long-term protection. We developed an intranasal, rationally designed adjuvant integrating a nanoemulsion (NE) that activates TLRs and NLRP3 with an RNA agonist of RIG-I (IVT DI). The combination adjuvant with spike protein antigen elicited robust responses to SARS-CoV-2 in mice, with markedly enhanced TH1-biased cellular responses and high virus-neutralizing antibody titers towards both homologous SARS-CoV-2 and a variant harboring the N501Y mutation shared by B1.1.7, B.1.351 and P.1 variants. Furthermore, passive transfer of vaccination-induced antibodies protected naive mice against heterologous viral challenge. NE/IVT DI enables mucosal vaccination, and has the potential to improve the immune profile of a variety of SARS-CoV-2 vaccine candidates to provide effective cross-protection against future drift variants.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sonia Jangra", - "author_inst": "Icahn School of Medicine at Mount Sinai New York, NY, USA" - }, - { - "author_name": "Jeffrey J Landers", - "author_inst": "University of Michigan Medical School, Ann Arbor, MI, USA" - }, - { - "author_name": "Raveen Rathnasinghe", - "author_inst": "Icahn School of Medicine at Mount Sinai New York, NY, USA" - }, - { - "author_name": "Katarzyna W Janczak", - "author_inst": "University of Michigan Medical School, Ann Arbor, MI, USA" - }, - { - "author_name": "Marilia Cascalho", - "author_inst": "University of Michigan Medical School, Ann Arbor, MI, USA" - }, - { - "author_name": "Andrew A Kennedy", - "author_inst": "University of Michigan Medical School, Ann Arbor, MI, USA" - }, - { - "author_name": "Andrew W Tai", - "author_inst": "University of Michigan Medical School, Ann Arbor, MI, USA" - }, - { - "author_name": "James R Baker Jr.", - "author_inst": "University of Michigan Medical School, Ann Arbor, MI, USA" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Pamela T Wong", - "author_inst": "University of Michigan Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.17.431722", "rel_title": "Homologous and heterologous serological response to the N-terminal domain of SARS-CoV-2", @@ -940879,6 +944298,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.15.21251781", + "rel_title": "Epidemiological dynamics of the incidence of COVID-19 in children and the relationship with the opening of schools in Catalonia (Spain)", + "rel_date": "2021-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251781", + "rel_abs": "Here we analyse the epidemiological trend of the incidence of COVID-19 in children in Catalonia (Spain) during the first 20 weeks of the 2020-2021 school year. This study demonstrates that while schools were open the incidence rate among children remained significantly lower than in general population, despite a greater diagnostic effort in children. These results suggest that schools have not played a significant role in the SARS-CoV-2 dissemination in Catalonia.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Aida Perramon", + "author_inst": "Universitat Pompeu Fabra, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Antoni Soriano-Arandes", + "author_inst": "Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "David Pino", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya (UPC BarcelonaTech), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Uxue Lazcano", + "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Cristina Andres", + "author_inst": "Respiratory Viruses Unit, Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Marti Catala", + "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Fundacio Institut d'Investigacio en Ciencies de la Salut Germans Trias i Pujol (IGTP), Badalona, " + }, + { + "author_name": "Anna Gatell", + "author_inst": "Equip Pediatria Territorial Alt Penedes-Garraf, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Mireia Carulla", + "author_inst": "ABS Pla d'Urgell (Mollerussa), Lleida, Catalonia, Spain" + }, + { + "author_name": "Dolors Canadell", + "author_inst": "CAP Barbera del Valles, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Gemma Ricos", + "author_inst": "CAP Drassanes, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Maria Teresa Riera-Bosch", + "author_inst": "EAP Vic Nord, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Silvia Burgaya", + "author_inst": "EAP Manlleu, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Olga Salvado", + "author_inst": "CAP Llibertat Reus, Tarragona, Catalonia, Spain" + }, + { + "author_name": "Javier Cantero", + "author_inst": "Corporacio del Maresme i la Selva, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Monica Vila", + "author_inst": "EAP Horta, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Miriam Poblet", + "author_inst": "Equip Territorial Pediatric Sabadell Nord, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Almudena Sanchez", + "author_inst": "CAP Les Hortes, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Anna Maria Ristol", + "author_inst": "CAP Can Serra Hospitalet de Llobregat, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Pepe Serrano", + "author_inst": "Equip Pediatria Territorial Alt Penedes-Garraf, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Andres Anton", + "author_inst": "Respiratory Viruses Unit, Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Clara Prats", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya (UPC BarcelonaTech), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Pere Soler-Palacin", + "author_inst": "Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.15.21251788", "rel_title": "COVID-19 European Regional Tracker", @@ -941646,61 +945168,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.02.17.431652", - "rel_title": "How the replication and transcription complex of SARS-CoV-2 functions in leader-to-body fusion", - "rel_date": "2021-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431652", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although unprecedented efforts are underway to develop therapeutic strategies against this disease, scientists have acquired only a little knowledge regarding the structures and functions of the CoV replication and transcription complex (RTC) and 16 non-structural proteins, named NSP1-16.\n\nResultsIn the present study, we proposed a two-route model to answer how the RTC functions in the jumping transcription of CoVs. The key step leading to this model was that the motif AAACH for METTL3 recognition flanking the transcription regulatory sequence (TRS) motif was discovered to determine the m6A methylation of SARS-CoV-2 RNAs, by reanalyzing public Nanopore RNA-seq data. As the most important finding, TRS hairpins were reported for the first time to interpret NSP15 cleavage, RNA methylation of CoVs and their association at the molecular level. In addition, we reported canonical TRS motifs of all CoVs to prove the importance of our findings.\n\nConclusionsThe main conclusions are: (1) TRS hairpins can be used to identify recombination regions in CoV genomes; (2) RNA methylation of CoVs participates in the determination of the RNA secondary structures by affecting the formation of base pairing; and (3) The eventual determination of the CoV RTC global structure needs to consider METTL3 in the experimental design. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, providing a crucial basis for future studies.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jianguang Liang", - "author_inst": "School of Pharmacy, Changzhou University" - }, - { - "author_name": "Jinsong Shi", - "author_inst": "National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine" - }, - { - "author_name": "Shunmei Chen", - "author_inst": "Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University" - }, - { - "author_name": "Guangyou Duan", - "author_inst": "Qilu Normal University+School of Life Sciences" - }, - { - "author_name": "Fan Yang", - "author_inst": "National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine" - }, - { - "author_name": "Cheng Zhi", - "author_inst": "College of Life Sciences, Nankai University" - }, - { - "author_name": "Xin Li", - "author_inst": "College of Life Sciences, Nankai University" - }, - { - "author_name": "Jishou Ruan", - "author_inst": "Nankai University+School of Mathematical Sciences" - }, - { - "author_name": "Dong Mi", - "author_inst": "Department of Clinical Laboratory, Tianjin Central Hospital of Obstetrics and Gynecology, Affiliated Maternity Hospital, Nankai University" - }, - { - "author_name": "Gao Shan", - "author_inst": "College of Life Sciences, Nankai University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.16.431437", "rel_title": "Phase transitions may explain why SARS-CoV-2 spreads so fast and why new variants are spreading faster", @@ -942684,6 +946151,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.15.431291", + "rel_title": "Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases", + "rel_date": "2021-02-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.15.431291", + "rel_abs": "Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained and the impact of underlying immune dysfunction or suppression unknown. Here, we examined the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM) and juvenile systemic lupus erythematosus (JSLE), against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. Despite immune dysfunction and immunosuppressive treatment, JIA, JDM and JSLE patients mounted comparable or stronger responses than healthier peers, dominated by IgG antibodies to HCoV-OC43 spike, and harboured IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM and JSLE patients, arguing against increased exposure. Consequently, autoimmune rheumatic diseases and their treatment were associated with a favourable ratio of spike to nucleoprotein antibodies.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Claire Deakin", + "author_inst": "UCL" + }, + { + "author_name": "Georgina Cornish", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Kevin Ng", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nikhil Faulkner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "William Bolland", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Veera Panova", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Joshua Hope", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Annachiara Rosa", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Saira Hussain", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Chris Earl", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Bethany Jebson", + "author_inst": "UCL" + }, + { + "author_name": "Merry Wilkinson", + "author_inst": "UCL" + }, + { + "author_name": "Lucy Marshall", + "author_inst": "UCL" + }, + { + "author_name": "Lizzy Rosser", + "author_inst": "UCL" + }, + { + "author_name": "Ania Radziszewska", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Peckham", + "author_inst": "UCL" + }, + { + "author_name": "Judith Heaney", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Rickman", + "author_inst": "UCL" + }, + { + "author_name": "Stavroula Paraskevopoulou", + "author_inst": "UCL" + }, + { + "author_name": "Catherine Houlihan", + "author_inst": "UCL" + }, + { + "author_name": "Moria Spyer", + "author_inst": "UCL" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Mccauley", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCL" + }, + { + "author_name": "Peter Cherepanov", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Coziana Ciurtin", + "author_inst": "UCL" + }, + { + "author_name": "Lucy Wedderburn", + "author_inst": "UCL" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.15.430863", "rel_title": "Live attenuated SARS-CoV-2 vaccine candidate: Protective immunity without serious lung lesions in Syrian hamsters", @@ -943235,105 +946833,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.12.21251298", - "rel_title": "SARS-CoV2- infection as a trigger of humoral response against apolipoprotein A-1", - "rel_date": "2021-02-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.12.21251298", - "rel_abs": "AimsUnravelling autoimmune targets triggered by SARS-CoV-2 infection may provide crucial insights in the physiopathology of the disease and foster the development of potential therapeutic candidate targets and prognostic tools. We aimed at determining i) the association between anti-SARS-CoV-2 and anti-apoA-1 humoral response, ii) their relationship to prognosis, and iii) the degree of linear homology between SARS-CoV-2, apoA-1, and Toll-like receptor-2 (TLR2) epitopes.\n\nMethods and ResultsImmunoreactivity against different engineered peptides as well as cytokines were assessed by immunoassays, on a case-control (n=101), an intensive care unit (ICU; n=126) with a 28-days follow-up, and a general population cohort (n=663) with available samples in the pre and post-pandemic period. Using bioinformatics modelling a linear sequence homologies between apoA-1, TLR2, and Spike epitopes were identified. Overall, anti-apoA-1IgG levels were higher in COVID-19 patients or anti-SARS-CoV-2 seropositive individuals than in healthy donors or anti-SARS-CoV-2 seronegative individuals (p<0.0001). Significant and similar associations were noted between anti-apoA-1, anti-SARS-CoV-2IgG, cytokines, and lipid profile. In ICU patients, anti-SARS-CoV-2 and anti-apoA-1 seroconversion rates displayed similar 7-days kinetics, reaching 82% for anti-apoA-1 seropositivity. C-statistics (CS) indicated that anti-Spike/TLR2 mimic-peptide IgGs displayed a significant prognostic accuracy for overall mortality at 28 days (CS: 0.64; p=0.02). In the general population, SARS-CoV-2 exposure increased baseline anti-apoA-1 IgG levels.\n\nConclusionCOVID-19 induces a marked humoral response against the major protein of high-density lipoproteins. As a correlate of poorer prognosis in other clinical settings, such autoimmunity signatures may relate to long-term COVID-19 prognosis assessment and warrant further scrutiny in the current COVID-19 pandemic.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sabrina Pagano", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Sabine Yerly", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Benjamin Meyer", - "author_inst": "University of Geneva" - }, - { - "author_name": "Catherine Juillard", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Noemie Suh", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Christophe LeTerrier", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jean-Pierre Daguer", - "author_inst": "University of Geneva" - }, - { - "author_name": "Lluc Farrera Soler", - "author_inst": "University of Geneva" - }, - { - "author_name": "Sofia Barluenga", - "author_inst": "University of Geneva" - }, - { - "author_name": "Giovanni Piumatti", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Oliver Hartley", - "author_inst": "University of Geneva" - }, - { - "author_name": "Barbara Lemaitre", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Christiane Sigrid Eberhardt", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Claire-Anne Siegrist", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Silvia Stringhini", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jerome Pugin", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Nicolas Winssinger", - "author_inst": "University of Geneva" - }, - { - "author_name": "Nicolas Vuilleumier", - "author_inst": "Geneva University Hospitals" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.07.21251322", "rel_title": "Confirmation of an Inverse Relationship between Bioaerosol Count and Influenza-like Illnesses, Including COVID-19. On the Contribution of Mold Spores", @@ -944329,6 +947828,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.12.431032", + "rel_title": "Pulsed broad-spectrum UV light effectively inactivates SARS-CoV-2 on multiple surfaces", + "rel_date": "2021-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.431032", + "rel_abs": "The ongoing SARS-CoV-2 pandemic has resulted in an increased need for technologies capable of efficiently disinfecting public spaces as well as personal protective equipment. UV light disinfection is a well-established method for inactivating respiratory viruses. Here, we have determined that broad-spectrum, pulsed UV light is effective at inactivating SARS-CoV-2 on multiple surfaces. For hard, non-porous surfaces we observed that SARS-CoV-2 was inactivated to undetectable levels on plastic and glass with a UV dose of 34.9 mJ/cm2 and stainless steel with a dose of 52.5 mJ/cm2. We also observed that broad-spectrum, pulsed UV light is effective at reducing SARS-CoV-2 on N95 respirator material to undetectable levels with a dose of 103 mJ/cm2. We included UV dosimeter cards that provide a colorimetric readout of UV dose and demonstrated their utility as a means to confirm desired levels of exposure were reached. Together, the results present here demonstrate that broad-spectrum, pulsed UV light is an effective technology for the inactivation of SARS-CoV-2 on multiple surfaces.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alexander S Jureka", + "author_inst": "Georgia State University" + }, + { + "author_name": "Caroline G Williams", + "author_inst": "Georgia State University" + }, + { + "author_name": "Christopher F Basler", + "author_inst": "Georgia State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.12.431026", "rel_title": "Jumper Enables Discontinuous Transcript Assembly in Coronaviruses", @@ -945049,33 +948575,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.10.21251475", - "rel_title": "'Leading from the front implementation strategies increase the success of influenza vaccination drives among healthcare workers: A reanalysis of Systematic Review evidence using Intervention Component Analysis (ICA) and Qualitative Comparative Analysis (QCA)", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251475", - "rel_abs": "BackgroundSeasonal influenza vaccination of healthcare workers (HCW) is widely recommended to protect staff and patients. A previous systematic review examined interventions to encourage uptake finding that hard mandates, such as loss of employment for non-vaccination, were more effective than soft mandates, such as signing a declination form, or other interventions such as incentives. Despite these overarching patterns the authors of the review concluded that substantial heterogeneity remained requiring further analysis. This paper reanalyses the evidence using Intervention Component Analysis (ICA) and Qualitative Comparative Analysis (QCA) to examine whether the strategies used to implement interventions explain the residual heterogeneity.\n\nMethodsWe used ICA to extract implementation features and trialists reflections on what underpinned the success of the intervention they evaluated. The ICA findings then informed and structured two QCA analyses to systematically analyse associations between implementation features and intervention outcomes. Analysis 1 examined hard mandate studies. Analysis 2 examined soft mandates and other interventions.\n\nResultsIn Analysis 1 ICA revealed the significance of leading from the front rather than top-down implementation of hard mandates. Four key features underpinned this: providing education prior to implementation; two-way engagement so HCW can voice concerns prior to implementation; previous use of other strategies so that institutions dont-go-in-cold with hard-mandates; and support from institutional leadership. QCA revealed that either of two configurations were associated with greater success of hard mandates. The first involves two-way engagement, leadership support and a dont-go-in-cold approach. The second involves leadership support, education and a dont-go-in-cold approach. Reapplying the leading from the front theory in Analysis 2 revealed similar patterns.\n\nConclusionsRegardless of intervention type a leading from the front approach to implementation will likely enhance intervention success. While the results pertain to flu vaccination among HCWs, the components identified here may be relevant to public health campaigns regarding COVID-19 vaccination.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Katy Sutcliffe", - "author_inst": "EPPI-Centre, Social Research Institute, University College London" - }, - { - "author_name": "Dylan Kneale", - "author_inst": "EPPI-Centre, Social Research Institute, University College London" - }, - { - "author_name": "James Thomas", - "author_inst": "EPPI-Centre, Social Research Institute, University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.11.21251590", "rel_title": "Evaluating COVID-19 reporting data in the context of testing strategies across 31 LMICs", @@ -945879,6 +949378,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.02.10.21251478", + "rel_title": "CATALYST trial protocol: A multicentre, open-label, phase II, multi-arm trial for an early and accelerated evaluation of the potential treatments for COVID-19 in hospitalised adults", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251478", + "rel_abs": "IntroductionSevere SARS-CoV-2 infection is associated with a dysregulated immune response. Inflammatory monocytes and macrophages are crucial, promoting injurious, pro-inflammatory sequelae. Immunomodulation is, therefore, an attractive therapeutic strategy and we sought to test licensed and novel candidate drugs.\n\nMethods and analysisThe CATALYST trial is a multi-arm, open-label, multi-centre, phase II platform trial designed to identify candidate novel treatments to improve outcomes of patients hospitalised with COVID-19 compared with usual care. Treatments with evidence of biomarker improvements will be put forward for larger-scale testing by current national phase III platform trials. Hospitalised patients >16 years with a clinical picture strongly suggestive of SARS-CoV-2 pneumonia (confirmed by chest X-ray or CT scan, with or without a positive reverse transcription polymerase chain reaction (RT-PCR) assay) and a C-Reactive Protein (CRP) [≥]40 mg/L are eligible. The primary outcome measure is CRP, measured serially from admission to day 14, hospital discharge or death. Secondary outcomes include the WHO Clinical Progression Improvement Scale as a principal efficacy assessment.\n\nEthics and disseminationThe protocol was approved by the East Midlands - Nottingham 2 Research Ethics Committee (20/EM/0115) and given Urgent Public Health status; initial approval was received on 05-May-2020, current protocol version (v6.0) approval on 12-Oct-2020. The MHRA also approved all protocol versions. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.\n\nTrial registration numberEudraCT Number: 2020-001684-89\n\nISRCTN Number: 40580903\n\nStrengths and limitations of this trialO_LICATALYST will provide a rapid readout on the safety and proof-of-concept of candidate novel treatments\nC_LIO_LICATALYST will enable phase III trial resources to be focussed and allocated for agents with a high likelihood of success\nC_LIO_LICATALYST uses Bayesian multi-level models to allow for nesting of repeated measures data, with factors for each individual patient and treatment arm, and allowing for non-linear responses\nC_LIO_LICATALYST is not designed to provide a definitive signal on clinical outcomes\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Tonny Veenith", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Benjamin A Fisher", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Daniel Slade", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Anna Rowe", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Rowena Sharpe", + "author_inst": "University of Birmingham" + }, + { + "author_name": "David R Thickett", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tony Whitehouse", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Matthew Rowland", + "author_inst": "University of Oxford" + }, + { + "author_name": "James Scriven", + "author_inst": "University Hospitals Birmingham NHS Trust" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sarah J Bowden", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Joshua S Savage", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Duncan Richards", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julian Bion", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pamela Kearns", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Simon Gates", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.02.11.21251581", "rel_title": "A genetically-informed study disentangling the relationships between tobacco smoking, cannabis use, alcohol consumption, substance use disorders and respiratory infections, including COVID-19", @@ -946715,49 +950293,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.12.429482", - "rel_title": "Physical phenotype of blood cells is altered in COVID-19", - "rel_date": "2021-02-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.429482", - "rel_abs": "Clinical syndrome coronavirus disease 2019 (COVID-19) induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by rapid spreading and high mortality worldwide. While the pathology is not yet fully understood, hyper-inflammatory response and coagulation disorders leading to congestions of microvessels are considered to be key drivers of the still increasing death toll. Until now, physical changes of blood cells have not been considered to play a role in COVID-19 related vascular occlusion and organ damage. Here we report an evaluation of multiple physical parameters including the mechanical features of five frequent blood cell types, namely erythrocytes, lymphocytes, monocytes, neutrophils, and eosinophils. More than 4 million blood cells of 17 COVID-19 patients at different levels of severity, 24 volunteers free from infectious or inflammatory diseases, and 14 recovered COVID-19 patients were analyzed. We found significant changes in erythrocyte deformability, lymphocyte stiffness, monocyte size, and neutrophil size and deformability. While some of these changes recovered to normal values after hospitalization, others persisted for months after hospital discharge, evidencing the long-term imprint of COVID-19 on the body.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Marketa Kubankova", - "author_inst": "Max Planck Institute for the Science of Light & Max-Planck-Zentrum fuer Physik und Medizin, Staudtstrasse 2, 91058 Erlangen, Germany" - }, - { - "author_name": "Bettina Hohberger", - "author_inst": "Department of Ophthalmology, Friedrich-Alexander-University Erlangen-Nuernberg, Schwabachanlage 6, 91054 Erlangen, Germany" - }, - { - "author_name": "Jakob Hoffmanns", - "author_inst": "Department of Ophthalmology, Friedrich-Alexander-University Erlangen-Nuernberg, Schwabachanlage 6, 91054 Erlangen, Germany" - }, - { - "author_name": "Julia Fuerst", - "author_inst": "Department of Internal Medicine 1, University Medical Center Erlangen, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany" - }, - { - "author_name": "Martin Hermann", - "author_inst": "Department of Internal Medicine 3, University Medical Center Erlangen, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany" - }, - { - "author_name": "Jochen Guck", - "author_inst": "Max Planck Institute for the Science of Light & Max-Planck-Zentrum fuer Physik und Medizin, Staudtstrasse 2, 91058 Erlangen, Germany" - }, - { - "author_name": "Martin Krater", - "author_inst": "Max Planck Institute for the Science of Light & Max-Planck-Zentrum fuer Physik und Medizin, Staudtstrasse 2, 91058 Erlangen, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.02.12.430472", "rel_title": "Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies", @@ -947617,6 +951152,232 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.10.21251247", + "rel_title": "Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251247", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Shabir Ahmed Madhi", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Vicky Lynne Baillie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Clare Louise Cutland", + "author_inst": "Wits- Alive: African Leadership in Vaccinology Expertise, University of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Merryn Voysey", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Anthonet L Koen", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Lee Fairlie", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Sherman D Padayachee", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Keertan Dheda", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Shaun L Barnabas", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Qasim Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre" + }, + { + "author_name": "Carmen Briner", + "author_inst": "Perinatal HIV Research Unit, Faculty of Health Science, University of the Witwatersrand, South Africa" + }, + { + "author_name": "Gaurav Kwatra", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Khatija Ahmed", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Parvinder Aley", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Sutika Bhikha", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Jinal N Bhiman", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "As'ad Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre, Soweto, South Africa" + }, + { + "author_name": "Jeanine du plessis", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Aliasgar Esmail", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Marisa Groenewald", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Elizea Horne", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Shi-Hsia Hwa", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Aylin Jose", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" + }, + { + "author_name": "Matt Laubscher", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Mookho Malahleha", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Masebole Masenya", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Mduduzi Masilela", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Shakeel McKenzie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Kgaogelo Molapo", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Andrew Moultrie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Suzette Oelofse", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Faeezah Patel", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Sureshnee Pillay", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Sarah Rhead", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Hylton Rodel", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Lindie Rossouw", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Carol Taoushanis", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Houryiah Tegally", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Asha Thombrayil", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Samuel van Eck", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Constantinos Wibmer", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "Nicholas M Durham", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Elizabeth J Kelly", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Tonya Villafana", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Sarah Gilbert", + "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" + }, + { + "author_name": "Andrew J Pollard", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Penny L Moore", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Alane Izu", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "- Network for Genomic Surveillance in South Africa (NGS-SA)", + "author_inst": "" + }, + { + "author_name": "- Wits VIDA COVID vaccine trial group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.10.21251392", "rel_title": "COVID-19 and Influenza: Vaccination Before and During the Pandemic among the Lebanese Adult Population", @@ -948173,104 +951934,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.11.21251557", - "rel_title": "Inclusion of cycle threshold (CT) values when reporting SARS-CoV-2 RT-PCR results improves clinical Interpretation in suspected and confirmed COVID-19", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251557", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Naema Hassan Al Molawi", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohamed Ali Ben Hadj Kacem", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Reham Awni El Kahlout", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Einas Al Kuwari", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Abdullatif Al Khal", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Imtiaz Gilliani", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Hatoun Saeb", - "author_inst": "Ministry of Public Health, Doha, Qatar" - }, - { - "author_name": "Sheikh Mohammad Al Thani", - "author_inst": "Ministry of Public Health, Doha, Qatar" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health, Doha, Qatar" - }, - { - "author_name": "Hanan F. Abdul Rahim", - "author_inst": "Qatar University, Doha, Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" - }, - { - "author_name": "Patrick Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Saad Al Kaabi", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Muna A. Rahman S. AlMaslamani", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Brendan David Morris", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Nasser Al-Ansari", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.11.21251563", "rel_title": "Long stability of SARS-CoV-2 RNA in dry and saliva swab samples stored for diagnostics, Denmark", @@ -949427,6 +953090,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.02.08.21250309", + "rel_title": "Hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic - Insights from the German-wide Helios hospital network", + "rel_date": "2021-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250309", + "rel_abs": "BackgroundWhile there are numerous reports that describe emergency care during the early Covid-19 pandemic, there is scarcity of data for later stages. This study analyzes hospitalization rates for 37 emergency-sensitive conditions in the largest German-wide hospital network during different pandemic phases.\n\nMethodsUsing claims data of 80 hospitals, consecutive cases between January 1 and November 17, 2020 were analyzed and compared to a corresponding period in 2019. Incidence-rate ratios (IRR) comparing the both periods were calculated using Poisson regression to model the number of hospitalizations per day.\n\nResultsThere was a hospitalization deficit between March 12 and June 13, 2020 (coinciding with the 1st pandemic wave) with 32,807 hospitalizations as opposed to 39,379 in 2019 (IRR 0.83, 95% CI 0.82 - 0.85, P<0.01). During the following period (June 14 to November 17, 2020, including the start of 2nd wave), hospitalizations were reduced from 63,799 in 2019 to 59,910 in 2020, but this reduction was not that pronounced (IRR 0.94, 95% CI 0.93 - 0.95, P<0.01). There was an increase in hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave during which hospitalizations had been reduced for those conditions. In contrast, hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic.\n\nConclusionsThere was an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic with heterogeneous effects on different disease categories. The increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism is an alarming signal that requires attention and further studies.\n\nKEY MESSAGESO_ST_ABSWhat is already known on this subjectC_ST_ABSO_LIThere has been a reduction in emergency room visits and hospital admissions for several emergent medical and surgical conditions during the early Covid-19 pandemic (1st wave).\nC_LI\n\nWhat this study addsO_LIUsing claims data of 80 German-wide Helios hospitals, we found an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic until mid November 2020 with heterogeneous effects on different disease categories. While hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic. There was an alarming increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "ANDREAS BOLLMANN", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Sven Hohenstein", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Vincent Pellissier", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Sebastian Koenig", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Laura Ueberham", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Gerhard Hindricks", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Andreas Meier-Hellmann", + "author_inst": "Helios Hospitals" + }, + { + "author_name": "Ralf Kuhlen", + "author_inst": "Helios Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.02.10.430668", "rel_title": "Data-driven analysis of COVID-19 reveals specific severity patterns distinct from the temporal immune response", @@ -950487,65 +954197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.08.21251009", - "rel_title": "Population-Based Study of anti-SARS-CoV-2, Social Distancing and Government Responses in Joinville, Brazil", - "rel_date": "2021-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251009", - "rel_abs": "Background: The city of Joinville had been mildly affected by the COVID-19 pandemic until June 2020. This study aimed to longitudinally assess the prevalence of exposure to the virus and social distancing practices in the local population. Methods: A randomized selection of households stratified by region was created. From June 15 to August 7, 2020, a dweller was randomized in each household, answered a questionnaire, and performed a test for the detection of SARS-CoV-2 antibodies. The prevalence of positive tests was calculated for each week and adjusted for the test's sensitivity and specificity. Results: The adjusted proportion of positive results increased from 1.4% in the first week (margin of error [ME] 0% to 2.87%) to 13.38% in the eighth week (ME 10.22% to 16.54%). Among the 213 participants that tested positive, 55 (25.82%) were asymptomatic. Only 37 (17.37%) sought medical consultation for any symptom. Among the 77 (36.15%) that were leaving home to work or study, only 18 (23.38%) stopped due to any symptom. The proportion that referred going to bars, restaurants, or making non-essential shopping decreased from 20.56% in the first week to 8.61% during the peak of diagnoses. Conclusion: The low proportion of participants that sought medical consultation or stopped leaving home indicates strategies directed to isolate only those symptomatic reach a low proportion of infected patients.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Henrique Diegoli", - "author_inst": "Health Secretariat of Joinville" - }, - { - "author_name": "Vivianne Samara Conzatti", - "author_inst": "Health Secretariat of Joinville" - }, - { - "author_name": "Suleimy Cristina Mazin", - "author_inst": "Faculty of Medicine of Ribeirao Preto, University of Sao Paulo" - }, - { - "author_name": "Juliana Safanelli", - "author_inst": "Health Secretariat of Joinville" - }, - { - "author_name": "Louise Domenguini Chiaradia Delatorre", - "author_inst": "Health Secretariat of Joinville" - }, - { - "author_name": "Keli Bett", - "author_inst": "Health Secretariat of Joinville" - }, - { - "author_name": "Roselaine Elisa Radtke", - "author_inst": "Health Secretariat of Joinville" - }, - { - "author_name": "Giulia Murillo Wollmann", - "author_inst": "Faculty of Medicine, University of the Region of Joinville" - }, - { - "author_name": "Helbert do Nascimento Lima", - "author_inst": "Postgraduate Program in Health and Environment, University of the Region of Joinville" - }, - { - "author_name": "Paulo Henrique Condeixa de Franca", - "author_inst": "Postgraduate Program in Health and Environment, University of the Region of Joinville" - }, - { - "author_name": "Jean Rodrigues da Silva", - "author_inst": "Health Secretariat of Joinville" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.08.21251343", "rel_title": "Machine learning approach to dynamic risk modeling of mortality in COVID-19: a UK Biobank cohort study", @@ -951741,6 +955392,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.07.21251311", + "rel_title": "Poor antigen-specific responses to the second BNT162b2 mRNA vaccine dose in SARS-CoV-2-experienced individuals", + "rel_date": "2021-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251311", + "rel_abs": "The use of COVID-19 vaccines will play the major role in helping to end the pandemic that has killed millions worldwide. COVID-19 vaccines have resulted in robust humoral responses and protective efficacy in human trials, but efficacy trials excluded individuals with a prior diagnosis of COVID-19. As a result, little is known about how immune responses induced by mRNA vaccines differ in individuals who recovered from COVID-19. Here, we evaluated longitudinal immune responses to two-dose BNT162b2 mRNA vaccination in 15 adults who recovered from COVID-19, compared to 21 adults who did not have prior COVID-19 diagnosis. Consistent with prior studies of mRNA vaccines, we observed robust cytotoxic CD8+ T cell responses in both cohorts following the second dose. Furthermore, SARS-CoV-2-naive individuals had progressive increases in humoral and antigen-specific antibody-secreting cell (ASC) responses following each dose of vaccine, whereas SARS-CoV-2-experienced individuals demonstrated strong humoral and antigen-specific ASC responses to the first dose but muted responses to the second dose of the vaccine at the time points studied. Together, these data highlight the relevance of immunological history for understanding vaccine immune responses and may have significant implications for personalizing mRNA vaccination regimens used to prevent COVID-19, including booster shots.\n\nOne Sentence SummaryPrior history of COVID-19 affects adaptive immune responses to mRNA vaccination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Marie Ines Samanovic-Golden", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Amber R Cornelius", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sophie L Gray-Gaillard", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Joseph Richard Allen", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Trishala Karmacharya", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Jimmy P Wilson", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sara Wesley Hyman", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Michael Tuen", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sergei B Koralov", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Ramin Sedaghat Herati", + "author_inst": "NYU School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.07.21251309", "rel_title": "The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions", @@ -952313,53 +956023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.08.21250525", - "rel_title": "COVID-19 infection and outcomes in a population-based cohort of 17,173 adults with intellectual disabilities compared with the general population", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250525", - "rel_abs": "ObjectivesTo compare COVID-19 infection, severe infection, mortality, case-fatality, and excess deaths, among adults with intellectual disabilities and those without.\n\nDesignRecord-linkage of all adults recorded with intellectual disabilities in Scotlands Census, 2011, and a 5% sample of other adults, to COVID-19 test results (Electronic Communication of Surveillance in Scotland), hospitalisations (Scottish Morbidity Record 01), and deaths (National Records of Scotland).\n\nSettingGeneral population; 24th January 2020 - 15th August 2020\n\nParticipantsSuccessful linkage of 94.8% provided data on 17,173 adults with, and 195,859 without, intellectual disabilities.\n\nOutcomesCrude rates of COVID-19 infection, severe infection (hospitalisation/death), mortality, and case fatality; age-, sex- and deprivation-standardised severe infection and mortality ratios; annual all-cause mortality for 2020 and 2015-2019.\n\nResultsAdults with intellectual disabilities had higher rates of COVID-19 infection (957/100,000 versus 513/100,000); severe infection (549/100,000 versus 237/100,000); mortality (259/100,000 versus 114/100,000); and case-fatality (30% versus 24%). Poorer COVID-19 outcomes remained after standardising for age, sex and deprivation: standardised severe infection ratio 2.59 (95% CI 1.80, 3.39) and mortality ratio 3.20 (95% CI 2.16, 4.25). These were higher among 55-64 year olds: 7.12 (95% CI 3.73, 10.50) and 16.16 (95% CI7.69, 24.63) respectively. Among adults with intellectual disabilities, all-cause mortality was only slightly higher in 2020 than the previous five years: standardised mortality ratios 2.49 (95% CI 2.17, 2.81) and 2.38 (95% CI 2.26, 2.49) respectively.\n\nConclusionsAdults with intellectual disabilities were more likely to be infected with COVID-19, and had worse outcomes once infected, particularly those under 65 years. Non-pharmaceutical interventions directed at formal and informal carers are essential to reduce transmission and all adults with intellectual disabilities should be immediately prioritised for vaccination regardless of age.\n\nSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICOVID-19 mortality is higher within multi-occupancy residences.\nC_LIO_LIAdults with intellectual disabilities may be at higher risk of COVID-19 mortality than other adults, but there are gaps in the evidence.\nC_LIO_LICOVID-19 case-fatality may be no different, or as much as 2.75 times higher in adults with intellectual disabilities compared with other adults.\nC_LI\n\nWhat this study addsO_LICompared with general population adults, adults with intellectual disabilities were almost twice as likely to become infected with COVID-19, 2.3 times as likely to have severe infection, 2.3 times as likely to have COVID-19 mortality, and had 25% higher COVID-19 case-fatality.\nC_LIO_LIAfter standardising for age, sex and deprivation, people with intellectual disabilities were 3.2 times more at risk of covid-19 mortality and 2.6 times more at risk of severe infection relative to those with no intellectual disabilities\nC_LIO_LICompared with general population adults, adults with intellectual disabilities had poorer outcomes among non-elderly age-groups particularly those aged 55-65 years, men, and those living in less-deprived neighbourhoods.\nC_LIO_LINon-pharmaceutical initiatives are important for carers and care-provider organisations, and adults with intellectual disabilities should be prioritised in the national rollouts of COVID-19 vaccination programmes, regardless of age, sex, or neighbourhood deprivation.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Angela Henderson", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Micheal Fleming", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Sally-Ann Cooper", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Jill Pell", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Craig Melville", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Daniel MacKay", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Christopher Hatton", - "author_inst": "Manchester Metropolitan University" - }, - { - "author_name": "Deborah Kinnear", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.07.21251287", "rel_title": "Modelling the impact of reopening schools in early 2021 in the presence of the new SARS-CoV-2 variant and with roll-out of vaccination against COVID-19", @@ -953351,6 +957014,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.04.21251131", + "rel_title": "Using Machine Learning to Predict Mortality for COVID-19 Patients on Day Zero in the ICU", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251131", + "rel_abs": "RationaleGiven the expanding number of COVID-19 cases and the potential for upcoming waves of infection, there is an urgent need for early prediction of the severity of the disease in intensive care unit (ICU) patients to optimize treatment strategies.\n\nObjectivesEarly prediction of mortality using machine learning based on typical laboratory results and clinical data registered on the day of ICU admission.\n\nMethodsWe studied retrospectively 263 COVID-19 ICU patients. To find parameters with the highest predictive values, Kolmogorov-Smirnov and Pearson chi-squared tests were used. Logistic regression and random forest (RF) algorithms were utilized to build classification models. The impact of each marker on the RF model predictions was studied by implementing the local interpretable model-agnostic explanation technique (LIME-SP).\n\nResultsAmong 66 documented parameters, 15 factors with the highest predictive values were identified as follows: gender, age, blood urea nitrogen (BUN), creatinine, international normalized ratio (INR), albumin, mean corpuscular volume, white blood cell count, segmented neutrophil count, lymphocyte count, red cell distribution width (RDW), and mean cell hemoglobin along with a history of neurological, cardiovascular, and respiratory disorders. Our RF model can predict patients outcomes with a sensitivity of 70% and a specificity of 75%.\n\nConclusionsThe most decisive variables in our model were increased levels of BUN, lowered albumin levels, increased creatinine, INR, and RDW along with gender and age. Complete blood count parameters were also crucial for some patients. Considering the importance of early triage decisions, this model can be a useful tool in COVID-19 ICU decision-making.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Elham Jamshidi", + "author_inst": "Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland." + }, + { + "author_name": "Amirhossein Asgary", + "author_inst": "Department of Biotechnology, College of Sciences, University of Tehran, Tehran, Iran." + }, + { + "author_name": "Nader Tavakoli", + "author_inst": "Trauma and Injury Research Center, Iran University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Alireza Zali", + "author_inst": "Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehra" + }, + { + "author_name": "Hadi Esmaily", + "author_inst": "Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Seyed Hamid Jamaldini", + "author_inst": "Department of Genetic, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran" + }, + { + "author_name": "Amir Daaee", + "author_inst": "School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran" + }, + { + "author_name": "Amirhesam Babajani", + "author_inst": "Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Ali Sendani Kashi", + "author_inst": "Master of Business Administration (MBA)-University of Tehran, Tehran, Iran." + }, + { + "author_name": "Masoud Jamshidi", + "author_inst": "Department of Exercise Physiology, Tehran University, Iran." + }, + { + "author_name": "Sahand Rahi", + "author_inst": "Laboratory of the Physics of Biological Systems, Institute of Physics, Ecole polytechnique federale de Lausanne (EPFL), Lausanne, Switzerland" + }, + { + "author_name": "Nahal Mansouri", + "author_inst": "Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole polytechnique federale de Lausanne (EPFL), Lausanne, Switzerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.04.21251170", "rel_title": "Symptoms of COVID-19 infection and magnitude of antibody response in a large community-based study", @@ -954031,41 +957757,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.05.430022", - "rel_title": "Impact of cobas PCR Media Freezing on SARS-CoV-2 Viral RNA Integrity and Whole Genome Sequencing Analyses", - "rel_date": "2021-02-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.05.430022", - "rel_abs": "SARS-CoV-2 whole genome sequencing is an important molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swab samples and shipment to reference laboratories is usually required since RNA sequencing is rarely available in routine clinical microbiology laboratories where initial diagnosis and support to outbreak investigations occur. The cobas PCR Media transport medium developed by Roche facilitates high throughput analyses on cobas multianalyzer PCR platforms. There is no data on the stability of SARS-CoV-2 RNA after freezing and thawing of clinical samples in this transport medium, but potential denaturing of the molecular template could impair test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Genomic coverage and sequencing depth did not significantly differ between fresh and frozen samples (n=10). For samples with lower viral inoculum and PCR cycle threshold above 30, sequencing quality scores and detection of single nucleotide polymorphisms did not differ either. Freezing of cobas PCR Media does not negatively affect the quality of SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories. Those results support secondary use of diagnostic nasopharyngeal swab material for viral sequencing without requirement for additional clinical samples.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Patrick Benoit", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Cecile Tremblay", - "author_inst": "CRCHUM" - }, - { - "author_name": "P. Richard Harrigan", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Isabelle Hardy", - "author_inst": "Hopital Notre-Dame CHUM" - }, - { - "author_name": "Simon Grandjean Lapierre", - "author_inst": "CHUM" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.02.05.21251173", "rel_title": "Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity", @@ -955329,6 +959020,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.06.21251099", + "rel_title": "COVID-19 increases age- and sex-controlled 21-day fatality rates for patients with melanoma, hematologic malignancies, uterine cancer, or kidney cancer", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251099", + "rel_abs": "IntroductionPrior research has reported an increased risk of fatality for cancer patients, but most studies investigated the risk by comparing cancer patients to non-cancer patients among COVID-19 infections. Only a few studies have compared the impact of a COVID-19 infection to non-infection with matched cancer patients and types.\n\nMethods & MaterialsWe conducted survival analyses of 4,606 cancer patients with COVID-19 test results from March 16 to October 11, 2020 in UK Biobank and estimated the overall hazard ratio of fatality with and without COVID-19 infection. We also examined the hazard ratios of thirteen specific cancer types with at least 100 patients.\n\nResultsCOVID-19 resulted in an overall hazard ratio of 7.76 (95% CI: [5.78, 10.40], p<10-10) by studying the survival rate of 4,606 cancer patients for 21-days after the tests. The hazard ratio was shown to vary among cancer type, with over a 10-fold increase in fatality rate (false discovery rate[≤]0.02) for melanoma, hematologic malignancies, uterine cancer, and kidney cancer using a stratified analysis on each of the cancer types. Although COVID-19 imposed a higher risk for localized cancers compared to distant metastasis ones, those of distant metastasis yielded higher fatality rates due to their multiplicative effects.\n\nConclusionThe results highlight the importance of timely care for localized and hematological cancer patients and the necessity to vaccinate uninfected patients as soon as possible, particularly for the cancer types influenced most by COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Haiquan Li", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Edwin Alexander Baldwin", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Colleen Kenost", + "author_inst": "Department of Biomedical Informatics, University of Utah" + }, + { + "author_name": "Wenting Luo", + "author_inst": "Statistics and Data Science GIDP, Biosystems Analytics & Technology Program, University of Arizona" + }, + { + "author_name": "Elizabeth A Calhoun", + "author_inst": "Department of Population Health, University of Kansas Medical Center" + }, + { + "author_name": "Lingling An", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Charles L Bennett", + "author_inst": "Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina" + }, + { + "author_name": "Yves A Lussier", + "author_inst": "Department of Biomedical Informatics, University of Utah" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.02.05.21251085", "rel_title": "Molecular Mechanism of Parosmia", @@ -955937,33 +959679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.07.21251082", - "rel_title": "Pre-pandemic cognitive function and COVID-19 mortality: prospective cohort study", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251082", - "rel_abs": "BackgroundPoorer performance on standard tests of cognitive function is related to an elevated risk of death from lower respiratory tract infections. Whether pre-pandemic measures of cognition are related to COVID-19 mortality is untested.\n\nMethodsUK Biobank, a prospective cohort study, comprises around half a million people who were aged 40 to 69 years at study induction between 2006 and 2010 when a reaction time test was administered to the full sample, and verbal-numeric reasoning assessed in a subgroup. Death from COVID-19 was ascertained from participant linkage to a UK-wide national registry.\n\nResultsBetween April 1st and September 23rd 2020, there were 388 deaths (138 women) ascribed to COVID-19 in the 494,932 individuals (269,602 women) with a reaction time test result, and 125 such deaths (38 women) in the 180,198 (97,794 women) for whom there were data on verbal-numeric reasoning. In analyses adjusted for age, sex, and ethnicity, a one standard deviation (118.2 msec) slower reaction time was related to a higher rate of death from COVID-19 (hazard ratio; 95% confidence interval: 1.18; 1.09, 1.28). A one standard deviation disadvantage (2.16 point) on the verbal-numeric reasoning test was also associated with an elevated risk of death (1.32; 1.09, 1.59). Attenuation after adjustment for additional covariates followed a similar pattern for both measures of cognition. For verbal-numeric reasoning, for instance, the hazard ratios were 1.22 (0.98, 1.51) after control for socioeconomic status, 1.16 (0.96, 1.41) after lifestyle factors, 1.25 (1.04, 1.52) after co-morbidity, and 1.29 (1.01, 1.64) after physiological indices.\n\nConclusionsIn the present study, poorer performance on two pre-pandemic indicators of cognitive function, including reaction time, a knowledge-reduced measure, was related to death ascribed to COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "George David Batty", - "author_inst": "University College London" - }, - { - "author_name": "Ian Deary", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Catharine Gale", - "author_inst": "Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.06.21251221", "rel_title": "Social predictors of food insecurity during the stay-at-home order due to the COVID-19 pandemic in Peru. Results from a cross-sectional web-based survey", @@ -957123,6 +960838,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.04.21251111", + "rel_title": "SARS-CoV-2 Worldwide Replication Drives Rapid Rise and Selection of Mutations across the Viral Genome: A Time-Course StudyPotential Challenge for Vaccines and Therapies", + "rel_date": "2021-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251111", + "rel_abs": "Scientists and the public were alarmed at the first large viral variant of SARS-CoV2 reported in December 2020. We have followed the time course of emerging viral mutants and variants during the SARS-CoV-2 pandemic in ten countries on four continents. We examined complete SARS-CoV-2 nucleotide sequences in GISAID, (Global Initiative of Sharing All Influenza Data) with sampling dates extending until January 20, 2021. These sequences originated from ten different countries: United Kingdom, South Africa, Brazil, USA, India, Russia, France, Spain, Germany, and China. Among the novel mutations, some previously reported mutations waned and some of them increased in prevalence over time. VUI2012/01 (B.1.1.7) and 501Y.V2 (B.1.351), the so-called UK and South Africa variants, respectively, and two variants from Brazil, 484K.V2, now called P.1 and P.2, increased in prevalence. Despite lockdowns, worldwide active replication in genetically and socio-economically diverse populations facilitated selection of new mutations. The data on mutant and variant SARS-CoV-2 strains provided here comprise a global resource for easy access to the myriad mutations and variants detected to date globally. Rapidly evolving new variant and mutant strains might give rise to escape variants, capable of limiting the efficacy of vaccines, therapies, and diagnostic tests.\n\nSignificance and New Aspects of Study - SynopsisO_LIWe examine the time course of emerging mutations in the SARS-CoV-2 genome that have rapidly been selected in the worlds populations through the beginning of 2021. A study of the prevalence of viral mutations in the GISAID database in ten different countries - United Kingdom, South Africa, Brazil, US, India, Russia, France, Spain, Germany, and China - revealed widespread mutations along the genome.\nC_LIO_LIWe previously identified about 10 hotspot mutations in the SARS-CoV-2 genome that became prevalent in many of the countries studied1. Since the beginning of February, many new mutations arose in the ten countries (and worldwide). The preponderance of variants and mutations correlated with the increased spread of Covid-19.\nC_LIO_LIThere was a temporal progression from about 10 predominant mutants shared by several countries up to the end of May 2020, followed by a consistent and rapid increase in the number of new mutations between June and December along with the emergence of variants of concern, first reported in December 2020.\nC_LIO_LIWe examine the relative frequencies of mutations, along with variants of interest, in 10 countries up until January 20, 2021. Investigations on the pathogenic properties of individual SARS-CoV-2 mutations will be urgently needed to understand the kaleidoscopic patterns of worldwide Covid-19 outbreaks and symptoms. Monitoring the frequency and speed of mutant selection have direct relevance to diagnostic testing, vaccines and therapeutics.\nC_LIO_LIAs an explanation for efficient viral mutagenesis, we hypothesize that the viral spike protein - as documented - facilitates viral entry via the cells ACE receptor2. This in turn interacts with the APOBEC polypeptide, an m-RNA editing function. The actually observed frequent C to U (T) transitions and other base exchanges are thus effected. Hence, as one of the earliest steps upon viral entry, active mutagenesis commences, since SARS-CoV-2 exploits one of the cells defenses against viral infections.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stefanie Weber", + "author_inst": "University of Cologne/Erlangen University" + }, + { + "author_name": "Christina C.M. Ramirez", + "author_inst": "UCLA School of Public Health, Los Angeles" + }, + { + "author_name": "Barbara Weiser", + "author_inst": "University of California, Davis," + }, + { + "author_name": "Harold Burger", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Walter Doerfler", + "author_inst": "Friedrich-Alexander University Erlangen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.04.21250932", "rel_title": "The systemic inflammatory response and clinicopathological characteristics in patients admitted to hospital with COVID-19 infection: Comparison of 2 consecutive cohorts", @@ -957895,53 +961645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.02.02.21249309", - "rel_title": "Protocol for a nationwide Internet-based health survey in workers during the COVID-19 pandemic in 2020", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21249309", - "rel_abs": "The ever-changing social implications of the COVID-19 pandemic have resulted in an urgent need to understand the working environments and health status of workers. We conducted a nationwide Internet-based health survey in Japanese workers in December 2020, in the midst the countrys \"third wave\" of COVID-19 infection. Of 33,087 surveys collected, 6,051 were determined to have invalid responses. The 27,036 surveys included in the study were balanced in terms of geographical area, participant sex, and type of work, according to the sampling plan. Men were more likely than women to have telecommuted, while women were more likely to have resigned since April 2020. Moreover, 40% and 9.1% of respondents had a K6 score of 5 or higher and 13 or higher, respectively, they did not exhibit extremely poor health. The present study describes the protocol used to conduct an Internet-based health survey in workers and a summary of its results during a period when COVID-19 was spreading rapidly in Japan. In the future, we plan to use this survey to examine the impact of COVID-19 on workers work styles and health.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" - }, - { - "author_name": "Tomohiro Ishimaru", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hisashi Eguchi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Koji Mori", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.02.03.21251056", "rel_title": "Impact of personal protective equipment use on health care workers physical health during the COVID-19 pandemic: a systematic review and meta-analysis", @@ -958961,6 +962664,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.02.02.21251043", + "rel_title": "COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251043", + "rel_abs": "ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE).\n\nPatients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally.\n\nResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test.\n\nConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Frederick Ho", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Kenneth Man", + "author_inst": "UCL" + }, + { + "author_name": "Mark Toshner", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Colin Church", + "author_inst": "NHS Greater Glasgow and Clyde" + }, + { + "author_name": "Carlos Celis-Morales", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Ian Wong", + "author_inst": "UCL" + }, + { + "author_name": "Colin Berry", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Naveed Sattar", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jill Pell", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.02.03.21251011", "rel_title": "GPS-estimated foot traffic data and venue selection for COVID-19 serosurveillance studies", @@ -960741,145 +964495,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.02.05.429759", - "rel_title": "Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 in nonhuman primates following NVX-CoV2373 subunit vaccine with Matrix-M\u2122 vaccination", - "rel_date": "2021-02-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.05.429759", - "rel_abs": "Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.\n\nHighlightsO_LINVX-CoV2373 subunit vaccine elicits receptor blocking, virus neutralizing antibodies, and Fc-effector functional antibodies.\nC_LIO_LIThe vaccine protects against respiratory tract infection and virus shedding in non-human primates (NHPs).\nC_LIO_LIBoth neutralizing and Fc-effector functions contribute to protection, potentially through different mechanisms in the upper and lower respiratory tract.\nC_LIO_LIBoth macaque and human vaccine-induced antibodies exhibit altered Fc-receptor binding to emerging mutants.\nC_LI", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Matthew J Gorman", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Nita Patel", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Mimi Guebre-Xabier", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Alex Zhu", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Caroline Atyeo", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Krista Pullen", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Carolin Loos", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Yenny Goez-Gazi", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Ricardo Carrion Jr.", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Jing-Hui Tian", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Dansu Yuan", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Kathryn Bowman", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Bin Zhou", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Sonia Maciejewski", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Marisa McGrath", - "author_inst": "University of Maryland" - }, - { - "author_name": "James Logue", - "author_inst": "University of Maryland" - }, - { - "author_name": "Matthew Frieman", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Colin Mann", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Sharon Schendel", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erica Ollman Saphire", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Douglas A Lauffenburger", - "author_inst": "MIT" - }, - { - "author_name": "Ann M Greene", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Alyse D Portnoff", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Michael J Massare", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Larry Ellingsworth", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Gregory Glenn", - "author_inst": "Novavax Inc" - }, - { - "author_name": "Gale Smith", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.05.429937", "rel_title": "Post-infection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection", @@ -961811,6 +965426,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.02.03.429646", + "rel_title": "Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens", + "rel_date": "2021-02-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429646", + "rel_abs": "The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stephen A. Goldstein", + "author_inst": "University of Utah" + }, + { + "author_name": "Joe Brown", + "author_inst": "University of Utah" + }, + { + "author_name": "Brent S Pedersen", + "author_inst": "University of Utah" + }, + { + "author_name": "Aaron R. Quinlan", + "author_inst": "University of Utah" + }, + { + "author_name": "Nels C. Elde", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.02.04.429819", "rel_title": "Codon arrangement modulates MHC-I peptides presentation: implications for a SARS-CoV-2 peptide-based vaccine", @@ -962351,73 +966001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.01.21250929", - "rel_title": "One Year of Evidence on Mental Health in the COVID-19 Crisis - A Systematic Review and Meta-Analysis", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250929", - "rel_abs": "This paper provides a systematic review and meta-analysis on the prevalence rate of mental health issues of general population, general and frontline healthcare workers (HCWs) in China over one year of the COVID-19 crisis. We systematically searched PubMed, Embase, Web of Science, and Medrxiv at November 16th, 2020, pooled data using random-effects meta-analyses to estimate the prevalence rates, and ran meta-regression to tease out the heterogeneity. The meta-regression results uncovered several predictors of the prevalence rates, including severity, type of mental issues, population, sampling location, and study quality. Pooled prevalence rates are significantly different from, yet largely between, the findings of previous meta-analyses, suggesting the results of our larger study are consistent with yet more accurate than the findings of the smaller, previous meta-analyses. The prevalence rates of distress and insomnia and those of frontline HCWs are higher suggest future research and interventions should pay more attention to those mental outcomes and populations. Our findings suggest a need to examine the prevalence rates at varying levels of severity. The one-year cumulative evidence on sampling locations (Wuhan vs. non-Wuhan) corroborates the typhoon eye effect theory.\n\nTrial registrationCRD4202022059", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Xi Chen", - "author_inst": "Daodao Network Technology Co, Ltd." - }, - { - "author_name": "Jiyao Chen", - "author_inst": "College of Business, Oregon State University" - }, - { - "author_name": "Meimei Zhang", - "author_inst": "Department of Speech-Language-Hearing Sciences, Texas Tech University Health Sciences Center" - }, - { - "author_name": "Richard Z Chen", - "author_inst": "Crescent Valley High School, Corvallis" - }, - { - "author_name": "Rebecca Kechen Dong", - "author_inst": "School of Management, University of South Australia" - }, - { - "author_name": "Zhe Dong", - "author_inst": "College of Psychology, Capital Normal University" - }, - { - "author_name": "Yingying Ye", - "author_inst": "Department of psychology, Zhejiang University of Technology" - }, - { - "author_name": "Lingyao Tong", - "author_inst": "Department of Clinical, Neuro and Developmental Psychology, Vrije Universiteit Amsterdam" - }, - { - "author_name": "Bryan Chen", - "author_inst": "Crescent Valley High School, Corvallis" - }, - { - "author_name": "Ruiying Zhao", - "author_inst": "Department of Clinical, Neuro and Developmental Psychology, Vrije Universiteit Amsterdam" - }, - { - "author_name": "Wenrui Cao", - "author_inst": "Department of Social, Health and Organizational Psychology, Utrecht University" - }, - { - "author_name": "Peikai Li", - "author_inst": "Department of Social, Health and Organizational Psychology, Utrecht University" - }, - { - "author_name": "Stephen X. Zhang", - "author_inst": "University of Adelaide" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.02.01.21250919", "rel_title": "How lifestyle changes within the COVID-19 global pandemic have affected the pattern and symptoms of the menstrual cycle.", @@ -963689,6 +967272,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.02.21250825", + "rel_title": "Evaluation of Depression, Anxiety and Sleep Quality in the Brazilian Population During Social Isolation Due to the New Coronavirus (SARS-CoV-2) pandemic: the DEGAS-CoV Study", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250825", + "rel_abs": "IntroductionThe new coronavirus infection (COVID-19) has caused distress and repercussions in mental and physical health of individuals. Depression, anxiety and worsening of sleep quality have been reported in several recent articles that surveyed populations all over the globe. Our work meant to access, through a cross-sectional study, these disorders in the Brazilian population, through the application of an online questionnaire conducted on the second trimester of 2020.\n\nMaterials and MethodsWe applied an online questionnaire, filled with questions regarding social, economic, financial, educational and health status, as well as questions from the Hospital Anxiety and Depression Scale (HAD), and from the Pittsburgh Sleep Quality Index (PSQI).\n\nResultsWe collected 2,695 valid answers, from April 24th to May 31st, 2020. Age ranged from 18 to 79 years, mean of 31.3. Women were 76.3%, men 23.7%. Symptoms of Anxiety were found in 56.5%, of depression in 46.1%, and of bad sleep in 49.2%. Some groups were more prone than others to one or more of those conditions, such as: younger people, women, mestizos, Northeasterners, people with lesser years of education, of lower income or whose income dropped significantly during the pandemic, caregivers, students, sedentary or people practicing less physical activity, people who followed more hours of news of COVID-19 and those less engaged in social and instrumental activities.\n\nConclusionanxiety, depression and bad sleep quality were significantly high in our survey. Mental and sleep health is heterogeneously affected among individuals, depending on social, economic, financial, educational and health status.\n\nO_TEXTBOXHIGHLIGHTS\n\n- An online survey (DEGAS-CoV) was conducted between April 30th and May 31st, 2020, with people living in Brazil, aged 18 or more. The study obtained 2,695 valid answers.\n- Rates of possible anxiety, possible depression and bad sleep quality were 56.5%, 46.1% and 49.2%, respectively. Rates are similar to another Brazilian survey, with 45,161 participants, conducted in a similar time window.\n- Were more prone to mental and/or sleep conditions: younger participants, women, mestizos, unemployed, students, people with less years of education, people with lower income or with considerable drops of income during the virus outbreak, caregivers, people who followed more news of COVID-19, people less engaged in social and instrumental activities, smokers, sedentary or those who practiced less physical activity, and people who had symptoms suspected (confirmed or not) of SARS-CoV-2 infection.\n- Alcohol drinkers were slightly less likely to be possibly depressed. That finding needs more clarification and may be due to confounders.\n\n\nC_TEXTBOX", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Paulo Afonso Mei", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Amanda Sasse", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Ana Lara Navarrete Fernandez", + "author_inst": "Pontificia Universidade Catolica de Goias" + }, + { + "author_name": "Barbara Neiva Perri", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Breno Alexander Bispo", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Giselly Brito Santana", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Gabriela Sakita Munhos", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Giovanni Giuliani Verghetti", + "author_inst": "Universidade Sao Leopoldo Mandic Araras" + }, + { + "author_name": "Guilherme Barbosa de Almeida Oliveira Martins", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Jennifer Pereira da Rocha", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Jessyca Rosa Lopes Mendonca", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Julia Patel Lebl", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Valdemiro Da Rolt Jr", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Lais Grabner Ruivo", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Laura Loeb", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Marielly Isepon", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Marina Joseane Pachecco", + "author_inst": "Universidade Sao Leopoldo Mandic Araras" + }, + { + "author_name": "Cintia Zonta Baptista", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Fabio Soares Nespoli", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Paloma Ricciardi de Castro", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Paola Ricciardi de Castro", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Rafaela Dotta Brustolin", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Taysa Maria Pimentel Goncalves Gomes Silva", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Victoria Gomes Andreata", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Amilton Santos Jr", + "author_inst": "Universidade Estadual de Campinas" + }, + { + "author_name": "Tania Marchiori de Oliveira Cardoso", + "author_inst": "Universidade Estadual de Campinas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.02.01.21250943", "rel_title": "Seroprevalence of SARS-CoV-2 during pregnancy and associated outcomes: results from an ongoing prospective cohort study, New York City", @@ -964509,41 +968211,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.01.21250972", - "rel_title": "The role of the SwissCovid digital contact tracing app during the pandemic response: results for the Canton of Zurich", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250972", - "rel_abs": "ImportanceDigital proximity tracing (DPT) apps were released in several countries to help interrupt SARS-CoV-2 transmission chains in the population. However, the impact of DPT on pandemic mitigation still remains to be demonstrated.\n\nObjectiveTo estimate key populations and performance indicators along the DPT app notification cascade in a clearly defined regional (Canton of Zurich, using all of Switzerland as a comparison) and temporal context (September/October 2020).\n\nDesignPublicly available administrative and research data, including key DPT performance indicators, SARS-CoV-2 testing statistics, infoline call statistics, and observational study data, were compiled. A model of the DPT notification cascade was developed and key performance indicators for DPT processes were defined. Subpopulation sizes at each cascade step were estimated using data triangulation. Resulting estimates were systematically checked for internal consistency and consistency with other up- or downstream estimates in the cascade. Stochastic simulations were performed to explore robustness of results.\n\nResultsFor the Canton of Zurich, we estimate that 537 app users received a positive SARS-CoV-2 test in September 2020, of whom 324 received and entered a CovidCode. This triggered an app notification for an estimated 1374 proximity contacts and led to 722 infoline calls. In total, 170 callers received a quarantine recommendation, and 30 app users tested positive for SARS-CoV-2 after an app notification, reflecting a performance above the national level.\n\nBased on this quantification, key performance indicators were evaluated. For September 2020, these analyses suggest that SwissCovid triggered quarantine recommendations in the equivalent of 5% of all exposed contacts placed in quarantine by manual contact tracing. Per 11 CovidCodes entered in the app, we estimate that almost 1 contact tested positive for SARS-CoV-2 upon app notification.\n\nHowever, longitudinal indicator analyses demonstrate bottlenecks in the notification cascade, as capacity limits were reached due to large increases in SARS-CoV-2 incidence in October 2020.\n\nConclusionAlthough requiring confirmation, our estimations on the number of notified proximity contacts receiving quarantine recommendations or testing positive after notification suggest relevant contributions to mitigating the pandemic. Increasing SwissCovid app uptake and improving notification cascade performance may further enhance its impact.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat is the real-life impact of Digital proximity tracing (DPT) apps on interrupting SARS-CoV-2 transmission chains?\n\nFindingsThis data-informed simulation study found that, in the canton of Zurich, the number of app notified persons receiving a quarantine recommendation corresponds to the equivalent of up to 5% of all mandatory quarantined contacts identified by manual contact tracing. Furthermore, about 1 in 11 notification triggers led to SARS-CoV-2 testing of an exposed proximity contact who was consecutively tested positive.\n\nMeaningDPT apps exert a measurable impact that will further scale as more persons use the apps.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dominik Menges", - "author_inst": "University of Zurich" - }, - { - "author_name": "Helene E Aschmann", - "author_inst": "University of Zurich" - }, - { - "author_name": "Andre Moser", - "author_inst": "University of Bern" - }, - { - "author_name": "Christian L Althaus", - "author_inst": "University of Bern" - }, - { - "author_name": "Viktor von Wyl", - "author_inst": "University of Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.01.21250923", "rel_title": "A cautionary note on recall vaccination in ex-COVID-19 subjects", @@ -965587,6 +969254,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.02.429431", + "rel_title": "Potential global impact of the N501Y mutation on MHC-II presentation and immune escape", + "rel_date": "2021-02-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.02.429431", + "rel_abs": "The B.1.1.7 SARS-CoV-2 variant, characterized by the N501Y mutation, is rapidly emerging, raising concerns about its effectiveness on natural as well as vaccine-induced adaptive viral immunity at the population level. Since CD4 T cell responses are of critical importance to the antibody response, we examined the global effects of N501Y mutation on MHC-II presentation compared to the N501 wildtype and found poorer presentation across the majority of MHC-II alleles. This suggests that the N501Y mutation may not only diminish binding of antibodies to the RBD but also interfere with their production by weakening the cooperation between T and B cells, facilitating immune escape.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrea Castro", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Hannah Carter", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Maurizio Zanetti", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.02.03.429355", "rel_title": "Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike", @@ -966531,37 +970225,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.30.21250708", - "rel_title": "Radius of Gyration as predictor of COVID-19 deaths trend with three-weeks offset", - "rel_date": "2021-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250708", - "rel_abs": "Total and perimetral lockdowns were the strongest nonpharmaceutical interventions to fight against Covid-19, as well as the with the strongest socioeconomic collateral effects. Lacking a metric to predict the effect of lockdowns in the spreading of COVID-19, authorities and decision-makers opted for preventive measures that showed either too strong or not strong enough after a period of two to three weeks, once data about hospitalizations and deaths was available. We present here the radius of gyration as a candidate predictor of the trend in deaths by COVID-19 with an offset of three weeks. Indeed, the radius of gyration aggregates the most relevant microscopic aspects of human mobility into a macroscopic value, very sensitive to temporary trends and local effects, such as lockdowns and mobility restrictions. We use mobile phone data of more than 13 million users in Spain during a period of one year (from January 6th 2020 to January 10th 2021) to compute the users daily radius of gyration and compare the median value of the population with the evolution of COVID-19 deaths: we find that for all weeks where the radius of gyration is above a critical value (70% of its pre-pandemic score) the number of weekly deaths increases three weeks after. The reverse also stands: for all weeks where the radius of gyration is below the critical value, the number of weekly deaths decreased after three weeks. This observation leads to two conclusions: i) the radius of gyration can be used as a predictor of COVID-19-related deaths; and ii) partial mobility restrictions are as effective as a total lockdown as far the radius of gyration is below this critical value.\n\nBackgroundAuthorities around the World have used lockdowns and partial mobility restrictions as major nonpharmaceutical interventions to control the expansion of COVID-19. While effective, the efficiency of these measures on the number of COVID-19 cases and deaths is difficult to quantify, severely limiting the feedback that can be used to tune the intensity of these measures. In addition, collateral socioeconomic effects challenge the overall effectiveness of lockdowns in the long term, and the degree by which they are followed can be difficult to estimate. It is desirable to find both a metric to accurately monitor the mobility restrictions and a predictor of their effectiveness.\n\nMethodsWe correlate the median of the daily radius of gyration of more than 13M users in Spain during all of 2020 with the evolution of COVID-19 deaths for the same period. Mobility data is obtained from mobile phone metadata from one of the major operators in the country.\n\nResultsThe radius of gyration is a predictor of the trend in the number of COVID-19 deaths with 3 weeks offset. When the radius is above/below a critical threshold (70% of the pre-pandemic score), the number of deaths increases/decreases three weeks later.\n\nConclusionsThe radius of gyration can be used to monitor in real time the effectiveness of the mobility restrictions. The existence of a critical threshold suggest that partial lockdowns can be as efficient as total lockdowns, while reducing their socioeconomic impact. The mechanism behind the critical value is still unknow, and more research is needed.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alberto Hernando de Castro", - "author_inst": "KIDO DYNAMICS" - }, - { - "author_name": "David Mateo", - "author_inst": "KIDO DYNAMICS" - }, - { - "author_name": "Jordi Bayer", - "author_inst": "KIDO DYNAMICS" - }, - { - "author_name": "Ignacio Barrios", - "author_inst": "KIDO DYNAMICS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.29.21250784", "rel_title": "COVID-19 vaccine acceptability and inequity in the United States: Results from a nationally representative survey", @@ -967501,6 +971164,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.31.429023", + "rel_title": "Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'-O-methyl transfer by SARS-CoV-2 nsp16", + "rel_date": "2021-02-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.31.429023", + "rel_abs": "Capping viral messenger RNAs is essential for efficient translation and prevents their detection by host innate immune responses. For SARS-CoV-2, RNA capping includes 2'-O-methylation of the first ribonucleotide by methyltransferase nsp16 in complex with activator nsp10. The reaction requires substrates, a short RNA and SAM, and is catalyzed by divalent cations, with preference for Mn2+. Crystal structures of nsp16-nsp10 with capped RNAs revealed a critical role of metal ions in stabilizing interactions between ribonucleotides and nsp16, resulting in precise alignment of the substrates for methyl transfer. An aspartate residue that is highly conserved among coronaviruses alters the backbone conformation of the capped RNA in the binding groove. This aspartate is absent in mammalian methyltransferases and is a promising site for designing coronavirus-specific inhibitors.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "George Minasov", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Monica Rosas-Lemus", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Ludmilla Shuvalova", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Nicole L. Inniss", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Joseph S. Brunzelle", + "author_inst": "Northwestern Synchrotron Research Center" + }, + { + "author_name": "Courtney M. Daczkowski", + "author_inst": "Purdue University" + }, + { + "author_name": "Paul Hoover", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Andrew D Mesecar", + "author_inst": "Purdue University" + }, + { + "author_name": "Karla J Satchell", + "author_inst": "Northwestern University Feinberg School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.31.429001", "rel_title": "Identification of anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) oxysterol derivatives in vitro", @@ -968253,41 +971967,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.28.21250694", - "rel_title": "Uncovering Survivorship Bias in Longitudinal Mental Health Surveys", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250694", - "rel_abs": "AimsMarkedly elevated adverse mental health symptoms were widely observed early in the coronavirus disease 2019 (COVID-19) pandemic. Unlike the U.S., where cross-sectional data indicate anxiety and depression symptoms have remained elevated, such symptoms reportedly declined in the U.K., according to analysis of repeated measures from a largescale longitudinal study. However, nearly 40% of U.K. respondents (those who did not complete multiple follow-up surveys) were excluded from analysis, suggesting that survivorship bias might partially explain this discrepancy. We therefore sought to assess survivorship bias among participants in our longitudinal survey study as part of The COVID-19 Outbreak Public Evaluation (COPE) Initiative.\n\nMethodsSurvivorship bias was assessed 4,039 U.S. respondents who completed surveys including the assessment of mental health as part of The COPE Initiative in April 2020 and were invited to complete follow-up surveys. Participants completed validated screening instruments for symptoms of anxiety, depression, and insomnia. Survivorship bias was assessed for (1) demographic differences in follow-up survey participation, (2) differences in initial adverse mental health symptom prevalences adjusted for demographic factors, and (3) differences in follow-up survey participation based on mental health experiences adjusted for demographic factors.\n\nResultsAdjusting for demographics, individuals who completed only one or two out of four surveys had higher prevalences of anxiety and depression symptoms in April 2020 (e.g., one-survey versus four-survey, anxiety symptoms, adjusted prevalence ratio [aPR]: 1.30, 95% confidence interval [CI]: 1.08-1.55, P=0.0045; depression symptoms, aPR: 1.43, 95% CI: 1.17-1.75, P=0.00052). Moreover, individuals who experienced incident anxiety or depression symptoms had higher odds of not completing follow-up surveys (adjusted odds ratio [aOR]: 1.68, 95% CI: 1.22-2.31, P=0.0015, aOR: 1.56, 95% CI: 1.15-2.12, P=0.0046, respectively).\n\nConclusionsOur findings revealed significant survivorship bias among longitudinal survey respondents, indicating that restricting analytic samples to only respondents who provide repeated assessments in longitudinal survey studies could lead to overly optimistic interpretations of mental health trends over time. Cross-sectional or planned missing data designs may provide more accurate estimates of population-level adverse mental health symptom prevalences than longitudinal surveys.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mark \u00c9. Czeisler", - "author_inst": "Monash University" - }, - { - "author_name": "Joshua F. Wiley", - "author_inst": "Monash University" - }, - { - "author_name": "Charles A. Czeisler", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Shantha M.W. Rajaratnam", - "author_inst": "Monash University" - }, - { - "author_name": "Mark E. Howard", - "author_inst": "Austin Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.01.29.21250592", "rel_title": "Hot days and Covid19 - unusual heat stress for nursing professions in Germany", @@ -969239,6 +972918,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250407", + "rel_title": "12-lead Electrocardiogram in Hospitalized COVID 19 Patients", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250407", + "rel_abs": "COVID-19 pandemic resulted in considerable morbidity and mortality. We analyzed 345 Electrocardiograms of 100 COVID-19 patients admitted to our tertiary care center in Detroit, during the initial month of Covid-19. Findings were correlated with mortality, cardiac injury and inflammatory markers. Our cohort included 61% males and 77% African Americans. The median age and BMI were 66 years (57-74) and 31 kg/m2 (26.1-39), respectively. We observed atrial arrhythmias in 29% of the patients (17% new onset), First degree heart block in 12%, ST-T segment changes in 17%, S1Q3T3 pattern in 19%, premature ventricular complexes in 23%, premature atrial complexes in 13%, Q waves in 27%, T wave inversion in 42% of the cases. While presence of premature atrial complexes or left atrial abnormality correlated with mortality (P = 0.02 & 0.03, respectively), other findings did not show significant correlation in this small cohort of patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mohamed Shokr", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Omar Chehab", + "author_inst": "Department of Internal Medicine, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Mustafa Ajam", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA" + }, + { + "author_name": "Manmohan Singh", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Said Ashraf", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "John Dawdy", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Mohit Pahuja", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Vivek Reddy", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Ahmed Subahi", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "M. Chadi Alraies", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Luis Afonso", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Randy Lieberman", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.01.28.21250129", "rel_title": "Application of a 27-protein candidate cardiovascular surrogate endpoint to track risk ascendancy and resolution in COVID-19.", @@ -969963,45 +973705,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.01.29.21250804", - "rel_title": "A mathematical model to estimate percentage secondary infections from margin of error of diagnostic sensitivity: Useful tool for regulatory agencies to assess the risk of propagation due to false negative outcome of diagnostics", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250804", - "rel_abs": "False negative outcome of a diagnosis is one the major reasons for the dissemination of the diseases with high risk of propagation. Diagnostic sensitivity and the margin of error determine the false negative outcome of the diagnosis. A mathematical model had been developed to estimate the mean % secondary infections based on the margin of error of diagnostic sensitivity, % prevalence and R0 value. This model recommends a diagnostic test with diagnostic sensitivity [≥] 96% and at least 92% lower bound limit of the 95% CI or [≤] 4% margin of error for a highly infectious diseases like COVID-19 to curb the secondary transmission of the infection due to false negative cases. Positive relationship was found between mean % secondary infection and margin of error of sensitivity suggesting greater the margin of error of a diagnostic test sensitivity, higher the number of secondary infections in a population due to false negative cases. Negative correlation was found between number of COVID-19 test kits (>90% sensitivity) with regulatory approval and margin of error (R= -0.92, p=0.023) suggesting lesser the margin of error of a diagnostic test, higher the chances of getting approved by the regulatory agencies. However, there are no specific regulatory standards available for margin of error of the diagnostic sensitivity of COVID-19 diagnostic tests. Highly infectious disease such as COVID-19, certainly need specific regulatory standards on margin of error or 95% CI of the diagnostic sensitivity to curb the dissemination of the disease due to false negative cases and our model can be used to set the standards such as sensitivity, margin of error or lower bound limit of 95% CI.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Azhahianambi Palavesam", - "author_inst": "Tamil Nadu Veterinary and Animal Sciences University" - }, - { - "author_name": "Karthik Kumaragurubaran", - "author_inst": "Tamil Nadu Veterinary and Animal Sciences University" - }, - { - "author_name": "Aravindh Babu R Parthiban", - "author_inst": "Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India" - }, - { - "author_name": "Senthilkumar TMA", - "author_inst": "Tamil Nadu Veterinary and Animal Sciences University" - }, - { - "author_name": "Balachandran Chidambaram", - "author_inst": "Tamil Nadu Veterinary and Animal Sciences University" - }, - { - "author_name": "Dhinakar Raj Gopal", - "author_inst": "Tamil Nadu Veterinary and Animal Sciences University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.29.21250712", "rel_title": "MOATAI-VIR - an AI algorithm that predicts severe adverse events and molecular features for COVID-19's complications", @@ -970913,6 +974616,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.29.21250793", + "rel_title": "COVID-19 spread and Weather in U.S. states: a cross-correlative study on summer-autumn 2020.", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250793", + "rel_abs": "An effect of weather on sars-cov-2 transmission is regularly proposed as a putative cause of unexplained fluctuations of covid-19 new cases, but clear data supporting this hypothesis remains to be presented. Here I measured longitudinal time-series correlations between outdoor temperature, humidity and covid-19 reproduction number (Rt) in the 50 U.S. states (+DC). In order to mitigate the confounding influence of varying social restriction measures, the analysis spans a 5-month period during summer and autumn 2020 when restrictions were comparatively lower and more stable. I used a cross-covariance approach to account for a variable delay between infection and case report. For a delay near 11 days, most U.S. states exhibited a negative correlation between outdoor temperature and Rt, as well as between absolute humidity and Rt (mean r = -0.35). In 21 states, the correlation was strong (r < -0.5). Individual state data are presented, and associations between cold and/or dry weather episodes and short-term new case surges are proposed. After identifying potential confounding factors, I discuss 3 possible causal mechanisms that could explain a correlation between outdoor weather and indoor disease transmission: behavioral adaptations to cold weather, respiratory tract temperature, and the importing of outdoor absolute humidity to indoor spaces.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Emmanuel de Margerie", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.30.21250830", "rel_title": "Estimated SARS-CoV-2 Seroprevalence in Healthy Children and Those with Chronic Illnesses in The Washington Metropolitan Area as of October 2020", @@ -971389,165 +975111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.27.21250591", - "rel_title": "High-dimensional profiling reveals phenotypic heterogeneity and disease-specific alterations of granulocytes in COVID-19", - "rel_date": "2021-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250591", - "rel_abs": "Since the outset of the COVID-19 pandemic, increasing evidence suggests that the innate immune responses play an important role in the disease development. A dysregulated inflammatory state has been proposed as key driver of clinical complications in COVID-19, with a potential detrimental role of granulocytes. However, a comprehensive phenotypic description of circulating granulocytes in SARS-CoV-2-infected patients is lacking. In this study, we used high-dimensional flow cytometry for granulocyte immunophenotyping in peripheral blood collected from COVID-19 patients during acute and convalescent phases. Severe COVID-19 was associated with increased levels of both mature and immature neutrophils, and decreased counts of eosinophils and basophils. Distinct immunotypes were evident in COVID-19 patients, with altered expression of several receptors involved in activation, adhesion and migration of granulocytes (e.g. CD62L, CD11a/b, CD69, CD63, CXCR4). Paired sampling revealed recovery and phenotypic restoration of the granulocytic signature in the convalescent phase. The identified granulocyte immunotypes correlated with distinct sets of soluble inflammatory markers supporting pathophysiologic relevance. Furthermore, clinical features, including multi-organ dysfunction and respiratory function, could be predicted using combined laboratory measurements and immunophenotyping. This study provides a comprehensive granulocyte characterization in COVID-19 and reveals specific immunotypes with potential predictive value for key clinical features associated with COVID-19.\n\nSignificanceAccumulating evidence shows that granulocytes are key modulators of the immune response to SARS-CoV-2 infection and their dysregulation could significantly impact COVID-19 severity and patient recovery after virus clearance. In the present study, we identify selected immune traits in neutrophil, eosinophil and basophil subsets associated to severity of COVID-19 and to peripheral protein profiles. Moreover, computational modeling indicates that the combined use of phenotypic data and laboratory measurements can effectively predict key clinical outcomes in COVID-19 patients. Finally, patient-matched longitudinal analysis shows phenotypic normalization of granulocyte subsets 4 months after hospitalization. Overall, in this work we extend the current understanding of the distinct contribution of granulocyte subsets to COVID-19 pathogenesis.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Magda Lourda", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Majda Dzidic", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Laura Hertwig", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Helena Bergsten", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Laura M Palma Medina", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Egle Kvedaraite", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jagadeeswara Rao Muvva", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jean-Baptiste Gorin", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Martin Cornillet", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Johanna Emgard", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Kirsten Moll", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Marina Garcia", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Kimia T Maleki", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jonas Klingstrom", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jakob Michaelsson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Malin Flodstrom-Tullberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Susanna Brighenti", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Marcus Buggert", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jenny Mjosberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Karl-Johan Malmberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Johan K Sandberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jan-Inge Henter", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Elin Folkesson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Sara Gredmark-Russ", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anders Sonnerborg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Lars I Eriksson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Olav Rooyackers", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Soo Aleman", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Kristoffer Stralin", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Hans-Gustaf Ljunggren", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Niklas K Bjorkstrom", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Mattias Svensson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Andrea Ponzetta", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anna Norrby-Teglund", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Benedict J Chambers", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "- Karolinska KI/K COVID-19 Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.01.27.21250597", "rel_title": "Modeling the asymptomatic prevalence of SARS-CoV-2 epidemic in Italy and the ISTAT survey", @@ -972731,6 +976294,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.28.21250700", + "rel_title": "Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus - Georgia Institute of Technology, Fall 2020", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250700", + "rel_abs": "A SARS-CoV-2 testing program combining pooled saliva sample surveillance leading to diagnosis and intervention surveyed over 112,000 samples from 18,029 students, staff and faculty, as part of integrative efforts to mitigate transmission at the Georgia Institute of Technology in Fall 2020. Cumulatively, 1,508 individuals were confirmed diagnostically. The surveillance strategy, including focused intensification of testing given case clusters, was effective in disrupting transmission following rapid case increases upon entry in August 2020, and again in November 2020. Owing to broad adoption by the campus community, the program protected higher risk staff while allowing some normalization of research activities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Greg C Gibson", + "author_inst": "Georgia Tech" + }, + { + "author_name": "Joshua S Weitz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Michael P. Shannon", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Benjamin Holton", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anton Bryksin", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Brian Liu", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Sandra Bramblett", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Julianne Williamson", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Michael Farrell", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Alexander Ortiz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Chaouki T. Abdallah", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Andr\u00e9s Garc\u00eda", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.428890", "rel_title": "Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algae Chlamydomonas reinhardtii", @@ -973623,89 +977249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.27.21250517", - "rel_title": "SARS-CoV-2 infection and transmission in school settings during the second wave in Berlin, Germany: a cross-sectional study", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250517", - "rel_abs": "BackgroundSchool attendance during the SARS-CoV-2 pandemic is intensely debated. Modelling studies suggest that school closures contribute to community transmission reduction. However, data among school-attending students and staff are scarce. In November 2020, we examined SARS-CoV-2 infections and seroreactivity in 24 randomly selected school classes and connected households in Berlin, Germany.\n\nMethodsStudents and school staff were examined, oro-nasopharyngeal swabs and blood samples collected, and SARS-CoV-2 infection and IgG antibodies detected by RT-PCR and ELISA. Household members performed self-swabs. Individual and institutional infection prevention and control measures were assessed. Classes with SARS-CoV-2 infection and connected household members were re-tested after one week.\n\nFindings1119 participants were examined, including 177 primary and 175 secondary school students, 142 staff, and 625 household members. Participants reported mainly cold symptoms (19{middle dot}4%). SARS-CoV-2 infection occurred in eight of 24 classes affecting each 1-2 individuals. Infection prevalence was 2{middle dot}7% (95%CI; 1{middle dot}2-5{middle dot}0%; 9/338), 1{middle dot}4% (0{middle dot}2-5{middle dot}1%; 2/140), and 2{middle dot}3% (1{middle dot}3-3{middle dot}8%; 14/611) among students, staff and household members, respectively, including quarantined persons. Six of nine infected students were asymptomatic. Prevalence increased with inconsistent facemask use in school, way to school on foot, and case-contacts outside school. IgG antibodies were detected in 2{middle dot}0% (0{middle dot}8-4{middle dot}1%; 7/347), 1{middle dot}4% (0{middle dot}2-5{middle dot}0%; 2/141) and 1{middle dot}4% (0{middle dot}6-2{middle dot}7%; 8/576), respectively. For three of nine households with infection(s) detected at cross-sectional assessment, origin in school seemed possible. After one week, no school-related, secondary infections appeared in affected classes; the attack rate in connected households was 1{middle dot}1%.\n\nInterpretationThese data suggest that school attendance under preventive measures is feasible, provided their rigorous implementation. In balancing threats and benefits of open versus closed schools during the pandemic, parents and society need to consider possible spill-overs into their households. Deeper insight is needed into the infection risks due to being a schoolchild as compared to attending school.\n\nFundingSenate of Berlin.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Stefanie Theuring", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Marlene Thielecke", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Welmoed van Loon", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Franziska Hommes", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Claudia Huelso", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Annkathrin von der Haar", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Jennifer Koerner", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Michael Schmidt", - "author_inst": "German Red Cross Blood Transfusion Service, Frankfurt, Germany" - }, - { - "author_name": "Falko Boehringer", - "author_inst": "Labor Berlin - Charite Vivantes Services GmbH, Berlin, Germany" - }, - { - "author_name": "Marcus A. Mall", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Departmen" - }, - { - "author_name": "Alexander Rosen", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Departmen" - }, - { - "author_name": "Christof von Kalle", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Clinical " - }, - { - "author_name": "Valerie Kirchberger", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Medical D" - }, - { - "author_name": "Tobias Kurth", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Medical D" - }, - { - "author_name": "Frank P Mockenhaupt", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Institute" - }, - { - "author_name": "- BECOSS Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.26.21250543", "rel_title": "The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera.", @@ -974541,6 +978084,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250349", + "rel_title": "HLA-A*11:01:01:01, HLA*C*12:02:02:01-HLA-B*52:01:02:02, age and sex are associated with severity of Japanese COVID-19 with respiratory failure", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250349", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19) was announced as an outbreak by the World Health Organization (WHO) in January 2020 and as a pandemic in March 2020. The majority of infected individuals have experienced no or only mild symptoms, ranging from fully asymptomatic cases to mild pneumonic disease. However, a minority of infected individuals develop severe respiratory symptoms. The objective of this study was to identify susceptible HLA alleles and clinical markers for the early identification of severe COVID-19 among hospitalized COVID-19 patients. A total of 137 patients with mild COVID-19 (mCOVID-19) and 53 patients with severe COVID-19 (sCOVID-19) were recruited from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan for the period of February-August 2020. High-resolution sequencing-based typing for eight HLA genes was performed using next-generation sequencing. In the HLA association studies, HLA-A*11:01:01:01 [Pc = 0.013, OR = 2.26 (1.27-3.91)] and HLA-C*12:02:02:01-HLA-B*52:01:01:02 [Pc = 0.020, OR = 2.25 (1.24-3.92)] were found to be significantly associated with the severity of COVID-19. After multivariate analysis controlling for other confounding factors and comorbidities, HLA-A*11:01:01:01 [P = 3.34E-03, OR = 3.41 (1.50-7.73)], age at diagnosis [P = 1.29E-02, OR = 1.04 (1.01-1.07)] and sex at birth [P = 8.88E-03, OR = 2.92 (1.31-6.54)] remained significant. Early identification of potential sCOVID-19 could help clinicians prioritize medical utility and significantly decrease mortality from COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Seik-Soon Khor", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Yosuke Omae", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Nao Nishida", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Masaya Sugiyama", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Noriko Kinoshita", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Tetsuya Suzuki", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Michiyo Suzuki", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Satoshi Suzuki", + "author_inst": "Biobank, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Shinyu Izumi", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Masayuki Hojo", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Masashi Mizokami", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Katsushi Tokunaga", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.27.21250048", "rel_title": "A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR", @@ -975033,37 +978643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.27.21250648", - "rel_title": "Sequencing Data of North American SARS-CoV-2 Isolates Shows Widespread Complex Variants", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250648", - "rel_abs": "Several new variants of the SARS-CoV-2 have been isolated in the United States, Mexico, and Canada. Many of the variants contain single variants of functional significance (e.g. S: N501Y increases transmissibility). To study the occurrence and co-circulation of these variants, we have developed an easy-to-use dashboard at janieslab.github.io/sars-cov-2.\n\nWe created a multiple sequence alignment workflow and processing script to generate a variant dataset, which populates this dashboard. We then use the features of the dashboard, such as visualization of the single and complex nucleotide variants geospatially and in a color-coded matrix format. Users also interact with the dashboard to filter the underlying data to regions of interest and or variants of interest. The user can export reports based on the desired filters, which we intend to be used for regionally specific pandemic response. We find in Genbank, an isolate from Massachusetts containing [(S: Q677H), (ORF3a: Q57H), (M: A85S), (N: D377Y)] collected on September 11, 2020.\n\nMoreover, we find that many viral isolates bear a marker of increased transmissibility (S: N501Y) in linkage with at least one variant of concern isolated from Ohio also range across the Untied States and stretch from British Columbia, Canada to Mexico. When we analyze co-circulation of more complex variant constellations with (S: N501Y), we note that the Upper Midwest and Northeast United States contain these isolates.\n\nIn summary, the viral variants that have raised concern in a few US States in recent reports are widespread. Based on the increase in the proportion of variant viruses being sampled and some empirical evidence in the United Kingdom, South Africa, and Ohio, these variants are likely to lead to increased transmission of SARS-CoV-2 across North America in the coming months.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Colby T Ford", - "author_inst": "University of North Carolina at Charlotte" - }, - { - "author_name": "Rachel Scott", - "author_inst": "University of North Carolina at Charlotte" - }, - { - "author_name": "Denis Jacob Machado", - "author_inst": "University of North Carolina at Charlotte" - }, - { - "author_name": "Daniel Janies", - "author_inst": "University of North Carolina at Charlotte" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.27.21250612", "rel_title": "The effectiveness of the first dose of BNT162 b 2 vaccine in reducing SARS-CoV-2 infection 13-24 days after immunization: real-world evidence", @@ -976175,6 +979754,153 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.01.27.428516", + "rel_title": "SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines", + "rel_date": "2021-01-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428516", + "rel_abs": "The SARS-CoV-2 Spike glycoprotein mediates virus entry and is a major target for neutralizing antibodies. All current vaccines are based on the ancestral Spike with the goal of generating a protective neutralizing antibody response. Several novel SARS-CoV-2 variants with multiple Spike mutations have emerged, and their rapid spread and potential for immune escape have raised concerns. One of these variants, first identified in the United Kingdom, B.1.1.7 (also called VUI202012/01), contains eight Spike mutations with potential to impact antibody therapy, vaccine efficacy and risk of reinfection. Here we employed a lentivirus-based pseudovirus assay to show that variant B.1.1.7 remains sensitive to neutralization, albeit at moderately reduced levels (~2-fold), by serum samples from convalescent individuals and recipients of two different vaccines based on ancestral Spike: mRNA-1273 (Moderna), and protein nanoparticle NVX-CoV2373 (Novavax). Some monoclonal antibodies to the receptor binding domain (RBD) of Spike were less effective against the variant while others were largely unaffected. These findings indicate that B.1.1.7 is not a neutralization escape variant that would be a major concern for current vaccines, or for an increased risk of reinfection.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Haili Tang", + "author_inst": "Duke University" + }, + { + "author_name": "Charlene McDana", + "author_inst": "Duke University" + }, + { + "author_name": "Xiaoying Shen", + "author_inst": "Duke University" + }, + { + "author_name": "Kshitij Wagh", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Haili Tang", + "author_inst": "Duke University" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Charlene McDana", + "author_inst": "Duke University" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Kshitij Wagh", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Hyejin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Hyejin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "S. Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "Nicholas W Hengartner", + "author_inst": "Los Alamos Nationa Lab" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc" + }, + { + "author_name": "S. Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nicholas W Hengartner", + "author_inst": "Los Alamos Nationa Lab" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.27.428534", "rel_title": "Unbiased interrogation of memory B cells from convalescent COVID-19 patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein", @@ -976931,57 +980657,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.01.26.21249744", - "rel_title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in a higher education sample", - "rel_date": "2021-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21249744", - "rel_abs": "ObjectiveTo assess the feasibility of home antibody testing as part of large-scale study, the Kings College London Coronavirus Health and Experiences of Colleagues at Kings (KCL CHECK).\n\nMethodsParticipants of the KCL CHECK study were sent a SureScreen Diagnostics COVID-19 IgG/IgM Rapid Test Cassette to complete at home in June 2020 (phase 1) and September 2020 (phase 2). Participants were asked to upload a test result image to a study website. Test result images and sociodemographic information were analysed by the research team.\n\nResultsA total of n=2716 participants enrolled in the KCL CHECK study, with n=2003 (73.7%) and n=1825 (69.3%) consenting and responding to phase 1 and 2. Of these, n=1882 (93.9%; phase 1) and n=1675 (91.8%; phase 2) returned a valid result. n=123 (6.5%; phase 1) and n=91 (5.4%; phase 2) tested positive for SARS-CoV-2 antibodies. A total of n=1488 participants provided a result in both phases, with n=57 (3.8%) testing positive for SARS- CoV-2 antibodies across both phases, suggesting a reduction in the number of positive antibody results over time. Initial comparisons showed variation by age group, gender and clinical role.\n\nConclusionsOur study highlights the feasibility of rapid, repeated and low-cost SARS-CoV-2 serological testing without the need for face-to-face contact.\n\nWhat is already known about this subject?Higher education institutions have a duty of care to minimise the spread and transmission of COVID-19 in its campuses, and among staff and students. The reopening of higher education buildings and campuses has brought about a mass movement of students, academics and support staff from across the UK. Serological antibody studies can assist by highlighting groups of people and behaviours associated with high risk of COVID-19.\n\nWhat are the new findings?We report a framework for SARS-CoV-2 serological antibody testing in an occupational group of postgraduate research students and current members of staff at Kings College London. Over two phases of data collection, 6.5% (phase 1) and 5.4% (phase 2) tested positive for SARS-CoV-2 antibodies, with only 3.8% testing positive for antibodies in both phases, suggesting a reduction in positive antibody results over time.\n\nHow might this impact on policy or clinical practice in the foreseeable future?Our study highlights the feasibility of rapidly deploying low-cost and repeatable SARS-CoV-2 serological testing, without the need for face-to-face contact, to support the higher education system of the UK.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Daniel Leightley Dr", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Valentina Vitiello Dr", - "author_inst": "The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK." - }, - { - "author_name": "Alice Wickersham Ms", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Katrina A.S. Davis Dr", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Gabriella Bergin-Cartwright Ms", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Grace Lavelle Dr", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Sharon A.M. Stevelink Dr", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Matthew Hotopf Prof", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - }, - { - "author_name": "Reza Razavi Prof", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.01.26.21250246", "rel_title": "Lack of trust and social media echo chambers predict COVID-19 vaccine hesitancy", @@ -977953,6 +981628,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.26.428208", + "rel_title": "Do examinations prepare students for higher education? A lesson from the Covid-19 lockdown.", + "rel_date": "2021-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.26.428208", + "rel_abs": "The COVID-19 pandemic caused severe disruption to education in the UK in 2020, with most of the school teaching moving online and national school examinations being cancelled. This was particularly disruptive for those taking end of school examinations in preparation for higher education. Biological science courses require students to absorb a lot of new vocabulary and concepts, with examinations traditionally focusing on content recall rather than reasoning. Students who had entered university in September 2019 were compared with those arriving in September 2020 with respect to their knowledge of bioscience vocabulary and understanding of key concepts. Results showed no significant difference between those who had gone through the examination process in 2019 relative to those who had not, in 2020. This suggests the cramming of information for examinations has no detectable effect on the knowledge and understanding of biology that students take with them to university.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Harriet L Jones", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Valentina Zini", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Jon R Green", + "author_inst": "University of Birmingham" + }, + { + "author_name": "John R Prendergast", + "author_inst": "JRP Information Services" + }, + { + "author_name": "Jon Scott", + "author_inst": "University of Leicester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.01.21.21250249", "rel_title": "Evaluation of six commercial SARS-CoV-2 Enzyme-Linked Immunosorbent assays for clinical testing and serosurveillance.", @@ -978553,105 +982263,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.01.23.21249554", - "rel_title": "The longest persistence of viable SARS-CoV-2 with recurrence of viremia and relapsing symptomatic COVID-19 in an immunocompromised patient - a case study", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21249554", - "rel_abs": "BackgroundImmunocompromised patients show prolonged shedding of SARS-CoV-2 in nasopharyngeal swabs. We report a case of a prolonged persistence of viable SARS-CoV-2 associated with clinical relapses of COVID-19 in a lymphoma patient.\n\nMethodsNasopharyngeal swabs and blood samples were tested for SARS-CoV-2 by Real time-PCR (RT-PCR). On five positive nasopharyngeal swabs, we performed viral culture and next generation sequencing. We analysed the patients adaptive and innate immunity to characterize T and NK cell subsets.\n\nFindingsSARS-CoV-2 RT-PCR on nasopharyngeal swabs samples remained positive with cycle threshold mean values of 22 {+/-} 1{middle dot}3 for over 8 months. All five performed viral cultures were positive and genomic analysis confirmed a persistent infection with the same strain. Viremia resulted positive in three out of four COVID-19 clinical relapses and cleared each time after remdesivir treatment. T and NK cells dynamic was different in aviremic and viremic samples and no SARS-CoV-2 specific antibodies were detected throughout the disease course.\n\nInterpretationIn our patient, SARS-CoV-2 persisted with proven infectivity for over eight months. Viremia was associated with COVID-19 relapses and remdesivir treatment was effective in viremia clearance and symptoms remission, although it was unable to clear the virus from the upper respiratory airways. During the viremic phase, we observed a low frequency of terminal effector CD8+ T lymphocytes in peripheral blood that are probably recruited in inflammatory tissue for viral eradication. In addition we found a high level of NK cells repertoire perturbation with a relevant involvement during SARS-CoV-2 viremia.\n\nFundingNone.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Chiara Sepulcri Jr.", - "author_inst": "Infectious Diseases Unit, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Chiara Dentone Sr.", - "author_inst": "Infectious Diseases Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences, Genoa, Italy" - }, - { - "author_name": "Malgorzata Mikulska Sr.", - "author_inst": "Infectious Diseases Unit, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Bianca Bruzzone Sr.", - "author_inst": "Hygiene Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences Genoa, Italy" - }, - { - "author_name": "Alessia Lai Sr.", - "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan Italy" - }, - { - "author_name": "Daniela Fenoglio Sr.", - "author_inst": "Center of Excellence for Biomedical Research, Cytofluorimetry Unit, University of Genoa ; Department of Internal Medicine (DiMI), University of Genoa, Genoa, It" - }, - { - "author_name": "Federica Bozzano Sr.", - "author_inst": "Infectious Diseases Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences, Genoa, Italy" - }, - { - "author_name": "Annalisa Bergna Jr.", - "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan Italy" - }, - { - "author_name": "Alessia Parodi Sr.", - "author_inst": "Biotherapy Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences, Genoa, Italy" - }, - { - "author_name": "Tiziana Altosole Jr.", - "author_inst": "Center of Excellence for Biomedical Research, Cytofluorimetry Unit, University of Genoa" - }, - { - "author_name": "Emanuele Delfino Sr.", - "author_inst": "Infectious Diseases Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences, Genoa, Italy" - }, - { - "author_name": "Giulia Bartalucci Sr.", - "author_inst": "Clinic of Hematology, Department of Internal Medicine (DiMI), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Andrea Orsi Sr.", - "author_inst": "Hygiene Unit, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Antonio Di Biagio Sr.", - "author_inst": "Infectious Diseases Unit, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Gianguglielmo Zehender Sr.", - "author_inst": "Hygiene Unit, Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan Italy" - }, - { - "author_name": "Filippo Ballerini Sr.", - "author_inst": "Hematology Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences Genoa, Italy" - }, - { - "author_name": "Stefano Bonora Sr.", - "author_inst": "Infectious Diseases Unit, Ospedale Amedeo di Savoia, University of Turin, Turin, Italy" - }, - { - "author_name": "Raffaele De Palma Sr.", - "author_inst": "Immunology Unit, Ospedale Policlinico San Martino, IRCCS for Oncology and Neurosciences, Genoa, Italy" - }, - { - "author_name": "Guido Silvestri Sr.", - "author_inst": "Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, USA; Division of Microbiology and Immunology Yerkes National Prim" - }, - { - "author_name": "Andrea De Maria Sr.", - "author_inst": "Infectious Diseases Unit, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Matteo Bassetti Sr.", - "author_inst": "Infectious Diseases Unit, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.23.21250325", "rel_title": "Evaluation of a Commercial Culture-free Neutralization Antibody Detection Kit for Severe Acute Respiratory Syndrome-Related Coronavirus-2 and Comparison with an Anti-RBD ELISA Assay", @@ -979695,6 +983306,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.25.21250082", + "rel_title": "SARS-CoV-2 RNA screening in routine pathology specimens", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250082", + "rel_abs": "Virus detection methods are important to cope with the SARS-CoV-2 pandemics. Apart from the lung, SARS-CoV-2 was detected in multiple organs in severe cases. Less is known on organ tropism in patients developing mild or no symptoms, and some of such patients might be missed in symptom-indicated swab testing.\n\nHere we tested and validated several approaches and selected the most reliable RT-PCR protocol for the detection of SARS-CoV-2 RNA in patients routine diagnostic formalin-fixed and paraffin-embedded (FFPE) specimens available in pathology, to assess a) organ tropism in samples from COVID-19-positive patients, b) unrecognized cases in selected tissues from negative or not-tested patients during a pandemic peak, and c) retrospectively, pre-pandemic lung samples.\n\nWe identified SARS-CoV-2 RNA in four samples from confirmed COVID-19 patients, in two gastric biopsies, one colon resection, and one pleural effusion specimen, while all other specimens, particularly from patients with mild COVID-19 disease course, were negative. In the pandemic peak cohort, we identified one previously unrecognized COVID-19 case in tonsillectomy samples. All pre-pandemic lung samples were negative.\n\nIn conclusion, SARS-CoV-2 RNA detection in FFPE pathology specimens can potentially improve surveillance of COVID-19, allow retrospective studies, and advance our understanding of SARS-CoV-2 organ tropism and effects.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Saskia E von Stillfried", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Sophia Villwock", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Roman D Buelow", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Sonja Djudjaj", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Eva M Buhl", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Angela Maurer", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Nadina Ortiz-Bruechle", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Peter Celec", + "author_inst": "Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Institute of Pathophysiology, Faculty of Medicine, Comenius" + }, + { + "author_name": "Barbara M Klinkhammer", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Dickson WL Wong", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Claudio Cacchi", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Till Braunschweig", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Ruth Knuechel", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Edgar Dahl", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Peter Boor", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany and Departments of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.21.21249906", "rel_title": "Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil", @@ -980639,41 +984325,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.01.24.21250389", - "rel_title": "Biomarkers of endothelial dysfunction and outcomes in coronavirus disease 2019 (COVID-19) patients: a systematic review and meta-analysis", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250389", - "rel_abs": "BackgroundSeveral studies have reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can directly infect endothelial cells, and endothelial dysfunction is often found in severe cases of coronavirus disease 2019 (COVID-19). To better understand the pathological mechanisms underlying endothelial dysfunction in COVID-19-associated coagulopathy, we conducted a systematic review and meta-analysis to assess biomarkers of endothelial cells in patients with COVID-19.\n\nMethodsA literature search was conducted on online databases for observational studies evaluating biomarkers of endothelial dysfunction and composite poor outcomes in COVID-19 patients.\n\nResultsA total of 1187 patients from 17 studies were included in this analysis. The estimated pooled means for von Willebrand Factor (VWF) antigen levels in COVID-19 patients was higher compared to healthy control (306.42 [95% confidence interval (CI) 291.37-321.48], p<0.001; I2:86%), with the highest VWF antigen levels was found in deceased COVID-19 patients (448.57 [95% CI 407.20-489.93], p<0.001; I2:0%). Meta-analysis showed that higher plasma levels of VWF antigen, tissue-type plasminogen activator (t-PA), plasminogen activator inhibitor-1 antigen (PAI-1) antigen, and soluble thrombomodulin (sTM) were associated with composite poor outcome in COVID-19 patients ([standardized mean difference (SMD) 0.74 [0.33-1.16], p<0.001; I2:80.4%], [SMD 0.55 [0.19-0.92], p=0.003; I2:6.4%], [SMD 0.33 [0.04-0.62], p=0.025; I2:7.9%], and [SMD 0.55 [0.10-0.99], p=0.015; I2:23.6%], respectively).\n\nConclusionThe estimated pooled means shows increased levels of VWF antigen in COVID-19 patients. Several biomarkers of endothelial dysfunction, including VFW antigen, t-PA, PAI-1, and sTM, are significantly associated with increased composite poor outcome in patients with COVID-19.\n\nPROSPERO registration numberCRD42021228821", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrianto Andrianto", - "author_inst": "Department of Cardiology and Vascular Medicine, Soetomo General Hospital, Faculty of Medicine, Universitas Airlangga, Surabaya 60286, Indonesia" - }, - { - "author_name": "Makhyan Jibril Al-Farabi", - "author_inst": "Department of Cardiology and Vascular Medicine, Soetomo General Hospital, Faculty of Medicine, Universitas Airlangga, Surabaya 60286, Indonesia" - }, - { - "author_name": "Ricardo Adrian Nugraha", - "author_inst": "Department of Cardiology and Vascular Medicine, Soetomo General Hospital, Faculty of Medicine, Universitas Airlangga, Surabaya 60286, Indonesia" - }, - { - "author_name": "Bagas Adhimurda Marsudi", - "author_inst": "Department of Cardiology and Vascular Medicine, Harapan Kita National Heart Center, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Yusuf Azmi", - "author_inst": "Faculty of Medicine, Universitas Airlangga, Surabaya 60286, Indonesia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.25.21250440", "rel_title": "Non-Congruent SARS-CoV-2 Waves in England", @@ -981621,6 +985272,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250507", + "rel_title": "Estimation of the SARS-CoV-2 infection fatality rate in Germany", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250507", + "rel_abs": "Assessing the infection fatality rate (IFR) of SARS-CoV-2 is one of the most controversial issues during the pandemic. Due to asymptomatic or mild courses of COVID-19, many infections remain undetected. Reported case fatality rates - COVID-19-associated deaths divided by number of detected infections - are therefore poor estimates of the IFR. Endogenous changes of the population at risk of a SARS-CoV-2 infection, changing test practices and an improved understanding of the pathogenesis of COVID-19 further exacerbate the estimation of the IFR. Here, we propose a strategy to estimate the IFR of SARS-CoV-2 in Germany that combines official data on reported cases and fatalities supplied by the Robert Koch Institute (RKI) with data from seroepidemiological studies in two infection hotspots, the Austrian town Ischgl and the German municipality Gangelt, respectively. For this purpose, we use the law of total probability to derive an approximate formula for the IFR that is based on a set of assumptions regarding data quality and test specificity and sensitivity. The resulting estimate of the IFR in Germany of 0.83% (95% CI: [0.69%; 0.98%]) that is based on a combination of the RKI and Ischgl data is notably higher than the IFR estimate reported in the Gangelt study (0.36% [0.29%; 0.45%]). It is closer to the consolidated estimate based on a meta-analysis (0.68% [0.53%; 0.82%]), where the difference can be explained by Germanys disadvantageous age structure. As a result of virus mutations, vaccination strategies, and improved therapy, a re-estimation of the IFR will eventually be mandated; the proposed method is able to account for such developments.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Thomas Dimpfl", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + }, + { + "author_name": "Jantje S\u00f6nksen", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + }, + { + "author_name": "Ingo Bechmann", + "author_inst": "University of Leipzig, Institute of Anatomy" + }, + { + "author_name": "Joachim Grammig", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.25.21250505", "rel_title": "Community structured model for vaccine strategies to control COVID19 spread: a mathematical study", @@ -982369,45 +986051,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.01.25.428190", - "rel_title": "Computational Investigation of Increased Virulence and Pathogenesis of SARS-CoV-2 Lineage B.1.1.7", - "rel_date": "2021-01-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428190", - "rel_abs": "New variants of SARS-CoV-2 are being reported worldwide. More specifically, the variants reported in South Africa (501Y.V2) and United Kingdom (B.1.1.7) were found to be more contagious than the wild type. There are also speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19, occurs through the interaction of receptor binding domain (RBD) of the spike protein with peptidase domain of the human ACE-2 (hACE-2) receptor. So, possibly the mutations in the RBD domain of spike protein in the new variants could modulate the protein-protein interaction with hACE-2 receptor leading to the increased virulence. In this study, we aim to get molecular level understanding into the mechanism behind the increased infection rate due to such mutations in these variants. We have computationally studied the interaction of the spike protein in both wild-type and B.1.1.7 variant with hACE-2 receptor using combined molecular dynamics and binding free energy calculations using molecular mechanics-Generalized Born surface area (MM-GBSA) approach. The binding free energies computed using configurations from minimization run and low temperature simulation show that mutant variant of spike protein has increased binding affinity for hACE-2 receptor (i.e. {Delta}{Delta}G(N501Y,A570D) is in the range -20.4 to -21.4 kcal/mol)The residue-wise decomposition analysis and intermolecular hydrogen bond analysis evidenced that the N501Y mutation has increased interaction between RBD of spike protein with ACE-2 receptor. We have also carried out calculations using density functional theory and the results evidenced the increased interaction between three pairs of residues (TYR449 (spike)-ASP38 (ACE-2), TYR453-HIE34 and TYR501-LYS353) in the variant that could be attributed to its increased virulence. The free energies of wild-type and mutant variants of the spike protein computed from MM-GBSA approach suggests that latter variant is stable by about -10.4 kcal/mol when compared to wild type suggesting that it will be retained in the evolution due to increased stability. We demonstrate that with the use of the state-of-the art of computational approaches, we can in advance predict the more virulent nature of variants of SARS-CoV-2 and alert the world health-care system.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Murugan Arul Natarajan", - "author_inst": "KTH" - }, - { - "author_name": "Prashanth S. Javali", - "author_inst": "Alagappa University" - }, - { - "author_name": "Chitra Jeyaraj Pandian", - "author_inst": "Alagappa University" - }, - { - "author_name": "Muhammad Akhtar Ali", - "author_inst": "KTH" - }, - { - "author_name": "Vaibhav Srivastava", - "author_inst": "kth" - }, - { - "author_name": "Jeyakanthan Jeyaraman", - "author_inst": "Alagappa university" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.01.26.428207", "rel_title": "Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2", @@ -983339,6 +986982,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.21.21249176", + "rel_title": "Distinct Autoimmune Antibody Signatures Between Hospitalized Acute COVID-19 Patients, SARS-CoV-2 Convalescent Individuals, and Unexposed Pre-Pandemic Controls", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249176", + "rel_abs": "Increasing evidence suggests that autoimmunity may play a role in the pathophysiology of SARS-CoV-2 infection during both the acute and long COVID phases of disease. However, an assessment of autoimmune antibodies in convalescent SARS-CoV-2 patients has not yet been reported.\n\nMethodologyWe compared the levels of 18 different IgG autoantibodies (AABs) between four groups: (1) unexposed pre-pandemic subjects from the general population (n = 29); (2) individuals hospitalized with acute moderate-severe COVID-19 (n = 20); (3) convalescent SARS-COV-2-infected subjects with asymptomatic to mild viral symptoms during the acute phase with samples obtained between 1.8 and 7.3 months after infection (n = 9); and (4) unexposed pre-pandemic subjects with systemic lupus erythematous (SLE) (n = 6). Total IgG and IgA levels were also measured from subjects in groups 1-3 to assess non-specific pan-B cell activation.\n\nResultsAs expected, in multivariate analysis, AABs were detected at much higher odds in SLE subjects (5 of 6, 83%) compared to non-SLE pre-pandemic controls (11 of 29, 38%) [odds ratio (OR) 19.4,95% CI, 2.0 - 557.0, p = 0.03]. AAB detection (percentage of subjects with one or more autoantibodies) was higher in SARS-CoV-2 infected convalescent subjects (7 of 9, 78%) [OR 17.4, 95% CI, 2.0 - 287.4, p = 0.02] and subjects with acute COVID-19 (12 of 20, 60%) compared with non-SLE pre-pandemic controls, but was not statistically significant among the latter [OR 1.8,95% CI, 0.6 - 8.1, p = 0.23]. Within the convalescent subject group, AABs were detected in 5/5 with reported persistent symptoms and 2/4 without continued symptoms (p = 0.17). The multivariate computational algorithm Partial Least Squares Determinant Analysis (PLSDA) was used to determine if distinct AAB signatures distinguish subject groups 1-3. Of the 18 autoantibodies measured, anti-Beta 2-Glycoprotein, anti-Proteinase 3-ANCA, anti-Mi-2 and anti-PM/Scl-100 defined the convalescent group; anti-Proteinase 3-ANCA, anti-Mi-2, anti-Jo-1 and anti-RNP/SM defined acute COVID-19 subjects; and anti-Proteinase 3-ANCA, anti-Mi-2, anti-Jo-1, anti-Beta 2-Glycoprotein distinguished unexposed controls. The AABs defining SARS-COV-2 infected from pre-pandemic subjects are widely associated with myopathies, vasculitis, and antiphospholipid syndromes, conditions with some similarities to COVID-19. Compared to pre-pandemic non-SLE controls, subjects with acute COVID-19 had higher total IgG concentration (p-value=0.006) but convalescent subjects did not (p-value=0.08); no differences in total IgA levels were found between groups.\n\nConclusionsOur findings support existing studies suggesting induction of immune responses to self-epitopes during acute, severe COVID-19 with evidence of general B cell hyperactivation. Also, the preponderance of AAB positivity among convalescent individuals up to seven months after infection indicates potential initiation or proliferation, and then persistence of self-reactive immunity without severe initial disease. These results underscore the importance of further investigation of autoimmunity during SARS-CoV-2 infection and its role in the onset and persistence of post-acute sequelae of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nahid Bhadelia", + "author_inst": "Department of Medicine, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories (NEIDL), Boston University" + }, + { + "author_name": "Anna Belkina", + "author_inst": "Flow Cytometry Core Facility and Department of Pathology and Laboratory Medicine, Boston University School of Medicine" + }, + { + "author_name": "Alex Olson", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Thomas Winter", + "author_inst": "Research Occupational Health Program, Boston University" + }, + { + "author_name": "Patricia Urick", + "author_inst": "Research Occupational Health Program, Boston University" + }, + { + "author_name": "Nina Lin", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Ian Rifkin", + "author_inst": "Renal Section, Department of Medicine, Boston University School of Medicine and Renal Section, Department of Medicine, VA Boston Healthcare System" + }, + { + "author_name": "Yachana Kataria", + "author_inst": "Department of Pathology and Laboratory Medicine, Boston University School of Medicine" + }, + { + "author_name": "Rachel Yuen", + "author_inst": "Department of Microbiology; Boston University School of Medicine" + }, + { + "author_name": "Manish Sagar", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Jennifer Cappione", + "author_inst": "Department of Microbiology; Boston University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.22.21249716", "rel_title": "An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein", @@ -984183,33 +987885,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.25.21250437", - "rel_title": "Tracking the mental health of home-carers during the first COVID-19 national lockdown: evidence from a nationally representative UK survey", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250437", - "rel_abs": "BackgroundUnpaid carers who look after another member of their household (home-carers) have poorer mental health than the general population. The first COVID-19 national lockdown led to an increasing reliance on home-carers and we investigate the short and longer-term impact of lockdown on their mental health.\n\nMethodsData from 9,737 adult participants (aged 16+) from the UK Household Longitudinal Study (Understanding Society) were used to explore changes in 12-item General Health Questionnaire (GHQ-12) score between (a) pre-pandemic (2019) and early lockdown (April 2020) and (b) early and later (July 2020) lockdown.\n\nResultsGHQ-12 scores among home-carers were higher pre-lockdown and increased more than for non-carers from 2019 to April 2020 with further increases for home-carers compared with non-carers between April and July. Compared with respondents caring for a spouse/partner, those caring for a child under 18 had a particularly marked increase in GHQ-12 score between 2019 and April, as did those caring for someone with learning difficulties. Home-carers of children under 18 improved from April to July while those caring for adult children saw a marked worsening of their mental health. Home-carers with greater care burden saw larger increases in GHQ-12 score from 2019 to April and from April to July, and increases through both periods were greater for home-carers who had formal help prior to lockdown but then lost it.\n\nConclusionsThe mental health of home-carers deteriorated more during lockdown than non-carers. Policies that reinstate support for them and their care-recipients will benefit the health of both vulnerable groups.\n\nWhat is already known on this topicO_LICarers have poorer mental health than the general population.\nC_LIO_LIAmong carers who live with the care recipient (home-carers), some subgroups have poorer mental health than others: female versus male; those who provide more hours of care and have been caring for longer; spousal carers compared with those caring for children (including adult), parents, or other relationships; those caring for individuals whose impairment results in behavioural disturbances, than those who care for individuals with physical or long-term health conditions.\nC_LI\n\nWhat this study addsO_LIIn a large representative UK survey, the decline in mental health during lockdown was greater among home-carers than for the general population, and stayed poorer through to July, even as the general populations mental health recovered slightly.\nC_LIO_LICompared with respondents who were caring for a spouse/partner, those caring for a child under 18 had a particularly marked increase in GHQ-12 score between 2019 and April while those caring for an adult child experienced a substantial decline in their mental health between the beginning and end of the first lockdown (April to July).\nC_LIO_LIThe increase in GHQ-12 in April from 2019 was highest among those caring for someone with a learning disability and lowest for those caring for someone with a problem related to old age.\nC_LIO_LIHome-carers who had a greater care burden, in terms of hours of care provided, or lost formal support during lockdown, had poorer mental health.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Elise Whitley", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Kelly Reeve", - "author_inst": "Universityof Essex" - }, - { - "author_name": "Michaela Benzeval", - "author_inst": "University of Essex" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.22.21249968", "rel_title": "An external validation of the QCovid risk prediction algorithm for risk of mortality from COVID-19 in adults: national validation cohort study in England", @@ -985313,6 +988988,133 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.25.428136", + "rel_title": "mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge", + "rel_date": "2021-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428136", + "rel_abs": "The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Michelle Meyer", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yuan Wang", + "author_inst": "Princeton University" + }, + { + "author_name": "Darin Edwards", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Gregory R Smith", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aliza B Rubenstein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Palaniappan Ramanathan", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Chad E Mire", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Colette Pietzsch", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Xi Chen", + "author_inst": "Flatiron Institute, Simons Foundation" + }, + { + "author_name": "Yongchao Ge", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Wan Sze Cheng", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carole Henry", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Angela Woods", + "author_inst": "Moderna Inc" + }, + { + "author_name": "LingZhi Ma", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Guillaume B. E. Stewart-Jones", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Kevin W Bock", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Minai Mahnaz", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Bianca M Nagata", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sivakumar Periasamy", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Barney S Graham", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ian N Moore", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Irene Ramos", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Olga G. Troyanskaya", + "author_inst": "Princeton University" + }, + { + "author_name": "Elena Zaslavsky", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrea Carfi", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Stuart C Sealfon", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Bukreyev", + "author_inst": "University of Texas Medical Branch at Galveston" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.25.428122", "rel_title": "Profiling transcription factor sub-networks in type I interferon signaling and in response to SARS-CoV-2 infection", @@ -985861,113 +989663,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.01.24.427991", - "rel_title": "Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant", - "rel_date": "2021-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.24.427991", - "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths worldwide and massive societal and economic burden. Recently, a new variant of SARS-CoV-2, known as B.1.1.7, was first detected in the United Kingdom and is spreading in several other countries, heightening public health concern and raising questions as to the resulting effectiveness of vaccines and therapeutic interventions. We and others previously identified host-directed therapies with antiviral efficacy against SARS-CoV-2 infection. Less prone to the development of therapy resistance, host-directed drugs represent promising therapeutic options to combat emerging viral variants as host genes possess a lower propensity to mutate compared to viral genes. Here, in the first study of the full-length B.1.1.7 variant virus, we find two host-directed drugs, plitidepsin (aplidin; inhibits translation elongation factor eEF1A) and ralimetinib (inhibits p38 MAP kinase cascade), as well as remdesivir, to possess similar antiviral activity against both the early-lineage SARS-CoV-2 and the B.1.1.7 variant, evaluated in both human gastrointestinal and lung epithelial cell lines. We find that plitidepsin is over an order of magnitude more potent than remdesivir against both viruses. These results highlight the importance of continued development of host-directed therapeutics to combat current and future coronavirus variant outbreaks.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Ann-Kathrin Reuschl", - "author_inst": "University College London" - }, - { - "author_name": "Lucy Thorne", - "author_inst": "University College London" - }, - { - "author_name": "Lorena Zuliani Alvarez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mehdi Bouhaddou", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kirsten Obernier", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joseph Hiatt", - "author_inst": "University of California-San Francisco" - }, - { - "author_name": "Margaret Soucheray", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jane Turner", - "author_inst": "University College London" - }, - { - "author_name": "Jacqueline Fabius", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gina T. Nguyen", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Danielle Swaney", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Romel Rosales", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York" - }, - { - "author_name": "Kris M. White", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York" - }, - { - "author_name": "Pablo Aviles", - "author_inst": "PharmaMar" - }, - { - "author_name": "Ilsa T Kirby", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "James E Melnyk", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ying Shi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ziyang Zhang", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kevan Shokat", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Clare Jolly", - "author_inst": "University College London" - }, - { - "author_name": "Gregory J Towers", - "author_inst": "University College London" - }, - { - "author_name": "Nevan J Krogan", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.21.20240887", "rel_title": "The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.", @@ -986815,6 +990510,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.22.21250289", + "rel_title": "Development and validation of a predictive model for critical illness in adult patients requiring hospitalization for COVID-19", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250289", + "rel_abs": "BackgroundIdentifying factors that can predict severe disease in patients needing hospitalization for COVID-19 is crucial for early recognition of patients at greatest risk.\n\nObjective1) Identify factors predicting intensive care unit (ICU) transfer and (2) develop a simple calculator for clinicians managing patients hospitalized with COVID-19.\n\nMethodsA total of 2,685 patients with laboratory-confirmed COVID-19 admitted to a large metropolitan health system in Georgia, USA between March and July 2020 were included in the study. Seventy-five percent of patients were included in the training dataset (admitted March 1 to July 10). Through multivariable logistic regression, we developed a prediction model (probability score) for ICU transfer. Then, we validated the model by estimating its performance accuracy (area under the curve [AUC]) using data from the remaining 25% of patients (admitted July 11 to July 31).\n\nResultsWe included 2,014 and 671 patients in the training and validation datasets, respectively. Diabetes mellitus, coronary artery disease, chronic kidney disease, serum C-reactive protein, and serum lactate dehydrogenase were identified as significant risk factors for ICU transfer, and a prediction model was developed. The AUC was 0.752 for the training dataset and 0.769 for the validation dataset. We developed a free, web-based calculator to facilitate use of the prediction model (https://icucovid19.shinyapps.io/ICUCOVID19/).\n\nConclusionOur validated, simple, and accessible prediction model and web-based calculator for ICU transfer may be useful in assisting healthcare providers in identifying hospitalized patients with COVID-19, who are at high risk for clinical deterioration.\n\nTriage of such patients for early aggressive treatment can impact clinical outcomes for this potentially deadly disease.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Neha Paranjape", + "author_inst": "Wellstar Medical Group" + }, + { + "author_name": "Lauren Staples", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Christina Stradwick", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Herman Ray", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Ian Saldanha", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.21.21250261", "rel_title": "Using body temperature and variables commonly available in the EHR to predict acute infection: A proof-of-concept study showing improved pretest probability estimates for acute COVID-19 infection among discharged emergency department patients", @@ -987571,57 +991301,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.22.427749", - "rel_title": "Emerging SARS-CoV-2 variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies", - "rel_date": "2021-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.22.427749", - "rel_abs": "SARS-CoV-2 Spike-specific antibodies contribute the majority of the neutralizing activity in most convalescent human sera. Two SARS-CoV-2 variants, N501Y.V1 (also known as B.1.1.7 lineage or VOC-202012/01) and N501Y.V2 (B.1.351 lineage), reported from the United Kingdom and South Africa, contain several mutations in the receptor binding domain of Spike and are of particular concern. To address the infectivity and neutralization escape phenotypes potentially caused by these mutations, we used SARS-CoV-2 pseudovirus system to compare the viral infectivity, as well as the neutralization activities of convalescent sera and monoclonal antibodies (mAbs) against SARS-CoV-2 variants. Our results showed that N501Y Variant 1 and Variant 2 increase viral infectivity compared to the reference strain (wild-type, WT) in vitro. At 8 months after symptom onset, 17 serum samples of 20 participants (85%) retaining titers of ID50 >40 against WT pseudovirus, whereas the NAb titers of 8 samples (40%) and 18 samples (90%) decreased below the threshold against N501Y.V1 and N501Y.V2, respectively. In addition, both N501Y Variant 1 and Variant 2 reduced neutralization sensitivity to most (6/8) mAbs tested, while N501Y.V2 even abrogated neutralizing activity of two mAbs. Taken together the results suggest that N501Y.V1 and N501Y.V2 reduce neutralization sensitivity to some convalescent sera and mAbs.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jie Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Pai Peng", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Kai Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Bei-zhong Liu", - "author_inst": "Yong-Chuan Hospital, Chongqing Medical University" - }, - { - "author_name": "Liang Fang", - "author_inst": "Yong-Chuan Hospital, Chongqing Medical University" - }, - { - "author_name": "Fei-yang Luo", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" - }, - { - "author_name": "Ai-shun Jin", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" - }, - { - "author_name": "Ni Tang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ailong Huang", - "author_inst": "Chongqing Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.22.427813", "rel_title": "CCR1 regulatory variants linked to pulmonary macrophage recruitment in severe COVID-19", @@ -988493,6 +992172,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.15.21249893", + "rel_title": "COVID-19 propagation by diffusion - a two-dimensional approach for Germany", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249893", + "rel_abs": "Diffusion comes anytime and everywhere. If there is a gradient or a potential difference of a quantity a diffusion process happens and this ends if an equilibrium is reached only. The concentration of a species maybe such quantity, or the voltage. An electric currant will be driven by a voltage difference for example.\n\nIn this COVID-19 pandemic one observes both regions with low incidence and other ones with high incidence. The local different people density could be a reason for that. In populous areas like big cities or congested urban areas higher COVID-19 incidences could be observed than in rural regions.\n\nThe aim of this paper consists in the application of a diffusion concept to describe one possible issue of the the COVID-19 propagation.\n\nThis will be discussed for the German situation based on the quite different incidence data for the different federal states of Germany.\n\nWith this ansatz some phenomenoms of the actual development of the pandemic could be confirmed. The model gives a possibility to investigate certain scenarios like border-crossings or local spreading events and their influence on the COVID-19 propagation as well.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Guenter K.F. Baerwolff", + "author_inst": "Technical University Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.15.20249089", "rel_title": "Physician Perceptions of Catching COVID-19", @@ -988929,73 +992627,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.01.18.21250047", - "rel_title": "Impact of Public Health Education Program on the Novel Coronavirus Outbreak in the United States", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250047", - "rel_abs": "The coronavirus outbreak in the United States continues to pose a serious threat to human lives. Public health measures to slow down the spread of the virus involve using a face mask, social-distancing, and frequent hand washing. Since the beginning of the pandemic, there has been a global campaign on the use of non-pharmaceutical interventions (NPIs) to curtail the spread of the virus. However, the number of cases, mortality, and hospitalization continue to rise globally, including in the United States. We developed a mathematical model to assess the impact of a public health education program on the coronavirus outbreak in the US. Our simulation showed the prospect of an effective public health education program in reducing both the cumulative and daily mortality of the novel coronavirus. Finally, our result suggests the need to obey public health measures as loss of willingness would increase the cumulative and daily mortality in the US.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Enahoro A Iboi", - "author_inst": "Arizona State University" - }, - { - "author_name": "Ariana Richardson", - "author_inst": "Spelman College" - }, - { - "author_name": "Rachel Ruffin", - "author_inst": "Spelman College" - }, - { - "author_name": "DeAndrea Ingram", - "author_inst": "Spelman College" - }, - { - "author_name": "Jailyn Clark", - "author_inst": "Spelman College" - }, - { - "author_name": "Jala Hawkins", - "author_inst": "Spelman College" - }, - { - "author_name": "Maati McKinney", - "author_inst": "Spelman College" - }, - { - "author_name": "Nianza Horne", - "author_inst": "Spelman College" - }, - { - "author_name": "Reyla Ponder", - "author_inst": "Spelman College" - }, - { - "author_name": "Zoe Denton", - "author_inst": "Spelman College" - }, - { - "author_name": "Folashade B Agusto", - "author_inst": "University of Kansas" - }, - { - "author_name": "Bismark Oduro", - "author_inst": "California University of Pennsylvania" - }, - { - "author_name": "Lanre Akinyemi", - "author_inst": "Prairie View A & M University, Prairie View" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.01.15.20248217", "rel_title": "Hidden Parameters impacting resurgence of SARS-CoV-2 Pandemic", @@ -989899,6 +993530,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.18.21250012", + "rel_title": "Studying the course of Covid-19 by a recursive delay approach", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250012", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIn an earlier paper we proposed a recursive model for epidemics; in the present paper we generalize this model to include the asymptomatic or unrecorded symptomatic people, which we call dark people (dark sector). We call this the SEPARd-model. A delay differential equation version of the model is added; it allows a better comparison to other models. We carry this out by a comparison with the classical SIR model and indicate why we believe that the SEPARd model may work better for Covid-19 than other approaches.\n\nIn the second part of the paper we explain how to deal with the data provided by the JHU, in particular we explain how to derive central model parameters from the data. Other parameters, like the size of the dark sector, are less accessible and have to be estimated more roughly, at best by results of representative serological studies which are accessible, however, only for a few countries. We start our country studies with Switzerland where such data are available. Then we apply the model to a collection of other countries, three European ones (Germany, France, Sweden), the three most stricken countries from three other continents (USA, Brazil, India). Finally we show that even the aggregated world data can be well represented by our approach.\n\nAt the end of the paper we discuss the use of the model. Perhaps the most striking application is that it allows a quantitative analysis of the influence of the time until people are sent to quarantine or hospital. This suggests that imposing means to shorten this time is a powerful tool to flatten the curves.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Erhard Scholz", + "author_inst": "University of Wuppertal" + }, + { + "author_name": "Matthias Kreck", + "author_inst": "University of Bonn" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.18.21249998", "rel_title": "The Association between Early Country-level Testing Capacity and Later COVID-19 Mortality Outcomes", @@ -990579,109 +994233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.19.20248611", - "rel_title": "Safety and immunogenicity of SARS-CoV-2 recombinant protein vaccine formulations in healthy adults: a randomised, placebo-controlled, dose-ranging study", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.20248611", - "rel_abs": "BackgroundEffective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. CoV2 preS dTM is a stabilised pre-fusion S protein vaccine produced in a baculovirus expression system. We present interim safety and immunogenicity results of the first-in-human study of the CoV2 preS dTM vaccine with two different adjuvant formulations.\n\nMethodsThis Phase I/II, randomised, double-blind study (NCT04537208) is being conducted in healthy, SARS-CoV-2-seronegative adults in the USA. Participants were stratified by age (18-49 and [≥]50 years) and randomised to receive one (on Day[D]1) or two doses (D1, D22) of placebo or candidate vaccine, containing: low-dose (LD, effective dose 1.3 {micro}g) or high-dose (HD, 2.6 {micro}g) antigen with adjuvant AF03 (Sanofi Pasteur) or AS03 (GlaxoSmithKline); or unadjuvanted HD (18-49 years only). Safety was assessed up to D43. SARS-CoV-2 neutralising and binding antibody profiles were assessed in D1, D22 and D36 serum samples.\n\nFindingsThe interim safety analyses included 439/441 randomised participants. There were no related unsolicited immediate AEs, serious AEs, medically attended AEs classified as severe, or AE of special interest. More grade 3 solicited reactions were reported than expected after the second dose in the adjuvanted vaccine groups. Neutralising and binding antibody responses after two vaccine doses were higher in adjuvanted versus unadjuvanted groups, in AS03-versus AF03-adjuvanted groups, in HD versus LD groups, and in younger versus older age strata.\n\nInterpretationThe lower than expected immune responses, especially in the older age stratum, and the higher than anticipated reactogenicity post dose 2 were likely due to a higher than anticipated host cell protein content and lower than planned antigen dose in the clinical material. Further development of the AS03-adjuvanted candidate vaccine will focus on identifying the optimal antigen formulation and dose.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Paul A Goepfert", - "author_inst": "Department of Medicine, University of Alabama at Birmingham" - }, - { - "author_name": "Bo Fu", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Anne-Laure Chabanon", - "author_inst": "Sanofi Pasteur, Lyon, France" - }, - { - "author_name": "Matthew I Bonaparte", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Matthew G Davis", - "author_inst": "Rochester Clinical Research, Rochester, NY, USA" - }, - { - "author_name": "Brandon J Essink", - "author_inst": "Meridian Clinical Research, Omaha, NE, USA" - }, - { - "author_name": "Ian Frank", - "author_inst": "Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA" - }, - { - "author_name": "Owen Haney", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Helene Janosczyk", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Michael C Keefer", - "author_inst": "University of Pennsylvania, School of Medicine and Dentistry, Rochester, NY, USA" - }, - { - "author_name": "Marguerite Koutsoukos", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Murray A Kimmel", - "author_inst": "Optimal Research LLC, Melbourne, FL, USA" - }, - { - "author_name": "Roger Masotti", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Stephen J Savarino", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Lode Schuerman", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Howard Schwartz", - "author_inst": "Research Centers of America, Hollywood, FL, USA" - }, - { - "author_name": "Lawrence D Sher", - "author_inst": "Peninsula Research Associates, Rolling Hills Estates, CA, USA" - }, - { - "author_name": "Jon Smith", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Fernanda Tavares-Da-Silva", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Sanjay Gurunathan", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Carlos A DiazGranados", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - }, - { - "author_name": "Guy DeBruyn", - "author_inst": "Sanofi Pasteur, Swiftwater, PA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.21249921", "rel_title": "A comprehensive antigen production and characterization study for easy-to-implement, highly specific and quantitative SARS-CoV-2 antibody assays", @@ -991825,6 +995376,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.01.19.426622", + "rel_title": "Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays", + "rel_date": "2021-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.426622", + "rel_abs": "Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.\n\nOur results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Takeru Nakabayashi", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Yuki Kawasaki", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Koichiro Murashima", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Kazuya Omi", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Satoshi Yuhara", + "author_inst": "H.U. Group Research Institute G.K." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.01.20.427105", "rel_title": "Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity", @@ -992393,45 +995979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.19.21250134", - "rel_title": "Hyperinflammatory conditions, gender differences and mortality in Indian COVID-19 patients", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250134", - "rel_abs": "PurposeEvidence suggests that COVID-19 induces hyperinflammatory conditions and causes relatively more deaths in males than females. The purpose of this study was to analyze gender differences associated with various hyperinflammatory conditions (HIC) and mortality in the Indian COVID-19 patients\n\nMethodsThis study was conducted at the Eras Lucknow Medical College and Hospital (ELMCH), ERA University, which is located in the northern part of India. Starting from July 4, 2020 till December 3, 2020 a total of 2997 patients were treated at ELMCH. We randomly collected blood samples from 150 severe COVID-19 patients (required oxygen) between August 10 and September 15, 2020 for analyzing the following HIC and associated laboratory markers: hyperferritinaemia (serum ferritin), hematological dysfunctions (lymphocytopenia and neutrophil to lymphocyte ratio), cytokinaemia (C-reactive protein), coagulopathy (D-dimer), liver inflammation (aspartate aminotransferase), renal inflammation (blood urea and creatinine), and hyperglycemia (random blood glucose). The threshold values/cut off limits of these laboratory markers used for analyzing the risk of mortality in male and female COVID-19 patients were set according to the scale validated recently by Webb et al, (2020).\n\nResultsIn the above cohort of consecutively admitted COVID-19 patients, analysis of various HIC revealed hyperferritinaemia (odd ratio: 2.9, 95% CI 1.4-6.0), hematological dysfunctions (odd ratio: 2.10, 95% CI 1.0-4.2), hepatic inflammation (odd ratio: 2.0, 95% CI 0.52-7.40), and coagulopathy (odd ratio: 1.5, 95% CI 1.50, 95% CI 0.50-4.60) were more prevalent and sever in male COVID-19 patients. Approximately 86% male to 64% female COVID-19 patients developed lymphocytopenia. Regarding mortality, while hyperferritinaemia (odd ratio: 1.70, 95% CI 0.37-7.43) and cytokinaemia (odd ratio: 1.60, 95% CI 0.37 -7.30) were strongly associated with mortality in male COVID-19 patients, coagulopathy (odd ratio: 3.30, 95% CI 0.31-35), and hematological dysfunctions (odd ratio: 1.70, 95% CI 0.27-10) were more commonly associated with mortality in female COVID-19 patients. Nearly 80% male and female COVID-19 patients, who died had developed [≥]2 criteria of HIS criteria. Chronic renal disease was associated with more deaths in female than male COVID-19 patients (odd ratio: 2.0, 95% CI 0.54 - 7.4). While the mortality proportion was slightly higher in male (6.3%) than female (4.5%) COVID-19 patients, survival curves of the two genders were not different (hazard ratio: 1.02, 95% CI 0.71-1.40, P = 0. 953).\n\nConclusionDistinct HIC were associated with the severity, and mortality in male and female COVID-19 patients. Coagulopathy and renal injury were detrimental, specifically, for female COVID-19 patients. The overall mortality proportion was around 5.3%. The above results suggest that gender differences associated with COVID-19 severity and mortality arise due to differences in various HIC. These results may help in developing personalized or gender based treatments for COVID-19 patients.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fouzia Shoeb", - "author_inst": "ERA University" - }, - { - "author_name": "Imran Hussain", - "author_inst": "ERA University" - }, - { - "author_name": "Gazala Afrin", - "author_inst": "ERA University" - }, - { - "author_name": "Shagufta T Mufti", - "author_inst": "ERA University" - }, - { - "author_name": "Syed T Raza", - "author_inst": "ERA University" - }, - { - "author_name": "Farzana Mahdi", - "author_inst": "ERA University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.21250100", "rel_title": "Impact of immediate and preferential relaxation of social and travel restrictions for vaccinated people on the spreading dynamics of COVID-19 : a model-based analysis", @@ -993647,6 +997194,65 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.19.427282", + "rel_title": "SARS-CoV-2 infection of circulating immune cells is not responsible for virus dissemination in severe COVID-19 patients", + "rel_date": "2021-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.427282", + "rel_abs": "In late 2019 a novel coronavirus (SARS-CoV-2) emerged, and has since caused a global pandemic. Understanding the pathogenesis of COVID-19 disease is necessary to inform development of therapeutics, and management of infected patients. Using scRNAseq of blood drawn from SARS-CoV-2 patients, we asked whether SARS-CoV-2 may exploit immune cells as a Trojan Horse to disseminate and access multiple organ systems. Our data suggests that circulating cells are not actively infected with SARS-CoV-2, and do not appear to be a source of viral dissemination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nicole L Rosin", + "author_inst": "University of Calgary" + }, + { + "author_name": "Arzina Jaffer", + "author_inst": "University of Calgary" + }, + { + "author_name": "Sarthak Sinha", + "author_inst": "University of Calgary" + }, + { + "author_name": "Rory P Mulloy", + "author_inst": "University of Calgary" + }, + { + "author_name": "Carolyn Robinson", + "author_inst": "University of Calgary" + }, + { + "author_name": "Elodie Labit", + "author_inst": "University of Calgary" + }, + { + "author_name": "Luiz G Almeida", + "author_inst": "University of Calgary" + }, + { + "author_name": "Antoine Dufour", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jennifer A Corcoran", + "author_inst": "University of Calgary" + }, + { + "author_name": "Bryan Yipp", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jeff Biernaskie", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.19.427250", "rel_title": "COVID-19 Knowledge, Attitudes, and Practices of United Arab Emirates Medical and Health Sciences Students: A Cross Sectional Study", @@ -994995,153 +998601,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.13.21249735", - "rel_title": "A Serology Strategy for Epidemiological Studies Based on the Comparison of the Performance of Seven Different Test Systems - The Representative COVID-19 Cohort Munich", - "rel_date": "2021-01-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249735", - "rel_abs": "BackgroundSerosurveys are essential to understand SARS-CoV-2 exposure and enable population-level surveillance, but currently available tests need further in-depth evaluation. We aimed to identify testing-strategies by comparing seven seroassays in a population-based cohort.\n\nMethodsWe analysed 6,658 samples consisting of true-positives (n=193), true-negatives (n=1,091), and specimens of unknown status (n=5,374). For primary testing, we used Euroimmun-Anti-SARS-CoV-2-ELISA-IgA/IgG and Roche-Elecsys-Anti-SARS-CoV-2; and virus-neutralisation, GeneScript(R)cPass, VIRAMED-SARS-CoV-2-ViraChip(R), and Mikrogen-recomLine-SARS-CoV-2-IgG, including common-cold CoVs, for confirmatory testing. Statistical modelling generated optimised assay cut-off-thresholds.\n\nFindingsSensitivity of Euroimmun-anti-S1-IgA was 64.8%, specificity 93.3%; for Euroimmun-anti-S1-IgG, sensitivity was 77.2/79.8% (manufacturers/optimised cut-offs), specificity 98.0/97.8%; Roche-anti-N sensitivity was 85.5/88.6%, specificity 99.8/99.7%. In true-positives, mean and median titres remained stable for at least 90-120 days after RT-PCR-positivity. Of true-positives with positive RT-PCR (<30 days), 6.7% did not mount detectable seroresponses. Virus-neutralisation was 73.8% sensitive, 100.0% specific (1:10 dilution). Neutralisation surrogate tests (GeneScript(R)cPass, Mikrogen-recomLine-RBD) were >94.9% sensitive, >98.1% specific. Seasonality had limited effects; cross-reactivity with common-cold CoVs 229E and NL63 in SARS-CoV-2 true-positives was significant.\n\nConclusionOptimised cut-offs improved test performances of several tests. Non-reactive serology in true-positives was uncommon. For epidemiological purposes, confirmatory testing with virus-neutralisation may be replaced with GeneScript(R)cPass or recomLine-RBD. Head-to-head comparisons given here aim to contribute to the refinement of testing-strategies for individual and public health use.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Laura Olbrich", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany German Centre for Infection Researc" - }, - { - "author_name": "Noemi Castelletti", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany Institute of Radiation Medicine, He" - }, - { - "author_name": "Yannik Schaelte", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, 85764 Neuherberg, GermanyCenter for Mathematics, Technische Universitaet Muenchen, 85748 Garchin" - }, - { - "author_name": "Merce Gari", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany" - }, - { - "author_name": "Peter Puetz", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, 85764 Neuherberg, GermanyDepartment of Business Administration and Economics, Bielefeld Universi" - }, - { - "author_name": "Abhishek Bakuli", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Michael Pritsch", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Inge Kroidl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany German Centre for Infection Researc" - }, - { - "author_name": "Elmar Saathoff", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany German Centre for Infection Researc" - }, - { - "author_name": "Jessica Michelle Guggenbuehl Noller", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Volker Fingerle", - "author_inst": "German Centre for Infection Research (DZIF), Partner Site MunichBavarian Health and Food Safety Authority (LGL)" - }, - { - "author_name": "Ronan Le Gleut", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, 85764 Neuherberg, GermanyCore Facility Statistical Consulting, Helmholtz Zentrum Muenchen, 85764" - }, - { - "author_name": "Leonard Gilberg", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Isabel Brand", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Philine Falk", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Alisa Markgraf", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Flora Deak", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Friedrich Riess", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Max Diefenbach", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Tabea M Eser", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany" - }, - { - "author_name": "Franz Weinauer", - "author_inst": "BRK-Blutspendedienst, 80336 Munich, Germany" - }, - { - "author_name": "Silke Martin", - "author_inst": "BRK-Blutspendedienst, 80336 Munich, Germany" - }, - { - "author_name": "Ernst-Markus Quenzel", - "author_inst": "BRK-Blutspendedienst, 80336 Munich, Germany" - }, - { - "author_name": "Marc Becker", - "author_inst": "Department of Conservative Dentistry and Periodontology, University Hospital, LMU Munich Ludwig-Maximilians-University of Munich, Goethestr. 70, 80336 Munich, G" - }, - { - "author_name": "Juergen Durner", - "author_inst": "Department of Conservative Dentistry and Periodontology, University Hospital, LMU Munich Ludwig-Maximilians-University of Munich, Goethestr. 70, 80336 Munich, G" - }, - { - "author_name": "Philipp Girl", - "author_inst": "German Centre for Infection Research (DZIF), Partner Site MunichBundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "Katharina Mueller", - "author_inst": "German Centre for Infection Research (DZIF), Partner Site MunichBundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "Katja Radon", - "author_inst": "Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, 80336 Munich, GermanyCenter for Internatio" - }, - { - "author_name": "Christiane Fuchs", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, 85764 Neuherberg, GermanyCenter for Mathematics, Technische Universitaet Muenchen, 85748 Garchin" - }, - { - "author_name": "Roman Woelfel", - "author_inst": "German Centre for Infection Research (DZIF), Partner Site MunichBundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "Jan Hasenauer", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen, 85764 Neuherberg, GermanyCenter for Mathematics, Technische Universitaet Muenchen, 85748 Garchin" - }, - { - "author_name": "Michael Hoelscher", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany German Centre for Infection Researc" - }, - { - "author_name": "Andreas Wieser", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Leopoldstr. 5, 80802 Munich, Germany German Centre for Infection Researc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.13.21249645", "rel_title": "Metabolic markers distinguish COVID-19 from other intensive care patients and show potential to stratify for disease risk", @@ -996140,6 +999599,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.14.21249637", + "rel_title": "SARS-CoV-2 infection control implementation based on sources of infection showing directions for three age groups in Japan", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249637", + "rel_abs": "BackgroundSome aspects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in children and adults remain unclear. This report describes different SARS-CoV-2 transmission patterns by age group in Japan.\n\nMethods and findingsThis retrospective observational case series study analyzed transmission patterns of real-time polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections found by local health authorities and commercial laboratories during January 14 through July 31, 2020 in Japan. After ascertaining the infection source for every symptomatic case as clusters at households, daycare facilities, schools, hospitals and workplaces etc., their associated transmission patterns were analyzed. Identified cases were divided into three groups: underage, < 20; adults, 20-59; and elderly people 60 years old and older. The reproductive number (R)s of respective transmission directions found for the respective age groups were compared.\n\nOf 26,986 total cases, 23,746 unknown cases were found, leaving 3,240 ascertained sources of infection (12.0%) comprising 125 (3.9%) underage, 2350 (72.5%) adult, and 765 (23.6%) elderly people. The respective Rs of underage infection sources directed to underage, adult, and elderly people were estimated respectively as 0.0415 (95% CI, 0.0138-0.0691), 1.11 (95% CI, 0.9171-1.3226), and 0.2811 (95% CI, 0.2074-0.3687). The respective Rs of adult infection source directed to underage, adult, and elderly people were estimated respectively as 0.0140 (95% CI, 0.0120-0.0162), 0.5392 (95% CI, 0.5236-0.5550), and 0.1135 (95% CI, 0.1074-0.1197). The respective Rs of elderly infection source directed to underage, adult, and elderly people were estimated as 0.065 (95% CI, 0.0039-0.0091), 0.3264 (95% CI, 0.3059-0.3474), and 0.3991 (95% CI, 0.3757-0.4229).\n\nConclusionsThe main sources of SARS-CoV-2 infection were adults and elderly people. The R of underage people directed to adults was greater than 1 because of close familial contact but they were unlikely to become carriers transmitting SARS-CoV-2 because they accounted for a minority for transmissions. Apparently, SARS-CoV-2 was transmitted among adults and elderly people, suggesting that infection control of SARS-CoV-2 should be managed specifically by generation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Atsuko Hata", + "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" + }, + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Eri Muso", + "author_inst": "Kyoto Kacho University" + }, + { + "author_name": "Toshiro Katayama", + "author_inst": "Morinomiya University of Medical Sciences" + }, + { + "author_name": "Takahide Hata", + "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.15.21249863", "rel_title": "How to best test suspected cases of COVID-19: an analysis of the diagnostic performance of RT-PCR and alternative molecular methods for the detection of SARS-CoV-2", @@ -996908,41 +1000406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.14.21249854", - "rel_title": "An Estimation of Reproduction Number of SARS-CoV-2 by Age Class for Age Classes in Japan", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249854", - "rel_abs": "BackgroundInfectiousness of COVID-19 by age class inferred from the infection source and by infected people might be different. However, studies of such infectiousness have not been reported.\n\nObjectThe object of this study was estimation of reproduction numbers by age class of the source of infection and the infected persons. To do so, after examining a new procedure for reproduction number estimation, we checked infected places by age class of the source of infection and the infected persons.\n\nMethodWe ignore patients who infected no one because their reliability might be lower than that of patients who infected more than one person. We estimated the reproduction number from the histogram of the number of the infected people by the same patient, assuming that the histogram follows an exponential distribution.\n\nDiscussion and ConclusionThe obtained results demonstrated that the effective reproduction numbers for infection from children were very low. They were higher among adult and elderly people than among the same age class. Moreover, although the highest and second-highest infected places were other and at home with some exceptions, the data for infection at hospitals were remarkable among adults and elderly people. Among elderly people, infection at facilities for elderly was also high. Infections at nursing schools, schools, restaurants, and entertainment venues at night were negligible.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Junko Kurita", - "author_inst": "Tokiwa University, Ibaraki, Japan" - }, - { - "author_name": "Takahide Hata", - "author_inst": "Kitano Hospital, Tazuke Kofukai Medical Research Institute, Osaka, Japan" - }, - { - "author_name": "Tamie Sugawara", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - }, - { - "author_name": "Yasushi Ohkusa", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - }, - { - "author_name": "Atsuko Hata", - "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.15.426526", "rel_title": "In vivo structure and dynamics of the RNA genome of SARS-Cov-2", @@ -998070,6 +1001533,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.12.21249603", + "rel_title": "Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249603", + "rel_abs": "We used a Sioutas personal cascade impactor sampler (PCIS) to screen for SARS-CoV-2 in a car driven by a COVID-19 patient. SARS-CoV-2 was detectable at all PCIS stages by PCR and was cultured from the section of the sampler collecting particles in the 0.25 to 0.50 {square}m size range.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "John A Lednicky", + "author_inst": "University of Florida" + }, + { + "author_name": "Michael Lauzardo", + "author_inst": "University of Florida" + }, + { + "author_name": "Md. Mabubul Alam", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Maha Elbadry", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Caroline Stephenson", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Julia C. Gibson", + "author_inst": "University of Florida" + }, + { + "author_name": "John Glenn Morris Jr.", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.10.20248871", "rel_title": "Emergence of multiple SARS-CoV-2 mutations in an immunocompromised host", @@ -998926,53 +1002432,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, - { - "rel_doi": "10.1101/2021.01.13.21249576", - "rel_title": "Evaluation of Urine SARS-COV-2 RT-PCR as a predictor of Acute Kidney Injury and disease severity in critical COVID-19 patients", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249576", - "rel_abs": "The novel coronavirus disease (COVID-19) is an emerging infectious disease caused by SARS-CoV-2, which began as an outbreak in Wuhan, China and spread rapidly throughout the globe. Although the majority of infections are mild, severe and critical COVID-19 patients face deterioration of respiratory function, and may also present extrapulmonary manifestations, mostly affecting the kidney, digestive tract, heart and nervous system. Here, we prospectively evaluated the presence of SARS-CoV-2 genetic material by RT-PCR in urine samples obtained from critical care COVID-19 patients. In 51 patients included, we found higher serum creatinine levels, a longer hospital stay and a more frequent dialysis need in urine-positive patients. These findings could suggest that, in predisposed patients, a direct viral cytopathic effect may contribute to a more severe disease phenotype.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sergio Pinto de Souza", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Marcelo Augusto Duarte Silveira", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Bruno Solano de Freitas Souza", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Carolina Kymie Vasques Nonaka", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Erica de Melo", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Julia Barros Cabral", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Fernanda Coelho", - "author_inst": "Hospital Sao Rafael" - }, - { - "author_name": "Rogerio da Hora Passos", - "author_inst": "Hospital Sao Rafael" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.01.14.21249793", "rel_title": "Real-Time Electronic Health Record Mortality Prediction During the COVID-19 Pandemic: A Prospective Cohort Study", @@ -1000052,6 +1003511,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.12.20248588", + "rel_title": "Bacterial superinfection pneumonia in SARS-CoV-2 respiratory failure", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.20248588", + "rel_abs": "BackgroundSevere community-acquired pneumonia secondary to SARS-CoV-2 is a leading cause of death. Current guidelines recommend patients with SARS-CoV-2 pneumonia receive empirical antibiotic therapy for suspected bacterial superinfection, but little evidence supports these recommendations.\n\nMethodsWe obtained bronchoscopic bronchoalveolar lavage (BAL) samples from patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. We analyzed BAL samples with multiplex PCR and quantitative culture to determine the prevalence of superinfecting pathogens at the time of intubation and identify episodes of ventilator-associated pneumonia (VAP) over the course of mechanical ventilation. We compared antibiotic use with guideline-recommended care.\n\nResultsThe 179 ventilated patients with severe SARS-CoV-2 pneumonia discharged from our hospital by June 30, 2020 were analyzed. 162 (90.5%) patients had at least one BAL procedure; 133 (74.3%) within 48 hours after intubation and 112 (62.6%) had at least one subsequent BAL during their hospitalization. A superinfecting pathogen was identified within 48 hours of intubation in 28/133 (21%) patients, most commonly methicillin-sensitive Staphylococcus aureus or Streptococcus species (21/28, 75%). BAL-based treatment reduced antibiotic use compared with guideline-recommended care. 72 patients (44.4%) developed at least one VAP episode. Only 15/72 (20.8%) of initial VAPs were attributable to multidrug-resistant pathogens. The incidence rate of VAP was 45.2/1000 ventilator days.\n\nConclusionsWith use of sensitive diagnostic tools, bacterial superinfection at the time of intubation is infrequent in patients with severe SARS-CoV-2 pneumonia. Treatment based on current guidelines would result in substantial antibiotic overuse. The incidence rate of VAP in ventilated patients with SARS-CoV-2 pneumonia are higher than historically reported.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Chiagozie O. Pickens", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Catherine A. Gao", + "author_inst": "Northwestern" + }, + { + "author_name": "Michael J. Cuttica", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Sean B. Smith", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Lorenzo Pesce", + "author_inst": "Department of Pharmacology, Northwestern University Department of Pharmacology School of Medicine" + }, + { + "author_name": "Rogan Grant", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Mengjia Kang", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Luisa Morales-Nebreda", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Avni A. Bavishi", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Jason Arnold", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Anna Pawlowski", + "author_inst": "Clinical Translational Sciences Institute, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Chao Qi", + "author_inst": "Department of Pathology, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "GR Scott Budinger", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Benjamin D. Singer", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Richard G. Wunderink", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "- NU COVID Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.14.21249831", "rel_title": "Increased peripheral blood neutrophil activation phenotypes and NETosis in critically ill COVID-19 patients", @@ -1000696,157 +1004234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.01.14.426475", - "rel_title": "N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2", - "rel_date": "2021-01-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.14.426475", - "rel_abs": "SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Matthew McCallum", - "author_inst": "University of Washington" - }, - { - "author_name": "Anna De Marco", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Florian Lempp", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "M. Alejandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Dora Pinto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "Martina Beltramello", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Alex Chen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Zhuoming Liu", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Fabrizia Zatta", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Samantha Zepeda", - "author_inst": "University of Washington" - }, - { - "author_name": "Julia di Iulio", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "John E Bowen", - "author_inst": "University of Washington" - }, - { - "author_name": "Martin Montiel-Ruiz", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Jiayi Zhou", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Laura Rosen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Siro Bianchi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Barbara Guarino", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Chiara Silacci Fregni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Rana Abdelnabi", - "author_inst": "KU Leuven" - }, - { - "author_name": "Shi-Yan Caroline Foo", - "author_inst": "KU Leuven" - }, - { - "author_name": "Paul W Rothlauf", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Louis-Marie Bloyet", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Fabio Benigni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Elisabetta Cameroni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Agostino Riva", - "author_inst": "University of Milan" - }, - { - "author_name": "Gyorgy Snell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Amalio Telenti", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Sean PJ Whelan", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Herbert W Virgin", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Matteo Samuele Pizzuto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.13.426626", "rel_title": "A highly thermotolerant, trimeric SARS-CoV-2 receptor binding domain derivative elicits high titers of neutralizing antibodies", @@ -1001966,6 +1005353,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.11.21249630", + "rel_title": "Determining the optimal COVID-19 policy response using agent-based modelling linked to health and cost modelling: Case study for Victoria, Australia", + "rel_date": "2021-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249630", + "rel_abs": "ImportanceDetermining the best policy on social restrictions and lockdowns for the COVID-19 pandemic is challenging.\n\nObjectiveTo determine the optimal policy response ranging from aggressive and moderate elimination, tight suppression (aiming for 1 to 5 cases per million per day) and loose suppression (5 to 25 cases per million per day).\n\nDesignTwo simulation models in series: an agent-based model to estimate daily SARS-CoV-2 infection rates and time in four stages of social restrictions; a proportional multistate lifetable model to estimate long-run health impacts (health adjusted life years (HALYs) arising from SARS-CoV-2) and costs (health systems, and health system plus GDP).\n\nThe net monetary benefit (NMB) of each policy option at varying willingness to pay (WTP) per HALY was calculated: NMB = HALYs x WTP - cost. The optimal policy response was that with the highest NMB.\n\nSetting and participantsThe State of Victoria, Australia, using simulation modeling of all residents.\n\nMain Outcome and MeasuresSARS-CoV-2 infection rates, time under various stages of restrictions, HALYs, health expenditure and GDP losses.\n\nResultsAggressive elimination resulted in the highest percentage of days with the lowest level of restrictions (median 31.7%, 90% simulation interval 6.6% to 64.4%). However, days in hard lockdown were similar across all four strategies (medians 27.5% to 36.1%).\n\nHALY losses (compared to a no-COVID-19 scenario) were similar for aggressive elimination (286, 219 to 389) and moderate elimination (314, 228 to 413), and nearly eight and 40-times higher for tight and loose suppression. The median GDP loss was least for moderate elimination ($US41.7 billion, $29.0 to $63.6 billion), but there was substantial overlap in simulation intervals between the four strategies.\n\nFrom a health system perspective aggressive elimination was optimal in 64% of simulations above a willingness to pay of $15,000 per HALY, followed by moderate elimination in 35% of simulations.\n\nModerate elimination was optimal from a partial societal perspective in half the simulations followed by aggressive elimination in a quarter.\n\nShortening the pandemic duration to 6 months saw loose suppression become preferable under a partial societal perspective.\n\nConclusions and RelevanceElimination strategies were preferable over a 1-year pandemic duration.\n\nFundingAnonymous philanthropic donation to the University of Melbourne.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSTo determine the optimal of four policy responses to COVID-19 in the State of Victoria, Australia (aggressive and moderate elimination, tight suppression (aiming for 1 to 5 cases per million per day) and loose suppression (5 to 25 cases per million per day), based on estimated future health loss and costs from both a health system and partial societal perspective.\n\nFindingsFrom a health system perspective aggressive elimination was optimal in 64% of simulations above a willingness to pay of $15,000 per HALY, followed by moderate elimination in 35% of simulations. Moderate elimination was optimal from a partial societal perspective (i.e., including GDP losses) in half the simulations followed by aggressive elimination in a quarter.\n\nMeaningWhilst there is considerable uncertainty in outcomes for all the four policy options, the two elimination options are usually optimal from both a health system and a partial societal (health expenditure plus GDP cost) perspective.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Professor Tony Blakely", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Jason Thompson", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Laxman Bablani", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Patrick Andersen", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Driss Ait Ouakrim", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Natalie Carvalho", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Patrick Abraham", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Marie-Anne Boujaoude", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Ameera Katar", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Edifofon Akpan", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Nick Wilson", + "author_inst": "University of Otago, Wellington" + }, + { + "author_name": "Professor Mark Stevenson", + "author_inst": "University of Melbourne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.11.21249564", "rel_title": "The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions", @@ -1002754,57 +1006204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.11.20248930", - "rel_title": "Cardiorespiratory Fitness and Neuromuscular Performance in Patients Recovered from COVID-19", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.20248930", - "rel_abs": "ObjectiveCOVID-19 affects cardiorespiratory and muscular systems, causing dysfunctions that may persist after recovery from the acute infection and treatment. The aim of this study was to evaluate cardiorespiratory fitness and neuromuscular performance in these patients.\n\nMethodsPatients recovered from mild (n=31) and severe (n=17) COVID-19 were evaluated and compared to healthy subjects (n=15). All volunteers underwent a maximal cardiopulmonary exercise test with simultaneous acquisition of electromyography (EMG). Power output, oxygen uptake (VO2), pulse oxygen (O2Pulse), cardiovascular efficiency ({Delta}HR/{Delta}VO2), ventilation (VE), breathing reserve (BR) and ventilatory efficiency (VE/VCO2 slope) were analyzed. From EMG, power output for type Ia and IIa activation as well as total neuromuscular efficiency ({Delta}watts/{Delta}%RMS) were determined.\n\nResultsPatients with severe COVID-19 presented lower VO2, O2Pulse and VE than mild COVID-19 patients and healthy subjects (p < 0.05 for all comparisons). No differences in {Delta}HR/{Delta}VO2, BR or VE/VCO2 slope were observed among the groups (p > 0.05 for all comparisons). Type IIa and IIb fibers were activated at lower power output in severe than in mild COVID-19 patients and healthy subjects (p < 0.05). {Delta}watts/{Delta}%RMS was lower in severe than in mild COVID-19 patients and healthy subjects (p < 0.05).\n\nConclusionPatients recovered from severe COVID-19 present low cardiorespiratory fitness, activate glycolytic fibers at low power outputs, and show low neuromuscular efficiency; while patients recovered from mild COVID-19 do not present these sequels.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Murillo Frazao", - "author_inst": "Federal University of Paraiba" - }, - { - "author_name": "Amilton da Cruz Santos", - "author_inst": "Federal University of Paraiba" - }, - { - "author_name": "Lucas de Assis Pereira Cacau", - "author_inst": "Intervent" - }, - { - "author_name": "Paulo Eugenio Silva", - "author_inst": "Hospital de Base do Distrito Federal" - }, - { - "author_name": "Tullio Rocha Petrucci", - "author_inst": "CLINAR" - }, - { - "author_name": "Mariela Cometki Assis", - "author_inst": "Intervent" - }, - { - "author_name": "Romulo de Almeida Leal", - "author_inst": "Federal University of Paraiba" - }, - { - "author_name": "Claudia Lucia de Moraes Forjaz", - "author_inst": "USP" - }, - { - "author_name": "Maria do Socorro Brasileiro-Santos", - "author_inst": "Federal University of Paraiba" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2021.01.12.21249608", "rel_title": "The impact of the coronavirus disease 2019 (COVID-19) pandemic on university students' dietary intake, physical activity, and sedentary behaviour", @@ -1003664,6 +1007063,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.09.21249489", + "rel_title": "Impact of COVID-19 pandemic on use of Pediatric Emergency Health Services in a Tertiary Care Pediatric Hospital in North India", + "rel_date": "2021-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249489", + "rel_abs": "ObjectiveTo compare Pediatric Emergency attendance pre-COVID 19 to that during COVID 19 pandemic and to study changes in patient profiles attending Pediatric Emergency Department during COVID 19 pandemic.\n\nMethodsWe conducted a retrospective cross-sectional observational study and collected data from Medical Record Section during the COVID-19 pandemic from January to June 2020 and compared it with data from 2019 in similar months. Data collected was analyzed to find out the impact of COVID - 19 on use of pediatric emergency health services with respect to patient attendance, age and clinical profile before and during COVID-19 in a tertiary care hospital in New Delhi.\n\nResultsWe observed a 43% decline in PED visits which increased to 75% during the period of lock-down (p value = 0.005). There was a significant decrease in children of age group 1-5 years attending PED. Mortality rate during lockdown had gone up by nearly 3times than the average monthly mortality.\n\nConclusionsWhile children might not have been directly affected by the COVID-19 pandemic, but the fear of COVID 19 and measures taken to control the pandemic has affected the health seeking behavior of patients to an extent that indirectly caused more damage than anticipated.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ravitanaya Sodani", + "author_inst": "Lady Hardinge Medical College, New Delhi, India" + }, + { + "author_name": "Shalu Gupta", + "author_inst": "Lady Hardinge Medical College & Kalawati Saran Children's Hospital, New Delhi, India" + }, + { + "author_name": "Virendra Kumar", + "author_inst": "Lady Hardinge Medical College & Kalawati Saran Children's Hospital, New Delhi, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.01.06.20249030", "rel_title": "Convergence of Comorbidity and COVID-19 Infection to Fatality: An Investigation Based on Concurrent Health Status Evaluation among the Elderly Population in Kerala", @@ -1004252,109 +1007678,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.10.21249440", - "rel_title": "Serologic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Infection in Hospital Health Care Workers", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249440", - "rel_abs": "BACKGROUNDIt is unclear how, when and where health care workers (HCW) working in hospitals are infected with SARS-CoV-2.\n\nMETHODSProspective cohort study comprising 4-weekly measurement of SARS-CoV-2 specific antibodies and questionnaires from March to June 2020. We compared SARS-CoV-2 incidence between HCW working in Covid-19 patient care, HCW working in non-Covid-19 patient care and HCW not in patient care. Phylogenetic analyses of SARS-CoV-2 samples from patients and HCW were performed to identify potential transmission clusters.\n\nRESULTSWe included 801 HCW: 439 in the Covid-19 patient care group, 164 in the non-Covid-19 patient care group and 198 in the no patient care group. SARS-CoV-2 incidence was highest in HCW working in Covid-19 patient care (13.2%), as compared with HCW in non-Covid-19 patient care (6.7%, hazard ratio [HR] 2.2, 95% confidence interval [CI] 1.2 to 4.3) and in HCW not working in patient care (3.6%, HR 3.9, 95% CI 1.8 to 8.6). Within the group of HCW caring for Covid-19 patients, SARS-CoV-2 cumulative incidence was highest in HCW working on Covid-19 wards (25.7%), as compared with HCW working on intensive care units (7.1%, HR 3.6, 95% CI 1.9 to 6.9), and HCW working in the emergency room (8.0%, HR 3.3, 95% CI 1.5 to 7.1). Phylogenetic analyses on Covid-19 wards identified multiple potential HCW-to-HCW transmission clusters while no patient-to-HCW transmission clusters were identified.\n\nCONCLUSIONSHCW working on Covid-19 wards are at increased risk for nosocomial SARS-CoV-2 infection, with an important role for HCW-to-HCW transmission.\n\n(Funded by the Netherlands Organization for Health Research and Development ZonMw & the Corona Research Fund Amsterdam UMC; Netherlands Trial Register number NL8645)", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Jonne J Sikkens", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "David T.P. Buis", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Edgar J.G. Peters", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Mireille Dekker", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Michiel Schinkel", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Tom D.Y. Reijnders", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Alex R. Schuurman", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Justin de Brabander", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Ayesha Lavell", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Jaap J Maas", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Jelle Koopsen", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Alvin X Han", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Colin A. Russell", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Janke Schinkel", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Marcel Jonges", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Sebastien P.F. Matamoros", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Suzanne Jurriaans", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Rosa van Mansfeld", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "W. Joost Wiersinga", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Yvo M Smulders", - "author_inst": "Amsterdam UMC, location VUmc" - }, - { - "author_name": "Menno D. de Jong", - "author_inst": "Amsterdam UMC, location AMC" - }, - { - "author_name": "Marije K Bomers", - "author_inst": "Amsterdam UMC, location VUmc" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.10.21249382", "rel_title": "Epidemiological impact of prioritizing SARS-CoV-2 vaccination by antibody status: Mathematical modeling analyses", @@ -1005370,6 +1008693,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.01.10.21249548", + "rel_title": "Atmospheric PM2.5 before and after Lockdown in relation to COVID-19 Evolution and daily Viral Counts: Could Viral Natural Selection have occurred due to changes in the Airborne Pollutant PM2.5 acting as a Vector for SARS-CoV-2?", + "rel_date": "2021-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249548", + "rel_abs": "BackgroundGenes coding for SARS-CoV-2 have been detected on the microscopic airborne pollutant particulate matter, which has been suggested as a vector for COVID-19 transmission. Lockdown in China has been shown to be associated with significant reduction in pollution including the particulate matter component which coincided with the appearance of a viral mutant (Clade G) which steadily displaced the original Clade D after lockdown. The reason why Clade G developed a fitness advantage is as yet unknown. This paper examines the possible role of airborne particulate matter PM2.5 as selective pressure determining viral Clade predominance and further shedding light on the mode of SARS-CoV-2 transmission.\n\nMethodsThe average levels of PM2.5 of a number of cities were obtained from the Air Quality Index (AQI), a real-time assessment of atmospheric pollution. The daily average PM2.5 levels were assessed between January 23rd and April 29th 2020 determined by the timeline when viral counts in Beijing and other cities were available. Daily viral counts of Clades D and G were available starting from the 12th February as determined by the scientific literature published in August 2020. The cities chosen were Beijing, Sheffield, Nottingham, Sydney and Cambridge because of their substantially elevated viral counts compared to other cities. Cities as opposed to vaster areas/nations were chosen as PM2.5 levels vary across regions and countries.\n\nResultsFor the time period assessed, the Beijing PM2.5 pattern initiated with highly elevated mean PM2.5 levels of 155.8{micro}g/m3 (SD+/-73.6) during high viral counts, followed by 82.1{micro}g/m3 (SD+/-44.9) (p<0.04) when the viral counts decreased. In all the other cities assessed, the pattern differed whereby the PM2.5 levels increased significantly over the preceding baseline contemporaneously with the viral count rise. The changes in these cities PM2.5 levels were on average 31.5{micro}g/m3 before viral counts rose and 56.35{micro}g/m3 contemporaneous with viral count rise. The average levels of PM2.5 in these cities started to decrease one week after lockdown to 46{micro}g/m3 when measured over 2 weeks post-lockdown.\n\nAs regards the viral counts from data retrieved from Beijing, the latter part of the bell-shaped curve and a subsequent smaller curve of the viral count was available for evaluation. The average viral count for Clade D in Beijing was 11.1(SD+/-13.5) followed by a mean viral count for Clade G was 13.8(SD+/-9.2). Conversely in all the other cities besides Beijing, the viral counts averaged 45.8 for Clade D and 161 for Clade G. The variation in viral counts between cities suggests the strong possibility of variation in the availability of sampling between cities.\n\nThe newer variant, Clade G demonstrated viral counts initially appearing in mid-February in Beijing to later displace Clade D as the dominant viral Clade. The appearance of Clade G coincided with the decreasing gradient of PM2.5 levels. A number of significant correlations were obtained between PM2.5 levels and the viral count in all the cities reviewed.\n\nConclusionCOVID-19 viral counts appear to increase concomitant with increasing PM2.5 levels. Viral counts of both Clades correlated differentially with PM2.5 levels in all the cities assessed. The significantly highly elevated PM2.5 levels in Beijing resulted in correlating mainly with Clade D, however Clade G began to appear with decreasing PM2.5 levels, suggesting the beginnings for the initial SARS-CoV-2 Clade evolution. Clade G, the newer variant was able to flourish at lower levels of PM2.5 than Clade D. Clade G may possibly have utilized other sources of particulate matter as a viral vector, such as that derived from tobacco smoking, whereby 66% of Chinese males are smokers and 70% of the Chinese non-smoking population are exposed to 2nd hand smoking.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Yves Muscat Baron", + "author_inst": "Medical School, University of Malta." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.10.21249151", "rel_title": "Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples", @@ -1006318,41 +1009660,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.10.426143", - "rel_title": "Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment", - "rel_date": "2021-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.10.426143", - "rel_abs": "MotivationThe SARS-CoV-2 variants emerging from South Africa (501.V2) and the UK (B.1.1.7) necessitate rapid assessment of the effects of the corresponding amino acid substitutions in the spike (S) receptor-binding domain (RBD) of the variants on the interactions with the human ACE2 receptor and monoclonal antibodies (mAbs) reported earlier to neutralize the spike.\n\nResultsMolecular modeling and simulations reveal that N501Y, shared by both variants, increases ACE2 binding affinity, and may impact the collective dynamics of the ACE2-RBD complex, occupying a central hinge site that modulates the overall dynamics of the complex. In contrast, the substitutions K417N and E484K in the South African variant 501.V2 would reduce the ACE2-binding affinity by abolishing two interfacial salt bridges that facilitate RBD binding to ACE2, K417(S)-D30(ACE2) and E484 (S)-K31(ACE2). These two mutations may thus be more than compensating the attractive effect induced by N501Y, overall resulting in an ACE2-binding affinity comparable to that of the wildtype RBD. Further analysis of the impact of these mutations on the interactions with mAbs targeting the spike indicate that the substitutions K417N and E484K may also abolish the salt bridges between the spike and selected mAbs, such as REGN10933, BD23, H11_H4, and C105, thus reducing the binding affinity and effectiveness of these mAbs.\n\nContactbahar@pitt.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mary Hongying Cheng", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "James M Krieger", - "author_inst": "University of Pittsburgh, Pittsburgh, PA 15213, USA" - }, - { - "author_name": "Burak Kaynak", - "author_inst": "University of Pittsburgh, Pittsburgh, PA 15213, USA" - }, - { - "author_name": "Moshe A Arditi", - "author_inst": "Cedars Sinai Medical Center" - }, - { - "author_name": "Ivet Bahar", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.01.11.426227", "rel_title": "Microsecond simulation unravel the structural dynamics of SARS-CoV-2 Spike-C-terminal cytoplasmic tail (residues 1242-1273)", @@ -1007676,6 +1010983,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.08.20249041", + "rel_title": "The incremental value of computed tomography of COVID-19 pneumonia in predicting ICU admission", + "rel_date": "2021-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.20249041", + "rel_abs": "RationaleTriage is crucial for patients management and estimation of the required Intensive Care Unit (ICU) beds is fundamental for Health Systems during the COVID-19 pandemic.\n\nObjectiveTo assess whether chest Computed Tomography (CT) of COVID-19 pneumonia has an incremental role in predicting patients admission to ICU.\n\nMethodsWe performed volumetric and texture analysis of the areas of the affected lung in CT of 115 outpatients with COVID-19 infection presenting to the Emergency Room with dyspnea and unresponsive hypoxyemia. Admission blood laboratory including lymphocyte count, serum lactate dehydrogenase, D-dimer and C-Reactive Protein and the ratio between the arterial partial pressure of oxygen and inspired oxygen were collected. By calculating the areas under the receiver-operating characteristic curves (AUC), we compared the performance of blood laboratory-arterial gas analyses features alone and combined with the CT features in two hybrid models (Hybrid radiological and Hybrid radiomics)for predicting ICU admission. Following a machine learning approach, 63 patients were allocated to the training and 52 to the validation set.\n\nMeasurements and Main ResultsTwenty-nine (25%) of patients were admitted to ICU. The Hybrid radiological model comprising the lung %consolidation performed significantly (p=0.04) better in predicting ICU admission in the validation (AUC=0.82; 95%Confidence Interval 0.68-0.95) set than the blood laboratory-arterial gas analyses features alone (AUC=0.71; 95%Confidence Interval 0.56-0.86). A risk calculator for ICU admission was derived and is available at:https://github.com/cgplab/covidapp\n\nConclusionsThe volume of the consolidated lung in CT of patients with COVID-19 pneumonia has a mild but significant incremental value in predicting ICU admission.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Maurizio Bartolucci", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Matteo Benelli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Margherita Betti", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Sara Bicchi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Luca Fedeli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Federico Giannelli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Donatella Aquilini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Alessio Baldini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Guglielmo Consales", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Massimo Edoardo Di Natale", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Pamela Lotti", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Letizia Vannucchi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Michele Trezzi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Lorenzo Nicola Mazzoni", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Sandro Santini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Roberto Carpi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Daniela Matarrese", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Luca Bernardi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Mario Mascalchi", + "author_inst": "University of Florence" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.01.06.21249325", "rel_title": "Pregnancy and neonatal outcomes of COVID-19, co-reporting of common outcomes from the PAN-COVID and AAP SONPM registry", @@ -1008532,93 +1011930,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.20249009", - "rel_title": "SARS-CoV-2 patient self-testing with an antigen-detecting rapid test: a head-to-head comparison with professional testing", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.20249009", - "rel_abs": "BackgroundAntigen-detecting rapid diagnostic tests (Ag-RDTs) have been widely recommended as a complement to RT-PCR. Considering the possibility of nasal self-sampling and the ease-of-use in performing the test, self-testing may be an option.\n\nMethods and FindingsWe performed a manufacturer-independent, prospective diagnostic accuracy study of nasal mid-turbinate self-sampling and self-testing when using a WHO-listed SARS-CoV-2 Ag-RDT. Symptomatic participants suspected to have COVID-19 received written and illustrated instructions. Procedures were observed without intervention. For comparison, Ag-RDTs with nasopharyngeal sampling were professionally performed. Estimates of agreement, sensitivity, and specificity relative to RT-PCR on a combined oro-/nasopharyngeal sample were calculated. Feasibility was evaluated by observer and participant questionnaires.\n\nAmong 146 symptomatic adults, 40 (27.4%) were RT-PCR-positive for SARS-CoV-2. Sensitivity with self-testing was 82.5% (33/40 RT-PCR positives detected; 95% CI 68.1-91.3), and 85.0% (34/40; 95% CI 70.9-92.9) with professional testing. The positive percent agreement between self-testing and professional testing on Ag-RDT was 91.4% (95% CI 77.6-97.0), and negative percent agreement 99.1% (95% CI 95.0-100). At high viral load (>7.0 log10 SARS-CoV-2 RNA copies/ml), sensitivity was 96.6% (28/29; 95% CI 82.8-99.8) for both self- and professional testing. Deviations in sampling and testing (incomplete self-sampling or extraction procedure, or imprecise volume applied on the test device) were observed in 25 out of the 40 PCR-positives. Participants were rather young (mean age 35 years) and educated (59.6% with higher education degree). Most participants (80.9%) considered the Ag-RDT as rather easy to perform.\n\nConclusionsAmbulatory participants suspected for SARS-CoV-2 infection were able to reliably perform the Ag-RDT and test themselves. Procedural errors might be reduced by refinement of the Ag-RDTs for self-testing, such as modified instructions for use or product design/procedures. Self-testing may result in more wide-spread and more frequent testing. Paired with the appropriate information and education of the general public about the benefits and risks, self-testing may therefore have significant impact on the pandemic.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Andreas K. Lindner", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Chiara Rohardt", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Franka Kausch", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Mia Wintel", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Maximilian Gertler", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Susen Burock", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Charit\u00e9 Comp" - }, - { - "author_name": "Merle H\u00f6rig", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Julian Bernhard", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Frank Tobian", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Mary Gaeddert", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Federica Lainati", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Victor M. Corman", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Terry C. Jones", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Jilian A. Sacks", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland." - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Medical Dire" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Frank P. Mockenhaupt", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.07.21249353", "rel_title": "Inherent random fluctuations in COVID-19 outbreaks may explain rapid growth of new mutated virus variants", @@ -1009514,6 +1012825,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.07.21249381", + "rel_title": "Comparing the age and sex trajectories of SARS-CoV-2 morbidity with other respiratory pathogens points to potential immune mechanisms.", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249381", + "rel_abs": "Comparing age and sex differences in SARS-CoV-2 hospitalization and mortality with influenza and other health outcomes opens the way to generating hypotheses as to the underlying mechanisms, building on the extraordinary advances in immunology and physiology that have occurred over the last year. Notable departures in health outcomes starting around puberty suggest that burdens associated with influenza and other causes are reduced relative to the two emergent coronaviruses over much of adult life. Two possible hypotheses could explain this: protective adaptive immunity for influenza and other infections, or greater sensitivity to immunosenescence in the coronaviruses. Comparison of sex differences suggest an important role for adaptive immunity; but immunosenescence might also be relevant, if males experience faster immunosenescence. Involvement of the renin-angiotensin-system in SARS-CoV-2 infection might drive high sensitivity to disruptions of homeostasis. Overall, these results highlight the long tail of vulnerability in the age profile relevant to the emergent coronaviruses, which more transmissible variants have the potential to uncover at the younger end of the scale, and aging populations will expose at the other end of the scale.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Princeton University" + }, + { + "author_name": "Juliette Paireau", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Megan ODriscoll", + "author_inst": "Department of Genetics, Cambridge University" + }, + { + "author_name": "Mathilde Pivette", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Bruno Hubert", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Isabelle Pontais", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Derek Cummings", + "author_inst": "Department of Biology, University of Florida, Gainesville, USA" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Institut Pasteur, Paris" + }, + { + "author_name": "Henrik Salje", + "author_inst": "Department of Biology, University of Florida, Gainesville, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.07.21249392", "rel_title": "Predicting severity of Covid-19 using standard laboratory parameters", @@ -1010085,93 +1013447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.07.425729", - "rel_title": "Protection against reinfection with D614- or G614-SARS-CoV-2 isolates in hamsters", - "rel_date": "2021-01-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425729", - "rel_abs": "Reinfections with SARS-CoV-2 have already been documented in humans, although its real incidence is currently unknown. Besides having great impact on public health, this phenomenon raises the question if immunity generated by a single infection is sufficient to provide sterilizing/protective immunity to a subsequent SARS-CoV-2 re-exposure. The Golden Syrian hamster is a manageable animal model to explore immunological mechanisms able to counteract COVID-19, as it recapitulates pathological aspects of mild to moderately affected patients. Here, we report that SARS-CoV-2-inoculated hamsters resolve infection in the upper and lower respiratory tracts within seven days upon inoculation with the Cat01 (G614) SARS-CoV-2 isolate. Three weeks after primary challenge, and despite high titers of neutralizing antibodies, half of the animals were susceptible to reinfection by both identical (Cat01, G614) and variant (WA/1, D614) SARS-CoV-2 isolates. However, upon re-inoculation, only nasal tissues were transiently infected with much lower viral replication than those observed after the first inoculation. These data indicate that a primary SARS-CoV-2 infection is not sufficient to elicit a sterilizing immunity in hamster models but protects against lung disease.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Marco Brustolin", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "Jordi Rodon", - "author_inst": "IRTA-CRESA" - }, - { - "author_name": "Maria Luisa Rodriguez de la Concepcion", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Carlos Avila-Nieto", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Guillermo Cantero", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "Monica Perez", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "Te Nigeer", - "author_inst": "IRTA-CRESA" - }, - { - "author_name": "Marc Noguera-Julian", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Victor Guallar", - "author_inst": "Barcelona Supercomputing Center (BSC)" - }, - { - "author_name": "Alfonso Valencia", - "author_inst": "Barcelona Supercomputing Center (BSC)" - }, - { - "author_name": "Nuria Roca", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "Nuria Izquierdo-Useros", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Julia Blanco", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Albert Bensaid", - "author_inst": "IRTA-CReSA" - }, - { - "author_name": "Jorge Carrillo", - "author_inst": "irsiCaixa Institute for AIDS research" - }, - { - "author_name": "Julia Vergara-Alert", - "author_inst": "IRTA-CRESA" - }, - { - "author_name": "Joaquim Segales", - "author_inst": "IRTA-CReSA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.01.07.425745", "rel_title": "New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2", @@ -1010903,6 +1014178,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.05.21249247", + "rel_title": "SARS-CoV-2 seroprevalence in the urban population of Qatar: An analysis of antibody testing on a sample of 112,941 individuals", + "rel_date": "2021-01-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249247", + "rel_abs": "BackgroundQatar has experienced a large SARS-CoV-2 epidemic. Our first objective was to assess the proportion of the urban population that has been infected with SARS-CoV-2, by measuring the prevalence of detectable antibodies. Our second objective was to identify predictors for infection and for having higher antibody titers.\n\nMethodsResidual blood specimens from individuals receiving routine and other clinical care between May 12-September 9, 2020 were tested for anti-SARS-CoV-2 antibodies. Associations with seropositivity and higher antibody titers were identified through regression analyses. Probability weights were applied in deriving the epidemiological measures.\n\nResultsWe tested 112,941 individuals ([~]10% of Qatars urban population), of whom 51.6% were men and 66.0% were 20-49 years of age. Seropositivity was 13.3% (95% CI: 13.1-13.6%) and was significantly associated with sex, age, nationality, clinical-care type, and testing date. The proportion with higher antibody titers varied by age, nationality, clinical-care type, and testing date. There was a strong correlation between higher antibody titers and seroprevalence in each nationality, with a Pearson correlation coefficient of 0.85 (95% CI: 0.47-0.96), suggesting that higher antibody titers may indicate repeated exposure to the virus. The percentage of antibody-positive persons with prior PCR-confirmed diagnosis was 47.1% (95% CI: 46.1-48.2%), severity rate was 3.9% (95% CI: 3.7-4.2%), criticality rate was 1.3% (95% CI: 1.1-1.4%), and fatality rate was 0.3% (95% CI: 0.2-0.3%).\n\nConclusionsFewer than two in every 10 individuals in Qatars urban population had detectable antibodies against SARS-CoV-2 between May 12-September 9, 2020, suggesting that this population is still far from the herd immunity threshold and at risk from a subsequent epidemic wave.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Peter V. Coyle", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Mohamed Ali Ben Hadj Kacem", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Naema Hassan Abdulla Al Molawi", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Reham Awni El Kahlout", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Imtiaz Gilliani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Nourah Younes", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Gheyath K. Nasrallah", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.04.21249235", "rel_title": "Machine Learning Forecast of Growth in COVID-19 Confirmed Infection Cases with Non-Pharmaceutical Interventions and Cultural Dimensions: Algorithm Development and Validation", @@ -1011747,33 +1015129,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.05.425508", - "rel_title": "Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes", - "rel_date": "2021-01-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.425508", - "rel_abs": "BackgroundWhen a virus that has grown in a nonhuman host starts an epidemic in the human population, human cells may not provide growth conditions ideal for the virus. Therefore, the invasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is usually prevalent in the bat population, into the human population is thought to have necessitated changes in the viral genome for efficient growth in the new environment. In the present study, to understand host-dependent changes in coronavirus genomes, we focused on the mono- and oligonucleotide compositions of SARS-CoV-2 genomes and investigated how these compositions changed time-dependently in the human cellular environment. We also compared the oligonucleotide compositions of SARS-CoV-2 and other coronaviruses prevalent in humans or bats to investigate the causes of changes in the host environment.\n\nResultsTime-series analyses of changes in the nucleotide compositions of SARS-CoV-2 genomes revealed a group of mono- and oligonucleotides whose compositions changed in a common direction for all clades, even though viruses belonging to different clades should evolve independently. Interestingly, the compositions of these oligonucleotides changed towards those of coronaviruses that have been prevalent in humans for a long period and away from those of bat coronaviruses.\n\nConclusionsClade-independent, time-dependent changes are thought to have biological significance and should relate to viral adaptation to a new host environment, providing important clues for understanding viral host adaptation mechanisms.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yuki Iwasaki", - "author_inst": "Nagahama Institute of Bio-Science and Technology" - }, - { - "author_name": "Takashi Abe", - "author_inst": "Niigata University" - }, - { - "author_name": "Toshimichi Ikemura", - "author_inst": "Nagahama Institute of Bio-Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.05.425420", "rel_title": "COVID-19 virtual patient cohort reveals immune mechanisms driving disease outcomes", @@ -1012673,6 +1016028,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.06.425543", + "rel_title": "Heterogeneity versus the COVID-19 Pandemic", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.06.425543", + "rel_abs": "In this paper, heterogeneity is formally defined, and its properties are explored. We define and distinguish observable versus non-observable heterogeneity. It is proposed that heterogeneity among the vulnerable is a significant factor in the contagion impact of COVID-19, as demonstrated with incidence rates on a Diamond Princess Cruise ship in February 2020. Given the nature of the disease, its heterogeneity and human social norms, pre-voyage and post-voyage quick testing procedures may become the new standard for cruise ship passengers and crew. The technological advances in testing available today would facilitate more humanistic treatment as compared to more archaic quarantine and isolation practices for all onboard ship. With quick testing, identification of those infected and thus not allowed to embark on a cruise or quarantining those disembarking and other mitigation strategies, the popular cruise adventure could be available safely again. Whatever the procedures implemented, the methodological purpose of this study should add valuable insight in the modeling of disease and specifically, the COVID-19 virus.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ramalingam Shanmugam", + "author_inst": "Texas State University" + }, + { + "author_name": "Gerald Ledlow", + "author_inst": "University of Texas Health Science Center at Tyler: The University of Texas Health Science Center at Tyler" + }, + { + "author_name": "Karan P. Singh", + "author_inst": "University of Texas Health Science Center Tyler" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.01.06.425544", "rel_title": "Complex Systems Analysis Informs on the Spread of COVID-19", @@ -1013289,33 +1016671,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.30.20249060", - "rel_title": "Syncope and COVID-19 disease - a systematic review.", - "rel_date": "2021-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249060", - "rel_abs": "BackgroundSyncope is not a common manifestation of COVID-19, but it may occur in this context and it can be the presenting symptom in some cases. Although several mechanisms may explain the pathophysiology behind COVID-19 related syncope, a valid relationship has not been established yet. In this systematic review, we aimed to examine the current incidence of syncope in COVID-19 patients and to explore different patterns observed in this setting.\n\nMethodsA systematic review across PubMed, ISI Web of Knowledge and SCOPUS was performed, according to PRISMA guidelines, in order to identify all relevant articles regarding both COVID-19 and syncope.\n\nResultsWe identified 81 publications, of which 62 were excluded. The cumulative incidence of syncope and pre-syncope across the selected studies was 7.1% (256/3584 patients). Unspecified syncope was the most common type (76.2% of the reported episodes), followed by reflex syncope (18.1% of the cases). Orthostatic hypotension was responsible for 3.6% of the cases and syncope of presumable cardiac cause accounted for 2.0%. Arterial hypertension was present in 64.7% of the patients and either angiotensin receptor blockers or angiotensin converting enzyme inhibitors were used by 39.5% of hypertensive patients with syncope.\n\nConclusionSyncope, although not considered a typical symptom of the COVID-19 disease, can be associated with it, particularly in early stages. Different types of syncope were seen in this context, each with different implications requiring distinct approaches. A careful reevaluation of blood pressure whenever a patient develops COVID-19 is suggested, including reassessment of antihypertensive therapy.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Raquel Falcao de Freitas", - "author_inst": "Faculdade de Medicina da Universidade do Porto, Portugal" - }, - { - "author_name": "Sofia Cardoso Torres", - "author_inst": "Centro Hospitalar Universitario Sao Joao, Porto, Portugal" - }, - { - "author_name": "Jose Pedro L. Nunes", - "author_inst": "Faculdade de Medicina da Universidade do Porto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.12.31.20249084", "rel_title": "Hospitalization as reliable indicator of second wave COVID-19 pandemic in eight European countries", @@ -1013911,6 +1017266,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.01.04.21249195", + "rel_title": "The incidence, characteristics and outcomes of pregnant women hospitalized with symptomatic and asymptomatic SARS-CoV-2 infection in the UK from March to September 2020: a national cohort study using the UK Obstetric Surveillance System (UKOSS)", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249195", + "rel_abs": "BackgroundEvidence on risk factors, incidence and impact of SARS-CoV-2 infection in pregnant mothers and their babies has rapidly expanded but there is a lack of population level data to inform accurate incidence rates and unbiased descriptions of characteristics and outcomes. The primary aim of this study was to describe the incidence, characteristics and outcomes of hospitalized pregnant women with symptomatic and asymptomatic SARS-CoV-2 in the UK compared to pregnant women without SARS-CoV-2 in order to inform future clinical guidance and management.\n\nMethods and FindingsWe conducted a national, prospective cohort study of all hospitalized pregnant women with confirmed SARS-CoV-2 from 1st March 2020 to 31st August 2020 using the UK Obstetric Surveillance System (UKOSS) across all 194 hospitals in the UK with a consultant-led maternity unit. Incidence was estimated using the latest national maternity data. Overall, 1148 hospitalized women had confirmed SARS-CoV-2 in pregnancy, 63% of which were symptomatic. Therefore, the estimated incidence of hospitalization with symptomatic SARS-CoV-2 was 2.0 per 1000 maternities (95% CI 1.9-2.2) and for asymptomatic SARS-CoV-2 was 1.2 per 1000 maternities (95% CI 1.1-1.4). Compared to pregnant women without SARS-CoV-2, women hospitalized with symptomatic SARS-CoV-2 were more likely to be overweight or obese (adjusted OR 1.86, 95% CI 1.39-2.48 and aOR 2.07, 95% CI 1.53-2.29 respectively), to be of Black, Asian or Other minority ethnic group (aOR 6.24, 95% CI 3.93-9.90, aOR 4.36, 95% CI 3.19-5.95 and aOR 12.95, 95% CI 4.93-34.01 respectively), and to have a relevant medical comorbidity (aOR 1.83, 95% CI 1.32-2.54). Compared to pregnant women without SARS-CoV-2, hospitalized pregnant women with symptomatic SARS-CoV-2 were more likely to be admitted to intensive care (aOR 57.67, 95% CI 7.80-426.70) but the absolute risk of poor outcomes was low. Cesarean births and neonatal unit admission were increased regardless of symptom status (symptomatic aOR 2.60, 95% CI 1.97-3.42 and aOR 3.08, 95% CI 1.99-4.77 respectively; asymptomatic aOR 2.02, 95% CI 1.52-2.70 and aOR 1.84, 95% 1.12-3.03 respectively). Iatrogenic preterm births were more common in women with symptomatic SARS-CoV-2 (aOR 11.43, 95% CI 5.07-25.75). The risks of stillbirth or neonatal death were not significantly increased, regardless of symptom status but numbers were small. The limitations of this study include the restriction to women hospitalized with SARS-CoV-2, who may by nature of their admission have been at greater risk of adverse outcome.\n\nConclusionsWe have identified factors that increase the risk of symptomatic and asymptomatic SARS-CoV-2 in pregnancy. The increased risks of cesarean and iatrogenic preterm birth provide clear evidence of the indirect impact of SARS-CoV-2 on mothers and maternity care in high income settings. Clinicians can be reassured that the majority of women do not experience severe complications of SARS-CoV-2 in pregnancy and women with mild disease can be discharged to continue their pregnancy safely.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nicola Vousden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kathryn Bunch", + "author_inst": "University of Oxford" + }, + { + "author_name": "Edward Morris", + "author_inst": "Royal College of Obstetricians and Gynaecologists" + }, + { + "author_name": "Nigel Simpson", + "author_inst": "University of Leeds" + }, + { + "author_name": "Christopher Gale", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick O'Brien", + "author_inst": "University College London" + }, + { + "author_name": "Maria Quigley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Brocklehurst", + "author_inst": "University College London" + }, + { + "author_name": "Jennifer J Kurinczuk", + "author_inst": "University of Oxford" + }, + { + "author_name": "Marian Knight", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.01.04.425336", "rel_title": "SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses", @@ -1014659,53 +1018069,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.28.20248807", - "rel_title": "Autoimmunity to the Lung Protective Phospholipid-Binding Protein Annexin A2 Predicts Mortality Among Hospitalized COVID-19 Patients", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248807", - "rel_abs": "BackgroundAnnexin A2 is a phospholipid-binding protein involved in fibrinolysis, cell membrane stabilization and repair, and ensuring the integrity of the pulmonary microvasculature. Given the autoantibodies observed in COVID-19 and that Annexin A2 is a known target of antiphospholipid antibodies, we studied autoimmunity directed against Annexin A2 among hospitalized COVID-19 patients.\n\nMethodsWe used ELISA to identify the levels of IgG autoantibodies recognizing Annexin A2 and A5 among 86 hospitalized cases of COVID-19. Using logistic regression, we analyzed the association between anti-Annexin A2 and A5 antibody levels with mortality after adjusting for age, sex, race and key comorbidities.\n\nResultsWe found higher average levels of anti-Annexin A2 antibodies among hospitalized COVID-19 patients that died when compared with non-critical hospitalized COVID-19 patients (p-value = 0.006) and critically ill COVID-19 patients (p-value = 0.04). No significant differences in anti-Annexin A5 antibody levels were identified. Regression analysis showed that anti-Annexin A2 antibody levels as measured in relative units strongly predicted mortality with an odds ratio of 9.3 (95% CI: 1.9 to 44.6, p=0.005). In contrast, anti-Annexin A5 antibody levels were not associated with higher mortality (95% CI: 0.5 to 15.2, p=0.22).\n\nConclusionsWe determined that anti-Annexin A2 antibodies were elevated among hospitalized COVID-19 patients and these levels predicted mortality. It is known that inhibition of Annexin A2 induces systemic thrombosis, cell death, and non-cardiogenic pulmonary edema. Autoimmunity to Annexin A2 is a potential mechanism that may explain the key clinical findings of severe COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Marisol Zuniga", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Claudia Gomes", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Steven E Carsons", - "author_inst": "NYU Long Island School of Medicine" - }, - { - "author_name": "Michael T Bender", - "author_inst": "NYU Long Island School of Medicine" - }, - { - "author_name": "Paolo Cotzia", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Qing Robert Miao", - "author_inst": "NYU Long Island School of Medicine" - }, - { - "author_name": "David C Lee", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Ana Rodriguez", - "author_inst": "NYU School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.28.20248950", "rel_title": "COVID-19 vaccine hesitancy worldwide: a systematic review of vaccine acceptance rates", @@ -1015573,6 +1018936,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.30.20248890", + "rel_title": "Detection of SARS-CoV-2 in the air from hospitals and closed rooms occupied by COVID-19 patients", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248890", + "rel_abs": "To understand air transmission characteristics of SARS-CoV-2 and risks for health care personnel and visitors to hospitals, we analyzed air samples collected from various enclosures in hospitals at Hyderabad and Mohali and performed closed room experiments with COVID-19 positive individuals. We collected 64 air samples from COVID and non-COVID areas of various hospitals and 17 samples from closed rooms occupied by COVID patients. 4 samples from COVID care areas were positive for SARS-CoV-2 with no obvious predilection towards ICU/non-ICU areas in the hospital samples. In the closed room experiments, where one or more COVID-19 patients spent a short duration of time, one sample - collected immediately after the departure of three symptomatic patients from the room - was positive. Our results indicate that the chance of picking up SARS-CoV-2 in the air is directly related to a number of COVID positive cases in the room, their symptomatic status, and the duration of exposure and that the demarcation of hospital areas into COVID and non-COVID areas is a successful strategy to prevent cross infections. In neutral environmental conditions, the virus does not seem to spread farther away from the patients, especially if they are asymptomatic, giving an objective evidence for the effectiveness of physical distancing in curbing the spread of the epidemic.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shivranjani Moharir", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Sharat Sharath Chandra", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Arushi Goel", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Bhuwaneshwar Thakur", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Gurpreet Singh Bhalla", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Dinesh Kumar", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Digvijay Singh Naruka", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Ashwani Kumar", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Amit Tuli", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Swathi Suravaram", + "author_inst": "ESI Hospital and Medical College, Hyderabad, India" + }, + { + "author_name": "Thrilok Chander Bingi", + "author_inst": "COVID-19 nodal centre, Hyderabad, India" + }, + { + "author_name": "M Srinivas", + "author_inst": "ESI Hospital and Medical College, Hyderabad, India" + }, + { + "author_name": "Rajarao Mesipogu", + "author_inst": "COVID-19 nodal centre, Hyderabad, India" + }, + { + "author_name": "Krishna Reddy", + "author_inst": "Durgabai Deshmukh Hospital, Hyderabad, India" + }, + { + "author_name": "Sanjeev Khosla", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Karthik Bharadwaj Tallapaka", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Rakesh K Mishra", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.23.20248803", "rel_title": "Clinical diagnosis of COVID-19: a prompt, feasible, and sensitive diagnostic tool for COVID-19 based on a 1,757-patient cohort (The AndroCoV Clinical Scoring for COVID-19 diagnosis).", @@ -1016025,33 +1019471,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.29.20247833", - "rel_title": "Characterizing Two Outbreak Waves of COVID-19 in Spain Using Phenomenological Epidemic Modelling", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20247833", - "rel_abs": "Since the first case reported of SARS-CoV-2 the end of December 2019 in China, the number of cases quickly climbed following an exponential growth trend, demonstrating that a global pandemic is possible. As of December 3, 2020, the total number of cases reported are around 65,527,000 contagions worldwide, and 1,524,000 deaths affecting 218 countries and territories. In this scenario, Spain is one of the countries that has suffered in a hard way, the ongoing epidemic caused by the novel coronavirus SARS-CoV-2, namely COVID-19 disease. In this paper, we present the utilization of phenomenological epidemic models to characterize the two first outbreak waves of COVID-19 in Spain. The study is driven using a two-step phenomenological epidemic approach. First, we use a simple generalized growth model to fit the main parameters at the early epidemic phase; later, we apply our previous finding over a logistic growth model to that characterize both waves completely. The results show that even in the absence of accurate data series, it is possible to characterize the curves of case incidence, and even construct short-term forecast in the near time horizon.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Miguel Lopez", - "author_inst": "University of Malaga" - }, - { - "author_name": "Alberto Peinado", - "author_inst": "University of Malaga" - }, - { - "author_name": "Andres Ortiz", - "author_inst": "University of Malaga" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.30.20248929", "rel_title": "Antemortem vs. postmortem histopathological and ultrastructural findings in paired transbronchial biopsies and lung autopsy samples from three patients with confirmed SARS-CoV-2 infection", @@ -1016875,6 +1020294,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.31.20249088", + "rel_title": "Stages of COVID-19 pandemic and paths to herd immunity by vaccination: dynamical model comparing Austria, Luxembourg and Sweden", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.31.20249088", + "rel_abs": "BackgroundWorldwide more than 72 million people have been infected and 1.6 million died with SARS-CoV-2 by 15th December 2020. Non-pharmaceutical interventions which decrease social interaction have been implemented to reduce the spread of SARS-CoV-2 and to mitigate stress on healthcare systems and prevent deaths. The pandemic has been tackled with disparate strategies by distinct countries resulting in different epidemic dynamics. However, with vaccines now becoming available, the current urgent open question is how the interplay between vaccination strategies and social interaction will shape the pandemic in the next months.\n\nMethodsTo address this question, we developed an extended Susceptible-Exposed-Infectious-Removed (SEIR) model including social interaction, undetected cases and the progression of patients trough hospitals, intensive care units (ICUs) and death. We calibrated our model to data of Luxem-bourg, Austria and Sweden, until 15th December 2020. We incorporated the effect of vaccination to investigate under which conditions herd immunity would be achievable in 2021.\n\nResultsThe model reveals that Sweden has the highest fraction of undetected cases, Luxembourg displays the highest fraction of infected population, and all three countries are far from herd immunity as of December 2020. The model quantifies the level of social interactions, and allows to assess the level which would keep Reff (t) below 1. In December 2020, this level is around 1/3 of what it was before the pandemic for all the three countries. The model allows to estimate the vaccination rate needed for herd immunity and shows that 2700 vaccinations/day are needed in Luxembourg to reach it by mid of April and 45,000 for Austria and Sweden. The model estimates that vaccinating the whole countrys population within 1 year could lead to herd immunity by July in Luxembourg and by August in Austria and Sweden.\n\nConclusionThe model allows to shed light on the dynamics of the epidemics in different waves and countries. Our results emphasize that vaccination will help considerably but not immediately and therefore social measures will remain important for several months before they can be fully alleviated.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Francoise Kemp", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Daniele Proverbio", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Atte Aalto", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Laurent Mombaerts", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Aymeric Fouquier d Herouel", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Andreas Husch", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Christophe Ley", + "author_inst": "University of Ghent" + }, + { + "author_name": "Jorge Goncalves", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Alexander Skupin", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Stefano Magni", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.30.20249066", "rel_title": "Need of care in interpreting Google Trends-based COVID-19 infodemiological study results: potential risk of false-positivity", @@ -1017595,57 +1021069,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.04.20249054", - "rel_title": "Autoimmune anti-DNA antibodies predict disease severity in COVID-19 patients", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.20249054", - "rel_abs": "COVID-19 can lead to severe disease and death, however the mechanisms of pathogenesis in these patients remain poorly understood. High levels of autoimmune antibodies have been observed frequently in COVID-19 patients but their specific contribution to disease severity and clinical manifestations remain unknown.\n\nWe performed a retrospective study of 115 COVID-19 hospitalized patients with different degrees of severity to analyze the generation of autoimmune antibodies to common antigens: a lysate of erythrocytes, the lipid phosphatidylserine (PS) and DNA.\n\nHigh levels of IgG autoantibodies against erythrocyte lysates were observed in a large percentage (up to 41%) of patients. Anti-DNA antibodies determined upon hospital admission correlated strongly with later development of severe disease, showing a positive predictive value of 89.5% and accounting for 22% of total severe cases. Statistical analysis identified strong correlations between anti-DNA antibodies and markers of cell injury, coagulation, neutrophil levels and erythrocyte size.\n\nAnti-DNA autoantibodies may play an important role in the pathogenesis of COVID-19 and could be developed as a predictive biomarker for disease severity and specific clinical manifestations.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Claudia Gomes", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Marisol Zuniga", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Kelly A. Crotty", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Kun Qian", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Lawrence Hsu Lin", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Kimon Argyropoulos", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Huilin Li", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Paolo Cotzia", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Ana Rodriguez", - "author_inst": "NYU School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.03.21249162", "rel_title": "SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection", @@ -1018413,6 +1021836,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.26.20248878", + "rel_title": "Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes", + "rel_date": "2021-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.26.20248878", + "rel_abs": "The worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive LAMPshade dyes as novel readouts in an isothermal RT-LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Timothy A Brown", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Katherine S. Schaefer", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Arthur Tsang", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Hyun Ah Yi", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Jonathan B. Grimm", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Andrew L. Lemire", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Fadi M. Jradi", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Charles Kim", + "author_inst": "Sensei Biotherapeutics" + }, + { + "author_name": "Kevin McGowan", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Kimberly Ritola", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Derek T Armstrong", + "author_inst": "Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba H. Mostafa", + "author_inst": "Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Wyatt Korff", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Ronald D. Vale", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Luke D Lavis", + "author_inst": "HHMI Janelia Research Campus" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.31.424987", "rel_title": "Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses", @@ -1019293,41 +1022791,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.26.20248872", - "rel_title": "The new Coronavirus (SARS-CoV-2) in Central America: Demographic-spatial simulations, Analyses of Molecular Variance (AMOVA) and Neutrality Tests in complete genomes from Belize, Guatemala, Cuba, Jamaica and Puerto Rico", - "rel_date": "2021-01-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.26.20248872", - "rel_abs": "In this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2 from five Central American countries (Belize, Guatemala, Cuba, Jamaica and Puerto Rico) with 04, 10, 2, 8 and 14 haplotypes, respectively, with an extension of up to 29,885 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform. Using specific methodologies for paired FST, AMOVA, mismatch, demographic-spatial expansion, molecular diversity and for the time of evolutionary divergence, it was possible to notice that only 79 sites remained conserved and that the high number of polymorphisms found helped to establish a clear pattern of genetic non-structuring, based on the time of divergence between the groups. The analyses also showed that significant evolutionary divergences within and between the five countries corroborate the fact that possible rapid and silent mutations are responsible for the increase in genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and medications in general.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Robson da Silva Ramos", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Dallynne Barbara Ramos Venancio", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Eduarda Doralice Alves Braz Da Silva", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Rosane Maria de Albuquerque", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Pierre Teodosio Felix Sr.", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.27.20248894", "rel_title": "Prevalence and clinical profile of SARS-CoV-2 infection among farmworkers in Monterey County, California: June-November, 2020", @@ -1020083,6 +1023546,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.29.424728", + "rel_title": "In vitro Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19", + "rel_date": "2020-12-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424728", + "rel_abs": "Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drug combinations on inflammatory cytokine production in peripheral blood mononuclear cells, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Clarissa S Santoso", + "author_inst": "Boston University" + }, + { + "author_name": "Zhaorong Li", + "author_inst": "Boston University" + }, + { + "author_name": "Jaice T Rottenberg", + "author_inst": "Boston University" + }, + { + "author_name": "Xing Liu", + "author_inst": "Boston University" + }, + { + "author_name": "Vivian X Shen", + "author_inst": "Boston University" + }, + { + "author_name": "Juan I Fuxman Bass", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.30.424801", "rel_title": "Pharmacophore-based peptide biologics neutralize SARS-CoV-2 S1 and deter S1-ACE2 interaction in vitro", @@ -1020695,85 +1024197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.25.20248668", - "rel_title": "Contact Tracing of COVID-19 in Karnataka, India: Superspreading and Determinants of Infectiousness and Symptomaticity", - "rel_date": "2020-12-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.25.20248668", - "rel_abs": "Brief AbstractWe analysed SARS-CoV-2 surveillance and contact tracing data from Karnataka, India up to 21 July 2020. We estimated metrics of infectiousness and the tendency for superspreading (overdispersion), and evaluated potential determinants of infectiousness and symptomaticity in COVID-19 cases. Among 956 cases confirmed to be forward-traced, 8.7% of index cases had 14.4% of contacts but caused 80% of all secondary cases, suggesting significant heterogeneity in individual-level transmissibility of SARS-CoV-2 which could not be explained by the degree of heterogeneity in underlying number of contacts. Secondary attack rate was 3.6% among 16715 close contacts. Transmission was higher when index case was aged >18 years, or was symptomatic (adjusted risk ratio, aRR 3.63), or was lab-confirmed [≥]4 days after symptom onset (aRR 3.01). Probability of symptomatic infection increased with age, and symptomatic infectors were 8.16 times more likely to generate symptomatic secondaries. This could potentially cause a snowballing effect on infectiousness and clinical severity across transmission generations; further studies are suggested to confirm this. Mean serial interval was 5.4 days. Adding backward contact tracing and targeting control measures to curb super-spreading may be prudent. Due to low symptomaticity and infectivity, interventions aimed at children might have a relatively small impact on reducing transmission.\n\nStructured AbstractO_ST_ABSBackgroundC_ST_ABSIndia has experienced the second largest outbreak of COVID-19 globally, yet there is a paucity of studies analysing contact tracing data in the region. Such studies can elucidate essential transmission metrics which can help optimize disease control policies.\n\nMethodsWe analysed contact tracing data collected under the Integrated Disease Surveillance Programme from Karnataka, India between 9 March and 21 July 2020. We estimated metrics of disease transmission including the reproduction number (R), overdispersion (k), secondary attack rate (SAR), and serial interval. R and k were jointly estimated using a Bayesian Markov Chain Monte Carlo approach. We evaluated the effect of age and other factors on the risk of transmitting the infection, probability of asymptomatic infection, and mortality due to COVID-19.\n\nFindingsUp to 21 July, we found 111 index cases that crossed the super-spreading threshold of [≥]8 secondary cases. R and k were most reliably estimated at R 0.75 (95% CI, 0.62-0.91) and k 0.12 (0.11-0.15) for confirmed traced cases (n=956); and R 0.91 (0.72-1.15) and k 0.22 (0.17-0.27) from the three largest clusters (n=394). Among 956 confirmed traced cases, 8.7% of index cases had 14.4% of contacts but caused 80% of all secondary cases. Among 16715 contacts, overall SAR was 3.6% (3.4-3.9) and symptomatic cases were more infectious than asymptomatic cases (SAR 7.7% vs 2.0%; aRR 3.63 [3.04-4.34]). As compared to infectors aged 19-44 years, children were less infectious (aRR 0.21 [0.07-0.66] for 0-5 years and 0.47 [0.32-0.68] for 6-18 years). Infectors who were confirmed [≥]4 days after symptom onset were associated with higher infectiousness (aRR 3.01 [2.11-4.31]). Probability of symptomatic infection increased with age, and symptomatic infectors were 8.16 (3.29-20.24) times more likely to generate symptomatic secondaries. Serial interval had a mean of 5.4 (4.4-6.4) days with a Weibull distribution. Overall case fatality rate was 2.5% (2.4-2.7) which increased with age.\n\nConclusionWe found significant heterogeneity in the individual-level transmissibility of SARS-CoV-2 which could not be explained by the degree of heterogeneity in the underlying number of contacts. To strengthen contact tracing in over-dispersed outbreaks, testing and tracing delays should be minimised, retrospective contact tracing should be considered, and contact tracing performance metrics should be utilised. Targeted measures to reduce potential superspreading events should be implemented. Interventions aimed at children might have a relatively small impact on reducing SARS-CoV-2 transmission owing to their low symptomaticity and infectivity. There is some evidence that symptomatic cases produce secondary cases that are more likely to be symptomatic themselves which may potentially cause a snowballing effect on infectiousness and clinical severity across transmission generations; further studies are needed to confirm this finding.\n\nFundingGiridhara R Babu is funded by an Intermediate Fellowship by the Wellcome Trust DBT India Alliance (Clinical and Public Health Research Fellowship); grant number: IA/CPHI/14/1/501499.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Mohak Gupta", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Giridara G Parameswaran", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Manraj S Sra", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Rishika Mohanta", - "author_inst": "Indian Institute of Science Education and Research (IISER), Pune" - }, - { - "author_name": "Devarsh Patel", - "author_inst": "Indian Institute of Science Education and Research (IISER), Pune" - }, - { - "author_name": "Amulya Gupta", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Bhavik Bansal", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Archisman Mazumder", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Mehak Arora", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Nishant Aggarwal", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Tarun Bhatnagar", - "author_inst": "ICMR- National Institute of Epidemiology, Chennai" - }, - { - "author_name": "Jawaid Akhtar", - "author_inst": "Secretariat, Health & Family Welfare Services, Government of Karnataka" - }, - { - "author_name": "Pankaj Pandey", - "author_inst": "Office of Commissioner, Health, Family Welfare and AYUSH Services, Government of Karnataka" - }, - { - "author_name": "Vasanthapuram Ravi", - "author_inst": "National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru" - }, - { - "author_name": "Giridhara R Babu", - "author_inst": "Indian Institute of Public Health, Bengaluru, Public Health Foundation of India" - }, - { - "author_name": "- iCART (India COVID-19 Apex Research Team)", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.25.20248851", "rel_title": "Genomic Diversity of the SARS-CoV-2 in Turkey and the Impact of Virus Genome Mutations on Clinical Outcomes", @@ -1021756,6 +1025179,169 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.12.28.424622", + "rel_title": "Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients", + "rel_date": "2020-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424622", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patients immunological status, and found dramatic changes in the IGH within the patients immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Haitao Xiang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Yingze Zhao", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xinyang Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Peipei Liu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Longlong Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Meiniang Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Lei Tian", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Haixi Sun", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Department of Computer Science, City University of Hong Kong" + }, + { + "author_name": "Ziqian Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Beiwei Ye", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaoju Yuan", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Pengyan Wang", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Ning Zhang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yuhuan Gong", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Chengrong Bian", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Zhaohai Wang", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Linxiang Yu", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Jin Yan", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Fanping Meng", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Changqing Bai", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Xiaoshan Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Xiaopan Liu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Kai Gao", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Liang Wu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Longqi F. Liu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Ying Gu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Yuhai J. Bi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yi Shi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Shaogeng Zhang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Chen Zhu", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Guizhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "George Gao", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Naibo Yang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "William Liu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Penghui Yang", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.29.424682", "rel_title": "ACE2 peptide fragment interacts with several sites on the SARS-CoV-2 spike protein S1", @@ -1022363,45 +1025949,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.28.424029", - "rel_title": "SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity", - "rel_date": "2020-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424029", - "rel_abs": "COVID-19 outbreak is the biggest threat to human health in recent history. Currently, there are over 1.5 million related deaths and 75 million people infected around the world (as of 22/12/2020). The identification of virulence factors which determine disease susceptibility and severity in different cell types remains an essential challenge. The serine protease TMPRSS2 has been shown to be important for S protein priming and viral entry, however, little is known about its regulation. SPINT2 is a member of the family of Kunitz type serine protease inhibitors and has been shown to inhibit TMPRSS2. Here, we explored the existence of a co-regulation between SPINT2/TMPRSS2 and found a tightly regulated protease/inhibitor expression balance across tissues. We found that SPINT2 negatively correlates with SARS-CoV-2 expression in Calu-3 and Caco-2 cell lines and was down-regulated in secretory cells from COVID-19 patients. We validated our findings using Calu-3 cell lines and observed a strong increase in viral load after SPINT2 knockdown. Additionally, we evaluated the expression of SPINT2 in datasets from comorbid diseases using bulk and scRNA-seq data. We observed its down-regulation in colon, kidney and liver tumors as well as in alpha pancreatic islets cells from diabetes Type 2 patients, which could have implications for the observed comorbidities in COVID-19 patients suffering from chronic diseases.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Carlos Ramirez", - "author_inst": "Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany" - }, - { - "author_name": "Ashwini Kumar Sharma", - "author_inst": "Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany" - }, - { - "author_name": "Carmon Kee", - "author_inst": "Department of Infectious Diseases, Virology, Heidelberg University, Germany" - }, - { - "author_name": "Leonie Thomas", - "author_inst": "Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany" - }, - { - "author_name": "Steeve Boulant", - "author_inst": "Department of Infectious Diseases, Virology, Heidelberg University, Germany" - }, - { - "author_name": "Carl Herrmann", - "author_inst": "Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "confirmatory results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.12.26.424429", "rel_title": "Analysis and Forecasting of Global of RT-PCR Primers for SARS-CoV-2", @@ -1023493,6 +1027040,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.23.20248444", + "rel_title": "Association between Use of Qingfei Paidu Tang and Mortality in Hospitalized Patients with COVID-19: A national retrospective registry study", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248444", + "rel_abs": "BackgroundQingfei Paidu Tang (QPT), a formula of traditional Chinese medicine, which was suggested to be able to ease symptoms in patients with Coronavirus Disease 2019 (COVID-19), has been recommended by clinical guidelines and widely used to treat COVID-19 in China. However, whether it decreases mortality remains unknown.\n\nPurposeWe aimed to explore the association between QPT use and in-hospital mortality among patients hospitalized for COVID-19.\n\nStudy designA retrospective study based on a real-world database was conducted.\n\nMethodsWe identified patients consecutively hospitalized with COVID-19 in 15 hospitals from a national retrospective registry in China, from January through May 2020. Data on patients characteristics, treatments, and outcomes were extracted from the electronic medical records. The association of QPT use with mortality was evaluated using Cox proportional hazards models based on propensity score analysis.\n\nResultsOf the 8939 patients included, 28.7% received QPT. The crude mortality was 1.2% (95% confidence interval [CI] 0.8% to 1.7%) among the patients receiving QPT and 4.8% (95% CI 4.3% to 5.3%) among those not receiving QPT. After adjustment for patient characteristics and concomitant treatments, QPT use was associated with a relative reduction of 50% in in-hospital mortality (hazard ratio, 0.50; 95% CI, 0.37 to 0.66 P <0.001). This association was consistent across subgroups by sex and age. Meanwhile, the incidence of acute liver injury (8.9% [95% CI, 7.8% to 10.1%]vs. 9.9% [95% CI, 9.2% to 10.7%]; odds ratio, 0.96 [95% CI, 0.81% to 1.14%], P =0.658) and acute kidney injury (1.6% [95% CI, 1.2% to 2.2%] vs. 3.0% [95% CI, 2.6% to 3.5%]; odds ratio, 0.85 [95% CI, 0.62 to 1.17], P =0.318) was comparable between patients receiving QPT and those not receiving QPT. The major study limitations included that the study was an observational study based on real-world data rather than a randomized control trial, and the quality of data could be affected by the accuracy and completeness of medical records.\n\nConclusionsQPT was associated with a substantially lower risk of in-hospital mortality, without extra risk of acute liver injury or acute kidney injury among patients hospitalized with COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Lihua Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xin Zheng", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xueke Bai", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Qing Wang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Bowang Chen", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Haibo Wang", + "author_inst": "Clinical Trial Unit, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou Province,PRC" + }, + { + "author_name": "Jiapeng Lu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Shuang Hu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xiaoyan Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Haibo Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Jiamin Liu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Ying Shi", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Zhiye Zhou", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Lanxia Gan", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Xi Li", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Jing Li", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.23.20248784", "rel_title": "The importance of continued non-pharmaceutical interventions during the upcoming SARS-COV-2 vaccination campaign", @@ -1024029,61 +1027655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.24.424245", - "rel_title": "Single point mutations can potentially enhance infectivity of SARS-CoV-2 revealed by in silico affinity maturation and SPR assay", - "rel_date": "2020-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.24.424245", - "rel_abs": "The RBD (receptor binding domain) of the SARS-CoV-2 virus S (spike) protein mediates the viral cell attachment and serves as a promising target for therapeutics development. Mutations on the S-RBD may alter its affinity to cell receptor and affect the potency of vaccines and antibodies. Here we used an in-silico approach to predict how mutations on RBD affect its binding affinity to hACE2 (human angiotensin-converting enzyme2). The effect of all single point mutations on the interface was predicted. SPR assay result shows that 6 out of 9 selected mutations can strengthen binding affinity. Our prediction has reasonable agreement with the previous deep mutational scan results and recently reported mutants. Our work demonstrated in silico method as a powerful tool to forecast more powerful virus mutants, which will significantly benefit for the development of broadly neutralizing vaccine and antibody.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ting Xue", - "author_inst": "Targeted Tracer Research and Development Laboratory, Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospit" - }, - { - "author_name": "Weikun Wu", - "author_inst": "XtalPi - AI Research Center (XARC)" - }, - { - "author_name": "Ning Guo", - "author_inst": "XtalPi - AI Research Center (XARC)" - }, - { - "author_name": "Chengyong Wu", - "author_inst": "Targeted Tracer Research and Development Laboratory, Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospit" - }, - { - "author_name": "Jian Huang", - "author_inst": "XtalPi - AI Research Center (XARC)" - }, - { - "author_name": "Lipeng Lai", - "author_inst": "XtalPi - AI Research Center (XARC)" - }, - { - "author_name": "Hong Liu", - "author_inst": "Targeted Tracer Research and Development Laboratory, Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospit" - }, - { - "author_name": "Yalun Li", - "author_inst": "Targeted Tracer Research and Development Laboratory, Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospit" - }, - { - "author_name": "Tianyuan Wang", - "author_inst": "XtalPi" - }, - { - "author_name": "Yuxi Wang", - "author_inst": "Targeted Tracer Research and Development Laboratory, Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospit" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.12.26.424442", "rel_title": "Establishment of a well-characterized SARS-CoV-2 lentiviral pseudovirus neutralization assay using 293T cells with stable expression of ACE2 and TMPRSS2", @@ -1025191,6 +1028762,77 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.23.424254", + "rel_title": "Cell-type apoptosis in lung during SARS-CoV-2 infection", + "rel_date": "2020-12-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424254", + "rel_abs": "The SARS-CoV-2 pandemic has inspired renewed interest in understanding the fundamental pathology of acute respiratory distress syndrome (ARDS) following infection because fatal COVID-19 cases are commonly linked to respiratory failure due to ARDS. The pathologic alteration known as diffuse alveolar damage in endothelial and epithelial cells is a critical feature of acute lung injury in ARDS. However, the pathogenesis of ARDS following SRAS-CoV-2 infection remains largely unknown.\n\nIn the present study, we examined apoptosis in post-mortem lung sections from COVID-19 patients and lung tissues from a non-human primate model of SARS-CoV-2 infection, in a cell-type manner, including type 1 and 2 alveolar cells and vascular endothelial cells (ECs), macrophages, and T cells. Multiple-target immunofluorescence (IF) assays and western blotting suggest both intrinsic and extrinsic apoptotic pathways are activated during SARS-CoV-2 infection. Furthermore, we observed that SARS-CoV-2 fails to induce apoptosis in human bronchial epithelial cells (i.e., BEAS2B cells) and primary human umbilical vein endothelial cells (HUVECs), which are refractory to SARS-CoV-2 infection. However, infection of co-cultured Vero cells and HUVECs or Vero cells and BEAS2B cells with SARS-CoV-2 induced apoptosis in both Vero cells and HUVECs/BEAS2B cells, but did not alter the permissiveness of HUVECs or BEAS2B cells to the virus. Post-exposure treatment of the co-culture of Vero cells and HUVECs with an EPAC1-specific activator ameliorated apoptosis in HUVECs. These findings may help to delineate a novel insight into the pathogenesis of ARDS following SARS-CoV-2 infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yakun Liu", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Tania M. Garron", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Qing Chang", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Zhengchen Su", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Changcheng Zhou", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Eric C. Gong", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Junying Zheng", + "author_inst": "The University of Texas Medical Branch" + }, + { + "author_name": "Whitney Yin", + "author_inst": "University of Texas Medical Branch, Galveston" + }, + { + "author_name": "Thomas Ksiazek", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Trevor Brasel", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yang Jin", + "author_inst": "Boston University Medical Campus" + }, + { + "author_name": "Paul Boor", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jason Edward Comer", + "author_inst": "UTMB" + }, + { + "author_name": "Bin Gong", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.12.23.424189", "rel_title": "Berberine and obatoclax inhibit SARS-CoV-2 replication in primary human nasal epithelial cells in vitro", @@ -1025927,93 +1029569,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.22.20248657", - "rel_title": "Adenovirus and RNA-based COVID-19 vaccines: perceptions and acceptance among healthcare workers", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248657", - "rel_abs": "ObjectivesThe aim of this study was to compare the perception, confidence, hesitancy, and acceptance rate of various COVID-19 vaccine types among healthcare workers (HCWs) in Saudi Arabia, a nation with MERS-CoV experience.\n\nDesignNational cross-sectional, pilot-validated questionnaire.\n\nSettingOnline, self-administered questionnaire among HCWs.\n\nParticipantsA total of 2,007 HCWs working in the Kingdom of Saudi Arabia participated; 75.3% completed the survey and were included in the analysis.\n\nInterventionData were collected through an online survey sent to HCWs during November 1-15, 2020. The main outcome measure was HCW acceptance of COVID-19 candidate vaccines. The associated factors of vaccination acceptance were identified through a logistic regression analysis and via measurement of the level of anxiety, using the generalized anxiety disorder 7 (GAD7) scale.\n\nResultsAmong the 1512 HCWs who were included, 62.4% were women, 70.3% were between 21 and 40 years of age, and the majority (62.2%) were from tertiary hospitals. In addition, 59.5% reported knowing about at least one vaccine; 24.4% of the participants were sure about their willingness to receive the ChAdOx1 nCoV-19 vaccine, and 20.9% were willing to receive the RNA BNT162b2 vaccine. However, 18.3% reported that they would refuse to receive the Ad5-vectored vaccine, and 17.9% would refuse the Gam-COVID-Vac vaccine. Factors that influenced the differential readiness of HCWs included their perceptions of the vaccines efficiency in preventing the infection (33%), their personal preferences (29%), and the vaccines manufacturing country (28.6%).\n\nConclusionsAwareness by HCWs of the several COVID-19 candidate vaccines could improve their perceptions and acceptance of vaccination. Reliable sources on vaccine efficiency could improve vaccine uptake, so healthcare authorities should use reliable information to decrease vaccine hesitancy among frontline healthcare providers.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Mohamad Hani Temsah", - "author_inst": "King Saud University" - }, - { - "author_name": "Mazin Barry", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fadi Aljamaan", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Abdullah Alhuzaimi", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Ayman Al-Eyadhy", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Basema Saddik", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Fahad Alsohime", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Ali Alhaboob", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Khalid Alhasan", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Abdulkarim Alrabiaah", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Ali Alaraji", - "author_inst": "Qassim University, Qassim, Saudi Arabia" - }, - { - "author_name": "Rabih Halwani", - "author_inst": "Sharjah University, UAE" - }, - { - "author_name": "Nurah Alamro", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fatimah Alshahrani", - "author_inst": "King Saud University" - }, - { - "author_name": "Amr Jamal", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Sarah Alsubaie", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Ziad Memish", - "author_inst": "Alfaisal University" - }, - { - "author_name": "Jafar A Al-Tawfiq", - "author_inst": "Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.22.20223651", "rel_title": "Toward a COVID-19 testing policy: where and how to test when the purpose is to isolate silent spreaders", @@ -1026917,6 +1030472,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.23.20248790", + "rel_title": "A Systematic Review of the Incubation Period of SARS-CoV-2: The Effects of Age, Biological Sex, and Location on Incubation Period", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248790", + "rel_abs": "A systematic review of the incubation period of COVID-19 was compiled and analyzed from 21 quantitative studies. We investigated the incubation period of COVID-19 with regard to age, biological sex, location, and severity of the disease. Based on the data extracted, we report an overall mean and median incubation period for SARS-CoV-2 of 5.894 days and 5.598 days, respectively. The incubation period did not statistically vary for biological sex or age, but some studies suggest a longer incubation period in the young and elderly. Cases of COVID-19 in Wuhan and Hubei Province of China may have a shorter incubation period for COVID-19 but the shorter incubation period may be due to an increase in viral load. In studying coronavirus strains such as SARS and MERS, researchers have discovered an inverse relationship between incubation period length and virus severity. Taking into consideration that SARS-CoV-2 is part of the beta-coronavirus family, as well as the study mentioned above, we suggest that people who experience more severe disease due to SARS-CoV-2 may have a shorter incubation period.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Caitlin Daley", + "author_inst": "Wheaton College" + }, + { + "author_name": "Megan Fydenkevez", + "author_inst": "Wheaton College" + }, + { + "author_name": "Shari Ackerman-Morris", + "author_inst": "Wheaton College" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.22.20248736", "rel_title": "REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY", @@ -1027604,73 +1031186,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.12.19.20243428", - "rel_title": "Combined RT-qPCR and Pyrosequencing of a SARS-CoV-2 Spike Glycoprotein Polybasic Cleavage Motif Uncovers Rare Pediatric COVID-19 Spectrum Diseases of Unusual Presentation", - "rel_date": "2020-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20243428", - "rel_abs": "BackgroundSurveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is essential for the global containment measures with regard to the ongoing pandemic. Diagnostic gold standard is currently reverse transcription of the (+)RNA genome and subgenomic RNAs and subsequent quantitative polymerase chain reaction (RT-qPCR) from nasopharyngeal swabs or bronchoalveolar lavages. In order to further improve the diagnostic accuracy, particularly for the reliable discrimination between negative and false-negative specimens, we propose the combination of the RT-qPCR workflow with subsequent pyrosequencing of a S-gene amplicon. This extension might add important value mainly in cases with low SARS-CoV-2 load, where RT-qPCR alone can deliver conflicting results.s\n\nResultsWe successfully established a combined RT-qPCR and S-gene pyrosequencing method which can be optionally exploited after routine diagnostics or for epidemiologic studies. This allows a more reliable interpretation of conflicting RT-qPCR results in specimens with relatively low viral loads and close to the detection limits of qPCR (CT values >30). After laboratory implementation and characterization of a best practice protocol we tested the combined method in a large pediatric cohort from two German medical centers (n=769). Pyrosequencing after RT-qPCR enabled us to uncover 6 previously unrecognized cases of pediatric SARS-CoV-2 associated diseases, partially exhibiting unusual and heterogeneous presentation. Moreover, it is notable that in the course of RT-qPCR/pyrosequencing method establishment we did not observe any case of false-positive diagnosis when confirmed SARS-CoV-2-positive specimens were used from foregoing routine testing.\n\nConclusionsThe proposed protocol allows a specific and sensitive detection of SARS-CoV-2 close to the detection limits of RT-qPCR. Combined RT-qPCR/pyrosequencing does not negatively affect preceding RT-qPCR pipeline in SARS-CoV-2 diagnostics and can be optionally applied in routine to inspect conflicting RT-qPCR results.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Patrick Philipp Weil", - "author_inst": "Clinical Molecular Genetics and Epigenetics, Faculty of Health, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Alfred-Herrhau" - }, - { - "author_name": "Jacqueline Hentschel", - "author_inst": "Clinical Molecular Genetics and Epigenetics, Faculty of Health, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Alfred-Herrhau" - }, - { - "author_name": "Frank Schult", - "author_inst": "HELIOS University Hospital Wuppertal, Childrens Hospital, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University, Heusnerstr. 40, 42" - }, - { - "author_name": "Anton Pembaur", - "author_inst": "Clinical Molecular Genetics and Epigenetics, Faculty of Health, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Alfred-Herrhau" - }, - { - "author_name": "Beniam Ghebremedhin", - "author_inst": "HELIOS University Hospital Wuppertal, Institute of Medical Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke Unive" - }, - { - "author_name": "Olivier Mboma", - "author_inst": "HELIOS University Hospital Wuppertal, Childrens Hospital, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University, Heusnerstr. 40, 42" - }, - { - "author_name": "Andreas Heusch", - "author_inst": "HELIOS University Hospital Wuppertal, Childrens Hospital, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University, Heusnerstr. 40, 42" - }, - { - "author_name": "Anna-Christin Reuter", - "author_inst": "Clinical Molecular Genetics and Epigenetics, Faculty of Health, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Alfred-Herrhau" - }, - { - "author_name": "Daniel Mueller", - "author_inst": "Clinical Molecular Genetics and Epigenetics, Faculty of Health, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Alfred-Herrhau" - }, - { - "author_name": "Stefan Wirth", - "author_inst": "HELIOS University Hospital Wuppertal, Childrens Hospital, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University, Heusnerstr. 40, 42" - }, - { - "author_name": "Malik Aydin", - "author_inst": "HELIOS University Hospital Wuppertal, Childrens Hospital, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University, Heusnerstr. 40, 42" - }, - { - "author_name": "Andreas C. W. Jenke", - "author_inst": "Kinikum Kassel, Zentrum fuer Kinder und Jugendmedizin, Neonatologie und allgemeine Paediatrie, Moenchebergstr. 41-43, 34125 Kassel, Germany" - }, - { - "author_name": "Jan Postberg", - "author_inst": "Clinical Molecular Genetics and Epigenetics, Faculty of Health, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Alfred-Herrhau" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.23.424177", "rel_title": "Identification of COVID-19-relevant transcriptional regulatory networks and associated kinases as potential therapeutic targets", @@ -1028562,6 +1032077,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.17.20248234", + "rel_title": "Airflow and air velocity measurements while playing wind instruments, with respect to risk assessment of a SARS-CoV-2 infection", + "rel_date": "2020-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248234", + "rel_abs": "Due to airborne transmission of infection with the coronavirus, the question arose as to how high the risk of spreading infectious particles can be while playing a wind instrument.\n\nTo contribute to this question and to help clarify the possible risks, we analyzed 14 wind instruments, first qualitative by making airflows visible while playing and second quantitative by measuring air velocities at three distances (1m, 1.5m and 2m) in direction of the instruments bell.\n\nMeasurements took place with wind instrumentalists of the Bamberg Symphony in their concert hall.\n\nOur findings highlight that while playing all wind instruments no airflow escaping from the instruments - from the bell with brass instruments, from the mouthpiece, keyholes and bell with woodwinds - was measured beyond a distance of 1.5m from the instruments bell, regardless of volume, pitch or what was played. With that, air velocity while playing corresponded to the usual value of hall-like rooms, of 0.1 m/s. For air-jet woodwinds, alto flute and piccolo, significant air movements were seen close to their mouthpieces, which escaped directly into the room without passing through the instrument and therefore generating directed air movements.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Claudia Spahn", + "author_inst": "Freiburg Institute for Musicians' Medicine" + }, + { + "author_name": "Anna Maria Hipp", + "author_inst": "Freiburg Institute for Musicians' Medicine" + }, + { + "author_name": "Bernd Schubert", + "author_inst": "Tintschl BioEnergie und Stroemungstechnik AG" + }, + { + "author_name": "Marcus Rudolf Axt", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Markus Stratmann", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Christian Schmoelder", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Bernhard Richter", + "author_inst": "Freiburg Institute for Musicians' Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.12.21.20248608", "rel_title": "Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study", @@ -1029422,77 +1032980,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.22.20248712", - "rel_title": "Content analysis and characterization of medical tweets during the early Covid-19 pandemic", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248712", - "rel_abs": "ObjectiveThe novel coronavirus disease 2019 (Covid-19) has infected millions worldwide and impacted the lives of many folds more. Many clinicians share new Covid-19 related resources, research, and ideas within the online Free Open Access to Medical Education (FOAM) community of practice. This study provides a detailed content and contributor analysis of Covid-19 related tweets among the FOAM community.\n\nDesign, Setting, ParticipantsTwitter was searched from November 1st, 2019 to March 21st, 2020 for English tweets discussing Covid-19 in the FOAM community. Tweets were classified into one of 13 pre-specified content categories: original research, editorials, FOAM resource, public health, podcast or video, learned experience, refuting false information, policy discussion, emotional impact, blatantly false information, other Covid-19, and non-Covid-19. Further analysis of linked original research and FOAM resources was performed. 1000 randomly selected contributor profiles and those deemed to have contributed false information were analyzed.\n\nResultsThe search yielded 8541 original tweets from 4104 contributors. The number of tweets in each content category were: 1557 other Covid-19 (18{middle dot}2%), 1190 emotional impact (13{middle dot}9%), 1122 FOAM resources (13{middle dot}1%), 1111 policy discussion (13{middle dot}0%), 928 advice (10{middle dot}9%), 873 learned experience (10{middle dot}2%), 424 non-Covid-19 (5{middle dot}0%), 410 podcast or video (4{middle dot}8%), 304 editorials (3{middle dot}6%), 275 original research (3{middle dot}2%), 245 public health (2{middle dot}9%), 83 refuting false information (1{middle dot}0%), and 19 blatantly false (0{middle dot}2%).\n\nConclusionsEarly in the Covid-19 pandemic, the FOAM community used Twitter to share Covid-19 learned experiences, online resources, crowd-sourced advice, research, and to discuss the emotional impact of Covid-19. Twitter also provided a forum for post-publication peer review of new research. Sharing blatantly false information within this community was infrequent. This study highlights several potential benefits from engaging with the FOAM community on Twitter.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ross Prager", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Michael Pratte", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Rudy R Unni", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Sudarshan Bala", - "author_inst": "McMaster University" - }, - { - "author_name": "Nicholas Ng Fat Hing", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Kay Wu", - "author_inst": "McMaster University" - }, - { - "author_name": "Trevor A McGrath", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Adam Thomas", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Laura Hilary Thompson", - "author_inst": "Ottawa Hospital Research Institute" - }, - { - "author_name": "Julia Hajjar", - "author_inst": "Ottawa Hospital Research Institute" - }, - { - "author_name": "Brent Thoma", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Philippe Rola", - "author_inst": "Santa Cabrini Hospital" - }, - { - "author_name": "Alan Karovitch", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Kwadwo Kyeremanteng", - "author_inst": "University of Ottawa" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.12.20.423682", "rel_title": "Analysis of 46,046 SARS-CoV-2 whole-genomes leveraging principal component analysis (PCA)", @@ -1030548,6 +1034035,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.21.20248627", + "rel_title": "COVID-19 pandemic dynamics in Ukraine after September 1, 2020", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248627", + "rel_abs": "BackgroundThe threats of the COVID-19 pandemic require the mobilization of scientists, including mathematicians. To understand how the number of cases increases versus time, various models based on direct observations of a random number of new cases and differential equations can be used. Complex mathematical models contain many unknown parameters, the values of which must be determined using a limited number of observations of the disease over time. Even long-term monitoring of the epidemic may not provide reliable estimates of its parameters due to the constant change of testing conditions, isolation of infected and quarantine. Therefore, simpler approaches should also be used, for example, some smoothing of the dependence of the number of cases on time and the known SIR (susceptible-infected-removed) model. These approaches allowed to detect the waves of pandemic in different countries and regions and to make adequate predictions of the duration, hidden periods, reproduction numbers, and final sizes of its waves. In particular, seven waves of the COVID-19 pandemic in Ukraine were investigated.\n\nObjectiveWe will detect new epidemic waves in Ukraine that occurred after September 1, 2020 and estimate the epidemic characteristics with the use of generalized SIR model. Some predictions of the epidemic dynamics will be presented.\n\nMethodsIn this study we use the smoothing method for the dependence of the number of cases on time; the generalized SIR model for the dynamics of any epidemic wave, the exact solution of the linear differential equations and statistical approach developed before.\n\nResultsSeventh and eights epidemic waves in Ukraine were detected and the reasons of their appearance were discussed. The optimal values of the SIR model parameters were calculated. The prediction for the COVID-19 epidemic dynamics in Ukraine is not very optimistic: new cases will not stop appearing until June 2021. Only mass vaccination and social distancing can change this trend.\n\nConclusionsNew waves of COVID-19 pandemic can be detected, calculated and predicted with the use of rather simple mathematical simulations. The expected long duration of the pandemic forces us to be careful and in solidarity.The government and all Ukrainians must strictly adhere to quarantine measures in order to avoid fatal consequences.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Igor Nesteruk", + "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.22.20248622", "rel_title": "Optimal strategies for combining vaccine prioritization and social distancing to reduce hospitalizations and mitigate COVID19 progression", @@ -1030980,97 +1034486,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.12.21.20248593", - "rel_title": "Factors Associated with Longitudinal Psychological and Physiological Stress in Health Care Workers During the COVID-19 Pandemic", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248593", - "rel_abs": "IntroductionThe Coronavirus Disease 2019 (COVID-19) pandemic has resulted in psychological distress in health care workers (HCWs). There is a need to characterize which HCWs are at increased risk of psychological sequela from the pandemic.\n\nMethodsHCWs across seven hospitals in New York City were prospectively followed in an ongoing observational digital study using the custom Warrior Watch Study App. Participants wore an Apple Watch for the duration of the study measuring HRV throughout the follow up period. Surveys were obtained daily.\n\nResultsThree hundred and sixty-one HCWs were enrolled. Multivariable analysis found New York City COVID-19 case count to be significantly associated with increased longitudinal stress (p=0.008). A non-significant decrease in stress (p=0.23) was observed following COVID-19 diagnosis, though there was a borderline significant increase following the 4-week period after a COVID-19 diagnosis via nasal PCR (p=0.05). Baseline emotional support, baseline quality of life and baseline resilience were associated with decreased longitudinal stress (p<0.001). Baseline resilience and emotional support were found to buffer against stressors, with a significant reduction in stress during the 4-week period after COVID-19 diagnosis observed only in participants in the highest tertial of emotional support and resilience (effect estimate -0.97, p=0.03; estimate -1.78, p=0.006). A significant trend between New York City COVID-19 case count and longitudinal stress was observed only in the high tertial emotional support group (estimate 1.22, p=0.005), and was borderline significant in the high and medium resilience tertials (estimate 1.29, p=0.098; estimate 1.14, p=0.09). Participants in the highest tertial of baseline emotional support and resilience had significantly reduced amplitude and acrophase of the circadian pattern of longitudinally collected heart rate variability.\n\nConclusionOur findings demonstrate that low resilience, emotional support, and quality of life identify HCWs at risk of high perceived longitudinal stress secondary to the COVID-19 pandemic and have a distinct physiological stress profile. Assessment of HCWs for these features can identify and permit allocation of psychological support to these at-risk individuals as the COVID-19 pandemic and its psychological effects continue in this vulnerable population.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Robert P Hirten", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Matteo Danieletto", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Lewis Tomalin", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Katie Hyewon Choi", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Micol Zweig", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Eddye Golden", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Sparshdeep Kaur", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Drew Helmus", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Anthony Biello", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Renata Pyzik", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Claudia Calcogna", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Robert Freeman", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Bruce E Sands", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Dennis Charney", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Erwin P Bottinger", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Laurie Keefer", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Mayte Suarez Farinas", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Girish Nadkarni", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Zahi A Fayad", - "author_inst": "Icahn School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.12.21.20248607", "rel_title": "Time use and social mixing during and around festive periods: Potential changes in the age distribution of COVID-19 cases from increased intergenerational interactions", @@ -1031882,6 +1035297,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.20.20248587", + "rel_title": "Predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model and the Theory of Planned Behavior Model", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248587", + "rel_abs": "BackgroundA novel coronavirus (COVID-19) was declared a global pandemic by the World Health Organization (WHO) in March, 2020. Until such time as a vaccine becomes available, it is important to identify the determining factors that influence the intention of the general public to accept a future COVID-19 vaccine. Consequently, we aim to explore behavioral-related factors predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model (HBM) and the Theory of Planned Behavior (TPB) model.\n\nMethodsAn online survey was conducted among adults aged 18 years and older from May 24 to June 24, 2020. The survey included socio-demographic and health-related questions, questions related to the HBM and TPB dimensions, and intention to receive COVID-19 vaccine. Associations between questionnaire variables and COVID-19 vaccination intention were assessed by univariate and multivariate analyses.\n\nResultsEighty percent of 398 eligible respondents stated their willingness to receive COVID-19 vaccine. A unified model including HBM and TPB covariates as well as demographic and health-related factors, proved to be a powerful predictor of intention to receive COVID-19 vaccine, explaining 78% of the variance (adjusted R2 = 0.78). Men (OR=4.35, 95% CI 1.58-11.93), educated respondents (OR=3.54, 95% CI 1.44-8.67) and respondents who had received the seasonal influenza vaccine in the previous year (OR=3.31, 95% CI 1.22-9.00) stated higher intention to receive COVID-19 vaccine. Participants were more likely to be willing to get vaccinated if they reported higher levels of perceived benefits of COVID-19 vaccine (OR=4.49, 95% CI 2.79-7.22), of perceived severity of COVID-19 infection (OR=2.36, 95% CI 1.58-3.51) and of cues to action (OR=1.99, 95% CI 1.38-2.87), according to HBM, and if they reported higher levels of subjective norms (OR=3.04, 95% CI 2.15-4.30) and self-efficacy (OR=2.05, 95% CI 1.54-2.72) according to TPB. Although half of the respondents reported they had not received influenza vaccine last year, 40% of them intended to receive influenza vaccine in the coming winter and 66% of them intended to receive COVID-19 vaccine.\n\nConclusionsProviding data on the public perspective and predicting intention for COVID-19 vaccination using HBM and TPB is important for health policy makers and healthcare providers and can help better guide compliance as the COVID-19 vaccine becomes available to the public.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Liora Shmueli", + "author_inst": "Bar-Ilan university" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.19.20248559", "rel_title": "Changes in UK hospital mortality in the first wave of COVID-19: the ISARIC WHO Clinical Characterisation Protocol prospective multicentre observational cohort study", @@ -1033154,41 +1036588,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.20.20248599", - "rel_title": "Projecting the combined healthcare burden of seasonal influenza and COVID-19", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248599", - "rel_abs": "The overlapping 2020-2021 influenza season and COVID-19 pandemic may overwhelm hospitals throughout the Northern Hemisphere. Using a mathematical model, we project that COVID-19 burden will dwarf that of influenza. If non-pharmacological mitigation efforts fail, increasing influenza vaccination coverage by 30% points would avert 54 hospitalizations per 100,000 people.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zhanwei Du", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Spencer J. Fox", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Tanvi Ingle", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Michael P. Pignone", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.19.20248513", "rel_title": "Clustering and longitudinal change in SARS-CoV-2 seroprevalence in school-children: prospective cohort study of 55 schools in Switzerland", @@ -1034252,6 +1037651,85 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.22.423893", + "rel_title": "Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection", + "rel_date": "2020-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423893", + "rel_abs": "SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA, and that sgRNA modifications are stable across transcript clusters, host cells and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Our results are available via an interactive web-app at http://coinlab.mdhs.unimelb.edu.au/.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jessie J.-Y. Chang", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Daniel Rawlinson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Miranda E. Pitt", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "George Taiaroa", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Josie Gleeson", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Chenxi Zhou", + "author_inst": "Department of Clinical Pathology, University of Melbourne," + }, + { + "author_name": "Francesca L. Mordant", + "author_inst": "Department of Clinical Pathology, University of Melbourne," + }, + { + "author_name": "Ricardo De Paoli-Iseppi", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Leon Caly", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Damian F. J. Purcell", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Tim P. Stinear", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Sarah L. Londrigan", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Michael B. Clark", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Deborah A. Williamson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Kanta Subbarao", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Lachlan J M Coin", + "author_inst": "Department of Microbiology and Immunology, The University of Melbourne" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.22.423920", "rel_title": "Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations", @@ -1035084,41 +1038562,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.20.423670", - "rel_title": "From infection to immunity: understanding the response to SARS-CoV2 through in-silico modeling", - "rel_date": "2020-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.423670", - "rel_abs": "BackgroundImmune system conditions of the patient is a key factor in COVID-19 infection survival. A growing number of studies have focused on immunological determinants to develop better biomarkers for therapies.\n\nAimThe dynamics of the insurgence of immunity is at the core of the both SARS-CoV-2 vaccine development and therapies. This paper addresses a fundamental question in the management of the infection: can we describe the insurgence (and the span) of immunity in COVID-19? The in-silico model developed here answers this question at individual (personalized) and population levels.\n\nWe simulate the immune response to SARS-CoV-2 and analyze the impact of infecting viral load, affinity to the ACE2 receptor and age in the artificially infected population on the course of the disease.\n\nMethodsWe use a stochastic agent-based immune simulation platform to construct a virtual cohort of infected individuals with age-dependent varying degree of immune competence. We use a parameter setting to reproduce known inter-patient variability and general epidemiological statistics.\n\nResultsWe reproduce in-silico a number of clinical observations and we identify critical factors in the statistical evolution of the infection. In particular we evidence the importance of the humoral response over the cytotoxic response and find that the antibody titers measured after day 25 from the infection is a prognostic factor for determining the clinical outcome of the infection.\n\nOur modeling framework uses COVID-19 infection to demonstrate the actionable effectiveness of simulating the immune response at individual and population levels. The model developed is able to explain and interpret observed patterns of infection and makes verifiable temporal predictions.\n\nWithin the limitations imposed by the simulated environment, this work proposes in a quantitative way that the great variability observed in the patient outcomes in real life can be the mere result of subtle variability in the infecting viral load and immune competence in the population.\n\nIn this work we i) show the power of model predictions, ii) identify the clinical end points that could be more suitable for computational modeling of COVID-19 immune response, iii) define the resolution and amount of data required to empower this class of models for translational medicine purposes and, iv) we exemplify how computational modeling of immune response provides an important view to discuss hypothesis and design new experiments, in particular paving the way to further investigations about the duration of vaccine-elicited immunity especially in the view of the blundering effect of immunesenescence.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Filippo Castiglione", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Debashrito Deb", - "author_inst": "REVA University, School of Applied Sciences, Department of Biochemistry, Bangalore, Karnataka, India" - }, - { - "author_name": "Anurag P. Srivastava", - "author_inst": "Garden City University, Deaprtment of Life Sciences, Bangalore, Karnataka, India" - }, - { - "author_name": "Pietro Li\u00f2", - "author_inst": "Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Arcangelo Liso", - "author_inst": "Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.12.20.423708", "rel_title": "Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma", @@ -1036129,6 +1039572,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.19.423597", + "rel_title": "A comprehensive transcriptome analysis reveals broader but weaker host response of SARS-CoV-2 than SARS-CoV", + "rel_date": "2020-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.19.423597", + "rel_abs": "COVID-19, which has resulted a worldwide health crisis with more than 74.9 million confirmed cases worldwide by December 2020, is caused by a newly emerging coronavirus identified and named SARS-CoV-2 in February in Wuhan, China. Experiences in defeating SARS, which infested during 2002-2003, can be used in treating the new disease. However, comparative genomics and epidemiology studies have shown much difference between SARS-CoV and SARS-CoV-2, which underlies the different clinical features and therapies in between those two diseases. Further studies comparing transcriptomes infected by these two viruses to uncover the differences in host responses would be necessary. Here we conducted a comprehensive transcriptome analysis of SARS-CoV and SARS-CoV-2-infected human cell lines, including Caco-2, Calu-3, H1299. Clustering analysis and expression of ACE2 show that SARS-CoV-2 has broader but weaker infection, where the largest discrepancy occurs in the epithelial lung cancer cell, Calu-3. SARS-CoV-2 genes also show less tissue specificity than SARS-CoV genes. Furthermore, we detected more general but moderate immune responses in SARS-CoV-2 infected transcriptomes by comparing weighted gene co-expression networks and modules. Our results suggest a different immune therapy and treatment scheme for COVID-19 patients than the ones used on SARS patients. The wider but weaker permissiveness and host responses of virus infection may also imply a long-term existence of SARS-CoV-2 among human populations.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Chi Sum Leung", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Songhong Xie", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Jiali Feng", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Dongjing Chen", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Aimei Dai", + "author_inst": "School of Life Science, Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.18.20248455", "rel_title": "The impact of the first UK Covid-19 lockdown on carers and people living with low prevalence dementia: results from the Rare Dementia Support survey", @@ -1037017,125 +1040495,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.18.423507", - "rel_title": "SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes", - "rel_date": "2020-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423507", - "rel_abs": "CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control, though direct evidence has been lacking so far. Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV- 2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding, which was associated with a loss of recognition and functional responses by CD8+ T cells isolated from HLA-matched COVID-19 patients. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through escape mutations in MHCI-restricted viral epitopes. This provides evolutionary evidence for CD8+ T cell immunity controlling SARS-CoV-2 with consequences for COVID-19 vaccine design.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Benedikt Agerer", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Maximilian Koblischke", - "author_inst": "Center for Virology, Medical University of Vienna" - }, - { - "author_name": "Venugopal Gudipati", - "author_inst": "Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna" - }, - { - "author_name": "Mark Smyth", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Alexandra Popa", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Jakob-Wendelin Genger", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Lukas Endler", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "David M Florian", - "author_inst": "Center for Virology, Medical University of Vienna" - }, - { - "author_name": "Vanessa Muehlgrabner", - "author_inst": "Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna" - }, - { - "author_name": "Alexander Lercher", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Pia Gattinger", - "author_inst": "Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna" - }, - { - "author_name": "Ricard Torralba-Gombau", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Thomas Penz", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Ingrid Fae", - "author_inst": "Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna" - }, - { - "author_name": "Sabine Wenda", - "author_inst": "Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna" - }, - { - "author_name": "Marianna Traungott", - "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital" - }, - { - "author_name": "Gernot Walder", - "author_inst": "Division of Hygiene and Medical Microbiology, Medical University of Innsbruck" - }, - { - "author_name": "Gottfried Fischer", - "author_inst": "Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna" - }, - { - "author_name": "Wolfgang Hoepler", - "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital" - }, - { - "author_name": "Erich Pawelka", - "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital" - }, - { - "author_name": "Alexander Zoufaly", - "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital" - }, - { - "author_name": "Rudolf Valenta", - "author_inst": "Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna" - }, - { - "author_name": "Christoph Bock", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - }, - { - "author_name": "Johannes B. Huppa", - "author_inst": "Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna" - }, - { - "author_name": "Judith H. Aberle", - "author_inst": "Center for Virology, Medical University of Vienna" - }, - { - "author_name": "Andreas Bergthaler", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.18.423509", "rel_title": "Fast and scalable lipid nanoparticle formulation of niclosamide (nano NCM) effectively inhibits SARS-CoV-2 replication in vitro", @@ -1038119,6 +1041478,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.18.20248434", + "rel_title": "Excess deaths among Latino people in California during the COVID-19 pandemic", + "rel_date": "2020-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248434", + "rel_abs": "BackgroundLatino people in the US are experiencing higher excess deaths during the COVID-19 pandemic than any other racial/ethnic group, but it is unclear which subgroups within this diverse population are most affected. Such information is necessary to target policies that prevent further excess mortality and reduce inequities.\n\nMethodsUsing death certificate data for January 1, 2016 through February 29, 2020 and time-series models, we estimated the expected weekly deaths among Latino people in California from March 1 through October 3, 2020. We quantified excess mortality as observed minus expected deaths and risk ratios (RR) as the ratio of observed to expected deaths. We considered subgroups defined by age, sex, place of birth, education, occupation, and combinations of these factors.\n\nFindingsDuring the first seven months of the pandemic, Latino deaths in California exceeded expected deaths by 10,316, a 31% increase. Excess death rates were greatest for individuals born in Mexico (RR 1.44; 95% PI, 1.41, 1.48) or Central America (RR 1.49; 95% PI, 1.37, 1.64), with less than a high school degree (RR 1.41; 95% PI, 1.35, 1.46), or in food-and-agriculture (RR 1.60; 95% PI, 1.48, 1.74) or manufacturing occupations (RR 1.59; 95% PI, 1.50, 1.69). Immigrant disadvantages in excess death were magnified among working-age Latinos in essential occupations.\n\nInterpretationThe pandemic has disproportionately impacted mortality among Latino immigrants and Latinos in unprotected essential jobs; Interventions to reduce these disparities should include early vaccination, workplace safety enforcement, and expanded access to medical care.\n\nFundingNational Institute on Aging; UCSF\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSSeveral articles have suggested all-cause excess mortality estimates are superior to official COVID-19 counts for assessing the impact of the pandemic on marginalized populations that lack access to testing and healthcare. We searched PubMed, Google scholar, and the medRxiv preprint database through December 22, 2020 for studies of (\"excess mortality\" or \"excess death\") AND (\"COVID-19\" or \"coronavirus\") set in the United States and we identified two empirical studies with estimates of excess mortality among Latinos during the pandemic. The study set in California (from our research team) found per capita excess mortality was highest among Black and Latino people. The national study found percent excess mortality was significantly higher among Latino people than any other racial/ethnic group. Neither study further disaggregated the diverse Latino population or provided subgroup estimates to clarify why excess pandemic mortality is so high in this population. In the U.S., official COVID-19 statistics are rarely disaggregated by place of birth, education, or occupation which has resulted in a lack of evidence of how these factors have impacted mortality during the pandemic. No study to date of excess mortality in the U.S. has provided estimates for immigrant or occupational subgroups.\n\nAdded value of this studyOur population-based observational study of all-cause mortality during the COVID-19 pandemic provides the first estimates of within-group heterogeneity among the Latino population in California - one of the populations hardest hit by COVID-19 in the U.S. We provide the first subgroup estimates by place of birth and occupational sector, in addition to combined estimates by foreign-birth and participation in an essential job and education. In doing so, we reveal that Latino immigrants in essential occupations have the highest risk of excess death during the pandemic among working-age Latinos. We highlight the heightened risk of excess mortality associated with food/agriculture and manufacturing occupational sectors, essential sectors in which workers may lack COVID-19 protections.\n\nImplications of all the available evidenceOur study revealed stark disparities in excess mortality during the COVID-19 pandemic among Latinos, pointing to the particularly high vulnerability of Latino immigrants and Latinos in essential jobs. These findings may offer insight into the disproportionate COVID-19 mortality experienced by immigrants or similarly marginalized groups in other contexts. Interventions to reduce these disparities should include policies enforcing occupational safety, especially for immigrant workers, early vaccination, and expanded access to medical care.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alicia R. Riley", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Yea-Hung Chen", + "author_inst": "Institute for Global Health Sciences, University of California, San Francisco" + }, + { + "author_name": "Ellicott C. Matthay", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "M. Maria Glymour", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Jacqueline M. Torres", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Alicia Fernandez", + "author_inst": "Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.18.20248449", "rel_title": "Coinfection with Respiratory Pathogens in COVID-19 in Korea", @@ -1038983,73 +1042385,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.12.18.423415", - "rel_title": "A recombinant fragment of Human surfactant protein D binds Spike protein and inhibits infectivity and replication of SARS-CoV-2 in clinical samples", - "rel_date": "2020-12-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423415", - "rel_abs": "RationaleCOVID-19 is an acute infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Human surfactant protein D (SP-D) is known to interact with spike protein of SARS-CoV, but its immune-surveillance against SARS-CoV-2 is not known.\n\nObjectiveThis study aimed to examine the potential of a recombinant fragment of human SP-D (rfhSP-D) as an inhibitor of replication and infection of SARS-CoV-2.\n\nMethodsrfhSP-D interaction with spike protein of SARS-CoV-2 and hACE-2 receptor was predicted via docking analysis. The inhibition of interaction between spike protein and ACE-2 by rfhSP-D was confirmed using direct and indirect ELISA. The effect of rfhSP-D on replication and infectivity of SARS-CoV-2 from clinical samples was studied by measuring the expression of RdRp gene of the virus using qPCR.\n\nMeasurements and Main ResultsIn-silico interaction studies indicated that three amino acid residues in the RBD of spike of SARS-CoV-2 were commonly involved in interacting with rfhSP-D and ACE-2. Studies using clinical samples of SARS-CoV-2 positive cases (asymptomatic, n=7 and symptomatic, n=8 and negative controls n=15) demonstrated that treatment with 5M rfhSP-D inhibited viral replication by ~5.5 fold and was more efficient than Remdesivir (100 M). Approximately, a 2-fold reduction in viral infectivity was also observed after treatment with 5M rfhSP-D.\n\nConclusionsThese results conclusively demonstrate that the calcium independent rfhSP-D mediated inhibition of binding between the receptor binding domain of the S1 subunit of the SARS-CoV-2 spike protein and human ACE-2, its host cell receptor, and a significant reduction in SARS-CoV-2 infection and replication in-vitro.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Taruna Madan", - "author_inst": "Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Barnali Biswas", - "author_inst": "Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Praveen Varghese", - "author_inst": "Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK" - }, - { - "author_name": "Rambhadur Subedi", - "author_inst": "Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Hrishikesh Pandit", - "author_inst": "Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Susan Idicula-Thomas", - "author_inst": "Biomedical Informatics Centre, ICMR- National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Indra Kundu", - "author_inst": "Biomedical Informatics Centre, ICMR- National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Sheetalnath Babasaheb Rooge", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "Reshu Aggarwal", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "Dinesh Tripathi", - "author_inst": "Department of Virology, Institute of Liver and Biliary Sciences, Delhi, India" - }, - { - "author_name": "Savneet Kaur", - "author_inst": "Department of Virology, Institute of Liver and Biliary Sciences, Delhi, India" - }, - { - "author_name": "Ekta Gupta", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "Sanjeev Gupta", - "author_inst": "Intrust Consulting, Mumbai, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.18.423420", "rel_title": "A new concept on anti-SARS-CoV-2 vaccines: strong CD8+ T-cell immune response in both spleen and lung induced in mice by endogenously engineered extracellular vesicles", @@ -1040057,6 +1043392,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.17.20248382", + "rel_title": "Sub-national forecasts of COVID-19 vaccine acceptance across the UK: a large-scale cross-sectional spatial modelling study", + "rel_date": "2020-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248382", + "rel_abs": "The rollout of COVID-19 vaccines has begun to at-risk populations around the world. It is currently unclear whether rejection of the vaccine will pose challenges for achieving herd/community immunity either through large-scale rejection or localised pockets. Here we predict uptake of the vaccine at unprecedented spatial resolution across the UK using a large-scale survey of over 17,000 individuals. Although the majority of the UK population would likely take the vaccine, there is substantial heterogeneity in uptake intent across the UK. Large urban areas, including London and North West England, females, Black or Black British ethnicities, and Polish-speakers are among the least accepting. This study helps identify areas and socio-demographic groups where vaccination levels may not reach those levels required for herd immunity. Identifying clusters of non-vaccinators is extremely important in the context of achieving herd immunity as vaccination \"cold-spots\" can amplify epidemic spread and disproportionately increase vaccination levels required for herd protection.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alex de Figueiredo", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.15.20247981", "rel_title": "SIREN protocol: Impact of detectable anti-SARS-CoV-2 on the subsequent incidence of COVID-19 in 100,000 healthcare workers: do antibody positive healthcare workers have less reinfection than antibody negative healthcare workers?", @@ -1040717,45 +1044071,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.16.20248303", - "rel_title": "Clinical validation of a point-of-care antibody test for COVID-19", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248303", - "rel_abs": "The objective of this study was to evaluate the performance of a lateral flow antibody test for COVID-19, approved for use in India. Although many point-of-care antibody tests are available globally, they have been subjected to limited clinical validation. This has led to suboptimal outcomes in the field, where antibody tests play a significant role in tracking the immunity of individuals and communities. In this study an antibody test, ImmunoQuick that recognizes antibodies to the Nucleocapsid and Spike proteins of SARS CoV-2 was tested in 100 symptomatic patients with a positive or negative diagnosis of COVID-19, based on RT-PCR results. The overall sensitivity of the test was found to be 86.1% (95% CI: 76.4% to 92.8%) and specificity 100% (95% confidence interval: 73.5% to 100%). The sensitivity reached a peak of 95.7% with samples taken 17 days after the onset of symptoms. Overall, the sensitivity and specificity of the test are sufficient for assessing seroprevalence.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Monila Patel", - "author_inst": "Department of Medicine, Smt NHL Municipal Medical College, Ahmedabad, India" - }, - { - "author_name": "Yogesh Lakhotia", - "author_inst": "HealthCubed India Private Limited, Bangalore, India" - }, - { - "author_name": "Sneha Shah", - "author_inst": "Department of Medicine, Smt NHL Municipal Medical College, Ahmedabad, India" - }, - { - "author_name": "Nilay Suthar", - "author_inst": "Department of Medicine, Smt NHL Municipal Medical College, Ahmedabad, India" - }, - { - "author_name": "Sankarrao Kola", - "author_inst": "Centre for Cellular Molecular Biology, Hyderabad, India" - }, - { - "author_name": "Radha Rangarajan", - "author_inst": "HealthCubed India Private Limited, Bangalore, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.16.20214106", "rel_title": "Transmission of SARS-CoV-2 before and after symptom onset: impact of nonpharmaceutical interventions in China", @@ -1041655,6 +1044970,45 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.12.17.423130", + "rel_title": "Suppression of miR-155 attenuates lung cytokine storm induced by SARS-CoV-2 infection in human ACE2-transgenic mice", + "rel_date": "2020-12-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.17.423130", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a recent global pandemic. It is a deadly human viral disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a high rate of infection, morbidity and mortality. Therefore, there is a great urgency to develop new therapies to control, treat and prevent this disease. Endogenous microRNAs (miRNAs, miRs) of the viral host are key molecules in preventing viral entry and replication, and building an antiviral cellular defense. Here, we have analyzed the role of miR-155, one of the most powerful drivers of host antiviral responses including immune and inflammatory responses, in the pathogenicity of SARS-CoV-2 infection. Subsequently, we have analyzed the potency of anti-miR-155 therapy in a COVID-19 mouse model (mice transgenic for human angiotensin I-converting enzyme 2 receptor (tg-mice hACE2)). We report for the first time that miR-155 expression is elevated in COVID-19 patients. Further, our data indicate that the viral load as well as miR-155 levels are higher in male relative to female patients. Moreover, we find that the delivery of anti-miR-155 to SARS-CoV-2-infected tg-mice hACE2 effectively suppresses miR-155 expression, and leads to improved survival and clinical scores. Importantly, anti-miR-155-treated tg-mice hACE2 infected with SARS-CoV-2 not only exhibit reduced levels of pro-inflammatory cytokines, but also have increased anti-viral and anti-inflammatory cytokine responses in the lungs. Thus, our study suggests anti-miR-155 as a novel therapy for mitigating the lung cytokine storm induced by SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dharmendra Kumar Soni", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Juan Cabrera-Luque", + "author_inst": "GeneDx" + }, + { + "author_name": "Swagata Kar", + "author_inst": "Bioqual Inc." + }, + { + "author_name": "Chaitali Sen", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Joseph Devaney", + "author_inst": "GeneDx" + }, + { + "author_name": "Roopa Biswas", + "author_inst": "Uniformed Services University of the Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.16.423166", "rel_title": "Molecular diversity analysis of the spike glycoprotein (S) gene from Hong Kong - China", @@ -1042239,25 +1045593,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.14.20248182", - "rel_title": "Mathematical model for the mitigation of the economic effects of Covid-19 in the Democratic Republic of the Congo", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248182", - "rel_abs": "A Mathematical model for the spread of Covid-19 in Democratic Republic of Congo taking into account the vulnerability of congolese economy is proposed. The reproduction number for the Covid-19 is calculated and numerical simulations are performed using Python software. A clear advice for policymakers is deduced from the forecasting of the model.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Zirhumanana Dieudonne Balike", - "author_inst": "Institut Superieur Pedagogique de Bukavu" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.14.20248186", "rel_title": "Vaccine Prioritisation Using Bluetooth Exposure Notification Apps", @@ -1043377,6 +1046712,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248181", + "rel_title": "Predicting the need for escalation of care or death from repeated daily clinical observations and laboratory results in patients with SARS-CoV-2 during 2020: a retrospective population-based cohort study from the United Kingdom", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248181", + "rel_abs": "ObjectivesCurrently used prognostic tools for patients with SARS-CoV-2 infection are based on clinical and laboratory parameters measured at a single point in time, usually on admission. We aimed to determine how dynamic changes in clinical and laboratory parameters relate to SARS-CoV-2 prognosis.\n\nDesignretrospective, observational cohort study using routinely collected clinical data to model the dynamic change in prognosis of SARS-CoV-2.\n\nSettinga single, large hospital in England.\n\nParticipantsall patients with confirmed SARS-CoV-2 admitted to Nottingham University Hospitals (NUH) NHS Trust, UK from 1st February 2020 until 30th November 2020.\n\nMain outcome measuresIntensive Care Unit (ICU) admission, death and discharge from hospital.\n\nStatistical MethodsWe split patients into 1st (admissions until 30th June) and 2nd (admissions thereafter) waves. We incorporated all clinical observations, blood tests and other covariates from electronic patient records and follow up until death or 30 days from the point of hospital discharge. We modelled daily risk of admission to ICU or death with a time varying Cox proportional hazards model.\n\nResults2,964 patients with confirmed SARS-CoV-2 were included. Of 1,374 admitted during the 1st wave, 593 were eligible for ICU escalation, and 466 had near complete ascertainment of all covariates at admission. Our validation sample included 1,590 confirmed cases, of whom 958 were eligible for ICU admission. Our model had good discrimination of daily need for ICU admission or death (C statistic = 0.87 (IQR 0.85-0.90)) and predicted this daily prognosis better than previously published scores (NEWS2, ISCARIC 4C). In validation in the 2nd wave the score overestimated escalation (calibration slope 0.55), whilst retaining a linear relationship and good discrimination (C statistic = 0.88 (95% CI 0.81 -0.95)).\n\nConclusionsA bespoke SARS-CoV-2 escalation risk prediction score can predict need for clinical escalation better than a generic early warning score or a single estimation of risk at admission.\n\nWhat is already known on this topicSARS-CoV-2 is a recently emerged viral infection, which presents typically with flu like symptoms, can have severe sequelae and has caused a pandemic during 2020.\n\nA number of risk factors for poor outcomes including obesity, age and comorbidity have been recognized.\n\nRisk scores have been developed to stratify risk of poor outcome for patients with SARS-CoV-2 at admission, but these do not take account of dynamic changes in severity of disease on a daily basis.\n\nWhat this study addsWe have developed a dynamic risk score to predict escalation to ICU or death within the next 24 hours.\n\nOur score has good discrimination between those who will and not require ICU admission (or die) in both our derivation and validation cohorts.\n\nOur bespoke SARS-CoV-2 escalation risk prediction score can predict need for clinical escalation better than a generic early warning score or a single estimation of risk at admission.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Colin J Crooks", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Joe West", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Andrew Fogarty", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Joanne R Morling", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Matthew J Grainge", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Sherif Gonem", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Mark Simmonds", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Andrea Race", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Irene Juurlink", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Stephen Briggs", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Simon Cruikshank", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Susan Hammond-Pears", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Timothy R Card", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.15.20248279", "rel_title": "Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity", @@ -1044049,45 +1047451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.16.20248321", - "rel_title": "The association between work situation and life satisfaction during the COVID-19 pandemic: prospective cohort study in Norway", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248321", - "rel_abs": "ObjectivesTo analyse the population effects on life quality of being laid off from work, having to work from home, or having been diagnosed with COVID-19.\n\nDesignNationwide population-based cohort study.\n\nSettingNorway.\n\nParticipantsWe followed more than 80,000 participants in an ongoing cohort study, the Norwegian Mother, Father and Child Cohort Study (MoBa) during the COVID-19 pandemic. We analysed current life satisfaction in April and again in September/October 2020 for subjects whose work situation and infection status had changed.\n\nMain outcome measuresSelf-reported satisfaction with life, using a scale from 0 (worst) to 10 (best).\n\nResultsTemporary and permanent layoffs, working from a home-based office, and getting a COVID-19 diagnosis were associated with modestly, but significantly lower concurrent life satisfaction, both on a population level and for subjects who changed status. The associations with change in work situation were stronger for men. For men with permanent job loss, the adjusted odds ratio for low life satisfaction (<6) was 3.2 (95% CI 2.4 to 4.2) in April and 4.9 (95% CI 3.5 to 6.9) in autumn. A suspected or confirmed COVID-19 diagnosis was associated with an adjusted odds ratio for low life satisfaction of 1.9 (95% CI 1.6 to 2.3) in spring. The strength of associations between work situation and life satisfaction did not vary much across socio-economic strata, but layoffs were more common among those with low education.\n\nConclusionLayoffs, home office and infection status had clear impact on the quality of life as measured with a global life satisfaction scale. These findings suggest that social differentials in quality of life, are increasing during the pandemic.\n\nFundingThis work was funded by the Norwegian Research Councils Centres of Excellence Funding Scheme (no. 262700) and by the Norwegian Institute of Public Health (NIPH).\n\nSUMMARY BOXESO_ST_ABSWhat is already known on this topicC_ST_ABS- Being laid off from work or having to work from a home-based office is usually associated with reduced life quality.\n- The population effect has not been estimated during the present surge in cases of COVID-19 in Europe.\n\n\nWhat this study adds- This population-based study shows that life satisfaction in Norway has been stable from the first to the second wave of the pandemic, but that both layoffs and working from home is associated with reduced life satisfaction, especially among men.\n- The reduced life satisfaction in people working from a home-based office implies that large proportions of the population are affected.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ellen Oen Carlsen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Ida Henriette Caspersen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Helga Ask", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Ragnhild Eek Brandlistuen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Lill Trogstad", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Per Magnus", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.15.20244160", "rel_title": "The role of metabolic comorbidity in COVID-19 mortality of middle-aged adults. The case of Mexico.", @@ -1045043,6 +1048406,33 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.14.422793", + "rel_title": "Genomic diversity analysis of SARS-CoV-2 genomes in Rwanda", + "rel_date": "2020-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.422793", + "rel_abs": "COVID-19 (Coronavirus disease 2019) is an emerging pneumonia-like respiratory disease of humans and is recently spreading across the globe.\n\nObjectiveTo analyze the genome sequence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) isolated from Rwanda with other viral strains from African countries.\n\nMethodsWe downloaded 75 genomes sequences of clinical SARS-CoV-2 from the GISAID (global initiative on sharing all influenza data) database and we comprehensively analyzed these SARS-CoV-2 genomes sequences alongside with Wuhan SARS-CoV-2 sequences as the reference strains.\n\nResultsWe analyzed 75 genomes sequences of SARS-CoV-2 isolated in different African countries including 10 samples of SARS-CoV-2 isolated in Rwanda between July and August 2020. The phylogenetic analysis of the genome sequence of SARS-CoV-2 revealed a strong identity with reference strains between 90-95%. We identified a missense mutation in four proteins including orf1ab polyprotein, NSP2, 2-O-ribose methyltransferase and orf1a polyprotein. The most common changes in the base are C > T. We also found that all clinically SARS-CoV-2 isolated from Rwanda had genomes belonging to clade G and lineage B.1.\n\nConclusionsTracking the genetic evolution of SARS-CoV-2 over time is important to understand viral evolution pathogenesis. These findings may help to implement public health measures in curbing COVID-19 in Rwanda.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nzungize Lambert", + "author_inst": "Synthetic Biology Rwanda" + }, + { + "author_name": "Ndishimye Pacifique", + "author_inst": "Rwanda Joint Task Force COVID-19, Rwanda Biomedical Center, Ministry of Health, Kigali, Rwanda." + }, + { + "author_name": "Fathiah Zakham", + "author_inst": "Laboratory of Virology, University of Helsinki, Helsinki 00014, Finland." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.10.20245944", "rel_title": "Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", @@ -1045739,41 +1049129,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.13.20247254", - "rel_title": "Predicting mortality in SARS-COV-2 (COVID-19) positive patients in the inpatient setting using a Novel Deep Neural Network", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.13.20247254", - "rel_abs": "BackgroundThe second wave of COVID-19 pandemic is anticipated to be worse than the initial one and will strain the healthcare systems even more during the winter months. Our aim was to develop a machine learning-based model to predict mortality using the deep learning Neo-V framework. We hypothesized this novel machine learning approach could be applied to COVID-19 patients to predict mortality successfully with high accuracy.\n\nMethodsThe current Deep-Neo-V model is built on our previously statistically rigorous machine learning framework [Fahad-Liaqat-Ahmad Intensive Machine (FLAIM) framework] that evaluated statistically significant risk factors, generated new combined variables and then supply these risk factors to deep neural network to predict mortality in RT-PCR positive COVID-19 patients in the inpatient setting. We analyzed adult patients ([≥]18 years) admitted to the Aga Khan University Hospital, Pakistan with a working diagnosis of COVID-19 infection (n=1228). We excluded patients that were negative on COVID-19 on RT-PCR, had incomplete or missing health records. The first phase selection of risk factor was done using Cox-regression univariate and multivariate analyses. In the second phase, we generated new variables and tested those statistically significant for mortality and in the third and final phase we applied deep neural networks and other traditional machine learning models like Decision Tree Model, k-nearest neighbor models and others.\n\nResultsA total of 1228 cases were diagnosed as COVID-19 infection, we excluded 14 patients after the exclusion criteria and (n=)1214 patients were analyzed. We observed that several clinical and laboratory-based variables were statistically significant for both univariate and multivariate analyses while others were not. With most significant being septic shock (hazard ratio [HR], 4.30; 95% confidence interval [CI], 2.91-6.37), supportive treatment (HR, 3.51; 95% CI, 2.01-6.14), abnormal international normalized ratio (INR) (HR, 3.24; 95% CI, 2.28-4.63), admission to the intensive care unit (ICU) (HR, 3.24; 95% CI, 2.22-4.74), treatment with invasive ventilation (HR, 3.21; 95% CI, 2.15-4.79) and laboratory lymphocytic derangement (HR, 2.79; 95% CI, 1.6-4.86). Machine learning results showed our DNN (Neo-V) model outperformed all conventional machine learning models with test set accuracy of 99.53%, sensitivity of 89.87%, and specificity of 95.63%; positive predictive value, 50.00%; negative predictive value, 91.05%; and area under the curve of the receiver-operator curve of 88.5.\n\nConclusionOur novel Deep-Neo-V model outperformed all other machine learning models. The model is easy to implement, user friendly and with high accuracy.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Maleeha Naseem", - "author_inst": "Department of Epidemiology & Biostatistics, Community Health Sciences, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Hajra Arshad", - "author_inst": "Department of Epidemiology & Biostatistics, Community Health Sciences, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Syeda Amrah Hashmi", - "author_inst": "Department of Epidemiology & Biostatistics, Community Health Sciences, Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Furqan Irfan", - "author_inst": "College of Osteopathic Medicine, Michigan State University, East Lansing, MI USA" - }, - { - "author_name": "Fahad Shabbir Ahmed", - "author_inst": "Clinicaro Machine Learning Group and Depart of Pathology, Wayne State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.10.20235747", "rel_title": "Human Safety, Tolerability, and Pharmacokinetics of a Novel Broad-Spectrum Oral Antiviral Compound, Molnupiravir, with Activity Against SARS-CoV-2", @@ -1046797,6 +1050152,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248160", + "rel_title": "Acceptability and feasibility of strategies to shield the vulnerable during the COVID-19 outbreak: a qualitative study in six Sudanese communities", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248160", + "rel_abs": "BackgroundShielding of high-risk groups from coronavirus disease (COVID-19), either within their households or safe communal structures, has been suggested as a realistic alternative to severe movement restrictions in response to the COVID-19 epidemic in low-income countries. To our knowledge, this concept has not been tested or evaluated in resource-poor settings. This study aimed to explore the acceptability and feasibility of strategies to shield persons at higher risk of severe COVID-19 outcomes, during the COVID-19 epidemic in six communities in Sudan.\n\nMethodsWe purposively sampled participants from six communities, illustrative of urban, rural and forcibly-displaced settings. In-depth telephone interviews were held with 59 members of households with one or more members at higher risk of severe COVID-19 outcomes. Follow-up interviews were held with 30 community members after movement restrictions were eased across the country. All interviews were audio-recorded, transcribed verbatim, and analysed using a two-stage deductive and inductive thematic analysis.\n\nResultsMost participants were aware that some people are at higher risk of severe COVID-19 outcomes but were unaware of the concept of shielding. Most participants found shielding acceptable and consistent with cultural inclinations to respect elders and protect the vulnerable. However, extra-household shielding arrangements were mostly seen as socially unacceptable. Participants reported feasibility concerns related to the social isolation of shielded persons and loss of income for shielding families. The acceptability and feasibility of shielding strategies were reduced after movement restrictions were eased, as participants reported lower perception of risk in their communities and increased pressure to comply with social commitments outside the house.\n\nConclusionShielding is generally acceptable in the study communities. Acceptability is influenced by feasibility, and by contextual changes in the epidemic and associated policy response. The promotion of shielding should capitalise on the cultural and moral sense of duty towards elders and vulnerable groups. Communities and households should be provided with practical guidance to implement feasible shielding options. Households must be socially, psychologically and financially supported to adopt and sustain shielding effectively.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nada Abdelmagid", + "author_inst": "London School of Hygiene and Tropical Medicine, (Department of Infectious Disease Epidemiology), London, (London), United Kingdom / Sudan COVID-19 Research Grou" + }, + { + "author_name": "Salma A.E. Ahmed", + "author_inst": "Independent public health researcher, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Nazik Nurelhuda", + "author_inst": "University of Khartoum, Faculty of Dentistry, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Israa Zainalabdeen", + "author_inst": "Y-PEER Sudan, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Aljaile Ahmed", + "author_inst": "Y-PEER Sudan, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Mahmoud Ali Fadlallah", + "author_inst": "Asian Institute of Technology, Bangkok, (Bangkok), Thailand / Public Health Institute (PHI), Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Maysoon Dahab", + "author_inst": "London School of Hygiene and Tropical Medicine, (Department of Infectious Disease Epidemiology), London, (London), United Kingdom / Sudan COVID-19 Research Grou" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.11.20247262", "rel_title": "COVID-19 in persons affected by Hansen's disease in Brazil", @@ -1047553,57 +1050951,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.12.14.422714", - "rel_title": "Neuroinvasion and encephalitis following intranasal inoculation of SARS-CoV-2 in K18-hACE2 mice", - "rel_date": "2020-12-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.422714", - "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can cause neurological disease in humans, but little is known about the pathogenesis of SARS-CoV-2 infection in the central nervous system. Herein, using K18-hACE2 mice, we demonstrate that SARS-CoV-2 neuroinvasion and encephalitis is associated with mortality in these mice. Intranasal infection of K18-hACE2 mice with 105 plaque-forming units of SARS-CoV-2 resulted in 100% mortality by day 6 after infection. The highest virus titers in the lungs were observed at day 3 and declined at days 5 and 6 after infection. In contrast, very high levels of infectious virus were uniformly detected in the brains of all the animals at days 5 and 6. Onset of severe disease in infected mice correlated with peak viral levels in the brain. SARS-CoV-2-infected mice exhibited encephalitis hallmarks characterized by production of cytokines and chemokines, leukocyte infiltration, hemorrhage and neuronal cell death. SARS-CoV-2 was also found to productively infect cells within the nasal turbinate, eye and olfactory bulb, suggesting SARS-CoV-2 entry into the brain by this route after intranasal infection. Our data indicate that direct infection of CNS cells together with the induced inflammatory response in the brain resulted in the severe disease observed in SARS-CoV-2-infected K18-hACE2 mice.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Pratima Kumari", - "author_inst": "Georgia State University" - }, - { - "author_name": "Hussin A Rothan", - "author_inst": "Georgia State University" - }, - { - "author_name": "Janhavi P Natekar", - "author_inst": "Georgia State University" - }, - { - "author_name": "Shannon Stone", - "author_inst": "Georgia State University" - }, - { - "author_name": "Heather Pathak", - "author_inst": "Georgia State University" - }, - { - "author_name": "Philip G Strate", - "author_inst": "Georgia State University" - }, - { - "author_name": "Komal Arora", - "author_inst": "Georgia State University" - }, - { - "author_name": "Margo A Brinton", - "author_inst": "Georgia State University" - }, - { - "author_name": "Mukesh Kumar", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.14.422710", "rel_title": "Surface proteins of SARS-CoV-2 drive airway epithelial cells to induce interferon-dependent inflammation", @@ -1048538,6 +1051885,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2020.11.22.20235184", + "rel_title": "Neurological Disorders associated with COVID-19 Hospital Admissions : Experience of a Single Tertiary Healthcare Centre", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20235184", + "rel_abs": "BackgroundEarly reports have detailed a range of neurological symptoms in patients with the SARS-CoV-2 infection. However, there is a lack of detailed description and incidence of the neurological disorders amongst hospitalized COVID-19 patients. We describe a range of neurological disorders (other than non-specific neurological symptoms), including their clinical, radiological and laboratory findings, encountered in our cohort of COVID-19 patients admitted to a large tertiary institution.\n\nMethodsWe reviewed our prospectively collated database of all adult Neurology referrals, Neurology and Stroke admissions and Neurological multi-disciplinary team meetings for all hospitalized patients with suspected or proven COVID-19 from 17 March 2020 to 31 August 2020.\n\nResultsTwenty-nine of 1243 COVID-19 inpatients (2.3%) presented with COVID-19-related neurological disorders. The mean age was 68.9 +/- 13.5(SD) years, age range of 34-97 years, and there were 16 males. 22 patients had confirmed, 5 were probable and 2 had suspected COVID-19 infection according to the WHO case classification. Eight patients (27%) required critical care admission. Neurological symptoms at presentation included acute confusion and delirium, seizures, and new focal neurological deficits. Based on the pre-defined neurological phenotype, COVID-19 patients were grouped into four main categories. 16 patients had cerebrovascular events (13 with acute ischaemic stroke and 3 had haemorrhagic features), 7 patients were found to have inflammatory, non-inflammatory and autoimmune encephalopathy (including 2 with known Multiple Sclerosis), whilst disorders of movement and peripheral nervous system were diagnosed in 3 patients each.\n\nConclusionAlthough the exact prevalence and aetiology remain unclear, new onset of neurological disorders, in addition to anosmia, is non-sporadic during the acute COVID-19-infection. Longitudinal follow-up of these patients is required to determine the clinical and functional outcome, treatment response and long-term effects of the SARS-CoV-2 infection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Permesh Singh Dhillon", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Robert Dineen", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Haley Morris", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Radu Tanasescu", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Esmaeil Nikfekr", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Jonathan Evans", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Cris S Constantinescu", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Akram A Hosseini", + "author_inst": "Nottingham University Hospitals NHS Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.12.08.20246140", "rel_title": "How detection ranges and usage stops impact digital contact tracing effectiveness for COVID-19", @@ -1049306,49 +1052700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.08.20240382", - "rel_title": "Multimodal Data Acquisition at SARS-CoV-2 Drive Through Screening Centers: Setup Description and Experiences in Saarland, Germany", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20240382", - "rel_abs": "SARS-CoV-2 drive through screening centers (DTSC) have been implemented worldwide as a fast and secure way of mass screening. We use DTSCs as a platform for the acquisition of multimodal datasets that are needed for the development of remote screening methods. Our acquisition setup consists of an array of thermal, infrared and RGB cameras as well as microphones and we apply methods from computer vision and computer audition for the contactless estimation of physiological parameters. We have recorded a multimodal dataset of DTSC participants in Germany for the development of remote screening methods and symptom identification. Acquisition in the early stages of a pandemic and in regions with high infection rates can facilitate and speed up the identification of infection specific symptoms and large scale data acquisition at DTSC is possible without disturbing the flow of operation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Philipp Flotho", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htw saar" - }, - { - "author_name": "Mayur Bhamborae", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htwsaar" - }, - { - "author_name": "Tobias Grun", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htwsaar" - }, - { - "author_name": "Carlos Trenado", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htwsaar" - }, - { - "author_name": "David Thinnes", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htwsaar" - }, - { - "author_name": "Dominik Limbach", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htwsaar" - }, - { - "author_name": "Daniel J Strauss", - "author_inst": "Systems Neuroscience & Neurotechnology Unit, Saarland University & htw saar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.08.20246074", "rel_title": "The impact of the COVID-19 pandemic on college students' health and financial stability in New York City: Findings from a population-based sample of City University of New York (CUNY) students", @@ -1050376,6 +1053727,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.10.20246884", + "rel_title": "SARS-CoV-2/COVID-19 hospitalised patients in Switzerland: a prospective cohort profile", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20246884", + "rel_abs": "BackgroundSARS-CoV-2/COVID-19, which emerged in China in late 2019, rapidly spread across the world causing several million victims in 213 countries. Switzerland was severely hit by the virus, with 43000 confirmed cases as of September 1st, 2020.\n\nAimIn cooperation with the Federal Office of Public Health, we set up a surveillance database in February 2020 to monitor hospitalised patients with COVID-19 in addition to their mandatory reporting system.\n\nMethodsPatients hospitalised for more than 24 hours with a positive PCR test, from 20 Swiss hospitals, are included. Data collection follows a custom Case Report Form based on WHO recommendations and adapted to local needs. Nosocomial infections were defined as infections for which the onset of symptoms started more than 5 days after the patients admission date.\n\nResultsAs of September 1st, 2020, 3645 patients were included. Most patients were male (2168 - 59.5%),and aged between 50 and 89 years (2778 - 76.2%), with a median age of 68 (IQR 54-79). Community infections dominated with 3249 (89.0%) reports. Comorbidities were frequently reported: hypertension (1481 - 61.7%), cardiovascular diseases (948 - 39.5%), and diabetes (660 - 27.5%) being the most frequent in adults; respiratory diseases and asthma (4 -21.1%), haematological and oncological diseases (3 - 15.8%) being the most frequent in children. Complications occurred in 2679 (73.4%) episodes, mostly for respiratory diseases (2470 - 93.2% in adults, 16 - 55.2% in children), renal (681 - 25.7%) and cardiac (631 - 23.8%) complication for adults. The second and third most frequent complications in children affected the digestive system and the liver (7 - 24.1%). A targeted treatment was given in 1299 (35.6%) episodes, mostly with hydroxychloroquine (989 - 76.1%). Intensive care units stays were reported in 578 (15.8%) episodes. 527 (14.5%) deaths were registered, all among adults.\n\nConclusionThe surveillance system has been successfully initiated and provides a very representative set of data for Switzerland. We therefore consider it to be a valuable addition to the existing mandatory reporting, providing more precise information on the epidemiology, risk factors, and clinical course of these cases.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Amaury Thiabaud", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + }, + { + "author_name": "Anne Iten", + "author_inst": "Service de pr\u00e9vention et contr\u00f4le de l'infection, Direction m\u00e9dicale et qualit\u00e9, HUG, Geneva, Switzerland" + }, + { + "author_name": "Carlo Balmelli", + "author_inst": "Infection Control Programme, EOC Hospitals, Ticino, Switzerland" + }, + { + "author_name": "Laurence Senn", + "author_inst": "Service de m\u00e9decine pr\u00e9ventive hospitali\u00e8re, CHUV, Lausanne, Switzerland" + }, + { + "author_name": "Nicolas Troillet", + "author_inst": "Service of Infectious Diseases, Central Institute, Valais Hospitals, Sion, Switzerland" + }, + { + "author_name": "Andreas Widmer", + "author_inst": "Department of Infectious Diseases, University Hospital Basel, Basel, Switzerland" + }, + { + "author_name": "Domenica Flury", + "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Peter W. Schreiber", + "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Miriam V\u00e1zquez", + "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" + }, + { + "author_name": "Lauro Damonti", + "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" + }, + { + "author_name": "Michael Buettcher", + "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Children's Hospital, Cantonal Hospital Lucerne, Switzerland" + }, + { + "author_name": "Danielle Vuichard-Gysin", + "author_inst": "Department of Infectious Diseases, Thurgau Cantonal Hospital, Thurgau, Switzerland" + }, + { + "author_name": "Christoph Kuhm", + "author_inst": "Department of Infectious Diseases, Thurgau Cantonal Hospital, Thurgau, Switzerland" + }, + { + "author_name": "Alexia Cusini", + "author_inst": "Department of Infectious Diseases, Cantonal Hospital Graubuenden, Chur, Switzerland" + }, + { + "author_name": "Thomas Riedel", + "author_inst": "Department of Pediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland" + }, + { + "author_name": "Yvonne Nussbaumer", + "author_inst": "Klinik f\u00fcr Innere Medizin, Kantonsspital Spit\u00e4ler Schaffhausen, Schaffhausen, Switzerland" + }, + { + "author_name": "Roman Gaudenz", + "author_inst": "Innere Medizin und Infektiologie, Kantonsspital Nidwalden, Stans, Switzerland" + }, + { + "author_name": "Ulrich Heininger", + "author_inst": "Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland" + }, + { + "author_name": "Christoph Berger", + "author_inst": "Division of Infectious Diseases, and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland" + }, + { + "author_name": "Franziska Zucol", + "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Cantonal Hospital Winterthur, Winterthur, Switzerland" + }, + { + "author_name": "Sara Bernhard-Stirnemann", + "author_inst": "Children's Hospital Aarau, Aarau, Switzerland" + }, + { + "author_name": "Natascia Corti", + "author_inst": "Unit of General Internal Medicine, Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Petra Zimmermann", + "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; and Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" + }, + { + "author_name": "Anita Uka", + "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; and Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" + }, + { + "author_name": "Anita Niederer-Loher", + "author_inst": "Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland" + }, + { + "author_name": "C\u00e9line Gardiol", + "author_inst": "Swiss Federal Office of Public Health, Bern, Switzerland" + }, + { + "author_name": "Maroussia Roelens", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.09.20246363", "rel_title": "Risk of adverse outcomes with COVID-19 in the Republic of Ireland", @@ -1051000,57 +1054478,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.10.20244509", - "rel_title": "Short of Breath for the Long Haul: Diaphragm Muscle Dysfunction in Survivors of Severe COVID-19 as Determined by Neuromuscular Ultrasound", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20244509", - "rel_abs": "Many survivors from severe coronavirus disease 2019 (COVID-19) suffer from persistent dyspnea and fatigue long after resolution of the active infection. In a cohort of 25 consecutive COVID-19 survivors admitted to an inpatient rehabilitation hospital (76% male), 80% of them had at least one sonographic abnormality of diaphragm muscle structure or function.\n\nSpecifically, when compared to established normative data, 76% had reduced diaphragm thickening ratio (impaired contractility), and 20% patients had reduced diaphragm muscle thickness (atrophy). These findings support neuromuscular respiratory dysfunction as a highly prevalent underlying cause for prolonged functional impairments after hospitalization for COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ellen Farr", - "author_inst": "McGaw Medical Center of Northwestern University" - }, - { - "author_name": "Alexis R Wolfe", - "author_inst": "McGaw Medical Center of Northwestern University" - }, - { - "author_name": "Swati Deshmukh", - "author_inst": "Northwestern University" - }, - { - "author_name": "Leslie Rydberg", - "author_inst": "Shirley Ryan AbilityLab" - }, - { - "author_name": "Rachna Soriano", - "author_inst": "Shirley Ryan AbilityLab" - }, - { - "author_name": "James M Walter", - "author_inst": "Northwestern University" - }, - { - "author_name": "Andrea J Boon", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Lisa F Wolfe", - "author_inst": "Northwestern University" - }, - { - "author_name": "Colin K. Franz", - "author_inst": "Shirley Ryan AbilityLab" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.12.10.20246959", "rel_title": "First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain", @@ -1052074,6 +1055501,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.10.20247361", + "rel_title": "COVID-19 prediction in South Africa: Understanding the unascertained cases -- the hidden part of the epidemiological iceberg", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247361", + "rel_abs": "Understanding the impact of non-pharmaceutical interventions as well as acscounting for the unascertained cases remain critical challenges for epidemiological models for understanding the transmission dynamics of COVID-19 spread. In this paper, we propose a new epidemiological model (eSEIRD) that extends the widely used epidemiological models such as extended Susceptible-Infected-Removed model (eSIR) and SAPHIRE (initially developed and used for analyzing data from Wuhan). We fit these models to the daily ascertained infected (and removed) cases from March 15, 2020 to Dec 31, 2020 in South Africa that reported the largest number of confirmed COVID-19 cases and deaths from the WHO African region. Using the eSEIRD model, the COVID-19 transmission dynamics in South Africa was characterized by the estimated basic reproduction number (R0) starting at 3.22 (95%CrI: [3.19, 3.23]) then dropping below 2 following a mandatory lockdown implementation and subsequently increasing to 3.27 (95%CrI: [3.27, 3.27]) by the end of 2020. The initial decrease of effective reproduction number followed by an increase suggest the effectiveness of early interventions and the combined effect of relaxing strict interventions and emergence of a new coronavirus variant in South Africa. The low estimated ascertainment rate was found to vary from 1.65% to 9.17% across models and time periods. The overall infection fatality ratio (IFR) was estimated as 0.06% (95%CrI: [0.04%, 0.22%]) accounting for unascertained cases and deaths while the reported case fatality ratio was 2.88% (95% CrI: [2.45%, 6.01%]). The models predict that from December 31, 2020, to April 1, 2021, the predicted cumulative number of infected would reach roughly 70% of total population in South Africa. Besides providing insights on the COVID-19 dynamics in South Africa, we develop powerful forecasting tools that enable estimation of ascertainment rates and IFR while quantifying the effect of intervention measures on COVID-19 spread.\n\nAMS ClassificationPlace Classification here. Leave as is, if there is no classification", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xuelin Gu", + "author_inst": "Department of Biostatistics, University of Michigan" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "Department of Biostatistics, University of Michigan; Department of Epidemiology, University of Michigan" + }, + { + "author_name": "Sonali Das", + "author_inst": "Department of Business Management, University of Pretoria" + }, + { + "author_name": "Jyotishka Datta", + "author_inst": "Department of Statistics, Virginia Polytechnic Institute and State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.10.20247247", "rel_title": "Mathematical modelling projections versus the actual course of the COVID-19 epidemic following the nationwide lockdown in Kyrgyzstan", @@ -1053162,89 +1056620,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.11.416180", - "rel_title": "Profound Treg perturbations correlate with COVID-19 severity", - "rel_date": "2020-12-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.11.416180", - "rel_abs": "The hallmark of severe COVID-19 disease has been an uncontrolled inflammatory response, resulting from poorly understood immunological dysfunction. We explored the hypothesis that perturbations in FoxP3+ T regulatory cells (Treg), key enforcers of immune homeostasis, contribute to COVID-19 pathology. Cytometric and transcriptomic profiling revealed a distinct Treg phenotype in severe COVID-19 patients, with an increase in both Treg proportions and intracellular levels of the lineage-defining transcription factor FoxP3, which correlated with poor outcomes. Accordingly, these Tregs over-expressed a range of suppressive effectors, but also pro-inflammatory molecules like IL32. Most strikingly, they acquired similarity to tumor-infiltrating Tregs, known to suppress local anti-tumor responses. These traits were most marked in acute patients with severe disease, but persisted somewhat in convalescent patients. These results suggest that Tregs may play nefarious roles in COVID-19, via suppressing anti-viral T cell responses during the severe phase of the disease, and/or via a direct pro-inflammatory role.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Silvia Galvan-Pena", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Juliette Leon", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Kaitavjeet Chowdhary", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Daniel A. Michelson", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Brinda Vijaykumar", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Liang Yang", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Angela Magnuson", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Zachary Manickas-Hill", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Alicja Piechocka-Trocha", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Daniel P. Worrall", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Kathryn E. Hall", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Musie Ghebremichael", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Bruce D. Walker", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Xu G. Yu", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "- MGH COVID-19 Collection & Processing Team", - "author_inst": "-" - }, - { - "author_name": "Diane Mathis", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Christophe Benoist", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.10.418855", "rel_title": "Identification of eight SARS-CoV-2 ORF7a deletion variants in 2,726 clinical specimens", @@ -1054233,6 +1057608,20 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.08.416677", + "rel_title": "Intranasal administration of SARS-CoV-2 neutralizing human antibody prevents infection in mice", + "rel_date": "2020-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416677", + "rel_abs": "Prevention of SARS-CoV-2 infection at the point of nasal entry is a novel strategy that has the potential to help contain the ongoing pandemic. Using our proprietary technologies, we have engineered a human antibody that recognizes SARS-CoV-2 S1 spike protein with an enhanced affinity for mucin to improve the antibodys retention in respiratory mucosa. The modified antibody, when administered into mouse nostrils, was shown to block infection in mice that were exposed to high titer SARS-CoV-2 pseudovirus 10 hours after the initial antibody treatment. Our data show that the protection against SARS-CoV-2 infection is effective in both nasal and lung areas 7 days after viral exposure. The modified antibody is stable in a nasal spray formulation and maintains its SARS-CoV-2 neutralizing activity. Nasal spray of the modified antibody can be developed as an affordable and effective prophylactic product to protect people from infection by exposure to SARS-CoV-2 virus in the air.\n\nOne-sentence summaryA Fc-modified human antibody prevents SARS-CoV-2 viral infection via nasal administration", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.12.09.417741", "rel_title": "Characterization of protease activity of Nsp3 from SARS-CoV-2 and its in vitro inhibition by nanobodies", @@ -1054925,29 +1058314,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.07.20241018", - "rel_title": "Neighbourhood-level Racial/Ethnic and Economic Inequities in COVID-19 Burden Within Urban Areas in the US and Canada", - "rel_date": "2020-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20241018", - "rel_abs": "The COVID-19 pandemic exhibits stark social inequities in infection and mortality outcomes. We investigated neighborhood-level inequities across cities in the US and Canada for COVID-19 cumulative case rates (46 cities), death rates (12 cities), testing rates and test positivity (12 cities), using measures that characterize social gradients by race/ethnicity, socioeconomic composition, or both jointly. We found consistent evidence of social gradients for case, death and positivity rates, with the most privileged neighborhoods having the lowest rates, but no meaningful variation in the magnitude of inequities between cities. Gradients were not apparent in testing rates, suggesting inadequate testing in the most deprived neighborhoods. Health agencies should monitor and compare inequities as part of their COVID-19 reporting practices and to guide pandemic response efforts.\n\nHIGHLIGHTSO_LIWithin urban regions with available data in the US and Canada, there were strong social gradients for case, death and positivity rates\nC_LIO_LIThe most racially and/or economically privileged neighborhoods had the lowest rates\nC_LIO_LISocial gradients were similar for neighborhood-level measures of racial/ethnic composition, income, racialized economic segregation, and racialized occupational segregation\nC_LIO_LITesting rates did not show consistent social gradients, which suggests that the most deprived neighborhoods have inadequate access to testing relative to their higher disease burden\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sudipta Saha", - "author_inst": "Li Ka Shing Knowledge Institute, St Michael's Hospital" - }, - { - "author_name": "Justin M Feldman", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.08.20245803", "rel_title": "A Selective Increase in OC Symptoms is Driving Information Seeking and Guideline Adherence During the Covid-19 Pandemic", @@ -1056006,6 +1059372,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.06.20243691", + "rel_title": "What is the probability that this patient, who presents to a UK hospital, will be diagnosed with Covid-19? Prospective validation of the open-source CovidCalculatorUK resource.", + "rel_date": "2020-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.06.20243691", + "rel_abs": "IntroductionThe novel coronavirus SARS-CoV2 and the associated disease, Covid-19, continue to pose a global health threat. The CovidCalculatorUK is an open-source online tool (covidcalculatoruk.org) that estimates the probability that an individual patient, who presents to a UK hospital, will later test positive for SARS-CoV2. The objective is to aid cohorting decisions and minimise nosocomial transmission of SARS-CoV2.\n\nMethodsThis n = 500 prospective, observational, multicentre, validation study compared the CovidCalculatorUKs estimated probability of Covid-19 with the first SARS-CoV2 oropharyngeal/nasopharyngeal swab result for individual patients admitted to hospital during the study period (01.04.20 - 18.05.20). A comparison with senior clinicians estimates of the probability of Covid-19 was also made.\n\nResultsPatients who were prospectively grouped, by the CovidCalculatorUK, into 0-30% estimated probability, 30-60% and 60-100% estimated probability went on to have first swab SARS-CoV2 positive results in: 15.7%, 30.5% and 61.9% of cases, respectively. CovidCalculatorUK performance demonstrated an area under the curve of 0.76 (95% CI 0.71 - 0.81) (p < 0.001). Senior clinician stratification of the estimated probability of Covid-19 performed similarly to the CovidCalculatorUK.\n\nConclusionThe CovidCalculatorUK provides a reasonably accurate estimate of the probability of an individual testing positive on their first SARS-CoV2 nasopharyngeal/oropharyngeal swab. The CovidCalculatorUK output performs similarly to a senior clinicians estimate. Further evolution of the calculator may improve performance.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "George A Chapman", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Lewis Mundell", + "author_inst": "Lanarkshire NHS Trust" + }, + { + "author_name": "Charlotte H Harrison", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Tamsin Cargill", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Odhran Keating", + "author_inst": "Buckinghamshire Healthcare NHS Trust" + }, + { + "author_name": "Mark Johnson", + "author_inst": "Buckinghamshire Healthcare NHS Trust" + }, + { + "author_name": "Andrew Smith", + "author_inst": "Lanarkshire NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.06.20244756", "rel_title": "Comparing Decision Tree-Based Ensemble Machine Learning Models for COVID-19 Death Probability Profiling", @@ -1056674,65 +1060083,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.12.07.415216", - "rel_title": "Engineered receptor binding domain immunogens elicit pan-coronavirus neutralizing antibodies", - "rel_date": "2020-12-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.07.415216", - "rel_abs": "Effective countermeasures are needed against emerging coronaviruses of pandemic potential, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Designing immunogens that elicit broadly neutralizing antibodies to conserved viral epitopes on the major surface glycoprotein, spike, such as the receptor binding domain (RBD) is one potential approach. Here, we report the generation of homotrimeric RBD immunogens from different sarbecoviruses using a stabilized, immune-silent trimerization tag. In mice, we find that a cocktail of these homotrimeric sarbecovirus RBDs elicits antibodies to conserved viral epitopes outside of the ACE2 receptor binding motif (RBM). Importantly, these responses neutralize all sarbecovirus components even in context of prior SARS-CoV-2 imprinting. We further show that a substantial fraction of the neutralizing antibodies elicited after vaccination in humans also engages non-RBM epitopes on the RBD. Collectively, our results suggest a strategy for eliciting broadly neutralizing responses leading to a pan-sarbecovirus vaccine.\n\nAuthor summaryImmunity to SARS-CoV-2 in the human population will be widespread due to natural infection and vaccination. However, another novel coronavirus will likely emerge in the future and may cause a subsequent pandemic. Humoral responses induced by SARS-CoV-2 infection and vaccination provide limited protection against even closely related coronaviruses. We show immunization with a cocktail of trimeric coronavirus receptor binding domains induces a neutralizing antibody response that is broadened to related coronaviruses with pandemic potential. Importantly, this broadening occurs in context of an initial imprinted SARS-CoV-2 spike immunization showing that preexisting immunity can be expanded to recognize other related coronaviruses. Our immunogens focused the serum antibody response to conserved epitopes on the receptor binding domain outside of the ACE2 receptor binding motif; this contrasts with current SARS-CoV-2 therapeutic antibodies, which predominantly target the receptor binding motif.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Blake M. Hauser", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Maya Sangesland", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Evan C. Lam", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Kerri J. St. Denis", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Jared Feldman", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Ashraf S. Yousif", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Timothy M. Caradonna", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Ty Kannegieter", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Alejandro Benjamin Balazs", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Daniel Lingwood", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "Ragon Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.07.415422", "rel_title": "Circular RNA profiling reveals abundant and diverse circRNAs of SARS-CoV-2, SARS-CoV and MERS-CoV origin", @@ -1057523,6 +1060873,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.12.05.20244426", + "rel_title": "Exploring drugs and vaccines associated with altered risks and severity of COVID-19: a UK Biobank cohort study of all ATC level-4 drug categories", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244426", + "rel_abs": "BackgroundCOVID-19 is a major public health concern, yet its risk factors are not well-understood and effective therapies are lacking. It remains unclear how different drugs may increase or decrease the risks of infection and severity of disease.\n\nMethodsWe studied associations of prior use of all level-4 ATC drug categories (including vaccines) with COVID-19 diagnosis and outcome, based on a prospective cohort of UK Biobank(UKBB). Drug history was based on general practitioner(GP) records. Effects of prescribed medications/vaccinations on the risk of infection, severity of disease and mortality were investigated separately. Hospitalized and fatal cases were categorized as severe infection. We also considered different study designs and conducted analyses within infected patients, tested subjects and the whole population respectively, and for 5 different time-windows of prescriptions. Missing data were accounted for by multiple imputation and inverse probability weighting was employed to reduce testing bias. Multivariable logistic regression was conducted which controls for main confounders.\n\nResultsWe placed a greater focus on protective associations here, as (residual) confounding by indication and comorbidities tends to bias towards harmful effects. Across all categories, statins showed the strongest and most consistent protective associations. Significant protective effects against severe infection were seen among infected subjects (OR for prescriptions within a 12-month window, same below: 0.50, 95% CI:0.42-0.60), tested subjects (OR=0.63, 0.54-0.73) or in the general population (OR=0.49, 0.42-0.57). A number of top-listed drugs with protective effects were also cardiovascular medications, such as angiotensin converting enzyme inhibitors, angiotensin receptor blockers, calcium channel blocker and beta-blockers. Some other drugs showing protective associations included biguanides (metformin), estrogens, thyroid hormones and proton pump inhibitors, among others.\n\nInterestingly, we also observed protective associations by numerous vaccines. The most consistent association was observed for influenza vaccines, which showed reduced odds of infection (OR= 0.73 for vaccination in past year, CI 0.65-0.83) when compared cases to general population controls or test-negative controls (OR=0.60, 0.53-0.68). Protective associations were also observed when severe or fatal infection was considered as the outcome. Pneumococcal, tetanus, typhoid and combined bacterial and viral vaccines (ATC code J07CA) were also associated with lower odds of infection/severity.\n\nFurther subgroup and interaction analyses revealed difference in protective effects in different clinical subgroups. For example, protective effects of flu and pneumococcal vaccines were weaker in obese individuals, while we observed stronger protective effects of statins in those with cardiometabolic disorders, such as diabetes, coronary artery disease, hypertension and obesity.\n\nConclusionsA number of drugs, including many for cardiometabolic disorders, may be associated with lower odds of infection/severity of infection. Several existing vaccines, especially flu vaccines, may be beneficial against COVID-19 as well. However, causal relationship cannot be established due to risk of confounding. While further studies are required to validate the findings, this work provides a useful reference for future meta-analyses, clinical trials or experimental studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yong XIANG", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kenneth Chi-Yin WONG", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Hon-Cheong SO", + "author_inst": "Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2020.12.04.20244327", "rel_title": "COVID-19 RELATED IMMUNIZATION DISRUPTIONS IN RAJASTHAN, INDIA: A RETROSPECTIVE OBSERVATIONAL STUDY", @@ -1058111,41 +1061488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.07.20244681", - "rel_title": "Diagnostic and monitoring utilities of saliva for SARS-CoV-2", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20244681", - "rel_abs": "IntroductionNasopharyngeal (NP) swab is an invasive procedure that is difficult to perform in pediatric cases and those with special needs. On the other hand, saliva has been a proposed sample given the ease of collection, comfort and the ability to self-collect. The research project aims to study the presence of SARS-CoV-2 in the saliva of suspected COVID-19 patients in comparison to its presence in NP swabs.\n\nMethodologyA cross-sectional study was conducted in October 2020 in COVID19 clinic in the Bahrain Defense Force Hospital. The study compared the presence of SARS-CoV2 by PCR in saliva samples to nasopharyngeal samples. COVID-19 Clinic tests symptomatic, staff, close contacts and pre-operation patients.\n\nResultsThe saliva PCR has shown a sensitivity of 72.9% (95% CI: 58.2% - 84.7%) and a specificity of 98.8% (95% CI: 97.8% - 99.4%). The PPV was 74.5% (95% CI 59.7% to 86.1%) and the NPV was 98.6% (95% CI 97.7% to 99.3%). Kappa coefficient of agreement between saliva and NP was 0.723 (95% CI 0.62 to 0.82, p<0.001). Moreover, when restricting cases to symptomatic only, the sensitivity of saliva increased to 86.7% (95% CI 59.5% to 98.3%) while specificity remained high at 97.2%.\n\nConclusionThe findings of the study suggest that saliva samples have the potential to be used as a screening tool for SARS-CoV-2, especially in symptomatic individuals. This is especially important when it is difficult to collect NP samples. Saliva samples are however at risk of producing more false negative tests.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Abdulkarim Abdulrahman", - "author_inst": "National Taskforce for Combating the Coronavirus (COVID-19), Bahrain ; Mohammed Bin Khalifa Cardiac Centre, Bahrain" - }, - { - "author_name": "Ahmed Albastaki", - "author_inst": "King Hamad University hospital" - }, - { - "author_name": "Abdulla Ismael AlAwadhi", - "author_inst": "National Taskforce for Combating the Coronavirus (COVID-19), Bahrain ; Bahrain Defence Force hospital, Bahrain" - }, - { - "author_name": "Asma AlWazzan", - "author_inst": "Bahrain Defence Force hospital, Bahrain" - }, - { - "author_name": "Manaf AlQahtani", - "author_inst": "Royal College of Surgeons in Ireland, Bahrain ; National Taskforce for Combating the Coronavirus (COVID-19), Bahrain ; Bahrain Defence Force hospital, Bahrain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.05.20244541", "rel_title": "IgG Antibodies against SARS-CoV-2 Correlate with Days from Symptom Onset, Viral Load and IL-10", @@ -1058981,6 +1062323,73 @@ "type": "contradictory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.06.413443", + "rel_title": "Efficient inhibition of SARS-CoV-2 strains by a novel ACE2-IgG4-Fc fusion protein with a stabilized hinge region", + "rel_date": "2020-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.06.413443", + "rel_abs": "The novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) enters its host cells after binding to the angiotensin-converting enzyme 2 (ACE2) via its spike glycoprotein. This interaction is critical for virus entry and virus-host membrane fusion. Soluble ACE2 ectodomains bind and neutralize the virus but the short in vivo half-lives of soluble ACE2 limits its therapeutic use. Fusion of the fragment crystallizable (Fc) part of human immunoglobulin G (IgG) to the ACE2 ectodomain can prolong the in vivo half-life but bears the risk of unwanted Fc-receptor activation and antibody-dependent disease enhancement. Here, we describe optimized ACE2-Fc fusion constructs that avoid Fc-receptor binding by using IgG4-Fc as a fusion partner. The engineered ACE2-IgG4-Fc fusion proteins described herein exhibit promising pharmaceutical properties and a broad antiviral activity at single-digit nanomolar concentration. In addition, they allow to maintain the beneficial enzymatic activity of ACE2 and thus are very promising candidate antivirals broadly acting against coronaviruses.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Hristo L Svilenov", + "author_inst": "Department of Chemistry, Technical University of Munich, Garching, Germany" + }, + { + "author_name": "Julia Sacherl", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + }, + { + "author_name": "Alwin Reiter", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Lisa Wolff", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + }, + { + "author_name": "Cho-Chin Chen", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany / German Center for Infection Research, Munich partner site, M" + }, + { + "author_name": "Marcel Stern", + "author_inst": "Max von Pettenkofer Institute & Gene Center, Virology, LMU Muenchen, Munich, Germany / German Center for Infection Research, Munich partner site, Munich, German" + }, + { + "author_name": "Frank-Peter Wachs", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Nicole Simonavicius", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Susanne Pippig", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Florian Wolschin", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Johannes Buchner", + "author_inst": "Department of Chemistry, Technical University of Munich, Garching, Germany" + }, + { + "author_name": "Carsten Brockmeyer", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Ulrike Protzer", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.06.412759", "rel_title": "The new generation hDHODH inhibitor MEDS433 hinders the in vitro replication of SARS-CoV-2", @@ -1059817,49 +1063226,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.12.02.20234989", - "rel_title": "Unraveling US National COVID-19 Racial/Ethnic Disparities using County Level Data Among 328 Million Americans", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20234989", - "rel_abs": "Identifying areas with high COVID-19 burden and their characteristics can help improve vaccine distribution and uptake, reduce burdens on health care systems, and allow for better allocation of public health intervention resources. Synthesizing data from various government and nonprofit institutions of 3,142 United States (US) counties as of 12/21/2020, we studied county-level characteristics that are associated with cumulative case and death rates using regression analyses. Our results showed counties that are more rural, counties with more White/non-White segregation, and counties with higher percentages of people of color, in poverty, with no high school diploma, and with medical comorbidities such as diabetes and hypertension are associated with higher cumulative COVID-19 case and death rates. We identify the hardest hit counties in US using model-estimated case and death rates, which provide more reliable estimates of cumulative COVID-19 burdens than those using raw observed county-specific rates. Identification of counties with high disease burdens and understanding the characteristics of these counties can help inform policies to improve vaccine distribution, deployment and uptake, prevent overwhelming health care systems, and enhance testing access, personal protection equipment access, and other resource allocation efforts, all of which can help save more lives for vulnerable communities.\n\nSignificance statementWe found counties that are more rural, counties with more White/non-White segregation, and counties with higher percentages of people of color, in poverty, with no high school diploma, and with medical comorbidities such as diabetes and hypertension are associated with higher cumulative COVID-19 case and death rates. We also identified individual counties with high cumulative COVID-19 burden. Identification of counties with high disease burdens and understanding the characteristics of these counties can help inform policies to improve vaccine distribution, deployment and uptake, prevent overwhelming health care systems, and enhance testing access, personal protection equipment access, and other resource allocation efforts, all of which can help save more lives for vulnerable communities.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniel Li", - "author_inst": "Harvard. T.H. Chan School of Public Health" - }, - { - "author_name": "Sheila M. Gaynor", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Corbin Quick", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Jarvis T. Chen", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Briana J.K. Stephenson", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Brent A. Coull", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Xihong Lin", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.01.20241364", "rel_title": "Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity", @@ -1060851,6 +1064217,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.02.20242925", + "rel_title": "Mapping each pre-existing conditions association to short-term and long-term COVID-19 complications", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242925", + "rel_abs": "Understanding the relationships between pre-existing conditions and complications of COVID-19 infection is critical to identifying which patients will develop severe disease. Here, we leverage 1.1 million clinical notes from 1,903 hospitalized COVID-19 patients and deep neural network models to characterize associations between 21 pre-existing conditions and the development of 20 complications (e.g. respiratory, cardiovascular, renal, and hematologic) of COVID-19 infection throughout the course of infection (i.e. 0-30 days, 31-60 days, and 61-90 days). Pleural effusion was the most frequent complication of early COVID-19 infection (23% of 383 complications) followed by cardiac arrhythmia (12% of 383 complications). Notably, hypertension was the most significant risk factor associated with 10 different complications including acute respiratory distress syndrome, cardiac arrhythmia and anemia. Furthermore, novel associations between cancer (risk ratio: 3, p=0.02) or immunosuppression (risk ratio: 4.3, p=0.04) with early-onset heart failure have also been identified. Onset of new complications after 30 days is rare and most commonly involves pleural effusion (31-60 days: 24% of 45 patients, 61-90 days: 25% of 36 patients). Overall, the associations between pre-COVID conditions and COVID-associated complications presented here may form the basis for the development of risk assessment scores to guide clinical care pathways.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Colin Pawlowski", + "author_inst": "nference" + }, + { + "author_name": "David Zemmour", + "author_inst": "nference" + }, + { + "author_name": "Travis Hughes", + "author_inst": "nference" + }, + { + "author_name": "Akash Anand", + "author_inst": "nference Labs" + }, + { + "author_name": "Gabriela Berner", + "author_inst": "nference" + }, + { + "author_name": "Nikhil Kayal", + "author_inst": "nference" + }, + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Ian Conrad", + "author_inst": "nference" + }, + { + "author_name": "Sairam Bade", + "author_inst": "nference Labs" + }, + { + "author_name": "Rakesh Barve", + "author_inst": "nference Labs" + }, + { + "author_name": "Purushottam Sinha", + "author_inst": "nference Labs" + }, + { + "author_name": "Jack O'Horo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.02.20242958", "rel_title": "Longitudinal lab test analysis confirms pre-existing anemia as a severe risk factor for post-viral clearance hospitalization in COVID-19 patients", @@ -1061623,57 +1065064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.03.20243162", - "rel_title": "Tolerability and Pharmacokinetic Evaluation of Inhaled Dry Powder Hydroxychloroquine in Healthy Volunteers", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243162", - "rel_abs": "RationaleInhaled antimicrobials enable high local concentrations where needed and, compared to orally administration, greatly reduce the potential for systemic side effects. In SARS-CoV-2 infections, hydroxychloroquine (HCQ) administered as dry powder via inhalation could be safer than oral HCQ allowing for higher and therefore more effective pulmonary concentrations without dose limiting toxic effects.\n\nObjectivesTo assess the local tolerability, safety and pharmacokinetic parameters of HCQ inhalations in single ascending doses of 5, 10 and 20 mg using the Cyclops dry powder inhaler.\n\nMethods12healthy volunteers were trained in inhaling HCQ correctly. Local tolerability and safety were assessed by pulmonary function tests, ECG and recording adverse events. To estimate systemic exposure, serum samples were collected before and 0.5, 2 and 3.5 h after inhalation.\n\nResults and discussionDry powder HCQ inhalations were well tolerated by the participants, except for transient bitter taste in all participants and minor coughing irritation. There was no significant change in QTc-interval or drop in FEV1 post inhalation. The serum HCQ concentration remained below 10 {micro}g/L in all samples.\n\nConclusionInhaled dry powder HCQ is safe and well tolerated. Our data support further studies with inhaled HCQ dry powder to evaluate pulmonary pharmacokinetics and efficacy is warranted.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yvette de Reus", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Paul Hagedoorn", - "author_inst": "University of Groningen" - }, - { - "author_name": "Marieke Sturkenboom", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Floris Grasmeijer", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Mathieu Bolhuis", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Imco Sibum", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Huib Kerstjens", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "Erik Frijlink", - "author_inst": "University of Groningen" - }, - { - "author_name": "Onno Akkerman", - "author_inst": "University Medical Center Groningen" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.03.20239863", "rel_title": "Detailed disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic: An exploratory analysis", @@ -1062505,6 +1065895,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.12.03.20239681", + "rel_title": "Spatial risk factors for Pillar 1 COVID-19 case counts and mortality in rural eastern England, UK", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20239681", + "rel_abs": "Understanding is still developing about risk factors for COVID-19 infection or mortality. This is especially true with respect to identifying spatial risk factors and therefore identifying which geographic areas have populations who are at greatest risk of acquiring severe disease. This is a secondary analysis of patient records in a confined area of eastern England, covering persons who tested positive for SARS-CoV-2 through end May 2020, including dates of death and residence area. For each residence area (local super output area), we obtained data on air quality, deprivation levels, care home bed capacity, age distribution, rurality, access to employment centres and population density. We considered these covariates as risk factors for excess cases and excess deaths in the 28 days after confirmation of positive covid status relative to the overall case load and death recorded for the study area as a whole. We used the conditional autoregressive Besag-York-Mollie model to investigate the spatial dependency of cases and deaths allowing for a Poisson error structure. Structural equation models were also applied to clarify relationships between predictors and outcomes. Excess case counts or excess deaths were both predicted by the percentage of population age 65 years, care home bed capacity and less rurality: older population and more urban areas saw excess cases. Greater deprivation did not correlate with excess case counts but was significantly linked to higher mortality rates after infection. Neither excess cases nor excess deaths were predicted by population density, travel time to local employment centres or air quality indicators. Only 66% of mortality could be explained by locally high case counts. The results show a clear link between greater deprivation and higher COVID-19 mortality that is separate from wider community prevalence and other spatial risk factors.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Julii S Brainard", + "author_inst": "university of east anglia" + }, + { + "author_name": "Steve Rushton", + "author_inst": "Newcastle University" + }, + { + "author_name": "Tim Winters", + "author_inst": "Norfolk County Council" + }, + { + "author_name": "Paul R Hunter", + "author_inst": "University of East Anglia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.03.20243535", "rel_title": "OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England", @@ -1063353,41 +1066774,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.12.01.20241588", - "rel_title": "The Impact of Coronavirus Disease 2019 Pandemic on People with Diabetes in Indonesia: A Cross Sectional National Scale Web-Survey", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241588", - "rel_abs": "BackgroundAs the country with the 7th largest number of People with Diabetes (PWD) in the world, the COVID-19 pandemic, and the Large Social Scale Restriction (LSSR) policy taken by the Indonesian government to reduce the number of COVID-19 transmissions is estimated to interfere diabetes management and will increase the incidence of diabetes complications. This study aims to determine the difficulties of diabetes management and its impact on diabetes morbidity during the COVID-19 pandemic in Indonesia.\n\nMethodologyThis study is a cross-sectional study using a national scale web survey. This research was conducted in Indonesia enrolling 1,124 PWD aged 18 years or older. Diabetes complications are defined as any incidence of hypoglycaemia, or Diabetic Foot Ulcer (DFU), or hospital admission experienced by PWD in Indonesia during the COVID-19 pandemic. The correlation between diabetes management difficulties and diabetes-related complications was measured using a modified cox regression test.\n\nResultsDiabetes management difficulties were experienced by 69.8% of PWD in Indonesia. The difficulties include attending diabetes consultation 30.1%, access to diabetes medication 12.4%, checking blood sugar levels 9.5%, controlling diet 23.8%, and performing regular exercise 36.5%. Diabetes-related complications occurred in 24.6% of subjects. Those who had diabetes management difficulties during the COVID-19 pandemic are prone to have diabetes complications by 1.4 times greater (PR: 1.41, 95% CI: 1.09-1.83) than those who did not.\n\nConclusionThe COVID-19 pandemic and LSSR have a substantial impact on diabetes management and indirectly increased diabetes morbidity in Indonesia.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ida Ayu Kshanti", - "author_inst": "Division of Endocrinology, Metabolism and Diabetes, Department of Internal Medicine, Fatmawati General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Marina Epriliawati", - "author_inst": "Division of Endocrinology, Metabolism and Diabetes, Department of Internal Medicine, Fatmawati General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Md Ikhsan Mokoagow", - "author_inst": "Division of Endocrinology, Metabolism and Diabetes, Department of Internal Medicine, Fatmawati General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Jerry Nasarudin", - "author_inst": "Division of Endocrinology, Metabolism and Diabetes, Department of Internal Medicine, Fatmawati General Hospital, Jakarta, Indonesia" - }, - { - "author_name": "Nadya Magfira", - "author_inst": "Diabetes Integrated Care Center, Fatmawati General Hospital, Jakarta, Indonesia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.12.01.20242099", "rel_title": "Is the end near? When the different countries will surmount COVID-19 pandemic: new approach applying physical, mathematical and game theory models.", @@ -1064051,6 +1067437,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.01.20241885", + "rel_title": "Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241885", + "rel_abs": "The Covid-19 disease has caused a world-wide pandemic with more than 60 million positive cases and more than 1.4 million deaths by the end of November 2020. As long as effective medical treatment and vaccination are not available, non-pharmaceutical interventions such as social distancing, self-isolation and quarantine as well as far-reaching shutdowns of economic activity and public life are the only available strategies to prevent the virus from spreading. These interventions must meet conflicting requirements where some objectives, like the minimization of disease-related deaths or the impact on health systems, demand for stronger counter-measures, while others, such as social and economic costs, call for weaker counter-measures. Therefore, finding the optimal compromise of counter-measures requires the solution of a multi-objective optimization problem that is based on accurate prediction of future infection spreading for all combinations of counter-measures under consideration. We present a strategy for construction and solution of such a multi-objective optimization problem with real-world applicability. The strategy is based on a micro-model allowing for accurate prediction via a realistic combination of person-centric data-driven human mobility and behavior, stochastic infection models and disease progression models including micro-level inclusion of governmental intervention strategies. For this micro-model, a surrogate macro-model is constructed and validated that is much less computationally expensive and can therefore be used in the core of a numerical solver for the multi-objective optimization problem. The resulting set of optimal compromises between counter-measures (Pareto front) is discussed and its meaning for policy decisions is outlined.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hanna Wulkow", + "author_inst": "Zuse Institute Berlin" + }, + { + "author_name": "Tim Conrad", + "author_inst": "Zuse Institute Berlin and Freie Universitaet Berlin" + }, + { + "author_name": "Natasa Djurdjevac Conrad", + "author_inst": "Zuse Institute Berlin" + }, + { + "author_name": "Sebastian Alexander Mueller", + "author_inst": "TU Berlin" + }, + { + "author_name": "Kai Nagel", + "author_inst": "TU Berlin" + }, + { + "author_name": "Christof Schuette", + "author_inst": "FU Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.01.20242289", "rel_title": "The COVID-19 herd immunity threshold is not low: A re-analysis of European data from spring of 2020", @@ -1064607,185 +1068032,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.12.03.409318", - "rel_title": "A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients by phage display is binding to the ACE2-RBD interface and is tolerant to known RBD mutations", - "rel_date": "2020-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.03.409318", - "rel_abs": "The novel betacoranavirus SARS-CoV-2 causes a form of severe pneumonia disease, termed COVID-19 (coronavirus disease 2019). Recombinant human antibodies are proven potent neutralizers of viruses and can block the interaction of viral surface proteins with their host receptors. To develop neutralizing anti-SARS-CoV-2 antibodies, antibody gene libraries from convalescent COVID-19 patients were constructed and recombinant antibody fragments (scFv) against the receptor binding domain (RBD) of the S1 subunit of the viral spike (S) protein were selected by phage display. The selected antibodies were produced in the scFv-Fc format and 30 showed more than 80% inhibition of spike (S1-S2) binding to cells expressing ACE2, assessed by flow cytometry screening assay. The majority of these inhibiting antibodies are derived from the VH3-66 V-gene. The antibody STE90-C11 showed a sub nM IC50 in a plaque-based live SARS-CoV-2 neutralization assay. The in vivo efficacy of the antibody was demonstrated in the Syrian hamster and in the hACE2 mice model using a silenced human IgG1 Fc part. The crystal structure of STE90-C11 Fab in complex with SARS-CoV-2-RBD was solved at 2.0 [A] resolution showing that the antibody binds at the same region as ACE2 to RBD. The binding and inhibtion of STE90-C11 is not blocked by many known RBD mutations including N439K, L452R, E484K or L452R+E484Q (emerging B.1.617). STE90-C11 derived human IgG1 with Fc{gamma}R silenced Fc (COR-101) is currently undergoing Phase Ib/II clinical trials for the treatment of moderate to severe COVID-19.\n\nIn BriefHuman antibodies were selected from convalescent COVID-19 patients using antibody phage display. The antibody STE90-C11 is neutralizing authentic SARS-CoV-2 virus in vitro and in vivo and the crystal structure of STE90-C11 in complex with SARS-CoV-2-RBD revealed that this antibody is binding in the RBD-ACE2 interface. S1 binding of STE90-C11 and inhibition of ACE2 binding is not blocked by many known RBD mutations.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Federico Bertoglio", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Viola F\u00fchner", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Maximilian Ruschig", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Philip Alexander Heine", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Leila Abasi", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Thomas Kl\u00fcnemann", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Ulfert Rand", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Doris Meier", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Nora Langreder", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Stephan Steinke", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Rico Ballmann", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Kai-Thomas Schneider", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Kristian Daniel Ralph Roth", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Philipp Kuhn", - "author_inst": "YUMAB GmbH" - }, - { - "author_name": "Peggy Riese", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Dorina Sch\u00e4ckermann", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Janin Korn", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Allan Koch", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "M. Zeeshan Chaudhry", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Kathrin Eschke", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Yeonsu Kim", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Susanne Zock-Emmenthal", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Marlies Becker", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Margitta Scholz", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Gustavo Mar\u00e7al Schmidt Garcia Moreira", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Esther Veronika Wenzel", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Giulio Russo", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Hendrikus S.P. Garritsen", - "author_inst": "St\u00e4dtisches Klinikum Braunschweig" - }, - { - "author_name": "Sebastian Casu", - "author_inst": "Helios Klinikum Salzgitter" - }, - { - "author_name": "Andreas Gerstner", - "author_inst": "St\u00e4dtisches Klinikum Braunschweig" - }, - { - "author_name": "G\u00fcnter Roth", - "author_inst": "BioCopy GmbH" - }, - { - "author_name": "Julia Adler", - "author_inst": "Institute of Virology, Freie Universitaet Berlin" - }, - { - "author_name": "Jakob Trimpert", - "author_inst": "Institute of Virology, Freie Universitaet Berlin" - }, - { - "author_name": "Andreas Hermann", - "author_inst": "CORAT Therapeutics GmbH" - }, - { - "author_name": "Thomas Schirrmann", - "author_inst": "YUMAB GmbH" - }, - { - "author_name": "Stefan D\u00fcbel", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Andr\u00e9 Frenzel", - "author_inst": "YUMAB GmbH" - }, - { - "author_name": "Joop Van den Heuvel", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Luka Cicin-Sain", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Maren Schubert", - "author_inst": "TU Braunschweig" - }, - { - "author_name": "Michael Hust", - "author_inst": "TU Braunschweig" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.12.02.409037", "rel_title": "SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, Sao Paulo, Parana and Tocantins", @@ -1065537,6 +1068783,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.12.01.20241570", + "rel_title": "The Acceleration Index as a Test-Controlled Reproduction Number: Application to COVID-19 in France", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241570", + "rel_abs": "We provide a novel way to correct the effective reproduction number for the time-varying amount of tests, using the acceleration index (Baunez et al., 2021) as a simple measure of viral spread dynamics. Not correcting results in the reproduction number being a biased estimate of viral acceleration and we provide a formal decomposition of the resulting bias, involving the useful notions of test and infectivity intensities. When applied to French data for the COVID-19 pandemic (May 13, 2020 - October 26, 2022), our decomposition shows that the reproduction number, when considered alone, characteristically underestimates the resurgence of the pandemic, compared to the acceleration index which accounts for the time-varying volume of tests. Because the acceleration index aggregates all relevant information and captures in real time the sizable time variation featured by viral circulation, it is a more parsimonious indicator to track the dynamics of an infectious disease outbreak in real time, compared to the equivalent alternative which would combine the reproduction number with the test and infectivity intensities.\n\nJEL Classification NumbersI18; H12", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Christelle Baunez", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Mickael Degoulet", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille School of Economics" + }, + { + "author_name": "Matteo Louis Pintus", + "author_inst": "AgroParisTech" + }, + { + "author_name": "Patrick Pintus", + "author_inst": "Aix-Marseille University and CNRS" + }, + { + "author_name": "Miriam Teschl", + "author_inst": "Aix-Marseille School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.11.30.20240986", "rel_title": "A Net Benefit Approach for the Optimal Allocation of a COVID-19 Vaccine", @@ -1066217,33 +1069502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.11.30.20241166", - "rel_title": "Social network-based strategies for classroom size reduction can help limit outbreaks of SARS-CoV-2 in high schools. A simulation study in classrooms of four European countries.", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241166", - "rel_abs": "Dividing classrooms may reduce the risk of SARS-CoV-2 outbreaks in schools. We investigate how classroom cohorting strategies, which downsize and isolate groups, may curb the spread of SARS-CoV-2. Using agent-based modelling based on a rich multi-country network dataset comprising 507 classrooms and 12,291 students, we assess random cohorting and three network-based strategies that consider students out-of-school contacts with classmates. Investigating effects on the number of cross-cohort transmissions, overall infections, and quarantines, our findings suggest that all cohorting strategies help to contain outbreaks, but that minimizing out-of-school contact between cohorts is most effective. Since this strategy may be hard to implement in practice, we show that a network chain nomination procedure and splitting classes by gender, both of which are easier to realize, also outperform random cohorting considerably. For all cohorting strategies, we find that rota-systems with instruction in alternating weeks contain outbreaks more effectively than same-day in-person instruction.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anna Karoline Kaiser", - "author_inst": "Affiliated Researcher INCITE, Columbia University" - }, - { - "author_name": "David Kretschmer", - "author_inst": "Mannheim Centre for European Social Research, University of Mannheim" - }, - { - "author_name": "Lars Leszczensky", - "author_inst": "Mannheim Centre for European Social Research, University of Mannheim" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.30.20241331", "rel_title": "Serological prevalence of SARS-CoV-2 infection and associated factors in health care workers in a \"non-COVID\" hospital in Mexico City", @@ -1067163,6 +1070421,137 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.12.01.405738", + "rel_title": "Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples", + "rel_date": "2020-12-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.405738", + "rel_abs": "BackgroundSARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution.\n\nResultsWe used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020.\n\nConclusionsWe present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Slawomir Kubik", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Ana Claudia Marques", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Xiaobin Xing", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Janine Silvery", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Claire Bertelli", + "author_inst": "Genomics and Metagenomics Laboratory, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland" + }, + { + "author_name": "Flavio De Maio", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Universita Cattolica del Sacro Cuore, L.go Agostino Gemelli 8, 00168 Roma, Italy" + }, + { + "author_name": "Spyros Pournaras", + "author_inst": "Laboratory of Clinical Microbiology, Attikon University Hospital Medical School, National and Kapodistrian University of Athens, Athens, Rimini 1, Chaidari 124 " + }, + { + "author_name": "Tom Burr", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Yannis Duffourd", + "author_inst": "Equipe GAD - Inserm U1231, CHU Francois Mitterrand; 21000 Dijon, France" + }, + { + "author_name": "Helena Siemens", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Chakib Alloui", + "author_inst": "Laboratoire de Virologie, CHU Avicenne, AP-HP, 93000 Bobigny, France" + }, + { + "author_name": "Lin Song", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Yvan Wenger", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Alexandra Saitta", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Morgane Macheret", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Ewan W Smith", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Philippe Menu", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Marion Brayer", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Lars M Steinmetz", + "author_inst": "Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA" + }, + { + "author_name": "Ali Si-Mohammed", + "author_inst": "Laboratoire de Virologie, CHU Francois Mitterrand; 2, rue Angelique Ducoudray, 2100 Dijon, France" + }, + { + "author_name": "Josiane Chuisseu", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Richard Stevens", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Pantelis Constantoulakis", + "author_inst": "BioAnalytica Genotypos SA, 3-5 Ilision str, 115 28 Athens, Greece" + }, + { + "author_name": "Michela Sali", + "author_inst": "Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Universita Cattolica del Sacro Cuore, Ro" + }, + { + "author_name": "Gilbert Greub", + "author_inst": "Genomics and Metagenomics Laboratory, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland" + }, + { + "author_name": "Carsten Tiemann", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Vicent Pelechano", + "author_inst": "SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden" + }, + { + "author_name": "Adrian Willig", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Zhenyu Xu", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.11.30.405340", "rel_title": "Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2", @@ -1068279,105 +1071668,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.25.20235150", - "rel_title": "T cell and antibody functional correlates of severe COVID-19", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20235150", - "rel_abs": "Comorbid medical illnesses, such as obesity and diabetes, are associated with more severe COVID-19, hospitalization, and death. However, the role of the immune system in mediating these clinical outcomes has not been determined. We used multi-parameter flow cytometry and systems serology to comprehensively profile the functions of T cells and antibodies targeting spike, nucleocapsid, and envelope proteins in a convalescent cohort of COVID-19 subjects who were either hospitalized (n=20) or not hospitalized (n=40). To avoid confounding, subjects were matched by age, sex, ethnicity, and date of symptom onset. Surprisingly, we found that the magnitude and functional breadth of virus-specific CD4 T cell and antibody responses were consistently higher among hospitalized subjects, particularly those with medical comorbidities. However, an integrated analysis identified more coordination between polyfunctional CD4 T-cells and antibodies targeting the S1 domain of spike among subjects that were not hospitalized. These data reveal a functionally diverse and coordinated response between T cells and antibodies targeting SARS-CoV-2 which is reduced in the presence of comorbid illnesses that are known risk factors for severe COVID-19. Our data suggest that isolated measurements of the magnitudes of spike-specific immune responses are likely insufficient to anticipate vaccine efficacy in high-risk populations.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Krystle K.Q. Yu", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Stephanie Fischinger", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Boston, MA PhD program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany" - }, - { - "author_name": "Malisa T. Smith", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Caroline Atyeo", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA PhD program in Virology, Division of Medical Sciences, Harvard University, Boston, MA" - }, - { - "author_name": "Deniz Cizmeci", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Boston, MA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA" - }, - { - "author_name": "Caitlin R. Wolf", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Erik D. Layton", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Jennifer K. Logue", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Melissa S. Aguilar", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Kiel Shuey", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Carolin Loos", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Boston, MA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA" - }, - { - "author_name": "Jingyou Yu", - "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA" - }, - { - "author_name": "Nicholas Franko", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Robert Y. Choi", - "author_inst": "Providence Medical Group, Everett, WA" - }, - { - "author_name": "Anna Wald", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Dan H. Barouch", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Boston, MA Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Bost" - }, - { - "author_name": "David M. Koelle", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Douglas Lauffenburger", - "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA" - }, - { - "author_name": "Helen Y. Chu", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Boston, MA" - }, - { - "author_name": "Chetan Seshadri", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle, WA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.25.20238915", "rel_title": "Alcohol Consumption is Associated with Poor Prognosis in Obese Patients with COVID-19: a Mendelian Randomization Study using UK Biobank", @@ -1069205,6 +1072495,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.11.26.20239103", + "rel_title": "I'm alone but not lonely. U-shaped pattern of perceived loneliness during the COVID-19 pandemic in the UK and Greece", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239103", + "rel_abs": "Many countries have adopted lengthy lockdown measures to mitigate the spreading of the COVID-19 virus. In this study, we train a RandomForest model using 10 variables quantifying individuals living environment, physical and mental health statuses to predict how long each of the UK participants (N=382) had been in lockdown. Self-perceived loneliness was found to be the most important variable predicting time in lockdown and, therefore, the aspect most influenced by the time the participant spent in lockdown. Subsequent statistical analysis showed a significant U-shaped curve for the levels of perceived loneliness (p<0.012), specifically decreasing during the 4th and 5th lockdown weeks. The same pattern was found on data from Greek citizens (N=129, p<0.041). These results suggest that lockdown measures may have affected how people evaluated their social support while in lockdown, leading to a decreased sense of loneliness. Implications of this study should be reflected on policies and countermeasures to current and future pandemics.\n\nState of relevanceThis study aims to inform policies for the current and/or future pandemics, particularly those involving lockdown restrictions. It highlights that self-perceived loneliness was the trait most affected by the time spent in lockdown: data show that the very first period of lockdown was characterised by a decrease in levels of perceived loneliness. The machine learning approach adopted and the statistical validation on two different Western European countries ensure that the uncovered pattern is substantial. This result highlights the dissociation between objective social support and perceived loneliness: initially, restrictions may have triggered better social behaviours among communities or increased the level of gratitude for the social support people have always received. The short duration of these desirable effects suggests that measures and campaigns promoting better social support strategies could be potentially effective, even in social isolation, to keep the levels of perceived loneliness low.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alessandro Carollo", + "author_inst": "University of Trento" + }, + { + "author_name": "Andrea Bizzego", + "author_inst": "University of Trento" + }, + { + "author_name": "Giulio Gabrieli", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Keri Ka-Yee Wong", + "author_inst": "Department of Psychology and Human Development, University College London, London, UK" + }, + { + "author_name": "Adrian Raine", + "author_inst": "Departments of Criminology, Psychiatry, and Psychology, University of Pennsylvania" + }, + { + "author_name": "Gianluca Esposito", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.25.20238741", "rel_title": "I dont feel safe sitting in my own yard: Chicago resident experiences with urban rats during a COVID-19 stay-at-home order", @@ -1069773,37 +1073102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.26.20239376", - "rel_title": "Modelling the impact of health-related variables, age, migration, and socio-economic factors in the geographical distribution of early tested case-fatality risks associated with COVID-19 in Mexico", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239376", - "rel_abs": "COVID-19 is a respiratory disease caused by SARS-CoV-2, which has significantly impacted economic and public healthcare systems world-wide. SARS-CoV-2 is highly lethal in older adults (>65 years old) and in cases with underlying medical conditions including chronic respiratory diseases, immunosuppression, and cardio-metabolic diseases including severe obesity, diabetes, and hypertension. The course of the COVID-19 pandemic in Mexico has led to many fatal cases in younger patients attributable to cardio-metabolic conditions. Here, we aimed to perform an early spatial epidemiological analysis for the COVID-19 outbreak in Mexico to evaluate how tested case-fatality risks (t-CFRs) are geographically distributed and to explore spatial predictors of early t-CFRs considering the variation of their impact on COVID-19 fatality across different states in Mexico, controlling for the severity of the disease. As results, considering health related variables; diabetes and obesity were highly associated with COVID-19 fatality. We identified that both external and internal migration had an important impact over early COVID-19 risks in Mexico, with external migration having the second highest impact when analyzing Mexico as a whole. Physicians-to-population ratio, as a representation of urbanity, population density, and overcrowding households, has the highest impact on t-CFRs, whereas the age group of 10 to 39 years was associated with lower risks. Geographically, the states of Quintana Roo, Baja California, Chihuahua, and Tabasco had higher t-CFRs and relative risks comparing with a national standard, suggesting that risks in these states were above of what was nationally expected; additionally, the strength of the association between some spatial predictors and the COVID-19 fatality risks variates by zone depending on the predictor.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ricardo Ram\u00edrez-Aldana", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Juan Carlos Gomez-Verjan", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Carmen Garcia-Pe\u00f1a", - "author_inst": "Instituto Nacional de Geriatria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.26.20239368", "rel_title": "Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2", @@ -1070871,6 +1074169,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.28.20240259", + "rel_title": "Threatening second wave of COVID-19 is imminent: A deep learning perspective", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240259", + "rel_abs": "When the entire world is waiting restlessly for a safe and effective COVID-19 vaccine that could soon become a reality, numerous countries around the globe are grappling with unprecedented surges of new COVID-19 cases. As the number of new cases is skyrocketing, pandemic fatigue and public apathy towards different intervention strategies are posing new challenges to the government officials to combat the pandemic. Henceforth, it is indispensable for the government officials to understand the future dynamics of COVID-19 flawlessly in order to develop strategic preparedness and resilient response planning. In light of the above circumstances, probable future outbreak scenarios in Brazil, Russia and the United kingdom have been sketched in this study with the help of four deep learning models: long short term memory (LSTM), gated recurrent unit (GRU), convolutional neural network (CNN) and multivariate convolutional neural network (MCNN). In our analysis, CNN algorithm has outperformed other deep learning models in terms of validation accuracy and forecasting consistency. It has been unearthed in our study that CNN can provide robust long term forecasting results in time series analysis due to its capability of essential features learning, distortion invariance and temporal dependence learning. However, the prediction accuracy of LSTM algorithm has been found to be poor as it tries to discover seasonality and periodic intervals from any time series dataset, which were absent in our studied countries. Our study has highlighted the promising validation of using convolutional neural networks instead of recurrent neural networks when it comes to forecasting with very few features and less amount of historical data.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Khondoker Nazmoon Nabi", + "author_inst": "Bangladesh University of Engineering and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.27.20240036", "rel_title": "Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario", @@ -1071311,29 +1074628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.29.20240499", - "rel_title": "Predicting Trends of Coronavirus Disease (COVID19) Using SIRD and Gaussian-SIRD Models", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20240499", - "rel_abs": "Eruption of COVID-19 patients in 215 countries worldwide have urged for robust predictive methods that can detect as early as possible size and duration of the contagious disease and also providing precision predictions. In many recent literatures reported on COVID-19, one or more essential parts of such investigation were missed. One of crucial elements for any predictive method is that such methods should fit simultaneously as many data as possible; these data could be total infected cases, daily hospitalized cases, cumulative recovered cases and deceased cases and so on. Other crucial elements include sensitivity and precision of such predictive methods on amount of data as the contagious disease evolved day by day. To show importance of these aspects, we have evaluated the standard SIRD model and a newly introduced Gaussian-SIRD model on development of COVID-19 in Kuwait. It is observed that SIRD model quickly pick up main trends of COVID-19 development; but Gaussian-SIRD model provides precise prediction at longer period of time.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ahmad Sedaghat", - "author_inst": "School of Engineering Australian College of Kuwait Safat 13015, Kuwait" - }, - { - "author_name": "Amir MOSAVI", - "author_inst": "Obuda University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.29.20237875", "rel_title": "CLINICAL TRIALS IN COVID-19 MANAGEMENT & PREVENTION: A META-EPIDEMIOLOGICAL STUDY EXAMINING METHODOLOGICAL QUALITY", @@ -1072357,6 +1075651,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.11.30.20240721", + "rel_title": "Remote working in mental health services: a rapid umbrella review of pre-COVID-19 literature", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20240721", + "rel_abs": "BackgroundTele-mental health care has been rapidly adopted to maintain services during the pandemic, and there is now substantial interest in its future role. Service planning and policy making for recovery from the pandemic and beyond should draw not only on COVID-19 experiences, but also on the substantial research evidence accumulated prior to this.\n\nAimsto conduct an umbrella review of systematic reviews of research literature and evidence-based guidance on remote working in mental health, including both qualitative and quantitative literature.\n\nMethodThree databases were searched between January 2010 and August 2020 for systematic reviews meeting pre-defined criteria. Reviews retrieved were independently screened and those meeting inclusion criteria were synthesised and assessed for risk of bias. Narrative synthesis was used to report findings\n\nResultsNineteen systematic reviews met inclusion criteria. Fifteen examined clinical effectiveness, eight reported on aspects of tele-mental health implementation, ten reported on acceptability to service users and clinicians, two on cost-effectiveness and one on guidance. Most reviews were assessed as low quality. Findings suggested that video-based communication could be as effective and acceptable as face-face formats, at least in the short-term. Evidence was lacking on extent of digital exclusion and how it can be overcome, or on significant context such as children and young people and inpatient settings.\n\nConclusionsThis umbrella review suggests that tele-mental health has potential to be an effective and acceptable form of service delivery. However, we found limited evidence on impacts of large-scale implementation across catchment areas. Combining previous evidence and COVID-19 experiences may allow realistic planning for future tele-mental health implementation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Phoebe Barnett", + "author_inst": "University College London" + }, + { + "author_name": "Lucy Goulding", + "author_inst": "King's College London" + }, + { + "author_name": "Cecilia Casetta", + "author_inst": "King's College London" + }, + { + "author_name": "Harriet Jordan", + "author_inst": "King's College London" + }, + { + "author_name": "Luke Sheridan Rains", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Steare", + "author_inst": "University College London" + }, + { + "author_name": "Julie Williams", + "author_inst": "King's College London" + }, + { + "author_name": "Lisa Wood", + "author_inst": "University College London" + }, + { + "author_name": "Fiona Gaughran", + "author_inst": "King's College London" + }, + { + "author_name": "Sonia Johnson", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.25.20234914", "rel_title": "The efficacy and safety of hydroxychloroquine in COVID19 patients : a multicenter national retrospective cohort", @@ -1073013,41 +1076362,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.25.20238642", - "rel_title": "COVID-19 Growth in Rural versus Urban Counties with Major Universities at the Start of the 2020 Academic Year", - "rel_date": "2020-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238642", - "rel_abs": "Universities play a central role in a rural or small towns economy. They are often the main forms of enrichment to the lives of the longtime residents, the students, and the employees. Unfortunately, during a global pandemic, the migration and movement of young people in these communities can likely cause a rapid infection spike and drive spread easily, especially relative to larger urban areas. The current study investigates the relationship between COVID-19 case growth, university-county rurality, and time at the beginning of the Fall 2020 academic semester. Findings showed that small metro and non-metro counties with universities had a dramatic infection spike near the beginning of the semester and infection growth remained significantly higher than their large and medium metro counterparts for the duration of the study. Suggestions to slow the spread in rural communities are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Michael S Penuliar", - "author_inst": "Texas Tech University - Health Sciences Center" - }, - { - "author_name": "Candice Clark", - "author_inst": "Texas Tech University - Health Sciences Center" - }, - { - "author_name": "Debbie Curti", - "author_inst": "Texas Tech University - Health Sciences Center" - }, - { - "author_name": "Cathy Hudson", - "author_inst": "Texas Tech University - Health Sciences Center" - }, - { - "author_name": "Billy Philips", - "author_inst": "Texas Tech University - Health Sciences Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.24.20238295", "rel_title": "The Relationship between Weekly Periodicity and COVID-19 Progression", @@ -1073647,6 +1076961,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.24.20238139", + "rel_title": "Prediction of evolution of the second wave of Covid-19 pandemic in Italy", + "rel_date": "2020-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20238139", + "rel_abs": "A relevant problem in the study of the Covid-19 pandemic is the study of its temporal evolution. Such evolution depends on a number of factors, among which the average rate of contacts between susceptible and infected individuals, the duration of infectiousness and the transmissibility, that is the probability of infection after a contact between susceptible and infected individuals. In a previous study, we analyzed the potentiality of a number of distributions to describe the evolution of the pandemic and the potentiality of each distribution to mathematically predict the evolution of the pandemic in Italy. Since the number of daily tests was changing and increasing with time, we used the ratio of the new daily cases per swab. We considered distributions of the type of Gauss (normal), Gamma, Beta, Weibull, Lognormal and in addition of the type of the Planck blackbody radiation law. The Planck law, describing the amount of energy of the electromagnetic radiation emitted by a black body at each wavelength or at each frequency, marked in 1900 the beginning of Quantum Mechanics. The result of our analysis was that, among the considered distributions, the Planck law has the best potentiality to mathematically predict the evolution of the pandemic and the best fitting capability. In this paper, we analyze the time evolution of the second wave of the Covid-19 pandemic in Italy and in particular we predict the ratio of the new daily cases per swab at Christmas 2020 using the data in the interval from 17 Oct to 21 Nov. According to Figure 4 and Figure 8, the prediction for such a ratio around Christmas is approximately within 6% and 7%. In this study there is also an attempt to account for the effects of the governmental containment measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignazio Ciufolini", + "author_inst": "University of Salento" + }, + { + "author_name": "Antonio Paolozzi", + "author_inst": "School of Aerospace Engineering, Sapienza University of Rome" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.25.20237776", "rel_title": "Body mass index and risk of COVID-19 diagnosis, hospitalisation, and death: a population-based multi-state cohort analysis including 2,524,926 people in Catalonia, Spain", @@ -1074247,73 +1077584,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.19.20234245", - "rel_title": "Validation and implementation of a direct RT-qPCR method for rapid screening of SARS-CoV-2 infection by using non-invasive saliva samples", - "rel_date": "2020-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234245", - "rel_abs": "BackgroundThere is an urgent need to curb COVID-19 pandemic through early identification of asymptomatic but infectious cases. We aimed to validate and implement an optimised screening method for detection of SARS-CoV-2 RNA combining use of self-collected raw saliva samples, single-step heat-treated virus inactivation and RNA extraction, and direct RT-qPCR.\n\nMethods and findingsThe study was conducted in Sant Joan de Deu University Hospital (Barcelona, Spain), including: i) analytical validation against standard RT-qPCR in saliva samples; ii) diagnostic validation against standard RT-qPCR using paired saliva-nasopharyngeal samples obtained from asymptomatic teenagers and young and older adults in a youth sports academy; and iii) high throughput pilot screening of asymptomatic health workers and other staff in the study site.\n\nThe proposed method had comparable analytical performance to standard RT-qPCR in saliva. Diagnostic validation included saliva samples self-collected with supervision by 173 participants during 9-12 weeks and nasopharyngeal samples collected from them. At baseline, all participants (100.0%) were negative for SARS-CoV-2 in both paired saliva-nasopharyngeal samples. In the following weeks, standard RT-qPCR yielded 23 positive results in nasopharyngeal samples whereas paired saliva specimens yielded 22 (95.7%) positive and one inconclusive result.\n\nA total of 2,709 participants engaged in the pilot screening, with high rate of participation (83.4% among health workers). Only 17 (0.6%) of saliva samples self-collected by participants in an unsupervised manner were invalid. Saliva was positive in 24 (0.9%) out of 2,692 valid specimens and inconclusive in 27 (1.0%). All 24 saliva-positive participants and 4 with saliva inconclusive results were positive by standard RT-qPCR in nasopharyngeal samples. The pilot showed potential for rapid analytical workflow (up to 384 batched samples can be processed in <2 hours).\n\nConclusionDirect RT-qPCR on self-collected raw saliva is a simple, rapid, and accurate method with potential to be scaled up for enhanced SARS-CoV-2 community-wide screening.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Pedro Brotons", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Amaresh Perez-Arguello", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Cristian Launes", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Francesc Torrents", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Jesica Saucedo", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Joana Claverol", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Juan Jose Garcia-Garcia", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Gil Rodas", - "author_inst": "Futbol Club Barcelona" - }, - { - "author_name": "Vicky Fumado", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Iolanda Jordan", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Eduard Gratacos", - "author_inst": "Hospital Sant Joan de Deu" - }, - { - "author_name": "Quique Bassat", - "author_inst": "ISGlobal" - }, - { - "author_name": "Carmen Munoz-Almagro", - "author_inst": "Hospital Sant Joan de Deu" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.25.20229088", "rel_title": "Use of dialysis, tracheostomy, and extracorporeal membrane oxygenation among 240,392 patients hospitalized with COVID-19 in the United States", @@ -1075601,6 +1078871,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.11.25.399055", + "rel_title": "Triple Combination Nitazoxanide, Ribavirin, and Hydroxychloroquine results in the multiplicative reduction of in vitro SARS-CoV-2 viral replication", + "rel_date": "2020-11-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.399055", + "rel_abs": "BackgroundAn immediate unmet medical need exists to test and develop existing approved drugs against SARS-COV-2. Despite many efforts, very little progress has been made regarding finding low-cost oral medicines that can be made widely available worldwide to address the global pandemic.\n\nMethodsWe sought to examine if a triple combination of nitazoxanide (using its active metabolite tizoxanide), ribavirin, and hydroxychloroquine would lead to a multiplicative effects on viral replication of SARS-COV-2 resulting in a significant reduction of virus yield using VERO E6 cells as a model of viral replication.\n\nResultsVirus yield measured in PFU/ml was ~ 2 logs lower with triple combination versus either drug alone, resulting in the prolongation of time to peak cytopathic effects (CPE). The time to produce 50% CPE increased from 2.8 days for viral controls versus 5.3 days for triple combination therapy. Finally, for each 1-log reduction in virus yield 24 hours post-infection, there was an additional 0.7-day delay in onset of CPE.\n\nConclusionsA triple combination of tizoxanide, ribavirin, and hydroxychloroquine produced a reduction in SARS-COV-2 viral replication in Vero E6 cells, warranting exploration in additional cell lines as well as human clinical trials.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elena Lian", + "author_inst": "Colorado State University" + }, + { + "author_name": "Carley McAlister", + "author_inst": "Colorado State University" + }, + { + "author_name": "Gabriela Ramirez", + "author_inst": "Colorado State University" + }, + { + "author_name": "David N Chernoff", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Gregory Went", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Justin Hoopes", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Rushika Perera", + "author_inst": "Colorado State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.26.399436", "rel_title": "Host-directed FDA-approved drugs with antiviral activity against SARS-CoV-2 identified by hierarchical in silico/in vitro screening methods", @@ -1076341,77 +1079654,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.11.22.20232959", - "rel_title": "Use of Artificial Intelligence on spatio-temporal data to generate insights during COVID-19 pandemic: A Review", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20232959", - "rel_abs": "The COVID-19 pandemic, within a short time span, has had a significant impact on every aspect of life in almost every country on the planet. As it evolved from a local epidemic isolated to certain regions of China, to the deadliest pandemic since the influenza outbreak of 1918, scientists all over the world have only amplified their efforts to combat it. In that battle, Artificial Intelligence, or AI, with its wide ranging capabilities and versatility, has played a vital role and thus has had a sizable impact. In this review, we present a comprehensive analysis of the use of AI techniques for spatio-temporal modeling and forecasting and impact modeling on diverse populations as it relates to COVID-19. Furthermore, we catalogue the articles in these areas based on spatio-temporal modeling, intrinsic parameters, extrinsic parameters, dynamic parameters and multivariate inputs (to ascertain the penetration of AI usage in each sub area). The manner in which AI is used and the associated techniques utilized vary for each body of work. Majority of articles use deep learning models, compartment models, stochastic methods and numerous statistical methods. We conclude by listing potential paths of research for which AI based techniques can be used for greater impact in tackling the pandemic.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gihan Chanaka Jayatilaka", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "Jameel Hassan", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "Umar Marikkar", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "Rumali Perera", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "Suren Sritharan", - "author_inst": "Sri Lanka Technological Campus" - }, - { - "author_name": "Harshana Weligampola", - "author_inst": "Sri Lanka Technological Campus" - }, - { - "author_name": "Mevan Ekanayake", - "author_inst": "Sri Lanka Technological Campus" - }, - { - "author_name": "Roshan Godaliyadda", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "Parakrama Ekanayake", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "Vijitha Herath", - "author_inst": "University of Peradeniya" - }, - { - "author_name": "G.M. Dilshan Godaliyadda", - "author_inst": "Researcher, Texas, USA" - }, - { - "author_name": "Anuruddhika Rathnayake", - "author_inst": "University of Colombo" - }, - { - "author_name": "Samath D. Dharmaratne", - "author_inst": "University of Peradeniya and University of Washington" - }, - { - "author_name": "Janaka Ekanayake", - "author_inst": "University of Peradeniya and Cardiff University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.11.23.20236711", "rel_title": "Statistical Analyses of the Public Health and Economic Performance of Nordic Countries in Response to the COVID-19 Pandemic", @@ -1077315,6 +1080557,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.23.20237198", + "rel_title": "The sensitivity of SARS-CoV-2 antigen tests in the view of large-scale testing", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237198", + "rel_abs": "ObjectivesAntigen tests have recently emerged as an interesting alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity of two point-of-care antigen tests when applied to a cohort of COVID-19 symptomatic, COVID-19 asymptomatic and healthy persons.\n\nMethodsWe examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 Ag Rapid Test, Abbott) and antigen test 2 (Standard F Covid-19 Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 associated symptoms.\n\nResultsWhile PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 (sensitivity 0.664, 95% CI 0.599 - 0.722) and 141 (sensitivity 0.623, 95% CI 0.558 - 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity increased to 0.738 (95% CI 0.667 - 0.799) for the antigen test 1 and to 0.685 (95% CI 0.611 - 0.750) for the antigen test 2. The substantial drop in sensitivity to 12.9% (95% CI 0.067 - 0.234) was observed for samples with the PCR threshold cycle above > 30.\n\nConclusionsLow sensitivity of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Pavel Drevinek", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + }, + { + "author_name": "Jakub Hurych", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + }, + { + "author_name": "Zdenek Kepka", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Ales Briksi", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Michal Kulich", + "author_inst": "Faculty of Mathematics and Physics, Charles University" + }, + { + "author_name": "Miroslav Zajac", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Petr Hubacek", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.24.20237560", "rel_title": "Demography, social contact patterns and the COVID-19 burden in different settings of Ethiopia: a modeling study", @@ -1078059,53 +1081344,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.24.20237743", - "rel_title": "COVI-Prim survey: Challenges for Austrian and German general practitioners during initial phase of COVID-19", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237743", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) represents a significant challenge to health care systems around the world. A well-functioning primary care system is crucial in epidemic situations as it plays an important role in the development of a system-wide response.\n\nMethods2,187 Austrian and German GPs answered an internet suvey on preparedness, testing, staff protection, perception of risk, self-confidence, a decrease in the number of patient contacts, and efforts to control the spread of the virus in the practice during the early phase of the COVID-pandemic (3rd to 30th April).\n\nResultsThe completion rate of the questionnaire was high (90.9%). GPs gave low ratings to their preparedness for a pandemic, testing of suspected cases and efforts to protect staff. The provision of information to GPs and the perception of risk were rated as moderate. On the other hand, the participants rated their self-confidence, a decrease in patient contacts and their efforts to control the spread of the disease highly.\n\nConclusionPrimary care is an important resource for dealing with a pandemic like COVID-19. The workforce is confident and willing to take an active role, but needs to be provided with the appropriate surrounding conditions. This will require that certain conditions are met.\n\nRegistrationTrial registration at the German Clinical Trials Register: DRKS00021231\n\nPrimary Funding SourceThe study was financed by the cooperating University Institutes without any external financial support.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Andrea Siebenhofer", - "author_inst": "Medical University of Graz Austria; Johann Wolfgang Goethe University Frankfurt, Germany" - }, - { - "author_name": "Sebastian Huter", - "author_inst": "Paracelsus Medical University Salzburg, Austria" - }, - { - "author_name": "Alexander Avian", - "author_inst": "Medical University of Graz, Austria" - }, - { - "author_name": "Karola Mergenthal", - "author_inst": "Johann Wolfgang Goethe University Frankfurt, Germany" - }, - { - "author_name": "Dagmar Schaffler-Schaden", - "author_inst": "Paracelsus Medical University Salzburg, Austria" - }, - { - "author_name": "Ulrike Spary-Kainz", - "author_inst": "Medical University Graz, Austria" - }, - { - "author_name": "Herbert Bachler", - "author_inst": "Medical University Innsbruck, Austria" - }, - { - "author_name": "Maria Flamm", - "author_inst": "Paracelsus Medical University Salzburg, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.11.24.20237586", "rel_title": "The experience of distress during the COVID-19 outbreak: a cross-country examination on the fear of COVID-19 and the sense of loneliness", @@ -1079089,6 +1082327,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.20.20233890", + "rel_title": "A Data Driven Change-point Epidemic Model for Assessing the Impact of Large Gathering and Subsequent Movement Control Order on COVID-19 Spread in Malaysia", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20233890", + "rel_abs": "The second wave of COVID-19 in Malaysia is largely attributed to a mass gathering held in Sri Petaling between February 27, 2020 and March 1, 2020, which contributed to an exponential rise of COVID-19 cases in the country. Starting March 18, 2020, the Malaysian government introduced four consecutive phases of a Movement Control Order (MCO) to stem the spread of COVID-19. The MCO was implemented through various non-pharmaceutical interventions (NPIs). The reported number of cases reached its peak by the first week of April and then started to reduce, hence proving the effectiveness of the MCO. To gain a quantitative understanding of the effect of MCO on the dynamics of COVID-19, this paper develops a class of mathematical models to capture the disease spread before and after MCO implementation in Malaysia. A heterogeneous variant of the Susceptible-Exposed-Infected-Recovered (SEIR) model is developed with additional compartments for asymptomatic transmission. Further, a change-point is incorporated to model the before and after disease dynamics, and is inferred based on data. Related statistical analyses for inference are developed in a Bayesian framework and are able to provide quantitative assessments of (1) the impact of the Sri Petaling gathering, and (2) the extent of decreasing transmission during the MCO period. The analysis here also quantitatively demonstrates how quickly transmission rates fall under effective NPI implemention within a short time period.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sarat Chandra Dass", + "author_inst": "Heriot-Watt University Malaysia Campus" + }, + { + "author_name": "Wai Meng Kwok", + "author_inst": "Heriot-Watt University Malaysia Campus" + }, + { + "author_name": "Gavin J Gibson", + "author_inst": "Heriot-Watt University Edinburgh Campus" + }, + { + "author_name": "Balvinder S Gill", + "author_inst": "Institute for Medical Research Malaysia" + }, + { + "author_name": "Bala M Sundram", + "author_inst": "Institute for Medical Research Malaysia" + }, + { + "author_name": "Sarbhan Singh", + "author_inst": "Institute for Medical Research Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.20.20220749", "rel_title": "Community Transmission of SARS-CoV-2 by Fomites: Risks and Risk Reduction Strategies", @@ -1079601,49 +1082878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.20.20224691", - "rel_title": "The risk of COVID hospital admission and COVID mortality during the first COVID 19 wave with a special emphasis on Ethnic Minorities: an observational study of a single, deprived, multi ethnic UK health economy", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20224691", - "rel_abs": "ObjectivesTo address the generalisability of COVID-19s outcomes to the well-defined but diverse communities of a single City area.\n\nDesignAn observational study of COVID-19 outcomes using quality-assured and integrated data from a single UK hospital contextualised to its feeder population and its associated factors (comorbidities, ethnicity, age, deprivation).\n\nSetting/ParticipantsSingle city hospital with a feeder population of 228,632 adults in Wolverhamptons city area.\n\nMain Outcome MeasuresHospital admissions and mortality.\n\nResults5558 patients admitted, 686 died (556 in hospital); 930 were COVID-19 admissions (CA),of which 270 were hospital COVID deaths, 47 non-COVID deaths, 36 deaths post-discharge; 4628 non-COVID-19 admissions (NCA), 239 in-hospital deaths (2 COVID), 94 deaths post-discharge. 223,074 adults not admitted, 407 died. Age, gender, multi-morbidity and Black ethnicity (OR 2.1 [95% CI 1.5-3.2] p<0.001, absolute excess risk of <1/1,000) were associated with COVID-19 admission and mortality. The South Asian cohort had lower CA and NCA, lower mortality (CA (0.5 [0.3-0.8], p<0.01), NCA (0.4 [0.3-0.6] p<0.001), community deaths (0.5 [0.3-0.7] p<0.001). Despite many common risk factors for CA and NCA, ethnic groups had different admission rates, and within-groups differing association of risk factors. Deprivation impacted only in White ethnicity, in the oldest age bracket and in a lesser (not most) deprived quintile.\n\nConclusionsWolverhamptons results, reflecting high ethnic diversity and deprivation, are similar to other studies for Black ethnicity, age and comorbidity risk in COVID-19 but strikingly different in South Asians and for deprivation. Sequentially considering population and then hospital based NCA and CA outcomes, we present a complete single health-economy picture. Risk factors may differ within ethnic groups; our data may be more representative of communities with high BAME populations, highlighting the need for locally focussed public health strategies. We emphasise the need for a more comprehensible and nuanced conveyance of risk.\n\nStrengths and limitations of this studyO_LIThe rapidly developing COVID-19 pandemic has led to numerous studies (published, preprints and national public health reports) of its health impacts in relation to ethnicity, co-morbidities and other factors; few studies, however, have attempted to evaluate infection patient data in terms of morbidity and mortality in context of the feeder population and most are limited by incompleteness of data and inability to account for regional variations in factors such as ethnicity and deprivation\nC_LIO_LIOur observational study used a high quality and complete dataset from the local population and the hospital serving it to examine the association of purported risk factors with severity and mortality and the results reveal the importance of evaluating such risks in the local, and not just national, population setting taking into account the local variations in patient backgrounds\nC_LIO_LIWe found an increased risk of COVID-19 mortality for Black ethnicity (OR 2.1) but a decreased risk (OR 0.5) for South Asians, compared with white ethnicity; Our analysis reveals that a nuanced approach to studying risk factors associated with COVID-19 severity and mortality is important - factoring in regional variation in ethnicity, deprivation etc. specifically linked to the source population\nC_LIO_LIWe suggest, based on our findings, that understandably rapid analysis and dissemination of studies of COVID-19 risk needs to be tempered by careful consideration of the real implications; we further urge caution in conveying risk messages to the wider community because of an ethical imperative to ensure such messages do not lead to unnecessary fear and deter individuals, particularly from specific ethnic backgrounds, from seeking needed medical assistance.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Baldev M Singh", - "author_inst": "Royal Wolverhampton NHS Trust" - }, - { - "author_name": "James Bateman", - "author_inst": "Royal Wolverhampton NHS Trust" - }, - { - "author_name": "Ananth Viswanath", - "author_inst": "Royal Wolverhampton NHS Trust" - }, - { - "author_name": "Vijay Klaire", - "author_inst": "Royal Wolverhampton NHS Trust" - }, - { - "author_name": "Sultan Mahmud", - "author_inst": "Royal Wolverhampton NHS Trust" - }, - { - "author_name": "Alan M Nevill", - "author_inst": "University of Wolverhampton" - }, - { - "author_name": "Simon J Dunmore", - "author_inst": "University of Wolverhampton" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.20.20235341", "rel_title": "Diagnostic accuracy of two commercial SARS-CoV-2 Antigen-detecting rapid tests at the point of care in community-based testing centers", @@ -1080495,6 +1083729,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.21.392555", + "rel_title": "Interactions of anti-COVID-19 drug candidates with multispecific ABC and OATP drug transporters", + "rel_date": "2020-11-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.21.392555", + "rel_abs": "In the COVID-19 epidemic, several repurposed drugs have been proposed to alleviate the major health effects of the disease. These drugs are often applied together with analgesics or non-steroid anti-inflammatory compounds, and co-morbid patients may also be treated with anticancer, cholesterol-lowering or antidiabetic agents. Since drug ADME-tox properties may be significantly affected by multispecific transporters, here we examined the interactions of the repurposed drugs with the key human multidrug transporters, present in the major tissue barriers and strongly affecting pharmacokinetics. Our in vitro studies, using a variety of model systems, explored the interactions of the antimalarial agents chloroquine and hydroxychloroquine, the antihelmintic ivermectin, and the proposed antiviral compounds, ritonavir, lopinavir, favipiravir and remdesivir with the ABCB1/Pgp, ABCG2/BCRP and ABCC1/MRP1 exporters, as well as the OATP2B1 and OATP1A2 uptake transporters. The results presented here show numerous pharmacologically relevant transporter interactions and may provide a warning for the potential toxicities of these repurposed drugs, especially in drug combinations at the clinic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Agnes Telbisz", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Csilla Ambrus", + "author_inst": "Solvo Biotechnology Ltd" + }, + { + "author_name": "Orsolya Mozner", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Edit Szabo", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Gyorgy Varady", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Eva Bakos", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Balazs Sarkadi", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Csilla Ozvegy-Laczka", + "author_inst": "Research Centre for Natural Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.11.21.392670", "rel_title": "A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2", @@ -1081151,57 +1084432,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.20.20234898", - "rel_title": "On-site rapid molecular testing, mobile sampling teams and eHealth to support primary care physicians during the COVID-19 pandemic", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20234898", - "rel_abs": "ObjectivesWe evaluated the effects of on-site rapid molecular testing at a drive-through sampling facility, deployment of mobile sampling teams and implementation of an online eHealth platform as supportive measures for general practitioners (GPs) during the COVID-19 pandemic.\n\nMethodsAn eHealth platform was developed that allowed GPs to either refer patients to a drive-through sampling facility or to request a home visit by a sampling team. Nasopharyngeal swab samples from patients marked as urgent (n=333) were tested immediately on-site using a GeneXpert System. Non-urgent samples (n=1,460) were sent once a day to a university hospital laboratory for routine testing. Time stamps starting from referral to the moment of test report sent were recorded to calculate the turnaround time.\n\nResultsThe eHealth platform was rapidly adopted and used by a total of 517 GPs to test 1,793 patients in a period of 13 weeks. On-site rapid molecular testing reduced the median turnaround time to 03h:41m compared to 29h:15m for routine testing. Positive SARS-CoV-2 test results were identified amongst 84/1,477 (5.7%) and 33/316 (10.4%) patients sampled at the drive-through or at home, respectively. In the age category of >80 years, 80.4% of patients were tested by a mobile sampling team.\n\nConclusionsThe combination of rapid molecular testing and eHealth reduced the time between referral and results sent back to the GP to less than four hours. In addition, mobile sampling teams helped in reaching non-mobile, elderly patient populations with a higher prevalence of COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "N.N. Cheung", - "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" - }, - { - "author_name": "S.A. Boers", - "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" - }, - { - "author_name": "S. Kiani deh Kiani", - "author_inst": "HADOKS, Haaglandse Dokters, Den Haag, the Netherlands" - }, - { - "author_name": "R.W. Jansen", - "author_inst": "HADOKS, Haaglandse Dokters, Den Haag, the Netherlands" - }, - { - "author_name": "D.O. Mook-Kanamori", - "author_inst": "Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands" - }, - { - "author_name": "L. Janssens", - "author_inst": "Netherlands Red Cross, Den Haag, the Netherlands" - }, - { - "author_name": "M.C.W. Feltkamp", - "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" - }, - { - "author_name": "A.C.M. Kroes", - "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" - }, - { - "author_name": "B.C. Mourik", - "author_inst": "Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.20.20235333", "rel_title": "Is Standard Personal Protective Equipment Effective Enough To Prevent COVID-19 Transmission During Aerosol Generating Dental, Oral and Maxillofacial Procedures ? A Systematic Review", @@ -1082253,6 +1085483,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.19.20234849", + "rel_title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "rel_date": "2020-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "rel_abs": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bethan Davies", + "author_inst": "Imperial College London" + }, + { + "author_name": "Brandon L Parkes", + "author_inst": "Imperial College London" + }, + { + "author_name": "James Bennett", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniela Fecht", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marta Blangiardo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Majid Ezzati", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.21.392639", "rel_title": "Anti-COVID-19 efficacy of ivermectin in the golden hamster", @@ -1083561,45 +1086834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.11.18.20234419", - "rel_title": "Modeling and Sensitivity Analysis of Coronavirus Disease(COVID-19) Outbreak Prediction", - "rel_date": "2020-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234419", - "rel_abs": "Susceptible-infectious-recovered-deceased (SIRD) model is an essential model for outbreak prediction. This paper evaluates the performance of the SIRD model for the outbreak of COVID-19 in Kuwait, which initiated on 24 February 2020 by five patients in Kuwait. This paper investigates the sensitivity of the SIRD model for the development of COVID-19 in Kuwait based on the duration of the progressed days of data. For Kuwait, we have fitted the SIRD model to COVID-19 data for 20, 40, 60, 80, 100, and 116 days of data and assessed the sensitivity of the model with the number of days of data. The parameters of the SIRD model are obtained using an optimization algorithm (lsqcurvefit) in MATLAB. The total population of 50,000 is equally applied for all Kuwait time intervals. Results of the SIRD model indicate that after 40 days, the peak infectious day can be adequately predicted. Although error percentage from sensitivity analysis suggests that different exposed population sizes are not correctly predicted. SIRD type models are too simple to robustly capture all features of COVID-19, and more precise methods are needed to tackle the correct trends of a pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ahmad Sedaghat", - "author_inst": "Australian College of Kuwait, Safat 13015, Kuwait" - }, - { - "author_name": "Seyed Amir Abbas Oloomi", - "author_inst": "Industrial Engineering Department, Yazd University, Yazd, Iran." - }, - { - "author_name": "Mahdi Ashtian Malayer", - "author_inst": "Young Researchers and Elite Club, Yazd Branch, Azad University, Yazd, Iran" - }, - { - "author_name": "Shahab S. Band", - "author_inst": "Future Technology Research Center, National Yunlin University of Science and Technology, Yunlin, Taiwan" - }, - { - "author_name": "Amir MOSAVI", - "author_inst": "Obuda University" - }, - { - "author_name": "Laszlo Nadai", - "author_inst": "John von Neumann Faculty of Infromatics, Obuda University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.18.20234039", "rel_title": "The detection and stability of the SARS-CoV-2 RNA biomarkers in wastewater influent in Helsinki, Finland", @@ -1084751,6 +1087985,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20225029", + "rel_title": "The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20225029", + "rel_abs": "BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic.\n\nMethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed.\n\nFindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures.\n\nInterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Angela B Brueggemann", + "author_inst": "University of Oxford" + }, + { + "author_name": "Melissa J Jansen van Rensburg", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Shaw", + "author_inst": "University of Oxford" + }, + { + "author_name": "Noel D McCarthy", + "author_inst": "University of Warwick" + }, + { + "author_name": "Keith A Jolley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Martin CJ Maiden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mark PG van der Linden", + "author_inst": "University Hospital RWTH Aachen" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.388140", "rel_title": "Detecting SARS-CoV-2 variants with SNP genotyping", @@ -1085383,65 +1088660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.18.389312", - "rel_title": "Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance", - "rel_date": "2020-11-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.18.389312", - "rel_abs": "Mutation-driven evolution of SARS coronavirus-2 (SARS-CoV-2) highlights the need for innovative approaches that simultaneously suppress viral replication and circumvent viral escape routes from host immunity and antiviral therapeutics. Here, we employed genome-wide computational prediction and singlenucleotide resolution screening to reprogram CRISPR-Cas13b against SARS-CoV-2 genomic and subgenomic RNAs. Reprogrammed Cas13b effectors targeting accessible regions of Spike and Nucleocapsid transcripts achieved >98% silencing efficiency in virus free-models. Further, optimized and multiplexed gRNAs suppressed viral replication by up to 90% in mammalian cells infected with replication-competent SARS-CoV-2. Unexpectedly, the comprehensive mutagenesis of guide-target interaction demonstrated that single-nucleotide mismatches do not impair the capacity of a potent single gRNA to simultaneously suppress ancestral and mutated SARS-CoV-2 in infected mammalian cells, including the highly infectious and globally disseminated Spike D614G mutant. The specificity, efficiency and rapid deployment properties of reprogrammed Cas13b described here provide a molecular blueprint of antiviral therapeutics to simultaneously suppress a wide range of SARS-CoV-2 mutants, and is readily adaptable to other emerging pathogenic viruses.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Mohamed Fareh", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - }, - { - "author_name": "Wei Zhao", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital" - }, - { - "author_name": "Wenxin Hu", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - }, - { - "author_name": "Joshua ML Casan", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - }, - { - "author_name": "Amit Kumar", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - }, - { - "author_name": "Jori Symons", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital" - }, - { - "author_name": "Ilia Voskoboinik", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - }, - { - "author_name": "Paul G Ekert", - "author_inst": "Childrens Cancer Institute Randwick NSW Australia" - }, - { - "author_name": "Rajeev Rudraraju", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - }, - { - "author_name": "Sharon R Lewin", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital" - }, - { - "author_name": "Joseph A Trapani", - "author_inst": "Sir Peter MacCallum Department of Oncology, The University of Melbourne" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.18.388413", "rel_title": "Long-chain polyphosphates impair SARS-CoV-2 infection and replication: a route for therapy in man", @@ -1086385,6 +1089603,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.16.20232850", + "rel_title": "The impact of COVID-19 employment shocks on suicide and poverty alleviation programs: An early-stage investigation", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232850", + "rel_abs": "This paper examines whether the COVID-19-induced employment shocks are associated with increases in suicides and safety net use in the second and third quarters of 2020. We exploit plausibly exogenous regional variation in the magnitude of the employment shocks in Japan and adopt a difference-in-differences research design to examine and control for possible confounders. Our preferred point estimates suggest that a one-percentage-point increase in the unemployment rate in the second quarter of 2020 is associated with, approximately, an additional 0.52 suicides, 28 unemployment benefit recipients, 88 recipients of a temporary loan program, and 10 recipients of public assistance per 100,000 population per month. A simple calculation based on these estimates suggests that if a region experienced a one-percentage-point increase in the unemployment rate caused by the COVID-19 crisis in the second quarter of 2020, which is roughly equivalent to the third-highest regional employment shock, this would be associated with 37.4%, 60.5%, and 26.5% increases in the total, female, and male suicide rates respectively in July 2020 compared with July 2019. Our baseline findings are robust to several different model specifications, although we do not assert that our research design perfectly solves the problem of estimation bias.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michihito Ando", + "author_inst": "Rikkyo University" + }, + { + "author_name": "Masato Furuichi", + "author_inst": "Teikyo University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.11.16.20227389", "rel_title": "Designing Efficient Contact Tracing Through Risk-Based Quarantining", @@ -1087077,85 +1090318,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.17.20232918", - "rel_title": "SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20232918", - "rel_abs": "In the United States, state-level re-openings in spring 2020 presented an opportunity for the resurgence of SARS-CoV-2 transmission. One important question during this time was whether human contact and mixing patterns could increase gradually without increasing viral transmission, the rationale being that new mixing patterns would likely be associated with improved distancing, masking, and hygiene practices. A second key question to follow during this time was whether clinical characteristics of the epidemic would improve after the initial surge of cases. Here, we analyze age-structured case, hospitalization, and death time series from three states - Rhode Island, Massachusetts, and Pennsylvania - that had successful re-openings in May 2020 without summer waves of infection. Using a Bayesian inference framework on eleven daily data streams and flexible daily population contact parameters, we show that population-average mixing rates dropped by >50% during the lockdown period in March/April, and that the correlation between overall population mobility and transmission-capable mobility was broken in May as these states partially re-opened. We estimate the reporting rates (fraction of symptomatic cases reporting to health system) at 96.0% (RI), 72.1% (MA), and 75.5% (PA); in Rhode Island, when accounting for cases caught through general-population screening programs, the reporting rate estimate is 94.5%. We show that elderly individuals were less able to reduce contacts during the lockdown period when compared to younger individuals. Attack rate estimates through August 31 2020 are 6.4% (95% CI: 5.8% - 7.3%) of the total population infected for Rhode Island, 5.7% (95% CI: 5.0% - 6.8%) in Massachusetts, and 3.7% (95% CI: 3.1% - 4.5%) in Pennsylvania, with some validation available through published seroprevalence studies. Infection fatality rates (IFR) estimates for the spring epidemic are higher in our analysis (>2%) than previously reported values, likely resulting from the epidemics in these three states affecting the most vulnerable sub-populations, especially the most vulnerable of the [≥]80 age group.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Nathan B Wikle", - "author_inst": "Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University" - }, - { - "author_name": "Thu Nguyen-Anh Tran", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Bethany Gentilesco", - "author_inst": "Department of Medicine, Brown University, Providence, RI" - }, - { - "author_name": "Scott M Leighow", - "author_inst": "Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University" - }, - { - "author_name": "Emmy Albert", - "author_inst": "Department of Physics, Pennsylvania State University" - }, - { - "author_name": "Emily R Strong", - "author_inst": "Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University" - }, - { - "author_name": "Karel Brinda", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Haider Inam", - "author_inst": "Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University" - }, - { - "author_name": "Fuhan Yang", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" - }, - { - "author_name": "Sajid Hossain", - "author_inst": "Yale School of Medicine, Yale University" - }, - { - "author_name": "Philip Chan", - "author_inst": "Department of Medicine, Brown University" - }, - { - "author_name": "William P Hanage", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Maria Messick", - "author_inst": "Rhode Island Office of the Governor and Rhode Island Department of Health" - }, - { - "author_name": "Justin R Pritchard", - "author_inst": "Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University" - }, - { - "author_name": "Ephraim M Hanks", - "author_inst": "Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University" - }, - { - "author_name": "Maciej F Boni", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.17.20229583", "rel_title": "Secondary transmission of COVID-19 in preschool and school settings after their reopening in northern Italy: a population-based study", @@ -1087803,6 +1090965,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.16.20232884", + "rel_title": "Comparative Efficacy and Safety of Current Drugs against COVID-19: a Systematic Review and Net-work Meta Analysis", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232884", + "rel_abs": "The rapid spread of coronavirus disease (COVID-19) has greatly disrupted the livelihood of many people around the world. To date, more than 35.16 million COVID-19 cases with 1.037million total deaths have been reported worldwide. Compared with China, where the disease was first reported, cases of COVID-19, the number of confirmed cases for the disease in the rest of the world have been incredibly high. Even though several dugs have been suggested to be used against the disease, the said interventions should be backed by empirical clinical evidence. Therefore, this paper provides a systematic review and a meta-analysis of efficacy and safety of different COVID-19 drugs.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCurrently, Covid-19 is one of the most urgent and significant health challenge, globally. However, so far there is no specific and effective treatment strategy against the disease. Nonetheless, there are numerous debates over the effectiveness and potential adverse effects of different COVID-19 antivirals. In general, there is invaluable need to continually report on new advances and successes against COVID-19, apparently to aid in managing the pandemic.\n\nAdded value of this studyThis study provides a comprehensive, evidence-based guide on the management of multiple COVID-19 symptoms. In particular, we provide a review of 14 drugs, placebos and standard treatments against COVID 19. Meanwhile, we also performed a meta-analysis based on four clinical outcome indicators, to measure and compare the efficacy and safety of current interventions.\n\nImplications of all the available evidenceFindings of this research will guide clinical decision in COVID-19 patients. It will also provide a basis for predicting clinical outcomes such as efficacy, mortality and safety of interventions against the disease.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yi Li", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "Wei He", + "author_inst": "China Pharmaceutical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.17.20233080", "rel_title": "COVID-19: more than a little flu? Insights from the Swiss hospital-based surveillance of Influenza and COVID-19", @@ -1088347,129 +1091532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.11.17.20233460", - "rel_title": "Global seroprevalence of SARS-CoV-2 antibodies: a systematic review and meta-analysis", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233460", - "rel_abs": "BackgroundMany studies report the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. We aimed to synthesize seroprevalence data to better estimate the level and distribution of SARS-CoV-2 infection, identify high-risk groups, and inform public health decision making.\n\nMethodsIn this systematic review and meta-analysis, we searched publication databases, preprint servers, and grey literature sources for seroepidemiological study reports, from January 1, 2020 to December 31, 2020. We included studies that reported a sample size, study date, location, and seroprevalence estimate. We corrected estimates for imperfect test accuracy with Bayesian measurement error models, conducted meta-analysis to identify demographic differences in the prevalence of SARS-CoV-2 antibodies, and meta-regression to identify study-level factors associated with seroprevalence. We compared region-specific seroprevalence data to confirmed cumulative incidence. PROSPERO: CRD42020183634.\n\nResultsWe identified 968 seroprevalence studies including 9.3 million participants in 74 countries. There were 472 studies (49%) at low or moderate risk of bias. Seroprevalence was low in the general population (median 4.5%, IQR 2.4-8.4%); however, it varied widely in specific populations from low (0.6% perinatal) to high (59% persons in assisted living and long-term care facilities). Median seroprevalence also varied by Global Burden of Disease region, from 0.6 % in Southeast Asia, East Asia and Oceania to 19.5% in Sub-Saharan Africa (p<0.001). National studies had lower seroprevalence estimates than regional and local studies (p<0.001). Compared to Caucasian persons, Black persons (prevalence ratio [RR] 3.37, 95% CI 2.64-4.29), Asian persons (RR 2.47, 95% CI 1.96-3.11), Indigenous persons (RR 5.47, 95% CI 1.01-32.6), and multi-racial persons (RR 1.89, 95% CI 1.60-2.24) were more likely to be seropositive. Seroprevalence was higher among people ages 18-64 compared to 65 and over (RR 1.27, 95% CI 1.11-1.45). Health care workers in contact with infected persons had a 2.10 times (95% CI 1.28-3.44) higher risk compared to health care workers without known contact. There was no difference in seroprevalence between sex groups. Seroprevalence estimates from national studies were a median 18.1 times (IQR 5.9-38.7) higher than the corresponding SARS-CoV-2 cumulative incidence, but there was large variation between Global Burden of Disease regions from 6.7 in South Asia to 602.5 in Sub-Saharan Africa. Notable methodological limitations of serosurveys included absent reporting of test information, no statistical correction for demographics or test sensitivity and specificity, use of non-probability sampling and use of non-representative sample frames.\n\nDiscussionMost of the population remains susceptible to SARS-CoV-2 infection. Public health measures must be improved to protect disproportionately affected groups, including racial and ethnic minorities, until vaccine-derived herd immunity is achieved. Improvements in serosurvey design and reporting are needed for ongoing monitoring of infection prevalence and the pandemic response.\n\nFundingPublic Health Agency of Canada through the COVID-19 Immunity Task Force.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Niklas Bobrovitz", - "author_inst": "University of Toronto, University of Calgary" - }, - { - "author_name": "Rahul Krishan Arora", - "author_inst": "University of Oxford, University of Calgary" - }, - { - "author_name": "Christian Cao", - "author_inst": "University of Calgary" - }, - { - "author_name": "Emily Boucher", - "author_inst": "University of Calgary, University of Oxford" - }, - { - "author_name": "Michael Liu", - "author_inst": "Harvard University, University of Oxford" - }, - { - "author_name": "Claire Donnici", - "author_inst": "University of Calgary" - }, - { - "author_name": "Mercedes Yanes-Lane", - "author_inst": "McGill University" - }, - { - "author_name": "Mairead Whelan", - "author_inst": "University of Calgary" - }, - { - "author_name": "Sara Perlman-Arrow", - "author_inst": "McGill University" - }, - { - "author_name": "Judy Chen", - "author_inst": "McGill University" - }, - { - "author_name": "Hannah Rahim", - "author_inst": "University of Calgary" - }, - { - "author_name": "Natasha Ilincic", - "author_inst": "University of Toronto" - }, - { - "author_name": "Mitchell Segal", - "author_inst": "University of Toronto" - }, - { - "author_name": "Nathan Duarte", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Jordan Van Wyk", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Tingting Yan", - "author_inst": "Univeristy of Toronto" - }, - { - "author_name": "Austin Atmaja", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Simona Rocco", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Abel Joseph", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Lucas Penny", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Clifton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tyler Williamson", - "author_inst": "University of Calgary" - }, - { - "author_name": "Cedric P Yansouni", - "author_inst": "McGill University" - }, - { - "author_name": "Timothy Evans Grant", - "author_inst": "McGill University" - }, - { - "author_name": "Jonathan Chevrier", - "author_inst": "McGill University" - }, - { - "author_name": "Jesse Papenburg", - "author_inst": "McGill University" - }, - { - "author_name": "Matthew P Cheng", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.18.20233908", "rel_title": "A sense of being needed: an interpretative phenomenological analysis of hospital-based allied health professionals' experiences during the COVID-19 pandemic", @@ -1089441,6 +1092503,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.16.20231100", + "rel_title": "Deconditioning in people living with dementia during the COVID-19 pandemic: findings from the Promoting Activity, Independence and Stability in Early Dementia (PrAISED) process evaluation", + "rel_date": "2020-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20231100", + "rel_abs": "BackgroundRestrictions introduced in response to the COVID-19 pandemic led to increased risk of deconditioning in the general population. No empirical evidence of this effect however has been empirically gathered in people living with dementia.\n\nObjectiveThis study aims to identify the causes and effects of COVID-19-related deconditioning in people living with dementia.\n\nDesignLongitudinal phenomenological qualitative study.\n\nSubjectsParticipants living with dementia, their carers and therapists involved in the Promoting Activity, Independence and Stability in Early Dementia (PrAISED) process evaluation during the COVID-19 pandemic.\n\nMethodsQualitative interviews with participants were conducted remotely at two time points. The data were analysed through deductive thematic analysis.\n\nResultsTwenty-four participants living with dementia, 19 carers and 15 therapists took part in the study. A self-reinforcing pattern was common, whereby lockdown made the person apathetic, demotivated, socially-disengaged, and frailer. This reduced activity levels, which in turn reinforced the effects of deconditioning over time. Without external supporters, most participants lacked the motivation / cognitive abilities to keep active. Provided the proper infrastructure and support, some participants could use tele-rehabilitation to combat deconditioning.\n\nConclusionThe added risks and effects of deconditioning on people with dementia require considerable efforts from policy makers and clinicians to ensure that they initiate and maintain physical activity in prolonged periods of social distancing. Delivering rehabilitation in the same way as before the pandemic might not be feasible or sustainable and innovative approaches must be found. Digital support for this population has shown promising results, but still remains a challenge.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Claudio Di Lorito", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Tahir Masud", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "John Gladman", + "author_inst": "University of Notitngham" + }, + { + "author_name": "Maureen Godfrey", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Marianne Dunlop", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rowan H Harwood", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.11.16.20232009", "rel_title": "The total number and mass of SARS-CoV-2 virions in an infected person", @@ -1090153,121 +1093254,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.17.385500", - "rel_title": "An Engineered Antibody with Broad Protective Efficacy in Murine Models of SARS and COVID-19", - "rel_date": "2020-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.17.385500", - "rel_abs": "The recurrent zoonotic spillover of coronaviruses (CoVs) into the human population underscores the need for broadly active countermeasures. Here, we employed a directed evolution approach to engineer three SARS-CoV-2 antibodies for enhanced neutralization breadth and potency. One of the affinity-matured variants, ADG-2, displays strong binding activity to a large panel of sarbecovirus receptor binding domains (RBDs) and neutralizes representative epidemic sarbecoviruses with remarkable potency. Structural and biochemical studies demonstrate that ADG-2 employs a unique angle of approach to recognize a highly conserved epitope overlapping the receptor binding site. In murine models of SARS-CoV and SARS-CoV-2 infection, passive transfer of ADG-2 provided complete protection against respiratory burden, viral replication in the lungs, and lung pathology. Altogether, ADG-2 represents a promising broad-spectrum therapeutic candidate for the treatment and prevention of SARS-CoV-2 and future emerging SARS-like CoVs.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "C. Garrett Rappazzo", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Longping V. Tse", - "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Chengzi I. Kaku", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Daniel Wrapp", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin" - }, - { - "author_name": "Mrunal Sakharkar", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Deli Huang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "Laura M. Deveau", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Thomas J. Yockachonis", - "author_inst": "Paul G. Allen School of Global Animal Health, Washington State University" - }, - { - "author_name": "Andrew S. Herbert", - "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases; The Geneva Foundation" - }, - { - "author_name": "Michael B. Battles", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Michael E. Brown", - "author_inst": "Adimab LLC" - }, - { - "author_name": "James C. Geoghegan", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Jonathan Belk", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Linghang Peng", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "Linlin Yang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "Trevor D. Scobey", - "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute; IAVI Neutralizing Antibody Center; Consortium for HIV/AIDS Vaccine Development (CHAVD" - }, - { - "author_name": "David Nemazee", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "John M. Dye", - "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "James E. Voss", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "Bronwyn M. Gunn", - "author_inst": "Paul G. Allen School of Global Animal Health, Washington State University" - }, - { - "author_name": "Jason S. McLellan", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill; Departments of Microbiology and Immunology, The University of North Carolina at Cha" - }, - { - "author_name": "Lisa E. Gralinski", - "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Laura M. Walker", - "author_inst": "Adimab LLC; Adagio Therapeutics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.11.16.384040", "rel_title": "A continuously self-sterilizing form of copper capable of 99% SARS-CoV-2 deactivation in 30 seconds.", @@ -1091543,6 +1094529,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.12.20230912", + "rel_title": "Prevalence of IgG antibodies against the severe acute respiratory syndrome coronavirus-2 among healthcare workers in Tennessee during May and June, 2020", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230912", + "rel_abs": "SARS-CoV-2 seroprevalence was low (<1%) in this large population of healthcare workers (HCWs) across the state of Tennessee (n=11,787) in May-June 2020. Among those with PCR results, 81.5% of PCR and antibody test results were concordant. SARS-CoV-2 seroprevalence was higher among HCWs working in high-community-transmission regions and among younger workers.\n\nImportanceThese results may be seen as a baseline assessment of SARS-CoV-2 seroprevalence among HCWs in the American South during a period of growth, but not yet saturation, of infections among susceptible populations. In fact, this period of May-June 2020 was marked by the extension of renewed and sustained community-wide transmission after mandatory quarantine periods expired in several more populous regions of Tennessee. Where community transmission remains low, HCWs may still be able to effectively mitigate SARS-CoV-2 transmission, preserving resources for populations at high risk of severe disease, and these sorts of data help highlight such strategies.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Peter F Rebeiro", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Divisions of Infectious Diseases & Epidemiology; Department of Biostatistics" + }, + { + "author_name": "Kara J Levinson", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Lindsay Jolly", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Elizabeth Kassens", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "George J Dizikes", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Richard S Steece", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "David C Metzger", + "author_inst": "Ballad Health" + }, + { + "author_name": "Matthew Loos", + "author_inst": "Ballad Health" + }, + { + "author_name": "Ron Buchheit", + "author_inst": "Department Of Emergency Medicine, University Of Tennessee College of Medicine Chattanooga, Erlanger Health System" + }, + { + "author_name": "Lisa D Duncan", + "author_inst": "University of Tennessee Medical Center, Department of Pathology" + }, + { + "author_name": "Lori A Rolando", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Division of General Internal Medicine & Public Health and Vanderbilt Health and Wellness" + }, + { + "author_name": "Jonathan Schmitz", + "author_inst": "Vanderbilt University School of Medicine , Department of Pathology, Microbiology and Immunology" + }, + { + "author_name": "Heather A Hart", + "author_inst": "Vanderbilt University School of Medicine, Department of Surgery, Division of Trauma" + }, + { + "author_name": "David M Aronoff", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Division of Infectious Diseases; Department of Pathology, Microbiology and Immunology" + }, + { + "author_name": "- Tennessee COVID-19 Serology Study Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.12.20230656", "rel_title": "Development and validation of a highly sensitive and specific electrochemical assay to quantify anti-SARS-CoV-2 IgG antibodies to facilitate pandemic surveillance and monitoring of vaccine response", @@ -1092215,57 +1095276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.13.20231118", - "rel_title": "Quantitative Assessment of Chest CT Patterns in COVID-19 and Bacterial Pneumonia patients: A Deep Learning Perspective", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231118", - "rel_abs": "As the number of COVID-19 patients has increased worldwide, many efforts have been made to find common patterns in CT images of COVID-19 patients and to confirm the relevance of these patterns against other clinical information. The aim of this paper is to propose a new method that allowed us to find patterns which observed on CTs of patients, and further we use these patterns for disease and severity diagnosis. For the experiment, we performed a retrospective cohort study of 170 confirmed patients with COVID-19 and bacterial pneumonia acquired at Yeungnam University hospital in Daegu, Korea. We extracted lesions inside the lungs from the CT images and classified whether these lesions were from COVID-19 patients or bacterial pneumonia patients by applying a deep learning model. From our experiments, we found 20 patterns that have a major effect on the classification performance of the deep learning model. Crazy-paving was extracted as a major pattern of bacterial pneumonia, while Ground-glass opacities (GGOs) in the peripheral lungs as that of COVID-19. Diffuse GGOs in the central and peripheral lungs was considered to be a key factor for severity classification. The proposed method achieved an accuracy of 91.2% for classifying COVID-19 and bacterial pneumonia with 95% reported for severity classification. Chest CT analysis with constructed lesion clusters revealed well-known COVID-19 CT manifestations comparable to manual CT analysis. Moreover, the constructed patient level histogram with/without radiomics features showed feasibility and improved accuracy for both disease and severity classification with key clinical implications.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Myeongkyun Kang", - "author_inst": "Daegu Gyeongbuk Institute of Science and Technology (DGIST)" - }, - { - "author_name": "Philip Chikontwe", - "author_inst": "Daegu Gyeongbuk Institute of Science and Technology (DGIST)" - }, - { - "author_name": "Miguel Luna", - "author_inst": "Daegu Gyeongbuk Institute of Science and Technology (DGIST)" - }, - { - "author_name": "Kyung Soo Hong", - "author_inst": "Yeungnam University Medical Center" - }, - { - "author_name": "Jong Geol Jang", - "author_inst": "Yeungnam University Medical Center" - }, - { - "author_name": "Jongsoo Park", - "author_inst": "Seoul National University Hospital" - }, - { - "author_name": "Kyeong-Cheol Shin", - "author_inst": "Yeungnam University Medical Center" - }, - { - "author_name": "June Hong Ahn", - "author_inst": "Yeungnam University Medical Center" - }, - { - "author_name": "Sang Hyun Park", - "author_inst": "Daegu Gyeongbuk Institute of Science and Technology (DGIST)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.11.13.20229625", "rel_title": "Performance of SARS-CoV-2 Serology tests: Are they good enough?", @@ -1093189,6 +1096199,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.11.13.20231571", + "rel_title": "No evidence of increase in suicide in Greece during the first wave of Covid-19", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231571", + "rel_abs": "Background and ObjectiveMental health outcomes have reportedly worsened in several countries during the Covid-19 pandemic and associated lockdowns. In the present study we examined whether suicides increased in Greece during the first wave of the pandemic.\n\nMethodsWe used daily suicide estimates from a Suicide Observatory in Greece from 2015-2020 and followed three methodologies: A descriptive approach, an interrupted time series analysis, and a differences-in-differences econometric model.\n\nResultsWe did not find any empirical evidence of any increase in suicides during the first wave of Covid-19 and the lockdown in any of the three approaches used.\n\nConclusionsSuicides did not seem to increase during the first wave of covid-19 and lockdown in Greece. However, this does not mean that mental health did not deteriorate, or that we will not observe an increase in suicides during the second wave. Protective factors for Greece during the first wave may include working from home (for those able to tele-work), strong family ties, advertising of a suicide hotline and income support for the unemployed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sotiris Vandoros", + "author_inst": "King's College London and Harvard T.H. Chan School of Public Health, Harvard University" + }, + { + "author_name": "Olga Theodorikakou", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Kyriakos Katsadoros", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Dimitra Zafeiropoulou", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Ichiro Kawachi", + "author_inst": "Harvard T.H. Chan School of Public Health, Harvard University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.14.20229096", "rel_title": "Chest CT features of COVID-19 in the region of Abu Dhabi, UAE- A single institute study", @@ -1093849,65 +1096894,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.11.16.384594", - "rel_title": "Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate", - "rel_date": "2020-11-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.16.384594", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of Nov 15, 2020 has claimed 1,319,946 lives worldwide. Vaccine development focuses on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralisation. Immunogen integrity is therefore important for glycoprotein-based vaccine candidates. Here we show how site-specific glycosylation differs between virus-derived spikes and spike proteins derived from a viral vectored SARS-CoV-2 vaccine candidate. We show that their distinctive cellular secretion pathways result in different protein glycosylation and secretion patterns, which may have implications for the resulting immune response and future vaccine design.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Juliane Brun", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Snezana Vasiljevic", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Bevin Gangadharan", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Mario Hensen", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Anu V. Chandran", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Michelle L. Hill", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "J.L. Kiappes", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Raymond A. Dwek", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Dominic S. Alonzi", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - }, - { - "author_name": "Weston B. Struwe", - "author_inst": "Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford" - }, - { - "author_name": "Nicole Zitzmann", - "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.11.15.383927", "rel_title": "Transcriptome Profiling of different types of human respiratory tract cells infected by SARS-CoV-2 Highlight an unique Role for Inflammatory and Interferon Response", @@ -1095131,6 +1098117,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.11.20229815", + "rel_title": "Excess mortality for care home residents during the first 23 weeks of the COVID-19 pandemic in England: a national cohort study", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229815", + "rel_abs": "BackgroundTo estimate excess mortality for care home residents during the COVID-19 pandemic in England, exploring associations with care home characteristics.\n\nMethodsDaily number of deaths in all residential and nursing homes in England notified to the Care Quality Commission (CQC) from 1st January 2017 to 7th August 2020. Care home level data linked with CQC care home register to identify homes characteristics: client type (over 65s/children and adults), ownership status (for-profit/not-for-profit; branded/independent), and size (small/medium/large).\n\nExcess deaths computed as the difference between observed and predicted deaths using local authority fixed-effect Poisson regressions on pre-pandemic data. Fixed-effect logistic regressions were used to model odds of experiencing COVID-19 suspected/confirmed deaths.\n\nFindingsUp to 7th August 2020 there were 29,542 (95%CI: 25,176 to 33,908) excess deaths in all care homes. Excess deaths represented 6.5% (95%CI: 5.5% to 7.4%) of all care home beds, higher in nursing (8.4%) than residential (4.6%) homes. 64.7% (95%CI: 56.4% to 76.0%) of the excess deaths were confirmed/suspected COVID-19. Almost all excess deaths were recorded in the quarter (27.4%) of homes with any COVID-19 fatalities.\n\nThe odds of experiencing COVID-19 attributable deaths were higher in homes providing nursing services (OR: 1.8, 95%CI: 1.6 to 2.0); to older people and/or with dementia (OR: 5.5, 95%CI: 4.4 to 6.8); among larger (vs. small) homes (OR: 13.3, 95%CI: 11.5 to 15.4); belonging to a large provider/brand (OR: 1.2, 95%CI: 1.1 to 1.3). There was no significant association with for-profit status of providers.\n\nInterpretationTo limit excess mortality, policy should be targeted at care homes to minimise the risk of ingress of disease and limit subsequent transmission. Our findings provide specific characteristic targets for further research on mechanisms and policy priority.\n\nFundingNIHR.\n\nSummary boxO_ST_ABSEvidence before this studyC_ST_ABSGlobally, residents in care homes have experienced disproportionately high morbidity and mortality from COVID-19. Excess mortality incorporates all direct and indirect mortality effects of the pandemic.\n\nWe searched MEDLINE for published literature, pre-publication databases (medRxiv and Lancet pre-print) and grey literature (ONS and Google) for care homes AND COVID-19 AND mortality, to 31st October 2020. We screened for evidence on excess deaths in care homes in England, and international evidence of the association of COVID-19 deaths and outbreaks with care home characteristics.\n\nOfficial estimates from England and Wales have reported aggregated excess deaths by place of occurrence, but we identified no peer-reviewed excess deaths study in this setting. These aggregates, however, do not account for care home residents dying in other settings (e.g. hospital), nor provide sufficient information to reflect on the impacts of enacted policies over the period, or to inform new policies for future virus waves.\n\nPrevious peer-reviewed and pre-publication studies have also shown the heterogeneous effects of COVID-19 by care home characteristics in other countries. Particularly important from the current literature appears to be care home size, with larger care homes tending to be associated with more negative outcomes in studies with smaller sample sizes. A study from the Lothian region of Scotland additionally found excess deaths concentrated in a minority of homes that experienced an outbreak. However, a national breakdown of excess deaths by care home characteristics is largely lacking from the current literature in England, with a specific market structure and policy context.\n\nAdded value of this studyWe use nationally representative administrative data from all care homes in England to estimate overall excess deaths and by care home characteristics: setting type (nursing or residential home), client types (offering services for people aged 65+ and/or people with dementia or offering services to children and adults), ownership status (whether not-for-profit - charity/NHS/LA-run homes - or for-profit), whether known to be affiliated to a large provider/brand or independent, and classification according to their registered maximum bed capacity (small, medium and large).\n\nWe then used multivariable logistic regression to estimate the adjusted odds of a care home experiencing a suspected or confirmed COVID-19 death across these characteristics.\n\nWe found that only 65% of excess deaths were flagged as officially confirmed/suspected COVID-19 attributed. However, almost all excess deaths occurred in the roughly quarter of care homes that reported at least one suspected/confirmed COVID-19 death. After adjusting for other care home characteristics, larger care homes (vs. small) had the highest odds of experiencing at least one suspected/confirmed COVID-19 death. These findings confirm those from the previous literature, in a unique policy context and with national data.\n\nImplications of all the available evidenceThe fact that nearly all excess deaths occurred in care homes with at least one COVID-19 attributed death suggests that directly-attributed deaths are very likely to be under-recorded. It also suggests that any indirect mortality effect, of COVID-19 and any enacted policies, were predominantly constrained to those homes experiencing an outbreak.\n\nLarger homes are likely to experience higher footfall in general, and so higher probability of contact with an infected individual, which is likely a contributing factor to the association. Furthermore, it might be easier to ensure person-centred protocols in small care homes due to the scale.\n\nThere is an urgent need for further research to explore the mechanisms in relation to care home characteristics. Also, to empirically test effective interventions, in consideration of additional impacts on quality of life and psychological wellbeing. However, until this is possible, prioritising existing resources, such as testing and PPE equipment, for care homes to prevent ingress of disease is key to preventing large excess mortality.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marcello Morciano", + "author_inst": "University of Manchester" + }, + { + "author_name": "Jonathan M Stokes", + "author_inst": "University of Manchester" + }, + { + "author_name": "Evangelos Kontopantelis", + "author_inst": "University of Manchester" + }, + { + "author_name": "Ian Hall", + "author_inst": "University of Manchester" + }, + { + "author_name": "Alexander J Turner", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.11.20229393", "rel_title": "Using Convergent Sequential Design for Rapid Complex Case Study Descriptions: Example of Public Health Briefings During the Onset of the COVID-19 Pandemic", @@ -1095935,53 +1098956,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.13.381533", - "rel_title": "Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2", - "rel_date": "2020-11-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.13.381533", - "rel_abs": "The SARS-CoV-2 viral spike (S) protein mediates attachment and entry into host cells and is a major target of vaccine and drug design. Potent SARS-CoV-2 neutralizing antibodies derived from closely related antibody heavy chain genes (IGHV3-53 or 3-66) have been isolated from multiple COVID-19 convalescent individuals. These usually contain minimal somatic mutations and bind the S receptor-binding domain (RBD) to interfere with attachment to the cellular receptor angiotensin-converting enzyme 2 (ACE2). We used antigen-specific single B cell sorting to isolate S-reactive monoclonal antibodies from the blood of a COVID-19 convalescent individual. The seven most potent neutralizing antibodies were somatic variants of the same IGHV3-53-derived antibody and bind the RBD with varying affinity. We report X-ray crystal structures of four Fab variants bound to the RBD and use the structures to explain the basis for changes in RBD affinity. We show that a germline revertant antibody binds tightly to the SARS-CoV-2 RBD and neutralizes virus, and that gains in affinity for the RBD do not necessarily correlate with increased neutralization potency, suggesting that somatic mutation is not required to exert robust antiviral effect. Our studies clarify the molecular basis for a heavily germline-biased human antibody response to SARS-CoV-2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sarah Ashley Clark", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Lars Eric Clark", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Adrian Coscia", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Lindsay G.A. McKay", - "author_inst": "Boston University School of Medicine NEIDL" - }, - { - "author_name": "Sundaresh Shankar", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Rebecca I. Johnson", - "author_inst": "Boston University School of Medicine NEIDL" - }, - { - "author_name": "Anthony Griffiths", - "author_inst": "Boston University School of Medicine NEIDL" - }, - { - "author_name": "Jonathan Abraham", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.12.380931", "rel_title": "The Preclinical Inhibitor GS441524 in Combination with GC376 Efficaciously Inhibited the Proliferation of SARS-CoV-2 in the Mouse Respiratory Tract", @@ -1096833,6 +1099807,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.10.20229005", + "rel_title": "Non-occupational and occupational factors associated with specific SARS-CoV-2 antibodies among Hospital Workers - a multicentre cross-sectional study", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229005", + "rel_abs": "ObjectivesProtecting healthcare workers (HCW) from Coronavirus Disease-19 (COVID-19) is critical to preserve the functioning of healthcare systems. We therefore assessed seroprevalence and identified risk factors for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) seropositivity in this population.\n\nMethodsBetween June 22nd and August 15th 2020, HCW from institutions in Northern/Eastern Switzerland were screened for SARS-CoV-2 antibodies. We recorded baseline characteristics, non-occupational and occupational risk factors. We used pairwise tests of associations and multivariable logistic regression to identify factors associated with seropositivity.\n\nResultsAmong 4664 HCW from 23 healthcare facilities, 139 (3%) were seropositive. Non-occupational exposures independently associated with seropositivity were contact with a COVID-19-positive household (adjusted OR=54, 95%-CI: 31-97) and stay in a COVID-19 hotspot (aOR=2.2, 95%-CI: 1.1-3.9). Blood group 0 vs. non-0 (aOR=0.4, 95%-CI: 0.3-0.7), active smoking (aOR=0.5, 95%-CI: 0.3-0.9) and living with children <12 years (aOR=0.3, 95%-CI: 0.2-0.6) were associated with decreased risk. Occupational risk factors were close contact to COVID-19 patients (aOR=2.8, 95%-CI: 1.5-5.5), exposure to COVID-19-positive co-workers (aOR=2.0, 95%-CI: 1.2-3.1), poor knowledge of standard hygiene precautions (aOR=2.0, 95%-CI: 1.3-3.2), and frequent visits to the hospital canteen (aOR=1.9, 95%-CI: 1.2-3.1).\n\nConclusionsLiving with COVID-19-positive households showed by far the strongest association with SARS-CoV-2 seropositivity. We identified several potentially modifiable risk factors, which might allow mitigation of the COVID-19 risk among HCW. The lower risk among those living with children, even after correction for multiple confounders, is remarkable and merits further study.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Christian R. Kahlert", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland; Children's Hospital of Eastern Switzerland, Depa" + }, + { + "author_name": "Raphael Persi", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Sabine Guesewell", + "author_inst": "Clinical Trials Unit, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Thomas Egger", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Onicio B. Leal-Neto", + "author_inst": "Epitrack, Recife, Brazil; Department of Economics, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Johannes Sumer", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Domenica Flury", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Angela Brucher", + "author_inst": "Psychiatry Services of the Canton of St. Gallen (South), Switzerland" + }, + { + "author_name": "Eva Lemmenmeier", + "author_inst": "Clienia Littenheid AG, Private Clinic for Psychiatry and Psychotherapy, Littenheid, Switzerland" + }, + { + "author_name": "Carsten Moeller", + "author_inst": "Rehabilitation Clinic, Zihlschlacht, Switzerland" + }, + { + "author_name": "Philip Rieder", + "author_inst": "Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Reto Stocker", + "author_inst": "Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Danielle Vuichard-Gysin", + "author_inst": "Thurgau Hospital Group, Division of Infectious Diseases and Hospital Epidemiology, Muensterlingen, Switzerland; Swiss National Center for Infection Prevention (" + }, + { + "author_name": "Benedikt Wiggli", + "author_inst": "Kantonsspital Baden, Division of Infectious Diseases and Hospital Epidemiology, Baden, Switzerland" + }, + { + "author_name": "Werner C. Albrich", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Baharak Babouee Flury", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Ulrike Besold", + "author_inst": "Geriatric Clinic St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Jan Fehr", + "author_inst": "Department of Public and Global Health, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Stefan P. Kuster", + "author_inst": "Federal Office of Public Health, Bern, Switzerland; University Hospital and University of Zurich, Division of Infectious Diseases and Hospital Epidemiology, Zur" + }, + { + "author_name": "Allison McGeer", + "author_inst": "Sinai Health System, Toronto, Canada" + }, + { + "author_name": "Lorenz Risch", + "author_inst": "Labormedizinisches Zentrum Dr Risch Ostschweiz AG, Buchs, Switzerland; Private Universitaet im Fuerstentum Liechtenstein, Triesen, Liechtenstein; Center of Labo" + }, + { + "author_name": "Matthias Schlegel", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Pietro Vernazza", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Andree Friedl", + "author_inst": "Kantonsspital Baden, Division of Infectious Diseases and Hospital Epidemiology, Baden, Switzerland" + }, + { + "author_name": "Philipp Kohler", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.10.20228973", "rel_title": "Comparison of SARS-COV-2 nasal antigen test to nasopharyngeal RT-PCR in mildly symptomatic patients", @@ -1097517,29 +1100606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.11.20229641", - "rel_title": "A computational analysis on Covid-19 transmission raises imuuno-epidemiology concerns.", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229641", - "rel_abs": "For Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) the investigation of the heterogeneity of individual infectiousness becomes important due to the cross reactive immunity of general population. Using a sample of infected population with SARS-COV-2 in close geographical proximity to the initial Severe Advanced Respiratory Syndrome-1 (SARS-1) outbreak, we explored the association between infectors age and dispersion (or heterogeneity) of individual infectiousness (k) in order to investigate the relatedness with the age of an individuals capability to disperse SARS-COV-2. Interestingly, we find a negative association between k and increase of infectors age. Significantly this becomes more evident for the age group of 20-60 years comparing with the infectors with younger age. This raises important immuno-epidemiology concerns for effectiveness of public health measures to contain the disease.\n\nOne Sentence SummaryDispersion of Coronavirus Disease-19 in China differed with age.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Anthony Kyriakopoulos", - "author_inst": "nasco ad biotech. lab" - }, - { - "author_name": "Shi Zhao", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.11.20229559", "rel_title": "Secondary Household Covid-19 Transmission Modelling of Students Returning Home from University", @@ -1098671,6 +1101737,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.11.08.20227819", + "rel_title": "Detection of COVID-19 Disease from Chest X-Ray Images: A Deep Transfer Learning Framework", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20227819", + "rel_abs": "World economy as well as public health have been facing a devastating effect caused by the disease termed as Coronavirus (COVID-19). A significant step of COVID-19 affected patients treatment is the faster and accurate detection of the disease which is the motivation of this study. In this paper, implementation of a deep transfer learning-based framework using a pre-trained network (ResNet-50) for detecting COVID-19 from the chest X-rays was done. Our dataset consists of 2905 chest X-ray images of three categories: COVID-19 affected (219 cases), Viral Pneumonia affected (1345 cases), and Normal Chest X-rays (1341 cases). The implemented neural network demonstrates significant performance in classifying the cases with an overall accuracy of 96%. Most importantly, the model has shown a significantly good performance over the current research-based methods in detecting the COVID-19 cases in the test dataset (Precision = 1.00, Recall = 1.00, F1-score = 1.00 and Specificity = 1.00). Therefore, our proposed approach can be adapted as a reliable method for faster and accurate COVID-19 affected case detection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shadman Sakib", + "author_inst": "Leading University" + }, + { + "author_name": "Md. Abu Bakr Siddique", + "author_inst": "International University of Business Agriculture and Technology" + }, + { + "author_name": "Mohammad Mahmudur Rahman Khan", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Nowrin Yasmin", + "author_inst": "Ahsanullah University of Science and Technology" + }, + { + "author_name": "Anas Aziz", + "author_inst": "Military Institute of Science and Technology" + }, + { + "author_name": "Madiha Chowdhury", + "author_inst": "Bangladesh University of Engineering and Technology" + }, + { + "author_name": "Ihtyaz Kader Tasawar", + "author_inst": "BRAC University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.08.20227884", "rel_title": "Host genetic liability for severe COVID-19 overlaps with alcohol drinking behavior and diabetic outcomes and in over 1 million participants", @@ -1099231,53 +1102340,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.08.20227744", - "rel_title": "Public Health response to an outbreak of SARS-CoV-2 infection in a Barcelona prison", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20227744", - "rel_abs": "An outbreak of SARS-CoV2 infection in a Barcelona prison was studied after seven cases appeared in nine days. One hundred and eighty-four people (148 inmates and 36 prison staff) were evaluated by rt-PCR. Thirty-nine (24.1%) were positive: 33 inmates and six staff members. The inmates were isolated in prison module 4, which was converted into an emergency COVID unit. Two people (one inmate and one health worker) were admitted to hospital for clinical deterioration. There were no deaths. Outbreaks pose a huge risk, must be detected early, are difficult to manage, and require optimal coordination between health and prison authorities.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Andres Marco", - "author_inst": "Prison Health Program. Catalan Institute of Health. CIBERESP, Spain" - }, - { - "author_name": "Carlos Gallego", - "author_inst": "Primary Penitentiary Care Team. La Roca del Valles, Barcelona. Spain." - }, - { - "author_name": "Violeta Perez-Caceres", - "author_inst": "Primary Penitentiary Care Team. La Roca del Valles. Barcelona. Spain." - }, - { - "author_name": "Rafael A Guerrero", - "author_inst": "Prison Health Program. Catalan Institute of Health. Spain." - }, - { - "author_name": "Montserrat Sanchez-Roig", - "author_inst": "Primary Penitentiary Care Team. La Roca del Valles, Barcelona. Spain." - }, - { - "author_name": "M Rosa Sala", - "author_inst": "Epidemiological Surveillance Unit, Public Health Agency of Catalonia. Generalitat of Catalonia. Spain." - }, - { - "author_name": "Juan Fernandez-Nager", - "author_inst": "Primary Penitentiary Care Team. La Roca del Valles, Barceloan. Spain." - }, - { - "author_name": "Elisabet Turu", - "author_inst": "Prison Health Program. Catalan Institute of Health. Institut of Health. Spain." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.08.20228056", "rel_title": "Protocol for a Sequential, Prospective Meta-Analysis to Describe COVID-19 in Pregnancy and Newborn Periods", @@ -1100649,6 +1103711,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.09.20228684", + "rel_title": "Retrospective Analyses of Interventions to Epidemics using a Continuously Updated Model, with Application to the COVID-19 Crisis in New York City", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228684", + "rel_abs": "Retrospective analyses of interventions to epidemics, in which the effectiveness of strategies implemented are compared to hypothetical alternatives, are valuable for performing the cost-benefit calculations necessary to optimize infection countermeasures. SIR (susceptible-infected-removed) models are useful in this regard but are limited by the challenge of deciding how and when to update the numerous parameters as the epidemic changes in response to population behaviors. Behaviors of particular interest include facemasks adoption (at various levels) and social distancing. We present a method that uses a \"dynamic spread function\" to systematically capture the continuous variation in the population behavior, and the gradual change in infection evolution, resulting from interventions. No parameter updates are made by the user. We use the tool to quantify the reduction in infection rate realizable from the population of New York City adopting different facemask strategies during COVID-19. Assuming a baseline facemask of 67% filtration efficiency, calculations show that increasing the efficiency to 80% could have reduced the roughly 5000 new infections per day occurring at the peak of the epidemic to around 4000. Population behavior that may not be varied as part of the retrospective analysis, such as social distancing in a facemask analysis, are automatically captured as part of the calibration of the dynamic spread function.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jenna Osborn", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Shayna Berman", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Sara Bender_Bier", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Gavin D'Souza", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Matthew Myers", + "author_inst": "U. S. FDA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.09.20228098", "rel_title": "Peginterferon-lambda for the treatment of COVID-19 in outpatients", @@ -1101465,33 +1104562,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.12.379917", - "rel_title": "Identifying and prioritizing potential human-infecting viruses from their genome sequences", - "rel_date": "2020-11-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.12.379917", - "rel_abs": "Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly-discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (AUC = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalisable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from non-human primates, but not other mammalian or avian host groups. A second application showed that our models could have identified SARS-CoV-2 as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic SARS-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterisation of viruses.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nardus Mollentze", - "author_inst": "MRC - University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Simon Babayan", - "author_inst": "Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow" - }, - { - "author_name": "Daniel Streicker", - "author_inst": "Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2020.11.11.378828", "rel_title": "Bifurcations and mutation hot-spots in the SARS-CoV-2 spike protein", @@ -1102887,6 +1105957,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.07.20227462", + "rel_title": "Synthetic Reproduction and Augmentation of COVID-19 Case Reporting Data by Agent-Based Simulation", + "rel_date": "2020-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227462", + "rel_abs": "We generate synthetic data documenting COVID-19 cases in Austria by the means of an agent-based simulation model. The model simulates the transmission of the SARS-CoV-2 virus in a statistical replica of the population and reproduces typical patient pathways on an individual basis while simultaneously integrating historical data on the implementation and expiration of population-wide countermeasures. The resulting data semantically and statistically aligns with an official epidemiological case reporting data set and provides an easily accessible, consistent and augmented alternative. Our synthetic data set provides additional insight into the spread of the epidemic by synthesizing information that cannot be recorded in reality.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nikolas Popper", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "Melanie Zechmeister", + "author_inst": "DEXHELPP - Decision Support for Health Policy and Planning" + }, + { + "author_name": "Dominik Brunmeir", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Claire Rippinger", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Nadine Weibrecht", + "author_inst": "DEXHELPP - Decision Support for Health Policy and Planning" + }, + { + "author_name": "Christoph Urach", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Martin Bicher", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "G\u00fcnter Schneckenreither", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "Andreas Rauber", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.06.20227330", "rel_title": "The COVID-19 epidemic in the Czech Republic: retrospective analysis of measures (not) implemented during the spring first wave", @@ -1103415,97 +1106536,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.08.20224790", - "rel_title": "Therapeutic use of convalescent plasma in COVID-19 patients with immunodeficiency: A systematic review", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20224790", - "rel_abs": "0In the absence of effective countermeasures, human convalescent plasma has been widely used to treat severe acute respiratory syndrome coronavirus 2 including among patients with innate or acquired immunodeficiency. However, the association between COVID-19-associated mortality in patients with immunodeficiency and therapeutic use of convalescent plasma is unknown. We review clinical features and treatment protocols of COVID-19 patients with immunodeficiency after treatment with human convalescent plasma. We also discuss the time course and clinical features of recovery. These insights provide evidence for the need to develop a clear treatment protocol for COVID-19 patients with immunodeficiency and support the efficacy of convalescent plasma in patients with primary or secondary immunodeficiency.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Jonathon Senefeld", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Stephen A Klassen", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Shane K Ford", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Chad C Wiggins", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Bruce C Bostrom", - "author_inst": "Children's Hospital of Minnesota" - }, - { - "author_name": "Michael A Thompson", - "author_inst": "Aurora Cancer Care, Advocate Aurora Health" - }, - { - "author_name": "Sarah E Baker", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Wayne T Nicholson", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Patrick W Johnson", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Rickey E Carter", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Jeffrey P Henderson", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "William R Hartman", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Liise-anne Pirofski", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "R. Scott Wright", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "DeLisa Fairweather", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Katelyn A Bruno", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Nigel S Paneth", - "author_inst": "Michigan State University" - }, - { - "author_name": "Arturo Casadevall", - "author_inst": "Johns Hopkins School of Public Health" - }, - { - "author_name": "Michael J Joyner", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.06.20227363", "rel_title": "Performance of qualitative and quantitative antigen tests for SARS-CoV-2 in early symptomatic patients using saliva", @@ -1104449,6 +1107479,93 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.11.10.376673", + "rel_title": "SARS-CoV-2 infection causes transient olfactory dysfunction in mice", + "rel_date": "2020-11-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.10.376673", + "rel_abs": "Olfactory dysfunction caused by SARS-CoV-2 infection represents as one of the most predictive and common symptoms in COVID-19 patients. However, the causal link between SARS-CoV-2 infection and olfactory disorders remains lacking. Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), resulting in transient olfactory dysfunction in humanized ACE2 mice. The sustentacular cells and Bowmans gland cells in OE were identified as the major targets of SARS-CoV-2 before the invasion into olfactory sensory neurons. Remarkably, SARS-CoV-2 infection triggers cell death and immune cell infiltration, and impairs the uniformity of OE structure. Combined transcriptomic and proteomic analyses reveal the induction of antiviral and inflammatory responses, as well as the downregulation of olfactory receptors in OE from the infected animals. Overall, our mouse model recapitulates the olfactory dysfunction in COVID-19 patients, and provides critical clues to understand the physiological basis for extrapulmonary manifestations of COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Cheng-Feng Qin", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qing Ye", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Jia Zhou", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Guan Yang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Rui-Ting Li", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qi He", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Yao Zhang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Shu-Jia Wu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Qi Chen", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Jia-Hui Shi", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Rong-Rong Zhang", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Hui-Min Zhu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Hong-Ying Qiu", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Tao Zhang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Yong-Qiang Deng", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Xiao-Feng Li", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Ping Xu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Xiao Yang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.05.20224436", "rel_title": "Anxiety and depression among people living in quarantine centers during COVID-19 pandemic: A mixed method study from western Nepal", @@ -1104981,33 +1108098,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.11.09.374173", - "rel_title": "Towards Targeting the Disordered SARS-CoV-2 Nsp2 C-terminal Region: Partial Structure and Dampened Mobility Revealed by NMR Spectroscopy", - "rel_date": "2020-11-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.09.374173", - "rel_abs": "Intrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many virus use their own IDPs to \"hack\" these processes to disactive host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational perferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2 interacts with human proteins that regulate translation initiation and endosome vesicle sorting, and the C-terminal region of this protein is predicted to be disordered. Molecules that block these interactions could be valuable leads for drug development. To enable inhibitor screening and to uncover conformational preferences and dynamics, we have expressed and purified the 13C,15N-labeled C-terminal region of Nsp2. The 13C{beta} and backbone 13CO, 1HN, 13C and 15N nuclei were assigned by analysis of a series of 2D 1H-15N HSQC and 13C-15N CON as well as 3D HNCO, HNCA, CBCAcoNH and HncocaNH spectra. Overall, the chemical shift data confirm that this region is chiefly disordered, but contains two five-residue segments that adopt a small population of {beta}-strand structure. Whereas the region is flexible on ms/ms timescales as gauged by T1{rho} measurements, the {1H}-15N NOEs reveal a flexibility on ns/ps timescales that is midway between a fully flexible and a completely rigid chain.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Miguel Mompe\u00e1n", - "author_inst": "Spanish National Research Council" - }, - { - "author_name": "Miguel \u00c1. Trevi\u00f1o", - "author_inst": "Rocasolano Institute for Physical Chemistry, Spanish National Research Council (IQFR/CSIC)" - }, - { - "author_name": "Douglas V. Laurents", - "author_inst": "\"Rocasolano\" Institute for Physical Chemistry, Spanish National Research Council (IQFR/CSIC)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.11.08.372581", "rel_title": "Resistance of endothelial cells to SARS-CoV-2 infection in vitro", @@ -1106130,6 +1109220,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.06.20226977", + "rel_title": "Team contact sports in times of the COVID-19 pandemic- a scientific concept for the Austrian football league", + "rel_date": "2020-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20226977", + "rel_abs": "BackgroundSince the beginning of the COVID -19 pandemic, many contact sport teams are facing major challenges to safely continue training and competition.\n\nObjectiveWe present the design and implementation of a structured monitoring concept for the Austrian national football league\n\nMethods146 professional players from five clubs of the professional Austrian football league were monitored for a period of 12 weeks. Subjective health parameters, PCR- test results and data obtained from a geo-tracking app were collected. Simulations modelling the consequences of a COVID-19 case with increasing reproduction number were computed.\n\nResultsNo COVID-19 infection occurred during the observation period in the players. Infections in the nearer surroundings lead to increased perceived risk of infection. Geo tracking was particularly hindered due to technical problems and reluctance of users. Simulation models suggested a hypothetical shut-down of all training and competition activities.\n\nConclusionsA structured monitoring concept can help to continue contact sports safely in times of a pandemic. Cooperation of all involved is essential.\n\nTrial registrationID: DRKS00022166 15/6/2020 https://www.who.int/ictrp/search/en/\n\nKey Points- The results of this study can inform the development of future prevention and monitoring strategies in professional football and beyond, potentially serving as a blueprint for the safe continuation of sports and physical activity, across a broad range of settings, during and following a pandemic such as COVID-19.\n- Health parameters should be digitally recorded and closely monitored to enable quick response in case of a COVID-19 infection.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Antje van der Zee-Neuen", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Dagmar Schaffler-Schaden", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Juergen Herfert", + "author_inst": "Red Bull Athlete Performance Centre" + }, + { + "author_name": "James O Brien", + "author_inst": "Red Bull Athlete Performance Centre" + }, + { + "author_name": "Tim Johansson", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Patrick Kutschar", + "author_inst": "patrick.kutschar@pmu.ac.at" + }, + { + "author_name": "Alexander Seymer", + "author_inst": "University of Salzburg" + }, + { + "author_name": "Stephan Ludwig", + "author_inst": "University of Muenster" + }, + { + "author_name": "Thomas Stoeggl", + "author_inst": "University of Salzburg" + }, + { + "author_name": "David Keeley", + "author_inst": "Electronic Caregiver" + }, + { + "author_name": "Herbert Resch", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Juergen Osterbrink", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Maria Flamm", + "author_inst": "Paracelsus Medical University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.05.20226654", "rel_title": "Multiplexed, quantitative serological profiling of COVID-19 from a drop of blood by a point-of-care test", @@ -1107018,105 +1110175,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.06.20226803", - "rel_title": "Longitudinal Physiological Data from a Wearable Device Identifies SARS-CoV-2 Infection and Symptoms and Predicts COVID-19 Diagnosis", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20226803", - "rel_abs": "BackgroundChanges in autonomic nervous system function, characterized by heart rate variability (HRV), have been associated with and observed prior to the clinical identification of infection. We performed an evaluation of this metric collected by wearable devices, to identify and predict Coronavirus disease 2019 (COVID-19) and its related symptoms.\n\nMethodsHealth care workers in the Mount Sinai Health System were prospectively followed in an ongoing observational study using the custom Warrior Watch Study App which was downloaded to their smartphones. Participants wore an Apple Watch for the duration of the study measuring HRV throughout the follow up period. Surveys assessing infection and symptom related questions were obtained daily.\n\nFindingsUsing a mixed-effect COSINOR model the mean amplitude of the circadian pattern of the standard deviation of the interbeat interval of normal sinus beats (SDNN), a HRV metric, differed between subjects with and without COVID-19 (p=0.006). The mean amplitude of this circadian pattern differed between individuals during the 7 days before and the 7 days after a COVID-19 diagnosis compared to this metric during uninfected time periods (p=0.01). Significant changes in the mean MESOR and amplitude of the circadian pattern of the SDNN was observed between the first day of reporting a COVID-19 related symptom compared to all other symptom free days (p=0.01).\n\nInterpretationLongitudinally collected HRV metrics from a commonly worn commercial wearable device (Apple Watch) can identify the diagnosis of COVID-19 and COVID-19 related symptoms. Prior to the diagnosis of COVID-19 by nasal PCR, significant changes in HRV were observed demonstrating its predictive ability to identify COVID-19 infection.\n\nFundingSupport was provided by the Ehrenkranz Lab For Human Resilience, the BioMedical Engineering and Imaging Institute, The Hasso Plattner Institute for Digital Health at Mount Sinai, The Mount Sinai Clinical Intelligence Center and The Dr. Henry D. Janowitz Division of Gastroenterology.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Robert P Hirten", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Matteo Danieletto", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lewis Tomalin", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Katie Hyewon Choi", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Micol Zweig", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Eddye Golden", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sparshdeep Kaur", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Drew Helmus", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Anthony Biello", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Renata Pyzik", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ismail Nabeel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexander Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin S Glicksberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Matthew Levin", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "David Reich", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Dennis Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erwin P Bottinger", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Laurie Keefer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Mayte Suarez-Farinas", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Girish N Nadkarni", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Zahi A Fayad", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.06.20225938", "rel_title": "Validation of home oxygen saturations as a marker of clinical deterioration in patients with suspected COVID-19", @@ -1107932,6 +1110990,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.11.05.20226472", + "rel_title": "How has Covid-19 affected mental health nurses and the delivery of mental health nursing care in the UK? Results of a mixed methods study", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226472", + "rel_abs": "IntroductionWhile evidence has emerged concerning the impact of Covid-19 on the general population and the challenges facing health services, much less is known regarding how the pandemic has directly affected the delivery of mental health nursing care.\n\nAimThis paper aims to explore how Covid-19 has affected the ability of mental health nurses to deliver care in community and inpatient mental health services in the UK.\n\nMethodWe investigated staff reports regarding the impact of the Covid-19 pandemic on mental healthcare and mental health service users in the UK, using a mixed methods online survey. A total of 897 nurses across a range of inpatient and community settings participated.\n\nDiscussionKey themes within the data explore: new ways of working; remote working; risks of infection/infection control challenges; and the impact on service users. Targeted guidelines are required to support mental health nurses providing care and support during a pandemic to people in severe mental distress, often in unsuitable environments.\n\nImplications for PracticeService developments need to occur alongside tailored guidance and support for staff welfare supported by clear leadership. These findings identify areas requiring attention and investment to prepare for future crises and the consequences of the pandemic.\n\nAccessible SummaryO_ST_ABSWhat is known on the subject?C_ST_ABSDuring the Covid-19 pandemic there has been research considering the impact on medical healthcare professionals and the mental health needs of the general population. However, limited focus has been placed on mental health services or mental health staff providing care in the community and in hospitals. Whilst nurses make up the largest section of the mental health workforce in the UK, the impact that this pandemic has had on their work has been largely ignored.\n\nWhat the paper adds to existing knowledge?This paper provides a unique insight into the experiences and impact that the Covid-19 pandemic has had on mental health nurses across a range of community and inpatient settings to understand what has changed in their work and the care they can and do provide during this crisis. This includes exploring how services have changed, the move to remote working, the impact of the protective equipment crisis on nurses, and the difficult working conditions facing those in inpatient settings where there is minimal guidance provided.\n\nWhat are the implications for practice?By understanding the impact the pandemic has had on mental health nursing care, we can understand the gaps in guidance that exist, the challenges being faced, and the impact the crisis has had on care for mental health service users. By doing so we can plan for the ongoing nature of this pandemic as well as the aftermath that the crisis may leave for our service users and workforce alike.\n\nRelevance StatementThis paper provides insight into the impact that the Covid-19 pandemic has had on the service and care that mental health nurses are expected to and can provide. As a workforce that often requires ongoing face to face contact with service users, many in serious distress, in inpatient and community settings, it is important that we understand their experiences and the challenges and risks that face this workforce. This will enable us to ensure that future planning, guidance, support and safeguarding can take place during the ongoing and future crises.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Una Foye", + "author_inst": "King's College London" + }, + { + "author_name": "Christian Dalton-Locke", + "author_inst": "University College London" + }, + { + "author_name": "Jasmine Harju-Seppanen", + "author_inst": "University College London" + }, + { + "author_name": "Rebecca Lane", + "author_inst": "Kings College London" + }, + { + "author_name": "Lewys Beams", + "author_inst": "South London and Maudsley Foundation Trust" + }, + { + "author_name": "Norha Vera San Juan", + "author_inst": "King's College London" + }, + { + "author_name": "Sonia Johnson", + "author_inst": "University College London" + }, + { + "author_name": "Alan Simpson", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2020.11.04.20226118", "rel_title": "Elevated COVID-19 outcomes among persons living with diagnosed HIV infection in New York State: Results from a population-level match of HIV, COVID-19, and hospitalization databases", @@ -1108892,45 +1111997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.11.04.20226233", - "rel_title": "Effectiveness of an Ozone Disinfecting and Sanitizing Cabinet to Decontaminate a Surrogate Virus for SARS-CoV-2 on N-95 Masks", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20226233", - "rel_abs": "Medical demands during the COVID-19 pandemic have triggered a grave shortage of medical-grade personal protective equipment (PPE), especially, N95 respirators. N95 respirators are critical for the personal protection of medical providers and others when being exposed to individuals with infections caused by the SARS-CoV-2 coronavirus. To address the shortage of N95 respirators, innovative methods are needed to decontaminate coronaviruses from N95 respirators, allowing them to be safely reused by healthcare workers. For this research, we use a commercial ozone disinfecting cabinet to examine the efficacy of ozone-based disinfection of a conservative surrogate virus for SARS-CoV-2, the MS2 bacteriophage. Treatment of mask materials with enhanced ozone treatment resulted in 2.38-log 10 (>99%) reduction of phage from household dust masks and a range of 1.43-log 10 (96.2%) to 4-log 10 (99.99%) reductions of phage from common N95 mask materials.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Megan S. Beaudry", - "author_inst": "University of Georgia" - }, - { - "author_name": "Julia C. Frederick", - "author_inst": "University of Georgia" - }, - { - "author_name": "Megan E. J. Lott", - "author_inst": "University of Georgia" - }, - { - "author_name": "William A. Norfolk", - "author_inst": "University of Georgia" - }, - { - "author_name": "Travis C Glenn", - "author_inst": "University of Georgia" - }, - { - "author_name": "Erin K. Lipp", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.05.20226415", "rel_title": "Psychological resilience, coping behaviors, and social support among healthcare workers during the COVID-19 pandemic: a systematic review of quantitative studies", @@ -1109914,6 +1112980,125 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.11.06.370676", + "rel_title": "Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago", + "rel_date": "2020-11-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.06.370676", + "rel_abs": "Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The SARS-CoV-2 pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, we used a combinatorial human antibody library constructed 20 years before the COVID-19 pandemic to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in crystal structures with SARS-CoV-2 spike RBD. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of human immune responses to SARS-CoV-2.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Min Qiang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Peixiang Ma", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Yu Li", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Hejun Liu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Adam Harding", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chenyu Min", + "author_inst": "Velox Pharmaceuticals" + }, + { + "author_name": "Lili Liu", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Meng Yuan", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Qun Ji", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Pingdong Tao", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Xiaojie Shi", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Zhean Li", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Fulian Wang", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Yu Zhang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Nicholas C. Wu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Chang-Chun D. Lee", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Xueyong Zhu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Javier Gilbert-Jaramillo", + "author_inst": "University of Oxford" + }, + { + "author_name": "Abhishek Saxena", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Xingxu Huang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Hou Wang", + "author_inst": "ShOx Science Limited" + }, + { + "author_name": "William James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Raymond A. Dwek", + "author_inst": "Oxford Glycobiology Institute" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Guang Yang", + "author_inst": "ShanghaiTech University;Velox Pharmaceuticals" + }, + { + "author_name": "Richard A. Lerner", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.03.367391", "rel_title": "Evolution of Antibody Immunity to SARS-CoV-2", @@ -1110649,185 +1113834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2020.11.04.20225680", - "rel_title": "Shorter androgen receptor polyQ alleles protect against life-threatening COVID-19 disease in males.", - "rel_date": "2020-11-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225680", - "rel_abs": "BackgroundCOVID-19 presentation ranges from asymptomatic to fatal. The variability in severity may be due in part to impaired Interferon type I response due to specific mutations in the host genome or to autoantibodies, explaining about 15% of the cases when combined. Exploring the host genome is thus warranted to further elucidate disease variability.\n\nMethodsWe developed a synthetic approach to genetic data representation using machine learning methods to investigate complementary genetic variability in COVID-19 infected patients that may explain disease severity, due to poly-amino acids repeat polymorphisms. Using host whole-exome sequencing data, we compared extreme phenotypic presentations (338 severe versus 300 asymptomatic cases) of the entire (men and women) Italian GEN-COVID cohort of 1178 subjects infected with SARS-CoV-2. We then applied the LASSO Logistic Regression model on Boolean gene-based representation of the poly-amino acids variability.\n\nFindingsShorter polyQ alleles ([≤]22) in the androgen receptor (AR) conferred protection against a more severe outcome in COVID-19 infection. In the subgroup of males with age <60 years, testosterone was higher in subjects with AR long-polyQ ([≥]23), possibly indicating receptor resistance (p=0.004 Mann-Whitney U test). Inappropriately low testosterone levels for the long-polyQ alleles predicted the need for intensive care in COVID-19 infected men. In agreement with the known anti-inflammatory action of testosterone, patients with long-polyQ ([≥]23) and age>60 years had increased levels of C Reactive Protein (p=0.018).\n\nInterpretationOur results may contribute to design reliable clinical and public health measures and provide a rationale to test testosterone treatment as adjuvant therapy in symptomatic COVID-19 men expressing AR polyQ longer than 23 repeats.\n\nFundingMIUR project \"Dipartimenti di Eccellenza 2018-2020\" to Department of Medical Biotechnologies University of Siena, Italy (Italian D.L. n.18 March 17, 2020). Private donors for COVID research and charity funds from Intesa San Paolo.\n\nBoxesO_ST_ABSEvidence before this studyC_ST_ABSWe searched on Medline, EMBASE, and Pubmed for articles published from January 2020 to August 2020 using various combinations of the search terms \"sex-difference\", \"gender\" AND SARS-Cov-2, or COVID. Epidemiological studies indicate that men and women are similarly infected by COVID-19, but the outcome is less favorable in men, independently of age. Several studies also showed that patients with hypogonadism tend to be more severely affected. A prompt intervention directed toward the most fragile subjects with SARS-Cov2 infection is currently the only strategy to reduce mortality. glucocorticoid treatment has been found cost-effective in improving the outcome of severe cases. Clinical algorithms have been proposed, but little is known on the ability of genetic profiling to predict outcome and disclose novel therapeutic strategies.\n\nAdded-value of this studyIn a cohort of 1178 men and women with COVID-19, we used a supervised machine learning approach on a synthetic representation of the uncovered variability of the human genome due to poly-amino acid repeats. Comparing the genotype of patients with extreme manifestations (severe vs. asymptomatic), we found that the poly-glutamine repeat of the androgen receptor (AR) gene is relevant for COVID-19 disease and defective AR signaling identifies an association between male sex, testosterone exposure, and COVID-19 outcome. Failure of the endocrine feedback to overcome AR signaling defect by increasing testosterone levels during the infection leads to the fact that polyQ becomes dominant to T levels for the clinical outcome.\n\nImplications of all the available evidenceWe identify the first genetic polymorphism predisposing some men to develop a more severe disease irrespectively of age. Based on this, we suggest that sizing the AR poly-glutamine repeat has important implications in the diagnostic pipeline of patients affected by life-threatening COVID-19 infection. Most importantly, our studies open to the potential of using testosterone as adjuvant therapy for severe COVID-19 patients having defective androgen signaling, defined by this study as [≥]23 PolyQ repeats and inappropriate levels of circulating androgens.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Margherita Baldassarri", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Nicola Picchiotti", - "author_inst": "University of Siena, DIISM-SAILAB, Siena, Italy; Department of Mathematics, University of Pavia, Pavia, Italy" - }, - { - "author_name": "Francesca Fava", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica" - }, - { - "author_name": "Chiara Fallerini", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Elisa Benetti", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Sergio Daga", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Floriana Valentino", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Gabriella Doddato", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Simone Furini", - "author_inst": "2)\tMed Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Annarita Giliberti", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Rossella Tita", - "author_inst": "Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy" - }, - { - "author_name": "Sara Amitrano", - "author_inst": "Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy" - }, - { - "author_name": "Mirella Bruttini", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica" - }, - { - "author_name": "Susanna Croci", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Ilaria Meloni", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Anna Maria Pinto", - "author_inst": "Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy" - }, - { - "author_name": "Chiara Gabbi", - "author_inst": "Independent Medical Scientist, Milan, Italy" - }, - { - "author_name": "Francesca Sciarra", - "author_inst": "Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy" - }, - { - "author_name": "Mary Anna Venneri", - "author_inst": "Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy" - }, - { - "author_name": "Marco Gori", - "author_inst": "University of Siena, DIISM-SAILAB, Siena, Italy; Universite Cote d Azur, Inria, CNRS, I3S, Maasai" - }, - { - "author_name": "Maurizio Sanarico", - "author_inst": "Independent Data Scientist, Milan, Italy" - }, - { - "author_name": "Francis P Crawley", - "author_inst": "Good Clinical Practice Alliance-Europe (GCPA) and Strategic Initiative for Developing Capacity in Ethical Review-Europe (SIDCER), Leuven, Belgium" - }, - { - "author_name": "Uberto Pagotto", - "author_inst": "Unit of Endocrinology and Prevention and Care of Diabetes, Center for Applied" - }, - { - "author_name": "Flaminia Fanelli", - "author_inst": "Unit of Endocrinology and Prevention and Care of Diabetes, Center for Applied" - }, - { - "author_name": "Marco Mezzullo", - "author_inst": "Unit of Endocrinology and Prevention and Care of Diabetes, Center for Applied" - }, - { - "author_name": "Elena Dominguez-Garrido", - "author_inst": "Molecular Diagnostic Unit, Fundacion Rioja Salud, Logrono, La Rioja, Spain" - }, - { - "author_name": "Laura Planas-Serra", - "author_inst": "Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; CIBERER, Centro de Investigacion Biomedica en Red de En" - }, - { - "author_name": "Agatha Schluter", - "author_inst": "Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; CIBERER, Centro de Investigacion Biomedica en Red de En" - }, - { - "author_name": "Roger Colobran", - "author_inst": "Immunology Division, Genetics Department. Hospital Universitari Vall d Hebron. \tVall d Hebron Research Institute. Vall d Hebron Barcelona Hospital Campus. Unive" - }, - { - "author_name": "Pere Soler-Palacin", - "author_inst": "Immunology Division, Genetics Department. Hospital Universitari Vall d Hebron. \tVall d Hebron Research Institute. Vall d Hebron Barcelona Hospital Campus. Unive" - }, - { - "author_name": "Pablo Lapunzina", - "author_inst": "CIBERER, Centro de Investigacion Biomedica en Red de Enfermedades Raras, ISCIII, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; Institute of Medical and Mol" - }, - { - "author_name": "Jair Tenorio", - "author_inst": "CIBERER, Centro de Investigacion Biomedica en Red de Enfermedades Raras, ISCIII, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; Institute of Medical and Mol" - }, - { - "author_name": "- Spanish Covid HGE", - "author_inst": "" - }, - { - "author_name": "Aurora Pujol", - "author_inst": "Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain CIBERER, Centro de Investigacion Biomedica en Red de Enf" - }, - { - "author_name": "Maria Grazia Castagna", - "author_inst": "Department of Medical, Surgical and Neurological Sciences, University of Siena, \tItaly" - }, - { - "author_name": "Marco Marcelli", - "author_inst": "Department of Medicine, Baylor College of Medicine, Houston TX, USA" - }, - { - "author_name": "Andrea M Isidori", - "author_inst": "Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy" - }, - { - "author_name": "- GEN-COVID Multicenter Study", - "author_inst": "" - }, - { - "author_name": "Alessandra Renieri", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetic" - }, - { - "author_name": "Elisa Frullanti", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Francesca Mari", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.11.03.20225375", "rel_title": "Adaptive responses to SARS-CoV-2 infection linked to accelerated aging measures predict adverse outcomes in patients with severe COVID-19", @@ -1112435,6 +1115441,101 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.11.05.370239", + "rel_title": "SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging", + "rel_date": "2020-11-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.05.370239", + "rel_abs": "Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, investigation of the SARS-CoV-2 infection in the native cellular context is scarce, and there is a lack of comprehensive knowledge on SARS-CoV-2 replicative cycle. Understanding the genome replication, assembly and egress of SARS-CoV-2, a multistage process that involves different cellular compartments and the activity of many viral and cellular proteins, is critically important as it bears the means of medical intervention to stop infection. Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Our results reveal at the whole cell level profound cytopathic effects of SARS-CoV-2 infection, exemplified by a large amount of heterogeneous vesicles in the cytoplasm for RNA synthesis and virus assembly, formation of membrane tunnels through which viruses exit, and drastic cytoplasm invasion into nucleus. Furthermore, cryoET of cell lamellae reveals how viral RNAs are transported from double-membrane vesicles where they are synthesized to viral assembly sites; how viral spikes and RNPs assist in virus assembly and budding; and how fully assembled virus particles exit the cell, thus stablishing a model of SARS-CoV-2 genome replication, virus assembly and egress pathways.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Luiza Mendonca", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew Howe", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "James B Gilchrist", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Dapeng Sun", + "author_inst": "University of Oxford" + }, + { + "author_name": "Michael Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura C Zanetti-Domingues", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Benji Bateman", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Anna-Sophia Krebs", + "author_inst": "University of Oxford" + }, + { + "author_name": "Long Chen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julika Radecke", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Yuewen Sheng", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Vivian D Li", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Tao Ni", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ilias Kounatidis", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Mohamed A Koronfel", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Marta Szynkiewicz", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Maria Harkiolaki", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Marisa L Martin-Fernandez", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "William James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peijun Zhang", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.05.368647", "rel_title": "SLAMF7 engagement super-activates macrophages in acute and chronic inflammation", @@ -1112943,49 +1116044,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.30.20223446", - "rel_title": "Investigating the effects of absolute humidity and human encounters on transmission of COVID-19 in the United States", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223446", - "rel_abs": "BackgroundMounting evidence suggests that the primary mode of transmission of SARS-CoV-2 is aerosolized transmission from close contact with infected individuals. Even though transmission is a direct result of human encounters, environmental conditions, such as lower humidity, may enhance aerosolized transmission risks similar to other respiratory viruses such as influenza.\n\nMethodsWe utilized dynamic time warping to cluster all 3,137 counties in the United States based on temporal data on absolute humidity from March 10 to September 29, 2020. We then used a multivariate generalized additive model (GAM) combining data on human mobility derived from mobile phone data with humidity data to identify the potential effect of absolute humidity and mobility on new daily cases of COVID-19 while considering the temporal differences between seasons.\n\nResultsThe clustering analysis found ten groups of counties with similar humidity levels. We found a significant negative effect between increasing humidity and new cases of COVID-19 in most regions, particularly in the period from March to July. The effect was greater in regions with generally lower humidity in the Western, Midwest, and Northeast regions of the US. In the two regions with the largest effect, a 1 g/m3 increase of absolute humidity resulted in a 0.21 and 0.15 decrease in cases. The effect of mobility on cases was positive and significant across all regions in the July-Sept time period, though the relationship in some regions was more mixed in the March to June period.\n\nConclusionsWe found that increasing humidity played an important role in falling cases in the spring, while increasing mobility in the summer contributed more significantly to increases in the summer. Our findings suggest that, similar to other respiratory viruses, the decreasing humidity in the winter is likely to lead to an increase in COVID-19 cases. Furthermore, the fact that mobility data were positively correlated suggests that efforts to counteract the rise in cases due to falling humidity can be effective in limiting the burden of the pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gary Lin", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Alisa Hamilton", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Oliver Gatalo", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Fardad Haghpanah", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Takeru Igusa", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Eili Klein", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "- CDC MInD-Healthcare Network", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.01.20223982", "rel_title": "Filtration Performance Degradation of In-Use Masks by Vapors from Alcohol-Based Hand Sanitizers and the Mitigation Solutions", @@ -1113893,6 +1116951,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.11.02.20224519", + "rel_title": "Are Mobile Phones part of the chain of transmission of SARS-CoV-2 in the hospital?", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224519", + "rel_abs": "SARS-CoV-2 cross-transmission has become an concern in hospitals. We investigate healthcare workers(HCWs) knowledge about SARS-CoV-2 cross-transmission and conceptions whether the virus can remain on HCWs mobile phones(MPs) and be part of the chain of transmission.\n\nA cross-sectional study was conducted at a COVID-19 Intensive Care Unit of a teaching-hospital. Fifty-one MPs were swabbed and a questionnaire about hand hygiene and MP use and disinfection was applied after an educational campaign. Although most of HCWs believed on the importance of cross-transmission and increased hand hygiene adhesion and MP disinfection during the pandemic, SARS-CoV-2 RNA was detected in two MPs(culture of the samples was negative).\n\nImplementation of official hospital policies to guide HCWs regarding disinfection and care of personal MP are needed.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Evelyn Patricia Sanchez Espinoza", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Marina Farrel Cortes", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Saidy Vasconez Nogueira", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Anderson Vincente de Paula", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Thais Guimaraes", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Lucy Santos Vilas Boas", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Marcelo Park", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Cristina Carvalho da Silva", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Ingra Morales", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Lauro Vieira Perdigao Neto", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Tania Regina Tozetto-Mendoza", + "author_inst": "Instituto de Medicina Tropical de Sao Paulo. Universidade de Sao Paulo." + }, + { + "author_name": "Icaro Boszczowski", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Ester Sabino", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Maria Cassia Mendes-Correa", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Anna Sara Shafferman Levin", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil." + }, + { + "author_name": "Silvia Figueiredo Costa", + "author_inst": "Department of Infectious diseases, Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.11.01.20214122", "rel_title": "Simulation model for productivity, risk and GDP impact forecasting of the COVID-19 portfolio vaccines", @@ -1114449,101 +1117586,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.02.20223636", - "rel_title": "Caspases in COVID-19 Disease and Sequela and the Therapeutic Potential of Caspase Inhibitors", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20223636", - "rel_abs": "Currently, there is no effective vaccine and only one FDA approved early-stage therapy against SARS-CoV-2 infection as an indication to prevent disease progression. Cellular caspases play a role in the pathophysiology of a number of disorders that the co-morbid conditions seen in severe COVID-19 disease. In this study, we assessed transcriptional states of caspases in blood cells from COVID-19 patients. Gene expression levels of select caspases were increased in in vitro SARS-CoV-2 infection models and single cell RNA-Seq data of blood from COVID-19 patients showed a distinct caspase expression in T cells, neutrophils, and dendritic cells. Flow cytometric evaluation of CD4 T cells showed up-regulation of caspase-1 in hospitalized COVID-19 patients compared to unexposed controls. Convalescent COVID-19 patients with lingering symptoms (\"long haulers\") showed persistent up-regulation of caspase-1 in CD4 T cells that was attenuated ex vivo following co-culture with a select pan-caspase inhibitor. Further, we observed elevated caspase-3 levels in red blood cells from COVID-19 patients compared to controls that were responsive to caspase inhibition. Our results expose an exuberant caspase response in COVID-19 that may facilitate immune-related pathological processes leading to severe outcomes. Pan-caspase inhibition could emerge as a therapeutic strategy to ameliorate or prevent severe COVID-19 outcomes.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Matthew Plassmeyer", - "author_inst": "Amerimmune" - }, - { - "author_name": "Oral Alpan", - "author_inst": "Amerimmune" - }, - { - "author_name": "Michael Corley", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Kimberleigh Lillard", - "author_inst": "Amerimmune" - }, - { - "author_name": "Paige Coatney", - "author_inst": "Amerimmune" - }, - { - "author_name": "Tina Vaziri", - "author_inst": "Amerimmune" - }, - { - "author_name": "Suzan Michalski", - "author_inst": "Amerimmune" - }, - { - "author_name": "Thomas A Premeaux", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Alina P.S. Pang", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Zaheer Bukhari", - "author_inst": "S.U.N.Y. Downstate Medical Center" - }, - { - "author_name": "Stephen Y Yueng", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Teresa Evering", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Gail Naughton", - "author_inst": "Histogen, Inc" - }, - { - "author_name": "Martin Latterich", - "author_inst": "Histogen, Inc." - }, - { - "author_name": "Philip A Mudd", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Alfred Spada", - "author_inst": "Histogen, Inc." - }, - { - "author_name": "Nicole Rindone", - "author_inst": "Amerimmune" - }, - { - "author_name": "Denise Loizou", - "author_inst": "Amerimmune" - }, - { - "author_name": "Lishomwa Ndhlovu", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Raavi Gupta", - "author_inst": "State University of New York, Downstate Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.11.02.20224832", "rel_title": "Preferential observation of large infectious disease outbreaks leads to consistent overestimation of intervention efficacy.", @@ -1115491,6 +1118533,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.11.02.20224642", + "rel_title": "Vascular Thrombosis in COVID-19: A Potential Association with Antiphospholipid Antibodies. A Rapid Systematic Review", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224642", + "rel_abs": "BackgroundVascular thrombosis is common in patients with coronavirus disease 2019 (COVID-19). Etiologies underlying this complication are unclear.\n\nPurposeTo determine the prevalence of antiphospholipid (aPL), including lupus anticoagulant, anti-cardiolipin and anti-{beta}2-glycoprotein-1 antibodies, and its possible association with thrombotic manifestations of COVID-19.\n\nData SourcesWe searched MEDLINE indexed journals on September 24, 2020 using the tool LitCovid and the pre-print server medRxIV.\n\nStudy SelectionOriginal investigations (cross-sectional studies, cohort studies, case series, and research letters) on COVID-19 and thrombosis were included.\n\nData ExtractionData were independently extracted, and compiled into spreadsheets based on the PRISMA principles.\n\nData SynthesisHospitalized patients with COVID-19 showed a higher prevalence of lupus anticoagulant compared to non-COVID-19 patients. Temporally, lupus anticoagulant was generally positive early in the course of illness, whereas anti-cardiolipin and anti-{beta}2-glycoprotein-1 antibodies appeared to emerge later in the disease. Some patients who were aPL-negative at an early time-point after disease onset became aPL-positive at a later time-point. Lupus anticoagulant was independently associated with thrombosis in 60 COVID-19 patients in New York had who had 32 thrombotic events (8 arterial and 24 venous). In 88 patients in Wuhan, who had more than 20 each of arterial and venous thrombotic events, medium/high positivity for multiple aPL was significantly associated with arterial thrombosis. However, the association of aPL with thrombosis was not evident in reports that had an overall lower number of or predominantly venous thrombotic events. Analysis of pooled patients revealed that aPL were significantly more frequent in COVID-19 patients with stroke than stroke patients in the general population. Furthermore, injection of IgG aPL fractions from COVID-19 patients into mice accelerated venous thrombosis.\n\nLimitationLimited data and paucity of prospective studies.\n\nConclusionThe aPL are prevalent in patients with COVID-19 and their presence is associated with thrombosis. Importantly, these antibodies may be a key mechanism of thrombosis in COVID-19. Follow-up studies are required to understand the relationship between aPL and the spectrum of vascular thrombosis during and after infection with SARS-CoV-2.\n\nPrimary Funding SourceNone.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aneesh S Kallapur", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Eric Y Yen", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ram Raj Singh", + "author_inst": "UCLA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.11.02.20224709", "rel_title": "Gender-affirming care, mental health, and economic stability in the time of COVID-19: a global cross-sectional study of transgender and non-binary people", @@ -1116159,85 +1119228,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.03.20225169", - "rel_title": "Experiences of living with mental health problems during the COVID-19 pandemic in the UK: a coproduced, participatory qualitative interview study", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225169", - "rel_abs": "PurposeResearch is beginning to quantify the impact of COVID-19 on people with pre-existing mental health conditions. Our paper addresses a lack of in-depth qualitative research exploring their experiences and perceptions of how life has changed at this time.\n\nMethodsWe used qualitative interviews (N=49) to explore experiences of the pandemic for people with pre-existing mental health conditions. In a participatory, coproduced approach, researchers with lived experiences of mental health conditions conducted interviews and analysed data as part of a multi-disciplinary research team.\n\nResultsExisting mental health difficulties were exacerbated for many people. People experienced specific psychological impacts of the pandemic, struggles with social connectedness, and inadequate access to mental health services, while some found new ways to cope and connect to community. New remote ways to access mental health care, including digital solutions, provided continuity of care for some but presented substantial barriers for others. People from black and ethnic minority (BAME) communities experienced heightened anxiety, stigma and racism associated with the pandemic, further impacting their mental health.\n\nConclusionThere is a need for evidence-based solutions to achieve accessible and effective mental health care in response to the pandemic, especially remote approaches to care. Further research should explore the long-term impacts of COVID-19 on people with pre-existing mental health conditions. Particular attention should be paid to understanding inequalities of impact on mental health, especially for people from BAME communities.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Steven Gillard", - "author_inst": "Centre for Mental Health Research, City, University of London, 1 Myddelton Street, London EC1R 1UW" - }, - { - "author_name": "Ceri Dare", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Jackie Hardy", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Patrick Nyikavaranda", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Rachel Rowan Olive", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Prisha Shah", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Mary Birken", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Una Foye", - "author_inst": "Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF" - }, - { - "author_name": "Josephine Ocloo", - "author_inst": "Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF" - }, - { - "author_name": "Ellie Pearce", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Theodora Stefanidou", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Alexandra Pitman", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Alan Simpson", - "author_inst": "Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF" - }, - { - "author_name": "Sonia Johnson", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "Bryn Lloyd-Evans", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - }, - { - "author_name": "NIHR Mental Health Policy Research Unit COVID Coproduction Research Group", - "author_inst": "Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.11.02.20220038", "rel_title": "Benefits and risks of zinc for adults during covid-19: rapid systematic review and meta-analysis of randomised controlled trials.", @@ -1117093,6 +1120083,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221077", + "rel_title": "Simple discrete-time self-exciting models can describe complex dynamic processes: a case study of COVID-19", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221077", + "rel_abs": "Hawkes processes are a form of self-exciting process that has been used in numerous applications, including neuroscience, seismology, and terrorism. While these self-exciting processes have a simple formulation, they are able to model incredibly complex phenomena. Traditionally Hawkes processes are a continuous-time process, however we enable these models to be applied to a wider range of problems by considering a discrete-time variant of Hawkes processes. We illustrate this through the novel coronavirus disease (COVID-19) as a substantive case study. While alternative models, such as compartmental and growth curve models, have been widely applied to the COVID-19 epidemic, the use of discrete-time Hawkes processes allows us to gain alternative insights. This paper evaluates the capability of discrete-time Hawkes processes by retrospectively modelling daily counts of deaths as two distinct phases in the progression of the COVID-19 outbreak: the initial stage of exponential growth and the subsequent decline as preventative measures become effective. We consider various countries that have been adversely affected by the epidemic, namely, Brazil, China, France, Germany, India, Italy, Spain, Sweden, the United Kingdom and the United States. These countries are all unique concerning the spread of the virus and their corresponding response measures, in particular, the types and timings of preventative actions. However, we find that this simple model is useful in accurately capturing the dynamics of the process, despite hidden interactions that are not directly modelled due to their complexity, and differences both within and between countries. The utility of this model is not confined to the current COVID-19 epidemic, rather this model could be used to explain many other complex phenomena. It is of interest to have simple models that adequately describe these complex processes with unknown dynamics. As models become more complex, a simpler representation of the process can be desirable for the sake of parsimony.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Raiha Browning", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Deborah Sulem", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kerrie Mengersen", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Vincent Rivoirard", + "author_inst": "Universit\u00e9 Paris-Dauphine" + }, + { + "author_name": "Judith Rousseau", + "author_inst": "University of Oxford; Universit\u00e9 Paris-Dauphine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221408", "rel_title": "ROLE OF CYTOKINES AND OTHER PROPHETIC VARIABLES IN THE DEVELOPMENT AND PROGRESSION OF DISEASE IN PATIENTS SUFFERING FROM COVID-19", @@ -1117625,53 +1120650,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.29.20221960", - "rel_title": "Socioeconomic Vulnerabilities and the Intensity of RT-PCR SARS-CoV-2 Testing Efforts in the Public Health System in Sao Paulo State", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20221960", - "rel_abs": "BackgroundThe testing of infected persons with SARS-CoV-2 is one of the cornerstones of an effective strategy deployed for pandemic control. The public health diagnostic effort is particularly important in regions with a critical transmission scenario and in vulnerable populations in these districts, such as Sao Paulo state, the Brazilian epicenter of the COVID-19 pandemic.\n\nMethodsWe developed an RT-PCR testing intensity effort index (RT-PCR TIEI) composed of seven indicators to assess the survelliance efforts in the Sao Paulo State. We used dynamic time-series cross-sectional models to analyze the association between the RT-PCR TIEI, the population living under high socioeconomic vulnerability levels, dependent on public health service (SUS), per capita income, and population density.\n\nResultsOn average, the RT-PCR TIEI score was 21.07. In the long-run, the RT-PCR TIEI is negatively associated with socioeconomic vulnerability (p-value=0.000, 95% CI -0.887, - 0.811), with a higher proportion of the population dependent on SUS (p-value= 0.000, 95% CI -0.871, -0.805), per capita income (p-value= 0.000, 95% CI -0.849,-0.792) and with population density (p-value=0.000, 95% CI -0.853; -0.801).\n\nConclusionTesting efforts declined as the pandemic advanced, and the the lowest RT-PCR TIEI values were found in the most socioeconomic vulnerable RHDs. Local public laboratory presence was a predictor of a higher score. Thus, the low testing RT-PCR efforts and local laboratory inequalities affected surveillance capability, especially for socioeconomic vulnerable populations.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Tatiane Cristina Moraes de Sousa", - "author_inst": "Oswaldo Cruz Foundation - Fiocruz" - }, - { - "author_name": "Natalia de Paula Moreira", - "author_inst": "Department of Political Science, University of Sao Paulo." - }, - { - "author_name": "Jose Krieger", - "author_inst": "Department of Cardiopneumology, Heart Institute (InCor) University of Sao Paulo Medical School" - }, - { - "author_name": "Isabel Seelaender C. Rosa", - "author_inst": "Faculty of Philosophy, Humanities and Social Science, University of Sao Paulo." - }, - { - "author_name": "Marcela Zamudio", - "author_inst": "Faculty of Philosophy, Humanities and Social Science, University of Sao Paulo." - }, - { - "author_name": "Maria Amelia S M Veras", - "author_inst": "Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo" - }, - { - "author_name": "Brigina Kemp", - "author_inst": "Conselho de Secretarios Municipais de Saude do Estado de Sao Paulo" - }, - { - "author_name": "Lorena Barberia", - "author_inst": "Department of Political Science, University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.29.20222422", "rel_title": "Avoiding versus contracting COVID-19: On the effectiveness of social distancing at the level of the individual", @@ -1119031,6 +1122009,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.29.20222505", + "rel_title": "The use of compassionate Ivermectin in the management of symptomatic outpatients and hospitalized patients with clinical diagnosis of COVID-19 at the Medical Center Bournigal and the Medical Center Punta Cana, Rescue Group, Dominican Republic, from may 1 to august 10, 2020.", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222505", + "rel_abs": "No antiviral has been shown to reduce mortality in SARS-COV-2 patients to date. In the present observational and retrospective report, 3,099 patients with a definitive or highly probable diagnosis of infection due to COVID-19 were evaluated between May 1st to August 10th, 2020, at Centro Medico Bournigal (CMBO) and Centro Medico Punta Cana (CMPC), and all received compassionate treatment with Ivermectin. A total of 2,706 (87.3%) were discharged for outpatient treatment, all with mild severity of the infection. In 2,688 (99.33%) with outpatient treatment, the disease did not progress to warrant further hospitalization and there were no deaths. In 16 (0.59%) with outpatient treatment, it was necessary their subsequent hospitalization to a room without any death. In 2 (0.08%) with outpatient treatment, it was necessary their admission to the Intensive Care Unit (ICU) and 1 (0.04%) patient died. There were 411 (13.3%) patients hospitalized, being admitted at a COVID-19 room with a moderate disease 300 (9.7%) patients of which 3 (1%) died; and with a severe to critical disease were hospitalized in the ICU 111 (3.6%), 34 (30.6%) of whom died. The mortality percentage of patients admitted to the ICU of 30.6%, is similar with the percentage found in the literature of 30.9%. Total mortality was 37 (1.2%) patients, which is much lower than that reported in world statistics, which are around 3%.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jose Morgenstern", + "author_inst": "Rescue Group" + }, + { + "author_name": "Jose N Redondo", + "author_inst": "Rescue Group" + }, + { + "author_name": "Albida De Leon", + "author_inst": "Rescue Group" + }, + { + "author_name": "Juan M Canela", + "author_inst": "Rescue Group" + }, + { + "author_name": "Nelson Torres", + "author_inst": "Rescue Group" + }, + { + "author_name": "Johnny Tavares", + "author_inst": "Rescue Group" + }, + { + "author_name": "Migulina Minaya", + "author_inst": "Rescue Group" + }, + { + "author_name": "Oscar Lopez", + "author_inst": "Rescue Group" + }, + { + "author_name": "Ana M Placido", + "author_inst": "Rescue Group" + }, + { + "author_name": "Ana Castillo", + "author_inst": "Rescue Group" + }, + { + "author_name": "Rafael Pena Cruz", + "author_inst": "Rescue Group" + }, + { + "author_name": "Yudelka Merrete", + "author_inst": "Rescue Group" + }, + { + "author_name": "Marlenin Toribio", + "author_inst": "Rescue Group" + }, + { + "author_name": "Juan A Francisco", + "author_inst": "Rescue Group" + }, + { + "author_name": "Santiago Roca", + "author_inst": "Rescue Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.29.20219931", "rel_title": "A longitudinal comparison of spike and nucleocapsid SARS-CoV-2 antibody responses in a tertiary hospitals laboratory workers with validation of DBS specimen analysis.", @@ -1119710,41 +1122763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.30.20223149", - "rel_title": "Availability of personal protective equipment and satisfaction of healthcare professionals during COVID-19 pandemic in Ethiopia", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223149", - "rel_abs": "Healthcare professionals (HCPs) are at the frontline in the fight against COVID-19 and are at an increased risk of becoming infected with coronavirus. Risk of infection can be minimized by use of proper personal protective equipment (PPE). This study assessed the availability of PPE and satisfaction of HCPs in six public hospitals in Addis Ababa, Ethiopia. A cross-sectional study was conducted from 9th to 26th June 2020. The study hospitals included: Tikur Anbessa Specialized Hospital, Zewditu Memorial Hospital, Ghandi Memorial Hospital, Menelik II Hospital, Yekatit 12 Hospital Medical College and St. Paul Hospital Millennium Medical College. Data were collected using a self-administered questionnaire. Descriptive statistics were used to describe the data and Chi-square test was used to assess the association between the groups. Bivariate and multivariable logistic regression models were used to assess factors associated with the satisfaction level of healthcare workers with regard to the availability and use of proper PPE during the current COVID-19 pandemic. A total of 1,134 (92.3%) valid questionnaires from a possible 1,228 were included in the analysis. The mean ({+/-}SD) age of the participants was 30.26{+/-}6.43 year and 52.6% were females. Nurses constituted about 40% of the overall sample, followed by physicians (22.2%), interns (10.8%), midwives (10.3%) and others (16.7%). An overall shortage of PPE was reported in all study hospitals. The majority (77%) of the healthcare professionals reported that their hospital did not have adequate PPE. A critical shortage of N95 respirator was particularly reported, the self-reported availability of N95 increased from 13% to 24% before and during COVID-19, respectively. The self-reported use of N95 increased from 9% to 21% before and during COVID-19, respectively. Almost 72% of the respondents were dissatisfied with the availability of PPE in their hospital. The independent predictors of the respondents satisfaction level about PPE were male gender (adjusted OR=1.39, 95% CI:1.05-1.85), healthcare workers who reported that PPE was adequately available in the hospital (adjusted OR=7.53, 95% CI:5.08-11.16), and preparedness to provide care to COVID-19 cases (adjusted OR=1.65, 95% CI:1.22-2.12). A critical shortage of appropriate PPE both before and during COVID-19 was identified. The high level of dissatisfaction with the availability of PPE might potentially lead to a lower level of preparedness and readiness to fight against COVID-19. Therefore, urgent efforts are needed to adequately supply the healthcare facilities with appropriate PPE to alleviate the challenges.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Wakgari Deressa", - "author_inst": "School of Public Health, College of Health Sciences, Addis Ababa University" - }, - { - "author_name": "Alemayehu Worku", - "author_inst": "School of Public Health, College of Health Sciences, Addis Ababa University" - }, - { - "author_name": "Workeabeba Abebe", - "author_inst": "School of Medicine, College of Health Sciences, Addis Ababa University" - }, - { - "author_name": "Muluken Gizaw", - "author_inst": "School of Public Health, College of Health Sciences, Addis Ababa University" - }, - { - "author_name": "Wondwossen Amogne", - "author_inst": "School of Medicine, College of Health Sciences, Addis Ababa University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.30.20223081", "rel_title": "Transmission routes of SARS-CoV-2 among healthcare workers of a French university hospital in Paris, France: a case-control study", @@ -1120712,6 +1123730,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.27.20220707", + "rel_title": "Association of Mass Gatherings and COVID-19 Hospitalization", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220707", + "rel_abs": "We examined COVID-19 hospitalizations following mass gatherings in Wisconsin and Minnesota, United States (September 17-18, 2020). We found that the hospitalization rate increased 15-fold in the Minnesota gathering county, and 12.7-fold in the Wisconsin gathering county. On the state level, it increased 2-fold in Minnesota, and 2.3-fold in Wisconsin, while not increasing significantly in states without gatherings. Our findings suggest that mass gatherings are followed by increased COVID-19 hospitalizations, and that precautions should be taken.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Oren Miron", + "author_inst": "Ben Gurion University" + }, + { + "author_name": "Kun-Hsing Yu", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Rachel Wilf-Miron", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Nadav Davidovitch", + "author_inst": "Ben Gurion University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.03.366609", "rel_title": "Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design", @@ -1121536,45 +1124585,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.01.361766", - "rel_title": "Rapid inactivation of SARS-CoV-2 with ozone water", - "rel_date": "2020-11-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.01.361766", - "rel_abs": "Although ozone water is one of the promising candidates for hand hygiene to prevent fomite infection, the detailed effects of ozone water on SARS-CoV-2 have not been clarified. We evaluated the inactivating effect of ozone water against SARS-CoV-2 by its concentration and exposure time. The reduction rates of virus titer after 5 sec treatment with ozone concentrations of 1, 4, 7, and 10 mg/L were 81.4%, 93.2%, 96.6%, and 96.6%, respectively. No further decrease in virus titer was observed by the extended exposure time over 5 sec. High-concentration ozone water was considered to be effective in promptly inactivating SARS-CoV-2 virus.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hiroko Inagaki", - "author_inst": "University of Miyazaki" - }, - { - "author_name": "Akatsuki Saito", - "author_inst": "University of Miyazaki," - }, - { - "author_name": "Putu Eka Sudaryatma", - "author_inst": "University of Miyazaki" - }, - { - "author_name": "Hironobu Sugiyama", - "author_inst": "University of Miyazaki" - }, - { - "author_name": "Tamaki Okabayashi", - "author_inst": "University of Miyazaki" - }, - { - "author_name": "Shouichi Fujimoto", - "author_inst": "University of Miyazaki" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.01.364364", "rel_title": "Photocatalyst under visible light irradiation inactivates SARS-CoV-2 on an abiotic surface", @@ -1122558,6 +1125568,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221093", + "rel_title": "Features of creatine-kinase in COVID-19 patients with different ages, clinical types and outcomes: A cohort study", + "rel_date": "2020-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221093", + "rel_abs": "ObjectivesTo study the features of creatine-kinase (CK) in COVID-19 patients with different ages, clinical types and outcomes and quantify the relationship between CK value and clinical type.\n\nMethodsAll laboratory confirmed COVID-19 patients hospitalized in Xiangyang No.1 Peoples Hospital were included. Patients general information, clinical type, all CK values and outcome were collected.\n\nResultsThe peak median value of CK in cases aged [≥] 71 years old (appeared at T2) was higher than that in cases aged [≤] 70 years old. There was statistical difference between the two groups (P=0.001). Similarly, the peak in critical cases (appeared at T2) was higher than moderate and severe types, and significant difference were existed among moderate, severe, and critical types (P=0.000). Moreover, the peak value in death group (appeared at T2) was higher than those in survival group. Significant difference was also found between them (P=0.000). According to the optimal scale regression model, the CK value (P=0.000) and age (P=0.000) were associated with the clinical type.\n\nConclusionsDifference of the CK in different ages, clinical types, and outcomes were significant. The results of the optimal scale regression model are helpful to judge the clinical type of COVID-19 patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shanshan Wan", + "author_inst": "Postgraduate Training Basement of Jinzhou Medical University, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Gaojing Qu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Hui Yu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Haoming Zhu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Guoxin Huang", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Lei Chen", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Meiling Zhang", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Jiangtao Liu", + "author_inst": "Department of Orthopedics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Bin Pei", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221069", "rel_title": "Psychological and social impact of COVID-19 in Pakistan: Need for Gender Responsive Policies", @@ -1123094,57 +1126155,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.27.20216366", - "rel_title": "Excess mortality during the COVID-19 pandemic in Aden governorate, Yemen: a geospatial and statistical analysis", - "rel_date": "2020-10-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20216366", - "rel_abs": "BackgroundThe burden of COVID-19 in low-income and conflict-affected countries is still unclear, largely reflecting low testing rates. In parts of Yemen, reports indicated a peak in hospital admissions and burials during May-June 2020. To estimate excess mortality during the epidemic period, we quantified activity across all identifiable cemeteries within Aden governorate in Yemen (population approximately one million) by analysing very high-resolution satellite imagery, and compared estimates to Civil Registry office records from the city.\n\nMethodsAfter identifying active cemeteries through remote and ground information, we applied geospatial analysis techniques to manually identify new grave plots and measure changes in burial surface area over a period from July 2016 to September 2020. After imputing missing grave counts using surface area data, we used alternative approaches, including simple interpolation and a generalised additive mixed growth model, to predict both actual and counterfactual (no epidemic) burial rates by cemetery and across the governorate during the most likely period of COVID-19 excess mortality (from 1 April 2020), and thereby compute excess burials. We also analysed death notifications to the Civil Registry office during April-July 2020 and in previous years.\n\nResultsWe collected 78 observations from 11 cemeteries, of which 10 required imputation from burial surface area. Cemeteries ranged in starting size from 0 to 6866 graves. In all but one a peak in daily burial rates was evident from April to July 2020. Interpolation and mixed model methods estimated {approx} 1500 excess burials up to 6 July, and 2120 up to 19 September, corresponding to a peak weekly increase of 230% from the counterfactual. Satellite imagery estimates were generally lower than Civil Registry data, which indicated a peak 1823 deaths in May alone. However, both sources suggested the epidemic had waned by September 2020.\n\nDiscussionTo our knowledge this is the first instance of satellite imagery being used for population mortality estimation. Findings suggest a substantial, under-ascertained impact of COVID-19 in this urban Yemeni governorate, and are broadly in line with previous mathematical modelling predictions, though our method cannot distinguish direct from indirect virus deaths. Satellite imagery burial analysis appears a promising novel approach for monitoring epidemics and other crisis impacts, particularly where ground data are difficult to collect.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Emilie S. Koum Besson", - "author_inst": "Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Keppel St, London School of Hygiene and Tropical Medicine, London," - }, - { - "author_name": "Andy Norris", - "author_inst": "Satellite Applications Catapult, Electron Building, Didcot, United Kingdom" - }, - { - "author_name": "Abdulla S. Bin Ghouth", - "author_inst": "Department of Community Medicine, Hadhramout University, Hadhramout, Yemen" - }, - { - "author_name": "Terri Freemantle", - "author_inst": "Satellite Applications Catapult, Electron Building, Didcot, United Kingdom" - }, - { - "author_name": "Mervat Alhaffar", - "author_inst": "Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Keppel St, London School of Hygiene and Tropical Medicine, London," - }, - { - "author_name": "Yolanda Vazquez", - "author_inst": "Satellite Applications Catapult, Electron Building, Didcot, United Kingdom" - }, - { - "author_name": "Chris Reeve", - "author_inst": "Satellite Applications Catapult, Electron Building, Didcot, United Kingdom" - }, - { - "author_name": "Patrick J. Curran", - "author_inst": "Department of Psychology, University of North Carolina, Chapel Hill, NC, United States of America" - }, - { - "author_name": "Francesco Checchi", - "author_inst": "Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Keppel St, London School of Hygiene and Tropical Medicine, London," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.19.20215673", "rel_title": "Structural Entropy of Daily Number of COVID-19 Related Fatalities", @@ -1124140,6 +1127150,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.27.20220731", + "rel_title": "Mental Health Impact of the First Wave of COVID-19 Pandemic on Spanish Healthcare Workers: a Large Cross-sectional Survey", + "rel_date": "2020-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220731", + "rel_abs": "IntroductionHealthcare workers are vulnerable to adverse mental health impacts of COVID-19. We assessed prevalence of mental disorders and associated factors during the first wave of the pandemic among healthcare professionals in Spain.\n\nMethodsAll workers in 18 healthcare institutions (6 AACC) in Spain were invited to a series of online surveys assessing a wide range of individual characteristics, COVID-19 infection status and exposure, and mental health status. Here we report: current mental disorders (Major Depressive Disorder-MDD- [PHQ-8[≥]10], Generalized Anxiety Disorder-GAD- [GAD-7[≥]10], Panic attacks, Posttraumatic Stress Disorder -PTSD- [PCL-5[≥]7]; and Substance Use Disorder -SUD-[CAGE-AID[≥]2]. Severe disability assessed by the Sheehan Disability Scale was used to identify \"disabling\" current mental disorders.\n\nResults9,138 healthcare workers participated. Prevalence of screen-positive disorder: 28.1% MDD; 22.5% GAD, 24.0% Panic; 22.2% PTSD; and 6.2% SUD. Overall 45.7% presented any current and 14.5% any disabling current mental disorder. Healthcare workers with prior lifetime mental disorders had almost twice the prevalence of current disorders than those without. Adjusting for all other variables, odds of any disabling mental disorder were: prior lifetime disorders (TUS: OR=5.74; 95%CI 2.53-13.03; Mood: OR=3.23; 95%CI:2.27-4.60; Anxiety: OR=3.03; 95%CI:2.53-3.62); age category 18-29 years (OR=1.36; 95%CI:1.02-1.82), caring \"all of the time\" for COVID-19 patients (OR=5.19; 95%CI: 3.61-7.46), female gender (OR=1.58; 95%CI: 1.27-1.96) and having being in quarantine or isolated (OR= 1.60; 95CI:1.31-1.95).\n\nConclusionsCurrent mental disorders were very frequent among Spanish healthcare workers during the first wave of COVID-19. As the pandemic enters its second wave, careful monitoring and support is needed for healthcare workers, especially those with previous mental disorders and those caring COVID-19 very often.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Jordi Alonso", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Gemma Vilagut", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Philippe Mortier", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Montse Ferrer", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Itxaso Alayo", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Andr\u00e9s Arag\u00f3n-Pe\u00f1a", + "author_inst": "Epidemiology Unit, Regional Ministry of Health, Community of Madrid" + }, + { + "author_name": "Enric Aragon\u00e8s", + "author_inst": "Institut d'Investigaci\u00f3 en Atenci\u00f3 Prim\u00e0ria IDIAP Jordi Gol" + }, + { + "author_name": "Mireia Campos", + "author_inst": "Service of Prevention of Labor Risks, Medical Emergencies System, Generalitat de Catalunya" + }, + { + "author_name": "Isabel del Cura-Gonz\u00e1lez", + "author_inst": "Research Unit. Primary Care Management. Madrid Health Service" + }, + { + "author_name": "Jos\u00e9 I. Emparanza", + "author_inst": "Hospital Universitario Donostia" + }, + { + "author_name": "Meritxell Espuga", + "author_inst": "Occupational Health Service. Hospital Universitari Vall d'Hebron" + }, + { + "author_name": "Joao Forjaz", + "author_inst": "National Center of Epidemiology, Instituto de Salud Carlos III (ISCIII)" + }, + { + "author_name": "Ana Gonz\u00e1lez Pinto", + "author_inst": "Hospital Universitario Araba-Santiago" + }, + { + "author_name": "Josep M. Haro", + "author_inst": "Parc Sanitari Sant Joan de D\u00e9u" + }, + { + "author_name": "Nieves L\u00f3pez Fresne\u00f1a", + "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n" + }, + { + "author_name": "Alma Mart\u00ednez de Sal\u00e1zar", + "author_inst": "UGC Salud Mental, Hospital Universitario Torrec\u00e1rdenas" + }, + { + "author_name": "Juan D. Molina", + "author_inst": "Villaverde Mental Health Center. Clinical Management Area of Psychiatry and Mental Health, Psychiatric Service, Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Rafael M. Ort\u00ed Lucas", + "author_inst": "Hospital Cl\u00ednic Universitari de Valencia" + }, + { + "author_name": "Mara Parellada", + "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n" + }, + { + "author_name": "Jos\u00e9 Maria Pelayo-Ter\u00e1n", + "author_inst": "Hospital El Bierzo" + }, + { + "author_name": "Aurora P\u00e9rez Zapata", + "author_inst": "Pr\u00edncipe de Asturias University Hospital" + }, + { + "author_name": "Jos\u00e9 I. Pijoan", + "author_inst": "Hospital Universitario Cruces/ OSI EEC" + }, + { + "author_name": "Nieves Plana", + "author_inst": "Pr\u00edncipe de Asturias University Hospital" + }, + { + "author_name": "Teresa Puig", + "author_inst": "Department of Epidemiology and Public Health, Hospital de la Santa Creu i Sant Pau" + }, + { + "author_name": "Cristina Rius", + "author_inst": "Ag\u00e8ncia de Salut P\u00fablica de Barcelona" + }, + { + "author_name": "Carmen Rodriguez-Blazquez", + "author_inst": "National Center of Epidemiology, Instituto de Salud Carlos III (ISCIII)" + }, + { + "author_name": "Ferran Sanz", + "author_inst": "Research Progamme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)" + }, + { + "author_name": "Consol Serra", + "author_inst": "Parc de Salut Mar PSMAR" + }, + { + "author_name": "Ronald C. Kessler", + "author_inst": "Department of Health Care Policy, Harvard Medical School" + }, + { + "author_name": "Ronny Bruffaerts", + "author_inst": "Center for Public Health Psychiatry, Universitair Psychiatrisch Centrum, KU Leuven" + }, + { + "author_name": "Eduard Vieta", + "author_inst": "Fundaci\u00f3 Cl\u00ednic per a la Recerca Biom\u00e8dica de Barcelona" + }, + { + "author_name": "V\u00edctor P\u00e9rez-Sol\u00e1", + "author_inst": "Parc de Salut Mar PSMAR" + }, + { + "author_name": "- MINDCOVID Working group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.29.20222372", "rel_title": "The COVID-19 Healthcare Personnel Study (CHPS): Overview, Methods and Preliminary Report", @@ -1124688,53 +1127845,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.29.20218750", - "rel_title": "Rapid Support for older adults during the initial stages of the COVID-19 Pandemic: Results from a Geriatric Psychiatry helpline", - "rel_date": "2020-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20218750", - "rel_abs": "BackgroundThe COVID-19 pandemic and governmental lockdown measures disproportionally impacts older adults. This study presents the results from a psychiatric helpline for older adults in Mannheim, Germany, during the lockdown, set up to provide information and psychosocial support measures. We aim to elucidate the needs of older adults, their reported changes and the psychological impact during the initial stages of the health crisis.\n\nMethods55 older adults called the psychiatric helpline between April and June 2020. Information on demographics, previous diagnosis of psychiatric and somatic diseases as well as changes in daily life due to the pandemic was collected anonymously. Current mental health status was assessed using the depression HAMD-7 and the anxiety HAM-A scales.\n\nResultsMost callers were women, older adults (M = 74.69 years), single and retired. 69% of callers reported new or an increase in psychiatric symptoms, with anxiety and depressive symptoms being the most common ones. Age was significantly negatively correlated to higher levels of anxiety and depression symptoms. Individuals with a previous diagnosis of a psychiatric disease reported significantly higher levels of depressive and anxiety symptoms than those without a diagnosis.\n\nConclusionIn older adults, the perceived psychological impact of the COVID-19 crisis appears to ameliorate with age. Individuals with a history of psychiatric disease are most vulnerable to negative mental health outcomes. Rapid response in the form of a geriatric helpline are useful initiatives to support the needs and the psychological well-being of older adults during a health crisis.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Anna-Sophia Wahl", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - }, - { - "author_name": "Gloria S. Benson", - "author_inst": "Central Institute of Mental Health Mannheim, University of Heidelberg" - }, - { - "author_name": "Lucrezia Hausner", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - }, - { - "author_name": "Sandra Schmitt", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - }, - { - "author_name": "Annika Knoll", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - }, - { - "author_name": "Adriana Ferretti-Bondy", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - }, - { - "author_name": "Dimitri Hefter", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - }, - { - "author_name": "Lutz Froelich", - "author_inst": "Central Institute of Mental Health, Mannheim, University of Heidelberg" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.28.20217455", "rel_title": "Anakinra To Prevent Respiratory Failure In COVID-19", @@ -1126950,6 +1130060,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.28.355305", + "rel_title": "5-amino levulinic acid inhibits SARS-CoV-2 infection in vitro", + "rel_date": "2020-10-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.355305", + "rel_abs": "The current COVID-19 pandemic requires urgent development of effective therapeutics. 5-amino levulinic acid (5-ALA) is a naturally synthesized amino acid and has been used for multiple purposes including as an anticancer therapy and as a dietary supplement due to its high bioavailability. In this study, we demonstrated that 5-ALA treatment potently inhibited infection of SARS-CoV-2, a causative agent of COVID-19. The antiviral effects could be detected in both human and non-human cells, without significant cytotoxicity. Therefore, 5-ALA is a candidate as an oral antiviral drug for COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yasuteru Sakurai", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Mya Myat Ngwe Tun", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Yohei Kurosaki", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Takaya Sakura", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Daniel Ken Inaoka", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kiyotaka Fujine", + "author_inst": "neopharma Japan Co., Ltd." + }, + { + "author_name": "Kiyoshi Kita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kouichi Morita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Jiro Yasuda", + "author_inst": "Nagasaki University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.28.359257", "rel_title": "In vitro assessment of the virucidal activity of four mouthwashes containing Cetylpyridinium Chloride, ethanol, zinc and a mix of enzyme and proteins against a human coronavirus", @@ -1127670,77 +1130831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.26.20219352", - "rel_title": "Pandemic impacts on healthcare utilisation: a systematic review", - "rel_date": "2020-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219352", - "rel_abs": "ObjectivesTo determine the extent and nature of changes in utilisation of healthcare services during COVID-19 pandemic.\n\nDesignSystematic review\n\nEligibilityEligible studies compared utilisation of services during COVID-19 pandemic to at least one comparable period in prior years. Services included visits, admissions, diagnostics, and therapeutics. Studies were excluded if from single-centres or studied only COVID-19 patients.\n\nData sourcesPubMed, Embase, Cochrane COVID-19 Study Register, and pre-prints were searched, without language restrictions, until August 10, using detailed searches with key concepts including COVID-19, health services and impact.\n\nData analysisRisk of bias was assessed by adapting ROBINS-I and Cochrane Effective Practice and Organization of Care tool. Results were analysed using descriptive statistics, graphical figures, and narrative synthesis.\n\nOutcome measuresPrimary outcome was change in service utilisation between pre-pandemic and pandemic periods. Secondary outcome was the change in proportions of users of healthcare services with milder or more severe illness (e.g. triage scores).\n\nResults3097 unique references were identified, and 81 studies across 20 countries included, reporting on >11 million services pre-pandemic and 6.9 million during pandemic. For the primary outcome, there were 143 estimates of changes, with a median 37% reduction in services overall (interquartile range -51% to -20%), comprising median reductions for visits of 42%(-53% to -32%), admissions, 28%(-40% to -17%), diagnostics, 31%(-53% to -24%), and for therapeutics, 30%(-57% to -19%). Among 35 studies reporting secondary outcomes, there were 60 estimates, with 27(45%) reporting larger reductions in utilisation among people with a milder spectrum of illness, and 33 (55%) reporting no change.\n\nConclusionsHealthcare utilisation decreased by about a third during the pandemic, with considerable variation, and with greater reductions among people with less severe illness. While addressing unmet need remains a priority, studies of health impacts of reductions may help health-systems prioritise higher-value care in the post-pandemic recovery.\n\nFunding, Study registrationNo funding was required. PROSPERO: CRD42020203729\n\nStrengths and limitations of this study- The review is the first broad synthesis of global studies of pandemic related changes in utilisation across all categories of healthcare services.\n- The review provides novel findings informing design of future studies of pandemic-related changes in utilisation and its impacts.\n- Limitations include the possibility of publication bias and the potential of our eligibility criteria to exclude important data sources such as studies in single-centres and unpublished datasets from health systems.\n- Heterogenous designs and settings precluding meta-analysis.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ray Moynihan", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University, Gold Coast, QLD, 4229, Australia" - }, - { - "author_name": "Sharon Sanders", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University, Gold Coast, QLD, 4229, Australia" - }, - { - "author_name": "Zoe A Michaleff", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University, Gold Coast, QLD, 4229, Australia" - }, - { - "author_name": "Anna Scott", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University, Gold Coast, QLD, 4229, Australia" - }, - { - "author_name": "Justin Clark", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University, Gold Coast, QLD, 4229, Australia" - }, - { - "author_name": "Emma J To", - "author_inst": "University of Calgary, 2500 University Drive, Calgary, Alberta, T2N1N4, Canada" - }, - { - "author_name": "Mark Jones", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University, Gold Coast, QLD, 4229, Australia" - }, - { - "author_name": "Eliza Kitchener", - "author_inst": "Griffith University, Brisbane, Queensland, Australia" - }, - { - "author_name": "Melissa Fox", - "author_inst": "Health Consumers Queensland, Level 3, 340 Adelaide St., Brisbane, Queensland, 4000, Australia" - }, - { - "author_name": "Minna Johansson", - "author_inst": "Cochrane Sustainable Healthcare Field, Sweden" - }, - { - "author_name": "Eddy Lang", - "author_inst": "University of Calgary, 2500 University Drive, Calgary, Alberta, T2N1N4, Canada" - }, - { - "author_name": "Anne Duggan", - "author_inst": "Australian Commission on Safety and Quality in Healthcare, Sydney, Australia" - }, - { - "author_name": "Ian Scott", - "author_inst": "Princess Alexander Hospital, 199 Ipswich Rd, Brisbane, Queensland, Australia" - }, - { - "author_name": "Loai Albarqouni", - "author_inst": "Institute for Evidence-Based Healthcare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.10.27.20220566", "rel_title": "Prevalence and outcomes of co-infection and super-infection with SARS-CoV-2 and other pathogens: A Systematic Review and Meta-analysis", @@ -1128516,6 +1131606,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.23.20218255", + "rel_title": "Characteristics and outcomes of hospitalized adult COVID-19 patients in Georgia", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218255", + "rel_abs": "ObjectiveDescribe presenting characteristics of hospitalized patients and explore factors associated with in-hospital mortality during the first wave of pandemic in Georgia.\n\nMethodsThis retrospective study included 582 adult patients admitted to 9 dedicated COVID-19 hospitals as of July 30, 2020 (72% of all hospitalizations). Data were abstracted from medical charts. Factors associated with mortality were evaluated in multivariable Poisson regression analysis.\n\nResultsAmong 582 adults included in this analysis 14.9% were 65+ years old, 49.1% were women, 59.3% had uni- or bi-lateral lung involvement on chest computed tomography, 27.1% had any co-morbidity, 13.2% patients had lymphopenia, 4.1% had neutophilosis, 4.8% had low platelet count, 37.6% had d-dimer levels of >0.5 mcg/l. Overall mortality was 2.1% (12/582). After excluding mild infections, mortality among patients with moderate-to-critical disease was 3.0% (12/399), while among patients with severe-to-critical disease mortality was 12.7% (8/63). Baseline characteristics associated with increased risk of mortality in multivariate regression analysis included: age [≥]65 years (RR: 10.38, 95% CI: 1.30-82.75), presence of any chronic co-morbidity (RR: 20.71, 95% CI: 1.58-270.99), lymphopenia (RR: 4.76, 95% CI: 1.52-14.93), neutrophilosis (RR: 7.22, 95% CI: 1.27-41.12), low platelet count (RR: 6.92, 95% CI: 1.18-40.54), elevated d-dimer (RR: 4.45, 95% CI: 1.48-13.35), elevated AST (RR: 6.33, 95% CI: 1.18-33.98).\n\nConclusionIn-hospital mortality during the first wave of pandemic in Georgia was low. We identified several risk factors (older age, co-morbidities and laboratory abnormalities) associated with poor outcome that should provide guidance for planning health sector response as pandemic continues to evolve.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tengiz Tsertsvadze", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; 2) Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia" + }, + { + "author_name": "Marina Ezugbaia", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Marina Endeladze", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Levani Ratiani", + "author_inst": "First University Clinic, Tbilisi, Georgia" + }, + { + "author_name": "Neli Javakhishvili", + "author_inst": "Giorgi Abramishvili Military Hospital, Gori, Georgia" + }, + { + "author_name": "Lika Mumladze", + "author_inst": "St. King Mirian and Queen Nana Mtskheta Regional Medical Center, Georgia" + }, + { + "author_name": "Manana Khotcholava", + "author_inst": "Childrens Infectious Diseases Hospital, Tbilisi, Georgia" + }, + { + "author_name": "Maiko Janashia", + "author_inst": "University Clinic Rukhi, Georgia" + }, + { + "author_name": "Diana Zviadadze", + "author_inst": "LJ Clinic, Kutaisi, Georgia" + }, + { + "author_name": "Levan Gopodze", + "author_inst": "Central Republican Hospital, Tbilisi, Georgia" + }, + { + "author_name": "Alex Gokhelashvili", + "author_inst": "Medalpha Clinic, Batumi, Georgia" + }, + { + "author_name": "Revaz Metchurchtlishvili", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Akaki Abutidze", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; 2) Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia" + }, + { + "author_name": "Nikoloz Chkhartishvili", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center; 2) Caucasus International University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.23.20218164", "rel_title": "SARS-CoV-2 seroprevalence in healthcare workers of dedicated COVID hospitals and non COVID hospitals of District Srinagar, Kashmir", @@ -1128972,93 +1132133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.23.20154302", - "rel_title": "Association between Hydroxyzine Use and Reduced Mortality in Patients Hospitalized for Coronavirus Disease 2019: Results from a multicenter observational study", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20154302", - "rel_abs": "ObjectiveTo examine the association between hydroxyzine use and mortality in patients hospitalized for COVID-19, based on its anti-inflammatory and antiviral properties.\n\nDesignMulticenter observational retrospective cohort study.\n\nSettingGreater Paris University hospitals, France.\n\nParticipants7,345 adults hospitalized for COVID-19 between 24 January and 1 April 2020, including 138 patients (1.9%) who received hydroxyzine during the visit at a mean dose of 49.8 mg (SD=51.5) for an average of 22.4 days (SD=25.9).\n\nData sourceAssistance Publique-Hopitaux de Paris Health Data Warehouse.\n\nMain outcome measuresThe study endpoint was death. We compared this endpoint between patients who received hydroxyzine and those who did not in time-to-event analyses adjusting for patient characteristics (such as age, sex, and comorbidities), clinical and biological markers of diseases severity, and use of other medications. The primary analysis was a multivariable Cox model with inverse probability weighting. Sensitivity analyses included a multivariable Cox model and a univariate Cox regression model in a matched analytic sample in a 1:1 ratio.\n\nResultsOver a mean follow-up of 20.3 days (SD=27.5), 994 patients (13.5%) had a primary end-point event. The primary multivariable analysis with inverse probability weighting showed a significant association between hydroxyzine use and reduced mortality (HR, 0.42; 95% CI, 0.25 to 0.71; p=0.001) with a significant dose-effect relationship (HR, 0.10; 95% CI, 0.02 to 0.45; p=0.003). This association was similar in sensitivity analyses. In secondary analyses conducted among subsamples of patients, we found a significant association between hydroxyzine use and a faster decrease in biological inflammatory markers associated with COVID-19-related mortality, including neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-C-reactive protein ratio (LCRP), and circulating interleukin 6 levels (IL-6) (all p<0.016), with a significant dose-effect relationship for NLR and LCRP (both p<0.037).\n\nConclusionsIn this retrospective observational study, hydroxyzine use was associated with reduced mortality in patients hospitalized for COVID-19. This association may be partially mediated by specific anti-inflammatory properties of H1 antihistamines. Double-blind controlled randomized clinical trials of hydroxyzine for COVID-19 are needed to confirm these results.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Nicolas Hoertel", - "author_inst": "Universit\u00e9 de Paris" - }, - { - "author_name": "Marina S\u00e1nchez", - "author_inst": "Universidad Complutense de Madrid" - }, - { - "author_name": "Rapha\u00ebl Vernet", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Nathana\u00ebl Beeker", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Antoine Neuraz", - "author_inst": "Necker-Enfants Malades Hospital" - }, - { - "author_name": "Carlos Blanco", - "author_inst": "National Institute on Drug Abuse" - }, - { - "author_name": "Mark Olfson", - "author_inst": "Columbia University" - }, - { - "author_name": "C\u00e9dric Lemogne", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Pierre Meneton", - "author_inst": "Sorbonne Universit\u00e9" - }, - { - "author_name": "Christel Daniel", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Nicolas Paris", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Alexandre Gramfort", - "author_inst": "Universit\u00e9 Paris-Saclay" - }, - { - "author_name": "Guillaume Lemaitre", - "author_inst": "Universit\u00e9 Paris-Saclay" - }, - { - "author_name": "Elisa Salamanca", - "author_inst": "Banque Nationale de Donn\u00e9es Maladies Rares" - }, - { - "author_name": "M\u00e9lodie Bernaux", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Ali Bellamine", - "author_inst": "Assistance Publique - H\u00f4pitaux de Paris" - }, - { - "author_name": "Anita Burgun", - "author_inst": "INSERM" - }, - { - "author_name": "Fr\u00e9d\u00e9ric Limosin", - "author_inst": "Universit\u00e9 de Paris" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.23.20217844", "rel_title": "Standard blood laboratory results in SARS-CoV-19 positive patients: do they show a typical pattern?", @@ -1130082,6 +1133156,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.24.20218685", + "rel_title": "Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218685", + "rel_abs": "ObjectivesLimited testing capacity has characterized the ongoing COVID-19 pandemic in Spain, hampering a timely control of outbreaks and the possibilities to reduce the escalation of community transmissions. Here we investigated the potential of using pooling of samples followed by one-step retrotranscription and quantitative PCR (RT-qPCR) to increase SARS-CoV-2 testing capacity.\n\nMethodsWe first evaluated different sample pooling (1:5, 1:10 and 1:15) prior to RNA extractions followed by standard RT-qPCR for SARS-CoV-2/COVID-19 diagnosis. The pool size achieving reproducible results in independent tests was then used for assessing nasopharyngeal samples in a tertiary hospital during August 2020.\n\nResultsWe found that pool size of five samples achieved the highest sensitivity compared to pool sizes of 10 and 15, showing a mean ({+/-} SD) Ct shift of 3.5 {+/-} 2.2 between the pooled test and positive samples in the pool. We then used a pool size of five to test a total of 895 pools (4,475 prospective samples) using two different RT-qPCR kits available at that time. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct ({+/-} SD) shift (2.2 {+/-} 2.4) among the pool and the individual samples. The strategy allows detecting individual samples in the positive pools with Cts in the range of 16.7-39.4.\n\nConclusionsWe found that pools of five samples combined with RT-qPCR solutions helped to increase SARS-CoV-2 testing capacity with minimal loss of sensitivity compared to that resulting from testing the samples independently.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Julia Alcoba-Florez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Helena Gil-Campesino", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Diego Garcia-Martinez de Artola", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Oscar Diez-Gil", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Agustin Valenzuela-Fernandez", + "author_inst": "Laboratorio de Inmunologia Celular y Viral, Unidad de Farmacologia, Universidad de La Laguna" + }, + { + "author_name": "Rafaela Gonzalez-Montelongo", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Laura Ciuffreda", + "author_inst": "Unidad de Investigacion, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Carlos Flores", + "author_inst": "Hospital Universitario Nuestra Senora de Candelaria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.24.20218974", "rel_title": "Low serum vitamin D level and COVID-19 infection and outcomes, a multivariate meta-analysis", @@ -1130542,57 +1133663,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.26.20219360", - "rel_title": "Features of C-reactive protein in COVID-19 patients within various period: a cohort study", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219360", - "rel_abs": "BACKGROUNDCoronavirus disease 2019 (COVID-19) has been declared as a threat to the global. Due to the lack of efficient treatments, indicators were urgently needed during the evolvement of disease to analyze the illness and prognosis and prevent the aggravation of COVID-19.\n\nMETHODSAll laboratory confirmed COVID-19 patients hospitalized in Xiangyang No.1 Peoples Hospital were included. Patients general information, clinical type, CRP value and outcome were collected. CRP values of all patients during disease course from different initial time were analyzed.\n\nRESULTSThe 131 enrolled patients were 50.13{+/-}17.13 years old. All cases underwent 724 tests of CRP since symptom onset, 53.18% of the test results were abnormal and the median value was 9.52(2.63-34.10) mg/L. The first median value on the day 8 from exposure onset was 39.08(11.92-47.89) mg/L then fluctuated around it until the day 28. The CRP median increased from 15.93 mg/L to 41.44 mg/L and then decreased to 18.26 mg/L before transformation of severe type, and then increased to 62.25 mg/L on the transforming date. Conversely, the CRP median increased from 56.17 mg/L 102.75 mg/L before transformation of critical type but decreased to 68.68 mg/L on the transforming date. The changes of CRP median over time before death ranged from 77.77 mg/L to 133.52 mg/L.\n\nCONCLUSIONSCRP increased before symptom onset and substantially increased during the early-to-mid stage (especially early stage), which was different from other virus-infected diseases. The changes of CRP before the transformation of clinical type was inconsistent with the aggravating of illness. And the CRP maintained over 100.00 mg/L prompted poor prognosis.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Guoxin Huang", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Gaojing Qu", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Hui Yu", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Meiling Zhang", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Xiaoming Song", - "author_inst": "Department of Equipment Division, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Lei Chen", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Haoming Zhu", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - }, - { - "author_name": "Yunfu Wang", - "author_inst": "Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan 442000,China" - }, - { - "author_name": "Bin Pei", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.26.20219428", "rel_title": "Community prevalence of SARS-CoV-2 in England during April to September 2020: Results from the ONS Coronavirus Infection Survey", @@ -1131556,6 +1134626,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.26.20219626", + "rel_title": "Hyper-Exponential Growth of COVID-19 during Resurgence of the Disease in Russia", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219626", + "rel_abs": "In Russia, COVID-19 has currently been growing hyper-exponentially. This type of a spread pattern was not seen during the first wave of the pandemic the world over. Indeed when the disease had first appeared, in the accelerating stage the spread pattern was observed to have followed a highly nonlinear pattern that could be said to be approximately exponential or sub-exponential. As to why in the resurgence the growth has become hyper-exponential is another matter. But this has been happening in Europe and how long this would continue cannot be predicted. It may so happen that in the countries in which retardation has already been taking place, there may be resurgence of the disease. It was observed that in the World as a whole, retardation was on the threshold during the second half of September. But if the resurgence happens to follow the hyper-exponential growth pattern in different countries, there may be resurgence in the World as a whole.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hemanta Kumar Baruah", + "author_inst": "The Assam Royal Global University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.22.20184630", "rel_title": "COVID-19 infections following outdoor mass gatherings in low incidence areas: retrospective cohort study", @@ -1132272,221 +1135361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.26.20219089", - "rel_title": "Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219089", - "rel_abs": "Despite signs of infection, the involvement of the oral cavity in COVID-19 is poorly understood. To address this, single-cell RNA sequencing data-sets were integrated from human minor salivary glands and gingiva to identify 11 epithelial, 7 mesenchymal, and 15 immune cell clusters. Analysis of SARS-CoV-2 viral entry factor expression showed enrichment in epithelia including the ducts and acini of the salivary glands and the suprabasal cells of the mucosae. COVID-19 autopsy tissues confirmed in vivo SARS-CoV-2 infection in the salivary glands and mucosa. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibiting ACE2 expression and SARS-CoV-2 RNA. Matched nasopharyngeal and saliva samples found distinct viral shedding dynamics and viral burden in saliva correlated with COVID-19 symptoms including taste loss. Upon recovery, this cohort exhibited salivary antibodies against SARS-CoV-2 proteins. Collectively, the oral cavity represents a robust site for COVID-19 infection and implicates saliva in viral transmission.", - "rel_num_authors": 50, - "rel_authors": [ - { - "author_name": "Kevin M Byrd", - "author_inst": "ADA Science & Research Institute" - }, - { - "author_name": "Ni Huang", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Paola Perez", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Takafumi Kato", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Yu Mikami", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Kenichi Okuda", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Rodney C. Gilmore", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Cecilia Dominguez Conde", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Billel Gasmi", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Sydney Stein", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Margaret Beach", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Eileen Pelayo", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jose Maldonado-Ortiz", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Bernard LaFont", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Ricardo Padilla", - "author_inst": "University of North Carolina Adams School of Dentistry" - }, - { - "author_name": "Valerie Murrah", - "author_inst": "University of North Carolina Adams School of Dentistry" - }, - { - "author_name": "Robert Maile", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Will Lovell", - "author_inst": "University of North Carolina Adams School of Dentistry" - }, - { - "author_name": "Shannon Wallet", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Natalie M Bowman", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Suzanne L Meinig", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Matthew C Wolfgang", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Saibyasachi N. Choudhury", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Mark Novotny", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Brian D Aevermann", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Richard Scheuermann", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Gabrielle Cannon", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Carlton Anderson", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Julie Marchesan", - "author_inst": "University of North Carolina Adams School of Dentistry" - }, - { - "author_name": "Mandy Bush", - "author_inst": "University of North Carolina Adams School of Dentistry" - }, - { - "author_name": "Marcelo Freire", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Adam Kimple", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Daniel L Herr", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Joseph Rabin", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Alison Grazioli", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Benjamin N. French", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Thomas JF Pranzatelli", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "John A. Chiorini", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "David E. Kleiner", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Stefania Pittaluga", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Stephen Hewitt", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Peter D. Burbelo", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Daniel Chertow", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "- NIH COVID-19 Autopsy Consortium", - "author_inst": "" - }, - { - "author_name": "- HCA Oral and Craniofacial Biological Network", - "author_inst": "" - }, - { - "author_name": "Karen M Frank", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Janice Lee", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Richard C. Boucher C. Boucher", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Sarah A. Teichmann", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Blake M Warner", - "author_inst": "National Institutes of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.26.20220137", "rel_title": "A quantitative exploration of symptoms in COVID-19 patients: an observational cohort study", @@ -1133734,6 +1136608,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.27.357954", + "rel_title": "Tuning Intrinsic Disorder Predictors for Virus Proteins", + "rel_date": "2020-10-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.27.357954", + "rel_abs": "Many virus-encoded proteins have intrinsically disordered regions that lack a stable folded threedimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy, e.g., a mean 36% gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to SARS-CoV-2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gal Almog", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + }, + { + "author_name": "Abayomi Samuel Olabode", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + }, + { + "author_name": "Art FY Poon", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.27.357731", "rel_title": "SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway", @@ -1134438,57 +1137339,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.22.20217661", - "rel_title": "Transmission of COVID-19 in the state of Georgia, United States: Spatiotemporal variation and impact of social distancing", - "rel_date": "2020-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217661", - "rel_abs": "BackgroundBeginning in early February 2020, COVID-19 spread across the state of Georgia, leading to 258,354 cumulative cases as of August 25, 2020. The time scale of spreading (i.e., serial interval) and magnitude of spreading (i.e., Rt or reproduction number) for COVID-19, were observed to be heterogenous by demographic characteristics, region and time period. In this study, we examined the COVID-19 transmission in the state of Georgia, United States.\n\nMethodsDuring February 1 to July 13, 2020, we identified 4080 transmission pairs using contact information from reports of COVID-19 cases from the Georgia Department of Public Health. We examined how various transmission characteristics were affected by disease symptoms, demographics (age, gender, and race), and time period (during shelter-in-place and after reopening). In addition, we estimated the time course of reproduction numbers during early February-mid-June for all 159 counties in the state of Georgia, using a total of 118,491 reported COVID-19 cases.\n\nFindingsOver this period, the serial interval appeared to decrease from 5.97 days in February-April to 4.40 days in June-July. With regard to age, transmission was assortative and patterns of transmission changed over time. COVID-19 mainly spread from adults to all age groups; transmission among and between children and the elderly was found less frequently. Younger adults (20- 50 years old) were involved in the majority of transmissions occurring during or after reopening subsequent to the shelter-in-place period. By mid-July, two waves of COVID-19 transmission were apparent, separated by the shelter-in-place period in the state of Georgia. Counties around major cities and along interstate highways had more intense transmission.\n\nInterpretationThe transmission of COVID-19 in the state of Georgia had been heterogeneous by area and changed over time. The shelter-in-place was not long enough to sufficiently suppress COVID-19 transmission in densely populated urban areas connected by major transportation links. Studying local transmission patterns may help in predicting and guiding states in prevention and control of COVID-19 according to population and region.\n\nFundingEmory COVID-19 Response Collaborative.\n\nResearch in context\n\nEvidence before this studyThe ongoing COVID-19 pandemic has caused 37,109,581 cases and 1,070,355 deaths worldwide as of October 11, 2020. We searched PubMed for articles published on and before October 11, 2020 using keywords \"novel coronavirus\", \"SARS-nCoV-2\", \"COVID-19\", \"transmission\", \"serial interval\", \"reproduction number\", and \"shelter-in-place\". Few published studies have estimated the serial interval but no study was found that examined the time-varying serial interval. Few studies have examined the transmission patterns between groups with different characteristics. And no study has examined the timevarying reproduction number for COVID-19 and impact of shelter-in-place order at the county level in the United States.\n\nAdded value of this studyTo our knowledge, this is the first study showing the multiple aspects of COVID-19 transmission, including serial interval, transmission patterns between age, gender, or race groups, and spatiotemporal patterns, based on data from 118,491 confirmed COVID-19 cases and 4080 tracked pairs of infector and infectee. We found that during February-July the serial interval for symptom onset shortened, and the major contribution to the spread of COVID-19 shifted to younger ages (from 40-70 years old in February-April to 20-50 years old in June-July). We also found three to four weeks of the shelter-in-place slowed transmission but was insufficient to prevent transmission into urban and peri-urban counties connected with major transportation.\n\nImplications of all the available evidenceThe contracting serial intervals and increasing spread by younger generation show the COVID-19 transmission at county level changes over time. The spatiotemporal patterns of transmission in county level further provide important evidence to guide effective COVID-19 prevention and control measures (e.g., shelter-in-place) in different areas.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yuke Wang", - "author_inst": "Emory University" - }, - { - "author_name": "Casey Siesel", - "author_inst": "Emory University" - }, - { - "author_name": "Yangping Chen", - "author_inst": "Emory University" - }, - { - "author_name": "Ben Lopman", - "author_inst": "Emory University" - }, - { - "author_name": "Laura Edison", - "author_inst": "Centers for Disease Control and Prevention; Georgia Department of Public Health" - }, - { - "author_name": "Michael Thomas", - "author_inst": "Georgia Department of Public Health" - }, - { - "author_name": "Carly Adams", - "author_inst": "Emory University" - }, - { - "author_name": "Max SY Lau", - "author_inst": "Emory University" - }, - { - "author_name": "Peter F.M. Teunis", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.22.20217604", "rel_title": "Coronavirus Disease (COVID-19) Global Prediction Using Hybrid Artificial Intelligence Method of ANN Trained with Grey Wolf Optimizer", @@ -1135328,6 +1138178,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.25.354571", + "rel_title": "Comparison of the in vitro-efficacy of different mouthwash solutions targeting SARS-CoV-2 based on the European Standard EN 14476", + "rel_date": "2020-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.25.354571", + "rel_abs": "The SARS-Cov-2 pandemic is triggering a global health emergency alert, and recent research is indicating the relevance of aerosols in the spread of SARS-CoV-2. Thus, in this study antiseptic mouthwashes based on the actives chlorhexidine (CHX) and octenidine (OCT) were investigated regarding their efficacy against SARS-CoV-2 using EN 14476. Based on the requirement of EN 14476 (i.e. reduction of viral titer by [≥] 4 log 10), the OCT-based formulation was effective within only 15 sec against SARS-CoV-2, and thus constitutes an interesting candidate for future clinical studies to prove its effectiveness in a potential prevention of SARS-CoV-2 transmission by aerosols.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Katrin Steinhauer", + "author_inst": "Department Research & Scientific Services, Schuelke & Mayr GmbH, Norderstedt, Germany; Faculty of Mechanical Engineering, Kiel University of Applied Sciences, K" + }, + { + "author_name": "Toni Luise Meister", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany" + }, + { + "author_name": "Daniel Todt", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany" + }, + { + "author_name": "Adalbert Krawczyk", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany" + }, + { + "author_name": "Lars Passvogel", + "author_inst": "Department Research & Scientific Services, Schuelke & Mayr GmbH, Norderstedt, Germany" + }, + { + "author_name": "Britta Becker", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Dajana Paulmann", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Birte Bischoff", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Stephanie Pfaender", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany" + }, + { + "author_name": "Florian Brill", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Eike Steinmann", + "author_inst": "Ruhr University Bochum" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.23.353219", "rel_title": "The papain-like protease of coronaviruses cleaves ULK1 to disrupt host autophagy", @@ -1135840,25 +1138749,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20217398", - "rel_title": "Spatial autocorrelation and the dynamics of the mean center of COVID-19 infections in Lebanon", - "rel_date": "2020-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20217398", - "rel_abs": "In this paper we study the spatial spread of the COVID-19 infection in Lebanon. We inspect the spreading of the daily new infections across the 26 administrative districts of the country, and implement Morans I statistics in order to analyze the tempo-spatial clustering of the infection in relation to various variables parameterized by adjacency, proximity, population, population density, poverty rate and poverty density, and we find out that except for the poverty rate, the spread of the infection is clustered and associated to those parameters with varying magnitude for the time span between July (geographic adjacency and proximity) or August (population, population density and poverty density) through October. We also determine the temporal dynamics of geographic location of the mean center of new and cumulative infections since late March. The results obtained allow for regionally and locally adjusted health policies and measures that would provide higher levels of public health safety in the country.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Omar El Deeb", - "author_inst": "Lebanese International University and Lebanese University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.21.20217331", "rel_title": "Requirements for the containment of COVID-19 disease outbreaks through periodic testing, isolation, and quarantine", @@ -1136670,6 +1139560,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.20.20215608", + "rel_title": "Evidence for secondary thrombotic microangiopathy in COVID-19", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20215608", + "rel_abs": "The causes of coagulopathy associated with COVID-19 disease are poorly understood. We aimed to investigate the relationship between markers of endothelial activation, intravascular hemolysis, coagulation, and organ damage in COVID-19 patients and study their association with disease severity and mortality. We conducted a retrospective study of 181 hospitalized COVID-19 patients randomly selected with equal distribution of survivors and non-survivors. Patients who died had significantly lower ADAMTS13 activity, significantly higher LDH, schistocytes and von Willebrand Factor levels compared to patients discharged alive. Only 30% of patients with an initial ADAMTS13 activity <43% survived vs. 60% with ADAMTS13 [≥]43% who survived. In conclusion, COVID-19 may manifest as a TMA-like illness in a subset of hospitalized patients. Presence of schistocytes on admission may warrant a work-up for TMA. These findings indicate the need for future investigation to study the relationship between endothelial and coagulation activation and the efficacy of TMA treatments in COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Joseph Sweeney", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Mohammad Barouqa", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Gregory J J Krause", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Jesus Gonzalez Lugo", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Shafia Rahman", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Morayma Reyes Gil", + "author_inst": "Montefiore Medical Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.10.21.20216192", "rel_title": "Broadly-targeted autoreactivity is common in severe SARS-CoV-2 Infection", @@ -1137430,37 +1140359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.21.20216812", - "rel_title": "No lockdown policy for COVID-19 epidemic in Bangladesh: Good, bad or ugly?", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216812", - "rel_abs": "Bangladesh has been combating the COVID-19 pandemic with limited financial resources and poor health infrastructure since March, 2020. Although the government has imposed several restricted measures to curb the progression of the outbreak, these arrays of measures are not sustainable in the long run. In this study, we assess the impact of lift of flexible lockdown on the COVID-19 dynamics in Bangladesh. Our analysis demonstrates that the country might experience second infection peak in 6-7 months after the withdrawal of current lockdown. Moreover, a prolonged restrictions until January, 2021 will shift the infection peak towards August, 2021 and will reduce approximately 20 % COVID-19 cases in Bangladesh.\n\nWhat we knowO_LIBangladesh has been going through COVID-19 crisis and in response, the Government has implemented restricted array of measures to curb the COVID-19 outbreak in Bangladesh.\nC_LI\n\nWhat this article addsO_LIThe impact of no lockdown policies on COVID-19 pandemic in Bangladesh.\nC_LIO_LIAppearance of second infection peak in 6-7 months after the withdrawal of current lockdown.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zakaria Shams Siam", - "author_inst": "North South University" - }, - { - "author_name": "M. Arifuzzaman", - "author_inst": "North South University" - }, - { - "author_name": "Md. Harunur Rashid", - "author_inst": "North South University" - }, - { - "author_name": "md shariful islam", - "author_inst": "North South University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.21.20216846", "rel_title": "Prediction of the infection of COVID-19 in Bangladesh by classical SIR model", @@ -1138396,6 +1141294,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.21.20216960", + "rel_title": "Emergency Response for Evaluating SARS-CoV-2 Immune Status, Seroprevalence and Convalescent Plasma in Argentina", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216960", + "rel_abs": "We report the emergency development and application of a robust serologic test to evaluate acute and convalescent antibody responses to SARS-CoV-2 in Argentina. The assays, COVIDAR IgG and IgM, which were produced and provided for free to health authorities, private and public health institutions and nursing homes, use a combination of a trimer stabilized spike protein and the receptor binding domain (RBD) in a single enzyme-linked immunosorbent assay (ELISA) plate. Over half million tests have already been distributed to detect and quantify antibodies for multiple purposes, including assessment of immune responses in hospitalized patients and large seroprevalence studies in neighborhoods, slums and health care workers, which resulted in a powerful tool for asymptomatic detection and policy making in the country. Analysis of antibody levels and longitudinal studies of symptomatic and asymptomatic SARS-CoV-2 infections in over one thousand patient samples provided insightful information about IgM and IgG seroconversion time and kinetics, and IgM waning profiles. At least 35% of patients showed seroconversion within 7 days, and 95% within 45 days of symptoms onset, with simultaneous or close sequential IgM and IgG detection. Longitudinal studies of asymptomatic cases showed a wide range of antibody responses with median levels below those observed in symptomatic patients. Regarding convalescent plasma applications, a protocol was standardized for the assessment of end point IgG antibody titers with COVIDAR with more than 500 plasma donors. The protocol showed a positive correlation with neutralizing antibody titers, and was used to assess antibody titers for clinical trials and therapies across the country. Here, we demonstrate the importance of providing a robust and specific serologic assay for generating new information about antibody kinetics in infected individuals and mitigation policies to cope with pandemic needs.\n\nAUTHOR SUMMARYThe development of robust and specific serologic assays to detect antibodies to SARS-CoV-2 is essential to understand the pandemic evolution and to stablish mitigation strategies. Here, we report the emergency development, production and application of a versatile ELISA test for detecting antibodies against the whole spike protein and its receptor binding domain. Over half million tests have been freely distributed in public and private health institutions of Argentina for evaluating immune responses, convalescent plasma programs and for large seroprevalence studies in neighborhoods and health care workers. We are still learning how and when to use serologic testing in different epidemiological settings. This program allowed us to produce large amount of high quality data on antibody levels in symptomatic and asymptomatic SARS-CoV-2 infections and generate relevant information about IgM and IgG seroconversion time and kinetics. We also present standardized protocols for antibody quantification as guidance for convalescent donor plasma selection in hospitals throughout the country for compassionate use and clinical trials. Here, we provide a framework for generating widely available tools, protocols and information of antibody responses for pandemic management.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Diego Ojeda", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Maria Mora Gonzalez Lopez Ledesma", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Horacio Palleres", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Guadalupe Costa Navarro", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Lautaro Sanchez", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Beatriz Perazzi", + "author_inst": "Facultad de Farmacia y Bioquimica UBA" + }, + { + "author_name": "Sergio Villordo", + "author_inst": "Fundacion Instituto Leloir" + }, + { + "author_name": "Diego Alvarez", + "author_inst": "Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin" + }, + { + "author_name": "- BioBanco Working Group", + "author_inst": "" + }, + { + "author_name": "Marcela Echavarria", + "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas" + }, + { + "author_name": "Kasopefoluwa Y. Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Christian Stevens", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jorge Carradori", + "author_inst": "Laboratorio Lemos" + }, + { + "author_name": "Julio Caramelo", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Marcelo Yanovsky", + "author_inst": "Fundacion Instituto Leloir" + }, + { + "author_name": "Andrea Gamarnik", + "author_inst": "FUNDACION INSTITUTO LELOIR" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.21.20216945", "rel_title": "The effect of COVID-19 on critical care research: A prospective longitudinal multinational survey", @@ -1139000,97 +1141981,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.22.349415", - "rel_title": "Broad transcriptional dysregulation of brain and choroid plexus cell types with COVID-19", - "rel_date": "2020-10-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.22.349415", - "rel_abs": "Though SARS-CoV-2 primarily targets the respiratory system, it is increasingly appreciated that patients may suffer neurological symptoms of varied severity1-3. However, an unbiased understanding of the molecular processes across brain cell types that could contribute to these symptoms in COVID-19 patients is still missing. Here, we profile 47,678 droplet-based single-nucleus transcriptomes from the frontal cortex and choroid plexus across 10 non-viral, 4 COVID-19, and 1 influenza patient. We complement transcriptomic data with immunohistochemical staining for the presence of SARS-CoV-2. We find that all major cortex parenchymal and choroid plexus cell types are affected transcriptionally with COVID-19. This arises, in part, from SARS-CoV-2 infection of the cortical brain vasculature, meninges, and choroid plexus, stimulating increased inflammatory signaling into the brain. In parallel, peripheral immune cells infiltrate the brain, microglia activate programs mediating the phagocytosis of live neurons, and astrocytes dysregulate genes involved in neurotransmitter homeostasis. Among neurons, layer 2/3 excitatory neurons--evolutionarily expanded in humans4--show a specific downregulation of genes encoding major SNARE and synaptic vesicle components, predicting compromised synaptic transmission. These perturbations are not observed in terminal influenza. Many COVID-19 gene expression changes are shared with those in chronic brain disorders and reside in genetic variants associated with cognitive function, schizophrenia, and depression. Our findings and public dataset provide a molecular framework and new opportunities to understand COVID-19 related neurological disease.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Andrew Chris Yang", - "author_inst": "Stanford University" - }, - { - "author_name": "Fabian Kern", - "author_inst": "Saarland University" - }, - { - "author_name": "Patricia M Losada", - "author_inst": "Stanford University" - }, - { - "author_name": "Christina A Maat", - "author_inst": "Stanford University" - }, - { - "author_name": "Georges Schmartz", - "author_inst": "Saarland University" - }, - { - "author_name": "Tobias Fehlmann", - "author_inst": "Saarland University" - }, - { - "author_name": "Nicholas Schaum", - "author_inst": "Stanford University" - }, - { - "author_name": "Davis P Lee", - "author_inst": "Stanford University" - }, - { - "author_name": "Kruti Calcuttawala", - "author_inst": "Stanford University" - }, - { - "author_name": "Ryan T Vest", - "author_inst": "Stanford University" - }, - { - "author_name": "David Gate", - "author_inst": "Stanford University" - }, - { - "author_name": "Daniela Berdnik", - "author_inst": "Stanford University" - }, - { - "author_name": "M. Windy McNerney", - "author_inst": "Stanford University" - }, - { - "author_name": "Divya Channappa", - "author_inst": "Stanford University" - }, - { - "author_name": "Inma Cobos", - "author_inst": "Stanford University" - }, - { - "author_name": "Nicole Ludwig", - "author_inst": "Saarland University" - }, - { - "author_name": "Walter J. Schulz-Schaeffer", - "author_inst": "Saarland University" - }, - { - "author_name": "Andreas Keller", - "author_inst": "Saarland University" - }, - { - "author_name": "Tony Wyss-Coray", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.10.22.351056", "rel_title": "Small-Molecule In Vitro Inhibitors of the Coronavirus Spike - ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2", @@ -1140010,6 +1142900,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.19.20213421", + "rel_title": "PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20213421", + "rel_abs": "BackgroundCovid-19 Serology may document exposure and perhaps protection to the virus and serological test may help understand epidemic dynamics. We tested health workers form a public laboratory to evaluate previous exposure to the virus and estimate the prevalence of antibodies against-SARS-CoV-2 in Adolfo Lutz Institute, State of Sao Paulo, Brazil.\n\nMethodsThis study was an open, prospective evaluation among professionals of Adolfo Lutz Institute some administrative personnel from the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay. SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants.\n\nResultsA total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity.\n\nConclusionsWe documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, higher among outsourced workers and those residing with COVID-19 patients. COVID related work did not increased seropositivity. Some symptoms show strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Valeria Oliveira Silva", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Elaine Lopes de Oliveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Marcia Jorge Castejon", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Rosemeire Yamashiro", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Cintia Mayumi Ahagon", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Giselle Ibette Lopez-Lopes", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Edilene Peres Real da Silveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Marisa Ailin Hong", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Maria do Carmo Timenetsky", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Carmem aparecida de Freitas Oliveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Luis Fernando de Macedo Brigido", + "author_inst": "Instituto Adolfo Lutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.20.20212522", "rel_title": "Analytical solution of equivalent SEIR and agent-based model of COVID-19; showing the bounds of contact tracing", @@ -1140605,109 +1143554,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.20.20213793", - "rel_title": "Validation of expert system enhanced deep learning algorithm for automated screening for COVID-Pneumonia on chest X-rays", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20213793", - "rel_abs": "The coronavirus disease of 2019 (COVID-19) pandemic exposed a limitation of artificial intelligence (AI) based medical image interpretation systems. Early in the pandemic, when need was greatest, the absence of sufficient training data prevented effective deep learning (DL) solutions. Even now, there is a need for Chest-X-ray (CxR) screening tools in low and middle income countries (LMIC), when RT-PCR is delayed, to exclude COVID-19 pneumonia (Cov-Pneum) requiring transfer to higher care. In absence of local LMIC data and poor portability of CxR DL algorithms, a new approach is needed. Axiomatically, it is faster to repurpose existing data than to generate new datasets. Here, we describe CovBaseAI, an explainable tool which uses an ensemble of three DL models and an expert decision system (EDS) for Cov-Pneum diagnosis, trained entirely on datasets from the pre-COVID-19 period. Portability, performance, and explainability of CovBaseAI was primarily validated on two independent datasets. First, 1401 randomly selected CxR from an Indian quarantine-center to assess effectiveness in excluding radiologic Cov-Pneum that may require higher care. Second, a curated dataset with 434 RT-PCR positive cases of varying levels of severity and 471 historical scans containing normal studies and non-COVID pathologies, to assess performance in advanced medical settings. CovBaseAI had accuracy of 87% with negative predictive value of 98% in the quarantine-center data for Cov-Pneum. However, sensitivity varied from 0.66 to 0.90 depending on whether RT-PCR or radiologist opinion was set as ground truth. This tool with explainability feature has better performance than publicly available algorithms trained on COVID-19 data but needs further improvement.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Prashant Sadashiv Gidde", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan 333031, India" - }, - { - "author_name": "Shyam Sunder Prasad", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan 333031, India" - }, - { - "author_name": "Ajay Pratap Singh", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Nitin Batheja", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Satyartha Prakash", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Prateek Singh", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Aakash Saboo", - "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), New Delhi, India" - }, - { - "author_name": "Rohit Thakar", - "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), New Delhi, India" - }, - { - "author_name": "Salil Gupta", - "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), New Delhi, India" - }, - { - "author_name": "Sumeet Saurav", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan 333031, India" - }, - { - "author_name": "M V Raghunandan", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Amritpal Singh", - "author_inst": "Maulana Azad Medical College (MAMC), New Delhi, India" - }, - { - "author_name": "Viren Sardana", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Harsh Mahajan", - "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), New Delhi, India" - }, - { - "author_name": "Arjun Kalyanpur", - "author_inst": "Teleradiology Solutions, #7G, Opposite Graphite India, Whitefield, Bangalore, Karnataka, 560048, India" - }, - { - "author_name": "Atanendu Shekhar Mandal", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan 333031, India" - }, - { - "author_name": "Vidur Mahajan", - "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), New Delhi, India" - }, - { - "author_name": "Anurag Agrawal", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India" - }, - { - "author_name": "Anjali Agrawal", - "author_inst": "Teleradiology Solutions, 12B Sriram Road, Civil Lines, Delhi, 110054, India" - }, - { - "author_name": "Vasantha Kumar Venugopal", - "author_inst": "Centre for Advanced Research in Imaging, Neurosciences & Genomics (CARING), New Delhi, India" - }, - { - "author_name": "Sanjay Singh", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan 333031, India" - }, - { - "author_name": "Debasis Dash", - "author_inst": "CSIR - Institute of Genomics and Integrative Biology, Delhi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.10.21.347799", "rel_title": "Preclinical study of DNA vaccines targeting SARS-CoV-2", @@ -1141595,6 +1144441,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.14.20212662", + "rel_title": "Antibody Immunological Imprinting on COVID-19 Patients", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212662", + "rel_abs": "While the current pandemic remains a thread to human health, the polyclonal nature of the antibody response against SARS-CoV-2 is not fully understood. Other than SARS-CoV-2, humans are susceptible to six different coronaviruses, and previous exposure to antigenically related and divergent seasonal coronaviruses is frequent. We longitudinally profiled the early humoral immune response against SARS-CoV-2 on hospitalized COVID-19 patients, and quantify levels of pre-existing immunity to OC43, HKU1 and 223E seasonal coronaviruses. A strong back-boosting effect to conserved, but not variable regions of OC43 and HKU1 betacoronaviruses spike protein was observed. All patients developed antibodies against SARS-CoV-2 spike and nucleoprotein, with peak induction at day 7 post hospitalization. However a negative correlation was found between antibody memory boost to human coronaviruses and induction of IgG and IgM against SARS-CoV-2 spike. Our findings provide evidence of immunological imprinting that determine the antibody profile to COVID-19 patients in an original antigenic sin fashion.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Teresa Aydillo", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York;" + }, + { + "author_name": "Alexander Rombauts", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Daniel Stadlbauer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Sadaf Aslam", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Gabriela Abelenda-Alonso", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Alba Escalera", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Kaijun Jiang", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Jordi Carratala", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.15.20213223", "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Incorporating Outdoor Temperature and School Re-Opening Effects-September Update", @@ -1142239,165 +1145144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.15.20122523", - "rel_title": "Intravenous Mesenchymal Stem Cells in Extracorporeal Oxygenation Patients with Severe COVID-19 Acute Respiratory Distress Syndrome", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20122523", - "rel_abs": "BackgroundThere is an ongoing critical need to improve therapeutic strategies for COVID-19 pneumonia, particularly in the most severely affected patients. Adult mesenchymal stem cell (MSC) infusions have the potential to benefit critically ill patients with acute respiratory syndrome SARS-COV-2 infection, but clinical data supporting efficacy are lacking.\n\nMethodsWe conducted a case-control study of critically ill patients with laboratory-confirmed COVID-19, severe acute respiratory distress syndrome (ARDS). To evaluate clinical responsiveness in the most critically ill patient we examined outcomes in a sub-group of those requiring extracorporeal membrane oxygenation (ECMO) support. Patients (n=9) were administered with up to 3 infusions of intravenous (IV) MSCs and compared to a local ECMO control group (n=31). The primary outcome was safety, and the secondary outcomes were all-cause mortality (or rate of hospital discharge), cytokine levels, and viral clearance.\n\nFindingsMSC infusions (12 patients) were well tolerated and no side effects occurred. Of ECMO patients receiving MSC infusions, 2 out of 9 died (22.2%; 95%CI: 2.8%, 60.0%) compared with a mortality of 15 of 31 (48.4%; 95%CI: 30.2%, 66.9%; p = 0.25) in the ECMO control group. Isolated plasma exosomes containing the SARS-COV-2 Spike protein decreased after MSC infusions between day 14 or 21 after administration (p=0.003 and p=0.005, respectively) and was associated with a decrease in COVID-19 IgG Spike protein titer at same time points (p = 0.006 and p=0.007, respectively). Control ECMO patients receiving convalescent plasma did not clear COVID-19 IgG over the same time frame.\n\nInterpretationTogether these findings suggest that MSC IV infusion is well tolerated in patients with a broad range of severity including the most severe COVID-19 ARDS requiring ECMO. These data also raise the possibility that MSCs, in addition to exerting an immunomodulatory effect, contribute to viral clearance and strongly support the conduct of randomized placebo-controlled trial.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Sunjay Kaushal", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Aisha Khan", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Kristopher Deatrick", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Derek K Ng", - "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Abigail Snyder", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Aakash Shah", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Lina V Caceres", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Ketty Bacallao", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Melania Bembea", - "author_inst": "Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland." - }, - { - "author_name": "Allen Everett", - "author_inst": "Blalock-Taussig-Thomas Congenital Heart Center, Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland" - }, - { - "author_name": "Jie Zhu", - "author_inst": "Blalock-Taussig-Thomas Congenital Heart Center, Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland" - }, - { - "author_name": "David Kaczorowski", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Ronson Madathil", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Ali Tabatabai", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, University Maryland School of Medicine, Baltimore, Maryland." - }, - { - "author_name": "Geoffrey Rosenthal", - "author_inst": "Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Adriana Brooks", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Bangon Longsomboon", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Rachana Mishra", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Progyaparamita Saha", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Yvenie Desire", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Russell Saltzman", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Kim G Hankey", - "author_inst": "Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Sixto A Arias", - "author_inst": "Pulmonary and Critical Care, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Folusakin Ayoade", - "author_inst": "Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Jairo A. Tovar", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Rejane Lamazares", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Hayley B Gershengorn", - "author_inst": "Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Fontaine J Magali", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Matthias Loebe", - "author_inst": "Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Kristin Mullins", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Muthukumar Gunasekaran", - "author_inst": "Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, Maryland" - }, - { - "author_name": "Vela Karakeshishyan", - "author_inst": "Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Dushyantha T Jayaweera", - "author_inst": "Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Anthony Atala", - "author_inst": "Department of Urology, Wake Forest University, Winston Salem, North Carolina" - }, - { - "author_name": "Ali Ghodsizad", - "author_inst": "Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Joshua M Hare", - "author_inst": "University of Miami" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.10.15.20212308", "rel_title": "Indirect effects of the COVID-19 pandemic on paediatric health-care use and severe disease: a retrospective national cohort study", @@ -1143345,6 +1146091,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.17.20214312", + "rel_title": "Echo chambers as early warning signals of widespread vaccine refusal in social-epidemiological networks", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.17.20214312", + "rel_abs": "Sudden shifts in population health and vaccination rates occur as the dynamics of some epidemiological models go through a critical point; literature shows that this is sometimes foreshadowed by early warning signals (EWS). We investigate different structural measures of a network as candidate EWS of infectious disease outbreaks and changes in popular vaccine sentiment. We construct a multiplex disease model coupling infectious disease spread and social contact dynamics. We find that the number and mean size of echo chambers predict transitions in the infection dynamics, as do opinion-based communities. Graph modularity also gives early warnings, though the clustering coefficient shows no significant pre-outbreak changes. Change point tests applied to the EWS show decreasing efficacy as social norms strengthen. Therefore, many measures of social network connectivity can predict approaching critical changes in vaccine uptake and aggregate health, thereby providing valuable tools for improving public health.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Brendon C Phillips", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Chris Bauch", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.16.20214049", "rel_title": "Quantifying Asymptomatic Infection and Transmission of COVID-19 in New York City using Observed Cases, Serology and Testing Capacity", @@ -1143821,41 +1146590,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2020.10.18.20214650", - "rel_title": "2008 financial crisis vs 2020 economic fallout: How COVID-19 might influence fertility treatment and live births", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20214650", - "rel_abs": "BackgroundThe economic and reproductive medicine response to the COVID-19 pandemic in the United States has reduced the affordability and accessibility of fertility care. We sought to determine the impact of the 2008 financial recession and the COVID-19 recession on fertility treatments and cumulative live-births.\n\nMethodsWe examined annual US natality, CDC IVF cycle activity and live birth data from 1999 to 2018 encompassing 3,286,349 treatment cycles, to estimate the age-stratified reduction in IVF cycles undertaken after the 2008 financial recession, with forward quantitative modelling of IVF cycle activity and cumulative live-births for 2020 to 2023.\n\nResultsThe financial recession of 2008 caused a four-year plateau in fertility treatments with a predicted 53,026 (95% CI 49,581 to 56,471) fewer IVF cycles and 16,872 (95% CI 16,713 to 17,031) fewer live births. A similar scale of economic recession would cause 67,386 (95% CI: 61,686 to 73,086) fewer IVF cycles between 2020 and 2023, with women younger than 35 years overall undertaking 22,504 (95% CI 14,320 to 30,690) fewer cycles, as compared to 4,445 (95% CI 3,144 to 5749) fewer cycles in women over the age of 40 years. This equates to overall 25,143 (95% CI: 22,408 to 27,877) fewer predicted live-births from IVF, of which only 490 (95% CI 381 to 601) are anticipated to occur in women over the age of 40 years.\n\nConclusionsThe COVID-19 recession could have a profound impact on US IVF live-birth rates in young women, further aggravating pre-existing declines in total fertility rates.\n\nTrial registration numbernot applicable", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Piotr S. Gromski", - "author_inst": "School of Medicine, University of Glasgow, UK" - }, - { - "author_name": "Andrew D.A.C. Smith", - "author_inst": "Applied Statistics Group, University of the West of England, Bristol, UK" - }, - { - "author_name": "Deborah A. Lawlor", - "author_inst": "MRC Epidemiology Unit at the University of Bristol, Bristol, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; Population Health Science, Bristol Medica" - }, - { - "author_name": "Fady I. Sharara", - "author_inst": "Virginia Center for Reproductive Medicine, Reston, VA, USA; George Washington University, Washington, DC, USA" - }, - { - "author_name": "Scott M. Nelson", - "author_inst": "School of Medicine, University of Glasgow, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; The Fertility Partnership, Oxford, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.10.16.20214023", "rel_title": "Age-Stratified SARS-CoV-2 Infection Fatality Rates in New York City estimated from serological data", @@ -1144895,6 +1147629,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.15.20208041", + "rel_title": "Analysis of respiratory and systemic immune responses in COVID-19 reveals mechanisms of disease pathogenesis", + "rel_date": "2020-10-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20208041", + "rel_abs": "Immune responses to respiratory viruses like SARS-CoV-2 originate and function in the lung, yet assessments of human immunity are often limited to blood. Here, we conducted longitudinal, high-dimensional profiling of paired airway and blood samples from patients with severe COVID-19, revealing immune processes in the respiratory tract linked to disease pathogenesis. Survival from severe disease was associated with increased CD4+T cells and decreased monocyte/macrophage frequencies in the airway, but not in blood. Airway T cells and macrophages exhibited tissue-resident phenotypes and activation signatures, including high level expression and secretion of monocyte chemoattractants CCL2 and CCL3 by airway macrophages. By contrast, monocytes in blood expressed the CCL2-receptor CCR2 and aberrant CD163+ and immature phenotypes. Extensive accumulation of CD163+monocyte/macrophages within alveolar spaces in COVID-19 lung autopsies suggested recruitment from circulation. Our findings provide evidence that COVID-19 pathogenesis is driven by respiratory immunity, and rationale for site-specific treatment and prevention strategies.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Peter A. Szabo", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Pranay Dogra", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Joshua I. Gray", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Steven B. Wells", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Thomas J. Connors", + "author_inst": "Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Stuart P. Weisberg", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Izabela Krupska", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Rei Matsumoto", + "author_inst": "Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Maya M.L. Poon", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 and Medical Scientist Training Program, Columbia Univer" + }, + { + "author_name": "Emma Idzikowski", + "author_inst": "Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Sinead E. Morris", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Pasin Chloe", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Andrew J. Yates", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Amy Ku", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Michael Chait", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Julia M. Davis-Porada", + "author_inst": "Medical Scientist Training Program, Columbia University" + }, + { + "author_name": "Jing Zhou", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Matthew Steinle", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Sean Mackay", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Anjali Saqi", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Matthew R. Baldwin", + "author_inst": "Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Peter A. Sims", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032 and Department of Biochemistry and Molecular Biophysics, Columbia U" + }, + { + "author_name": "Donna L Farber", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.17.343863", "rel_title": "Development and pre-clinical characterization of two therapeutic equine formulations towards SARS-CoV-2 proteins for the potential treatment of COVID-19", @@ -1145707,61 +1148548,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.16.20213959", - "rel_title": "HIV testing by public health centers and municipalities, and new HIV cases during the COVID-19 pandemic in Japan", - "rel_date": "2020-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20213959", - "rel_abs": "BackgroundDuring the COVID-19 outbreak, medical resources were primarily allocated to COVID-19, which might have reduced facility capacity for HIV testing. Further, people may have opted against HIV testing during this period to avoid COVID-19 exposure. We investigate the influence of the COVID-19 pandemic on HIV testing and its consequences in Japan.\n\nMethodsWe analysed quarterly HIV/AIDS-related data from 2015 to the second quarter of 2020 using an anomaly detection approach. The data included the number of consultations that public health centers received, the number of HIV tests performed by public health centers or municipalities, and the number of newly reported HIV cases with and without AIDS diagnosis. As sensitivity analyses, we performed the same analysis for two subgroups: men who have sex with men (MSM) and non-Japanese.\n\nFindingsThe number of HIV tests (9,584 vs. 35,908 in the year-before period) and consultations (11,689 vs. 32,565) performed by public health centers significantly declined in the second quarter of 2020, while the proportion of HIV cases with AIDS diagnosis among all HIV cases (36{middle dot}2% vs. 26{middle dot}4%) significantly increased after removing the trend and seasonality effects. The number of HIV cases without AIDS diagnosis numerically decreased (166 vs. 217), although the reduction was not significant. We confirmed similar trend for the MSM and non-Japanese groups.\n\nInterpretationThe current HIV testing system including public health centers misses more HIV cases at the early phase of the infection during the pandemic. Given that the clear epidemiological picture of HIV incidence during the pandemic is still uncertain, continuously monitoring the situation as well as securing sufficient test resources using self-test is essential.\n\nFundingJapan Society for the Promotion of Science, Japan Science and Technology Agency, Japan Agency for Medical Research and Development.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSBefore this study, we searched PubMed, Medline, and Google Scholar on Oct 12, 2020, for articles investigated the number of HIV test and HIV cases during the COVID-19 pandemic in Japan, using the search terms \"novel coronavirus\" or \"SARS-CoV-2\", and \"HIV\" or \"AIDS\", and \"Japan\", with no time restrictions. We found no published work relevant to our study.\n\nAdded value of this studyDuring the COVID-19 pandemic in Japan, the public health centers and municipalities temporarily suspended facility-based HIV testing to concentrate their limited resources to COVID-19 testing. We investigated the impact of the COVID-19 pandemic on the number of HIV tests in public health centers and municipalities, and on the number of HIV cases with and without AIDS diagnosis. We confirmed that the number of the test declined in the second quarter (April to June) of 2020, and the proportion of HIV with AIDS diagnosis among all HIV cases increased during the same period.\n\nImplications of all the available evidenceProviding sufficient HIV testing opportunities even during the pandemic, when facility-based testing is challenging, is necessary for better clinical and public health outcomes. Self-testing and home specimen collection (e.g. dried blood spot or oral fluid test) could be a key to fill the gap between the need for HIV testing and the constraints related to the COVID-19 outbreak.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Keisuke Ejima", - "author_inst": "Indiana University" - }, - { - "author_name": "Yoshiki Koizumi", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Nao Yamamoto", - "author_inst": "Arizona State University" - }, - { - "author_name": "Molly Rosenberg", - "author_inst": "Indiana University School of Public Health-Bloomington" - }, - { - "author_name": "Christina Ludema", - "author_inst": "Indiana University School of Public Health-Bloomington" - }, - { - "author_name": "Ana I Bento", - "author_inst": "Indiana University" - }, - { - "author_name": "Daisuke Yoneoka", - "author_inst": "St. Luke's International University" - }, - { - "author_name": "Seiichi Ichikawa", - "author_inst": "Kinjo Gakuin University" - }, - { - "author_name": "Daisuke Mizushima", - "author_inst": "AIDS Clinical Center, National Center for Global Health and Medicine" - }, - { - "author_name": "Shingo Iwami", - "author_inst": "Kyushu University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.14.20212993", "rel_title": "White blood cells and severe COVID-19: a Mendelian randomization study", @@ -1146456,6 +1149242,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.14.20212449", + "rel_title": "TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA", + "rel_date": "2020-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212449", + "rel_abs": "BackgroundSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a virus that causes COVID-19, which has become a worldwide pandemic. However, until now, there is no vaccine or specific drug to prevent or treat COVID-19.\n\nObjectivesTo find out the effective treatment as an antiviral agent for COVID-19, to determine the correlation between sociodemography with clinical outcomes and duration of treatment, and to determine the relationship between comorbidities with clinical outcomes and duration of treatment for COVID-19 patients.\n\nMethodsA prospective cohort study was conducted in this study. This study included only confirmed COVID-19 patients who were admitted to the hospital during April-May 2020. Convenience sampling was used to select 103 patients, but only 72 patients were suitable for inclusion.\n\nResultsThe survival analysis for COVID-19 patients using the Kaplan Meier method showed that patients receiving Oseltamivir + Hydroxychloroquine had an average survival rate of about 83% after undergoing treatment for about ten days. Gender (p = 0.450) and age (p = 0.226) did not have a significant correlation with the duration of treatment for COVID-19 patients. Gender (p = 0.174) and age (p = 0.065) also did not have a significant correlation with clinical outcome of COVID-19 patients. Comorbidities showed a significant correlation with duration of treatment (p = 0.002) and clinical outcome (p = 0.014) of COVID-19 patients.\n\nConclusionThe most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine. The higher the patients average treatment duration, the lower the average survival rate for COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Diana Laila Ramatillah", + "author_inst": "Universitas 17 Agustus 1945 Jakarta" + }, + { + "author_name": "Suri Isnaini", + "author_inst": "Pharmacy Faculty, Universitas 17 Agustus 1945 Jakarta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.10.20207449", "rel_title": "Recovery of monocyte exhaustion is associated with resolution of lung injury in COVID-19 convalescence.", @@ -1147228,97 +1150037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.14.20212340", - "rel_title": "Early Prediction of COVID-19 Severity Using Extracellular Vesicles and Extracellular RNAs", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212340", - "rel_abs": "The clinical manifestations of COVID-19 vary broadly, ranging from asymptomatic infection to acute respiratory failure and death. But the predictive biomarkers for characterizing the variability are still lacking. Since emerging evidence indicates that extracellular vesicles (EVs) and extracellular RNAs (exRNAs) are functionally involved in a number of pathological processes, we hypothesize that these extracellular components may be key determinants and/or predictors of COVID-19 severity. To test our hypothesis, we collected serum samples from 31 patients with mild COVID-19 symptoms at the time of their admission. After standard therapy without corticosteroids, 9 of the 31 patients developed severe COVID-19 symptoms. We analyzed EV protein and exRNA profiles to look for correlations between these profiles and COVID-19 severity. Strikingly, we identified three distinct groups of markers (antiviral response-related EV proteins, coagulation-related markers, and liver damage-related exRNAs) with the potential to serve as early predictive biomarkers for COVID-19 severity. Among these markers, EV COPB2 has the best predictive value for severe deterioration of COVID-19 patients in this cohort. This type of information concerning functional extracellular component profiles could have great value for patient stratification and for making early clinical decisions about strategies for COVID-19 therapy.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Yu Fujita", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Tokio Hoshina", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Juntaro Matsuzaki", - "author_inst": "Tokyo Medical University" - }, - { - "author_name": "Tsukasa Kadota", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Shota Fujimoto", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Hironori Kawamoto", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Naoaki Watanabe", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Kenji Sawaki", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Yohei Sakamoto", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Makiko Miyajima", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Kwangyole Lee", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Kazuhiko Nakaharai", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Tetsuya Horino", - "author_inst": "The Jikei University School of Medicine," - }, - { - "author_name": "Ryo Nakagawa", - "author_inst": "Omiya City Clinic" - }, - { - "author_name": "Jun Araya", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Mitsuru Miyato", - "author_inst": "Tokyo Medical University" - }, - { - "author_name": "Masaki Yoshida", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Kazuyoshi Kuwano", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Takahiro Ochiya", - "author_inst": "Tokyo Medical University," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.14.20212431", "rel_title": "How to remove the testing bias in CoV-2 statistics", @@ -1148314,6 +1151032,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.14.20090985", + "rel_title": "An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland", + "rel_date": "2020-10-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20090985", + "rel_abs": "Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. We showed that immigration and the logarithm of general mobility is the best predictor of SARS-CoV-2 arrival times, while emigration, industrialization and air quality explain the most of the size of the epidemic in poviats. On the other hand, infection dynamics is driven to a lesser extent by previously postulated variables such as population size and density, income or the size of the elderly population. Our analyses could support Polish authorities in preparation for the second wave of infections and optimal management of resources as we have provided a proposition of optimal distribution of human resources between poviats.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrzej Jarynowski", + "author_inst": "Institute for Interdisciplinary Research" + }, + { + "author_name": "Monika Wojta-Kempa", + "author_inst": "Wroclaw Medical Universtity" + }, + { + "author_name": "Lukasz Krzowski", + "author_inst": "Military University of Technology in Warsaw" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.13.20211284", "rel_title": "Stay-at-home policy: is it a case of exception fallacy? An internet-based ecological study", @@ -1148918,113 +1151663,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.10.15.340612", - "rel_title": "Systematic analysis of innate immune antagonism reveals vulnerabilities of SARS-CoV-2", - "rel_date": "2020-10-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.15.340612", - "rel_abs": "The innate immune system constitutes a powerful barrier against viral infections. However, it may fail because successful emerging pathogens, like SARS-CoV-2, evolved strategies to counteract it. Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Mechanistic analyses show that autophagy and type I IFN responses are effectively counteracted at different levels. For example, Nsp14 induces loss of the IFN receptor, whereas ORF3a disturbs autophagy at the Golgi/endosome interface. Comparative analyses revealed that antagonism of type I IFN and autophagy is largely conserved, except that SARS-CoV-1 Nsp15 is more potent in counteracting type I IFN than its SARS-CoV-2 ortholog. Altogether, however, SARS-CoV-2 counteracts type I IFN responses and autophagy much more efficiently than type II and III IFN signaling. Consequently, the virus is relatively resistant against exogenous IFN-/{beta} and autophagy modulation but remains highly vulnerable towards IFN-{gamma} and -{lambda} treatment. In combination, IFN-{gamma} and -{lambda} act synergistically, and drastically reduce SARS-CoV-2 replication at exceedingly low doses. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Manuel Hayn", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Maximilian Hirschenberger", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Lennart Koepke", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Jan Hendrik Straub", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Rayhane Nchioua", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Maria Honholt Christensen", - "author_inst": "Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany" - }, - { - "author_name": "Susanne Klute", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Caterina Prelli Bozzo", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Wasim Aftab", - "author_inst": "Biomedical Center, Protein Analysis Unit, Department of Molecular Biology, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Graduate School f" - }, - { - "author_name": "Fabian Zech", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Carina Conzelmann", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Janis Alexander Mueller", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Smitha Srinivasachar Badarinarayan", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Christina Martina Stuerzel", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Ignasi Forne", - "author_inst": "Biomedical Center, Protein Analysis Unit, Department of Molecular Biology, Ludwig-Maximilians- University of Munich, 82152 Planegg-Martinsried, Germany" - }, - { - "author_name": "Steffen Stenger", - "author_inst": "Institute for Medical Microbiology and Hygiene, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Karl-Klaus Conzelmann", - "author_inst": "Gene Center and Max von Pettenkofer-Institute of Virology, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany" - }, - { - "author_name": "Jan Muench", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Daniel Sauter", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Florian Ingo Schmidt", - "author_inst": "Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany" - }, - { - "author_name": "Axel Imhof", - "author_inst": "Biomedical Center, Protein Analysis Unit, Department of Molecular Biology, Ludwig-Maximilians- University of Munich, 82152 Planegg-Martinsried, Germany" - }, - { - "author_name": "Frank Kirchhoff", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - }, - { - "author_name": "Konstantin Maria Johannes Sparrer", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.15.340794", "rel_title": "Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs", @@ -1149848,6 +1152486,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.10.11.20211045", + "rel_title": "Understanding the Los Angeles County Coronavirus Epidemic: The Critical Role of Intrahousehold Transmission", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20211045", + "rel_abs": "We tracked the course of the COVID-19 epidemic among the approximately 300 communities comprising Los Angeles County. The epidemic, we found, had three distinct phases. During Phase I, from early March through about April 4, initial seeding of infection in relatively affluent areas was followed by radial geographic extension to adjoining communities. During Phase II, lasting until about July 11, COVID-19 cases continued to rise at a slower rate, and became increasingly concentrated in four geographic foci of infection across the county. Those communities with larger reductions in social mobility during April - as measured by the proportion of smartphones staying at home and number of smartphones visiting a gym - reported fewer COVID-19 cases in May. During Phase III, COVID-19 incidence only gradually declined, remaining as high as the incidence seen at the end of Phase I. Across communities, the prevalence of households at high risk for intergenerational transmission was strongly correlated with the persistence of continued COVID-19 propagation. This association was even stronger in those communities with a higher rate of gym attendance in Phase II. The map of the prevalence of at-risk households in Los Angeles County coincided strikingly with the map of cumulative COVID-19 incidence. These findings, taken together, support the critical role of household structure in the persistent propagation of COVID-19 infections in Los Angeles County. Public health policy needs to be reoriented from a focus on protecting the individual to a focus on protecting the household.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jeffrey E Harris", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.12.20211094", "rel_title": "Prioritisation of population groups with the most interactions for COVID-19 vaccination can substantially reduce total fatalities", @@ -1150320,181 +1152977,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.10.13.20201855", - "rel_title": "Validation of a Derived International Patient Severity Phenotype to Support COVID-19 Analytics from Electronic Health Record Data", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20201855", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSIntroductionC_ST_ABSThe Consortium for Clinical Characterization of COVID-19 by EHR (4CE) includes hundreds of hospitals internationally using a federated computational approach to COVID-19 research using the EHR.\n\nObjectiveWe sought to develop and validate a standard definition of COVID-19 severity from readily accessible EHR data across the Consortium.\n\nMethodsWe developed an EHR-based severity algorithm and validated it on patient hospitalization data from 12 4CE clinical sites against the outcomes of ICU admission and/or death. We also used a machine learning approach to compare selected predictors of severity to the 4CE algorithm at one site.\n\nResultsThe 4CE severity algorithm performed with pooled sensitivity of 0.73 and specificity 0.83 for the combined outcome of ICU admission and/or death. The sensitivity of single code categories for acuity were unacceptably inaccurate - varying by up to 0.65 across sites. A multivariate machine learning approach identified codes resulting in mean AUC 0.956 (95% CI: 0.952, 0.959) compared to 0.903 (95% CI: 0.886, 0.921) using expert-derived codes. Billing codes were poor proxies of ICU admission, with 49% precision and recall compared against chart review at one partner institution.\n\nDiscussionWe developed a proxy measure of severity that proved resilient to coding variability internationally by using a set of 6 code classes. In contrast, machine-learning approaches may tend to overfit hospital-specific orders. Manual chart review revealed discrepancies even in the gold standard outcomes, possibly due to pandemic conditions.\n\nConclusionWe developed an EHR-based algorithm for COVID-19 severity and validated it at 12 international sites.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Jeffrey G. Klann", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Griffin M Weber", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Hossein Estiri", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Bertrand Moal", - "author_inst": "Bordeaux University Hospital" - }, - { - "author_name": "Paul Avillach", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Chuan Hong", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Victor M Castro", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Thomas Maulhardt", - "author_inst": "Institute of Medical Biometry and Statistics, Medical Center, University of Freiburg" - }, - { - "author_name": "Amelia LM Tan", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Alon Geva", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Brett K Beaulieu-Jones", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Alberto Malovini", - "author_inst": "Istituti Clinici Scientifici Maugeri SpA SB IRCCS" - }, - { - "author_name": "Andrew M South", - "author_inst": "Brenner Children's Hospital, Wake Forest School of Medicine" - }, - { - "author_name": "Shyam Visweswaran", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Gilbert S Omenn", - "author_inst": "University of Michigan" - }, - { - "author_name": "Kee Yuan Ngiam", - "author_inst": "National Univerisity Health Systems Singapore" - }, - { - "author_name": "Kenneth D Mandl", - "author_inst": "Harvard Medical School, Boston Children's Hospital" - }, - { - "author_name": "Martin Boeker", - "author_inst": "Faculty of Medicine and Medical Center, University of Freiburg" - }, - { - "author_name": "Karen L Olson", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Danielle L Mowery", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Michele Morris", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Robert W Follett", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "David A Hanauer", - "author_inst": "University of Michigan Medical School" - }, - { - "author_name": "Riccardo Bellazzi", - "author_inst": "University of Pavia, Italy and IRCCS ICS Maugeri, Italy" - }, - { - "author_name": "Jason H Moore", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Ne Hooi Will Loh", - "author_inst": "National University Health System, Singapore" - }, - { - "author_name": "Douglas S Bell", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Kavishwar Wagholikar", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Luca Chiovato", - "author_inst": "IRCCS ICS Maugeri, Pavia and Department of Internal Medicine and Medical Therapy, University of Pavia" - }, - { - "author_name": "Valentina Tibollo", - "author_inst": "IRCCS ICS Maugeri, Pavia" - }, - { - "author_name": "Siegbert Rieg", - "author_inst": "Medical Center - University of Freiburg" - }, - { - "author_name": "Anthony LLJ Li", - "author_inst": "National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore" - }, - { - "author_name": "Vianney Jouhet", - "author_inst": "Bordeaux University Hospital / ERIAS - Inserm U1219 BPH" - }, - { - "author_name": "Emilly Schriver", - "author_inst": "University of Pennsylvania Health System" - }, - { - "author_name": "Malarkodi J Samayamuthu", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Zongqi Xia", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "- The Consortium for Clinical Characterization of COVID-19 by EHR (4CE)", - "author_inst": "" - }, - { - "author_name": "Isaac S Kohane", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Gabriel A Brat", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Shawn N Murphy", - "author_inst": "Massachusetts General Hospital and Mass General Brigham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.13.20212183", "rel_title": "Return to University Campuses Associated with 9% Increase in New COVID-19 Case Rate", @@ -1151462,6 +1153944,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.12.20211557", + "rel_title": "Nonspecific blood tests as proxies for COVID-19 hospitalization: are there plausible associations after excluding noisy predictors?", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211557", + "rel_abs": "This study applied causal criteria in directed acyclic graphs for handling covariates in associations for prognosis of severe COVID-19 (Corona virus disease 19) cases. To identify nonspecific blood tests and risk factors as predictors of hospitalization due to COVID-19, one has to exclude noisy predictors by comparing the concordance statistics (AUC) for positive and negative cases of SARS-CoV-2 (acute respiratory syndrome coronavirus 2). Predictors with significant AUC at negative stratum should be either controlled for their confounders or eliminated (when confounders are unavailable). Models were classified according to the difference of AUC between strata. The framework was applied to an open database with 5644 patients from Hospital Israelita Albert Einstein in Brazil with SARS-CoV-2 RT-PCR (Reverse Transcription - Polymerase Chain Reaction) exam. C-reactive Protein (CRP) was a noisy predictor: hospitalization could have happen due to causes other than COVID-19 even when SARS-CoV-2 RT-PCR is positive and CRP is reactive, as most cases are asymptomatic to mild. Candidates of characteristic response from moderate to severe inflammation of COVID-19 were: combinations of eosinophils, monocytes and neutrophils, with age as risk factor; and creatinine, as risk factor, sharpens the odds ratio of the model with monocytes, neutrophils, and age.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gerson Ishikawa", + "author_inst": "Universidade Tecnologica Federal do Parana" + }, + { + "author_name": "Graziela Argenti", + "author_inst": "Universidade Estadual de Ponta Grossa" + }, + { + "author_name": "Cristina Berger Fadel", + "author_inst": "Universidade Estadual de Ponta Grossa" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.13.20212118", "rel_title": "Does autism protect against COVID quarantine effects?", @@ -1152170,109 +1154679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.13.338095", - "rel_title": "Rapid Development of Neutralizing and Diagnostic SARS-COV-2 Mouse Monoclonal Antibodies", - "rel_date": "2020-10-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.13.338095", - "rel_abs": "The need for high-affinity, SARS-CoV-2-specific monoclonal antibodies (mAbs) is critical in the face of the global COVID-19 pandemic, as such reagents can have important diagnostic, research, and therapeutic applications. Of greatest interest is the ~300 amino acid receptor binding domain (RBD) within the S1 subunit of the spike protein because of its key interaction with the human angiotensin converting enzyme 2 (hACE2) receptor present on many cell types, especially lung epithelial cells. We report here the development and functional characterization of 29 nanomolar-affinity mouse SARS-CoV-2 mAbs created by an accelerated immunization and hybridoma screening process. Differing functions, including binding of diverse protein epitopes, viral neutralization, impact on RBD-hACE2 binding, and immunohistochemical staining of infected lung tissue, were correlated with variable gene usage and sequence.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Asheley Poole Chapman", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Xiaoling Tang", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Joo R. Lee", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Asiya Chida", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Kristina Mercer", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Rebekah E. Wharton", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Markus H Kainulainen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jennifer L. Harcourt", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Roosecelis B. Martines", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Michelle Schroeder", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Liangjun Zhao", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Anton Bryksin", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Bin Zhou", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Eric Bergeron", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Brigid C. Bollweg", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Azaibi Tamin", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Natalie Thornburg", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David E. Wentworth", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David Petway", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Dennis Bagarozzi Jr.", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "M.G. Finn", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Jason M. Goldstein", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.14.339150", "rel_title": "Therapeutic activity of an inhaled potent SARS-CoV-2 neutralizing human monoclonal antibody in hamsters", @@ -1153192,6 +1155598,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.09.20210039", + "rel_title": "EVALUATION OF ELEVEN IMMUNOCHROMATOGRAPHIC ASSAYS FOR SARS-CoV-2 DETECTION: INVESTIGATING DENGUE CROSS-REACTION", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20210039", + "rel_abs": "BackgroundCOVID-19 disease (Coronavirus disease 2019) caused by SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) is widespread worldwide, affecting more than 11 million people globally (July 6th, 2020). Diagnostic techniques have been studied in order to contain the pandemic. Immunochromatographic (IC) assays are feasible and low cost alternative for monitoring the spread of COVID-19 in the population.\n\nMethodsHere we evaluate the sensitivity and specificity of eleven different immunochromatographic tests in 98 serum samples from confirmed cases of COVID-19 through RT-PCR and 100 negative serum samples from blood donors collected in February 2019. Considering the endemic situation of Dengue in Brazil, we also evaluated the cross-reactivity with Dengue using 20 serum samples from patients with confirmed diagnosis for Dengue collected in early 2019 through four different tests.\n\nResultsOur results demonstrated agreement between immunochromatographic assays and RT-PCR, especially after 10 days since the onset of symptoms. The evaluation of IgG and IgM antibodies combined demonstrated a strong level of agreement (0.85) of IC assays and RT-PCR. It was observed cross-reactivity between Dengue and COVID-19 using four different IC assays for COVID-19 diagnosis. The specificity of IC assays to detected COVID-19 IgM antibodies using Dengue serum samples varied from 80% to 85%; the specificity of IgG detection was 100% and total antibody was 95%.\n\nConclusionsWe found high sensitivity, specificity and good agreement of IC assays, especially after 10 days onset of symptoms. However, we detected cross-reactivity between Dengue and COVID-19 mainly with IgM antibodies demonstrating the need for better studies about diagnostic techniques for these diseases.\n\nHighlightsO_LIImmunochromatographic assays demonstrated high sensitivity and specificity and good agreement with the gold-standard RT-PCR;\nC_LIO_LIIncrease in sensitivity and specificity of assays using samples collected after the 10th day of symptoms;\nC_LIO_LICross-reaction with Dengue serology in evaluation of IgM.\nC_LI", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Beatriz Araujo Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Lea Campos de Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Franciane Mendes de Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Geovana Maria Pereira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Regina Maia de Souza", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Erika Regina Manuli", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Fabricio Klerynton Marchini", + "author_inst": "Instituto Carlos Chagas, Fiocruz" + }, + { + "author_name": "Evelyn Patr\u00edcia Sanchez Espinoza", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Marcelo Park", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Leandro Taniguchi", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Pedro Vitale Mendes", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Lucas Augusto Moyses Franco", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Ana Catharina Nastri", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Maura Salaroli de Oliveira", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Jos\u00e9 Mauro Vieira Junior", + "author_inst": "Hospital S\u00edrio Liban\u00eas" + }, + { + "author_name": "Esper Georges Kallas", + "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" + }, + { + "author_name": "Anna Sara Levin", + "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" + }, + { + "author_name": "Ester Cerdeira Sabino", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Silvia Figueiredo Costa", + "author_inst": "Instituto de Medicina Tropical" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.08.20209544", "rel_title": "What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis", @@ -1153799,369 +1156296,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.10.09.20207464", - "rel_title": "SARS-CoV-2 infects brain astrocytes of COVID-19 patients and impairs neuronal viability", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20207464", - "rel_abs": "Although increasing evidence confirms neuropsychiatric manifestations associated mainly with severe COVID-19 infection, the long-term neuropsychiatric dysfunction has been frequently observed after mild infection. Here we show the spectrum of the cerebral impact of SARS-CoV-2 infection ranging from long-term alterations in mildly infected individuals (orbitofrontal cortical atrophy, neurocognitive impairment, excessive fatigue and anxiety symptoms) to severe acute damage confirmed in brain tissue samples extracted from the orbitofrontal region (via endonasal trans-ethmoidal approach) from individuals who died of COVID-19. We used surface-based analyses of 3T MRI and identified orbitofrontal cortical atrophy in a group of 81 mildly infected patients (77% referred anosmia or dysgeusia during acute stage) compared to 145 healthy volunteers; this atrophy correlated with symptoms of anxiety and cognitive dysfunction. In an independent cohort of 26 individuals who died of COVID-19, we used histopathological signs of brain damage as a guide for possible SARS-CoV-2 brain infection, and found that among the 5 individuals who exhibited those signs, all of them had genetic material of the virus in the brain. Brain tissue samples from these 5 patients also exhibited foci of SARS-CoV-2 infection and replication, particularly in astrocytes. Supporting the hypothesis of astrocyte infection, neural stem cell-derived human astrocytes in vitro are susceptible to SARS-CoV-2 infection through a non-canonical mechanism that involves spike-NRP1 interaction. SARS-CoV-2-infected astrocytes manifested changes in energy metabolism and in key proteins and metabolites used to fuel neurons, as well as in the biogenesis of neurotransmitters. Moreover, human astrocyte infection elicits a secretory phenotype that reduces neuronal viability. Our data support the model in which SARS-CoV-2 reaches the brain, infects astrocytes and consequently leads to neuronal death or dysfunction. These deregulated processes are also likely to contribute to the structural and functional alterations seen in the brains of COVID-19 patients.", - "rel_num_authors": 87, - "rel_authors": [ - { - "author_name": "Fernanda Crunfli", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Victor Corasolla Carregari", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Flavio Protasio Veras", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Pedro Henrique Vendramini", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Aline Gazzola Fragnani Valenca", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Andre Saraiva Leao Marcelo Antunes", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Carolina Brandao-Teles", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Giuliana da Silva Zuccoli", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Guilherme Reis-de-Oliveira", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Licia C. Silva-Costa", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Ver\u00f4nica Monteiro Saia-Cereda", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil" - }, - { - "author_name": "Bradley Joseph Smith", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazi" - }, - { - "author_name": "Ana Campos Codo", - "author_inst": "Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Gabriela Fabiano de Souza", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "St\u00e9fanie Primon Muraro", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Pierina Lorencini Parise", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Daniel A. Toledo-Teixeira", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Icaro Maia Santos de Castro", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Bruno Marcel Silva Melo", - "author_inst": "University of S\u00e3o Paulo" - }, - { - "author_name": "Glaucia M. Almeida", - "author_inst": "Department of Biochemistry and Immunology, Ribeir\u00e3o Preto Medical School (FMRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Egidi Mayara Silva Firmino", - "author_inst": "Department of Pharmacology, Ribeir\u00e3o Preto Medical School (FMRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Isadora Marques Paiva", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Bruna Manuella Souza Silva", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Rafaela Mano Guimaraes", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Niele D. Mendes", - "author_inst": "Department of Surgery and Anatomy, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo (FMRP-USP), Ribeirao Preto-SP, Brazil." - }, - { - "author_name": "Ra\u00edssa Guimar\u00e3es Ludwig", - "author_inst": "Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Gabriel Palermo Ruiz", - "author_inst": "Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Thiago Leite Knittel", - "author_inst": "Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Gustavo Gast\u00e3o Davanzo", - "author_inst": "Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Jaqueline Aline Gerhardt", - "author_inst": "Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Patr\u00edcia Brito Rodrigues", - "author_inst": "Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Pau" - }, - { - "author_name": "Julia Forato", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Mariene Ribeiro Amorim", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Nat\u00e1lia Brunetti Silva", - "author_inst": "Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo" - }, - { - "author_name": "Matheus Cavalheiro Martini", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Ma\u00edra Nilson Benatti", - "author_inst": "Department of Pathology and Legal Medicine, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Sabrina Batah", - "author_inst": "Department of Pathology and Legal Medicine, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Li Siyuan", - "author_inst": "Department of Pathology and Legal Medicine, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Rafael Batista Jo\u00e3o", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Lucas Scardua Silva", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Mateus Henrique Nogueira", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "\u00edtalo Karmann Aventurato", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Mariana Rabelo de Brito", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Marina Koutsodontis Machado Alvim", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Jos\u00e9 Roberto da Silva Junior", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "L\u00edvia Liviane Dami\u00e3o", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Maria Ercilia de Paula Castilho Stefano", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "I\u00eada Maria Pereira de Sousa", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Elessandra Dias da Rocha", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Solange Maria Gon\u00e7alves", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Luiz Henrique Lopes da Silva", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Vanessa Bettini", - "author_inst": "Department of Radiology, Clinical Hospital, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Brunno Machado de Campos", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Guilherme Ludwig", - "author_inst": "Department of Statistics, University of Campinas (UNICAMP), Campinas, Brazil;" - }, - { - "author_name": "Lucas Alves Tavares", - "author_inst": "Virology Research Center, Ribeirao Preto Medical School (FMRP), University of Sao Paulo (USP), Ribeirao Preto, Sao Paulo, Brazil;" - }, - { - "author_name": "Marjorie Cornejo Pontelli", - "author_inst": "Virology Research Center, Ribeirao Preto Medical School (FMRP), University of Sao Paulo (USP), Ribeirao Preto, Sao Paulo, Brazil;" - }, - { - "author_name": "Rosa Maria Mendes Viana", - "author_inst": "Virology Research Center, Ribeirao Preto Medical School (FMRP), University of Sao Paulo (USP), Ribeirao Preto, Sao Paulo, Brazil; Department of Cell and Molecul" - }, - { - "author_name": "Ronaldo Martins", - "author_inst": "Virology Research Center, Ribeirao Preto Medical School (FMRP), University of Sao Paulo (USP), Ribeirao Preto, Sao Paulo, Brazil;" - }, - { - "author_name": "Andre S. Vieira", - "author_inst": "Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Jos\u00e9 Carlos Alves-Filho", - "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeir\u00e3o Preto Medical School (FMRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto, S\u00e3o " - }, - { - "author_name": "Eurico de Arruda Neto", - "author_inst": "Virology Research Center, Ribeir\u00e3o Preto Medical School (FMRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil; Department o" - }, - { - "author_name": "Guilherme Podolski-Gondim", - "author_inst": "Division of Neurosurgery, Dept. of Surgery and Anatomy, Ribeirao Preto Clinics Hospital, Ribeirao Preto Medical School, University of Sao Paulo, SP, Brazil" - }, - { - "author_name": "Marcelo Volpon Santos", - "author_inst": "Division of Pediatric Neurosurgery, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil" - }, - { - "author_name": "Luciano Neder", - "author_inst": "Department of Pathology and Forensic Medicine, Ribeirao Preto Medical School, University of Sao Paulo, SP, Brazil" - }, - { - "author_name": "Fernando Cendes", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Paulo Louzada-Junior", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Rene Donizeti Oliveira", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Fernando Q Cunha Sr.", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Andr\u00e9 Dam\u00e1sio", - "author_inst": "Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil; 17- Experimental Medic" - }, - { - "author_name": "Marco Aur\u00e9lio Ramirez Vinolo", - "author_inst": "Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Pau" - }, - { - "author_name": "Carolina Demarchi Munhoz", - "author_inst": "Department of Pharmacology, Institute of Biomedical Science, University of S\u00e3o Paulo, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Stevens K Rehen Sr.", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Helder I Nakaya", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Thais Mauad", - "author_inst": "Department Pathology, School of Medicine (FM), University of S\u00e3o Paulo (USP), S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Amaro Nunes Duarte-Neto", - "author_inst": "Department Pathology, School of Medicine (FM), University of S\u00e3o Paulo (USP), S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Luiz Fernando Ferraz da Silva", - "author_inst": "Department Pathology, School of Medicine (FM), University of S\u00e3o Paulo (USP), S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Marisa Dolhnikoff", - "author_inst": "Department Pathology, School of Medicine (FM), University of S\u00e3o Paulo (USP), S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Paulo Saldiva", - "author_inst": "Department Pathology, School of Medicine (FM), University of S\u00e3o Paulo (USP), S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Alessandro S Farias", - "author_inst": "University of Campinas" - }, - { - "author_name": "Pedro Manoel M. Moraes-Vieira", - "author_inst": "Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Alexandre Todorovic Fabro", - "author_inst": "Department of Pathology and Legal Medicine, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Adriano Sebollela", - "author_inst": "Department of Biochemistry and Immunology, Ribeir\u00e3o Preto Medical School (FMRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Jos\u00e9 Luiz Proen\u00e7a M\u00f3dena", - "author_inst": "Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas" - }, - { - "author_name": "Clarissa Lin Yasuda", - "author_inst": "Laboratory of Neuroimaging, Department of Neurology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Marcelo A. Mori", - "author_inst": "Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Thiago Mattar Cunha", - "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeir\u00e3o Preto Medical School (FMRP), University of S\u00e3o Paulo (USP), Ribeir\u00e3o Preto, S\u00e3o Paulo, Brazil;" - }, - { - "author_name": "Daniel Martins-de-Souza", - "author_inst": "Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.10.09.20210260", "rel_title": "Group Testing with Homophily to Curb Epidemics with Asymptomatic Carriers", @@ -1155317,6 +1157451,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.08.20204750", + "rel_title": "Estimating the effect of social inequalities in the mitigation of COVID-19 across communities in Santiago de Chile", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20204750", + "rel_abs": "We study the spatio-temporal spread of SARS-CoV-2 in Santiago de Chile using anonymized mobile phone data from 1.4 million users, 22% of the whole population in the area, characterizing the effects of non-pharmaceutical interventions (NPIs) on the epidemic dynamics. We integrate these data into a mechanistic epidemic model calibrated on surveillance data. As of August 1st 2020, we estimate a detection rate of 102 cases per 1,000 infections (90% CI: [95 - 112 per 1,000]). We show that the introduction of a full lockdown on May 15th, 2020, while causing a modest additional decrease in mobility and contacts with respect to previous NPIs, was decisive in bringing the epidemic under control, highlighting the importance of a timely governmental response to COVID-19 outbreaks. We find that the impact of NPIs on individuals mobility correlates with the Human Development Index of comunas in the city. Indeed, more developed and wealthier areas became more isolated after government interventions and experienced a significantly lower burden of the pandemic. The hetero-geneity of COVID-19 impact raises important issues in the implementation of NPIs and highlights the challenges that communities affected by systemic health and social inequalities face adapting their behaviors during an epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicol\u00f2 Gozzi", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + }, + { + "author_name": "Michele Tizzoni", + "author_inst": "ISI Foundation, Turin, Italy" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Leo Ferres", + "author_inst": "Data Science Institute, Universidad del Desarrollo, Santiago, Chile" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Nicola Perra", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.08.20209437", "rel_title": "Estimating the Burden of COVID-19 Symptoms Among Participants at the 2020 USA Curling Club Nationals Tournament", @@ -1156033,29 +1158206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20209643", - "rel_title": "Explaining the Effective Reproduction Number of COVID-19 through Mobility and Enterprise Statistics: Evidence from the First Wave in Japan", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209643", - "rel_abs": "This study uses mobility statistics combined with business census data for the eight Japanese prefectures with the highest COVID-19 infection rates to study the effect of mobility reductions on the effective reproduction number (i.e., the average number of secondary cases caused by one infected person). Mobility statistics are a relatively new data source created by compiling smartphone location data. Based on data for the first wave of infections in Japan, we found that reductions targeting the hospitality industry were more effective than restrictions on general business activities. Specifically, we found that to hold back the pandemic (that is, to reduce the effective reproduction number to one or less for all days), a 20-35% reduction in weekly mobility is required, depending on the region. A lesser goal, 80% of days with one or less observed transmission, can be achieved with a 6-30% reduction in weekly mobility. These are the results if other potential causes of spread are ignored; more careful observations and expanded data sets are needed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yoshio Kajitani", - "author_inst": "Kagawa Univeristy" - }, - { - "author_name": "Michinori Hatayama", - "author_inst": "Kyoto University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.09.20209999", "rel_title": "COVID-19 Disease Severity and Determinants among Ethiopian Patients: A study of the Millennium COVID-19 Care Center", @@ -1156930,6 +1159080,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.10.20203034", + "rel_title": "Clarifying predictions for COVID-19 from testing data: the example of New-York State", + "rel_date": "2020-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20203034", + "rel_abs": "In this article, we use testing data as an input of a new epidemic model. We get nice a concordance between the best fit the model to the reported cases data for New-York state. We also get a good concordance of the testing dynamic and the epidemics dynamic in the cumulative cases. Finally, we can investigate the effect of multiplying the number of tests by 2, 5, 10, and 100 to investigate the consequences on the reduction of the number of reported cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Pierre Griette", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Pierre Magal", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.07.20208744", "rel_title": "One size fits all?: Modeling face-mask fit on population-based faces", @@ -1157630,33 +1159803,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.10.12.335521", - "rel_title": "Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin", - "rel_date": "2020-10-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.12.335521", - "rel_abs": "Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is the driving force in its evolution. Systematic analysis of CUP of the coding sequences (CDS) of representative major pangolin lineages A and B of SARS-CoV-2 indicate a single transmission event of a codon-optimized virus from its source into humans. Here, no direct congruence could be detected in CUP of all CDS of SARS-CoV-2 with the non-human natural SARS viruses further reiterating its novelty. Several CDS show similar CUP with bat or pangolin, while others have distinct CUP pointing towards a possible hybrid nature of the virus. At the same time, phylogenetic diversity suggests the role of even silent mutations in its success by adapting to host tRNA pool. However, genomes of SARS-CoV-2 from primary infections are required to investigate the origins amongst the competing natural or lab leak theories.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kanika Bansal", - "author_inst": "CSIR-Institute of Microbial Technology" - }, - { - "author_name": "Sanjeet Kumar", - "author_inst": "Gangadhar Meher University" - }, - { - "author_name": "Prabhu B Patil", - "author_inst": "CSIR- Institute of Microbial Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.10.334458", "rel_title": "SARS-CoV-2 infects carotid arteries: implications for vascular disease and organ injury in COVID-19", @@ -1158676,6 +1160822,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.10.20210328", + "rel_title": "SARS-CoV-2 infections in Italian schools: preliminary findings after one month of school opening during the second wave of the pandemic", + "rel_date": "2020-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210328", + "rel_abs": "IntroductionThe impact of school opening on the SARS-CoV-2 pandemic is still unknown. This study aims to provide preliminary information about the number of SARS-CoV-2 cases among students attending Italian schools.\n\nMethodsData are extracted and analysed from an open access, online dataset that monitor, on a daily basis, media news about SARS-CoV-2 infections of students attending Italian schools\n\nResultsAs of 5 October 2020, a total of 1350 cases of SARS-CoV-2 infections have been registered in the Italian territory schools (involving 1059 students, 145 teachers and 146 other school members), for a total of 1212 out of 65104 (1.8%) Italian schools involved. National schools reported only 1 case of SARS-CoV-2 infection in more than 90% of cases, and only in one high school a cluster of more than 10 cases have been described (P 0.015). The detection of one or more SARS-CoV-2 infections leaded to the closure of 192 (14.2%) entire schools, more frequently nursery/kindergartens (P<0.0005).\n\nDiscussionOur preliminary data support low transmission of SARS-CoV-2 within schools, at least among younger students. However, entire schools are frequently closed in the fear of larger outbreaks. Continuous monitoring of school settings, hopefully through daily updated open access datasets, are needed to better understand the impact of schools on the pandemic, and provide guidelines that better consider different risks within different age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Danilo Buonsenso", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Cristina De Rose", + "author_inst": "Fondazione Universitaria Policlinico Gemelli, IRCSS, Rome, Italy" + }, + { + "author_name": "Rosanna Moroni", + "author_inst": "Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Piero Valentini", + "author_inst": "Fondazione Universitaria Policlinico A. Gemelli, IRCSS, Rome, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.10.07.20208389", "rel_title": "A Comparative COVID 19 Characterizations and Clinical Course Analysis between ICU and Non ICU Settings", @@ -1159432,61 +1161609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.08.20209148", - "rel_title": "Epidemiology of sleep disorders during COVID-19 pandemic: A systematic scoping review", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209148", - "rel_abs": "BackgroundA growing burden of mental health problems has become a global concern amid the coronavirus disease (COVID-19) pandemic. Sleep disorders are major mental health problems associated with increased psychosocial stressors; however, no research synthesis is available on the epidemiology of it. In this systematic scoping review, we aimed to assess the current evidence on the epidemiological burden, associated factors, and interventions from the existing literature.\n\nMethodSeven major health databases and additional sources were searched to identify, evaluate, and synthesize empirical studies on the prevalence and correlates of sleep disorders and available interventions. The Joanna Briggs Institute Methodology for Scoping Review were used, and the findings were reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist.\n\nResultsA total of 78 articles were retrieved, the prevalence of sleeping disorders ranged from 2.3% to 76.6%. Age, sex, level of education, physical and mental health, COVID-19 related factors, occupation especially being health care workers (HCW) were the main associated factors. Only two intentions were identified to address the issue.\n\nConclusionThe finding of this review indicated a high burden of sleep disorder with limited interventions that necessitate informing policymakers and practitioners to facilitate future research and implementations.\n\nBrief summaryO_ST_ABSCurrent Knowledge/Study RationaleC_ST_ABSDespite the paramount importance of sleep for the physical and mental wellbeing of individuals, sleep hygiene is often neglected which resulted in a high prevalence of sleep disorders across the globe. This condition is likely to worsen amid this pandemic. This is the first systematic scoping review of sleep disorders during the COVID-19 pandemic.\n\nStudy ImpactThe findings of our study suggest a high prevalence of sleep disorder and highlight a wide range of socio-demographic factors to identify population groups vulnerable to the adverse outcomes of sleep disorder with limited interventions. These pieces of evidence will guide clinicians to make informed choices for better management of patients and aid public health professionals to prevent sleep disorder epidemic concurring with the current pandemic.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Samia Tasnim", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Mariya Rahman", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Priyanka Pawar", - "author_inst": "Mamta Foundation India" - }, - { - "author_name": "Xinli Chi", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Qian Yu", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Liye Zou", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Abida Sultana", - "author_inst": "EviSyn Health" - }, - { - "author_name": "E. Lisako J. McKyer", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Ping Ma", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Md Mahbub Hossain", - "author_inst": "Texas A&M School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.07.20208595", "rel_title": "When lockdown policies amplify social inequalities in COVID-19 infections. Evidence from a cross-sectional population-based survey in France.", @@ -1160494,6 +1162616,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.10.09.20209965", + "rel_title": "Pulmonary Embolism in Patients with COVID-19: A Systematic review and Meta-analysis", + "rel_date": "2020-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209965", + "rel_abs": "BackgroundThere is an increasing evidence that COVID-19 could be complicated by coagulopathy which may lead to death; especially in severe cases. Hence, this study aimed to build concrete evidence regarding the incidence and mortality of pulmonary embolism (PE) in patients with COVID-19.\n\nMethodsWe performed a systematic search for trusted databases/search engines including PubMed, Scopus, Cochrane library and Web of Science. After screening, the relevant data were extracted and the incidences and mortality rates from the different included studies were pooled for meta-analysis.\n\nResultsTwenty studies were finally included in our study consisting of 1896 patients. The results of the meta-analysis for the all included studies showed that the incidence of PE in patients with COVID-19 was 17.6% with the 95% confidence interval (CI) of 12.7 to 22.5%. There was significant heterogeneity (I2{square}={square}91.17%). Additionally, the results of meta-analysis including 8 studies showed that the mortality in patients with both PE and COVID-19 was 43.1% with the 95% confidence interval (CI) of 19 to 67.1%. There was significant heterogeneity (I2{square}={square}86.96%).\n\nConclusionPE was highly frequent in patients with COVID-19. The mortality in patients with both COVID-19 and PE was remarkable representing almost half of the patients. Appropriate prophylaxis and management are vital for better outcomes.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Omar Hamam", + "author_inst": "Alexandria Faculty of Medicine" + }, + { + "author_name": "Ahmed Goda", + "author_inst": "Faculty of Medicine, October 6th University, Cairo, 12585 Egypt" + }, + { + "author_name": "Radwa Awad", + "author_inst": "Faculty of Medicine, Benha University, Benha, 13518 Egypt" + }, + { + "author_name": "Amr Ussama", + "author_inst": "Faculty of Medicine, Al-azhar University, Cairo, 11651 Egypt" + }, + { + "author_name": "Moustafa Eldalal", + "author_inst": "Faculty of Medicine, Alexandria University, Alexandria21131, Egypt" + }, + { + "author_name": "Ahmed Fayez", + "author_inst": "Faculty of Medicine, October 6th University, Cairo, 12585 Egypt" + }, + { + "author_name": "Karim Elyamany", + "author_inst": "Faculty of Medicine, Alexandria University, Alexandria21131, Egypt" + }, + { + "author_name": "Renu Bhandari", + "author_inst": "Department of Internal Medicine, Manipal College of Medical Sciences, Kaski, 33700 Nepal." + }, + { + "author_name": "Waleed Ikram", + "author_inst": "Lahore Medical and Dental College, Lahore, 30022 Pakistan" + }, + { + "author_name": "Abdelrhman Elbaz", + "author_inst": "Bascom Palmer Eye Institute, Miami, FL 33136 United States of America" + }, + { + "author_name": "Smarika Baral", + "author_inst": "Department of Internal Medicine, Nepalgunj Medical College, Banke, 21900 Nepal." + }, + { + "author_name": "Yomna Elbandrawy", + "author_inst": "Faculty of Medicine, Tanta University, Tanta, 31951 Egypt" + }, + { + "author_name": "Alexander Egbe", + "author_inst": "Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, 55905 United States of America." + }, + { + "author_name": "Iraida Sharina", + "author_inst": "Division of Cardiology, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center Houston, Houston, TX 77225, Unit" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.10.07.20207845", "rel_title": "Isolation of infected people and their contacts is likely to be effective against many short-term epidemics", @@ -1161114,37 +1163307,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.08.332080", - "rel_title": "Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data", - "rel_date": "2020-10-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.08.332080", - "rel_abs": "Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. Batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Batch-Corrected Distance (BCD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate BCD on a simulated data as well as applied it to a mouse retina development dataset and a lung dataset. We also found the utility of our approach in understanding the progression of the Coronavirus Disease 2019 (COVID-19). BCD achieves more accurate clusters and better visualizations than state-of-the-art batch correction methods on longitudinal datasets. BCD can be directly integrated with most clustering and visualization methods to enable more scientific findings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Shaoheng Liang", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jinzhuang Dou", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Ramiz Iqbal", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Ken Chen", - "author_inst": "The University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.10.08.330456", "rel_title": "idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates", @@ -1162055,6 +1164217,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.06.20207993", + "rel_title": "Sars-Cov-2 in Argentina: Following Virus Spreading using Granger Causality", + "rel_date": "2020-10-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207993", + "rel_abs": "There is a debate in Argentina on how COVID-19 outbreak in one district ends up infecting its neighbor districts. This contribution aims to use tools of time series analysis for understanding processes of contagious through regions. I use VAR and Granger causality for testing neighbor spreading via sequential rate of contagion. Results show that in the case of Argentina, contagion began in the capital city of Buenos Aires and then spread to its hinterland via specific districts. Once interior districts were infected a positive feedback dynamics emerge creating regions of high reproducibility of the virus where interventions may be focus in the very near future. This specific use of time series analysis may provide a tool for tracing infectiousness along regions that may help to anticipate infection and then for intervening for reducing the problems derived by the disease.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Juan M.C. Larrosa", + "author_inst": "Universidad Nacional del Sur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.06.20208009", "rel_title": "Misinterpretation of viral load in COVID-19.", @@ -1162703,29 +1164884,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.06.20207910", - "rel_title": "Business Shutdowns and COVID-19 Mortality", - "rel_date": "2020-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207910", - "rel_abs": "Governments around the world have adopted unprecedented policies to deal with COVID-19. This paper zooms in on business shutdowns and investigates their effectiveness in reducing mortality. We leverage upon highly granular death registry data for over 4,000 Italian municipalities in a diff-in-diff approach that allows us to credibly mitigate endogeneity concerns. Our results, which are robust to controlling for a host of co-factors, offer strong evidence that business shutdowns are very effective in reducing mortality. We calculate that the death toll from the first wave of COVID-19 in Italy would have been twice as high in their absence. Our findings also highlight that timeliness is key - by acting one week earlier, the government could have reduced the death toll by an additional 25%. Finally, our estimates suggest that shutdowns should be targeted: closing shops, bars and restaurants saves the most lives, while shutting down manufacturing and construction activities has only mild effects.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Gabriele Ciminelli", - "author_inst": "Asia School of Business in collaboration with MIT Sloan" - }, - { - "author_name": "Silvia Garcia-Mandico", - "author_inst": "Organisation for Economic Co-operation and Development" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.10.05.20205872", "rel_title": "SARS-CoV-2 RNA detection using pooling of self-collected samples: Simple protocols may foster asymptomatic surveillance", @@ -1163877,6 +1166035,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20205328", + "rel_title": "The Impact of COVID-19 on the Management of Heart Failure -A United Kingdom Patient Questionnaire Study", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20205328", + "rel_abs": "AimThe coronavirus disease 2019 (COVID-19) pandemic has created significant challenges to healthcare globally, necessitating rapid restructuring of service provision. This questionnaire survey was conducted amongst adult heart failure (HF) patients in the United Kingdom (UK), to understand the impact of COVID-19 upon HF services.\n\nMethods and ResultsThe survey was conducted by the Pumping Marvellous Foundation (PMF), a UK HF patient charity. \"Survey Monkey\" was used to disseminate the questionnaire in the PMFs online patient group and in 10 UK hospitals (out-patient hospital and community HF clinics). 1050 responses were collected (693/1050-66% women); 55% (579/1050) were aged over 60 years. Anxiety level was significantly higher regarding COVID19 (mean 7{+/-}2.5 on anxiety scale of 0 to 10) compared to anxiety regarding HF (6.1{+/-}2.4; p<0.001). Anxiety was higher amongst patients aged [≤]60 years about HF (6.3{+/-}2.2 versus 5.9{+/-}2.5 in those aged >60 years; p=0.005) and COVID-19 (7.3{+/-}2.3 versus 6.7{+/-}2.6 those aged >60 years; p<0.001). 65% respondents (686/1050) reported disruption to HF appointments (cancellation or postponement) during the lockdown period. 37% reported disruption to medication prescription services and 34% reported inability to access their HF teams promptly. 32% expressed reluctance to attend hospital (25% stated they would only attend hospital if there was no alternative and 7% stated that they would not attend hospital at all).\n\nConclusionsThe COVID-19 pandemic has caused significant anxiety amongst HF patients regarding COVID-19 and HF. Cancellation or postponement of scheduled clinic appointments, investigations, procedures, prescription and monitoring services were implicated as sources of anxiety.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rajiv Sankaranarayanan", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Nick Hartshorne-Evans", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Sam Redmond-Lyon", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Jill Wilson", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Hani Essa", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Alastair Gray", + "author_inst": "Craigavon Area Hospital" + }, + { + "author_name": "Louise Clayton", + "author_inst": "University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Carys Barton", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Fozia Z Ahmed", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Colin Cunnington", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Duwarakan Satchithananda", + "author_inst": "University Hospital North Midlands" + }, + { + "author_name": "Clare Murphy", + "author_inst": "Royal Alexandra and Vale of Leven Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.10.04.20206318", "rel_title": "The relationship between neighborhood poverty and COVID-19 mortality within racial/ethnic groups (Cook County, Illinois)", @@ -1164345,25 +1166566,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.03.20206326", - "rel_title": "Comparative policy analysis of face mask mandates during COVID 19 pandemic on rate of mask use in the United States", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206326", - "rel_abs": "As COVID-19 continues to spread throughout the United States, there has been a search for policies to prevent individual infections, to slow the spread of the virus in general, and to mitigate the economic impact of the pandemic. Masks have proven to be a cost-effective measure in all regards, and as such some state governments have begun to mandate their use. However, while the efficacy of masks has been demonstrated, the efficacy of public policies which mandate the use of masks has not been demonstrated. This paper compares the rates of mask use in counties as defined by state policy. It finds that state mandates are strongly correlated with higher rates of mask use, and that mandating use by all individuals in public spaces is more effective than a less comprehensive mandate for mask use by all public facing employees.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Michael J Maloney", - "author_inst": "Proof School" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.03.20206193", "rel_title": "Development and comparison of a novel multiple cross displacement amplification (MCDA) assay with other nucleic acid amplification methods for SARS-CoV-2 detection", @@ -1165187,6 +1167389,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.05.20207100", + "rel_title": "Updating Herd Immunity Models for the U.S. in 2020: Implications for the COVID-19 Response", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20207100", + "rel_abs": "ObjectivesTo understand what levels of herd immunity are required in the COVID-19 pandemic, given spatial population heterogeneity, to best inform policy and action.\n\nMethodsUsing a network of counties in the United States connected by transit data we considered a set of coupled differential equations for susceptible-infectious-removed populations. We calculated the classical herd immunity level plus a version reflecting the heterogeneity of connections in the network by running the model forward in time until the epidemic completed.\n\nResultsNecessary levels of herd immunity vary greatly from county to county. A population weighted average for the United States is 47.5% compared to a classically estimated level of 77.1%.\n\nConclusionsCommon thinking argues that the nation needs to achieve at least 60% herd immunity to emerge from the COVID-19 pandemic. Heterogeneity in contact structure and individual variation in infectivity, susceptibility, and resistance are key factors that reduce the disease-induced herd immunity levels to 34.2-47.5% in our models. Looking forward toward vaccination strategies, these results suggest we should consider not just who is vaccinated but where those vaccinations will do the most good.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Natalie Elizabeth Sheils", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Gregory D Lyng", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Ethan M Berke", + "author_inst": "UnitedHealth Group" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.03.20206359", "rel_title": "PREDICTIONS FOR EUROPE FOR THE COVID-19 PANDEMICAFTER LOCKDOWN WAS LIFTED USING AN SIR MODEL", @@ -1165739,41 +1167968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.06.20207597", - "rel_title": "Consideration for the asymptomatic transmission of COVID-19: Systematic Review and Meta-Analysis", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207597", - "rel_abs": "ObjectiveWorldwide countries are experiencing viral load in their population, leading to potential infectivity of asymptomatic COVID-19. Current systematic review and meta-analysis aimed to investigate the role of asymptomatic infection worldwide reported in family-cluster, adults, children, health care workers, and travelers.\n\nDesignOnline literature search (PubMed, Google Scholar, medRixv, and BioRixv) was accomplished using standard Boolean operators, studies published till 07th June 2020.\n\nSettingStudies were included from case reports, short communication, and retrospective to cover sufficient asymptomatic COVID-19 transmission reported.\n\nParticipantsFamilial-clusters, adults, children, health care workers, and travelers.\n\nResultsWe observed asymptomatic transmission among familial-cluster, adults, children, health care workers, and travelers with a proportion of 32% 37%, 26%, 6%, and 32%, respectively. This study observed an overall proportion of 31% (95%CI: 0.19-0.44) with heterogeneity of I2 (97.28%, p=<0.001) among all asymptomatic populations mentioned in this study. Among children and healthcare workers, this study showed no heterogeneity; to overcome the interpretation from a fixed model, the random effect model was also applied to estimate the average distribution across studies included in the meta-analysis.\n\nConclusionWe found and suggest the rigorous epidemiological history, early isolation, social distancing, and increased quarantine period (at least 28 days) after screening asymptomatic cases as well as their close contacts for chest CT scan even after their negative nucleic acid testing to minimize the spread among the community. This systematic review and meta-analysis support asymptomatic COVID-19 transmission between person to person depending on the variation of virus incubation period among individuals. Children especially, school-going aged <18 years, need to be monitored and prevention strategy, e.g., chest CT and social distancing required to prevent the community transmission of COVID-19 in asymptomatic mode.\n\nStrengths and limitations of this studyO_LIExamine the possibility of asymptomatic COVID-19 transmission in the community at different levels.\nC_LIO_LISupports contact tracing, social distancing, early isolation, and increased quarantine period to minimize the risk of virus spread.\nC_LIO_LISupports chest CT scan and viral nucleic acid testing to identify the asymptomatic cases in the community.\nC_LIO_LISupports rigorous epidemiological history with multiple detection methods.\nC_LIO_LIA higher proportion of asymptomatic incidence was seen, suggests monitoring, and maintaining social distancing.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Khaiwal Ravindra", - "author_inst": "PGIMER, Chandigarh, India" - }, - { - "author_name": "Vivek Singh Malik", - "author_inst": "Post Graduate Institute of Medical Education and Research, Chandigarh" - }, - { - "author_name": "Bijaya K Padhi", - "author_inst": "Post Graduate Institute of Medical Education and Research (PGIMER)" - }, - { - "author_name": "Sonu Goel", - "author_inst": "Post graduate Institute of Medical Education and Research, Chandigarh" - }, - { - "author_name": "Madhu Gupta", - "author_inst": "Post Graduate Institute of Medical Education and Research, Chandigarh" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.01.20204214", "rel_title": "SARS-CoV-2 Inactivation Potential of Metal Organic Framework Induced Photocatalysis", @@ -1166785,6 +1168979,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.20200931", + "rel_title": "Association of Pre-COVID-19 Lymphocytopenia with Fatality", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20200931", + "rel_abs": "Lymphocytopenia during the COVID-19 has been associated with fatality. We tested whether pre-existing lymphocytopenia reported prior to any possible exposure to SARS-COV2 (from 2010 to 2019) was associated with fatality. Using all patients diagnosed on testing in a single regional laboratory, we identified 1137 subjects with PCR positive for SARS-COV2 and at least one available complete blood count from the decade prior to any possible exposure to the virus. Bivariate analysis indicated an association between pre-existing lymphocytopenia (defined as absolute lymphocyte count <0.9x109 /L) and fatality (18% versus 4%). Furthermore, a logistic regression model, accounting for both patient age and number of blood counts obtained, indicated the subjects with pre-existing lymphocytopenia were 1.4 times as likely to die. Because the absolute lymphocyte count is almost universally available and easily interpreted, this biomarker of the risk of fatality could be widely useful.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Richard Burack", + "author_inst": "University of Rochester" + }, + { + "author_name": "Philip Rock", + "author_inst": "University of Rochester" + }, + { + "author_name": "David Burtoon", + "author_inst": "University of Rochester" + }, + { + "author_name": "Xueya Cai", + "author_inst": "University of Rochester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.02.20205880", "rel_title": "Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity irrespective of virus", @@ -1167325,41 +1169550,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.02.20205906", - "rel_title": "Evaluating the Efficacy of COVID-19 Vaccines", - "rel_date": "2020-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205906", - "rel_abs": "A large number of studies are being conducted to evaluate the efficacy and safety of candidate vaccines against novel coronavirus disease-2019 (COVID-19). Most Phase 3 trials have adopted virologically confirmed symptomatic COVID-19 disease as the primary efficacy endpoint, although laboratory-confirmed SARS-CoV-2 is also of interest. In addition, it is important to evaluate the effect of vaccination on disease severity. To provide a full picture of vaccine efficacy and make efficient use of available data, we propose using SARS-CoV-2 infection, symptomatic COVID-19, and severe COVID-19 as dual or triple primary endpoints. We demonstrate the advantages of this strategy through realistic simulation studies. Finally, we show how this approach can provide rigorous interim monitoring of the trials and efficient assessment of the durability of vaccine efficacy.\n\nSummaryTo increase statistical power and meet vaccine success criteria, we propose to evaluate the efficacy of COVID-19 vaccines by using the dual or triple primary endpoints of SARS-CoV-2 infection, symptomatic COVID-19, and severe COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dan-Yu Lin", - "author_inst": "University of North Carolina, Chapel Hill" - }, - { - "author_name": "Donglin Zeng", - "author_inst": "University of North Carolina, Chapel Hill" - }, - { - "author_name": "Devan V. Mehrotra", - "author_inst": "Merck & Co., Inc." - }, - { - "author_name": "Lawrence Corey", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Peter B. Gilbert", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.02.20205567", "rel_title": "Impact of pathogen reduction technologies on immunological propertiesof the COVID-19 convalescent plasma", @@ -1168403,6 +1170593,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.09.30.20204537", + "rel_title": "SARS-CoV-2 seroprevalence and clinical features of COVID-19 in a German liver transplant recipient cohort: a prospective serosurvey study.", + "rel_date": "2020-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204537", + "rel_abs": "In liver transplant (LT) recipients with severe COVID-19 fatal outcome has been reported in a substantial subset of patients. Whether LT recipients are at increased risk for severe COVID-19 compared to the general population is controversial. Here we report the first results of a SARS-CoV-2 serosurvey in a large LT recipient cohort.\n\nTaking into account known risk factors, LT recipients a priori represented a high-risk cohort for severe COVID-19 with 101/219 (46.1 %) presenting with more than 2 risk factors for severe COVID-19. Out of 219 LT recipients 8 (3.7%) were either tested positive for nasopharyngeal SARS-CoV-2 RNA or anti-SARS-CoV-2 serum IgG. 5/8 (62.5 %) did not show any clinical signs of infection, 3/8 (37.5%) had self-limited disease, none required hospitalization for COVID-19. 5/8 (67.5%) SARS-CoV-2 positive patients showed high utilization of the healthcare system. 2/8 (25 %) had known exposure to infected health care personal. A majority of 65.4 % often or always avoided outside family social contacts. Face masks were commonly worn by all patients.\n\nIn summary, LT recipients showed a SARS-CoV-2 seroconversion rate similar to the general population with a substantial percentage of unrecognized infections. The health care system can be the assumed source of infection in most of these cases.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Conrad Rauber", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Shilpa Tiwari-Heckler", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Jan Pfeiffenberger", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Arianeb Mehrabi", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Frederike Lund", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Philip Gath", + "author_inst": "Staedtisches Klinikum Ludwigshafen" + }, + { + "author_name": "Markus Mieth", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Uta Merle", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Christian Rupp", + "author_inst": "Universitaetsklinikum Heidelberg" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.10.01.20204255", "rel_title": "COVID-19 Pandemic in University Hospital: Impact on Medical Training of Medical Interns", @@ -1169219,45 +1171460,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.01.20205146", - "rel_title": "An Integrated Framework with Machine Learning and Radiomics for Accurate and Rapid Early Diagnosis of COVID-19 from Chest X-ray", - "rel_date": "2020-10-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205146", - "rel_abs": "Early diagnosis of COVID-19 is considered the first key action to prevent spread of the virus. Currently, reverse transcription-polymerase chain reaction (RT-PCR) is considered as a gold standard point-of-care diagnostic tool. However, several limitations of RT-PCR have been identified, e.g., low sensitivity, cost, long delay in getting results and the need of a professional technician to collect samples. On the other hand, chest X-ray (CXR) is routinely used as a cost-effective diagnostic test for diagnosis and monitoring different respiratory abnormalities and is currently being used as a discriminating tool for COVID-19. However, visual assessment of CXR is not able to distinguish COVID-19 from other lung conditions. Several machine learning algorithms have been proposed to detect COVID-19 directly from CXR images with reasonably good accuracy on a data set that was randomly split into two subsets for training and test. Since these methods require a huge number of images for training, data augmentation with geometric transformation was applied to increase the number of images. It is highly likely that the images of the same patients are present in both the training and test sets resulting in higher accuracies in detection of COVID-19. It is, therefore, vital to assess the performance of COVID-19 detection algorithm on an independent data set with different degrees of the disease before being employed for clinical settings. On the other hand, machine learning techniques that depend on handcrafted features extraction and selection approaches can be trained with smaller data set. The features can also be analyzed separately for various lung conditions. Radiomics features are such kind of handcrafted features that represent heterogeneous appearance of the lung on CXR quantitatively and can be used to distinguish COVID-19 from other lung conditions. Based on this hypothesis, a machine learning based technique is proposed here that is trained on a set of suitable radiomics features (71 features) to detect COVID-19. It is found that Support Vector Machine (SVM) and Ensemble Bagging Model Trees (EBM) trained on these 71 radiomics features can distinguish between COVID-19 and other diseases with an overall sensitivity of 99.6% and 87.8% and specificity of 85% and 97% respectively. Though the performance is comparable for both methods, EBM is more robust across severity levels. Severity, in this case, was scored between 0 to 4 by two experienced radiologists for each lung segment of each CXR image represents the degree of severity of the disease. For the case of 0 severity, sensitivity and specificity of the EBM method are 91.7% and 100% respectively indicating that there are certain radiomics pattern that are not visibly distinguishable. Since the proposed method does not require any manual intervention (e.g., sample collection etc.), it can be integrated with any standard X-ray reporting system to be used as an efficient, cost-effective and rapid early diagnosis device. It can also be deployed in places where quick results of the COVID-19 test are required, e.g., airports, seaports, hospitals, health clinics, etc.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mahbubunnabi Tamal", - "author_inst": "Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia" - }, - { - "author_name": "Maha Alshammari", - "author_inst": "Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia" - }, - { - "author_name": "Meernah Alabdullah", - "author_inst": "Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia" - }, - { - "author_name": "Rana Hourani", - "author_inst": "Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia" - }, - { - "author_name": "Hossain Abu Alola", - "author_inst": "Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia" - }, - { - "author_name": "Tarek M. Hegazi", - "author_inst": "Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.09.30.20199828", "rel_title": "Exhaled aerosol increases with COVID-19 infection, and risk factors of disease symptom severity", @@ -1170097,6 +1172299,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.323915", + "rel_title": "A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion", + "rel_date": "2020-10-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.02.323915", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely \"bottom-up\" coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.\n\nSignificance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alvin Yu", + "author_inst": "University of Chicago" + }, + { + "author_name": "Alexander J Pak", + "author_inst": "University of Chicago" + }, + { + "author_name": "Peng He", + "author_inst": "University of Chicago" + }, + { + "author_name": "Viviana Monje-Galvan", + "author_inst": "University of Chicago" + }, + { + "author_name": "Lorenzo Casalino", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Zied Gaieb", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Abigail C Dommer", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Rommie E Amaro", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Gregory A Voth", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.10.02.324145", "rel_title": "SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs", @@ -1170945,45 +1173198,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.09.30.321596", - "rel_title": "A small interfering RNA (siRNA) database for SARS-CoV-2", - "rel_date": "2020-10-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.30.321596", - "rel_abs": "Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we propose a database of SARS-CoV-2 targets for siRNA approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. Beyond target sequences, it also displays more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess whether siRNAs targets bind or not off-target sequences. This dataset is available as a set of four tables in a single spreadsheet file, each table corresponding to sequences of 18, 19, 20, and 21 nucleotides length, respectively, aiming to meet the diversity of technology and expertise among labs around the world concerning siRNAs design of varied sizes, more specifically between 18 and 21nt length. We hope that this database helps to speed the development of new target antivirals for SARS-CoV-2, contributing to more rapid and effective responses to the COVID-19 pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "In\u00e1cio Gomes Medeiros", - "author_inst": "Bioinformatics Graduate Program, Metr\u00f3pole Digital Institute, Federal University of Rio Grande do Norte" - }, - { - "author_name": "Andr\u00e9 Salim Khayat", - "author_inst": "Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal do Para" - }, - { - "author_name": "Beatriz Stransky", - "author_inst": "Biomedical Engineering Department, Center of Technology, Federal University of Rio Grande do Norte; Bioinformatics Multidisciplinary Environment (BioME), Metr\u00f3p" - }, - { - "author_name": "Sidney Emanuel Batista dos Santos", - "author_inst": "Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal do Par\u00e1; N\u00facleo de Pesquisas em Oncologia, Universidade Federal do Par\u00e1" - }, - { - "author_name": "Paulo Pimentel Assump\u00e7\u00e3o", - "author_inst": "N\u00facleo de Pesquisas em Oncologia, Universidade Federal do Par\u00e1" - }, - { - "author_name": "Jorge Estefano Santana de Souza", - "author_inst": "Bioinformatics Graduate Program, Metr\u00f3pole Digital Institute, Federal University of Rio Grande do Norte; Bioinformatics Multidisciplinary Environment (BioME), M" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.28.20203463", "rel_title": "Efficacy of Famotidine for COVID-19: A Systematic Review and Meta-analysis", @@ -1171935,6 +1174149,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.29.20202416", + "rel_title": "Virus evolution affected early COVID-19 spread", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20202416", + "rel_abs": "As the SARS-Cov-2 virus spreads around the world afflicting millions of people, it has undergone divergent genetic mutations. Although most of these mutations are expected to be inconsequential, some mutations in the spike protein structure have been hypothesized to affect the critical stage at which the virus invades human cells, which could affect transmission probability and disease expression. If true, then we expect an increased growth rate of reported COVID-19 cases in regions dominated by viruses with these altered proteins. We modeled early global infection dynamics based on clade assignment along with other demographic and meteorological factors previously found to be important. Clade, but not variant D614G which has been associated with increased viral load, enhanced our ability to describe early COVID-19 growth dynamics. Including clade identity in models significantly improved predictions over earlier work based only on weather and demographic variables. In particular, higher proportions of clade 19A and 19B were negatively correlated with COVID-19 growth rate, whereas higher proportions of 20A and 20C were positively correlated with growth rate. A strong interaction between the prevalence of clade 20C and relative humidity suggests that the impact of clade identity might be more important when coupled with certain weather conditions. In particular, 20C an 20A generate the highest growth rates when coupled with low humidity. Projections based on data through April 2020 suggest that, without intervention, COVID-19 has the potential to grow more quickly in regions dominated by the 20A and 20C clades, including most of South and North America.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Derek Corcoran", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Mark C Urban", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Jill Wegrzyn", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Cory Merow", + "author_inst": "University of Connecticut" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.30.20204644", "rel_title": "Estimation of novel coronavirus (covid-19) reproduction number and case fatality rate: a systematic review and meta-analysis", @@ -1172655,49 +1174900,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.09.29.20204396", - "rel_title": "Examining Australian public perceptions and behaviors towards a future COVID-19 vaccine", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20204396", - "rel_abs": "BackgroundThere is an indication that vaccine(s) for COVID-19 could be available by early 2021. As immunisation program launches have previously demonstrated, it is essential that careful planning occurs now to ensure the readiness of the public for a COVID-19 vaccine. As part of that process, this study aimed to understand the public perceptions regarding a future COVID-19 vaccine in Australia.\n\nMethodsA national cross-sectional online survey of 1420 Australian adults (18 years and older) was undertaken between 18 and 24 March 2020. The statistical analysis of the data included univariate and multivariate logistic regression analysis.\n\nResultsParticipants generally held positive views towards vaccination. Eighty percent (n=1143) agreed with the statement that getting myself vaccinated for COVID-19 would be a good way to protect myself against infection. Females (614, 83%) were more likely to agree with the statement than males (529, 78%) (aOR=1.4 (95% CI: 1.1-1.8); P=0.029), while 90.9% aged 70 and above agreed compared to 76.6% aged 18-29 year old (aOR=2.3 (95% CI:1.2-4.1); 0.008). Agreement was also higher for those with a self-reported chronic disease (aOR=1.4 (95% CI: 1.1-2.0); P=0.043) and among those who held private health insurance (aOR=1.7 (95% CI: 1.3-2.3); P<0.001). Beyond individual perceptions, 78% stated that their decision to vaccinate would be supported by family and friends\n\nConclusionThis study presents an early indication of public perceptions towards a future COVID-19 vaccine and represents a starting point for mapping vaccine perceptions. To support an effective launch of these new vaccines, governments need to use this time to understand the communities concerns and to identify the strategies that will support engagement.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Holly Seale", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Anita E Heywood", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Julie Leask", - "author_inst": "University of Sydney" - }, - { - "author_name": "Meru Sheel", - "author_inst": "The Australian National University" - }, - { - "author_name": "David N Durrheim", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Katarzyna Bolsewicz", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Rajneesh Kaur", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.29.20204289", "rel_title": "Identification of biological correlates associated with respiratory failure in COVID-19", @@ -1173717,6 +1175919,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.09.28.20200915", + "rel_title": "COVID-19 seroprevalence surveys and antibody decline - A note of caution on antibody decline", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20200915", + "rel_abs": "We analyzed 21,676 residual specimens from Ontario, Canada collected between March-August, 2020 to investigate the effect of antibody decline on SARS-CoV-2 seroprevalence estimates. Testing specimens orthogonally using the Abbott (anti-nucleocapsid) and then the Ortho (anti-spike) assays, seroprevalence estimates ranged from 0.4%-1.4%, despite ongoing disease activity. The geometric mean concentration (GMC) of antibody-positive specimens decreased over time (p=0.015), and the GMC of antibody-negative specimens increased over time (p=0.0018). The association between the two tests decreased each month (p<0.001), suggesting anti-N antibody decline. Lowering the Abbott index cut-off from 1.4 to 0.7 resulted in a 16% increase in positive specimens.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shelly Bolotin", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa Tran", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Selma Osman", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Kevin A. Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A. Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Eugene Joh", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Shelley L. Deeks", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa G. Allen", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.27.20199737", "rel_title": "High-Quality Masks Can Reduce Infections and Deaths in the US", @@ -1174641,29 +1176890,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.27.20202564", - "rel_title": "Using COVID-19 deaths as a surrogate to measure the progression of the pandemics.", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20202564", - "rel_abs": "The IFR (Infection Fatality Risk) is one of the most important parameters of an infectious disease. If properly estimated, the observed number of deaths divided by the IFR can be used to estimate the current number of infections and, if immunity is permanent, we can estimate the fraction of susceptible which can be used to plan reopening of activities and vaccine deployment, when these become available. Here we suggest how to use the observed deaths by COVID-19 in an arbitrary population as a surrogate for the progression of the epidemic with the purpose of decision making. We compare several estimates of IFR for SARS-CoV-2 with our estimate that uses the number of additional deaths in households in a database population of 159,150 laboratory-confirmed (RT-qPCR) COVID-19 by SARS-COV-2 in Mexico. The main result is that if the number of deaths in a region is close to 2 per thousand individuals, the fraction of remaining susceptible may be too small for the vaccine to make a difference in the total number of infected.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "UNIVERSIDAD DE COLIMA" - }, - { - "author_name": "Efren Murillo-Zamora", - "author_inst": "Mexican Institute of Social Security" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.28.20202978", "rel_title": "A steady trickle-down from metro districts and improving epidemic-parameters characterize the increasing COVID-19 cases in India", @@ -1175527,6 +1177753,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.29.317289", + "rel_title": "Susceptibility of midge and mosquito vectors to SARS-CoV-2 by natural route of infection", + "rel_date": "2020-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.317289", + "rel_abs": "SARS-CoV-2 is a recently emerged, highly contagious virus and the cause of the current pandemic. It is a zoonotic virus, although its animal origin is not clear yet. Person-to-person transmission occurs by inhalation of infected droplets and aerosols, or by direct contact with contaminated fomites. Arthropods transmit numerous viral, parasitic, and bacterial diseases; however, the potential role of arthropods in SARS-CoV-2 transmission is not fully understood. Thus far, a few studies have demonstrated that SARS-CoV-2 replication is not supported in cells from certain insect species nor in certain species of mosquitoes after intrathoracic inoculation. In this study, we expanded the work of SARS-CoV-2 susceptibility to biting insects after ingesting a SARS-CoV-2infected blood meal. Species tested included Culicoides sonorensis biting midges, as well as Culex tarsalis and Culex quinquefasciatus mosquitoes, all known biological vectors for numerous RNA viruses. Arthropods were allowed to feed on SARS-CoV-2 spiked blood and at various time points post infection analyzed for the presence of viral RNA and infectious virus. Additionally, cell lines derived from C. sonorensis (W8a), Ae. aegypti (C6/36), Cx. quinquefasciatus (HSU), and Cx. tarsalis (CxTrR2) were tested for SARS-CoV-2 susceptibility. Our results indicate that none of the biting insects, nor the insect cell lines support SARS-CoV-2 replication. We conclude, that biting insect do not pose a risk for transmission of SARS-CoV-2 to humans or animals following a SARS-CoV-2 infected blood meal.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Velmurugan Balaraman", + "author_inst": "Kansas State University" + }, + { + "author_name": "Barbara S. Drolet", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Natasha N Gaudreault", + "author_inst": "Kansas State University" + }, + { + "author_name": "William C. Wilson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Jeana Owens", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Dashzeveg Bold", + "author_inst": "Kansas State University" + }, + { + "author_name": "Dustin A Swanson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Dane C Jasperson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Leela E Noronha", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Juergen A Richt", + "author_inst": "Kansas State University" + }, + { + "author_name": "Dana Mitzel", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.28.317685", "rel_title": "SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo", @@ -1176079,41 +1178364,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.26.20202259", - "rel_title": "Prevalence of SARS-CoV-2 IgG/IgM antibodies among Danish and Swedish Falck emergency and non-emergency healthcare workers", - "rel_date": "2020-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.26.20202259", - "rel_abs": "Background: Knowledge about the COVID-19 outbreak is still sparse especially in a cross-national setting. COVID-19 is caused by a SARS-CoV-2 infection. The aim of the study is to contribute to the surveillance of the pandemic by bringing new knowledge about SARS-CoV-2 seropositivity among healthcare workers and evaluating whether certain job functions is associated with a higher risk of being infected, and to clarify if such association is mediated by the number of individuals that the employees meet during a workday. Finally, we will investigate regional and national differences in seroprevalence. Methods: A bi-national prospective observational cohort study including 3,272 adults employed at Falck in Sweden and Denmark. Participants were tested for SARS-CoV-2 antibodies every second week for a period of 8 weeks from June 22, 2020 until August 10, 2020. Descriptive statistics as well as multivariable logistic regression analyses were applied. Results: Of the 3,272 Falck employees participating in this study, 159 (4.9%) tested positive for SARS-CoV-2 antibodies. The seroprevalence was lower among Danish Falck employees than among those from Sweden (2.8% in Denmark and 8.3% in Sweden). We also found that number of customer or patient contacts during a workday was the most prominent predictor for seropositivity, and that ambulance staff was the most vulnerable staff group. Conclusions: Our study presents geographical variations in seroprevalence within the Falck organization and shows evidence that social interaction is one of the biggest risk factors for getting infected with SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jannie Laursen", - "author_inst": "Department of Global Business Quality Management, Falck, Copenhagen, Denmark" - }, - { - "author_name": "Janne Petersen", - "author_inst": "Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg. Copenhagen, Denmark and Section of Biostatistics, Dep" - }, - { - "author_name": "Maria Didriksen", - "author_inst": "Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet" - }, - { - "author_name": "Kasper Karmark Iversen", - "author_inst": "Department of emergency medicine and department of cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark" - }, - { - "author_name": "Henrik Ullum", - "author_inst": "Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.26.20202150", "rel_title": "Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020", @@ -1177221,6 +1179471,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.27.315796", + "rel_title": "A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force", + "rel_date": "2020-09-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.27.315796", + "rel_abs": "The current COVID-19 pandemic has a devastating global impact and is caused by the SARS-CoV-2 virus. SARS-CoV-2 attaches to human host cells through interaction of its receptor binding domain (RBD) located on the viral Spike (S) glycoprotein with angiotensin converting enzyme-2 (ACE2) on the surface of host cells. RBD binding to ACE2 is a critical first step in SARS-CoV-2 infection. Viral attachment occurs in dynamic environments where forces act on the binding partners and multivalent interactions play central roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using specific molecular handles, we tether the fusion proteins between a functionalized flow cell surface and magnetic beads in magnetic tweezers. We observe repeated interactions of RBD and ACE2 under constant loads and can fully quantify the force dependence and kinetics of the binding interaction. Our results suggest that the SARS-CoV-2 ACE2 interaction has higher mechanical stability, a larger free energy of binding, and a lower off-rate than that of SARS-CoV-1, the causative agents of the 2002-2004 SARS outbreak. In the absence of force, the SARS-CoV-2 RBD rapidly (within [≤]1 ms) engages the ACE2 receptor if held in close proximity and remains bound to ACE2 for 400-800 s, much longer than what has been reported for other viruses engaging their cellular receptors. We anticipate that our assay will be a powerful tool investigate the roles of mutations in the RBD that might alter the infectivity of the virus and to test the modes of action of neutralizing antibodies and other agents designed to block RBD binding to ACE2 that are currently developed as potential COVID-19 therapeutics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Magnus S. Bauer", + "author_inst": "LMU Munich" + }, + { + "author_name": "Sophia Gruber", + "author_inst": "LMU Munich" + }, + { + "author_name": "Lukas F. Milles", + "author_inst": "University of Washington, Seattle" + }, + { + "author_name": "Thomas Nicolaus", + "author_inst": "LMU Munich" + }, + { + "author_name": "Leonard C. Schendel", + "author_inst": "LMU Munich" + }, + { + "author_name": "Hermann E. Gaub", + "author_inst": "LMU Munich" + }, + { + "author_name": "Jan Lipfert", + "author_inst": "LMU Munich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.09.27.316174", "rel_title": "Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach", @@ -1177741,37 +1180034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.25.20201772", - "rel_title": "Kinetics of SARS-CoV-2 infection in the human upper and lower respiratory tracts and their relationship with infectiousness", - "rel_date": "2020-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201772", - "rel_abs": "SARS-CoV-2 is a human pathogen that causes infection in both the upper respiratory tract (URT) and the lower respiratory tract (LRT). The viral kinetics of SARS-CoV-2 infection and how they relate to infectiousness and disease progression are not well understood. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection in both the URT and LRT. We fit the models to viral load data from patients with likely infection dates known, we estimated that infected individuals with a longer incubation period had lower rates of viral growth, took longer to reach peak viremia in the URT, and had higher chances of presymptomatic transmission. We then developed a model linking viral load to infectiousness. We found that to explain the substantial fraction of transmissions occurring presymptomatically, the infectiousness of a person should depend on a saturating function of the viral load, making the logarithm of the URT viral load a better surrogate of infectiousness than the viral load itself. Comparing the roles of target-cell limitation, the innate immune response, proliferation of target cells and spatial infection in the LRT, we found that spatial dissemination in the lungs is likely to be an important process in sustaining the prolonged high viral loads. Overall, our models provide a quantitative framework for predicting how SARS-CoV-2 within-host dynamics determine infectiousness and represent a step towards quantifying how viral load dynamics and the immune responses determine disease severity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ruian Ke", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Carolin Zitzmann", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Ruy M. Ribeiro", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Alan S. Perelson", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.25.20201863", "rel_title": "Deep Immune Profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19", @@ -1178627,6 +1180889,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.09.22.20195628", + "rel_title": "Public health information on COVID-19 for international travellers: Lessons learned from a rapid mixed-method evaluation in the UK containment phase", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20195628", + "rel_abs": "Introduction In the containment phase of the response to the COVID-19 outbreak, Public Health England (PHE) delivered advice to travellers arriving at major UK ports. We aimed to rapidly evaluate the impact and effectiveness of these communication materials for passengers in the early stages of the pandemic. Methods In stage I (Patient and Public Involvement, PPI) we interviewed seven travellers who had returned from China in January and February 2020. We used these results to develop a questionnaire and topic guides for stage II, a cross-sectional survey and follow-up interviews with passengers arriving at London Heathrow Airport on scheduled flights from China and Singapore. The survey assessed passengers' knowledge of symptoms, actions to take and attitudes towards PHE COVID-19 public health information; interviews explored their views of official public health information and self-isolation. Results In stage II, 121 passengers participated in the survey and 15 in follow-up interviews. 83% of surveyed passengers correctly identified all three COVID-19 associated symptoms listed in PHE information at that time. Most could identify the recommended actions and found the advice understandable and trustworthy. Interviews revealed that passengers shared concerns about the lack of wider official action, and that passengers' knowledge had been acquired elsewhere as much from PHE. Respondents also noted their own agency in choosing to self-isolate, partially as a self-protective measure. Conclusion PHE COVID-19 public health information was perceived as clear and acceptable, but we found that passengers acquired knowledge from various sources and they saw the provision of information alone on arrival as an insufficient official response. Our study provides fresh insights into the importance of taking greater account of diverse information sources and of the need for public assurance in creating public health information materials to address global health threats. Keywords COVID-19, public health advice, government, policy, airport, international travel", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tingting Zhang", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" + }, + { + "author_name": "Charlotte Robin", + "author_inst": "Field Epidemiology, Field Service, National Infection Service, Public Health England, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science a" + }, + { + "author_name": "Shenghan Cai", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" + }, + { + "author_name": "Clare Sawyer", + "author_inst": "UK Field Epidemiology Training Programme, Global Public Health Division, Public Health England, London, UK; Communicable Disease Surveillance Centre, Public Hea" + }, + { + "author_name": "Wendy Rice", + "author_inst": "Field Epidemiology, Field Service, National Infection Service, Public Health England, Bristol, UK" + }, + { + "author_name": "Louise E. Smith", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Resp" + }, + { + "author_name": "Richard Aml\u00f4t", + "author_inst": "NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection R" + }, + { + "author_name": "G. James Rubin", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Resp" + }, + { + "author_name": "Rosy Reynolds", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK; School of Psychological Scien" + }, + { + "author_name": "Matthew Hickman", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + }, + { + "author_name": "Isabel Oliver", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol; Field Epidemiology, Field Service, National Infection Service, Public Health England;" + }, + { + "author_name": "Helen Lambert", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.23.20200212", "rel_title": "Impact of Personal Care Habits on Post-Lockdown COVID-19 Contagion: Insights from Agent-based Simulations", @@ -1179523,53 +1181852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.24.20200790", - "rel_title": "Clinical manifestations along with biochemical and psychological outcomes of COVID-19 cases in diabetic individuals in Bangladesh", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200790", - "rel_abs": "Background and aimsThis study investigated the clinical manifestations, outcomes and long-term complications of COVID-19 inpatients in Bangladesh while emphasizing on individuals having diabetes.\n\nMethodsA cross-sectional study was conducted for a sample of COVID-19 inpatients across four different hospitals of Bangladesh between April 1st and June 30, 2020. Variation in clinical characteristics, contact history, comorbidities, treatment pattern, and long-term complications were investigated.\n\nResultsThere were 734 COVID-19 presentations in this study of which 19.8% of patients had diabetes. 76% were male and 85% of the patients had been administered with all vaccine doses during childhood. The most frequently occurring blood groups among patients with diabetes were B (+) ve (35%) and O (+) ve (31%). Among biochemical parameters, glucose, D-dimer, C-reactive protein (CRP) and Troponin levels were significantly elevated amidst the cohort with diabetes. The frequency of insulin dependent individuals increased three-fold during COVID-19. A number of COVID-19 patients with diabetes have been suffering from long term complications post recovery including pain, discomfort, memory loss and sleep disturbance.\n\nConclusionIndividuals with diabetes have experienced severe manifestation of COVID-19 and post disease complications. Further in-depth studies focused on larger sample sizes are entailed to assess the relationships elaborately.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Farhana Akter", - "author_inst": "Chittagong Medical College" - }, - { - "author_name": "Adnan Mannan", - "author_inst": "Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram-4331, Bangladesh." - }, - { - "author_name": "H. M. Hamidullah Mehedi", - "author_inst": "250 beded General Hospital Chittagong, Chattogram, Bangladesh." - }, - { - "author_name": "Abdur Rob", - "author_inst": "250 beded General Hospital Chittagong, Chattogram, Bangladesh." - }, - { - "author_name": "Shakeel Ahmed", - "author_inst": "Department of Microbiology, Bangladesh Institute of Tropical & Infectious Diseases, Chattogram 4217, Bangladesh" - }, - { - "author_name": "Asma Salauddin", - "author_inst": "Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram-4331, Bangladesh." - }, - { - "author_name": "Md. Shakhawat Hossain", - "author_inst": "Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram-4331, Bangladesh" - }, - { - "author_name": "Md Mahbub Hasan", - "author_inst": "Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram-4331, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.23.20165639", "rel_title": "First phylogenetic analysis of Malian SARS-CoV-2 sequences provide molecular insights into the genomic diversity of the Sahel region", @@ -1180369,6 +1182651,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.25.20201459", + "rel_title": "Performance of a point of care test for detecting IgM and IgG antibodies against SARS-CoV-2 and seroprevalence in blood donors and health care workers in Panama", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201459", + "rel_abs": "Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, which has reached 28 million cases worldwide in eight months. The serological detection of antibodies against the virus will play a pivotal role in complementing molecular tests to improve diagnostic accuracy, contact tracing, vaccine efficacy testing and seroprevalence surveillance. Here, we aimed first to evaluate a lateral flow assays ability to identify specific IgM and IgG antibodies against SARS-CoV-2 and second, to report the seroprevalence of these antibodies among health care workers and healthy volunteer blood donors in Panama. We recruited study participants between April 30th and July 7th, 2020. For the test validation and performance evaluation, we analyzed serum samples from participants with clinical symptoms and confirmed positive RT-PCR for SARS-CoV-2, participants with other confirmed infectious diseases, and a set of pre-pandemic serum samples. We used two by two table analysis to determine the test sensitivity and specificity as well as the kappa agreement value with a 95% confidence interval. Then, we used the lateral flow assay to determine seroprevalence among serum samples from COVID-19 patients, potentially exposed health care workers, and healthy volunteer donors. Our results show this assay reached a positive percent agreement of 97.2% (95% CI 84.2-100.0%) for detecting both IgM and IgG. The assay showed a kappa of 0.898 (95%CI 0.811-0.985) and 0.918 (95% CI 0.839-0.997) for IgM and IgG, respectively. The evaluation of serum samples from hospitalized COVID-19 patients indicates a correlation between test sensitivity and the number of days since symptom onset; the highest positive percent agreement (87% (95% CI 67.0-96.3%)) was observed at [≥]15 days post-symptom onset. We found an overall antibody seroprevalence of 11.6% (95% CI 8.5-15.8%) among both health care workers and healthy blood donors. Our findings suggest this lateral flow assay could contribute significantly to implementing seroprevalence testing in locations with active community transmission of SARS-CoV-2.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Alcibiades Villarreal", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Giselle Rangel", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Xu Zhang", + "author_inst": "CAS" + }, + { + "author_name": "Digna Wong", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Carolina De La Guardia", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Gabrielle Britton", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Patricia L. Fernandez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Carlos M Restrepo", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ambar Perez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Diana Oviedo", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Maria B Carreira", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Gilberto A. Eskildsen", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Dilcia Sambrano", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Yamitzel Zaldivar", + "author_inst": "GORGAS" + }, + { + "author_name": "Danilo Franco", + "author_inst": "GORGAS" + }, + { + "author_name": "Sandra Lopez Verges", + "author_inst": "GORGAS" + }, + { + "author_name": "Dexi Zhang", + "author_inst": "CAS" + }, + { + "author_name": "Fangjing Fan", + "author_inst": "CAS" + }, + { + "author_name": "Baojun Wang", + "author_inst": "KEWEI" + }, + { + "author_name": "Xavier Saez-Llorens", + "author_inst": "CEVAXIN" + }, + { + "author_name": "Rodrigo DeAntonio", + "author_inst": "CEVAXIN" + }, + { + "author_name": "Ivonne Torres-Atencio", + "author_inst": "UP" + }, + { + "author_name": "Fernando Diaz Subia", + "author_inst": "Pacifica Salud" + }, + { + "author_name": "Eduardo Ortega-Barria", + "author_inst": "GSK" + }, + { + "author_name": "Rao Kosagisharaf", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ricardo Lleonart", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Chong Li", + "author_inst": "CAS" + }, + { + "author_name": "Amador Goodridge", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "- COVID-19 SEROLOGY COLLABORATOR GROUP", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.24.20200394", "rel_title": "Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer", @@ -1181029,45 +1183442,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.09.25.310078", - "rel_title": "Sequence Analysis for SNP Detection and Phylogenetic Reconstruction of SARS-CoV-2 Isolated from Nigerian COVID-19 Cases", - "rel_date": "2020-09-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.25.310078", - "rel_abs": "BackgroundCoronaviruses are a group of viruses that belong to the Family Coronaviridae, Genus Betacoronavirus. In December 2019, a new coronavirus disease (COVID-19) characterized by severe respiratory symptoms was discovered. The causative pathogen was a novel coronavirus known as 2019-nCoV and later as SARS-CoV-2. Within two months of its discovery, COVID-19 became a pandemic causing widespread morbidity and mortality.\n\nMethodologyWhole genome sequence data of SARS-CoV-2 isolated from Nigerian COVID-19 cases were retrieved by downloading from GISAID database. A total of 18 sequences that satisfied quality assurance (length [≥] 29700 nts and number of unknown bases denoted as N [≤] 5%) were used for the study. Multiple sequence alignment (MSA) was done in MAFFT (Version 7.471) while SNP calling was implemented in DnaSP (Version 6.12.03) respectively and then visualized in Jalview (Version 2.11.1.0). Phylogenetic analysis was with MEGA X software.\n\nResultsNigerian SARS-CoV-2 had 99.9% genomic similarity with four large conserved genomic regions. A total of 66 SNPs were identified out of which 31 were informative. Nucleotide diversity assessment gave Pi = 0.00048 and average SNP frequency of 2.22 SNPs per 1000 nts. Non-coding genomic regions particularly 5UTR and 3UTR had a SNP density of 3.77 and 35.4 respectively. The region with the highest SNP density was ORF10 with a frequency of 8.55 SNPs/1000 nts). Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. Nigeria SARS-CoV-2 revealed 3 major clades namely Oyo, Ekiti and Osun on a maximum likelihood phylogenetic tree.\n\nConclusion and RecommendationNigerian SARS-CoV-2 reveals high mutation rate together with preponderance of L lineage and D614G mutants. Implication of these mutations for SARS-CoV-2 virulence and the need for more aggressive testing and treatment of COVID-19 in Nigeria is discussed. Additionally, attempt to produce testing kits for COVID-19 in Nigeria should consider the conserved regions identified in this study. Strict adherence to COVID-19 preventive measure is recommended in view of Nigerian SARS-CoV-2 phylogenetic clustering pattern, which suggests intensive community transmission possibly rooted in communal culture characteristic of many ethnicities in Nigeria.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Idowu A. Taiwo", - "author_inst": "University of Lagos" - }, - { - "author_name": "Nike Adeleye", - "author_inst": "University of Lagos" - }, - { - "author_name": "Fatimah O. Anwoju", - "author_inst": "University of Lagos" - }, - { - "author_name": "Adeyemi Adeyinka", - "author_inst": "University of Lagos" - }, - { - "author_name": "Ijeoma C. Uzoma", - "author_inst": "University of Nigeria, Nsukka" - }, - { - "author_name": "Taiwo T. Bankole", - "author_inst": "University of Lagos" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.25.309914", "rel_title": "Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model", @@ -1182091,6 +1184465,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.09.23.310565", + "rel_title": "COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest", + "rel_date": "2020-09-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.23.310565", + "rel_abs": "COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 Spike receptor binding domain (RBD) across different geographic regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the recent emergence of a dominant lineage harboring an S477N RBD mutation in Australia. To accelerate COVID-19 research and public health efforts, COVID-19 CG will be continually upgraded with new features for users to quickly and reliably pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Albert Tian Chen", + "author_inst": "Broad Institute of MIT & Harvard" + }, + { + "author_name": "Kevin Altschuler", + "author_inst": "NA" + }, + { + "author_name": "Shing Hei Zhan", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Yujia Alina Chan", + "author_inst": "Broad Institute of MIT & Harvard" + }, + { + "author_name": "Benjamin E Deverman", + "author_inst": "Broad Institute of MIT and Harvard" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.24.310490", "rel_title": "Broad-spectrum, patient-adaptable inhaled niclosamide-lysozyme particles are efficacious against coronaviruses in lethal murine infection models", @@ -1182907,69 +1185316,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.21.20199117", - "rel_title": "Features of patients that died for COVID-19 in a Hospital in the south of Mexico: A observational cohort study", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20199117", - "rel_abs": "BackgroundDue to the wide spread of SARS-CoV2 around the world, the risk of death in individuals with metabolic comorbidities has dangerously increased. Mexico has a high number of infected individuals and deaths by COVID-19, as well as an important burden of metabolic diseases. However, reports about features of Mexican individuals with COVID-19 are scarce. The aim of this study was to evaluate demographic features, clinical characteristics, and the pharmacological treatment of individuals who died by COVID-19 in the south of Mexico.\n\nMethodsWe performed an observational study including 185 deceased individuals with confirmed diagnosis of COVID-19. Data were retrieved from medical records. Categorical data was expressed as proportions (%) and numerical data were expressed as mean {+/-} standard deviation. Comorbidities and overlapping symptoms where plotted as Venn diagrams. Drug clusters were plotted as dendrograms.\n\nResultsThe mean age was 59.53 years. There was a male predominance (60.1%). The mean hospital stay was 4.75 {+/-} 4.43 days. The most frequent symptoms were dyspnea (88.77%), fever (71.42%) and dry cough (64.28%). Present comorbidities were diabetes (60.63%), hypertension (59.57%) and obesity (43.61%). The main drugs used were azithromycin (60.6%), hydroxychloroquine (53.0%) and oseltamivir (27.3%).\n\nConclusionsMexican individuals who died of COVID-19 had shorter hospital stays, higher frequency of shortness of breath, and higher prevalence of diabetes compared with individuals from other countries. Also, there was a high frequency of off-label use of drugs for their treatment.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jesus Arturo Ruiz-Quinonez Sr.", - "author_inst": "Hospital de Alta Especialidad Dr. Juan Graham Casasus" - }, - { - "author_name": "Crystell Guzman-Priego Sr.", - "author_inst": "Universidad Juarez Autonoma de Tabasco" - }, - { - "author_name": "German Alberto Nolasco-Rosales Sr.", - "author_inst": "Universidad Juarez Autonoma de Tabasco" - }, - { - "author_name": "Carlos Alfonso Tovilla-Zarate", - "author_inst": "Universidad Juarez Autonoma de Tabasco" - }, - { - "author_name": "Oscar Israel Flores-Barrientos", - "author_inst": "Hospital de Alta Especialidad Dr. Juan Graham Casasus" - }, - { - "author_name": "Victor Narvaez-Osorio", - "author_inst": "Hospital de Alta Especialidad Dr. Juan Graham Casasus" - }, - { - "author_name": "Guadalupe del Carmen Baeza-Flores", - "author_inst": "Universidad Juarez Autonoma de Tabasco" - }, - { - "author_name": "Thelma Beatriz Gonzalez-Castro", - "author_inst": "Universidad Juarez Autonoma de Tabasco" - }, - { - "author_name": "Carlos Ramon Lopez-Brito", - "author_inst": "Hospital de Alta Especialidad Dr. Juan Graham Casasus" - }, - { - "author_name": "Carlos Alberto Denis-Garcia", - "author_inst": "Hospital de Alta Especialidad Dr. Juan Graham Casasus" - }, - { - "author_name": "Agustin Perez-Garcia", - "author_inst": "Hospital de Alta Especialidad Dr. Juan Graham Casasus" - }, - { - "author_name": "Isela Esther Juarez-Rojop", - "author_inst": "Universidad Juarez Autonoma de Tabasco" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.09.21.20198804", "rel_title": "A Brief Burnout Evaluation Scale (BBES) as a potential tool to prevent collapse of the health care task force during the COVID-19 pandemic", @@ -1183837,6 +1186183,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2020.09.22.20198465", + "rel_title": "Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20198465", + "rel_abs": "Using serological test to estimate the prevalence and infection potential of coronavirus disease 2019 in ocular diseases patients help understand the relationship between ocular diseases and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We conducted a cross-sectional study assaying the IgG and IgM antibodies in 1331 individuals with ocular diseases by using a magnetic chemiluminescence enzyme immunoassay kit, during the period from February 2020 to May 2020. In our study, the seroposivity in total ocular disease patients was 0.83% (11/1331). The patients with different ocular diseases including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others had seroposivity of 2.94%, 12.5%, 25%, 4.41%, 2.63%, 1.6%, 2.22% and 0%, respectively. Among that, two ocular surface disease groups (keratitis and conjunctival cyst) had higher seroprevalence compared with others. All the participants were reverse transcription polymerase chain reaction negative for SARS-CoV-2 from throat swabs. Our study evaluated the seroprevalence in patients with different ocular diseases, which will help us understand the relationship between ocular disease and SARS-CoV-2 infection. Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "shengjie li Sr.", + "author_inst": "Fudan University" + }, + { + "author_name": "yichao qiu", + "author_inst": "fudan university" + }, + { + "author_name": "li tang", + "author_inst": "fudan university" + }, + { + "author_name": "zhujian wang", + "author_inst": "fudan university" + }, + { + "author_name": "wenjun cao", + "author_inst": "fudan university" + }, + { + "author_name": "xinghuai sun", + "author_inst": "fudan university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.20.20198432", "rel_title": "COVID-19 dynamics across the US: A deep learning study of human mobility and social behavior", @@ -1184473,121 +1186858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.09.22.20199125", - "rel_title": "Molecular Architecture of Early Disseminationand Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199125", - "rel_abs": "We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.\n\nIMPORTANCEThere is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, Texas, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture, evolution, and relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our study provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Scott Wesley Long", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Randall J Olsen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Paul A. Christensen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "David W Bernard", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "James J. Davis", - "author_inst": "University of Chicago" - }, - { - "author_name": "Maulik Shukla", - "author_inst": "University of Chicago" - }, - { - "author_name": "Marcus Nguyen", - "author_inst": "University of Chicago" - }, - { - "author_name": "Matthew Ojeda Saavedra", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Prasanti Yerramilli", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Layne Pruitt", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Sishir Subedi", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Hung-Che Kuo", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Heather Hendrickson", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Ghazaleh Eskandari", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Hoang A.T. Nguyen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "James Hunter Long", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Muthiah Kumaraswami", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Jule Goike", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Daniel Boutz", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jimmy Gollihar", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jason S. McLellan", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Chia-Wei Chou", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kamyab Javanmardi", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Ilya J. Finkelstein", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "James Musser", - "author_inst": "Houston Methodist Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.09.22.20199703", "rel_title": "Prognostic value of sTREM-1 in COVID-19 patients: a biomarker for disease severity and mortality", @@ -1185671,6 +1187941,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.09.20.20197608", + "rel_title": "At home and online during the early months of the COVID-19 pandemic and the relationship to alcohol consumption in a national sample of U.S. adults", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20197608", + "rel_abs": "ObjectiveThe current study seeks to understand the links between social media use and alcohol consumption during the early months of the COVID-19 pandemic.\n\nMethodData were from the national Understanding American Study, a probability-based Internet panel weighted to represent the U.S. population. Subjects (N=5874; 51% female) were adults, 18 years and older, who completed a March survey (wave 1) and a follow-up survey one month later (wave 3). Analyses assessed the relationship of social media use at wave 1 with wave 3 alcohol use, accounting for wave 1 alcohol use and the sociodemographic characteristics of the sample. We examined the effect of working or studying from home as a moderator.\n\nResultsTwitter and Instagram users, but not Facebook users, drank more frequently at wave 3 than non-users. For Instagram users, more frequent alcohol use at wave 3 was at least partially attributed to the frequency of drinking at wave 1. The interaction between Twitter use and working or studying from home was statistically significant. The combination of being on Twitter and working or studying from home was associated with drinking more days a week.\n\nConclusionsExposure to content about COVID-19 and increased alcohol consumption during the pandemic may contribute to more frequent alcohol use for some social media users, especially those sheltering at home. The study of public health messaging via social media to change alcohol use behaviors during traumatic events is warranted.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Karen G Chartier", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Jeanine P.D. Guidry", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Catherine A. Lee", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2020.09.20.20196907", "rel_title": "Microfluidic Affinity Profiling reveals a Broad Range of Target Affinities for Anti-SARS-CoV-2 Antibodies in Plasma of Covid Survivors", @@ -1186611,33 +1188908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.18.20197319", - "rel_title": "Uncovering clinical risk factors and prediction of severe COVID-19: A machine learning approach based on UK Biobank data", - "rel_date": "2020-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197319", - "rel_abs": "BackgroundCOVID-19 is a major public health concern. Given the extent of the pandemic, it is urgent to identify risk factors associated with disease severity. Accurate prediction of those at risk of developing severe infections is also of high clinical importance.\n\nMethodsBased on the UK Biobank(UKBB data), we built machine learning(ML) models to predict the risk of developing severe or fatal infections, and to evaluate major risk factors involved. We first restricted the analysis to infected subjects(N=7846), then performed analysis at a population level, considering those with no known infection as controls(N for controls=465,728). Hospitalization was used as a proxy for severity. Totally 97 clinical variables(collected prior to COVID-19 outbreak) covering demographic variables, comorbidities, blood measurements(e.g. hematological/liver/renal function/metabolic parameters etc.), anthropometric measures and other risk factors (e.g. smoking/drinking habits) were included as predictors. We also constructed a simplified ( lite) prediction model using 27 covariates that can be more easily obtained (demographic and comorbidity data). XGboost (gradient boosted trees) was used for prediction and predictive performance was assessed by cross-validation. Variable importance was quantified by Shapley values and accuracy gain. Shapley dependency and interaction plots were used to evaluate the pattern of relationship between risk factors and outcomes.\n\nResultsA total of 2386 severe and 477 fatal cases were identified. For the analysis among infected individuals (N=7846),our prediction model achieved AUCs of 0.723(95% CI:0.711-0.736) and 0.814(CI: 0.791-0.838) for severe and fatal infections respectively. The top five contributing factors for severity were age, number of drugs taken(cnt_tx), cystatin C(reflecting renal function), wait-hip ratio (WHR) and Townsend Deprivation index (TDI). For prediction of mortality, the top features were age, testosterone, cnt_tx, waist circumference(WC) and red cell distribution width (RDW).\n\nIn analyses involving the whole UKBB population, the corresponding AUCs for severity and fatality were 0.696(CI:0.684-0.708) and 0.802(CI:0.778-0.826) respectively. The same top five risk factors were identified for both outcomes, namely age, cnt_tx, WC, WHR and TDI. Apart from the above features, Type 2 diabetes(T2DM), HbA1c and apolipoprotein A were ranked among the top 10 in at least two (out of four) analyses. Age, cystatin C, TDI and cnt_tx were among the top 10 across all four analyses.\n\nAs for the lite models, the predictive performances in terms of AUC are broadly similar, with estimated AUCs of 0.716, 0.818, 0.696 and 0.811 respectively. The top-ranked variables were similar to above, including for example age, cnt_tx, WC, male and T2DM.\n\nConclusionsWe identified a number of baseline clinical risk factors for severe/fatal infection by an ML approach. For example, age, central obesity, impaired renal function, multi-comorbidities and cardiometabolic abnormalities may predispose to poorer outcomes. The presented prediction models may be useful at a population level to help identify those susceptible to developing severe/fatal infections, hence facilitating targeted prevention strategies. Further replications in independent cohorts are required to verify our findings.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kenneth C.Y. WONG", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Yong Xiang", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Hon-Cheong So", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.16.20195230", "rel_title": "Vent-Lock: A 3D Printed Ventilator Multiplexer to Enhance the Capacity of Treating Patients with COVID-19", @@ -1187461,6 +1189731,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.22.20199372", + "rel_title": "Limits and opportunities of SARS-CoV-2 antigen rapid Tests: an experience based perspective", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199372", + "rel_abs": "Due to the currently increasing case numbers of SARS-CoV-2 infections worldwide there is an increasing need for rapid diagnostic devices in addition to existing PCR-capacities. Therefore, rapid antigen assays including lateral flow assays are discussed as an alternative method. In comparison to an established RT-PCR protocol, however the novel lateral flow assay unfortunately lowered the expectations set in these assays.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Verena Schildgen", + "author_inst": "Kliniken der Stadt Koeln gGmbH, Klinikum der Privaten Universitaet Witten/Herdecke" + }, + { + "author_name": "Sabrina Demuth", + "author_inst": "Kliniken der Stadt Koeln" + }, + { + "author_name": "Jessica Lusebrink", + "author_inst": "Kliniken der Stadt Koeln" + }, + { + "author_name": "Oliver Schildgen", + "author_inst": "Kliniken der Stadt Koeln gGmbH, Klinikum der Privaten Universtaet Witten/Herdecke" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.21.20199133", "rel_title": "Reorganization of Substance Use Treatment and Harm Reduction Services during the COVID-19 Pandemic: A Global Survey", @@ -1188241,57 +1190542,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.09.21.307439", - "rel_title": "Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution", - "rel_date": "2020-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.21.307439", - "rel_abs": "In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the \"down\" conformation, indicating they are more prone to adopt this receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. These results collectively indicate that strong RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xinquan Wang", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Shuyuan Zhang", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Shuyuan Qiao", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Jinfang Yu", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Jianwei Zeng", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Sisi Shan", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Jun Lan", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Long Tian", - "author_inst": "Tsinghua university" - }, - { - "author_name": "Linqi Zhang", - "author_inst": "Tsinghua university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.09.22.308338", "rel_title": "NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response", @@ -1189266,6 +1191516,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.20.297242", + "rel_title": "Comparative analysis reveals the species-specific genetic determinants of ACE2 required for SARS-CoV-2 entry", + "rel_date": "2020-09-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.20.297242", + "rel_abs": "Coronavirus interaction with its viral receptor is a primary genetic determinant of host range and tissue tropism. SARS-CoV-2 utilizes ACE2 as the receptor to enter host cell in a species-specific manner. We and others have previously shown that ACE2 orthologs from New World monkey, koala and mouse cannot interact with SARS-CoV-2 to mediate viral entry, and this defect can be restored by humanization of the restrictive residues in New World monkey ACE2. To better understand the genetic determinants behind the ability of ACE2 orthologs to support viral entry, we compared koala and mouse ACE2 sequences with that of human and identified the key residues in koala and mouse ACE2 that restrict viral receptor activity. Humanization of these critical residues rendered both koala and mouse ACE2 capable of binding the spike protein and facilitating viral entry. The single mutation that allowed for mouse ACE2 to serve as a viral receptor provides a potential avenue for the development of SARS-CoV-2 mouse model.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wenlin Ren", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Gaowei Hu", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaomin Zhao", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yuyan Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Hongyang Shi", + "author_inst": "Institut Pasteur of Shanghai, Chinese Academy of Sciences" + }, + { + "author_name": "Jun Lan", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yunkai Zhu", + "author_inst": "Fudan University" + }, + { + "author_name": "Jianping Wu", + "author_inst": "Westlake University" + }, + { + "author_name": "Devin J. Kenney", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Douam Florian", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Yimin Tong", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Jin Zhong", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Fudan University" + }, + { + "author_name": "Xinquan Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Zhenghong Yuan", + "author_inst": "Fudan University" + }, + { + "author_name": "Dongming Zhou", + "author_inst": "School of Basic Medical Sciences, Tianjin Medical University" + }, + { + "author_name": "Rong Zhang", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Qiang Ding", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.21.306357", "rel_title": "Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19", @@ -1189758,41 +1192095,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.14.20193987", - "rel_title": "Death associated with coronavirus (COVID-19) infection in individuals with severe mental disorders in Sweden during the early months of the outbreak - a exploratory cross-sectional analysis of a population-based register study", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20193987", - "rel_abs": "BackgroundIndividuals with severe mental disorder (SMD) have a higher risk of somatic comorbidity and mortality than the rest of the population. We set up a population-based study to assess whether individuals with SMD had a higher risk of death associated with a COVID-19 infection (COVID-19 associated death) than individuals without SMD.\n\nMethodsExploratory analysis with a cross-sectional design in the framework of a population-based register study covering the entire Swedish population. The Swedish Board for Health and Welfare (Socialstyrelsen) provided anonymised tabulated summary data for further analysis. We compared numbers of COVID-19 associated death in individuals with SMD (cases) and without SMD (controls). We calculated the odds ratio (OR) for the whole sample and by age group and four potential risk factors, namely diabetes, cardiovascular disease, hypertension, chronic lung disease.\n\nResultsThe sample comprised of 7,923,859 individuals, 103,999 with SMD and 7,819,860 controls. There were 130 (0.1%) COVID-19 associated deaths in the SMD group and 4945 (0.06%) in the control group, corresponding to an OR of 1.98 (CI 1.66-2.35; p < 0.001). The odds were fourfold in the age group between 60 and 79 years. Cardiovascular diseases increased the odds by 50%. Individuals with SMD without any of the risk factors under study had three-folds odds of COVID-19 associated death.\n\nConclusionOur preliminary results suggest that individuals with SMD are a further group at increased risk of COVID-19 associated death. The factors contributing to this increased mortality risk require clarification.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Martin Maripuu", - "author_inst": "Department of Clinical Sciences, Division of Psychiatry, Ume\u00e5 University, Ume\u00e5, Sweden" - }, - { - "author_name": "Marie Bendix", - "author_inst": "Dep of Clinical Sciences, Div of Psychiatry, Ume\u00e5 University, Ume\u00e5, Sweden; Dep of Clinical Neuroscience, Karolinska Institutet, Centre for Psychiatry Research " - }, - { - "author_name": "Louise \u00d6hlund", - "author_inst": "Department of Clinical Sciences, Division of Psychiatry, Sunderby Research Unit, Ume\u00e5 University, Ume\u00e5, Sweden" - }, - { - "author_name": "Micael Widerstr\u00f6m", - "author_inst": "Department of Clinical Microbiology, Ume\u00e5 University, Ume\u00e5, Sweden" - }, - { - "author_name": "Ursula Werneke", - "author_inst": "Department of Clinical Sciences, Division of Psychiatry, Sunderby Research Unit, Ume\u00e5 University, Ume\u00e5, Sweden" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.09.15.20165886", "rel_title": "Genetically proxied inhibition of interleukin-6 signaling: opposing associations with susceptibility to COVID-19 and pneumonia", @@ -1190600,6 +1192902,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.15.20194258", + "rel_title": "COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194258", + "rel_abs": "Background: Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. International comparisons are hampered by highly variable conditions under which epidemics spread and differences in the timing and scale of interventions. Cumulative COVID-19 morbidity and mortality are functions of both the rate of epidemic growth and the duration of uninhibited growth before interventions were implemented. Incomplete and sporadic testing during the early COVID-19 epidemic makes it difficult to identify how long SARS-CoV-2 was circulating in different places. SARS-CoV-2 genetic sequences can be analyzed to provide an estimate of both the time of epidemic origin and the rate of early epidemic growth in different settings. Methods: We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were cross-referenced with dates of the most stringent interventions in each location as well as the number of cumulative COVID-19 deaths following maximum intervention. Phylodynamic methods were used to estimate the rate of early epidemic growth and proxy estimates of epidemic size. Findings: The time elapsed between epidemic origin and maximum intervention is strongly associated with different measures of epidemic severity and explains 46% of variance in numbers infected at time of maximum intervention. The reproduction number is independently associated with epidemic severity. In multivariable regression models, epidemic severity was not associated with census population size. The time elapsed between detection of initial COVID-19 cases to interventions was not associated with epidemic severity, indicating that many locations experienced long periods of cryptic transmission. Interpretation: Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Manon Ragonnet-Cronin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Olivia Boyd", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lily Geidelberg", + "author_inst": "Imperial College London" + }, + { + "author_name": "David Jorgensen", + "author_inst": "Imperial College London" + }, + { + "author_name": "Fabricia F Nascimento", + "author_inst": "Imperial College London" + }, + { + "author_name": "Igor Siveroni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robert Johnson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zulma M Cucunuba", + "author_inst": "Imperial College London" + }, + { + "author_name": "Elita Jauneikaite", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hayley A Thompson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "Imperial College London; University of Oxford" + }, + { + "author_name": "Erik Volz", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.14.20194589", "rel_title": "Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves", @@ -1191156,113 +1193537,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.09.15.20192765", - "rel_title": "An ELISA protocol with resolution at high sample concentration reveals reactive antibodies to SARS-CoV-2 in unexposed individuals", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20192765", - "rel_abs": "The COVID-19 pandemic has significantly impacted work, economy, and way of life. The SARS-CoV-2 virus displays unique features including widely varying symptoms and outcomes between infected individuals. Sensitive measurement of SARS-CoV-2 specific antibodies would provide new insight into virus transmission dynamics, pre-existing cross-reactive immunity, and the nuances of SARS-CoV-2 pathogenesis. To date, existing SARS-CoV-2 serology tests have limited utility due to insufficient detection of antibody levels lower than what is typically present after several days of symptoms. To measure lower quantities of SARS-CoV-2 IgM, IgG, and IgA with higher resolution than existing assays, we developed a new ELISA protocol with a distinct plate washing procedure and timed plate development via use of a standard curve. This BU ELISA method exhibits very low signal from plasma or serum samples added to uncoated wells at as low as a 1:5 dilution. Use of this method revealed circulating SARS-CoV-2 receptor binding domain (RBD) and nucleocapsid protein (NP) reactive antibodies from blood samples drawn prior to May 2019. Of our prepandemic cohort, no SARS-CoV-2 RBD-reactive IgG antibodies were detected in subjects over 70 years of age, and SARS-CoV-2 NP-reactive antibodies were present at similar levels to infected subjects in some individuals and very low in others. Also, samples drawn in May 2020 from two individuals with no symptoms or no known virus exposure contained SARS-CoV-2 RBD-reactive antibodies at intermediate amounts compared with other subject groups (higher than pre-pandemic and lower than confirmed SARS-CoV-2 infected). The one asymptomatic SARS-CoV-2 convalescent subject in our study possessed comparable amounts of SARS-CoV-2 NP-specific IgM and IgG but drastically lower IgA than the symptomatic counterparts. Also, our assay detected positive signal from samples that gave negative results in a commercially available Lateral Flow Device (LFD) and the EUA approved Abbott IgG chemiluminescent microparticle immunoassay for SARS-CoV-2 antibody detection. We propose that this improved ELISA protocol, which is straightforward to perform, low cost, and uses readily available commercial reagents, is a useful tool to elucidate new information about SARS-CoV-2 infection and has promising implications for improved detection of all analytes measurable by this platform.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Rachel Yuen", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Dylan Steiner", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Riley Pihl", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Elizabeth Chavez", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Alex Olson", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Lillia Baird", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Filiz Korkmaz", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Patricia Urick", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Manish Sagar", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Jacob Berrigan", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Rahm Gummuluru", - "author_inst": "Boston University Medical Center" - }, - { - "author_name": "Ronald Corley", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Karen Quillen", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Anna Belkina", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Gustavo Mostoslavsky", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Ian Rifkin", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Yachana Kataria", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Amedeo Cappione", - "author_inst": "MilliporeSigma" - }, - { - "author_name": "Nina Lin", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Nahid Bhadelia", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Jennifer Snyder-Cappione", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Erika L Smith", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Wenda Gao", - "author_inst": "Antagen Pharmaceuticals" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.20187369", "rel_title": "Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories", @@ -1192534,6 +1194808,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.09.16.20195685", + "rel_title": "Integrative Genomics Analysis Reveals a Novel 21q22.11 Locus Contributing to Susceptibility of COVID-19", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195685", + "rel_abs": "The systematic identification of host genetic risk factors is essential for the understanding and treatment of COVID-19. By performing a meta-analysis of two independent genome-wide association (GWAS) summary datasets (N = 680,128), a novel locus at 21q22.11 was identified to be associated with COVID-19 infection (rs9976829 in IFNAR2 and upstream of IL10RB, OR = 1.16, 95% CI = 1.09 - 1.23, P = 2.57x10-6). The rs9976829 represents a strong splicing quantitative trait locus (sQTL) for both IFNAR2 and IL10RB genes, especially in lung tissue (P 1.8x10-24). Gene-based association analysis also found IFNAR2 was significantly associated with COVID-19 infection (P = 2.58x10-7). Integrative genomics analysis of combining GWAS with eQTL data showed the expression variations of IFNAR2 and IL10RB have prominent effects on COVID-19 in various types of tissues, especially in lung tissue. The majority of IFNAR2-expressing cells were dendritic cells (40%) and plasmacytoid dendritic cells (38.5%), and IL10RB-expressing cells were mainly nonclassical monocytes (29.6%). IFNAR2 and IL10RB are targeted by several interferons-related drugs. Together, our results uncover 21q22.11 as a novel susceptibility locus for COVID-19, in which individuals with G alleles of rs9976829 have a higher probability of COVID-19 susceptibility than those with non-G alleles.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yunlong Ma", + "author_inst": "Wenzhou Medical University" + }, + { + "author_name": "Yukuan Huang", + "author_inst": "Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China" + }, + { + "author_name": "Sen Zhao", + "author_inst": "Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China" + }, + { + "author_name": "Yinghao Yao", + "author_inst": "Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, China" + }, + { + "author_name": "Yaru Zhang", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + }, + { + "author_name": "Jia Qu", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + }, + { + "author_name": "Nan Wu", + "author_inst": "Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China" + }, + { + "author_name": "Jianzhong Su", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.17.20190595", "rel_title": "The \"Great Lockdown\": Inactive Workers and Mortality by Covid-19", @@ -1193294,65 +1195615,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.15.20195313", - "rel_title": "Seroprevalence and seroconversion rates to SARS-CoV-2 in interns, residents, and medical doctors in a University Hospital in Bogota, Colombia", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20195313", - "rel_abs": "ObjectivesTo determine the prevalence of antibodies to SARS-CoV-2 and the incidence of seroconversion in the first month of follow-up among interns, residents, and medical doctors attending patients at a University Hospital, to explore for associations of seroprevalence and seroconversion with risk factors and symptoms compatible with COVID-19, and to explore the concordance of CLA, LFA, and ELFA.\n\nDesign or methodsWe conducted a cross-sectional and a prospective study among medical doctors and medical trainees at Hospital Universitario San Ignacio in Bogota (Colombia) during June, July, and August to assess seroprevalence and seroconversion rates in this population was performed using CLA IgG for SARS-CoV-2. LFA IgG and IgM and ELFA IgM were also determined to explore concordance with CLA IgG.\n\nResultsAt baseline, 8 (2.28% 95%CI 1.16-4.43%) individuals were IgG positive for SARS-CoV-2 by CLA. At the end of the study, 21 (5.98% 95%CI 3.94-8.97%) individuals seroconverted by CLA IgG. In all, 29 individuals had IgG by CLA and of these 11 (3.13% 95%CI 1.76-5.52%) were asymptomatic. No associations with risk factors for infection were identified. CLA had moderate concordance with LFA IgG and ELFA, but minimal with LFA IgM.\n\nConclusionsOur report is one of the first in Latina America on seroprevalence and seroconversion rates in medical healthcare workers. It emphasizes the importance of avoiding focusing only on symptomatic individuals to screen this population for SARS-CoV-2 infection, since of all individuals that have evidence of previous infection many (37.93%) may be pre-symptomatic or asymptomatic and may contribute to infection/disease spread.\n\nHighlightsO_LILatin America was one of the most severely compromised regions of the world during the SARS-CoV-2 pandemic, between June and August 2020.\nC_LIO_LIHealthcare workers are at increased risk for COVID-19 and studies of seroprevalence and seroconversion rates in these subjects have not been published in the area.\nC_LIO_LIWe conducted a cross-sectional and prospective study of medical doctors and medical trainees in a University Hosptial during June, July, and August 2020 to assess seroprevalence and seroconversion rates of SARS-CoV-2 in this population, using a Chemiluminescent assay (CLA).\nC_LIO_LIAt baseline, 8 (2.28% 95%CI 1.16-4.43%) individuals were IgG positive for SARS-CoV-2 by CLA. At the end of the study, 21 (5.98% 95%CI 3.94-8.97%) individuals had seroconverted by CLA IgG.\nC_LIO_LIIn all, 29 (8.26% 95%CI 5.81-11.61%) individuals had IgG for SARS-CoV-2 by CLA and of these 11 (3.13% 95%CI 1.76-5.52%) were asymptomatic.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Beatriz Elena Ariza", - "author_inst": "Hospital Universitario San Ignacio" - }, - { - "author_name": "Yulieth Ximena Torres", - "author_inst": "Pontificia Universidad Javeriana" - }, - { - "author_name": "Diana Salgado", - "author_inst": "Hospital Universitario San Ignacio" - }, - { - "author_name": "Magda Cepeda", - "author_inst": "Pontificia Universidad Javeriana" - }, - { - "author_name": "Carlos Gomez", - "author_inst": "Pontificia Universidad Javeriana" - }, - { - "author_name": "Julio Cesar Castellanos", - "author_inst": "Hospital Universitario San Ignacio" - }, - { - "author_name": "Fernando Suarez", - "author_inst": "Pontificia Universidad Javeriana" - }, - { - "author_name": "Adriana Cuellar", - "author_inst": "Pontificia Universidad Javeriana" - }, - { - "author_name": "Claudia Cecilia Cardozo", - "author_inst": "Hospital Universitario San Ignacio" - }, - { - "author_name": "Juana Angel", - "author_inst": "Pontificia Universidad Javeriana" - }, - { - "author_name": "Manuel Antonio Franco", - "author_inst": "Pontificia Universidad Javeriana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.16.20195958", "rel_title": "Physiological Effect of Prone Positioning in Mechanically Ventilated SARS- CoV-2 Infected Patients with Severe ARDS: Preliminary Analysis of an Observational Study", @@ -1194368,6 +1196630,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.17.20195131", + "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in US Blood Donors", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20195131", + "rel_abs": "BackgroundTo identify blood donors eligible to donate Coronavirus Disease-2019 (COVID-19) Convalescent Plasma (CCP), a large blood center began testing for antibodies to SARS-CoV-2, the etiologic agent of COVID-19. We report the seroprevalence of total immunoglobulin directed against the S1 spike protein of SARS-CoV-2 in US blood donors.\n\nMethodsUnique non-CCP donor sera from June 1-July 31, 2020 were tested with the Ortho VITROS Anti-SARS-CoV-2 total immunoglobulin assay (positive: signal-to-cutoff (S/C) [≥]1). Donor age, sex, race/ethnicity, ABO/RhD, education, and experience were compared to June and July 2019. Multivariate regressions were conducted to identify demographics associated with the presence of antibodies and with S/C values.\n\nResultsUnique donors (n=252,882) showed an overall seroprevalence of 1.83% in June (1.37%) and July (2.26%), with the highest prevalence in northern New Jersey (7.3%). In a subset of donors with demographic information (n=189,565), higher odds of antibody reactivity were associated with non-Hispanic Native American/Alaskan (NH-NAA/A) and Black (NH-B), and Hispanic (H) race/ethnicity, age 18-64, middle school or lesser education, blood Group A, and never or non-recent donor status. In positive donors (n=2,831), antibody signal was associated with male sex, race/ethnicity (NH-NAA/A, NH-B and H) and geographic location.\n\nConclusionsSeroprevalence remains low in US blood donors but varies significantly by region. Temporal trends in reactivity may be used to gauge the effectiveness of public health measures. Before generalizing these data from healthy donors to the general population however, rates must be corrected for false positive test results among low prevalence test subjects and adjusted to match the wider demography.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ralph R Vassallo", + "author_inst": "Vitalant" + }, + { + "author_name": "Marjorie D Bravo", + "author_inst": "Vitalant" + }, + { + "author_name": "Larry J Dumont", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Kelsey Hazegh", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Hany Kamel", + "author_inst": "Vitalant" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.17.20196832", "rel_title": "COVID-19 pediatric mortality rates are heterogenous between countries", @@ -1195020,65 +1197317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.17.20196402", - "rel_title": "RPA-Based Method For The Detection Of SARS-CoV2", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196402", - "rel_abs": "Background: Coronavirus disease 2019 (COVID-19) is a highly infectious disease with significant mortality, morbidity, and far-reaching economic and social disruptions. Testing is key in the fight against COVID-19 disease. The gold standard for COVID-19 testing is the reverse transcription polymerase chain reaction (RT-PCR) test. RT-PCR requires highly specialized, expensive, and advanced bulky equipment that is difficult to use in the field or in a point of care setting. There is need for a simpler, inexpensive, convenient, portable and accurate test. Our aims were to: (i) design primer-probe pairs for use in isothermal amplification of the S1, ORF3 and ORF8 regions of the SARS-CoV2 virus; (ii) optimize the recombinase polymerase amplification (RPA) assay for the isothermal amplification of the named SARS-COV2 regions; (iii) detect amplification products on a lateral flow device. and (ii) perform a pilot field validation of RPA on RNA extracted from nasopharyngeal swabs. Results: Assay validation was done at the National Reference Lab (NRL) at the Rwanda Biomedical Center (RBC) in Rwanda. Results were compared to an established, WHO-approved rRT-PCR laboratory protocol. The assay provides a faster and cheaper alternative to rRT-PCR with 100% sensitivity, 93% specificity, and positive and negative predictive agreements of 100% and 93% respectively. Conclusion: To the best of our knowledge, this is the first in-field and comparative laboratory validation of RPA for COVID-19 disease in low resource settings. Further standardization will be required for deployment of the RPA assay in field settings. Keywords: Recombinase Polymerase Amplification, COVID-19", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Angus A Nassir", - "author_inst": "Bioinformatics Institute of Kenya" - }, - { - "author_name": "Mazarati Jean Baptiste", - "author_inst": "National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda" - }, - { - "author_name": "Ivan Mwikarago", - "author_inst": "National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda" - }, - { - "author_name": "Majidi R Habimana", - "author_inst": "National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda" - }, - { - "author_name": "Janvier Ndinkabandi", - "author_inst": "University of Rwanda" - }, - { - "author_name": "Anthere Murangwa", - "author_inst": "Rwanda Military Hospital, Kigali, Rwanda" - }, - { - "author_name": "Thiery Nyatanyi", - "author_inst": "National COVID19 Taskforce, Kigali, Rwanda" - }, - { - "author_name": "Claude Mambo Muvunyi", - "author_inst": "University of Rwanda" - }, - { - "author_name": "Sabin Nsanzimana", - "author_inst": "Medical Research Center, Rwanda Biomedical Center, Kigali, Rwanda" - }, - { - "author_name": "Mutesa Leon", - "author_inst": "University of Rwanda" - }, - { - "author_name": "Clarisse Musanabaganwa", - "author_inst": "Medical Research Center, Rwanda Biomedical Center, Kigali, Rwanda" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.17.20196212", "rel_title": "Early Anti-SARS-CoV-2 Convalescent Plasma in Patients Admitted for COVID-19: A Randomized Phase II Clinical Trial", @@ -1196150,6 +1198388,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.16.300871", + "rel_title": "Distinct SARS-CoV-2 Antibody Reactivity Patterns in Coronavirus Convalescent Plasma Revealed by a Coronavirus Antigen Microarray", + "rel_date": "2020-09-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300871", + "rel_abs": "A coronavirus antigen microarray (COVAM) was constructed containing 11 SARS-CoV-2, 5 SARS-1, 5 MERS, and 12 seasonal coronavirus recombinant proteins. The array is designed to measure immunoglobulin isotype and subtype levels in serum or plasma samples against each of the individual antigens printed on the array. We probed the COVAM with COVID-19 convalescent plasma (CCP) collected from 99 donors who recovered from a PCR+ confirmed SARS-CoV-2 infection. The results were analyzed using two computational approaches, a generalized linear model (glm) and Random Forest (RF) prediction model, to classify individual specimens as either Reactive or Non-Reactive against the SARS-CoV-2 antigens. A training set of 88 pre-COVID-19 specimens (PreCoV) collected in August 2019 and102 positive specimens from SARS-CoV-2 PCR+ confirmed COVID-19 cases was used for these analyses. Results compared with an FDA emergency use authorized (EUA) SARS-CoV2 S1-based total Ig chemiluminescence immunoassay (Ortho Clinical Diagnostics VITROS(R) Anti-SARS-CoV-2 Total, CoV2T) and with a SARS-CoV-2 S1-S2 spike-based pseudovirus micro neutralization assay (SARS-CoV-2 reporter viral particle neutralization titration (RVPNT) showed high concordance between the 3 assays. Three CCP specimens that were negative by the VITROS CoV2T immunoassay were also negative by both COVAM and the RVPNT assay. Concordance between VITROS CoV2T and COVAM was 96%, VITROS CoV2T and RVPNT 93%, and RVPNT and COVAM 95%. The discordances were all weakly reactive samples near the cutoff threshold of the VITROS CoV2T immunoassay. The multiplex COVAM allows CCP to be grouped according to antibody reactivity patterns against 11 SARS-CoV-2 antigens. Unsupervised K-means analysis, via the gap statistics, as well as hierarchical clustering analysis revealed 3 main clusters with distinct reactivity intensities and patterns. These patterns were not recapitulated by adjusting the VITROS CoV2T or RVPNT assay thresholds. Plasma classified according to these reactivity patterns may be better associated with CCP treatment efficacy than antibody levels alone. The use of a SARS-CoV-2 antigen array may be useful to qualify CCP for administration as a treatment for acute COVID-19 and to interrogate vaccine immunogenicity and performance in preclinical and clinical studies to understand and recapitulate antibody responses associated with protection from infection and disease.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rafael Ramiro de Assis", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Aarti Jain", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Rie Nakajima", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Algis Jasinskas", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Saahir Khan", + "author_inst": "University of Southern California" + }, + { + "author_name": "Larry J Dumont", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Kathleen Kelly", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Graham Simmons", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Mars Stone", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Clara Di Germanio", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Michael P Busch", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Philip L Felgner", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.16.300319", "rel_title": "A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture", @@ -1197050,29 +1199351,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.16.299362", - "rel_title": "Structure Model Analysis Of Phosphorylation Dependent Binding And Sequestration Of SARS-COV-2 Encoded Nucleocapsid Protein By Protein 14-3-3", - "rel_date": "2020-09-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.299362", - "rel_abs": "Phosphorylation of serines 197 and 206 of SARS-COV-2 Nucleocapsid protein (NCp) enhanced the stability and binding efficiency and sequestration of NCp to Protein 14-3-3 by increasing the Stability Energy ({Delta}Gstability energy) and Binding Energy ({Delta}{Delta}Gbinding energy) from ~545 Kcal/mol to ~616 Kcal/mol, and from 108 Kcal/mol to ~228 Kcal/mol respectively. The calculated Binding Energy Difference ({Delta}{Delta}Gbinding energy difference) between dephospho-NCp-14-3-3 complex and phospho-NCp-13-3-3 complex was ~72 Kcal/mol. Phosphorylations of serines 186, 197, 202 and 206, and threonines 198 and 205 NCp also caused an increase in the Stability Energy ({Delta}Gstability energy) and Binding Energy ({Delta}{Delta}Gbinding energy) from ~545 Kcal/mol to ~617, 616, 583, 580, 574, 564 and 566 Kcal/mol and from ~108 Kcal/mol to ~228, 216, 184, 188, 184, 174 and 112 Kcal/mol respectively. Phosphorylation of NCp on serines 197 and 206 caused a decrease in Stability Energy and Binding Energy from ~698 Kcal/mol to 688 Kcal/mol, and from ~91 Kcal/mol to ~82 Kcal/mol for the dimerization of NCp. These results support the existence of a phosphorylation dependent cellular mechanism to bind and sequester NCp.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "H.Y. Lim Tung", - "author_inst": "Nacbraht Biomedical Research Institute" - }, - { - "author_name": "Pierre Limtung", - "author_inst": "Nacbraht Biomedical Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.09.16.300277", "rel_title": "Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques", @@ -1197968,6 +1200246,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.13.20193896", + "rel_title": "Are we there yet? An adaptive SIR model for continuous estimation of COVID-19 infection rate and reproduction number in the United States", + "rel_date": "2020-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193896", + "rel_abs": "BackgroundThe dynamics of the COVID-19 epidemic vary due to local population density and policy measures. When making decisions, policy makers consider an estimate of the effective reproduction number [R]t which is the expected number of secondary infections by a single infected individual.\n\nObjectiveWe propose a simple method for estimating the time-varying infection rate and reproduction number [R]t.\n\nMethodsWe use a sliding window approach applied to a Susceptible-Infectious-Removed model. The infection rate is estimated using the reported cases for a seven-day window to obtain continuous estimation of [R]t. The proposed adaptive SIR (aSIR) model was applied to data at the state and county levels.\n\nResultsThe aSIR model showed an excellent fit for the number of reported COVID-19 positive cases, a one-day forecast MAPE was less than 2.6% across all states. However, a seven-day forecast MAPE reached 16.2% and strongly overestimated the number of cases when the reproduction number was high and changing fast. The maximal [R]t showed a wide range of 2.0 to 4.5 across all states, with the highest values for New York (4.4) and Michigan (4.5). We demonstrate that the aSIR model can quickly adapt to an increase in the number of tests and associated increase in the reported cases of infections. Our results also suggest that intensive testing may be one of the effective methods of reducing [R]t.\n\nConclusionThe aSIR model provides a simple and accurate computational tool to obtain continuous estimation of the reproduction number and evaluate the efficacy of mitigation measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mark B Shapiro", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Fazle Karim", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Guido Muscioni", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Abel Saju Augustine", + "author_inst": "Anthem, Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.03.20187112", "rel_title": "Treatment with an Anti-CK2 Synthetic Peptide Improves Clinical Response in Covid-19 Patients with Pneumonia. A Randomized and Controlled Clinical Trial", @@ -1198912,65 +1201221,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.14.295956", - "rel_title": "Ceftazidime Is a Potential Drug to Inhibit SARS-CoV-2 Infection In Vitro by Blocking Spike Protein-ACE2 Interaction", - "rel_date": "2020-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.14.295956", - "rel_abs": "Coronavirus Disease 2019 (COVID-19) spreads globally as a sever pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cell entry of SARS-CoV-2 mainly depends on binding of the viral spike (S) proteins to angiotensin converting enzyme 2 (ACE2) on host cells. Therefore, repurposing of known drugs to inhibit S protein-ACE2 interaction could be a quick way to develop effective therapy for COVID-19. Using a high-throughput screening system to investigate the interaction between spike receptor binding domain (S-RBD) and ACE2 extracellular domain, we screened 3581 FDA-approved drugs and natural small molecules and identified ceftazidime as a potent compound to inhibit S-RBD-ACE2 interaction by binding to S-RBD. In addition to significantly inhibit S-RBD binding to HPAEpiC cells, ceftazidime efficiently prevented SARS-CoV-2 pseudovirus to infect ACE2-expressing 293T cells. The inhibitory concentration (IC50) was 113.2 M, which is far below the blood concentration (over 300 M) of ceftazidime in patients when clinically treated with recommended dose. Notably, ceftazidime is a drug clinically used for the treatment of pneumonia with minimal side effects compared with other antiviral drugs. Thus, ceftazidime has both anti-bacterial and anti-SARS-CoV-2 effects, which should be the first-line antibiotics used for the clinical treatment of COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "ChangDong Lin", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "Yue Li", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "MengYa Yuan", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "MengWen Huang", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "Cui Liu", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "Hui Du", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "XingChao Pan", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "YaTing Wen", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - }, - { - "author_name": "Xinyi Xu", - "author_inst": "State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy" - }, - { - "author_name": "Chenqi Xu", - "author_inst": "State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy" - }, - { - "author_name": "JianFeng Chen", - "author_inst": "State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of S" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.15.298067", "rel_title": "Antibody potency, effector function and combinations in protection from SARS-CoV-2 infection in vivo", @@ -1199866,6 +1202116,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.12.20193334", + "rel_title": "Analysis of the interventions adopted due to the COVID-19 on ARI morbility for Colombia", + "rel_date": "2020-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193334", + "rel_abs": "Acute Respiratory Infections are among the leading causes of death globally, particularly in developing countries, and are highly correlated with the quality of health and surveillance systems and effective early interventions in high-risk age groups. According to the World Health Organization, about four million people die each year from mostly preventable respiratory tract infections, making it a public health concern. The official declaration of a pandemic in March 2020 due to the Sars-CoV-2 virus coincided with the influenza season in Colombia and with environmental alerts about low air quality that increase its incidence. The objective of this document is the application of a flexible model for the identification of the pattern and monitoring of ARI morbility for Colombia by age group that shows atypical patterns in the reported series for 5 departments and that coincide with the decisions implemented to contain the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alvaro Quijano-Angarita", + "author_inst": "Instituto de Evaluacion Tecnologica en Salud - IETS" + }, + { + "author_name": "Oscar Espinosa", + "author_inst": "Instituto de Evaluacion Tecnologica en Salud - IETS" + }, + { + "author_name": "Marcela M Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Walteros", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Carolina Malo", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.12.20193409", "rel_title": "Clinical characteristics and outcomes of patients with COVID-19 and ARDS admitted to a third level health institution in Mexico City", @@ -1200522,33 +1202807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.13.20193565", - "rel_title": "AI for radiographic COVID-19 detection selects shortcuts over signal", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193565", - "rel_abs": "Artificial intelligence (AI) researchers and radiologists have recently reported AI systems that accurately detect COVID-19 in chest radiographs. However, the robustness of these systems remains unclear. Using state-of-the-art techniques in explainable AI, we demonstrate that recent deep learning systems to detect COVID-19 from chest radiographs rely on confounding factors rather than medical pathology, creating an alarming situation in which the systems appear accurate, but fail when tested in new hospitals.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Alex J DeGrave", - "author_inst": "University of Washington" - }, - { - "author_name": "Joseph D Janizek", - "author_inst": "University of Washington" - }, - { - "author_name": "Su-In Lee", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.09.10.20190017", "rel_title": "Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India", @@ -1201380,6 +1203638,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.09.20184143", + "rel_title": "The Effect of Early Hydroxychloroquine-based Therapy in COVID-19 Patients in Ambulatory Care Settings: A Nationwide Prospective Cohort Study", + "rel_date": "2020-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20184143", + "rel_abs": "ABSTRACT BACKGROUND: Currently, there is no proven effective therapy nor vaccine for the treatment of SARS-CoV-2. Evidence regarding the potential benefit of early administration of hydroxychloroquine (HCQ) therapy in symptomatic patients with Coronavirus Disease (COVID-19) is not clear. METHODS: This observational prospective cohort study took place in 238 ambulatory fever clinics in Saudi Arabia, which followed the Ministry of Health (MOH) COVID-19 treatment guideline. This guideline included multiple treatment options for COVID-19 based on the best available evidence at the time, among which was Hydroxychloroquine (HCQ). Patients with confirmed COVD-19 (by reverse transcriptase polymerase chain reaction (PCR) test) who presented to these clinics with mild to moderate symptoms during the period from 5-26 June 2020 were included in this study. Our study looked at those who received HCQ-based therapy along with supportive care (SC) and compared them to patients who received SC alone. The primary outcome was hospital admission within 28-days of presentation. The secondary outcome was a composite of intensive care admission (ICU) and/or mortality during the follow-up period. Outcome data were assessed through a follow-up telephonic questionnaire at day 28 and were further verified with national hospitalisation and mortality registries. Multiple logistic regression model was used to control for prespecified confounders. RESULTS: Of the 7,892 symptomatic PCR-confirmed COVID-19 patients who visited the ambulatory fever clinics during the study period, 5,541 had verified clinical outcomes at day 28 (1,817 patients in the HCQ group vs 3,724 in the SC group). At baseline, patients who received HCQ therapy were more likely to be males who did not have hypertension or chronic lung disease compared to the SC group. No major differences were noted regarding other comorbid conditions. All patients were presenting with active complaints; however, the HCQ groups had higher rates of symptoms compared to the SC group (fever: 84% vs 66.3, headache: 49.8 vs 37.4, cough: 44.5 vs 35.6, respectively). Early HCQ-based therapy was associated with a lower hospital admission within 28-days compared to SC alone (9.4% compared to 16.6%, RRR 43%, p-value <0.001). The composite outcome of ICU admission and/or mortality at 28-days was also lower in the HCQ group compared to the SC (1.2% compared to 2.6%, RRR 54%, p-value 0.001). Adjusting for age, gender, and major comorbid conditions, a multivariate logistic regression model showed a decrease in the odds of hospitalisation in patients who received HCQ compared to SC alone (adjusted OR 0.57 [95% CI 0.47-0.69], p-value <0.001). The composite outcome of ICU admission and/or mortality was also lower for the HCQ group compared to the SC group controlling for potential confounders (adjusted OR 0.55 [95% CI 0.34-0.91], p-value 0.019). CONCLUSION: Early intervention with HCQ-based therapy in patients with mild to moderate symptoms at presentation is associated with lower adverse clinical outcomes among COVID-19 patients, including hospital admissions, ICU admission, and/or death.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Tarek Sulaiman", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Abdulrhman Mohana", + "author_inst": "Saudi Center for Disease Prevention and Control" + }, + { + "author_name": "Laila Alawdah", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nagla Mahmoud", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Mustafa Hassanein", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Tariq Wani", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Amel Alfaifi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Eissa Alenazi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nashwa Radwan", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nasser AlKhalifah", + "author_inst": "King Fahad Medical City, Riyadh. Saudi Arabia" + }, + { + "author_name": "Ehab Elkady", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Manwer AlAnazi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Mohammed Alqahtani", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Khalid Abdalla", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Yousif Yousif", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fouad AboGazalah", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fuad Awwad", + "author_inst": "Quantitative analysis department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia" + }, + { + "author_name": "Khaled AlabdulKareem", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fahad AlGhofaili", + "author_inst": "King Fahad Medical City, Riyadh. Saudi Arabia" + }, + { + "author_name": "Ahmed AlJedai", + "author_inst": "Assistant Deputy Minister for Therapeutic Affairs, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Hani Jokhdar", + "author_inst": "Deputyship of Public Health, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fahad Alrabiah", + "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20180521", "rel_title": "On Machine Learning-Based Short-Term Adjustment of Epidemiological Projections of COVID-19 in US", @@ -1201820,85 +1204181,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.12.20186106", - "rel_title": "Cerebral Venous Sinus Thrombosis Associated with SARS-CoV-2; a Multinational Case Series", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20186106", - "rel_abs": "BackgroundSARS-CoV-2 induced coagulopathy can lead to thrombotic complications such as stroke. Cerebral venous sinus thrombosis (CVST) is a less common type of stroke which might be triggered by COVID-19. We present a series of CVST cases with SARS-CoV-2 infection.\n\nMethodsIn a multinational retrospective study, we collected all cases of CVST in SARS-CoV-2 infected patients admitted to nine tertiary stroke centers from the beginning of the pandemic to June 30th, 2020. We compared the demographics, clinical and radiological characteristics, risk factors, and outcome of these patients with a control group of non-SARS-CoV-2 infected CVST patients in the same seasonal period of the years 2012-2016 from the country where the majority of cases were recruited.\n\nResultsA total of 13 patients fulfilled the inclusion criteria (62% women, mean age 50.9{+/-} 11.2 years). Six patients were discharged with good outcomes (mRS[≤]2) and three patients died in hospital. Compared to the control group, the SARS-CoV-2 infected patients were significantly older (50.9 versus 36.7 years, p<0.001), had a lower rate of identified CVST risk factors (23.1% versus 84.2%, p<0.001), had more frequent cortical vein involvement (38.5% versus 10.5%, p: 0.025), and a non-significant higher rate of in-hospital mortality (23.1% versus 5.3%, p: 0.073).\n\nConclusionCVST should be considered as potential comorbidity in SARS-CoV-2 infected patients presenting with neurological symptoms. Our data suggest that compared to non-SARS-CoV-2 infected patients, CVST occurs in older patients, with lower rates of known CVST risk factors and might lead to a poorer outcome in the SARS-CoV-2 infected group.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ashkan Mowla", - "author_inst": "Division of Stroke and Endovascular Neurosurgery, Department of Neurological Surgery, Keck School of Medicine, University of Southern California, California, US" - }, - { - "author_name": "Banafsheh Shakibajahromi", - "author_inst": "Clinical Neurology Research Center, Shiraz University of Medical Sciences" - }, - { - "author_name": "Shima Shahjouei", - "author_inst": "Neurology Department, Neuroscience Institute, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Afshin Borhani-Haghighi", - "author_inst": "Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran" - }, - { - "author_name": "Nasrin Rahimian", - "author_inst": "Neurology Department, Yasrebi Hospital, Kashan, Iran" - }, - { - "author_name": "Humain Baharvahdat", - "author_inst": "Division of Neuroendovascular surgery, Department of Neurosurgery, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran" - }, - { - "author_name": "Soheil Naderi", - "author_inst": "Neurosurgery Department, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Fariborz Khorvash", - "author_inst": "Department of Neurology, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Davar Altafi", - "author_inst": "Department of Neurology, Alavi Hospital, Ardabil University of Medical Sciences, Ardabil, Iran" - }, - { - "author_name": "Seyed Amir Ebrahimzadeh", - "author_inst": "Department of Radiology, Yasrebi Hospital, Kashan, Iran" - }, - { - "author_name": "Ghasem Farahmand", - "author_inst": "Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Alaleh Vaghefi Far", - "author_inst": "Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Vijay K. Sharma", - "author_inst": "Division of Neurology, National University Health System, School of Medicine, National University of Singapore, Singapore" - }, - { - "author_name": "Saeideh Aghayari Sheikh Neshin", - "author_inst": "Neuroscience Research Center, Guilan University of Medical Sciences, Guilan, Iran" - }, - { - "author_name": "Georgios Tsivgoulis", - "author_inst": "Second Department of Neurology, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital, Athens, Greece" - }, - { - "author_name": "Ramin Zand", - "author_inst": "Geisinger Health System" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.09.11.20190520", "rel_title": "SARS2 simplified scores to estimate risk of hospitalization and death among patients with COVID-19", @@ -1203114,6 +1205396,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.10.20192195", + "rel_title": "Mathematical Modeling and a Month Ahead Forecast of the Coronavirus Disease 2019 (COVID-19) Pandemic: An Indian Scenario", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192195", + "rel_abs": "India, the second-most populous country in the world, has been lately witnessing a daily surge in the COVID-19 infected cases. India is currently among the worst-hit nations worldwide, due to the COVID-19 pandemic, and ranks just behind Brazil and USA. In order to prevent the further worsening of the situation, predicting the future course of the pandemic is of utmost importance. In this paper, we model the past trajectory (March 01, 2020 - July 25, 2020) and make a month-long (July 26, 2020 - August 24, 2020) forecast of the future evolution of the COVID-19 pandemic in India using an autoregressive integrated moving average (ARIMA) model. According to our forecasting results, India is likely to have 3,800,989 cumulative infected cases, 1,634,142 cumulative active cases, 2,110,697 cumulative recoveries and 56,150 cumulative deaths by August 24, 2020, if the current trend of the pandemic continues to prevail. The implications of these forecasts are that in the upcoming month the infection rate of COVID-19 in India is going to escalate, while as the rate of recovery and the case-fatality rate is likely to reduce. In order to avert these possible scenarios, the administration and health-care personnel need to formulate and implement robust control measures, while the general public needs to be more responsible and strictly adhere to the established and newly formulated guidelines to slow down the spread of the pandemic and prevent it from transforming into a catastrophe.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Suhail Ganiny", + "author_inst": "National Institute of Technology, Srinagar" + }, + { + "author_name": "Owais Nisar", + "author_inst": "SKUAST-K" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20192450", "rel_title": "Impacts of the COVID-19 epidemic on the department of stomatology in a tertiary hospital: a case study in the General Hospital of the Central Theater Command, Wuhan, China", @@ -1203590,105 +1205895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.10.20179135", - "rel_title": "The influence of pH on SARS-CoV-2 infection and COVID-19 severity", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20179135", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect a broad range of human tissues by using the host receptor angiotensin-converting enzyme 2 (ACE2). Individuals with comorbidities associated with severe COVID-19 display higher levels of ACE2 in the lungs compared to those without comorbidities, and conditions such as cell stress, elevated glucose levels and hypoxia may also increase the expression of ACE2. Here we showed that patients with Barretts esophagus (BE) have a higher expression of ACE2 in BE tissues compared to normal squamous esophagus, and that the lower pH associated with BE may drive this increase in expression. Human primary monocytes cultured in reduced pH displayed increased ACE2 expression and viral load upon SARS-CoV-2 infection. We also showed in two independent cohorts of COVID-19 patients that previous use of proton pump inhibitors is associated with 2- to 3-fold higher risk of death compared to those not using the drugs. Our work suggests that pH has a great influence on SARS-CoV-2 Infection and COVID-19 severity.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Leandro Jimenez", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Ana C Codo", - "author_inst": "University of Campinas" - }, - { - "author_name": "Vanderson S Sampaio", - "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" - }, - { - "author_name": "Antonio E.R. Oliveira", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Lucas KK Ferreira", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Gustavo G Davanzo", - "author_inst": "University of Campinas" - }, - { - "author_name": "Lauar B Monteiro", - "author_inst": "University of Campinas" - }, - { - "author_name": "Joao V Virgilio-da-Silva", - "author_inst": "University of Campinas" - }, - { - "author_name": "Mayla GS Borba", - "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" - }, - { - "author_name": "Gabriela F Souza", - "author_inst": "University of Campinas" - }, - { - "author_name": "Nathalia Zini", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Flora A Gandolfi", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Stefanie P Murano", - "author_inst": "University of Campinas" - }, - { - "author_name": "Jose L Proenca-Modena", - "author_inst": "University of Campinas" - }, - { - "author_name": "Fernando A Val", - "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" - }, - { - "author_name": "Gisely C Melo", - "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" - }, - { - "author_name": "Wuelton M Monteiro", - "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" - }, - { - "author_name": "Mauricio L Nogueira", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Marcus VG Lacerda", - "author_inst": "Fundacao de Medicina Tropical Dr Heitor Vieira Dourado" - }, - { - "author_name": "Pedro M Moraes-Vieira", - "author_inst": "University of Campinas" - }, - { - "author_name": "Helder I Nakaya", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.09.09.20191593", "rel_title": "Title: COVID-19Predict - Predicting Pandemic Trends.", @@ -1204708,6 +1206914,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.11.20192526", + "rel_title": "Increased extravascular lung water index (EVLWI) reflects rapid inflammatory oedema and mortality in COVID-19 associated ARDS", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192526", + "rel_abs": "OBJECTIVENearly 5 % of the patients with COVID-19 develop an acute respiratory distress syndrome (ARDS). Extravascular lung water index (EVLWI) is a marker of pulmonary oedema which is associated with mortality in ARDS. In this study we evaluate whether EVLWI is higher in patients with COVID-19 associated ARDS as compared to controls and whether EVLWI has the potential to monitor disease progression.\n\nMETHODSFrom the day of intubation, EVLWI, cardiac function were monitored by transpulmonary thermodilution in n=25 patients with COVID-19 and compared to a control group of 49 non-COVID-19 ARDS-patients.\n\nRESULTSEVLWI in COVID-19-patients was noticeably elevated and significantly higher than in the control group (17 (11-38) vs. 11 (6-26) mL/kg; p<0.001). High pulmonary vascular permeability index values (2.9 (1.0-5.2) versus 1.9 (1.0-5.2); p=0.003) suggest inflammatory oedema. By contrast, the cardiac parameters SVI, GEF and GEDVI were comparable. High EVLWI values were associated with viral persistence, prolonged intensive care treatment and mortality (23.2{+/-}6.7% vs. 30.3{+/-}6.0%, p=0.025).\n\nCONCLUSIONSCompared to the control group, COVID-19 results in markedly elevated EVLWI-values in patients with ARDS. EVLWI reflects a non-cardiogenic pulmonary oedema in COVID-19 associated ARDS and could serve as parameter to monitor ARDS progression.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sebastian Rasch", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Paul Schmidle", + "author_inst": "Technical University of Munich, School of Medicine, Department of Dermatology and Allergology, Biedersteiner Str. 29, 80802 Munich" + }, + { + "author_name": "Senguel Sancak", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Alexander Herner", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Christina Huberle", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Dominik Schulz", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Ulrich Mayr", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Jochen Schneider", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Christoph Spinner", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Fabian Geisler", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Roland M. Schmid", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Tobias Lahmer", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Wolfgang Huber", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.09.10.20191932", "rel_title": "Evaluating the effects of cardiometabolic exposures on circulating proteins which may contribute to SARS-CoV-2 severity", @@ -1205316,33 +1207589,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.11.20192542", - "rel_title": "Socio-demographic correlate of knowledge and practice toward novel coronavirus among people living in Mosul-Iraq: A cross-sectional study", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192542", - "rel_abs": "Background: Since the World Health Organization (WHO) announced that the 2019 novel coronavirus (2019-nCoV) is a worldwide pandemic, as the Iraqi authorities have started responding and taking action to control the spread of the pandemic. The knowledge and practices of the public play an important role in curbing the spreading of the virus by following the health guidelines. This study aimed to assess the socio-demographic correlate of knowledge and practices of Iraqi living in Mosul-Iraq towards novel coronavirus during its rapid rise. Methods: A cross-sectional online survey of 909 participants was conducted among Mosul-Iraq between 20th June to 1st July 2020. The survey included three parts: 1) socio-demographic characteristics, 2) participants' knowledge, 3) participants' practices. T-test, ANOVA, chi-square, and binary logistic regression were used. A p-value less than 0.05 (p < 0.05) was considered statistically significant. Results: The results showed knowledge and practice mean score of (12.91\\1.67) and (21.56\\2.92) with cumulative knowledge and practice of 86% and 76% respectively towards 2019-nCoV. Socio-demographic characteristics such as age, marital status, gender, level of education and employment were statistically related with a higher mean score of knowledge and practice towards the virus as P<0.05. Conclusions: We concluded that the majority of the respondents demonstrate a high level of knowledge and practices towards 2019-nCoV except respondents with socio-demographic characteristics such as those who were younger, male respondents, those with lower education and those unemployed as such campaigns that will increase the knowledge and encourage adequate preventive practice towards 2019-nCoV should be targeted towards this group.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Balsam Qubais", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Rula mudhafar Al-Shahrabi", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Obasanjo Afolabi Bolarinwa", - "author_inst": "University of KwaZulu-Natal, Durban, South Africa" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.293449", "rel_title": "Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2", @@ -1206254,6 +1208500,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.09.20191700", + "rel_title": "Altered blood cell traits underlie a major genetic locus of severe COVID-19", + "rel_date": "2020-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191700", + "rel_abs": "PurposeThe genetic locus 3p21.31 has been associated with severe coronavirus disease 2019 (COVID-19), but the underlying pathophysiological mechanism is unknown.\n\nMethodsTo identify intermediate traits of the COVID-19 risk variant, we performed a phenome-wide association study (PheWAS) with 923 phenotypes in 310,999 European individuals from UK Biobank. For candidate target genes, we examined associations between their expression and the polygenic score (PGS) of 1,263 complex traits in a meta-analysis of 31,684 blood samples.\n\nResultsOur PheWAS identified and replicated multiple blood cell traits to be associated with the COVID-19 risk variant, including monocyte count and percentage (p = 1.07x10-8, 4.09x10-13), eosinophil count and percentage (p = 5.73x10-3, 2.20x10-3), and neutrophil percentage (p = 3.23x10-3). The PGS analysis revealed positive associations between the expression of candidate genes and genetically predicted counts of specific blood cells: CCR3 with eosinophil and basophil (p = 5.73x10-21, 5.08x10-19); CCR2 with monocytes (p = 2.40x10-10); and CCRl with monocytes and neutrophil (p = 1.78x10-6, 7.17x10-5).\n\nConclusionsMultiple blood cell traits, especially monocyte, eosinophil, and neutrophil numbers, are associated with the COVID-19 risk variant and the expression of its candidate target genes, representing probable mechanistic links between the genetic locus 3p21.31 and severe COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jingqi Zhou", + "author_inst": "University of Georgia" + }, + { + "author_name": "Yitang Sun", + "author_inst": "University of Georgia" + }, + { + "author_name": "Weishan Huang", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Kaixiong Ye", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.08.20190884", "rel_title": "Prison population reductions and COVID-19: A latent profile analysis synthesizing recent evidence from the Texas state prison system", @@ -1206750,49 +1209027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.09.290247", - "rel_title": "rSWeeP: A R/Bioconductor package deal with SWeeP sequences representation", - "rel_date": "2020-09-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.290247", - "rel_abs": "The rSWeeP package is an R implementation of the SWeeP model, designed to handle Big Data. rSweeP meets to the growing demand for efficient methods of heuristic representation in the field of Bioinformatics, on platforms accessible to the entire scientific community. We explored the implementation of rSWeeP using a dataset containing 31,386 viral proteomes, performing phylogenetic and principal component analysis. As a case study we analyze the viral strains closest to the SARS-CoV, responsible for the current pandemic of COVID-19, confirming that rSWeeP can accurately classify organisms taxonomically. rSWeeP package is freely available at https://bioconductor.org/packages/release/bioc/html/rSWeeP.html.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Danrley R. Fernandes", - "author_inst": "Federal University of Parana" - }, - { - "author_name": "Mariane G. Kulik", - "author_inst": "Federal University of Parana" - }, - { - "author_name": "Diogo J. S. Machado", - "author_inst": "Federal University of Parana" - }, - { - "author_name": "Jeroniza N. Marchaukoski", - "author_inst": "Federal University of Parana" - }, - { - "author_name": "Fabio O. Pedrosa", - "author_inst": "Federal University of Parana" - }, - { - "author_name": "Camilla R. De Pierri", - "author_inst": "Federal University of Paran" - }, - { - "author_name": "Roberto Tadeu Raittz", - "author_inst": "Federal University of Parana" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.08.20190603", "rel_title": "Sleep Disturbances, Anxiety, and Burnout during the COVID-19 Pandemic: a nationwide cross-sectional study in Brazilian Healthcare Professionals.", @@ -1207768,6 +1210002,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.07.20188003", + "rel_title": "The Geography of Excess Deaths in England during the Covid-19 pandemic: Longer term impacts and monthly dynamics", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20188003", + "rel_abs": "Physical social interaction relevant to the spread of infectious diseases occurs, by its nature, at a local level. If infection and related mortality are associated with social background, it is therefore natural to study variation in them in relation to the social composition of local areas. The first part of the paper studies the geographical impact of Covid-19 infection on age-standardised sex-specific excess death rates during the peak months of the pandemic so far, March through May 2020. The second part examines monthly mortality dynamics in relation to predictions from a spatial SIR (Susceptible, Infected, Recovered) model of infection introduced by Bisin and Moro (2020). The analysis indicates that during the peak months of the Covid-19 pandemic, a larger non-white population and higher social deprivation in an area were associated with higher excess mortality, particularly among men. Regarding dynamics, higher population density accelerated the growth in mortality during the upsurge in infection and increased its rate of decline after the peak of the epidemic, thereby producing a more peaked mortality profile. There is also evidence of a slower post-peak decline in mortality in more socially deprived areas but a more rapid decline in areas with a larger non-white population.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Richard Breen", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Ermisch", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.04.20188235", "rel_title": "Trend prediction of COVID-19 based on ARIMA model in mainland of China", @@ -1208596,33 +1210853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.09.07.20189936", - "rel_title": "Self-learning on COVID-19 among medical students and their preparedness to participate in government's COVID-19 response in Bhutan: a cross-sectional study", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189936", - "rel_abs": "BackgroundBhutan lacks a medical school and all their medical students are trained outside in Sri Lanka, Bangladesh and India. When the COVID-19 pandemic let to closure of medical schools in these countries, the Bhutanese medical students were repatriated in March-April 2020. Upon return, they were kept in government-sponsored facility quarantine for 21 days. This study assessed their knowledge on COVID-19 as a part of self-learning and attitude as part of preparedness towards participation in governments health response to COVID-19.\n\nMethodThis was a cross-sectional study among medical students who had returned to the country. This survey was conducted through an online questionnaire while the students were in 21-day facility quarantine. The sample size calculated was 129 and a convenient sampling was used. Knowledge was assessed using 20 questions, each scored 1/20. Cumulative score of score of [≥]80% was categorized as \"good knowledge\", score of [≥]60 - 79% was considered \"satisfactory knowledge\", and score < 60% was considered \"poor knowledge.\" Correlation between knowledge score and duration of clinical clerkship was tested using Pearsons correlation coefficient. Attitude of students towards their willingness to participate in the national COVID-19 response were tested using rating scales. Data were analysed using Stata 13.1.\n\nResults120 medical students responded to this survey (response rate = 93%). Eighty-eight (74%) had good knowledge, 28 (23%) had satisfactory knowledge and only four (3%) had poor knowledge on COVID-19. The students scored high on the symptomatology, mode of transmission, prevention and treatment options and on local epidemiology; and scored low on the forms of mechanical ventilations and on the home-management of non-critical cases. The knowledge score correlated with duration of clinical clerkship (r = 0.326, p = 0.001). The primary source of information were social media sites (102, 85%), television (94, 78%) and newspapers (76, 63%). The majority (78, 65%) were willing to participate in the governments COVID-19 response but could not identify what roles they could play. The fear of contracting COVID-19 was reported in only in 8.7%.\n\nConclusionsThe medical students had good knowledge on COVID-19 and were self-learned through social media, television and newspapers. The students held positive attitude towards participation in the governments COVID-19 response.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Thinley Dorji", - "author_inst": "Jigme Dorji Wangchuck National Referral Hospital" - }, - { - "author_name": "Saran Tenzin Tamang", - "author_inst": "Faculty of Postgraduate Medicine, Khesar Gyalpo University of Medical Sciences of Bhutan, Thimphu" - }, - { - "author_name": "TVSVGK Tilak", - "author_inst": "Armed Forces Medical College, Maharashtra University of Health Sciences, India" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.09.08.20187559", "rel_title": "The role of NIH funding in vaccine readiness; foundational research and NIH funding underlying candidate SARS-CoV-2 vaccines", @@ -1209418,6 +1211648,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.08.20190397", + "rel_title": "The impact of COVID-19 restriction measures on loneliness among older adults in Austria", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190397", + "rel_abs": "BackgroundTo halt the spread of COVID-19, Austria implemented a 7-week shut-down of public life in March/April 2020 which was followed by a gradual withdrawal of these restriction measures in May/June 2020. We expect that the ensuing reduction in social contacts led to increased loneliness among older adults (60+).\n\nMethodsWe conducted three analyses to assess the association between COVID-19 public health restriction measures and loneliness: (1) A comparison between pre-pandemic (SHARE: 2013-2017) and pandemic (May 2020) levels of loneliness (UCLA-3 scale), (2) an analysis of the correlation between being affected by COVID-19 restriction measures and loneliness based on cross-sectional survey data from early May 2020, and (3) a longitudinal analysis of weekly changes in loneliness (Corona panel data) from late March to early June 2020.\n\nResultsWe found (1) loneliness levels to have increased in 2020 in comparison with previous years, (2) an association between the number of restriction measures older adults reported to be affected from and loneliness, and (3) that loneliness was higher during shut-down compared to the subsequent re-opening phase, particularly among those who live alone.\n\nDiscussionOur results provide evidence that COVID-19 restriction measures in Austria have indeed resulted in increased levels of loneliness among older adults. However, these effects seem to be short-lived, and thus we do not expect strong negative consequences for older adults mental health downstream. Nonetheless, effects of longer and/or repeated future restriction measures aiming at social distancing should be closely monitored.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Erwin Stolz", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Hannes Mayerl", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Wolfgang Freidl", + "author_inst": "Medical University of Graz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.08.20190470", "rel_title": "Modelling the epidemic growth of preprints on COVID-19 and SARS-CoV-2", @@ -1210110,125 +1212367,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.09.289892", - "rel_title": "Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions", - "rel_date": "2020-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.289892", - "rel_abs": "Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Chandni Radhakrishnan", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Mohit Kumar Divakar", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Abhinav Jain", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Prasanth Viswanathan", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Rahul C. Bhoyar", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Bani Jolly", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Mohamed Imran", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Disha Sharma", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Mercy Rophina", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Gyan Ranjan", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Beena Philomina Jose", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Rajendran Vadukkoot Raman", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Thulaseedharan Nallaveettil Kesavan", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Kalpana George", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Sheela Mathew", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Jayesh Kumar Poovullathil", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Sajeeth Kumar Keeriyatt Govindan", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Priyanka Raveendranadhan Nair", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Shameer Vadekkandiyil", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Vineeth Gladson", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Midhun Mohan", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Fairoz Cheriyalingal Parambath", - "author_inst": "Government Medical College, Kozhikode, Medical College PO, Kozhikode Kerala, INDIA" - }, - { - "author_name": "Mohit Mangla", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Afra Shamnath", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Sridhar Sivasubbu", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - }, - { - "author_name": "Vinod Scaria", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, INDIA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.09.09.289488", "rel_title": "Candidate screening of host cell membrane proteins involved in SARS-CoV-2 entry", @@ -1211388,6 +1213526,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.06.20189480", + "rel_title": "Antibody Responses to SARS-CoV-2 in Coronavirus Diseases 2019 Patients with Different Severity", + "rel_date": "2020-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189480", + "rel_abs": "BackgroundMore understanding of antibody responses in the SARS-CoV-2 infected population is useful for vaccine development.\n\nAimTo investigate SARS-CoV-2 IgA and IgG among COVID-19 Thai patients with different severity.\n\nMethodsWe used plasma from 118 adult patients who have confirmed SARS-CoV-2 infection and 49 patients under investigation without infection, 20 patients with other respiratory infections, and 102 healthy controls. Anti-SARS-CoV-2 IgA and IgG were performed by enzyme-linked immunosorbent assay from Euroimmun. The optical density ratio cut off for positive test was 1.1 for IgA and 0.8 for IgG. The association of antibody response with the severity of diseases and the day of symptoms was performed.\n\nResultsFrom Mar 10 to May 31, 2020, 289 participants were enrolled, and 384 samples were analyzed. Patients were categorized by clinical manifestations to mild (n = 59), moderate (n = 27) and severe (n = 32). The overall sensitivity of IgA and IgG from samples collected after day 7 is 87.9% (95% CI 79.8-93.6) and 84.8% (95% CI 76.2-91.3), respectively. The severe group had a significantly higher level of specific IgA and IgG to S1 antigen compared to the mild group. All moderate to severe patients have specific IgG while 20% of the mild group did not have any IgG detected after two weeks. Interestingly, SARS-CoV-2 IgG level was significantly higher in males compared to females among the severe group (p = 0.003).\n\nConclusionThe serologic test for SARS-CoV-2 has high sensitivity after the second week after onset of illness. Serological response differs among patients with different severity and different sex.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ekasit Kowitdamrong", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Thanyawee Puthanakit", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Watsamon Jantarabenjakul", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Eakachai Prompetchara", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Pintip Suchartlikitwong", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Opass Putcharoen", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Nattiya Hirankarn", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.05.20188821", "rel_title": "Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis", @@ -1211964,1077 +1214145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.03.20187252", - "rel_title": "Convalescent plasma in the management of moderate COVID-19 in India: An open-label parallel-arm phase II multicentre randomized controlled trial (PLACID Trial)", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187252", - "rel_abs": "ObjectivesConvalescent plasma (CP) as a passive source of neutralizing antibodies and immunomodulators is a century-old therapeutic option used for the management of viral diseases. We investigated its effectiveness for the treatment of COVID-19.\n\nDesignOpen-label, parallel-arm, phase II, multicentre, randomized controlled trial.\n\nSettingThirty-nine public and private hospitals across India.\n\nParticipantsHospitalized, moderately ill confirmed COVID-19 patients (PaO2/FiO2: 200-300 or respiratory rate > 24/min and SpO2 [≤] 93% on room air).\n\nInterventionParticipants were randomized to either control (best standard of care (BSC)) or intervention (CP + BSC) arm. Two doses of 200 mL CP was transfused 24 hours apart in the intervention arm.\n\nMain Outcome MeasureComposite of progression to severe disease (PaO2/FiO2< 100) or all-cause mortality at 28 days post-enrolment.\n\nResultsBetween 22nd April to 14th July 2020, 464 participants were enrolled; 235 and 229 in intervention and control arm, respectively. Composite primary outcome was achieved in 44 (18.7%) participants in the intervention arm and 41 (17.9%) in the control arm [aOR: 1.09; 95% CI: 0.67, 1.77]. Mortality was documented in 34 (13.6%) and 31 (14.6%) participants in intervention and control arm, respectively [aOR) 1.06 95% CI: -0.61 to 1.83].\n\nInterpretationCP was not associated with reduction in mortality or progression to severe COVID-19. This trial has high generalizability and approximates real-life setting of CP therapy in settings with limited laboratory capacity. A priori measurement of neutralizing antibody titres in donors and participants may further clarify the role of CP in management of COVID-19.\n\nTrial registrationThe trial was registered with Clinical Trial Registry of India (CTRI); CTRI/2020/04/024775.", - "rel_num_authors": 264, - "rel_authors": [ - { - "author_name": "Anup Agarwal", - "author_inst": "Clinical Trial & Health Systems Research Unit, Indian Council of Medical Research (ICMR), New Delhi, India" - }, - { - "author_name": "Aparna Mukherjee", - "author_inst": "Clinical Trial & Health Systems Research Unit, Indian Council of Medical Research (ICMR), New Delhi, India" - }, - { - "author_name": "Gunjan Kumar", - "author_inst": "Clinical Trial & Health Systems Research Unit, Indian Council of Medical Research (ICMR), New Delhi, India" - }, - { - "author_name": "Pranab Chatterjee", - "author_inst": "Scientist B, Translational Global Health Policy and Research Cell, Indian Council of Medical Research (ICMR), New Delhi, India" - }, - { - "author_name": "Tarun Bhatnagar", - "author_inst": "ICMR School of Public Health, Indian Council of Medical Research -National Institute of Epidemiology, Chennai, Tamil Nadu, India" - }, - { - "author_name": "Pankaj Malhotra", - "author_inst": "Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India" - }, - { - "author_name": "B Latha", - "author_inst": "Department of Transfusion Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "Sunita Bundas", - "author_inst": "Department of Immunohaematology and Transfusion Medicine, SMS Medical College and Hospital, Jaipur, Rajasthan, India" - }, - { - "author_name": "Vivek Kumar", - "author_inst": "Dept. of Critical Care Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Ravi Dosi", - "author_inst": "Department of Respiratory Medicine, Sri Aurobindo Institute of Medical Sciences, Indore, Madhya Pradesh, India" - }, - { - "author_name": "Janak Kumar Khambholja", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Rosemarie de Souza", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Raja Rao Mesipogu", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Hyderabad, Telangana, India" - }, - { - "author_name": "Saurabh Srivastava", - "author_inst": "Department of Internal Medicine, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India" - }, - { - "author_name": "Simmi Dube", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "Kiran Chaudhary", - "author_inst": "Department of Transfusion Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Subash S", - "author_inst": "Department of Transfusion Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "S. Anbuselvi Mattuvar K", - "author_inst": "Department of Physiology, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "V Rajendran", - "author_inst": "Department of Internal Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "A Sundararajaperumal", - "author_inst": "Department of Thoracic Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "P Balamanikandan", - "author_inst": "Department of Internal Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "R S Uma Maheswari", - "author_inst": "Department of Internal Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "R Jayanthi", - "author_inst": "Department of Internal Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "S Ragunanthanan", - "author_inst": "Department of Internal Medicine, Madras Medical College, Chennai, Tamil Nadu, India" - }, - { - "author_name": "Sudhir Bhandari", - "author_inst": "Department of Internal Medicine, SMS Medical College and Hospital, Jaipur, Rajasthan, India" - }, - { - "author_name": "Ajeet Singh", - "author_inst": "Department of Internal Medicine, SMS Medical College and Hospital, Jaipur, Rajasthan, India" - }, - { - "author_name": "Ashok Pal", - "author_inst": "Department of Immunohaematology and Transfusion Medicine, SMS Medical College and Hospital, Jaipur, Rajasthan, India" - }, - { - "author_name": "Anjali Handa", - "author_inst": "Department of Immunohaematology and Transfusion Medicine, SMS Medical College and Hospital, Jaipur, Rajasthan, India" - }, - { - "author_name": "Govind Rankawat", - "author_inst": "Department of Internal Medicine, SMS Medical College and Hospital, Jaipur, Rajasthan, India" - }, - { - "author_name": "Ketan Kargirwar", - "author_inst": "Dept. of Critical Care Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Joyce Regi", - "author_inst": "Dept. of Transfusion Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Darshana Rathod", - "author_inst": "Dept. of Critical Care Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Edwin Pathrose", - "author_inst": "Dept. of Critical Care Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Nirankar Bhutaka", - "author_inst": "Dept. of Critical Care Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Mayur H Patel", - "author_inst": "Dept. of Critical Care and Emergency Medicine, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Rahul J Verma", - "author_inst": "Dept. of Academics and Research, Sir H N Reliance Foundation Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Kamal Malukani", - "author_inst": "Department of Pathology, Sri Aurobindo Institute of Medical Sciences, Indore, Madhya Pradesh, India" - }, - { - "author_name": "Shivani Patel", - "author_inst": "Department of Hematology, Sri Aurobindo Institute of Medical Sciences, Indore, Madhya Pradesh, India" - }, - { - "author_name": "Apurv Thakur", - "author_inst": "Department of Community Medicine, Sri Aurobindo Institute of Medical Sciences, Indore, Madhya Pradesh, India" - }, - { - "author_name": "Satish Joshi", - "author_inst": "Department of Pathology, Sri Aurobindo Institute of Medical Sciences, Indore, Madhya Pradesh, India" - }, - { - "author_name": "Rashmi Kulkarni", - "author_inst": "Department of Forensic Medicine, Sri Aurobindo Institute of Medical Sciences, Indore, Madhya Pradesh, India" - }, - { - "author_name": "Nilay N Suthar", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Nehal M Shah", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Hemang M Purohit", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Cherry K Shah", - "author_inst": "Department of Pathology, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Monila N Patel", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Saket Shah", - "author_inst": "Department of Hematology, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Smit H Shah", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Tehsim Memon", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Vishal R Beriwala", - "author_inst": "Department of Internal Medicine, Smt NHL Municipal Medical College, Ahmedabad, Gujarat, India" - }, - { - "author_name": "Kusum Jashnani", - "author_inst": "Department of Pathology, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Fatema Ezzy", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Simran Agrawal", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Rakesh Bhadade", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Atish M N", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Tushar Madke", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Vikash Kavishwar", - "author_inst": "Department of Internal Medicine, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Ramesh Waghmare", - "author_inst": "Department of Pathology, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "Nitin Valvi", - "author_inst": "Department of Pathology, BYL Nair Charitable Hospital & TN Medical College, Mumbai, Maharashtra, India" - }, - { - "author_name": "B Thrilok Chander", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "A Vinaya Sekhar", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "Akhilesh Kumar Maurya", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "K Hemanth", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "K Nagamani", - "author_inst": "Department of Microbiology, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "K Sudha", - "author_inst": "Department of Blood Bank, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "T Ravi Chandra", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "K Tushara Rao", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "J Vyshnavi", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Secunderabad, Telangana, India" - }, - { - "author_name": "Rashmi Upadhyay", - "author_inst": "Department of Pulmonary Medicine, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India" - }, - { - "author_name": "Shalini Bahadur", - "author_inst": "Department of Pathalogy, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India" - }, - { - "author_name": "Rambha Pathak", - "author_inst": "Department of Community Medicine, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India" - }, - { - "author_name": "Shikha Seth", - "author_inst": "Department of Obstetrics and Gynecology, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India" - }, - { - "author_name": "Rakesh Gupta", - "author_inst": "Department of Pediatrics, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh, India" - }, - { - "author_name": "Rita Saxena", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "Preksha Dwivedi", - "author_inst": "Department of Internal Medicine, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "Reeni Malik", - "author_inst": "Department of Pathology Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "Deepti Chourasia", - "author_inst": "Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "Jaya Lalwani", - "author_inst": "Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "UM Sharma", - "author_inst": "Department of Pathology, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "JL Marko", - "author_inst": "Department of Pharmacology, Gandhi Medical College, Bhopal, Madhya Pradesh, India" - }, - { - "author_name": "Amit Suri", - "author_inst": "Department of Pulmonary Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Vijay Kumar", - "author_inst": "Department of Pathology, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Rajnish Kaushik", - "author_inst": "Department of Pulmonary Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Parul Kodan", - "author_inst": "Department of Internal Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Bhabani Prasad Acharya", - "author_inst": "Department of Community Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Kuldeep Kumar Gaur", - "author_inst": "Department of Internal Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Anubhav Gupta", - "author_inst": "Department of Transfusion Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Prerna Sachdeva", - "author_inst": "Department of Transfusion Medicine, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Shruti Dogra", - "author_inst": "Department of Pathology, Atal Bihari Vajpayee Institute of Medical Sciences and Ram Manohar Lohia Hospital, New Delhi, India" - }, - { - "author_name": "Aikaj Jindal", - "author_inst": "Department of Transfusion Medicine, Satguru Partap Singh Hospitals, Ludhiana, Punjab, India" - }, - { - "author_name": "M Joseph John", - "author_inst": "Department of Clinical Hematology, Christian Medical College, Ludhiana, Punjab, India" - }, - { - "author_name": "Avtar Singh Dhanju", - "author_inst": "Department of Internal Medicine, Government Medical College, Amritsar, Punjab, India" - }, - { - "author_name": "Ranjana Khetrepal", - "author_inst": "Department of Anesthesia, Government Medical College, Amritsar, Punjab, India" - }, - { - "author_name": "Neeraj Sharma", - "author_inst": "Department of Transfusion, Government Medical College, Amritsar, Punjab, India" - }, - { - "author_name": "Neetu Kukar", - "author_inst": "Department of Immunohematology and Blood Transfusion, Guru Gobind Singh Medical College and Hospital, Faridkot, Punjab, India" - }, - { - "author_name": "Divya Kavita", - "author_inst": "Department of Anaesthesia, Guru Gobind Singh Medical College and Hospital, Faridkot, Punjab, India" - }, - { - "author_name": "Rajesh Kumar", - "author_inst": "Department of Immunohematology and Blood Transfusion, Dayanand Medical College and Hospital, Ludhiana, Punjab, India" - }, - { - "author_name": "Rajesh Mahajan", - "author_inst": "Department of Internal Medicine, Dayanand Medical College and Hospital, Ludhiana, Punjab, India" - }, - { - "author_name": "Gurpreet Singh", - "author_inst": "Department of Respiratory Medicine, Satguru Partap Singh Hospitals, Ludhiana, Punjab, India" - }, - { - "author_name": "Jaspreet Kaur", - "author_inst": "Department of Microbiology, Satguru Partap Singh Hospitals, Ludhiana, Punjab, India" - }, - { - "author_name": "Raminder Pal Singh", - "author_inst": "Department of Internal Medicine, Government Medical College, Patiala, Punjab, India" - }, - { - "author_name": "Rajni Bassi", - "author_inst": "Department of Transfusion Medicine, Government Medical College, Patiala, Punjab, India" - }, - { - "author_name": "Swapneil Parikh", - "author_inst": "Department of Infectious Diseases, Kasturba Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Om Shrivastav", - "author_inst": "Department of Infectious Diseases, Kasturba Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Jayanthi Shastri", - "author_inst": "Department of Microbiology, Kasturba Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Maherra Desai", - "author_inst": "Clinical Research Department, Kasturba Hospital, Mumbai, Maharashtra, India" - }, - { - "author_name": "Shreevatsa Udupa", - "author_inst": "Clinical Research Department, Kasturba Hospital, Mumbai, Maharashtra, India" - 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"author_inst": "Department of Community Medicine Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - }, - { - "author_name": "Sonali Salvi", - "author_inst": "Department of Internal Medicine, Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - }, - { - "author_name": "Nalini Kadgi", - "author_inst": "Department of Pathology, Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - }, - { - "author_name": "Shashikala Sangle", - "author_inst": "Department of Internal Medicine, Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - }, - { - "author_name": "Leena Nakate", - "author_inst": "Department of Pathology, Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - }, - { - "author_name": "Samir Joshi", - "author_inst": "Department of E.N.T., Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - }, - { - "author_name": "Rajesh Karyakarte", - "author_inst": "Department of Microbiology, Byramjee Jeejeebhoy Medical College, Pune, Maharashtra, India" - 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"author_inst": "Department of Internal Medicine, Smt. 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"author_inst": "Department of Internal Medicine, Karnataka Institute of Medical Sciences, Hubballi, Karnataka, India" - }, - { - "author_name": "Medini S", - "author_inst": "Department of Internal Medicine, Karnataka Institute of Medical Sciences, Hubballi, Karnataka, India" - }, - { - "author_name": "Mohith HN", - "author_inst": "Department of Internal Medicine, Karnataka Institute of Medical Sciences, Hubballi, Karnataka, India" - }, - { - "author_name": "Anil Gurtoo", - "author_inst": "Department of Internal Medicine, Lady Hardinge Medical College, New Delhi, India" - }, - { - "author_name": "Ritika Sud", - "author_inst": "Department of Internal Medicine, Lady Hardinge Medical College, New Delhi, India" - }, - { - "author_name": "Sangeeta Pahuja", - "author_inst": "Department of Transfusion Medicine, Lady Hardinge Medical College, New Delhi, India" - }, - { - "author_name": "Anupam Prakash", - "author_inst": "Department of Internal Medicine, Lady Hardinge Medical College, New Delhi, India" - 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"author_inst": "Blood Center & Transplant Immunology Lab, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India" - }, - { - "author_name": "Ashish Jain", - "author_inst": "Department of Respiratory Medicine, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India" - }, - { - "author_name": "Shweta Sharma", - "author_inst": "Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India" - }, - { - "author_name": "Puneet Rijhwani", - "author_inst": "Department of Internal Medicine, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India" - }, - { - "author_name": "Naveen Gupta", - "author_inst": "Department of Clinical Hematology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India" - }, - { - "author_name": "Tinkal C Patel", - "author_inst": "Department of Internal Medicine, Government Medical College, Surat, Gujarat, India" - 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"author_inst": "Department of Transfusion Medicine, Sri Venkateswra Institute of Medical Sciences, Tirupati, Andhra Pradesh, India" - }, - { - "author_name": "B Suresh Babu", - "author_inst": "Department of Transfusion Medicine, Sri Venkateswra Institute of Medical Sciences, Tirupati, Andhra Pradesh, India" - }, - { - "author_name": "Alladi Mohan", - "author_inst": "Department of Internal Medicine, Sri Venkateswra Institute of Medical Sciences, Tirupati, Andhra Pradesh, India" - }, - { - "author_name": "B Vengamma", - "author_inst": "Department of Neurology, Sri Venkateswra Institute of Medical Sciences,Tirupati, Andhra Pradesh, India" - }, - { - "author_name": "K Chandra Sekhar", - "author_inst": "Department of Internal Medicine, Sri Venkateswra Institute of Medical Sciences,Tirupati, Andhra Pradesh, India" - }, - { - "author_name": "Srinivasulu Damam", - "author_inst": "Department of Internal Medicine, Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "K Narsimhulu", - "author_inst": "Department of Internal Medicine, Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "C Aparna", - "author_inst": "Department of Pathology, Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "G Baleswari", - "author_inst": "Professor, Department of Pathology, Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Ravindranath Reddy K", - "author_inst": "Professor, Department of Internal Medicine, Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "P Chandrasekhar", - "author_inst": "Department of Cardiology, Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Sunil Jodharam Panjwani", - "author_inst": "Department of Internal Medicine, Government Medical College, Bhavnagar, Gujarat, India" - }, - { - "author_name": "Pankaj J Akholkar", - "author_inst": "Department of Internal Medicine, Government Medical College, Bhavnagar, Gujarat, India" - 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}, - { - "author_name": "Gururaj Deshpande", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Sharda Sharma", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Rashmi Gunjikar", - "author_inst": "Senior Technical Officer, Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Anita Shete", - "author_inst": "Maximum Containment Laboratory, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Darpan Phagiwala", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Chetan Patil", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Snehal Shingade", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Kajal Jarande", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Himanshu Kaushal", - "author_inst": "Human Influenza Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Pragya Yadav", - "author_inst": "Maximum Containment Laboratory, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Gajanan Sapkal", - "author_inst": "Diagnostic Virology Group, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - }, - { - "author_name": "Priya Abraham", - "author_inst": "Director, Indian Council of Medical Research, National Institute Virology, Pune, Maharashtra, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.04.20188169", "rel_title": "In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-\u03b2-dominated adaptive immune response", @@ -1214246,6 +1215356,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.09.04.20185645", + "rel_title": "Predicting illness trajectory and hospital resource utilization of COVID-19 hospitalized patients - a nationwide study", + "rel_date": "2020-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20185645", + "rel_abs": "BackgroundThe spread of COVID-19 has led to a severe strain on hospital capacity in many countries. There is a need for a model to help planners assess expected COVID-19 hospital resource utilization.\n\nMethodsRetrospective nationwide cohort study following the day-by-day clinical status of all hospitalized COVID-19 patients in Israel from March 1st to May 2nd, 2020. Patient clinical course was modelled with a machine learning approach based on a set of multistate Cox regression-based models with adjustments for right censoring, recurrent events, competing events, left truncation, and time-dependent covariates. The model predicts the patients entire disease course in terms of clinical states, from which we derive the patients hospital length-of-stay, length-of-stay in critical state, the risk of in-hospital mortality, and total and critical care hospital-bed utilization. Accuracy assessed over eight cross-validation cohorts of size 330, using per-day Mean Absolute Error (MAE) of predicted hospital utilization averaged over 64 days; and area under the receiver operating characteristics (AUROC) for individual risk of critical illness and in-hospital mortality, assessed on the first day of hospitalization. We present predicted hospital utilization under hypothetical incoming patient scenarios.\n\nFindingsDuring the study period, 2,703 confirmed COVID-19 patients were hospitalized in Israel. The per-day MAEs for total and critical-care hospital-bed utilization, were 4{middle dot}72 {+/-} 1{middle dot}07 and 1{middle dot}68 {+/-} 0{middle dot}40 respectively; the AUROCs for prediction of the probabilities of critical illness and in-hospital mortality were 0{middle dot}88 {+/-} 0{middle dot}04 and 0{middle dot}96 {+/-} 0{middle dot}04, respectively. We further present the impact of several scenarios of patient influx on healthcare system utilization, and provide an R software package for predicting hospital-bed utilization.\n\nInterpretationWe developed a model that, given basic easily obtained data as input, accurately predicts total and critical care hospital utilization. The model enables evaluating the impact of various patient influx scenarios on hospital utilization and planning ahead of hospital resource allocation.\n\nFundingThe work was funded by the Israeli Ministry of Health. M.G. received support from the U.S.-Israel Binational Science Foundation (BSF, 2016126).\n\nO_TEXTBOXResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCOVID19 outbreaks are known to lead to severe case load in hospital systems, stretching resources, partially due to the long hospitalizations needed for some of the patients. There is a crucial need for tools helping planners assess future hospitalization load, taking into account the specific characteristics and heterogeneity of currently hospitalized COVID19 patients, as well as the characteristics of incoming patients. We searched PubMed for articles published up to September 9, 2020, containing the words \"COVID19\" and combinations of \"hospital\", \"utilization\", \"resource\", \"capacity\" and \"predict\". We found 145 studies; out of them, several included models that predict the future trend of hospitalizations using compartment models (e.g. SIR models), or by using exponential or logistic models. We discuss two of the more prominent ones, which model explicitly the passage of patients through the ICU. These models (i) do not take into account individual patient characteristics; (ii) do not consider length-of-stay heterogeneity, despite the fact that bed utilization is in part determined by a long tail of patients requiring significantly longer stays than others; (iii) do not correct for competing risks bias. We further searched for studies containing the words \"COVID19\" and \"multistate\", and \"COVID19\" and \"length\" and \"stay\". Out of 317 papers, we found two using multistate models focusing only on patients undergoing ECMO treatment.\n\nAdded value of this studyWe present the first model predicting hospital load based on the individual characteristics of hospitalized patients: age, sex, clinical state, and time already spent in-hospital. We combine this with scenarios for incoming patients, allowing for variations by age, sex and clinical state. The models precise predictions are based on a large sample of complete, day-by-day disease trajectories of patients, with a full coverage of the entire COVID-19 hospitalized population in Israel up to early May, 2020 (n =2, 703). We provide the model, as well as software for fitting such a model to local data, and an anonymized version of the dataset used to create the model.\n\nImplications of all the available evidenceAccurate predictions for hospital utilization can be made based on easy to obtain patient data: age, sex, and patient clinical state (moderate, severe or critical). The model allows hospital-and regional-level planners to allocate resources in a timely manner, preparing for different patient influx scenarios.\n\nC_TEXTBOX", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Michael Roimi", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Rom Gutman", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Jonathan Somer", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Asaf Ben Arie", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Ido Calman", + "author_inst": "Independent" + }, + { + "author_name": "Yaron Bar-Lavie", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Udi Gelbshtein", + "author_inst": "Israel Ministry of Health" + }, + { + "author_name": "Sigal Liverant-Taub", + "author_inst": "Israel Ministry of Health" + }, + { + "author_name": "Arnona Ziv", + "author_inst": "Gertner Institute for Epidemiology and Health Policy Research" + }, + { + "author_name": "Danny Eytan", + "author_inst": "Technion - Israel Institute of Technology and Rambam Health Care Campus" + }, + { + "author_name": "Malka Gorfine", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Uri Shalit", + "author_inst": "Technion - Israeli Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.09.04.20184523", "rel_title": "MOLECULAR EPIDEMIOLOGY TO UNDERSTAND THE SARS-CoV-2 EMERGENCE IN THE BRAZILIAN AMAZON REGION", @@ -1214870,33 +1216043,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.04.20187914", - "rel_title": "Social capital and psychological distress during Colombian coronavirus disease lockdown", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187914", - "rel_abs": "IntroductionThis study aims to establish the association between low capital social (CS) with some indicators of psychological distress.\n\nMethodsA cross-sectional study was carried out using an online questionnaire that evaluated demographic variables, social capital, coronavirus disease perceived stress, depression risk, insomnia risk, and suicide risk. SC was taken as an independent variable, and symptoms indicating psychological distress was handed as dependent variables. Odds ratios (OR) were established with 95% confidence intervals (CI), using binary logistic regression analysis.\n\nResultsA group of 700 adults participated in the survey; they were aged between 18 and 76 years (M = 37, SD = 13). Low SC was associated with depression risk (OR = 2.00, 95%CI 1.34-2.97), elevated suicide risk (OR = 2.62, 95%CI 1.40-4.91) high perceived stress related to coronavirus disease (OR = 2.08, 95%CI 1.15-3.76), and insomnia risk (OR = 2.42, 95%CI 1.69-3.47).\n\nConclusionsLow CS was associated with indicators of psychological distress represented in depression risk, elevated suicide risk, high perceived stress related to coronavirus disease and insomnia risk. SC is a community social resource that could help mitigate the impact of the coronavirus disease quarantine amidst the Colombian populations psychological health. It is necessary to deepen the SC role in psychological well-being during and after the coronavirus disease epidemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Carmen Cecilia Caballero-Dominguez", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - }, - { - "author_name": "Jeimmy De Luque-Salcedo", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - }, - { - "author_name": "Adalberto Campo-Arias", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.09.05.20187435", "rel_title": "The dichotomous and incomplete adaptive immunity in COVID-19", @@ -1215984,6 +1217130,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.09.03.20187757", + "rel_title": "The role of school reopening in the spread of COVID-19", + "rel_date": "2020-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187757", + "rel_abs": "Many countries chose to close schools as part of their response to the SARS-CoV2 coronavirus (COVID-19) pandemic. Whilst nations are gradually reopening schools, and many politicians advise that schools remain safe and the risks of increases in the spread of COVID-19 are low, little evidence has been presented to confirm those statements.\n\nA review of the numbers of new confirmed COVID-19 cases by country suggests that the reopening of schools is likely to be a driver in the increase of the number of new cases. This is likely exacerbated by accompanying changes and easing of restrictions. However, with the exception of China, notable for its robust test, track, trace, and isolate processes, no other countries that had significant numbers of COVID-19 cases have successfully reopened schools without an increase in cases as a consequence.\n\nWhilst reopening of schools following an initial peak and decrease in COVID-19 infections is desirable for a range of reasons, doing so without adequate controls and protections may lead to an exacerbation of spread within the school environment, which could then lead to increased community spread of disease.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Richard Beesley", + "author_inst": "Juvenile Arthritis Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.03.20187062", "rel_title": "College campuses and COVID-19 mitigation: clinical and economic value", @@ -1216580,41 +1217745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.03.20187617", - "rel_title": "COVID-19 hospitalizations in Brazil's Unified Health System (SUS)", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187617", - "rel_abs": "ObjectiveTo study the profile of hospitalizations due to COVID-19 in the Unified Health System (SUS) in Brazil and to identify factors associated with hospital mortality related to the disease.\n\nMethodsCross-sectional study, based on secondary data on COVID-19 hospitalizations that occurred in SUS, between the last days of February and June. Patients aged 18 years or older, with primary or secondary diagnoses indicative of COVID-19 were included. Bivariate analyses were performed and generalized linear mixed models (GLMM) were estimated with random effects intercept. The modeling followed three steps, including: attributes of the patients; elements of the care process; and characteristics of the hospital and place of hospitalization.\n\nResults89,405 hospitalizations were observed, of which 24.4% resulted in death. COVID-19 patients hospitalized in SUS were predominantly male (56.5%), with a mean age of 58.9 years. The length of stay ranged from less than 24 hours to 114 days, with a mean of 6.9 ({+/-}6.5) days. Of the total number of hospitalizations, 22.6% reported ICU use. The chances of hospital death among men were 16.8% higher than among women and increased with age. Black individuals had a higher chance of death. The behavior of the Charlson and Elixhauser indices was consistent with the hypothesis of a higher risk of death among patients with comorbidities, and obesity had an independent effect on increasing this risk. Some states had a higher risk of hospital death from COVID-19, such as Amazonas and Rio de Janeiro. The chances of hospital death were 72.1% higher in municipalities with at least 100,000 inhabitants and being hospitalized in the municipality of residence was a protective factor.\n\nConclusionThere was wide variation in hospital COVID-19 mortality in the SUS, associated with demographic and clinical factors, social inequality and differences in the structure of services and quality of health care.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Carla Louren\u00e7o Tavares de Andrade", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz" - }, - { - "author_name": "Claudia Cristina de Aguiar Pereira", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz" - }, - { - "author_name": "M\u00f4nica Martins", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz" - }, - { - "author_name": "Sheyla Maria Lemos Lima", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz" - }, - { - "author_name": "Margareth Cris\u00f3stomo Portela", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.03.20187807", "rel_title": "Assessment of COVID-19 Pandemic in Nepal: A Lockdown Scenario Analysis", @@ -1217534,6 +1218664,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.01.20185793", + "rel_title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "rel_abs": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Katie Biggs", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ben Thomas", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Steve Goodacre", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ellen Lee", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Laura Sutton", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Matthew Bursnall", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Amanda Loban", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Simon Waterhouse", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Richard Simmonds", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Carl Marincowitz", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jose Schutter", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Sarah Connelly", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Elena Sheldon", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jamie Hall", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Emma Young", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Andrew Bentley", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Kirsty Challen", + "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Chris Fitzsimmons", + "author_inst": "Sheffield Children's NHS Foundation Trust" + }, + { + "author_name": "Tim Harris", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Fiona Lecky", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Andrew Lee", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ian Maconochie", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Darren Walter", + "author_inst": "Manchester University NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.08.29.20184325", "rel_title": "Face-masking, an acceptable protective measure against COVID-19: Findings of Ugandan high-risk groups", @@ -1218066,45 +1219303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.09.01.20186304", - "rel_title": "Exploring the global impact of the COVID-19 pandemic on medical education: an international cross-sectional study of medical learners", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186304", - "rel_abs": "To broadly explore the extent that COVID-19 has initially impacted medical learners around the world and examine global trends and patterns across geographic regions and levels of training, a cross-sectional survey of medical learners was conducted between March 25-June 14th, 2020, shortly after the World Health Organization declared concurrent COVID-19 a pandemic. 6492 medical learners completed the survey from 140 countries, Students were concerned about the quality of their learning, training progression, and milestone fulfillment. Most trainees felt under-utilized and wanted to be engaged clinically in meaningful ways; however, some trainees felt that contributing to healthcare during a pandemic was beyond the scope of a medical learner. Statistically significant differences were detected between levels of training and geographic regions for satisfaction with organizational responses, the impact of COVID-19 on wellness, and state-trait anxiety. Overall, the initial disruption to medical training has been perceived by learners across all levels and geographic regions to have negatively affected their training and well-being, particularly amongst postgraduate trainees. These results provide initial insights into the areas that warrant future research as well as consideration for current and future policy planning, such as the policies for clinical utilization of medical learners during public health emergencies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Allison Brown", - "author_inst": "University of Calgary - Cumming School of Medicine, Department of Medicine and Community Health Sciences" - }, - { - "author_name": "Aliya Kassam", - "author_inst": "University of Calgary - Cumming School of Medicine, Office of Postgraduate Medical Education" - }, - { - "author_name": "Mike Paget", - "author_inst": "University of Calgary - Cumming School of Medicine, Undergraduate Medical Education" - }, - { - "author_name": "Kenneth Blades", - "author_inst": "University of Calgary" - }, - { - "author_name": "Megan Mercia", - "author_inst": "University of Calgary - Faculty of Science" - }, - { - "author_name": "Rahim Kachra", - "author_inst": "University of Calgary - Cumming School of Medicine, Department of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.09.02.20186502", "rel_title": "Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection", @@ -1218948,6 +1220146,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.02.20186916", + "rel_title": "Maximizing and evaluating the impact of test-trace-isolate programs", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186916", + "rel_abs": "September 2, 2020\n\nBackgroundTest-trace-isolate programs are an essential part of COVID-19 control that offer a more targeted approach than many other non-pharmaceutical interventions. Effective use of such programs requires methods to estimate their current and anticipated impact.\n\nMethods and FindingsWe present a mathematical modeling framework to evaluate the expected reductions in the reproductive number, R, from test-trace-isolate programs. This framework is implemented in a publicly available R package and an online application. We evaluated the effects of case detection, speed of isolation, contact tracing completeness and speed of quarantine using parameters consistent with COVID-19 transmission (R0 = 2.5, generation time 6.5 days). We show that R is most sensitive to changes to the proportion of infections detected in almost all scenarios, and other metrics have a reduced impact when case detection levels are low (< 30%). Although test-trace-isolate programs can contribute substantially to reducing R, exceptional performance across all metrics is needed to bring R below one through test-trace-isolate alone, highlighting the need for comprehensive control strategies. Formally framing the dynamical process also indicates that metrics used to evaluate performance of test-trace-isolate, such as the proportion of identified infections among traced contacts, may be misleading. While estimates of program performance are sensitive to assumptions about COVID-19 natural history, our qualitative findings are robust across numerous sensitivity analyses.\n\nConclusionsEffective test-trace-isolate programs first need to be strong in the \"test\" component, as case detection underlies all other program activities. Even moderately effective test-trace-isolate programs are an important tool for controlling the COVID-19 pandemic, and can alleviate the need for more restrictive social distancing measures.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kyra H Grantz", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lucy D'Agostino McGowan", + "author_inst": "Department of Mathematics and Statistics, Wake Forest University" + }, + { + "author_name": "Kyu Han Lee", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University; Princeton School of Public and International Affairs, Princeton University" + }, + { + "author_name": "Emily S Gurley", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.02.20186734", "rel_title": "Could seasonal influenza vaccination influence COVID-19 risk?", @@ -1219604,33 +1220845,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.02.20186650", - "rel_title": "COMPARISON OF ARTIFICIAL INTELLIGENCE ENABLED METHODS IN THE COMPUTED TOMOGRAPHIC ASSESSMENT OF COVID-19 DISEASE.", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186650", - "rel_abs": "ObjectivesComparison of three different Artificial intelligence (AI) methods of assessment for patients undergoing Computed tomography (CT) for suspected Covid-19 disease. Parameters studied were probability of diagnosis, quantification of disease severity and the time to reach the diagnosis.\n\nMethods107 consecutive patients of suspected Covid-19 patients were evaluated using the three AI methods labeled as Al-I,II, III alongwith visual analysis labeled as VT for predicting probability of Covid-19, determining CT severity score (CTSS) and index (CTSI), percentage opacification (PO) and high opacification (POHO). Sensitivity, specificity along with area under curves were estimated for each method and the CTSS and CTSI correlated using Friedman test.\n\nResultsOut of 107 patients 71 patients were Covid-19 positive and 20 negative by RT-PCR while 16 did not get RT-PCR done. Al-III method showed higher sensitivity and specificity of 93% and 88% respectively to predict probability of Covid 19. It had 2 false positive patients of interstitial lung disease. Al-II method had sensitivity and specificity of 66% and 83% respectively while visual (VT) analysis showed sensitivity and specificity of 59.7% and 62% respectively. Statistically significant differences were also seen in CTSI and PO estimation between Al-I and III methods (p< 0.0001) with Al-III showing fastest time to calculate results.\n\nConclusionsAl-III method gave better results to make an accurate and quick diagnosis of the Covid-19 with AUC of 0.85 to predict probability of Covid-19 alongwith quantification of Covid-19 lesions in the form of PO, POHO as compared to other AI methods and also by visual analysis.\n\nKEY POINTSCT examinations of the chest can be more accurate and informative in detecting Covid-19 if combined with AI methods which are being designed to achieve this objective. In this study we compared three AI methods with Visual analysis and the results show. O_LIAl-III method had a higher sensitivity and specificity of 93% and 88% compared to other methods in predicting probability of Covid-19.\nC_LIO_LISignificant inter method variations were seen in quantifying Covid-19 opacities as CTSS,CTSI, PO and POHO variables (p< 0.0001). Al-III method showed no statistical difference with VT method for PO variable (p = 0.24) and was the only method which depicted all the variables..\nC_LIO_LITime to processing results was the shortest with Al-III method.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Atul Kapoor", - "author_inst": "Advanced diagnostics" - }, - { - "author_name": "Goldaa Mahajan", - "author_inst": "Advanced Diagnostics" - }, - { - "author_name": "Aprajita Kapoor", - "author_inst": "Advanced Diagnostics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.09.01.20186213", "rel_title": "Performance of serum apolipoprotein-A1 as a sentinel of Covid-19", @@ -1220574,6 +1221788,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.01.20184101", + "rel_title": "Rapid 'mix and read' assay for scalable detection of SARS-CoV-2 antibodies in patient plasma", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20184101", + "rel_abs": "The human beta coronavirus SARS-CoV-2, causative virus of COVID-19, has infected more than 15 million people globally and continues to spread. Widespread, population level testing to detect active and past infections is critical to curb the COVID-19 pandemic. Antibody (serological) testing is the only option for detecting past infections outside the narrow window accessible to nucleic acid-based tests. However, currently available serological assays commonly lack scalability. Here, we describe the development of a rapid homogenous serological assay for the detection of antibodies to SARS-CoV-2 in patient plasma. We show that the fluorescence-based assay accurately detects seroconversion in COVID-19 patients from less than 1 L of plasma. Using a cohort of samples from COVID-19 infected or healthy individuals, we demonstrate detection with 100% sensitivity and specificity. This assay addresses an important need for a robust, low barrier to implementation, and scalable serological assay with complementary strengths to currently available serological platforms.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hong Yue", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Rados\u0142aw P Nowak", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Daan Overwijn", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "N Connor Payne", + "author_inst": "Harvard University" + }, + { + "author_name": "Stephanie Fischinger", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lindsey R Baden", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Eric James Nilles", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Elizabeth W Karlson", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Xu G Yu", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jonathan Z Li", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Ralph Mazitschek", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Eric S Fischer", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20186742", "rel_title": "The role of masks in reducing the risk of new waves of COVID-19 in low transmission settings: a modeling study", @@ -1221118,57 +1222403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.29.20184473", - "rel_title": "Entry screening and multi-layer mitigation of COVID-19 cases for a safe university reopening", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184473", - "rel_abs": "We have performed detailed modeling of the COVID-19 epidemic within the State of Illinois at the population level, and within the University of Illinois at Urbana-Champaign at a more detailed level of description that follows individual students as they go about their educational and social activities.\n\nWe ask the following questions:\n\nO_LIHow many COVID-19 cases are expected to be detected by entry screening?\nC_LIO_LIWill this initial \"bump\" in cases be containable using the mitigation steps being undertaken at UIUC?\nC_LI\n\nOur answers are:\n\nO_LIAssuming that there are approximately 45,000 students returning to campus in the week beginning August 15, 2020, our most conservative estimate predicts that a median of 270 {+/-} 90 (minimum-maximum range) COVID-19 positive cases will be detected by entry screening. The earliest estimate for entry screening that we report was made on July 24th and predicted 198 {+/-} 90 (68% CI) positive cases.\nC_LIO_LIIf the number of returning students is less, then our estimate just needs to be scaled proportionately.\nC_LIO_LIThis initial bump will be contained by entry screening initiated isolation and contact tracing, and once the semester is underway, by universal masking, a hybrid teaching model, twice-weekly testing, isolation, contact tracing, quarantining and the use of the Safer Illinois exposure notification app.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ahmed Elbanna", - "author_inst": "University of Illinois Urbana Champaign" - }, - { - "author_name": "George N. Wong", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Zach J. Weiner", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Tong Wang", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Hantao Zhang", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Zhiru Liu", - "author_inst": "Stanford University" - }, - { - "author_name": "Alexei V Tkachenko", - "author_inst": "Brookhaven National Laboratory" - }, - { - "author_name": "Sergei Maslov", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Nigel Goldenfeld", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.30.20184598", "rel_title": "The Uncertain COVID-19 Spread Pattern in India: A Statistical Analysis of the Current Situation", @@ -1222280,6 +1223514,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.20184176", + "rel_title": "Estimating Unreported Deaths Associated with COVID-19", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184176", + "rel_abs": "Efforts to mitigate the spread of coronavirus disease 2019 (COVID-19) in the United States require an accurate understanding of how the epidemic is progressing. The National Center for Health Statistics (NCHS) releases weekly numbers of deaths attributed to a set of select causes, including deaths from COVID-19 in the entire United States (US), by state, and cumulatively for individual counties. Comparing US and state level deaths from select causes recorded in 2020 with values from 2014-2019 identifies a number of differences that exceeded 95% confidence limits on historical mean values, including three states with deaths possibly from COVID-19 in December 2019. Comparing county-level NCHS datasets with county-level data on deaths from COVID-19 compiled by four public pandemic tracking sites suggests that a large number of COVID-19 deaths have not yet been reported to the NCHS. Dividing the numbers of COVID-19 deaths counted by the public tracking sites by the percentage of COVID-19 deaths reported to the NCHS suggests that approximately 20% of all US deaths from Natural Causes, as many as 200,000, may not yet have been reported to the NCHS. Evaluating changes in the fractions of deaths attributed to COVID-19 and other specific causes or nonspecific outcomes during the epidemic, relative to 2020 totals or historical mean values, can provide a valuable perspective on the public health consequences of COVID-19.\n\nSignificance StatementEstimating total deaths from natural causes using the percentage of natural cause deaths from COVID-19 reported to the CDC and the number of COVID-19 deaths counted by public tracking sites suggests that up to 200,000 deaths from natural causes between 22 April and 15 August, 2020, around 20% of the total recorded as of 26 August, have not yet been reported to the CDC.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Benjamin Stear", + "author_inst": "The Children's Hospital of Philadelphia" + }, + { + "author_name": "Kyle Hernandez", + "author_inst": "University of Chicago," + }, + { + "author_name": "Vidya Manian", + "author_inst": "University of Puerto Rico" + }, + { + "author_name": "Som Dutta", + "author_inst": "Utah State University" + }, + { + "author_name": "Deanne Taylor", + "author_inst": "University of Pennsylvania Perelman Medical School" + }, + { + "author_name": "Catharine Conley", + "author_inst": "NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.30.20184804", "rel_title": "To isolate or not to isolate: The impact of changing behavior on COVID-19 transmission", @@ -1223032,45 +1224305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.31.20183533", - "rel_title": "Prevalence of SARS-CoV-2 Infections in a Pediatric Orthopedic Hospital", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20183533", - "rel_abs": "This project assessed the prevalence of active and past infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a specialized pediatric institution that did not provide care for coronavirus disease 2019 (Covid-19). The study was performed in Montreal, the city with the highest number of Covid-19 cases in Canada during the early phase of the pandemic. Testing for SARS-CoV-2 RNA in 199 individuals (39 children, 61 accompanying persons, 99 hospital employees) did not reveal active infection in any of the study participants. However, 22 (11%) of study participants had SARSCoV-2 IgG antibodies, indicating prior infection. Ten of these participants did not report symptoms compatible with Covid-19 in the 6 months prior to the study. Thus, although no evidence for active infection was found within the institution, consideration should be given to regular staff testing to detect asymptomatic spreading of SARS-CoV-2. In addition, it could be useful to test accompanying persons in children presenting for surgical procedures.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ghalib Bardai", - "author_inst": "Shriners Hospital for Children - Canada, Montreal, Quebec, Canada" - }, - { - "author_name": "Jean A Ouellet", - "author_inst": "Shriners Hospital for Children - Canada, Montreal, Quebec, Canada" - }, - { - "author_name": "Thomas Engelhardt", - "author_inst": "Shriners Hospital for Children - Canada, Montreal, Quebec, Canada" - }, - { - "author_name": "Gianluca Bertolizio", - "author_inst": "Shriners Hospital for Children - Canada, Montreal, Quebec, Canada" - }, - { - "author_name": "Zenghui Wu", - "author_inst": "Shriners Hospital for Children - Canada, Montreal, Quebec, Canada" - }, - { - "author_name": "Frank Rauch", - "author_inst": "Shriners Hospital for Children - Canada, Montreal, Quebec, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.31.20184895", "rel_title": "Selecting COVID-19 Convalescent Plasma for Neutralizing Antibody Potency Using a High-capacity SARS-CoV-2 Antibody Assay", @@ -1224054,6 +1225288,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.08.31.20185314", + "rel_title": "HYDROXICLOROQUINE FOR PRE-EXPOSURE PROPHYLAXIS FOR SARS-CoV-2", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185314", + "rel_abs": "SARS-CoV-2 infection has a high transmission level. At the present time there is not a specific treatment approved but it is known that, in vitro, chloroquine and hydroxychloroquine can inhibit the coronavirus.\n\nObjectiveverifying if patients with autoimmune diseases that are on treatment with HCQ have less incidence and severity on COVID-19.\n\nMaterial and methodsthis is a retrospective cohort study. The exposed cohort was formed by individuals with autoimmune diseases with HCQ treatment. The control cohort was randomly selected using the Health Card database. To deal with confounding variables and evaluate the effect of HCQ on the incidence and severity of SARS-CoV-2 infection, propensity score matching was used. Risk difference and paired percentage difference between exposed and non-exposed groups was estimated.\n\nResults919 individuals formed the exposed cohort and 1351 the control cohort. After matching, there were 690 patients on each group. During the time of the study, in the exposed group there were 42 (6.1%) individuals with suspected COVID-19, 12(1.7%) with confirmed COVID-19 and 3(0.4%) were hospitalized. In the control group there were 30(4.3%) individuals with suspected COVID-19, 13(1.9%) with confirmed COVID-19 and 2(0.3%) were hospitalized. The risk difference between each cohort was: 0.017(-0.05-0.04) for suspected COVID-19; -0.014(-0.015-0.012) for confirmed COVID-19 and 0.001(-0.007-0.007) for hospitalized patients. There were not significant differences.\n\nConclusionthere is no difference neither on the incidence nor on the severity of COVID-19 between patients with autoimmune diseases with HCQ treatment and patients that do not take HCQ.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jaime Lopez de la Iglesia", + "author_inst": "GAP Leon" + }, + { + "author_name": "Naiara Cubelos", + "author_inst": "Licenciada en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Roi Naveiro", + "author_inst": "Instituto de Ciencias Matematicas. Estadistica e investigacion operativa. Consejo Superior de Investigacion Cientifica (ICMAT-CSIC)." + }, + { + "author_name": "Marina Montoro Gomez", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Francisco Javier Gonzalez de Haro", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Maria Ajenjo Gonzalez", + "author_inst": "Doctora en Medicina.GAP Leon (Spain)" + }, + { + "author_name": "Estefania Tobal Vicente", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Maria Lamuedra Gil de Gomez", + "author_inst": "Graduada en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Maria Teresa Nuevo Guisado", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Isabel Torio Gomez", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Ana Penalver Andrada", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Nuria Martinez Cao", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Paula Gonzalez Figaredo", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Carlos Robles Garcia", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Lidia Anastasia Alvarado Machon", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Angeles Lafont Alcalde", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Jose Cesareo Naveiro Rilo", + "author_inst": "Doctor en Salud Publica y Medicina Preventiva. Unidad Docente de Medicina Familiar y Comunitaria de Leon (Spain)." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2020.09.01.20183145", "rel_title": "Impact of COVID-19 pandemic on cancer care delivery : A Real World Experience", @@ -1224750,41 +1226067,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.09.02.20186759", - "rel_title": "Deep-learning convolutional neural networks with transfer learning accurately classify COVID19 lung infection on portable chest radiographs", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186759", - "rel_abs": "Portable chest x-ray (pCXR) has become an indispensable tool in the management of Coronavirus Disease 2019 (COVID-19) lung infection. This study employed deep-learning convolutional neural networks to classify COVID-19 lung infections on pCXR from normal and related lung infections to potentially enable more timely and accurate diagnosis. This retrospect study employed deep-learning convolutional neural network (CNN) with transfer learning to classify based on pCXRs COVID-19 pneumonia (N=455) on pCXR from normal (N=532), bacterial pneumonia (N=492), and non-COVID viral pneumonia (N=552). The data was split into 75% training and 25% testing. A five-fold cross-validation was used. Performance was evaluated using receiver-operating curve analysis. Comparison was made with CNN operated on the whole pCXR and segmented lungs. CNN accurately classified COVID-19 pCXR from those of normal, bacterial pneumonia, and non-COVID-19 viral pneumonia patients in a multiclass model. The overall sensitivity, specificity, accuracy, and AUC were 0.79, 0.93, and 0.79, 0.85 respectively (whole pCXR), and were 0.91, 0.93, 0.88, and 0.89 (CXR of segmented lung). The performance was generally better using segmented lungs. Heatmaps showed that CNN accurately localized areas of hazy appearance, ground glass opacity and/or consolidation on the pCXR. Deep-learning convolutional neural network with transfer learning accurately classifies COVID-19 on portable chest x-ray against normal, bacterial pneumonia or non-COVID viral pneumonia. This approach has the potential to help radiologists and frontline physicians by providing more timely and accurate diagnosis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shreeja Kikkisetti", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Jocelyn Zhu", - "author_inst": "stony brook university" - }, - { - "author_name": "Beiyi Shen", - "author_inst": "stony brook university" - }, - { - "author_name": "Haifang Li", - "author_inst": "stony brook university" - }, - { - "author_name": "Tim Duong", - "author_inst": "Stony Brook Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.31.20185074", "rel_title": "Fully automated detection and differentiation of pandemic and endemic coronaviruses (NL63, 229E, HKU1, OC43 and SARS-CoV-2) on the Hologic Panther Fusion", @@ -1225960,6 +1227242,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.08.27.20182923", + "rel_title": "Evaluation of production lots of a rapid point-of-care lateral flow serological test intended for identification of IgM and IgG against the N-terminal part of the spike protein (S1) of SARS-CoV-2", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182923", + "rel_abs": "Background and objectivesSeveral antibody tests are available to detect SARS-CoV-2 specific antibodies, many of which address different antigens. Rapid point-of-care (POC) tests have been doubted due to an eventual risk of production errors, although it is unstudied whether such error would affect test sensitivity and/or specificity. We aimed to evaluate two separate production lots of a commercially available test intended for rapid detection of IgM and IgG against the N-terminal part of the SARS-CoV-2 spike protein (S1).\n\nMaterials and methodsSerum samples from individuals with confirmed SARS-CoV-2 infection, by RT-PCR and/or serology, and pre-COVID-19 negative control sera gathered from a biobank during 2018 were collected. The presence of anti-S1 IgM/IgG was verified by an in-house Luminex-based serological assay, serving as reference method. The index test was a commercially available rapid POC-test (the COVID-19 IgG/IgM Rapid Test Cassette [Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China/Healgen Scientific, LLC, U.S.A.]).\n\nResultsOne hundred samples were verified positive for anti-S1 IgG (median fluorescence intensity (MFI) [≥]900) and 74 for anti-S1 IgM (MFI [≥]700), confirmed by RT-PCR (n=90) and/or serology (n=89). None of the negative controls (n=200; MFI <300) had SARS-CoV-2 anti-S1 IgM, while one tested positive for SARS-CoV-2 anti-S1 IgG. For the two lots, the sensitivities of the rapid test were 93.2% (69/74; 95% CI: 85.1% - 97.1%) and 87.8% (65/74; 95% CI: 78.5% - 93.5%) for IgM, respectively 93.0% (93/100; 95% CI: 86.3% - 96.6%) and 100.0% for IgG (100/100; 95% CI: 96.3% - 100.0%). The specificity for both lots was 100% for IgM (200/200; 95% CI: 98.1% - 100%) and 99.5% for IgG (199/200; 95% CI: 97.2% - 99.9%). The positive predictive value was 100% for IgM and 98.9% and 99.0% for IgG. The negative predictive value was 95.7% and 97.6% for IgM, and 96.6% and 100.0% for IgG.\n\nConclusionThe rapid POC-test used in this study is suitable to assess SARS-CoV-2 anti-S1 specific IgM/IgG, as a measure of previous virus exposure on an individual level. While the specificity was not affected by production lot, external validation of separate lots of rapid POC-tests is encouraged to ensure high sensitivity before market introduction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tove Hoffman", + "author_inst": "Uppsala University" + }, + { + "author_name": "Linda Kolstad", + "author_inst": "Uppsala University" + }, + { + "author_name": "Bengt Ronnberg", + "author_inst": "Uppsala University Hospital" + }, + { + "author_name": "Ake Lundkvist", + "author_inst": "Uppsala University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.26.20182675", "rel_title": "Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study", @@ -1226688,65 +1228001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.08.27.20182238", - "rel_title": "Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19.", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182238", - "rel_abs": "The increasing body of literature describing the role of host factors in COVID-19 pathogenesis demonstrates the need to combine diverse, multi-omic data to evaluate and substantiate the most robust evidence and inform development of therapies.\n\nHere we present a dynamic ranking of host genes implicated in human betacoronavirus infection (SARS-CoV-2, SARS-CoV, MERS-CoV, seasonal coronaviruses). Researchers can search and review the ranked genes and the contribution of different experimental methods to gene rank at https://baillielab.net/maic/covid19.\n\nWe conducted an extensive systematic review of experiments identifying potential host factors. Gene lists from diverse sources were integrated using Meta-Analysis by Information Content (MAIC). This previously described algorithm uses data-driven gene list weightings to produce a comprehensive ranked list of implicated host genes.\n\nFrom 32 datasets, the top ranked gene was PPIA, encoding cyclophilin A, a drug-gable target using cyclosporine.Other highly-ranked genes included proposed prognostic factors (CXCL10, CD4, CD3E) and investigational therapeutic targets (IL1A) for COVID-19. Gene rankings also inform the interpretation of COVID-19 GWAS results, implicating FYCO1 over other nearby genes in a disease-associated locus on chromosome 3.\n\nAs new data are published we will regularly update list of genes as a resource to inform and prioritise future studies.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Nicholas Parkinson", - "author_inst": "Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Natasha Rodgers", - "author_inst": "The Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Max Head Fourman", - "author_inst": "The Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Bo Wang", - "author_inst": "The Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Marie Zechner", - "author_inst": "The Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Maaike Swets", - "author_inst": "Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Jonathan E Millar", - "author_inst": "Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Andy Law", - "author_inst": "Roslin Institute, The University of Edinburgh" - }, - { - "author_name": "Clark Russell", - "author_inst": "The University of Edinburgh" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh" - }, - { - "author_name": "Sara Clohisey", - "author_inst": "Roslin Institute, University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.08.26.20182840", "rel_title": "On Statistical Power for Case-Control Host Genomic Studies of COVID-19", @@ -1227562,6 +1228816,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.26.20182477", + "rel_title": "Modelling COVID-19 contagion:Risk assessment and targeted mitigation policies", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182477", + "rel_abs": "We use a spatial epidemic model with demographic and geographic heterogeneity to study the regional dynamics of COVID-19 across 133 regions in England.\n\nOur model emphasises the role of variability of regional outcomes and heterogeneity across age groups and geographic locations, and provides a framework for assessing the impact of policies targeted towards sub-populations or regions. We define a concept of efficiency for comparative analysis of epidemic control policies and show targeted mitigation policies based on local monitoring to be more efficient than country-level or non-targeted measures. In particular, our results emphasise the importance of shielding vulnerable sub-populations and show that targeted policies based on local monitoring can considerably lower fatality forecasts and, in many cases, prevent the emergence of second waves which may occur under centralised policies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rama Cont", + "author_inst": "University of Oxford" + }, + { + "author_name": "RenYuan Xu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Artur Kotlicki", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.26.20181990", "rel_title": "Empowering the crowd: Feasible strategies to minimize the spread of COVID-19 in high-density informal settlements", @@ -1228106,45 +1229387,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.27.20183632", - "rel_title": "Acute kidney injury is associated with severe and fatal outcomes in patients with Coronavirus disease 2019 (COVID-19) infection: a systematic review and meta-analysis of observational studies", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183632", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a pandemic impacting 213 countries and territories with more than 17,918,582 cases worldwide. Kidney dysfunction has been reported to occur in severe and death cases. This meta-analysis was done to summarize available studies on the association between acute kidney injury and severity of COVID-19 infection. Online databases including Web of Science, PubMed/Medline, Cochrane Library, Scopus and Google Scholar were searched to detect relevant articles up to 1 July 2020, using relevant keywords. To pool data, a random- or fixed-effects model was used based on the heterogeneity between studies. In total, 50 studies with 8,180 COVID-19 confirmed cases (severe cases=1,823 and death cases=775), were included in this meta-analysis. Higher serum levels of creatinine (weighted mean difference (WMD) for disease severity=5.47 mol/L, 95% CI=2.89 to 8.05, P<0.001 and WMD for mortality=18.32 mol/L, 95% CI=12.88 to 23.75, P<0.001), blood urea nitrogen (BUN) (WMD for disease severity=1.10 mmol/L, 95% CI=0.67 to 1.54, P<0.001 and WMD for mortality=3.56 mmol/L, 95% CI=2.65 to 4.48, P<0.001) and lower levels of estimated glomerular filtration rate (eGFR) (WMD for disease severity=-15.34 mL/min/1.73 m2, 95% CI=-18.46 to -12.22, P<0.001 and WMD for mortality=-22.74 mL/min/1.73 m2, 95% CI=-27.18 to -18.31, P<0.001) were associated with a significant increase in the severity and mortality of COVID-19 infection. Acute kidney injury, as assessed by kidney biomarkers (serum creatinine, BUN and eGFR), was associated with severe outcome and death from COVID-19 infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mohammad Parohan", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Sajad Yaghoubi", - "author_inst": "Iranshahr University of Medical Sciences" - }, - { - "author_name": "Mahmoud Djalali", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Asal Seraji", - "author_inst": "Damavand Branch, Islamic Azad University" - }, - { - "author_name": "Mohammad Hassan Javanbakht", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Zahra Mousavi", - "author_inst": "Iranshahr University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.30.20183889", "rel_title": "Viral shedding dynamics reveals sputum as a reliable and cost-saving specimen for SARS-CoV-2 diagnosis within the first 10 days since symptom onset: A prospective cohort study", @@ -1229240,6 +1230482,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.08.29.20126201", + "rel_title": "Sex-based clinical and immunological differences in COVID-19", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20126201", + "rel_abs": "BackgroundMales and females differ in their immunological responses to foreign pathogens. However, most of the current COVID-19 clinical practices and trials do not take sex as consideration.\n\nMethodsWe performed an unbiased sex-based comparative analysis for the clinical outcomes, peripheral immune cells, and SARS-CoV-2 specific antibody levels of 1,558 males and 1,499 females COVID-19 patients from a single center. The lymphocyte subgroups were measured by Flow cytometry. Total antibody, Spike protein (S)-, receptor binding domain (RBD)-, and nucleoprotein (N)-specific IgM and IgG levels were measured by chemiluminescence.\n\nResultsWe found that the mortality and ICU admission rates were approximately 2-fold higher in males than that in females (P<0.005). Survival analysis revealed that sex is an independent prognostic factor for COVID-19 (Hazard ratio=2.2, P=0.003). The concentration of inflammatory factors in peripheral blood was significantly higher in males. Besides, the renal and hepatic abnormality induced by COVID-19 was more common in males during the hospitalization. The analysis of lymphocyte subsets revealed that the percentage of CD19+ B cell and CD4+ T cell was significantly higher in females (P<0.001) during hospitalization, indicating the stronger humoral immunity in females than males. Notably, the protective IgG sharply increased and reached a peak in the fourth week after symptom onset in females, while gradually increased and reached a peak in the seventh week in males.\n\nConclusionsThe unfavorable prognosis of male COVID-19 patients may result from the weak humoral immunity and indolent antibody responses during SARS-CoV-2 infection and recovery. Early medical intervention and close monitoring are important, especially for male COVID-19 patients. Hormonal or convalescent plasma therapy may help improve the immunity of males to fight against SARS-CoV-2 infection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kening Li", + "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" + }, + { + "author_name": "Bin Huang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Yun Cai", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Zhihua Wang", + "author_inst": "Department of Laboratory Medicine & Blood Transfusion, the 907th Hospital" + }, + { + "author_name": "Lu Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Lingxiang Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Mengyan Zhu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Jie Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Ziyu Wang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Min Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Wanlin Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Wei Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Lishen Zhang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Xinyi Xia", + "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" + }, + { + "author_name": "Shukui Wang", + "author_inst": "Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University" + }, + { + "author_name": "Qianghu Wang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20183616", "rel_title": "A Comparison of Covid-19 Patient Characteristics Before versus After Partial Lockdown in Vietnam", @@ -1229988,41 +1231309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.08.25.20181511", - "rel_title": "A comparison of Emergency Department presentations for Medically Unexplained Symptoms in Frequent Attenders during COVID-19", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181511", - "rel_abs": "BackgroundMedically Unexplained Symptoms (MUS) refer to symptoms with no identified organic aetiology, and are amongst the most challenging for patients and Emergency Department (ED) staff. Providers working in our ED perceived an increase in severity and frequency of these types of presentations during the COVID-19 pandemic.\n\nMethodsA retrospective list of frequent attenders (FA) presenting five or more times to the ED between two 122-day periods were examined: 01 Mar to 30 Jun 2019 (Control) and 2020 (COVID-19). The FA group were then examined to identify patients presenting with MUS (FA-MUS). Data were analysed in Prism; presented as n(%), % (95% confidence interval (95%CI) - Wilson/Brown method). Proportions were compared with a two-tailed Fishers exact test. A Baptista-Pike odds ratio was used to estimate magnitude and precision.\n\nResultsThe total number of ED attendances during the control period was n=42,785 which reduced to n=28,806 in the COVID-19 period, a decrease of 32.7%. The control FA cohort had n=44 FA-MUS patients with 149 ED visits. This increased to n=65 FA-MUS patients with 267 visits during COVID-19, p=0.44. There was a significant increase in the proportion of all ED visits that were FA-MUS: 0.3% (control) compared to 0.9% (COVID-19); OR 2.7, p<0.001. There was a significant increase in shortness of breath amongst MUS during the COVID-19 pandemic relative to the control period (p<0.01), with no significant difference in any other MUS category.\n\nConclusionWhilst the total number of ED attendances reduced by almost one third during COVID-19, the actual number of all visits by frequent attenders with MUS increased and the proportion of attendances by these tripled during the same period. This presents an increasing challenge to ED clinicians who may feel underprepared to manage these patients effectively.\n\nO_LSTWhat is already knownC_LSTO_LIMedically Unexplained Symptoms (MUS) are those that have no identified organic aetiology - they are amongst the most challenging presentations for patients and Emergency Department (ED) staff.\nC_LIO_LIDuring times of stress and uncertainty, frequent attenders (FA) appear to be disproportionately affected by MUS. However, there are few data examining the impact of COVID-19 on the FA population.\nC_LI\n\nO_LSTWhat this paper addsC_LSTO_LIThere was a significant increase in the proportion of all ED visits by FAs during the first four months of the COVID-19 pandemic.\nC_LIO_LIThere was a significant increase in the proportion of all ED visits by FAs with MUS during the first four months of the COVID-19 pandemic.\nC_LIO_LIThe proportion of MUS presentations that were shortness of breath was significantly higher in the COVID-19 period compared to the control period. There were no other proportional differences observed in MUS categories.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Natasha Faye Daniels", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Raiiq Ridwan", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK" - }, - { - "author_name": "Edward BG Barnard", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK" - }, - { - "author_name": "Talha Muneer Amanullah", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK" - }, - { - "author_name": "Catherine Hayhurst", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.08.25.20181453", "rel_title": "Phosphate levels and pulmonary damage in COVID-19 patients based on CO-RADS scheme: is there any link between parathyroid gland and COVID-19?", @@ -1231114,6 +1232400,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.25.20181487", + "rel_title": "Risk of COVID-19 hospitalisation rises exponentially with age, inversely proportional to T-cell production", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181487", + "rel_abs": "Here we report that COVID-19 hospitalisation rates follow an exponential relationship with age, doubling for every 16 years of age or equivalently increasing by 4.5% per year of life (R2=0.98). This mirrors the well studied exponential decline of both thymus volume and T-cell production, which halve every 16 years. COVID-19 can therefore be added to the list of other diseases with this property, including those caused by MRSA, MERS-CoV, West Nile virus, Streptococcus Pneumonia and certain cancers, such as chronic myeloid leukemia and brain cancers. In addition, incidence of severe disease and mortality due to COVID-19 are both higher in men, consistent with the degree to which thymic involution (and the decrease in T-cell production with age) is more severe in men compared to women. Since these properties are shared with some non-contagious diseases, we hypothesised that the age-dependence does not come from social-mixing patterns, i.e. that the probability of hospitalisation given infection rises exponentially, doubling every 16 years. A Bayesian analysis of daily hospitalisations, incorporating contact matrices, found that this relationship holds for every age group except for the under 20s. While older adults have less contacts than young adults, our analysis suggests that there is an approximate cancellation between the effects of less contacts for the elderly and higher infectiousness due to a higher probability of developing severe disease. Our model fitting suggests under 20s have 49-75% additional immune protection beyond that predicted by strong thymus function alone, consistent with increased juvenile cross-immunity from other viruses. We found no evidence for differences between age groups in susceptibility to infection or infectiousness to others (given disease state), i.e. the only important factor in the age-dependence of hospitalisation rates is the probability of hospitalisation given infection. These findings suggest the existence of a T-cell exhaustion threshold, proportional to thymic output, and that clonal expansion of peripheral T-cells does not affect disease risk. The strikingly simple inverse relationship between risk and thymic T-cell output adds to the evidence that thymic involution is an important factor in the decline of the immune system with age and may also be an important clue in understanding disease progression, not just for COVID-19 but other diseases as well.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sam Palmer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nik Cunniffe", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ruairi Donnelly", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.25.20154252", "rel_title": "SARS-CoV-2-RNA viremia is associated to hypercytokinemia and critical illness in COVID-19", @@ -1232006,97 +1233319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.31.275719", - "rel_title": "SARS-CoV-2 Cell Entry Factors ACE2 and TMPRSS2 are Expressed in the Pancreas but Not in Islet Endocrine Cells", - "rel_date": "2020-08-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.31.275719", - "rel_abs": "Summary/AbstractReports of new-onset diabetes and diabetic ketoacidosis in individuals with COVID-19 have led to the hypothesis that SARS-CoV-2, the virus that causes COVID-19, is directly cytotoxic to pancreatic islet {beta} cells. This would require binding and entry of SARS-CoV-2 into host {beta} cells via cell surface co-expression of ACE2 and TMPRSS2, the putative receptor and effector protease, respectively. To define ACE2 and TMPRSS2 expression in the human pancreas, we examined six transcriptional datasets from primary human islet cells and assessed protein expression by immunofluorescence in pancreata from donors with and without diabetes. ACE2 and TMPRSS2 transcripts were low or undetectable in pancreatic islet endocrine cells as determined by bulk or single cell RNA sequencing, and neither protein was detected in or {beta} cells from these donors. Instead, ACE2 protein was expressed in the islet and exocrine tissue microvasculature and also found in a subset of pancreatic ducts, whereas TMPRSS2 protein was restricted to ductal cells. The absence of significant ACE2 and TMPRSS2 co-expression in islet endocrine cells reduces the likelihood that SARS-CoV-2 directly infects pancreatic islet {beta} cells through these cell entry proteins.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Katie C Coate", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "JeeYeon Cha", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Shristi Shrestha", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Wenliang Wang", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Luciana Mateus Goncalves", - "author_inst": "University of Miami Miller School of Medicine" - }, - { - "author_name": "Joana Almaca", - "author_inst": "University of Miami Miller School of Medicine" - }, - { - "author_name": "Meghan E Kapp", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Maria Fasolino", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Ashleigh Morgan", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Chunhua Dai", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Diane C Saunders", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Rita Bottino", - "author_inst": "Institute of Cellular Therapeutics, Allegheny Health Network; Imagine Pharma" - }, - { - "author_name": "Radhika Aramandla", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Regina Jenkins", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Roland Stein", - "author_inst": "Vanderbilt University School of Medicine" - }, - { - "author_name": "Klaus H Kaestner", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Golnaz Vahedi", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Marcela Brissova", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Alvin C Powers", - "author_inst": "Vanderbilt University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.08.30.273979", "rel_title": "Ebselen derivatives are very potent dual inhibitors of SARS-CoV-2 proteases - PLpro and Mpro in in vitro studies", @@ -1233248,6 +1234470,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.272864", + "rel_title": "A simplified cell-based assay to identify coronavirus 3CL protease inhibitors", + "rel_date": "2020-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.29.272864", + "rel_abs": "We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Samuel J Resnick", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Sho Iketani", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Seo Jung Hong", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Arie Zask", + "author_inst": "Columbia University" + }, + { + "author_name": "Hengrui Liu", + "author_inst": "Columbia University" + }, + { + "author_name": "Sungsoo Kim", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Schuyler Melore", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Manoj S Nair", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Nicholas E S Tay", + "author_inst": "Columbia University" + }, + { + "author_name": "Tomislav Rovis", + "author_inst": "Columbia University" + }, + { + "author_name": "Hee Won Yang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Brent R Stockwell", + "author_inst": "Columbia University" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Alejandro Chavez", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.29.257360", "rel_title": "The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans.", @@ -1233964,61 +1235261,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.28.272518", - "rel_title": "A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice", - "rel_date": "2020-08-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.272518", - "rel_abs": "Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (S{Delta}C-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of S{Delta}C-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with S{Delta}C-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Abigail E. Powell", - "author_inst": "Stanford University" - }, - { - "author_name": "Kaiming Zhang", - "author_inst": "Stanford University" - }, - { - "author_name": "Mrinmoy Sanyal", - "author_inst": "Stanford University" - }, - { - "author_name": "Shaogeng Tang", - "author_inst": "Stanford University" - }, - { - "author_name": "Payton A. Weidenbacher", - "author_inst": "Stanford University" - }, - { - "author_name": "Shanshan Li", - "author_inst": "Stanford University" - }, - { - "author_name": "Tho D. Pham", - "author_inst": "Stanford University" - }, - { - "author_name": "John E. Pak", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Wah Chiu", - "author_inst": "Stanford University" - }, - { - "author_name": "Peter S. Kim", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.28.267567", "rel_title": "A PCR amplicon-based SARS-CoV-2 replicon for antiviral screening", @@ -1234997,6 +1236239,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.27.270637", + "rel_title": "Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion", + "rel_date": "2020-08-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.27.270637", + "rel_abs": "The molecular basis for the severity and rapid spread of the COVID-19 disease caused by SARS-CoV-2 is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04 [A] resolution by x-ray crystallography. The structure reveals a ~60 residue core similar to SARS-CoV ORF7a with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate non-covalent interface is formed by another SARS-CoV-2-specific sequence, 73YIDI76. Together the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Thomas G Flower", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Cosmo Z Buffalo", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Richard M Hooy", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Marc Allaire", + "author_inst": "Lawrence Berkeley National Laboratory" + }, + { + "author_name": "Xuefeng Ren", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "James H Hurley", + "author_inst": "UC Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.08.26.267781", "rel_title": "Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades", @@ -1235585,57 +1236866,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.24.20180851", - "rel_title": "Age-specific mortality and immunity patterns of SARS-CoV-2 infection in 45 countries", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180851", - "rel_abs": "The number of COVID-19 deaths is often used as a key indicator of SARS-CoV-2 epidemic size. However, heterogeneous burdens in nursing homes and variable reporting of deaths in elderly individuals can hamper comparisons of deaths and the number of infections associated with them across countries. Using age-specific death data from 45 countries, we find that relative differences in the number of deaths by age amongst individuals aged <65 years old are highly consistent across locations. Combining these data with data from 15 seroprevalence surveys we demonstrate how age-specific infection fatality ratios (IFRs) can be used to reconstruct infected population proportions. We find notable heterogeneity in overall IFR estimates as suggested by individual serological studies and observe that for most European countries the reported number of deaths amongst [≥]65s are significantly greater than expected, consistent with high infection attack rates experienced by nursing home populations in Europe. Age-specific COVID-19 death data in younger individuals can provide a robust indicator of population immunity.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Megan O'Driscoll", - "author_inst": "Imperial College London" - }, - { - "author_name": "Gabriel Ribeiro Dos Santos", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Lin Wang", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - }, - { - "author_name": "Andrew S Azman", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Juliette Paireau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Arnaud Fontanet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Simon Cauchemez", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Henrik Salje", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.24.20180927", "rel_title": "SARS-CoV-2 phylodynamics differentiates the effectiveness of non-pharmaceutical interventions", @@ -1236611,6 +1237841,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.26.266825", + "rel_title": "Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals", + "rel_date": "2020-08-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.266825", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease - referred to as COVID-19 - unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS-CoV-2 infections in animals once test systems are validated for use in different species. Here, we developed an indirect multi-species ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The newly established ELISA was validated using 59 sera of infected or vaccinated animals including ferrets, raccoon dogs, hamsters, rabbits, chickens, cattle and a cat, and a total of 220 antibody-negative sera of the same animal species. Overall, a diagnostic specificity of 100.0% and sensitivity of 98.31% was achieved, and the functionality with every species included in this study could be demonstrated. Hence, a versatile and reliable ELISA protocol was established that enables high-throughput antibody detection in a broad range of animal species, which may be used for outbreak investigations, to assess the seroprevalence in susceptible species or to screen for reservoir or intermediate hosts.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kerstin Wernike", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Andrea Aebischer", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anna Michelitsch", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Donata Hoffmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Conrad Freuling", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anne Balkema-Buschmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Annika Graaf", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Thomas Mueller", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Nikolaus Osterrieder", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Melanie Rissmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Dennis Rubbenstroth", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Jacob Schoen", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Claudia Schulz", + "author_inst": "University of Veterinary Medicine Hannover" + }, + { + "author_name": "Jakob Trimpert", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Lorenz Ulrich", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Asisa Volz", + "author_inst": "University of Veterinary Medicine Hannover" + }, + { + "author_name": "Thomas Mettenleiter", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Martin Beer", + "author_inst": "Friedrich-Loeffler-Institut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.25.267328", "rel_title": "A unique view of SARS-CoV-2 through the lens of ORF8 protein", @@ -1237427,41 +1238744,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.08.22.20178640", - "rel_title": "The Relationship between Deteriorating Mental Health Conditions and Longitudinal Behavioral Changes in Google and YouTube Usages among College Students in the United States during COVID-19: Observational Study", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20178640", - "rel_abs": "BackgroundMental health problems among the global population are worsened during the coronavirus disease (COVID-19). Yet, current methods for screening mental health issues rely on in-person interviews, which can be expensive, time-consuming, blocked by social stigmas and quarantines. Meanwhile, how individuals engage with online platforms such as Google Search and YouTube undergoes drastic shifts due to COVID-19 and subsequent lockdowns. Such ubiquitous daily behaviors on online platforms have the potential to capture and correlate with clinically alarming deteriorations in mental health profiles of users in a non-invasive manner.\n\nObjectiveThe goal of this study is to examine, among college students in the United States, the relationship between deteriorating mental health conditions and changes in user behaviors when engaging with Google Search and YouTube during COVID-19.\n\nMethodsThis study recruited a cohort of undergraduate students (N=49) from a U.S. college campus during January 2020 (prior to the pandemic) and measured the anxiety and depression levels of each participant. The anxiety level was assessed via the General Anxiety Disorder-7 (GAD-7). The depression level was assessed via the Patient Health Questionnaire-9 (PHQ-9). This study followed up with the same cohort during May 2020 (during the pandemic), and the anxiety and depression levels were assessed again. The longitudinal Google Search and YouTube history data of all participants were anonymized and collected. From individual-level Google Search and YouTube histories, we developed 5 signals that can quantify shifts in online behaviors during the pandemic. We then assessed the differences between groups with and without deteriorating mental health profiles in terms of these features.\n\nResultsOf the 49 participants, 41% (n=20) of them reported a significant increase (increase in the PHQ-9 score [≥] 5) in depression, denoted as DEP; 45% (n=22) of them reported a significant increase (increase in the GAD-7 score [≥] 5) in anxiety, denoted as ANX. Of the 5 features proposed to quantify online behavior changes, statistical significances were found between the DEP and non-DEP groups for all of them (P[≤].01, effect sizes [Formula] ranging between 0.130 to 0.320); statistical significances were found between the ANX and non-ANX groups for 4 of them (P[≤].02, effect sizes [Formula] ranging between 0.115 to 0.231). Significant features included late-night online activities, continuous usages and time away from the internet, porn consumptions, and keywords associated with negative emotions, social activities, and personal affairs.\n\nConclusionsThe results suggested strong discrepancies between college student groups with and without deteriorating mental health conditions in terms of behavioral changes in Google Search and YouTube usages during the COVID-19. Though further studies are required, our results demonstrated the feasibility of utilizing pervasive online data to establish non-invasive surveillance systems for mental health conditions that bypasses many disadvantages of existing screening methods.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Anis Zaman", - "author_inst": "University of Rochester" - }, - { - "author_name": "Boyu Zhang", - "author_inst": "University of Rochester" - }, - { - "author_name": "Ehsan Hoque", - "author_inst": "University of Rochester" - }, - { - "author_name": "Vincent Silenzio", - "author_inst": "Rutgers University" - }, - { - "author_name": "Henry Kautz", - "author_inst": "University of Rochester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.08.23.20179838", "rel_title": "Projecting COVID-19 disease severity in cancer patients using purposefully-designed machine learning", @@ -1238557,6 +1239839,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.23.20180307", + "rel_title": "Hesitant or not? A global survey of potential acceptance of a COVID-19 vaccine", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180307", + "rel_abs": "A number of COVID-19 vaccines are under development, with one or more possibly becoming available in 2021. We conducted a global survey in June 2020 of 13,426 people in 19 countries to determine potential acceptance rates of a COVID-19 vaccine and factors influencing acceptance. We ran univariate logistic regressions to examine the associations with demographic variables. 71.5% reported they would be very or somewhat likely to take a COVID-19 vaccine; 61.4% reported they would accept their employers recommendation to take a COVID-19 vaccine. Differences in acceptance across countries ranged from almost 9 in 10 (China) to fewer than 6 in 10 (Russia). Respondents reporting higher levels of trust in information from government sources were more likely to accept a vaccine, and take their employers advice to do so. Targeted interventions addressing age, sex, income, and education level are required to increase and sustain public acceptance of a COVID-19 vaccine.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jeffrey V Lazarus", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Scott Ratzan", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + }, + { + "author_name": "Adam Palayew", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Lawrence O Gostin", + "author_inst": "Georgetown University, Washington, DC, USA" + }, + { + "author_name": "Heidi J Larson", + "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Kenneth Rabin", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + }, + { + "author_name": "Spencer Kimball", + "author_inst": "Emerson College, Boston, Mass, USA" + }, + { + "author_name": "Ayman El-Mohandes", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.23.20180513", "rel_title": "3D Printed N95 Equivalent for PPE Shortages: The Kansas City Mask", @@ -1239033,233 +1240362,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.23.20178236", - "rel_title": "Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20178236", - "rel_abs": "SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.", - "rel_num_authors": 53, - "rel_authors": [ - { - "author_name": "Jacob Lemieux", - "author_inst": "Broad Institute" - }, - { - "author_name": "Katherine J Siddle", - "author_inst": "Broad Institute" - }, - { - "author_name": "Bennett M. Shaw", - "author_inst": "Massachusetts General Hospital, Division of Infectious Diseases" - }, - { - "author_name": "Christine Loreth", - "author_inst": "Broad Institute" - }, - { - "author_name": "Stephen Schaffner", - "author_inst": "Broad Institute" - }, - { - "author_name": "Adrianne Gladden-Young", - "author_inst": "Broad Institute" - }, - { - "author_name": "Gordon Adams", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Massachusetts General Hospital" - }, - { - "author_name": "Timelia Fink", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Chris H Tomkins-Tinch", - "author_inst": "Broad Institute" - }, - { - "author_name": "Lydia A Krasilnikova", - "author_inst": "Broad Institute, Harvard University Department of OEB" - }, - { - "author_name": "Katherine C Deruff", - "author_inst": "Broad Institute" - }, - { - "author_name": "Melissa Rudy", - "author_inst": "Broad Institute" - }, - { - "author_name": "Matthew R Bauer", - "author_inst": "Broad Institute and Harvard Program in Biological and Biomedical Sciences" - }, - { - "author_name": "Kim A Lagerborg", - "author_inst": "Broad Institute and Harvard Program and Biological and Biomedical Sciences" - }, - { - "author_name": "Erica Normandin", - "author_inst": "Broad Institute and Department of Systems Biology, Harvard Medical School" - }, - { - "author_name": "Sinead B Chapman", - "author_inst": "Broad Institute" - }, - { - "author_name": "Steven K Reilly", - "author_inst": "Broad Institute and Harvard University Department of Organismic and Evolutionary Biology" - }, - { - "author_name": "Melis N Anahtar", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Aaron E Lin", - "author_inst": "Broad Institute and Harvard University Department of Organismic and Evolutionary Biology" - }, - { - "author_name": "Amber Carter", - "author_inst": "Broad Institute" - }, - { - "author_name": "Cameron Myhrvold", - "author_inst": "Broad Institute and Harvard University Department of Organismic and Evolutionary Biology" - }, - { - "author_name": "Molly Kemball", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Harvard University" - }, - { - "author_name": "Suschma Chaluvadi", - "author_inst": "Broad Institute" - }, - { - "author_name": "Caroline Cusick", - "author_inst": "Broad Institute" - }, - { - "author_name": "Katelyn Flowers", - "author_inst": "Broad Institute" - }, - { - "author_name": "Anna Neumann", - "author_inst": "Broad Institute" - }, - { - "author_name": "Felecia Cerrato", - "author_inst": "Broad Institute" - }, - { - "author_name": "Maha Farhat", - "author_inst": "Harvard Medical School; Massachusetts General Hospital" - }, - { - "author_name": "Damien Slater", - "author_inst": "Massachusetts General Hospital, Division of Infectious Diseases" - }, - { - "author_name": "Jason B Harris", - "author_inst": "Massachusetts General Hospital, Division of Pediatric Infectious Diseases" - }, - { - "author_name": "John Branda", - "author_inst": "Massachusetts General Hospital, Department of Pathology" - }, - { - "author_name": "David Hooper", - "author_inst": "Massachusetts General Hospital, Division of Infectious Diseases" - }, - { - "author_name": "Jessie M Gaeta", - "author_inst": "Boston Health Care for the Homeless Program; Boston University Medical Center" - }, - { - "author_name": "Travis P. Baggett", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "James O'Connell", - "author_inst": "Boston Health Care for the Homeless Program; Massachusetts General Hospital" - }, - { - "author_name": "Andreas Gnirke", - "author_inst": "Broad Institute" - }, - { - "author_name": "Tami D Lieberman", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Anthony Philippakis", - "author_inst": "Broad Institute" - }, - { - "author_name": "Meagan Burns", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Catherine Brown", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Jeremy Luban", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Edward T Ryan", - "author_inst": "Massachusetts General Hospital, Division of Infectious Diseases" - }, - { - "author_name": "Sarah E Turbett", - "author_inst": "Massachusetts General Hospital, Division of Infectious Diseases" - }, - { - "author_name": "Regina C LaRocque", - "author_inst": "Massachusetts General Hospital, Division of Infectious Diseases" - }, - { - "author_name": "William P. Hanage", - "author_inst": "Harvard School of Public Health" - }, - { - "author_name": "Glen Gallagher", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Lawrence C Madoff", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Sandra Smole", - "author_inst": "Massachusetts Department of Public Health" - }, - { - "author_name": "Virginia M. Pierce", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Eric S Rosenberg", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Pardis Sabeti", - "author_inst": "Harvard University; The Broad Institute or MIT and Harvard; Howard Hughes Medical Institute" - }, - { - "author_name": "Daniel J Park", - "author_inst": "Broad Institute" - }, - { - "author_name": "Bronwyn L MacInnis", - "author_inst": "Broad Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.20.20178772", "rel_title": "Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study", @@ -1240318,6 +1241420,57 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.08.24.264077", + "rel_title": "An hACE2 peptide mimic blocks SARS-CoV-2 Pulmonary Cell Infection", + "rel_date": "2020-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.264077", + "rel_abs": "In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimics bind to the virus spike protein with high affinity and are able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. These first in class blocking peptide mimics represent powerful tools that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Philippe Karoyan", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Vincent Vieillard", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Estelle Odile", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Alexis Denis", + "author_inst": "Oncodesign" + }, + { + "author_name": "amelie guihot", + "author_inst": "Assistance Publique Hopitaux de Paris Hopital Pitie Salpetriere Service de Medecine Intensive Reanimation Institut de Cardiologie 75013, Paris, France" + }, + { + "author_name": "charles edouard luyt", + "author_inst": "Assistance Publique Hopitaux de Paris, Hopital Pitie Salpetriere, Service de Medecine Intensive Reanimation, Institut de Cardiologie 75013 Paris France" + }, + { + "author_name": "Luis Gomes-Morales", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Pascal Grondin", + "author_inst": "Oncodesign" + }, + { + "author_name": "Olivier Lequin", + "author_inst": "Sorbonne Universite" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.08.24.264630", "rel_title": "SARS-CoV-2 neutralizing human antibodies protect against lower respiratory tract disease in a hamster model", @@ -1241034,85 +1242187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.21.20179291", - "rel_title": "Untuned antiviral immunity in COVID-19 revealed by temporal type I/III interferon patterns and flu comparison", - "rel_date": "2020-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20179291", - "rel_abs": "A central paradigm of immunity is that interferon (IFN) mediated antiviral responses precede the pro-inflammatory ones, optimizing host protection and minimizing collateral damage1,2. Here, we report that for COVID-19 this does not apply. By investigating temporal IFN and inflammatory cytokine patterns in 32 COVID-19 patients hospitalized for pneumonia and longitudinally followed for the development of respiratory failure and death, we reveal that IFN-{lambda} and type I IFN production is both diminished and delayed, induced only in a fraction of patients as they become critically ill. On the contrary, pro-inflammatory cytokines such as TNF, IL-6 and IL-8 are produced before IFNs, in all patients, and persist for a prolonged time. By comparison, in 16 flu patients hospitalized for pneumonia with similar clinicopathological characteristics to COVID-19 and 24 milder non-hospitalized flu patients IFN-{lambda} and type I IFN are robustly induced, earlier, at higher levels and independently of disease severity, while pro-inflammatory cytokines are only acutely and transiently produced. Notably, higher IFN-{lambda} levels in COVID-19 patients correlate with lower viral load in bronchial aspirates and faster viral clearance, and a higher IFN-{lambda}:type I IFN ratio with improved outcome of critically ill patients. Moreover, altered cytokine patterns in COVID-19 patients correlate with longer hospitalization time and higher incidence of critical disease and mortality compared to flu. These data point to an untuned antiviral response in COVID-19 contributing to persistent viral presence, hyperinflammation and respiratory failure.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ioanna Evdokia Galani", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - }, - { - "author_name": "Nikoletta Rovina", - "author_inst": "ICU, 1st Department of Respiratory Medicine, National and Kapodistrian University of Athens, Medical School, Sotiria General Hospital of Chest Diseases, Athens," - }, - { - "author_name": "Vicky Lampropoulou", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - }, - { - "author_name": "Vasiliki Triantafyllia", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - }, - { - "author_name": "Maria Manioudaki", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - }, - { - "author_name": "Eleftherios Pavlos", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - }, - { - "author_name": "Evangelia Koukaki", - "author_inst": "1st Department of Respiratory Medicine, National and Kapodistrian University of Athens, Medical School, Sotiria General Hospital of Chest Diseases, Athens, Gree" - }, - { - "author_name": "Paraskevi C Fragkou", - "author_inst": "4th Department of Internal Medicine, Attikon University Hospital, University of Athens Medical School, Athens, Greece" - }, - { - "author_name": "Vasiliki Panou", - "author_inst": "1st Department of Respiratory Medicine, National and Kapodistrian University of Athens, Medical School, Sotiria General Hospital of Chest Diseases, Athens, Gree" - }, - { - "author_name": "Vasiliki Rapti", - "author_inst": "4th Department of Internal Medicine, Attikon University Hospital, University of Athens Medical School, Athens, Greece" - }, - { - "author_name": "Ourania Koltsida", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - }, - { - "author_name": "Andreas Mentis", - "author_inst": "Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece" - }, - { - "author_name": "Nikolaos Koulouris", - "author_inst": "1st Department of Respiratory Medicine, National and Kapodistrian University of Athens, Medical School, Sotiria General Hospital of Chest Diseases, Athens, Gree" - }, - { - "author_name": "Sotirios Tsiodras", - "author_inst": "4th Department of Internal Medicine, Attikon University Hospital, University of Athens Medical School, Athens, Greece" - }, - { - "author_name": "Antonia Koutsoukou", - "author_inst": "ICU, 1st Department of Respiratory Medicine, National and Kapodistrian University of Athens, Medical School, Sotiria General Hospital of Chest Diseases, Athens," - }, - { - "author_name": "Evangelos Andreakos", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Athens, Greece" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.21.20167965", "rel_title": "Implications of the school-household network structure on SARS-CoV-2 transmission under different school reopening strategies in England", @@ -1241904,6 +1242978,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.23.255364", + "rel_title": "Antiviral activity of lambda-carrageenan against influenza viruses in mice and severe acute respiratory syndrome coronavirus 2 in vitro", + "rel_date": "2020-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.23.255364", + "rel_abs": "Influenza virus and coronavirus, belonging to enveloped RNA viruses, are major causes of human respiratory diseases. The aim of this study was to investigate the broad spectrum antiviral activity of a naturally existing sulfated polysaccharide, lambda-carrageenan ({lambda}-CGN), purified from marine red algae. Cell culture-based assays revealed that the macromolecule efficiently inhibited both influenza A and B viruses, as well as currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with EC50 values ranging from 0.3-1.4 g/ml. No toxicity to host cells was observed at concentrations up to 300 g/ml. Plaque titration and western blot analysis verified that {lambda}-CGN reduced expression of viral proteins in cell lysates and suppressed progeny virus production in culture supernatants in a dose-dependent manner. This polyanionic compound exerts antiviral activity by targeting viral attachment to cell surface receptors and preventing entry. Moreover, intranasal administration to mice during influenza A viral challenge not only alleviated infection-mediated reductions in body weight but also protected 60% of mice from virus-induced mortality. Thus, {lambda}-CGN could be a promising antiviral agent for preventing infection by several respiratory viruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ye Jin Jang", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Heegwon Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Myoung Kyu Lee", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Oh Seung Kwon", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Jin Soo Shin", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Yongil Kim", + "author_inst": "Hanmi Pharmaceutical Co." + }, + { + "author_name": "Meehyein Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.20.20178723", "rel_title": "Automatic analysis system of COVID-19 radiographic lung images (XrayCoviDetector)", @@ -1242496,77 +1243613,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.21.262295", - "rel_title": "Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein", - "rel_date": "2020-08-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.21.262295", - "rel_abs": "SARS-CoV-2 is a novel coronavirus that emerged in 2019 and is now classified in the genus Coronavirus with closely related SARS-CoV. SARS-CoV-2 is highly pathogenic in humans and is classified as a biosafety level (BSL)-3 pathogen, which makes manipulating it relatively difficult due to its infectious nature. To circumvent the need for BSL-3 laboratories, an alternative assay was developed that avoids live virus and instead uses a recombinant VSV expressing luciferase and possesses the full length or truncated spike proteins of SARS-CoV-2. Furthermore, to measure SARS-CoV-2 neutralizing antibodies under BSL2 conditions, a chemiluminescence reduction neutralization test (CRNT) for SARS-CoV-2 was developed. The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The CRNT, which used whole blood collected from hospitalized patients with COVID-19, was also examined. As a result, the inhibition of pseudotyped virus infection was specifically observed in both serum and whole blood and was also correlated with the results of the IFA. In conclusion, the CRNT for COVID-19 is a convenient assay system that can be performed in a BSL-2 laboratory with high specificity and sensitivity for evaluating the occurrence of neutralizing antibodies against SARS-CoV-2.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Hideki Tani", - "author_inst": "Toyama Institute of Health" - }, - { - "author_name": "Long Tan", - "author_inst": "University of Toyama" - }, - { - "author_name": "Miyuki Kimura", - "author_inst": "University of Toyama" - }, - { - "author_name": "Yoshihiro Yoshida", - "author_inst": "University of Toyama" - }, - { - "author_name": "Hiroshi Yamada", - "author_inst": "University of Toyama" - }, - { - "author_name": "Shuetsu Fukushi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masayuki Saijo", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan." - }, - { - "author_name": "Hitoshi Kawasuji", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - }, - { - "author_name": "Akitoshi Ueno", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - }, - { - "author_name": "Yuki Miyajima", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - }, - { - "author_name": "Yasutaka Fukui", - "author_inst": "University of Toyama" - }, - { - "author_name": "Ippei Sakamaki", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - }, - { - "author_name": "Yoshihiro Yamamoto", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - }, - { - "author_name": "Yoshitomo Morinaga", - "author_inst": "Nagasaki University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.19.20177550", "rel_title": "This time is different: model-based evaluation of the implications of SARS-CoV-2 infection kinetics for disease control", @@ -1243590,6 +1244636,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.19.20178129", + "rel_title": "Epidemic Analysis of COVID-19 in Egypt, Qatar and Saudi Arabia using the Generalized SEIR Model", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178129", + "rel_abs": "BackgroundSince its emergence in late December 2019 and its declaration as a global pandemic by World Health Organization (WHO) on March 11, 2020, the novel coronavirus disease known as (COVID-19) has attracted global attention. The process of modeling and predicting the pandemic behavior became crucial as the different states needed accurate predictions to be able to adopt suitable policies to minimize the pressure on their health care systems. Researchers have employed modified variants of classical SIR/SEIR models to describe the dynamics of this pandemic. In this paper, after proven effective in numerous countries, a modified variant of SEIR is implemented to predict the behavior of COVID-19 in Egypt and other countries in the Middle East and North Africa region (MENA).\n\nMethodsWe built MATLAB simulations to fit the real data of COVID-19 Active, recovered and death Cases in Egypt, Qatar and Saudi Arabia to the modified SEIR model via Nelder-Mead algorithm to be able to estimate the future dynamics of the pandemic.\n\nFindingsWe estimate several characteristics of COVID-19 future dynamics in Egypt, Qatar and Saudi Arabia. We also estimate that the pandemic will resolve in the countries under investigation in February 2021, January 2021 and 28th August 2020 With total death cases of 9,742, 5,600, 185 and total cases of 187,600, 490,000, 120,000, respectively.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ahmed E Fahmy", + "author_inst": "Zewail University of Science and Technology" + }, + { + "author_name": "Mohammed M Eldesouky", + "author_inst": "Zewail University of Science and Technology" + }, + { + "author_name": "Ahmed S.A. Mohamed", + "author_inst": "Zewail University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.19.20177956", "rel_title": "Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area", @@ -1244094,61 +1245167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.19.20178350", - "rel_title": "CLINICAL COURSE, RISK FACTORS FOR TRANSFER TO ICU AND MORTALITY IN PATIENTS WITH COVID-19 AFFECTED BY ACUTE RESPIRATORY FAILURE REFERRED TO A RESPIRATORY INTERMEDIATATE CARE UNIT.", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178350", - "rel_abs": "IntroductionThere are no clear guidelines as yet for the selection of patients affected by COVID-19 who can be treated in intermediate RICU, neither shared criteria for their intubation and transfer in ICU.\n\nIn the present study we described the clinical course and risk factors for transfer to ICU and mortality of SARS-Cov-2 positive patients affected by acute respiratory failure, hospitalized in a Respiratory Intermediate Care Unit in the south of Italy.\n\nMethodsIn this retrospective, observational single centre study we evaluated 96 laboratory confirmed COVID-19 patients affected by acute respiratory failure (ARF). We compared demographic data, laboratory data and clinical outcomes between deceased and survived patients, aiming to identify risk factors for transfer to ICU and mortality, and possible gender-related differences.\n\nResultsOf 96 patients, 51 (53.1%) survived and 45 (46.9 %) died. Among those who died, 23 (51.1%) deceased in RICU. Twenty-nine (30.2%) were transferred to ICU, of whom 22 (75.9%) died in ICU. Patients affected by COPD have a higher mortality compared to patients without this comorbidity (p = 0.002). Lower baseline P/F ratio (p = 0,014) and neurologic comorbidities (p = 0,008) emerged as risk factors for death.\n\nMale were younger than female patients (66 vs 80 y.o.; p = 0.042). In female patients, lower peripheral blood lymphocyte count (p = 0.007) is a risk factor for death, characteristic gender-related in our sample.\n\nFemale sex was a protective parameter against transfer to ICU (p = 0,036) and P/F ratio wasnt a significant predictor of transfer to ICU (p = 0,227).\n\nOnly higher baseline CRP (p = 0,034) has shown a predictive role for transfer to ICU in our sample. Patients deceased after a transfer to ICU had younger age (p = 0,000), lower median comorbidity number (p = 0,000), lower D-dimer (p = 0,029) and lower prevalence of female sex (p = 0,029).\n\nDiscussionMortality in our study was similar to that found in other studies involving patients in non-invasive ventilation. In our study older age and comorbidities play as predictors of death in COVID-19 patients. COPD, despite presenting low prevalence, is a risk factor for death, both in men and women. In female patients chronic ischemic heart disease and congestive heart failure are death predictors. High CRP and lymphopenia, linked to inflammatory status, are predictors of transfer to ICU. Patients transferred to ICU higher mortality than the others, and patients who die in ICU are mostly men, younger and have less comorbidities. Baseline P/F ratio is not a good predictor of transfer to ICU, while in our sample is a sensible predictor of death. More studies need to be performed on COVID-19 patients, in the urgency of COVID-19 pandemic persistence.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Enrico Buonamico", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Vitaliano Nicola Quaranta", - "author_inst": "\"Di Venere\" Hospital of Bari, Italy" - }, - { - "author_name": "Esterina Boniello", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Michela Dimitri", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Marco Majorano", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Luciana Labate", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Paola Pierucci", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Federica Barratta", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Giovanna Elisiana Carpagnano", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - }, - { - "author_name": "Onofrio Resta", - "author_inst": "Department of Basic Medical Science, Neuroscience and Sense Organs - \"Aldo Moro\" University of Bari, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.08.21.261727", "rel_title": "The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera.", @@ -1245112,6 +1246130,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.17.20176735", + "rel_title": "Comparing the Fit of N95, KN95, Surgical, and Cloth Face Masks and Assessing the Accuracy of Fit Checking", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176735", + "rel_abs": "IntroductionThe COVID-19 pandemic has made well-fitting face masks a critical piece of protective equipment for healthcare workers and civilians. While the importance of wearing face masks has been acknowledged, there remains a lack of understanding about the role of good fit in rendering protective equipment useful. In addition, supply chain constraints have caused some organizations to abandon traditional quantitative or qualitative fit testing, and instead, have implemented subjective fit checking. Our study seeks to quantitatively evaluate the level of fit offered by various types of masks, and most importantly, assess the accuracy of implementing fit checks by comparing fit check results to quantitative fit testing results.\n\nMethodsSeven participants first evaluated N95 and KN95 masks by performing a fit check. Participants then underwent quantitative fit testing wearing five N95 masks, a KN95 mask, a surgical mask, and fabric masks.\n\nResultsN95 masks offered higher degrees of protection than the other categories of masks tested; however, it should be noted that most N95 masks failed to fit the participants adequately. Fit check responses had poor correlation with quantitative fit scores. All non-N95 masks achieved low fit scores.\n\nConclusionFit is critical to the level of protection offered by masks. For an N95 mask to provide the promised protection, it must fit the participant. Performing a fit check was an unreliable way of determining fit.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Eugenia O'Kelly", + "author_inst": "Cambridge University" + }, + { + "author_name": "Anmol Arora", + "author_inst": "Cambridge University" + }, + { + "author_name": "Sophia Pirog", + "author_inst": "Northwestern University" + }, + { + "author_name": "James Ward", + "author_inst": "Cambridge University" + }, + { + "author_name": "P John Clarkson", + "author_inst": "Cambridge University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.17.20175117", "rel_title": "Real-time spatial health surveillance: mapping the UK COVID-19 epidemic", @@ -1245912,77 +1246965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.17.20176594", - "rel_title": "ELISA detection of SARS-CoV-2 antibodies in saliva", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176594", - "rel_abs": "To facilitate containment of the COVID-19 pandemic currently active in the United States and across the world, options for easy, non-invasive antibody testing are required. Here we have adapted a commercially available, serum-based ELISA for use with saliva samples, which will enable widespread, affordable testing for patients who experienced this disease.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Melanie A MacMullan", - "author_inst": "Curative Inc, San Dimas, CA 91773, USA; Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of South" - }, - { - "author_name": "Albina Ibrayeva", - "author_inst": "Curative Inc, San Dimas, CA 91773, USA; Eli and Edythe Broad Center for Regenerative Medicine & Stem Cell Research at USC, Department of Stem Cell Biology and R" - }, - { - "author_name": "Kylie Trettner", - "author_inst": "Curative Inc, San Dimas, CA 91773, USA; Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of South" - }, - { - "author_name": "Laura Deming", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Sudipta Das", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Frances Tran", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Jose Ricardo Moreno", - "author_inst": "Curative Inc, San Dimas, CA 91773; Bridge Institute, Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California" - }, - { - "author_name": "Joseph G Casian", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Prithivi Chellamuthu", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Jeffrey Kraft", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Kenneth Kozak", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Fred E Turner", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Vladimir I Slepnev", - "author_inst": "Curative Inc, San Dimas, CA 91773" - }, - { - "author_name": "Lydia M Le Page", - "author_inst": "Curative Inc, San Dimas, CA 91773" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.17.20176917", "rel_title": "A DEEP LEARNING MODEL TO PREDICT THE NEED FOR MECHANICAL VENTILATION USING CHEST X-RAY IMAGES IN HOSPITALIZED COVID-19 PATIENTS", @@ -1246750,6 +1247732,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.20.260190", + "rel_title": "Astodrimer sodium, dendrimer antiviral, inhibits replication of SARS-CoV-2 in vitro", + "rel_date": "2020-08-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.20.260190", + "rel_abs": "An effective response to the ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will involve a range of complementary preventive modalities. The current studies were conducted to evaluate the in vitro SARS-CoV-2 antiviral and virucidal activity of astodrimer sodium, a dendrimer with broad spectrum antimicrobial activity, including against enveloped viruses in in vitro and in vivo models, that is marketed for antiviral and antibacterial applications. We report that astodrimer sodium inhibits replication of SARS-CoV-2 in Vero E6 and Calu-3 cells, with 50% effective concentrations (EC50) for i) reducing virus-induced cytopathic effect of 0.002 to 0.012 mg/mL in Vero E6 cells, and ii) infectious virus release by plaque assay of 0.019 to 0.031 mg/mL in Vero E6 cells and 0.031 to 0.045 mg/mL in Calu-3 cells. The selectivity index (SI) in these assays was as high as 2197. Astodrimer sodium was also virucidal, reducing SARS-CoV-2 infectivity by >99.9% (>3 log10) within 1 minute of exposure, and up to >99.999% (>5 log10) shown at astodrimer sodium concentrations of 10 to 30 mg/mL in Vero E6 and Calu-3 cell lines. Astodrimer sodium also inhibited infection in a primary human airway epithelial cell line. The data were similar for all investigations and were consistent with the potent antiviral and virucidal activity of astodrimer sodium being due to inhibition of virus-host cell interactions, as previously demonstrated for other viruses. Further studies will confirm if astodrimer sodium binds to SARS-CoV-2 spike protein and physically blocks initial attachment of the virus to the host cell. Given the in vitro effectiveness and significantly high SI, astodrimer sodium warrants further investigation for potential as a nasally administered or inhaled antiviral agent for SARS-CoV-2 prevention and treatment applications.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jeremy R.A. Paull", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Graham P. Heery", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Michael D Bobardt", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Alex Castellarnau", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Carolyn A. Luscombe", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Jacinth K. Fairley", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Philippe A Gallay", + "author_inst": "Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.21.261289", "rel_title": "Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses", @@ -1247454,65 +1248479,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.18.20177121", - "rel_title": "Persistence of SARS-CoV-2 in the first trimester placenta leading to vertical transmission and fetal demise from an asymptomatic mother", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177121", - "rel_abs": "Coronaviruses infect the respiratory tract and are known to survive in these tissues during the clinical course of infection. However, how long can SARS-CoV-2 survive in the tissues is hitherto unknown. Herein, we report a case where the virus is detected in the first trimester placental cytotrophoblast and syncytiotrophoblasts five weeks after the asymptomatic mother cleared the virus from the respiratory tract. This first trimester placental infection was vertically transmitted as the virus was detected in the amniotic fluid and fetal membranes. This congenitally acquired SARS-CoV-2 infection was associated with hydrops and fetal demise. This is the first study providing concrete evidences towards persistent tissue infection of SARS-CoV-2, its congenital transmission in early pregnancy leading to intrauterine fetal death.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Prajakta Shende", - "author_inst": "ESI- PGIMSR and Model Hospital Andheri; E.S.I.S. Hospital Kandivali" - }, - { - "author_name": "Pradip Gaikwad", - "author_inst": "ESI- PGIMSR and Model Hospital Andheri; E.S.I.S. Hospital Kandivali" - }, - { - "author_name": "Manisha Gandhewar", - "author_inst": "ESI- PGIMSR and Model Hospital Andheri; E.S.I.S. Hospital Kandivali" - }, - { - "author_name": "Pawankumar Ukey", - "author_inst": "ESI- PGIMSR and Model Hospital Andheri; E.S.I.S. Hospital Kandivali" - }, - { - "author_name": "Anshul Bhide", - "author_inst": "ICMR-National Institute for Research in Reproductive Health" - }, - { - "author_name": "Vainav Patel", - "author_inst": "ICMR-National Institute for Research in Reproductive Health" - }, - { - "author_name": "Sharad Bhagat", - "author_inst": "ICMR-National Institute for Research in Reproductive Health" - }, - { - "author_name": "Vikrant Bhor", - "author_inst": "ICMR-National Institute for Research in Reproductive Health" - }, - { - "author_name": "Smita Mahale", - "author_inst": "ICMR-National Institute for Research in Reproductive Health" - }, - { - "author_name": "Rahul Gajbhiye", - "author_inst": "ICMR-National Institute for Research in Reproductive Health" - }, - { - "author_name": "Deepak Modi", - "author_inst": "ICMR-National Institute for Research in Reproductive Heath" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.08.18.20177410", "rel_title": "Inadequate preparedness for response to COVID-19 is associated with stress and burnout among healthcare workers in Ghana", @@ -1248480,6 +1249446,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.16.20175901", + "rel_title": "Air pollution, SARS-CoV-2 transmission, and COVID-19 outcomes: A state-of-the-science review of a rapidly evolving research area", + "rel_date": "2020-08-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20175901", + "rel_abs": "BackgroundAs the coronavirus pandemic rages on, 692,000 (August 7, 2020) human lives and counting have been lost worldwide to COVID-19. Understanding the relationship between short- and long-term exposure to air pollution and adverse COVID-19 health outcomes is crucial for developing solutions to this global crisis.\n\nObjectivesTo conduct a scoping review of epidemiologic research on the link between short- and long-term exposure to air pollution and COVID-19 health outcomes.\n\nMethodWe searched PubMed, Web of Science, Embase, Cochrane, MedRxiv, and BioRxiv for preliminary epidemiological studies of the association between air pollution and COVID-19 health outcomes. 28 papers were finally selected after applying our inclusion/exclusion criteria; we categorized these studies as long-term studies, short-term time-series studies, or short-term cross-sectional studies. One study included both short-term time-series and a cross-sectional study design.\n\nResults27 studies of the 28 reported evidence of statistically significant positive associations between air pollutant exposure and adverse COVID-19 health outcomes; 11 of 12 long-term studies and all 16 short-term studies reported statistically significant positive associations. The 28 identified studies included various confounders, spatial and temporal resolutions of pollution concentrations, and COVID-19 health outcomes.\n\nDiscussionWe discuss methodological challenges and highlight additional research areas based on our findings. Challenges include data quality issues, ecological study design limitations, improved adjustment for confounders, exposure errors related to spatial resolution, geographic variability in testing, mitigation measures and pandemic stage, clustering of health outcomes, and a lack of publicly available data and code.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anushka Bhaskar", + "author_inst": "Harvard University" + }, + { + "author_name": "Jay Chandra", + "author_inst": "Harvard University" + }, + { + "author_name": "Danielle Braun", + "author_inst": "Harvard TH Chan School of Public Health" + }, + { + "author_name": "Jacqueline Cellini", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Francesca Dominici", + "author_inst": "Harvard TH Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.08.19.257493", "rel_title": "Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2", @@ -1249472,53 +1250473,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.16.20176230", - "rel_title": "Aeromedical retrieval diagnostic trends during a period of Coronavirus 2019 lockdown", - "rel_date": "2020-08-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20176230", - "rel_abs": "BackgroundWe aimed to compare the pre, lockdown, and post-lockdown aeromedical retrieval (AR) diagnostic reasons and patient demographics during a period of Coronavirus 2019 (COVID-19) social isolation.\n\nMethodsAn observational study with retrospective data collection, consisting of Australians who received an AR between the 26 January to the 23 June 2020. The main outcome measures were patient diagnostic category proportions and trends prior (28 January to 15 March), during (16 March to 4 May), and following (5 May to 23 June 2020) social isolation restrictions.\n\nResultsThere were 16981 ARs consisting of 1959 (11.5) primary evacuations (PE) and 12724 (88.5) inter-hospital transfer (IHT), with a population median age of 52 years old (interquartile range [IQR]\n\n29.0-69.0), with 49.0% (n = 8283) of the cohort being male and 38.0% (n = 6399) being female. There were a total of 6 confirmed and 209 suspected cases of COVID-19, with the majority of cases (n = 114;\n\n53.0%) in the social isolation period. As compared to pre-restriction, the odds of retrieval for the restriction and post-restriction period differed across time between the major diagnostic groups. This included, an increase in cardiovascular retrieval for both restriction and post-restriction periods (OR 1.12 95% CI 1.02-1.24 and OR 1.18 95% CI 1.08-1.30 respectively), increases in neoplasm in the post restriction period (OR 1.31 95% CI 1.04-1.64), and increases for congenital conditions in the restriction period (OR 2.56 95% CI 1.39-4.71). Cardiovascular and congenital conditions had increased rates of priority 1 patients in the restriction and post restriction periods. There was a decrease in endocrine and metabolic disease retrievals in the restriction period (OR 0.72 95% CI 0.53-0.98). There were lower odds during the post-restriction period for a retrievals of the respiratory system (OR 0.78 95% CI 0.67-0.93), and disease of the skin (OR 0.78 95% CI 0.6-1.0). Distribution between the 2019 and 2020 time periods differed (p< 0.05), with the lockdown period resulting in a significant reduction in activity.\n\nConclusionThe lockdown period resulted in increased AR rates of circulatory and congenital conditions. However, this period also resulted in a reduction of overall activity, possibly due to a reduction in other infectious disease rates, such as influenza, due to social distancing.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Fergus W Gardiner", - "author_inst": "Royal Flying Doctor Service" - }, - { - "author_name": "Marianne Gillam", - "author_inst": "University of South Australia" - }, - { - "author_name": "Leonid Churilov", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Pritish Sharma", - "author_inst": "The Royal Flying Doctor Service" - }, - { - "author_name": "Mardi Steere", - "author_inst": "The Royal Flying Doctor Service" - }, - { - "author_name": "Michelle Hannan", - "author_inst": "The Royal Flying Doctor Service" - }, - { - "author_name": "Andrew Hooper", - "author_inst": "The Royal Flying Doctor Service" - }, - { - "author_name": "Frank Quinlan", - "author_inst": "The Royal Flying Doctor Service" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.08.17.20176255", "rel_title": "Effects of case- and population-based COVID-19 interventions in Taiwan", @@ -1250426,6 +1251380,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.17.20174821", + "rel_title": "Quantifying the efficiency of non-pharmaceutical interventions against SARS-COV-2 transmission in Europe", + "rel_date": "2020-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20174821", + "rel_abs": "Since the emergence of SARS-CoV-2, governments around the World have implemented a combination of public health responses based on non-pharmaceutical interventions (NPIs), with significant social and economic consequences. Though most European countries have overcome the first epidemic wave, it remains of high priority to quantify the efficiency of different NPIs to inform preparedness for an impending second wave. In this study, combining capture-recapture methods with Bayesian inference in an age-structured mathematical model, we use a unique European dataset compiled by the European Centre for Disease Control (ECDC) to quantify the efficiency of 24 NPIs and their combinations (referred to as public health responses, PHR) in reducing SARS-Cov-2 transmission rates in 32 European countries. Of 166 unique PHR tested, we found that median decrease in viral transmission was 74%, which is enough to suppress the epidemic. PHR efficiency was positively associated with the number of NPIs implemented. We found that bans on mass gatherings had the largest effect among NPIs, followed by school closures, teleworking, and stay home orders. Partial implementation of most NPIs resulted in lower than average response efficiency. This first large-scale estimation of NPI and PHR efficiency against SARS-COV-2 transmission in Europe suggests that a combination of NPIs targeting different population groups should be favored to control future epidemic waves.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andres Garchitorena", + "author_inst": "Institut de Recherche pour le Developpement" + }, + { + "author_name": "Hugo Gruson", + "author_inst": "IRD" + }, + { + "author_name": "Bernard Cazelles", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Tommi Karki", + "author_inst": "European Centre for Disease Control" + }, + { + "author_name": "Bertrand Sudre", + "author_inst": "European Centre for Disese Control" + }, + { + "author_name": "Benjamin ROCHE", + "author_inst": "IRD" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.17.20176552", "rel_title": "SARS-CoV-2 antibody responses in children with MIS-C and mild and severe COVID-19", @@ -1251122,129 +1252115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.08.17.254375", - "rel_title": "Equine hyperimmune globulin raised against the SARS-CoV-2 spike glycoprotein has extremely high neutralizing titers", - "rel_date": "2020-08-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.17.254375", - "rel_abs": "We used the trimeric spike (S) glycoprotein (residues 1-1208) in the prefusion conformation to immunize horses for production of hyperimmune globulins against SARS-CoV-2. Serum antibody titers measured by anti-spike ELISA were above 1:1,000,000, and neutralizing antibody titer was 1:14,604 (average PRNT90), which is 140-fold higher than the average neutralizing titer of plasma from three convalescent COVID-19 patients analyzed for comparison. Using the same technology routinely used for industrial production of other horse hyperimmune products, plasma from immunized animals was pepsin digested to remove the Fc portion and purified, yielding a F(ab)2 preparation with PRNT90 titers 150-fold higher than the neutralizing titers in human convalescent plasma. Repeating the hyperimmunization in a second group of horses confirmed the very high neutralizing titers in serum and in a GMP clinical F(ab)2 lot. Virus-neutralizing activity in samples from mice that received the F(ab)2 preparation was detected even three days after injection, indicating an appropriate half-life for therapeutic intervention. These results supported the design of a clinical trial (identifier NCT04573855) to evaluate safety and efficacy of this horse F(ab)2 preparation.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Luis Eduardo R. Cunha", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Adilson A. Stolet", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Marcelo A. Strauch", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Victor A. R. Pereira", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Carlos H. Dumard", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Andre M. O. Gomes", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Patricia N. C. Souza", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Juliana G. Fonseca", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Francisco E. Pontes", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Leonardo G. R. Meirelles", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Jose W. M. Albuquerque", - "author_inst": "Vital Brazil Institute" - }, - { - "author_name": "Carolina Q. Sacramento", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Tulio M. Lima", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Renata G. F. Alvim", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Federico F. Marsili", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Marcella M. Caldeira", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Luisa M. Higa", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Fabio L. Monteiro", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Russolina Zingali", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Guilherme A. P. Oliveira", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Thiago M. L. Souza", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Amilcar Tanuri", - "author_inst": "UFRJ" - }, - { - "author_name": "Andrea C. Oliveira", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Herbert L. M. Guedes", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Leda R. Castilho", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Jerson L. Silva", - "author_inst": "Federal University of Rio de Janeiro" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.18.255877", "rel_title": "Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2", @@ -1252288,6 +1253158,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.15.20175513", + "rel_title": "Behavioral preventive measures and the use of medicines and herbal products among the public in response to Covid-19 in Bangladesh: A cross-sectional study", + "rel_date": "2020-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175513", + "rel_abs": "The present study was conducted to assess the behavioral preventive measures and the use of medicines and herbal foods/products among the public in response to Covid-19. A cross-sectional survey was conducted from 27 June to 20 July 2020, and 1222 people participated. Kruskal-Wallis test was used to identify the differences in behavioral preventive practices across different demographic categories. To identify the factors associated with the use of preventive medicines and herbal foods/products, multivariable logistic regression was performed. Most participants adopted the recommended preventive practices such as washing hands more frequently (87.5%), staying home more often (85.5%), avoiding crowds (86%), and wearing masks (91.6%). About half of the smokers reported a decreased rate of smoking during the pandemic. Also, 14.8% and 57.6% of the participants took medicines and herbal foods/products as preventive measures against Covid-19. Arsenicum album and Zinc supplements were the most commonly used preventive medicines. Gender, age, and fear of Covid-19 were significantly associated with the use of both preventive medicines and herbal products. For the management of Covid-19 related symptoms, Paracetamols, Fexofenadine, and Zinc supplements were used most often. Most participants sought information from non-medical sources while using medicines and herbal products. Moreover, potentially inappropriate and unnecessary use of drugs were identified.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Iftekhar Ahmed", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh" + }, + { + "author_name": "Maruf Hasan", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh" + }, + { + "author_name": "Rahima Akter", + "author_inst": "Department of Pharmacy, World University of Bangladesh, Dhaka, Bangladesh" + }, + { + "author_name": "Bidduth Kumar Sarkar", + "author_inst": "Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj, Bangladesh" + }, + { + "author_name": "Marufa Rahman", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Md Samun Sarker", + "author_inst": "Bangladesh Livestock Research Institute (BLRI), Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Mohammed A. Samad", + "author_inst": "Bangladesh Livestock Research Institute (BLRI), Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.15.20175786", "rel_title": "Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community", @@ -1252936,81 +1253849,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.08.16.20175752", - "rel_title": "Hydroxychloroquine Safety Outcome within Approved Therapeutic Protocol for COVID-19 Outpatients in Saudi Arabia", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20175752", - "rel_abs": "BackgroundHealthcare systems globally has been challenged following the COVID-19 pandemic, since late 2019. Multiple approaches and strategies have been performed to relieve the pressure and support existing healthcare systems. The Saudi Arabian Ministry of Health (MOH) launched an initiative to support the National Healthcare System. Since the 5th of June 2020, 238 outpatient fever clinics were established across Saudi Arabia.\n\nMethodsA cross-sectional study included 2,733 eligible patients subjected to MOH treatment protocol (hydroxychloroquine and zinc) and revisited the clinics within 3-7 days after treatment initiation. This study aimed to assess the safety outcome and reported adverse events from hydroxychloroquine use among suspected COVID-19 patients. The data was collected through an electronic link and cross-checked with that of the national database (Health Electronic Surveillance Network, HESN) and reports from the MOH Morbidity and Mortality (M&M) Committee.\n\nResultsMajority of the cases were males (70.4%). Upon reassessing the studied participants within 3-7 days, 240 patients (8.8%) discontinued the treatment protocol because of the development of side effects (4.1%) and for non-clinical reasons in the remaining (4.7%). Medication side effects overall were reported among (6.7%) of all studied participants, including mainly cardiovascular adverse events (2.5%), followed by gastrointestinal (GI) symptoms (2.4%). No Intensive Care Unit (ICU) admission or death were reported among these patients.\n\nConclusionIn our study, results show that the use of hydroxychloroquine for COVID-19 patients in mild to moderate cases in an outpatient setting, within the protocol recommendation and inclusion/exclusion criteria, is safe, highly tolerable, and with minimum side effects.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Abdulrhman Mohana", - "author_inst": "Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia" - }, - { - "author_name": "Tarek Suliman", - "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" - }, - { - "author_name": "Nagla Mahmoud", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Mustafa Hassanein", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Amel Alfaifi", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Eissa Alenazi", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Nashwa Radwan", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Nasser Alkhalifah", - "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" - }, - { - "author_name": "Ehab Elkady", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Abdullah Almohaizeie", - "author_inst": "King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fouad AboGazalah", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Khaled AbdulKareem", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fahad AlGhofaili", - "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" - }, - { - "author_name": "Hani Jokhdar", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fahad Alrabiah", - "author_inst": "King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.14.20175356", "rel_title": "SARS-Coronavirus-2 nucleocapsid protein measured in blood using a Simoa ultra-sensitive immunoassay differentiates COVID-19 infection with high clinical sensitivity.", @@ -1253970,6 +1254808,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.14.20170878", + "rel_title": "Estimating the epidemic growth dynamics within the first week", + "rel_date": "2020-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20170878", + "rel_abs": "Information about the early growth of infectious outbreaks are indispensable to estimate the epidemic spreading. A large number of mathematical tools have been developed to this end, facing as much large number of different dynamic evolutions, ranging from sub-linear to super-exponential growth. Of course, the crucial point is that we do not have enough data during the initial outbreak phase to make reliable inferences. Here we propose a methodology to estimate the epidemic growth dynamics from the infected cumulative data of just a week, provided a surveillance system is available over the whole territory. The methodology, based on the Newcomb-Benford Law, is applied to Italian covid 19 case-study. Results show that it is possible to discriminate the epidemic dynamics using the first seven data points collected over fifty Italian cities. Moreover, the form of the most probable approximating function of the growth, within a six weeks epidemic scenario, is identified.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "VINCENZO FIORITI", + "author_inst": "ENEA" + }, + { + "author_name": "IVAN ROSELLI", + "author_inst": "ENEA" + }, + { + "author_name": "MARTA CHINNICI", + "author_inst": "ENEA" + }, + { + "author_name": "ANDREA ARBORE", + "author_inst": "ICT CONSULTANT" + }, + { + "author_name": "NICOLA SIGISMONDI", + "author_inst": "ICT CONSULTANT" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.14.20175190", "rel_title": "Bidirectional associations between COVID-19 and psychiatric disorder: a study of 62,354 COVID-19 cases", @@ -1254858,25 +1255731,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.15.252411", - "rel_title": "Multifractal Analysis of SARS-CoV-2 Coronavirus genomes using the wavelet transform.", - "rel_date": "2020-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.15.252411", - "rel_abs": "In this paper, the 1D Wavelet Transform Modulus Maxima lines (WTMM) method is used to investigate the Long-Range Correlation (LRC) and to estimate the so-called Hurst exponent of 21 isolate RNA sequence downloaded from the NCBI database of patients infected by SARS-CoV-2, Coronavirus, the Knucleotidic, Purine, Pyramidine, Ameno, Keto and GC DNA coding are used. Obtained results show the LRC character in the most sequences; except some sequences where the anti-correlated or the Classical Brownian motion character is observed, demonstrating that the SARS-Cov2 coronavirus undergoes mutation from a country to another or in the same country, they reveals also the complexity and the heterogeneous genome structure organization far from the equilibrium and the self-organization.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sid-Ali Ouadfeul", - "author_inst": "Algerian Petroleum Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.08.14.20174896", "rel_title": "Modelling Suggests Limited Change in the Reproduction Number from Reopening Norwegian Kindergartens and Schools During the COVID-19 Pandemic", @@ -1255980,6 +1256834,97 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.08.14.248880", + "rel_title": "In plain sight: the role of alpha-1-antitrypsin in COVID-19 pathogenesis and therapeutics.", + "rel_date": "2020-08-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.248880", + "rel_abs": "RationaleSARS-CoV-2 entry into host cells is facilitated by endogenous and exogenous proteases that proteolytically activate the spike glycoprotein and antiproteases inhibiting this process. Understanding the key actors in viral entry is crucial for advancing knowledge of virus tropism, pathogenesis, and potential therapeutic targets.\n\nObjectivesWe aimed to investigate the role of naive serum and alpha-1-antitrypsin (AAT) in inhibiting protease-mediated SARS-CoV-2 entry and explore the implications of AAT deficiency on susceptibility to different SARS-CoV-2 variants.\n\nFindingsOur study demonstrates that naive serum exhibits significant inhibition of SARS-CoV-2 entry, with AAT identified as the major serum protease inhibitor potently restricting entry. Using pseudoparticles, replication-competent pseudoviruses, and authentic SARS-CoV-2, we show that AAT inhibition occurs at low concentrations compared with those in serum and bronchoalveolar tissues, suggesting physiological relevance. Furthermore, sera from subjects with an AAT-deficient genotype show reduced ability to inhibit entry of both Wuhan-Hu-1 (WT) and B.1.617.2 (Delta) but exhibit no difference in inhibiting B.1.1.529 (Omicron) entry.\n\nConclusionsAAT may have a variant-dependent therapeutic potential against SARS-CoV-2. Our findings highlight the importance of further investigating the complex interplay between proteases, antiproteases, and spike glycoprotein activation in SARS-CoV-2 and other respiratory viruses to identify potential therapeutic targets and improve understanding of disease pathogenesis.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Christian S Stevens", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kasopefoluwa Y Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shreyas Kowdle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aditya Gowlikar", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mohammed NA Siddiquey", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Joshua A Acklin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Griffin Haas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert M Schilke", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Matthew D Woolard", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Hongbo Zhang", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Luca Brambilla", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Satoshi Ikegame", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Chuan-tien Hung", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jean K Lim", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert W Cross", + "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" + }, + { + "author_name": "Thomas W Geisbert", + "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" + }, + { + "author_name": "Stanimir S Ivanov", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Jeremy P Kamil", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.13.20174508", "rel_title": "Data Mining Approach to Analyze Covid19 Dataset of Brazilian Patients", @@ -1256492,69 +1257437,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.13.243303", - "rel_title": "Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion", - "rel_date": "2020-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.243303", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells by binding to the host cell receptor Ace2 and undergoing virus-host membrane fusion. Fusion is triggered by the protease TMPRSS2, which processes the viral Spike (S) protein to reveal the fusion peptide. SARS-CoV-2 has evolved a multibasic site at the S1-S2 boundary, which is thought to be cleaved by furin in order to prime S protein for TMPRSS2 processing. Here we show that CRISPR-Cas9 knockout of furin reduces, but does not prevent, the production of infectious SARS-CoV-2 virus. Comparing S processing in furin knockout cells to multibasic site mutants reveals that while loss of furin substantially reduces S1-S2 cleavage it does not prevent it. SARS-CoV-2 S protein also mediates cell-cell fusion, potentially allowing virus to spread virion-independently. We show that loss of furin in either donor or acceptor cells reduces, but does not prevent, TMPRSS2-dependent cell-cell fusion, unlike mutation of the multibasic site that completely prevents syncytia formation. Our results show that while furin promotes both SARS-CoV-2 infectivity and cell-cell spread it is not essential, suggesting furin inhibitors will not prevent viral spread.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Guido Papa", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Donna Mallery", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Anna Albecka", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Lawrence Welch", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Jerome Cattin-Ortola", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Jakub Luptak", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "David Paul", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Harvey T McMahon", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Ian G. Goodfellow", - "author_inst": "Division of Virology, Department of Pathology, University of Cambridge Cambridge, UK" - }, - { - "author_name": "Andrew P Carter", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Sean Munro", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Leo C James", - "author_inst": "MRC-Laboratory of Molecular Biology, Cambridge, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.13.249953", "rel_title": "Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses", @@ -1257482,6 +1258364,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.11.20145086", + "rel_title": "Face Coverings and Respiratory Tract Droplet Dispersion", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20145086", + "rel_abs": "Respiratory droplets are the primary transmission route for SARS-CoV-2. Evidence suggests that virus transmission can be reduced by face coverings, but robust evidence for how mask usage might affect safe distancing parameters is lacking. Accordingly, we investigate the effectiveness of surgical masks and single-layer cotton masks on mitigating dispersion of large respiratory droplets (i.e. non aerosol). We tested a manikin ejecting fluorescent droplets and human volunteers in speaking and coughing conditions. We quantified the number of droplets in flight using laser sheet illumination and UV-light for those that had landed at table height at up to 2m. For human volunteers, expiratory droplets were caught on a microscope slide 5cm from the mouth. Whether manikin or human, wearing a face covering decreased the number of projected droplets by >1000-fold. We estimated that a person standing 2m from someone coughing without a mask is exposed to over 1000 times more respiratory droplets than from someone standing 5 cm away wearing a basic single layer mask. Our results indicate that face coverings show consistent efficacy at blocking respiratory droplets. If aerosol transmission is later determined to be a significant driver of infection, then our findings may overestimate the effectiveness of face coverings.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lucia Bandiera", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Geethanjali Pavar", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Gabriele Pisetta", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Shuji Otomo", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Enzo Mangano", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Jonathan R. Seckl", + "author_inst": "Queen`s Medical Research Institute, University of Edinburgh" + }, + { + "author_name": "Paul Digard", + "author_inst": "The Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Emanuela Molinari", + "author_inst": "School of Informatics, University of Edinburgh" + }, + { + "author_name": "Filippo Menolascina", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Ignazio Maria Viola", + "author_inst": "School of Engineering, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.11.20173062", "rel_title": "Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence", @@ -1258206,97 +1259143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.12.20173609", - "rel_title": "Frontline healthcare workers' knowledge and perception of COVID-19 and willingness to work during the pandemic in Nepal: a nationwide cross-sectional web-based study", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173609", - "rel_abs": "BackgroundThe health sectors effectiveness during a pandemic primarily depends on the availability, knowledge, skills, perceptions, and motivations of frontline healthcare workers. In this study, we aimed to investigate the contextual factors associated with the knowledge, perceptions, and the willingness of frontline healthcare workers to work during the COVID-19 pandemic in Nepal.\n\nMethodsA total of 1051 frontline health-workers from all seven Nepalese provinces were included in this web-based cross-sectional study, which was conducted in May 2020. Using a 5-point Likert scale questionnaire, we collected information on knowledge, perceptions, and the willingness of frontline healthcare workers to work during the COVID-19 pandemic. Multivariable logistic regression was applied to identify independent associations between predictors and outcome variables.\n\nResultsOf the 1051 frontline health-workers, 17.2% were found to have inadequate knowledge on COVID-19, 63.6% reported unsatisfactory perceptions of government response, and 35.9% showed an unwillingness to work during the pandemic. Health workers at local health facilities (AOR: 0.35; 95% CI: 0.17-0.68) and those with chronic diseases were less likely to have adequate knowledge of COVID-19. Nurses (AOR: 2.10; 95% CI: 1.38-3.18), health-workers from Karnali Province (AOR: 2.62; 95% CI: 1.52-4.53), and those who had adequate knowledge of COVID-19 (AOR: 3.86; 95% CI: 2.51-6.16) were more likely to have satisfactory perception towards government response to COVID-19. In addition, laboratory-workers, health workers from Karnali province, and those with adequate knowledge (AOR: 1.81; 95% CI: 1.27-2.58) were more likely to work during the COVID-19 pandemic.\n\nConclusionsWe concluded that frontline healthcare workers have some gaps in knowledge-related to COVID-19; about two-thirds of them had a negative perception of government response, and nearly one-third of them were unwilling to work. These observations demonstrate that prompt actions are required to improve health-worker knowledge of COVID-19, address negative perceptions to government responses, and motivate them to provide healthcare services during the pandemic.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "DIPAK PRASAD UPADHYAYA", - "author_inst": "Central Department of Public Health, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal" - }, - { - "author_name": "Rajan Paudel", - "author_inst": "Central Department of Public Health, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal" - }, - { - "author_name": "Daniel J Bromberg", - "author_inst": "Department of Social and Behavioral Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA" - }, - { - "author_name": "Dilaram Acharya", - "author_inst": "Department of Preventive Medicine, College of Medicine, Dongguk University, South Korea" - }, - { - "author_name": "Kaveh Khoshnood", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven CT, USA" - }, - { - "author_name": "Kwan Lee", - "author_inst": "Department of Preventive Medicine, College of Medicine, Dongguk University, Gyeongju 38066 South Korea" - }, - { - "author_name": "Ji-Huyuk Park", - "author_inst": "Department of Preventive Medicine, College of Medicine, Dongguk University, South Korea" - }, - { - "author_name": "Seok-Ju Yoo", - "author_inst": "Department of Preventive Medicine, College of Medicine, Dongguk University, South Korea" - }, - { - "author_name": "Archana Shrestha", - "author_inst": "Department of Public Health, Kathmandu University, Kathmandu, Nepal" - }, - { - "author_name": "Bom BC", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Sabin Bhandari", - "author_inst": "B.P Koirala Institute of Health Sciences, Dharan, Nepal" - }, - { - "author_name": "Ramgyan Yadav", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Ashish Timalsina", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Chetan Nidhi Wagle", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Brij Kumar Das", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Ramesh Kunwar", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Binaya Chalise", - "author_inst": "Hiroshima University, Graduate School for International Development and Cooperation, Hiroshima, Japan" - }, - { - "author_name": "Deepak Raj Bhatta", - "author_inst": "Ministry of Health and Population, Kathmandu, Nepal" - }, - { - "author_name": "Mukesh Adhikari", - "author_inst": "Department of Health Policy and Management, Yale School of Public Health, Yale University, New Haven CT, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.12.20173856", "rel_title": "Comparative Evaluation of SARS-CoV-2 IgG Assays in India", @@ -1259252,6 +1260098,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20174060", + "rel_title": "Comprehensive Systematic Review to Identify putative COVID-19 Treatments: Roles for Immunomodulator and Antiviral Treatments", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174060", + "rel_abs": "ObjectivesTo identify putative COVID-19 treatments and identify the roles of immunomodulators and antivirals in disease management.\n\nDesignSystematic review.\n\nData sourcesPubMed, bioRxiv.org and medRxiv.org were searched for studies suggestive of effective treatments for COVID-19. Additional studies were identified via a snowballing method applied to the references of retrieved papers as well as a subsequent targeted search for drug names.\n\nReview methodsInclusion criteria included any case series or randomised control trials in any language that were published from 18th December 2019 to 18th April 2020 and described COVID-19 treatment. Of an initial 2140 studies identified from the initial search, 29 studies were found to meet the inclusion criteria and included in this comprehensive systematic review.\n\nResults19 studies of antiviral treatments for COVID-19 have been reported and seven studies for immunomodulatory treatments. Six randomised controlled trials have been published with one positive trial for Hydroxychloroquine. This small study consisted of 31 patients though subsequent studies showed contradictory findings. All the remaining studies were observational studies, retrospective case reviews or non-randomised trials and these results are difficult to interpret due to methodological issues.\n\nConclusionsTo date, an impressive number of studies have been performed in a short space of time, indicative of a resilient clinical trials infrastructure. However, there is a lack of high quality evidence to support any novel treatments for COVID-19 to be incorporated into the current standard of care. The majority of the studies of treatments for COVID-19 could only be found in pre-print servers. Future clinical reviews should therefore be Comprehensive Systematic Reviews involving pre-print studies to prevent potential unnecessary replications of clinical studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Thomas Hill", + "author_inst": "Department of Oncology, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston, B152GW" + }, + { + "author_name": "Mark Baker", + "author_inst": "Birmingham Medical School, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT" + }, + { + "author_name": "Lawrence Isherwood", + "author_inst": "Birmingham Medical School, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT" + }, + { + "author_name": "Lennard YW Lee", + "author_inst": "Department of Oncology, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston B15 2GW, United Kingdom. Institute of Cancer and Genomic Sciences, Univer" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.12.20173104", "rel_title": "First report of tocilizumab use in a cohort of Latin American patients hospitalized for severe COVID-19 pneumonia", @@ -1259740,53 +1260617,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.08.13.20172494", - "rel_title": "Comparison of RNA extraction methods for the detection of SARS-CoV-2 by RT-PCR", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20172494", - "rel_abs": "ObjectivesThe SARS-CoV-2 pandemic outbreak has stressed health care systems as well as medical supply chains, but diagnostic testing is an essential public health measure to control viral spread. Here we test the suitability of different RNA extraction methods for integration into a diagnostic workflow for coronavirus testing.\n\nMethodsWe applied six RNA extraction methods on the same 24 SARS-CoV-2 positive patient samples and quantified their results by subsequent reverse-transcriptase PCR (RT-PCR) of three viral genes. These methods included a) column-based extraction, b) phenol-chloroform extraction, as well as c) extraction using magnetic beads (i.e., one commercial kit as well as three different magnetic beads in combination with home-brewed buffers and solutions).\n\nResultsWe achieved diagnostic-quality RT-PCR results with all methods, and there was no significant difference between the tested methods, except for one magnetic bead protocol with home-brewed buffers, in which the number of positive tested genes was significantly lower.\n\nConclusionsFive of the six RNA extraction methods are interchangeable in a diagnostic workflow. Since some methods are more scalable than others, and have comparable results on RT-PCR quantitation, they may be more amenable to high-throughput sample processing pipelines.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/20172494v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@f9ff33org.highwire.dtl.DTLVardef@e17c21org.highwire.dtl.DTLVardef@19c8c37org.highwire.dtl.DTLVardef@b9aa2d_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ossia M Eichhoff", - "author_inst": "Department of Dermatology, University Hospital Zurich, 8091 Zurich, Switzerland; Faculty of Medicine, University of Zurich, 8006 Zurich, Switzerland" - }, - { - "author_name": "Elisa Bellini", - "author_inst": "Department of Dermatology, University Hospital Zurich, 8091 Zurich, Switzerland Switzerland; Faculty of Medicine, University of Zurich, 8006 Zurich, Switzerland" - }, - { - "author_name": "Reto Lienhard", - "author_inst": "ADMED Microbiologie, 2300 La Chaux-de-Fonds, Switzerland" - }, - { - "author_name": "Wendelin J. Stark", - "author_inst": "Department of Chemical and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland" - }, - { - "author_name": "Philippe Bechtold", - "author_inst": "Department of Chemical and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland" - }, - { - "author_name": "Robert N. Grass", - "author_inst": "Department of Chemical and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland" - }, - { - "author_name": "Philipp P. Bosshard", - "author_inst": "Department of Dermatology, University Hospital Zurich, 8091 Zurich, Switzerland Switzerland; Faculty of Medicine, University of Zurich, 8006 Zurich, Switzerland" - }, - { - "author_name": "Mitchell P. Levesque", - "author_inst": "Department of Dermatology, University Hospital Zurich, 8091 Zurich, Switzerland Switzerland; Faculty of Medicine, University of Zurich, 8006 Zurich, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.12.20173781", "rel_title": "Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18 and SARS-CoV-2-specific IgA", @@ -1260614,6 +1261444,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.12.20172726", + "rel_title": "Testing of Healthcare Workers Exposed to COVID19 with Rapid Antigen Detection", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20172726", + "rel_abs": "There is a need to develop safe and cost-effective ways to test healthcare workers for COVID19. Here we describe a rapid antigen testing strategy in a cohort of 497 Healthcare workers exposed to SARS-CoV-2 that can be applied by systems facing a surge of COVID19 cases, increased number of exposures in their workforce and limited RT-PCR availability. Our findings support an expanded use for antigen testing beyond its current indication and highlights the importance of further evaluating this modality for the diagnosis of COVID19 on asymptomatic individuals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Victor Herrera", + "author_inst": "Adventhealth" + }, + { + "author_name": "Vincent Hsu", + "author_inst": "AdventHealth" + }, + { + "author_name": "Ademola Adewale", + "author_inst": "Adventhealth" + }, + { + "author_name": "Timothy Hendrix", + "author_inst": "AdventHealth" + }, + { + "author_name": "Lee Johnson", + "author_inst": "Adventhealth" + }, + { + "author_name": "Jeffrey Kuhlman", + "author_inst": "Adventhealth" + }, + { + "author_name": "Neil Finkler", + "author_inst": "Adventhealth" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20170068", "rel_title": "A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English Primary Schools with application of Structured Expert Judgement", @@ -1261222,201 +1262095,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.08.14.251207", - "rel_title": "SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2", - "rel_date": "2020-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.251207", - "rel_abs": "While vaccines are vital for preventing COVID-19 infections, it is critical to develop new therapies to treat patients who become infected. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. In particular, host kinases are highly druggable targets and a number of conserved coronavirus proteins, notably the nucleoprotein (N), require phosphorylation for full functionality. In order to understand how targeting kinases could be used to compromise viral replication, we used a combination of phosphoproteomics and bioinformatics as well as genetic and pharmacological kinase inhibition to define the enzymes important for SARS-CoV-2 N protein phosphorylation and viral replication. From these data, we propose a model whereby SRPK1/2 initiates phosphorylation of the N protein, which primes for further phosphorylation by GSK-3/{beta} and CK1 to achieve extensive phosphorylation of the N protein SR-rich domain. Importantly, we were able to leverage our data to identify an FDA-approved kinase inhibitor, Alectinib, that suppresses N phosphorylation by SRPK1/2 and limits SARS-CoV-2 replication. Together, these data suggest that repurposing or developing novel host-kinase directed therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Tomer M Yaron", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Brook E Heaton", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Tyler M Levy", - "author_inst": "Cell Signaling Technology, Danvers, MA, USA." - }, - { - "author_name": "Jared L Johnson", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Tristan X Jordan", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA." - }, - { - "author_name": "Benjamin M Cohen", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Alexander Kerelsky", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Ting-Yu Lin", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Katarina M Liberatore", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Danielle K Bulaon", - "author_inst": "Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Edward R Kastenhuber", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Marisa N Mercadante", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Kripa Shobana-Ganesh", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Long He", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Robert E Schwartz", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Shuibing Chen", - "author_inst": "Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, USA" - }, - { - "author_name": "Harel Weinstein", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Oliver Elemento", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA." - }, - { - "author_name": "Elena Piskounova", - "author_inst": "Department of Dermatology, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Benjamin E Nilsson-Payant", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Gina Lee", - "author_inst": "Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Irvine, CA, USA" - }, - { - "author_name": "Joseph D Trimarco", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Kaitlyn N Burke", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Cait E Hamele", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Ryan R Chaparian", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Alfred T Harding", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Aleksandra Tata", - "author_inst": "Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Xinyu Zhu", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Purushothama Rao Tata", - "author_inst": "Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Clare M Smith", - "author_inst": "Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA" - }, - { - "author_name": "Anthony P Possemato", - "author_inst": "Cell Signaling Technology, Danvers, MA, USA" - }, - { - "author_name": "Sasha L Tkachev", - "author_inst": "Cell Signaling Technology, Danvers, MA, USA" - }, - { - "author_name": "Peter V Hornbeck", - "author_inst": "Cell Signaling Technology, Danvers, MA, USA" - }, - { - "author_name": "Sean A Beausoleil", - "author_inst": "Cell Signaling Technology, Danvers, MA, USA" - }, - { - "author_name": "Shankara K Anand", - "author_inst": "Broad Institute of MIT & Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Fran\u00e7ois Aguet", - "author_inst": "Broad Institute of MIT & Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Gad Getz", - "author_inst": "Broad Institute of MIT & Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Andrew D Davidson", - "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK" - }, - { - "author_name": "Kate Heesom", - "author_inst": "Proteomics Facility, University of Bristol, Bristol, BS8 1TD, UK" - }, - { - "author_name": "Maia Kavanagh-Williamson", - "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK" - }, - { - "author_name": "David Matthews", - "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK" - }, - { - "author_name": "Benjamin R tenOever", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA." - }, - { - "author_name": "Lewis C Cantley", - "author_inst": "Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "John Blenis", - "author_inst": "Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Nicholas S Heaton", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.14.251090", "rel_title": "Methylene Blue has a potent antiviral activity against SARS-CoV-2 in the absence of UV-activation in vitro", @@ -1262388,6 +1263066,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20166868", + "rel_title": "Factors Associated with Disease Severity and Mortality among Patients with Coronavirus Disease 2019: A Systematic Review and Meta-Analysis", + "rel_date": "2020-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20166868", + "rel_abs": "BackgroundUnderstanding the factors associated with disease severity and mortality in Coronavirus disease (COVID-19) is imperative to effectively triage patients. We performed a systematic review to determine the demographic, clinical, laboratory and radiological factors associated with severity and mortality in COVID-19.\n\nMethodsWe searched PubMed, Embase and WHO database for English language articles from inception until May 8, 2020. We included Observational studies with direct comparison of clinical characteristics between a) patients who died and those who survived or b) patients with severe disease and those without severe disease. Data extraction and quality assessment were performed by two authors independently.\n\nResultsAmong 15680 articles from the literature search, 109 articles were included in the analysis. The risk of mortality was higher in patients with increasing age, male gender (RR 1.45, 95%CI 1.23-1.71), dyspnea (RR 2.55, 95%CI 1.88-2.46), diabetes (RR 1.59, 95%CI 1.41-1.78), hypertension (RR 1.90, 95%CI 1.69-2.15). Congestive heart failure (OR 4.76, 95%CI 1.34-16.97), hilar lymphadenopathy (OR 8.34, 95%CI 2.57-27.08), bilateral lung involvement (OR 4.86, 95%CI 3.19-7.39) and reticular pattern (OR 5.54, 95%CI 1.24-24.67) were associated with severe disease. Clinically relevant cut-offs for leukocytosis(>10.0 x109/L), lymphopenia(< 1.1 x109/L), elevated C-reactive protein(>100mg/L), LDH(>250U/L) and D-dimer(>1mg/L) had higher odds of severe disease and greater risk of mortality.\n\nConclusionKnowledge of the factors associated of disease severity and mortality identified in our study may assist in clinical decision-making and critical-care resource allocation for patients with COVID-19.\n\nPrimary Funding SourceNone.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Vignesh Chidambaram", + "author_inst": "Johns Hopkins Bloomberg school of Public health" + }, + { + "author_name": "Nyan Lynn Tun", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Waqas Haque", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Marie Gilbert Majella", + "author_inst": "Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India" + }, + { + "author_name": "Ranjith Kumar Sivakumar", + "author_inst": "Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China" + }, + { + "author_name": "Amudha Kumar", + "author_inst": "Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA" + }, + { + "author_name": "Angela Ting-Wei Hsu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Izza Ishak", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Aqsha Nur", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Samuel Ayeh", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Emmanuella Salia", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Ahsan Zil-E-Ali", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Muhammad Saeed", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ayu Sarena", + "author_inst": "Bhayangkara Setukpa Hospital, Sukabumi, Indonesia" + }, + { + "author_name": "Bhavna Seth", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Muzzammil Ahmadzada", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Eman Haque", + "author_inst": "Southern Methodist University, Dallas, TX, USA" + }, + { + "author_name": "Pranita Neupane", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Kuang-Heng Wang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Tzu-Miao Pu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Syed Ali", + "author_inst": "Fatima Memorial Hospital, Lahore, Pakistan" + }, + { + "author_name": "Muhammad Arshad", + "author_inst": "Nishtar Hospital, Multan, Pakistan" + }, + { + "author_name": "Lin Wang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Sheriza Baksh", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Petros Karakousis", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Panagis Galiatsatos", + "author_inst": "Johns Hopkins School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.26.20162008", "rel_title": "COVID-19 mild cases determination from correlating COVID-line calls to reported cases", @@ -1262924,37 +1263721,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.12.248732", - "rel_title": "Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load", - "rel_date": "2020-08-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.12.248732", - "rel_abs": "SARS-CoV-2 is a betacoronavirus responsible for human cases of COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load in both regions without selective pressure and across the genome, compared to nsp7, 8, and 12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates, and nsp14 mutations as potential predictors for high mutability strains.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Do\u011fa Eskier", - "author_inst": "Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey" - }, - { - "author_name": "Asl\u0131 Suner", - "author_inst": "Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey" - }, - { - "author_name": "Yavuz Oktay", - "author_inst": "Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey; Departmen" - }, - { - "author_name": "G\u00f6khan Karak\u00fclah", - "author_inst": "Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.08.12.246389", "rel_title": "Maraviroc inhibits SARS-CoV-2 multiplication and s-protein mediated cell fusion in cell culture", @@ -1263894,6 +1264660,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20171371", + "rel_title": "Impaired cellular immunity to SARS-CoV-2 in severe COVID-19 patients", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171371", + "rel_abs": "The World Health Organization has declared SARS-CoV-2 virus outbreak a world-wide pandemic. Individuals infected by the virus exhibited different degrees of symptoms, the basis of which remains largely unclear. Currently, though convalescent individuals have been shown with both cellular and humoral immune responses, there is very limited understanding on the immune responses, especially adaptive immune responses, in patients with severe COVID-19. Here, we examined 10 blood samples from COVID-19 patients with acute respiratory distress syndrome (ARDS). The majority of them (70%) mounted SARS-CoV-2-specific humoral immunity with production of neutralizing antibodies. However, compared to healthy controls, the percentages and absolute numbers of both NK cells and CD8+ T cells were significantly reduced, accompanied with decreased IFN{gamma} expression in CD4+ T cells in peripheral blood from severe patients. Most notably, we failed in detecting SARS-CoV-2-specific IFN{gamma} production by peripheral blood lymphocytes from these patients. Our work thus indicates that COVID-19 patients with severe symptoms are associated with defective cellular immunity, which not only provides insights on understanding the pathogenesis of COVID-19, but also has implications in developing an effective vaccine to SARS-CoV-2.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ling Ni", + "author_inst": "Institute for Immunology and School of Medicine,Tsinghua University" + }, + { + "author_name": "Meng-Li Cheng", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Hui Zhao", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Yu Feng", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Jingyuan Liu", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases," + }, + { + "author_name": "Fang Ye", + "author_inst": "Department of Hematology, Chui Yang Liu Hospital affiliated to Tsinghua University" + }, + { + "author_name": "Qing Ye", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences," + }, + { + "author_name": "Gengzhen Zhu", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Xiaoli Li", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Pengzhi Wang", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Jing Shao", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Yong-qiang Deng", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Peng Wei", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Fang Chen", + "author_inst": "Department of Cardiology, Chui Yang Liu Hospital affiliated to Tsinghua University" + }, + { + "author_name": "Cheng-feng Qin", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Guoqing Wang", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Fan Li", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Hui Zeng", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases" + }, + { + "author_name": "Chen Dong", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.08.10.20171439", "rel_title": "Extended SEIQR type model for COVID-19 epidemic and data analysis", @@ -1264602,57 +1265459,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.12.247825", - "rel_title": "TRIM28 regulates SARS-CoV-2 cell entry by targeting ACE2", - "rel_date": "2020-08-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.12.247825", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), it binds to angiotensin-converting enzyme 2 (ACE2) to enter into human cells. The expression level of ACE2 potentially determine the susceptibility and severity of COVID-19, it is thus of importance to understand the regulatory mechanism of ACE2 expression. Tripartite motif containing 28 (TRIM28) is known to be involved in multiple processes including antiviral restriction, endogenous retrovirus latency and immune response, it is recently reported to be co-expressed with SARS-CoV-2 receptor in type II pneumocytes; however, the roles of TRIM28 in ACE2 expression and SARS-CoV-2 cell entry remain unclear. This study showed that knockdown of TRIM28 induces ACE2 expression and increases pseudotyped SARS-CoV-2 cell entry of A549 cells and primary pulmonary alveolar epithelial cells (PAEpiCs). In a co-culture model of NK cells and lung epithelial cells, our results demonstrated that NK cells inhibit TRIM28 and promote ACE2 expression in lung epithelial cells, which was partially reversed by depletion of interleukin-2 and blocking of granzyme B in the co-culture medium. Furthermore, TRIM28 knockdown enhanced interferon-{gamma} (IFN-{gamma})-induced ACE2 expression through a mechanism involving upregulating IFN-{gamma} receptor 2 (IFNGR2) in both A549 and PAEpiCs. Importantly, the upregulated ACE2 induced by TRIM28 knockdown and co-culture of NK cells was partially reversed by dexamethasone in A549 cells but not PAEpiCs. Our study identified TRIM28 as a novel regulator of ACE2 expression and SARS-CoV-2 cell entry.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yinfang Wang", - "author_inst": "Central Laboratory, Basic and Translational Vascular Medicine Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine" - }, - { - "author_name": "Yingzhe Fan", - "author_inst": "Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine" - }, - { - "author_name": "Yitong Huang", - "author_inst": "Central Laboratory, Basic and Translational Vascular Medicine Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine" - }, - { - "author_name": "Tao Du", - "author_inst": "Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Zongjun Liu", - "author_inst": "Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine" - }, - { - "author_name": "Dekui Huang", - "author_inst": "Basic and Translational Vascular Medicine Laboratory, Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine" - }, - { - "author_name": "Ying Wang", - "author_inst": "Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic" - }, - { - "author_name": "Nanping Wang", - "author_inst": "The Advanced Institute for Medical Sciences, Dalian Medical University" - }, - { - "author_name": "Peng Zhang", - "author_inst": "Putuo Hospital, Shanghai University of TCM" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.08.12.247767", "rel_title": "Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2", @@ -1265712,6 +1266518,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20161737", + "rel_title": "LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20161737", + "rel_abs": "LamPORE is a rapid way of testing/screening large numbers of samples for the presence or absence of SARS-CoV-2, the virus causing COVID-19. It combines barcoded multi-target amplification, 15-minute barcoded library preparation and real-time nanopore sequencing. Starting with extracted RNA, results can be obtained from 12 samples in approximately an hour and from 96 samples in under 2 hours. High scalability is achieved by combinatorial barcoding. Performance characteristics are currently being established and regulatory clearance to market is underway.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Phillip James", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "David Stoddart", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Eoghan D Harrington", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "John Beaulaurier", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Lynn Ly", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Stuart Reid", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Daniel J Turner", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Sissel Juul", + "author_inst": "Oxford Nanopore Technologies" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.07.20170407", "rel_title": "Model-based projections for COVID-19 outbreak size and student-days lost to closure in Ontario childcare centres and primary schools", @@ -1266404,49 +1267257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.07.20170456", - "rel_title": "Considering indirect benefits is critical when evaluating SARS-CoV-2 vaccine candidates", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20170456", - "rel_abs": "Significant progress has already been made in development and testing of SARS-CoV-2 vaccines, and Phase III clinical trials have begun for 6 novel vaccine candidates to date. These Phase III trials seek to demonstrate direct benefits of a vaccine on vaccine recipients. However, vaccination is also known to bring about indirect benefits to a population through the reduction of virus circulation. The indirect effects of SARS-CoV-2 vaccination can play a key role in reducing case counts and COVID-19 deaths. To illustrate this point, we show through simulation that a vaccine with strong indirect effects has the potential to reduce SARS-CoV-2 circulation and COVID-19 deaths to a greater extent than an alternative vaccine with stronger direct effects but weaker indirect effects. Protection via indirect effects may be of particular importance in the context of this virus, because elderly individuals are at an elevated risk of death but are also less likely to be directly protected by vaccination due to immune senescence. We therefore encourage ongoing data collection and model development aimed at evaluating the indirect effects of forthcoming SARS-CoV-2 vaccines.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Molly E. Gallagher", - "author_inst": "Emory University" - }, - { - "author_name": "Andrew J. Sieben", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Kristin N. Nelson", - "author_inst": "Emory University Rollins School of Public Health" - }, - { - "author_name": "Alicia N. M. Kraay", - "author_inst": "Emory University Rollins School of Public Health" - }, - { - "author_name": "Ben Lopman", - "author_inst": "Emory University Rollins School of Public Health" - }, - { - "author_name": "Andreas Handel", - "author_inst": "University of Georgia" - }, - { - "author_name": "Katia Koelle", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.09.20171355", "rel_title": "Sensitivity, specificity and predictive values of molecular and serological tests for COVID-19. A longitudinal study in emergency room.", @@ -1267494,6 +1268304,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20172155", + "rel_title": "EPIDEMIC ANALYSIS OF COVID-19 IN ALGERIA BY A GENERALIZED SEIR MODEL", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172155", + "rel_abs": "The novel coronavirus diseases 2019 (COVID-19) in Wuhan is continuing to impress the world by its fast spread and the number of affected persons attracting an unprecedented attention. In this article, we used the classical SEIR model and a generalized SEIR model called SEIRDP model inspired in a model previously used during the outbreak in China to predict the evolution of COVID-19 in Algeria for a future period of 100 days using official reported data from early April to early August, 2020. Initial evaluation showed that thetwo models had a net correspondence with the reported data during this period for cumulative infected cases but the number of cumulative deaths was underestimated with the classical SEIR model. Model prediction with the SEIRDP concluded that the number of cumulative infected cases will increase in the next days reaching a number of about 60 k in middle November with a median of about 300 daily cases. Also, the number of estimated deaths will be around 2k. These results suggest that the COVID-19 is ongoing to infect more persons which may push national authorities to carefully act in the probable leaving of containment.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mohamed LOUNIS Sr.", + "author_inst": "University of Ziane Achour Djelfa" + }, + { + "author_name": "Juarez dos Santos AZEVEDO Sr.", + "author_inst": "Universidade Federal da Bahia (UFBA)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.10.20172189", "rel_title": "Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis", @@ -1268174,89 +1269007,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.11.246314", - "rel_title": "K18-hACE2 mice develop respiratory disease resembling severe COVID-19", - "rel_date": "2020-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.11.246314", - "rel_abs": "SARS-CoV-2 emerged in late 2019 and resulted in the ongoing COVID-19 pandemic. Several animal models have been rapidly developed that recapitulate the asymptomatic to moderate disease spectrum. Now, there is a direct need for additional small animal models to study the pathogenesis of severe COVID-19 and for fast-tracked medical countermeasure development. Here, we show that transgenic mice expressing the human SARS-CoV-2 receptor (angiotensin-converting enzyme 2 [hACE2]) under a cytokeratin 18 promoter (K18) are susceptible to SARS-CoV-2 and that infection resulted in a dose-dependent lethal disease course. After inoculation with either 104 TCID50 or 105 TCID50, the SARS-CoV-2 infection resulted in rapid weight loss in both groups and uniform lethality in the 105 TCID50 group. High levels of viral RNA shedding were observed from the upper and lower respiratory tract and intermittent shedding was observed from the intestinal tract. Inoculation with SARS-CoV-2 resulted in upper and lower respiratory tract infection with high infectious virus titers in nasal turbinates, trachea and lungs. The observed interstitial pneumonia and pulmonary pathology, with SARS-CoV-2 replication evident in pneumocytes, were similar to that reported in severe cases of COVID-19. SARS-CoV-2 infection resulted in macrophage and lymphocyte infiltration in the lungs and upregulation of Th1 and proinflammatory cytokines/chemokines. Extrapulmonary replication of SARS-CoV-2 was observed in the cerebral cortex and hippocampus of several animals at 7 DPI but not at 3 DPI. The rapid inflammatory response and observed pathology bears resemblance to COVID-19. Taken together, this suggests that this mouse model can be useful for studies of pathogenesis and medical countermeasure development.\n\nAuthors SummaryThe disease manifestation of COVID-19 in humans range from asymptomatic to severe. While several mild to moderate disease models have been developed, there is still a need for animal models that recapitulate the severe and fatal progression observed in a subset of patients. Here, we show that humanized transgenic mice developed dose-dependent disease when inoculated with SARS-CoV-2, the etiological agent of COVID-19. The mice developed upper and lower respiratory tract infection, with virus replication also in the brain after day 3 post inoculation. The pathological and immunological diseases manifestation observed in these mice bears resemblance to human COVID-19, suggesting increased usefulness of this model for elucidating COVID-19 pathogenesis further and testing of countermeasures, both of which are urgently needed.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Claude Kwe Yinda", - "author_inst": "RML" - }, - { - "author_name": "Julia R Port", - "author_inst": "RML" - }, - { - "author_name": "Trenton J Bushmaker", - "author_inst": "RML" - }, - { - "author_name": "Irene Offei Owusu", - "author_inst": "RML" - }, - { - "author_name": "Victoria A Avanzato", - "author_inst": "RML" - }, - { - "author_name": "Robert J Fischer", - "author_inst": "RML" - }, - { - "author_name": "Jonathan E Schulz", - "author_inst": "RML" - }, - { - "author_name": "Myndi G Holbrook", - "author_inst": "RML" - }, - { - "author_name": "Madison J Hebner", - "author_inst": "RML" - }, - { - "author_name": "Rebecca Rosenke", - "author_inst": "RML" - }, - { - "author_name": "Tina Thomas", - "author_inst": "RML" - }, - { - "author_name": "Andrea Marzi", - "author_inst": "RML" - }, - { - "author_name": "Sonja M Best", - "author_inst": "RML" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Carl Shaia", - "author_inst": "RML" - }, - { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIH" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.11.245993", "rel_title": "Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development", @@ -1269640,6 +1270390,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.09.242867", + "rel_title": "A potent neutralizing nanobody against SARS-CoV-2 with inhaled delivery potential", + "rel_date": "2020-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.09.242867", + "rel_abs": "The outbreak of COVID-19 has emerged as a global pandemic. The unprecedented scale and severity call for rapid development of effective prophylactics or therapeutics. We here reported Nanobody (Nb) phage display libraries derived from four camels immunized with the SARS-CoV-2 spike receptor-binding domain (RBD), from which 381 Nbs were identified to recognize SARS-CoV-2-RBD. Furthermore, seven Nbs were shown to block interaction of human angiotensin converting enzyme 2 (ACE2) with SARS-CoV-2-RBD-variants, bat-SL-CoV-WIV1-RBD and SARS-CoV-1-RBD. Among the seven candidates, Nb11-59 exhibited the highest activity against authentic SARS-CoV-2 with ND50 of 0.55 g/mL. Nb11-59 can be produced on a large-scale in Pichia pastoris, with 20 g/L titer and 99.36% purity. It also showed good stability profile, and nebulization did not impact its stability. Overall, Nb11-59 might be a promising prophylactic and therapeutic molecule against COVID-19, especially through inhalation delivery.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC=\"FIGDIR/small/242867v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@e4434org.highwire.dtl.DTLVardef@9fee79org.highwire.dtl.DTLVardef@1e15bb1org.highwire.dtl.DTLVardef@4adb0c_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Junwei Gai", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Linlin Ma", + "author_inst": "Shanghai University of Medicine and Health Sciences" + }, + { + "author_name": "Guanghui Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Min Zhu", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Peng Qiao", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Xiaofei Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Haiwei Zhang", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Yanmin Zhang", + "author_inst": "School of Science, China Pharmaceutical University" + }, + { + "author_name": "Yadong Chen", + "author_inst": "School of Science, China Pharmaceutical University" + }, + { + "author_name": "Weiwei Ji", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Hao Zhang", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Huanhuan Cao", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Xionghui Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Rui Gong", + "author_inst": "Wuhan Institute of Virology Chinese Academy of Sciences" + }, + { + "author_name": "Yakun Wan", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.08.04.20168054", "rel_title": "SARS-CoV-2 and the Role of Orofecal Transmission: Systematic Review", @@ -1270116,473 +1270941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.05.20169169", - "rel_title": "SARS-CoV-2 and Stroke Characteristics: A Report from the Multinational COVID-19 Stroke Study Group", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20169169", - "rel_abs": "BackgroundStroke is reported as a consequence of SARS-CoV-2 infection. However, there is a lack of regarding comprehensive stroke phenotype and characteristics\n\nMethodsWe conducted a multinational observational study on features of consecutive acute ischemic stroke (AIS), intracranial hemorrhage (ICH), and cerebral venous or sinus thrombosis (CVST) among SARS-CoV-2 infected patients. We further investigated the association of demographics, clinical data, geographical regions, and countries health expenditure among AIS patients with the risk of large vessel occlusion (LVO), stroke severity as measured by National Institute of Health stroke scale (NIHSS), and stroke subtype as measured by the TOAST criteria. Additionally, we applied unsupervised machine learning algorithms to uncover possible similarities among stroke patients.\n\nResultsAmong the 136 tertiary centers of 32 countries who participated in this study, 71 centers from 17 countries had at least one eligible stroke patient. Out of 432 patients included, 323(74.8%) had AIS, 91(21.1%) ICH, and 18(4.2%) CVST. Among 23 patients with subarachnoid hemorrhage, 16(69.5%) had no evidence of aneurysm. A total of 183(42.4%) patients were women, 104(24.1%) patients were younger than 55 years, and 105(24.4%) patients had no identifiable vascular risk factors. Among 380 patients who had known interval onset of the SARS-CoV-2 and stroke, 144(37.8%) presented to the hospital with chief complaints of stroke-related symptoms, with asymptomatic or undiagnosed SARS-CoV-2 infection. Among AIS patients 44.5% had LVO; 10% had small artery occlusion according to the TOAST criteria. We observed a lower median NIHSS (8[3-17], versus 11 [5-17]; p=0.02) and higher rate of mechanical thrombectomy (12.4% versus 2%; p<0.001) in countries with middle to high-health expenditure when compared to countries with lower health expenditure. The unsupervised machine learning identified 4 subgroups, with a relatively large group with no or limited comorbidities.\n\nConclusionsWe observed a relatively high number of young, and asymptomatic SARS-CoV-2 infections among stroke patients. Traditional vascular risk factors were absent among a relatively large cohort of patients. Among hospitalized patients, the stroke severity was lower and rate of mechanical thrombectomy was higher among countries with middle to high-health expenditure.", - "rel_num_authors": 113, - "rel_authors": [ - { - "author_name": "Shima Shahjouei", - "author_inst": "Neurology Department, Neuroscience Institute, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Georgios Tsivgoulis", - "author_inst": "Second Department of Neurology, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital" - }, - { - "author_name": "Ghasem Farahmand", - "author_inst": "Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences" - }, - { - "author_name": "Eric Koza", - "author_inst": "Geisinger Commonwealth School of Medicine" - }, - { - "author_name": "Ashkhan Mowla", - "author_inst": "Division of Stroke and Endovascular Neurosurgery, Department of Neurological Surgery, Keck School of Medicine, University of Southern California, California, US" - }, - { - "author_name": "Alireza Vafaei Sadr", - "author_inst": "Department de Physique Theorique and Center for Astroparticle Physics, University Geneva, Switzerland" - }, - { - "author_name": "Arash Kia", - "author_inst": "Icahn school of medicine at Mount Sinai, Department of Population Health Science and Policy, Institute for Healthcare Delivery Science, New York, USA" - }, - { - "author_name": "Alaleh Vaghefi Far", - "author_inst": "Neurology Department, Tehran University of medical sciences" - }, - { - "author_name": "Stefania Mondello", - "author_inst": "Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina" - }, - { - "author_name": "Achille Cernigliaro", - "author_inst": "Regional Health Authority of Sicily" - }, - { - "author_name": "Annemarei Ranta", - "author_inst": "Department of Neurology, Wellington Hospital" - }, - { - "author_name": "Martin Punter", - "author_inst": "Department of Neurology, Wellington Hospital" - }, - { - "author_name": "Faezeh Khodadadi", - "author_inst": "PES university,bengalore,India" - }, - { - "author_name": "Mrina Sabra", - "author_inst": "Lebanese University/Medical School, NRC (Neurosciences Research Center)" - }, - { - "author_name": "Mahtab Ramezani", - "author_inst": "Neurology Department,Shahid Beheshti University of medical sciences" - }, - { - "author_name": "Soheil Naderi", - "author_inst": "Neurosurgery Department, Tehran University of Medical Sciences" - }, - { - "author_name": "Oluwaseyi Olulana", - "author_inst": "Geisinger Commonwealth School of Medicine" - }, - { - "author_name": "Durgesh Chaudhary", - "author_inst": "Neurology Department, Neuroscience Institute, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Aicha Lyoubi", - "author_inst": "Neurology Department, Delafontaine Hospital, Saint Denis, France" - }, - { - "author_name": "Bruce Campbell", - "author_inst": "Royal Melbourne Hospital Department of Neurology and University of Melbourne." - }, - { - "author_name": "Juan F Arenillas", - "author_inst": "Department of Neurology, University of Valladolid, Valladolid, Spain." - }, - { - "author_name": "Daniel Bock", - "author_inst": "Department of Cardiology, Klinikum Frankfurt Hochst, Frankfurt Germany" - }, - { - "author_name": "Joan Montaner", - "author_inst": "Department of Neurology, Hospital Universitario Virgen Macarena, Sevilla, Spain" - }, - { - "author_name": "Saeideh Aghayari Sheikh Neshin", - "author_inst": "Neurology Department, Poursina Hospital" - }, - { - "author_name": "Diana Aguiar de Sousa", - "author_inst": "Hospital de Santa Maria, University of Lisbon, Lisbon, Portugal" - }, - { - "author_name": "Mattew Tenser", - "author_inst": "Division of Stroke and Endovascular Neurosurgery, Department of Neurological Surgery, Keck School of Medicine, University of Southern California, California, US" - }, - { - "author_name": "Ana Aires", - "author_inst": "Department of Neurology, Sao Joao Hospital Center, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal." - }, - { - "author_name": "Mercedes De Lera Alfonso", - "author_inst": "Department of Neurology, University of Valladolid, Valladolid, Spain." - }, - { - "author_name": "Orkhan Alizada", - "author_inst": "Neurosurgery Department, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty" - }, - { - "author_name": "Elsa Azevedo", - "author_inst": "Department of Neurology, Sao Joao Hospital Center, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal." - }, - { - "author_name": "Nitin Goyal", - "author_inst": "Neurology Department, University of Tennessee Health Science Center, Tennessee, USA" - }, - { - "author_name": "Zabihollah Babaeepour", - "author_inst": "Neurology ward, Valiasr Hospital, Borujen, Iran" - }, - { - "author_name": "Gelareh Banihashemi", - "author_inst": "Sina hospital (Neurology departement)" - }, - { - "author_name": "Leo H Bonati", - "author_inst": "Department of Neurology, Arak University of Medical Sciences, Arak,Iran" - }, - { - "author_name": "Carlo Cereda", - "author_inst": "Stroke Center, Neurocenter of Southern Switzerland, Lugano, Switzerland" - }, - { - "author_name": "Jason J Chang", - "author_inst": "Department of Neurology, Marry Washington Healthcare, Fredricksburg, Virginia, USA" - }, - { - "author_name": "Miljenko Crnjakovic", - "author_inst": "Intensive Care Unit, Department of Neurology, Clinical Hospital Dubrava, Zagreb, Croatia" - }, - { - "author_name": "GianMarco De Marchis", - "author_inst": "Neurorehabilitation Unit, University Center for Medicine of Aging and Rehabilitation Basel, Felix Platter Hospital, University of Basel, Switzerland." - }, - { - "author_name": "Massimo del Sette", - "author_inst": "Neurology Unit, Galliera Hospital, Genova, Italy" - }, - { - "author_name": "Seyed Amir Ebrahimadeh", - "author_inst": "Department of Radiology, Yasrebi Hospital, Kashan, Iran" - }, - { - "author_name": "Mehdi Farhoudi", - "author_inst": "Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences,Tabriz, Iran." - }, - { - "author_name": "Ilaria Gandoglia", - "author_inst": "Neurology Unit, Galliera Hospital, Genova, Italy" - }, - { - "author_name": "Bruno Goncalves", - "author_inst": "Department of Neurology, GHU Paris Psychiatrie et Neurosciences, Universite de Paris, INSERM U1266, Paris, France" - }, - { - "author_name": "Christoph Griessenauer", - "author_inst": "Neurology Department, Neuroscience Institute, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Mehmet Murat Hanci", - "author_inst": "Neurosurgery Department, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty" - }, - { - "author_name": "Aristeidis H. Katsanos", - "author_inst": "Second Department of Neurology, Attikon University Hospital, School of Medicine, National & Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Christos Krogias", - "author_inst": "epartment of Neurology, St. Josef-Hospital, Ruhr University Bochum, Bochum, Germany" - }, - { - "author_name": "Ronen Leker", - "author_inst": "Department of Neurology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Lev Lotman", - "author_inst": "Department of Neurology, Albany Medical Center, Albany, NY" - }, - { - "author_name": "Jeffrey Mai", - "author_inst": "Department of Neurology, Marry Washington Healthcare, Fredricksburg, Virginia, USA" - }, - { - "author_name": "Shailesh Male", - "author_inst": "Neurology Department, Vidant Medical Center" - }, - { - "author_name": "konark Malhotra", - "author_inst": "Department of Neurology, Allegheny Health Network (AHN),Pittsburgh, PA, USA" - }, - { - "author_name": "Branko Malojcic", - "author_inst": "TIA Clinic, Department of Neurology, University Hospital Centre Zagreb, Zagreb School of Medicine, University of Zagreb, Zagreb, Croatia." - }, - { - "author_name": "Tresa Mesquita", - "author_inst": "Department of Neurology, Hospital de Egas Moniz, Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal" - }, - { - "author_name": "Asadollah Mirghasemi", - "author_inst": "Department of Anesthesiology, University of Ottawa" - }, - { - "author_name": "Hany Mohamed Aref", - "author_inst": "Department of neurology, Ain Shams University, Cairo, Egypt" - }, - { - "author_name": "Zeinab Mohseni Afshar", - "author_inst": "Infection Disease Research Center, Kermanshah University of Medical Sciences" - }, - { - "author_name": "Junsun Moon", - "author_inst": "Department of Neurology, National Medical Center, Seoul, South Korea" - }, - { - "author_name": "Mika Niemela", - "author_inst": "Department of Neurosurgery, Helsinki University Hospital, Finland" - }, - { - "author_name": "Behnam Rezai Jahromi", - "author_inst": "Department of Neurosurgery, Helsinki University Hospital, Finland" - }, - { - "author_name": "Lawrence Nolan", - "author_inst": "Department of Neurology, Albany Medical Center, Albany, NY" - }, - { - "author_name": "Abhi Pandhi", - "author_inst": "Neurology Department, University of Tennessee Health Science Center, Tennessee, USA" - }, - { - "author_name": "Jong-Ho Park", - "author_inst": "Department of Neurology, Myongji Hospital, Hanyang University College of Medicine, South Korea." - }, - { - "author_name": "Joao Pedro Marto", - "author_inst": "Department of Neurology, Hospital de Egas Moniz, Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal" - }, - { - "author_name": "Francisco Purroy", - "author_inst": "Department of Neurology, Hospital Arnau de Vilanova, Lleida, Spain" - }, - { - "author_name": "Sakineh Ranji-Burachaloo", - "author_inst": "Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences" - }, - { - "author_name": "Nuno Reis Carreira", - "author_inst": "Department of Internal Medicine, Hospital de Santa Maria, University of Lisbon, Lisbon, Portugal" - }, - { - "author_name": "Manuel Requena", - "author_inst": "Stroke Unit, Department of Neurology, Hospital Vall d'Hebron, Departament de Medicina, Universitat Autonoma de Barcelona" - }, - { - "author_name": "Marta Rubiera", - "author_inst": "Stroke Unit, Department of Neurology, Hospital Vall d'Hebron, Departament de Medicina, Universitat Autonoma de Barcelona" - }, - { - "author_name": "Seyed Aidin Sajedi", - "author_inst": "Neuroscience Research Center, Golestan University of Medical Sciences, Iran" - }, - { - "author_name": "Joao SargentoFreitas", - "author_inst": "Department of Neurology, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal" - }, - { - "author_name": "Vijay Sharma", - "author_inst": "Division of Neurology, University Medicine Cluster, National University Health System, Singapore, Singapore" - }, - { - "author_name": "Thorsten Steiner", - "author_inst": "Department of Neurology, Klinikum Frankfurt Hochst, Frankfurt Germany" - }, - { - "author_name": "Kristi Tempro", - "author_inst": "Department of Neurology, Albany Medical Center, Albany, NY" - }, - { - "author_name": "Guillaume Turc", - "author_inst": "Department of Neurology, GHU Paris Psychiatrie et Neurosciences, Universite de Paris, INSERM U1266, Paris, France" - }, - { - "author_name": "Yassaman Ahmadzadeh", - "author_inst": "Hospital for Special Surgery, New York, USA" - }, - { - "author_name": "Mostafa Almasi-Dooghaee", - "author_inst": "Divisions of Vascular and Endovascular Neurosurgery and Neurology, Firoozgar Hospital and Rasoul-Akram hospital, Iran University of Medical Sciences, Tehran, Ir" - }, - { - "author_name": "Farhad Assarzadegan", - "author_inst": "Department of Neurology, Imam Hosein Hospital, Shahid Beheshti Medical University, Tehran, Iran" - }, - { - "author_name": "Arefeh Babazadeh", - "author_inst": "Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, I.R. Iran." - }, - { - "author_name": "Humain Baharvahdat", - "author_inst": "Neurosurgical Department, Ghaem Hospital, Mashhad University of Medical Sciences" - }, - { - "author_name": "Fabricio Cardoso", - "author_inst": "Neurology Department, Centro Medico de Campinas, Brazil" - }, - { - "author_name": "Apoorva Dev", - "author_inst": "PES university,Bengalore,India" - }, - { - "author_name": "Mohammad Ghorbani", - "author_inst": "Division of Vascular and Endovascular Neurosurgery, Firoozgar Hospital, Iran University of Medical Sciences" - }, - { - "author_name": "Ava Hamidi", - "author_inst": "Neutology ward, Gheshm Hospital, Gheshm, Iran" - }, - { - "author_name": "Zeynab Sadat Hasheminejad", - "author_inst": "Department of Neurology, Imam Hosein Hospital, Shahid Beheshti Medical University, Tehran, Iran" - }, - { - "author_name": "Sahar Hojjat-Anasri Komachali", - "author_inst": "Department of Neurology, Pirooz hospital, Gilan University of Medical Sciences, Lahijan,Iran" - }, - { - "author_name": "Fariborz Khorvash", - "author_inst": "Professor Of Neurology, Isfahan University Of Neurology, Isfahan, Iran" - }, - { - "author_name": "Firas Kobeissy", - "author_inst": "Program of Neurotrauma, Neuroproteomics and Biomarker Research (NNBR), University of Florida, Florida, USA" - }, - { - "author_name": "Hamidreza Mirkarimi", - "author_inst": "Neurology ward, Modarres Hospital, Kashmar, Iran" - }, - { - "author_name": "Elahe Mohammadi-Vosough", - "author_inst": "Neurology ward, Modarres Hospital, Kashmar, Iran" - }, - { - "author_name": "Debdipto Misra", - "author_inst": "Steele Institute of Health & Innovation, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Alierza Noorian", - "author_inst": "UCLA stroke program, US" - }, - { - "author_name": "Peyman Nowrouzi-Sohrabi", - "author_inst": "Student Research Committee, Shiraz University of Medical Sciences" - }, - { - "author_name": "Sepideh Paybast", - "author_inst": "Department of Neurology, Bou Ali hospital, Qazvin University of Medical Sciences, Qazvin,Iran" - }, - { - "author_name": "Leila Poorsaadat", - "author_inst": "Department of Neurology, Arak University of Medical Sciences, Arak,Iran" - }, - { - "author_name": "mehrdad Roozbeh", - "author_inst": "Brain Mapping Research Center, Shahid Beheshti University of Medical Sciences" - }, - { - "author_name": "Behnam Sabayan", - "author_inst": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Saeideh Salehizadeh", - "author_inst": "Salahadin Ayubi Hospital, Parastar street, Baneh, Iran." - }, - { - "author_name": "Alia Saberi", - "author_inst": "Neurology Department, Poursina Hospital, Iran" - }, - { - "author_name": "Mercedeh Sepehrnia", - "author_inst": "Department of Neurology, Imam Hosein Hospital, Shahid Beheshti Medical University, Tehran, Iran" - }, - { - "author_name": "Fahimeh Vahabizad", - "author_inst": "Sina Hospital" - }, - { - "author_name": "Thomas Yasuda", - "author_inst": "Neurology Department, Centro Medico de Campinas, Brazil" - }, - { - "author_name": "Ahmadreza Hojati Marvasti", - "author_inst": "Neurology Department, Tehran University of medical sciences, Iran" - }, - { - "author_name": "Mojdeh Ghabaee", - "author_inst": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Nasrin Rahimian", - "author_inst": "Department of Neurology, Yasrebi Hospital, Kashan, Iran" - }, - { - "author_name": "Mohammad Hosein Harirchian", - "author_inst": "Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences" - }, - { - "author_name": "Afshin Borhani-Haghighi", - "author_inst": "Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran" - }, - { - "author_name": "Rohan Arora", - "author_inst": "Northwell, USA" - }, - { - "author_name": "Saeed Ansari", - "author_inst": "Department of Neurology, University of Tennessee, Tennessee, USA" - }, - { - "author_name": "Venkatesh Avula", - "author_inst": "Neurology Department, Neuroscience Institute, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Jian Li", - "author_inst": "Geisinger health system, USA" - }, - { - "author_name": "Vida Abedi", - "author_inst": "Department of Molecular and Functional Genonic, Geisinger Health System, Pennsylvania, USA" - }, - { - "author_name": "Ramin Zand", - "author_inst": "Neurology Department, Neuroscience Institute, Geisinger Health System" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.08.06.20169276", "rel_title": "The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa", @@ -1271454,6 +1271812,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20169961", + "rel_title": "Neutralizing antibody response in non-hospitalized SARS-CoV-2 patients", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20169961", + "rel_abs": "The majority of infections with SARS-CoV-2 are asymptomatic or mild without the necessity of hospitalization. It is of importance to reveal if these patients develop an antibody response against SARS-CoV-2 and to define which antibodies confer virus neutralization. We conducted a comprehensive serological survey of 49 patients with a mild course of disease and quantified neutralizing antibody responses against a clinical SARS-CoV-2 isolate employing human cells as targets.\n\nFour patients (8%), even though symptomatic, did not develop antibodies against SARS-CoV-2 and two other patients (4%) were only positive in one of the six serological assays employed. For the remainder, antibody response against the S-protein correlated with serum neutralization whereas antibodies against the nucleocapsid were poor predictors of virus neutralization. Regarding neutralization, only six patients (12%) could be classified as highly neutralizers. Furthermore, sera from several individuals with fairly high antibody levels had only poor neutralizing activity. In addition, employing a novel serological Western blot system to characterize antibody responses against seasonal coronaviruses, we found that antibodies against the seasonal coronavirus 229E might contribute to SARS-CoV-2 neutralization.\n\nAltogether, we show that there is a wide breadth of antibody responses against SARS-CoV-2 in patients that differentially correlate with virus neutralization. This highlights the difficulty to define reliable surrogate markers for immunity against SARS-CoV-2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Natalia Ruetalo", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Ramona Businger", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Karina Althaus", + "author_inst": "Institute for Transfusion Medicine, University Hospital Tuebingen" + }, + { + "author_name": "Simon Fink", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Felix Ruoff", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Klaus Hamprecht", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Bertram Flehmig", + "author_inst": "Mediagnost GmbH, Reutlingen" + }, + { + "author_name": "Tamam Bakchoul", + "author_inst": "Institute for Transfusion Medicine, University Hospital Tuebingen" + }, + { + "author_name": "Markus F Templin", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Michael Schindler", + "author_inst": "University Hospital Tuebingen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.05.20168476", "rel_title": "Specificity and Performance of Nucleocapsid and Spike-based SARS-CoV-2 Serologic Assays", @@ -1272282,53 +1272695,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.08.06.20169409", - "rel_title": "Public perceptions and preventive behaviours during the early phase of the COVID-19 pandemic: a comparative study between Hong Kong and the United Kingdom", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169409", - "rel_abs": "BackgroundIn the absence of treatments and vaccines, the mitigation of COVID-19 relies on population engagement in non-pharmaceutical interventions, which is driven by their risk perception, anxiety level and knowledge. There may also be regional discrepancies in these drivers due to different historical exposure to disease outbreaks, government responses and cultures. As such, this study compared psycho-behavioral responses in two regions during the early phase of the pandemic.\n\nMethodsComparable cross-sectional surveys were administered among adults in Hong Kong (HK) and the United Kingdom (UK) during the early phase of each respective epidemic. Explanatory variables included demographics, risk perception and knowledge of COVID-19, anxiety level and preventive behaviors. Responses were weighted according to census data. Logistic regression models, including interaction terms to quantify regional differences, were used to assess the association between explanatory variables and the adoption of social-distancing measures.\n\nResultsData of 3431 complete responses (HK:1663; UK:1768) were analysed. Perceived severity differed by region (HK: 97.5%; UK: 20.7%). A large proportion of respondents were abnormally/borderline anxious (HK:64.8%; UK:45.9%) and regarded direct contact with infected individuals as the transmission route of COVID-19 (HK:94.0-98.5%; UK:69.2-93.5%), with HK identifying additional routes. HK reported high levels of adoption of social-distancing (HK:32.4-93.7%; UK:17.6-59.0%) and mask-wearing (HK:98.8%; UK:3.1%). The impact of perceived severity and perceived ease of transmission on the adoption of social-distancing varied by region. In HK, they had no impact, whereas in the UK, those who perceived severity as \"high\" were more likely to adopt social-distancing (aOR:1.58-3.01), and those who perceived transmission as \"easy\" were prone to both general social-distancing (aOR:2.00, 95% CI:1.57, 2.55) and contact avoidance (aOR:1.80, 95% CI: 1.41, 2.30). The impact of anxiety on adopting social-distancing did not vary by region.\n\nDiscussionThese results suggest that health officials should ascertain and consider baseline levels of risk perception and knowledge in the populations, as well as prior sensitisation to infectious disease outbreaks, during the development of mitigation strategies. Risk communication should be done through suitable media channels - and trust should be maintained - while early intervention remains the cornerstone of effective outbreak response.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Leigh Bowman", - "author_inst": "Imperial College London" - }, - { - "author_name": "Kin On Kwok", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Rozlyn Redd", - "author_inst": "Imperial College London" - }, - { - "author_name": "Yuanyuan Yi", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Helen Ward", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wan In Wei", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Christina J Atchison", - "author_inst": "Imperial College London" - }, - { - "author_name": "Samuel Yeung Shan Wong", - "author_inst": "The Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.06.20169870", "rel_title": "BEHAVIORAL CHANGES DURING THE COVID-19 PANDEMIC: RESULTS OF A NATIONAL SURVEY IN SINGAPORE", @@ -1273196,6 +1273562,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.05.20168799", + "rel_title": "COVID-19 Test & Trace Success Determinants: Modeling On A Network", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168799", + "rel_abs": "What determines the success of a COVID-19 Test & Trace policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing, we find that important determinants of successful containment are: (i) the time from symptom onset until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced. Comparatively less important is (iii) the time of test analysis and contact tracing. When the share of contacts successfully traced is higher, the Test & Trace Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace systems and policies could affect all three parameters, Symptom Onset to Test Time should be considered, alongside test turnaround time and contact tracing coverage, as a key determinant of Test & Trace success.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ofir Reich", + "author_inst": "Google" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.04.20168518", "rel_title": "Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations", @@ -1273896,41 +1274281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20168757", - "rel_title": "Epidemiology of Reopening in the COVID-19 Pandemic in the United States, Europe and Asia", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168757", - "rel_abs": "Since the discovery of the novel coronavirus (SARS-CoV-2), COVID-19 has become a global healthcare and economic crisis. The United States (US) and Europe exhibited wide impacts from the virus with more than six million cases by the time of our analysis. To inhibit spread, stay-at-home orders and other non-pharmaceutical interventions (NPIs) were instituted. Beginning late April 2020, some US states, European, and Asian countries lifted restrictions and started the reopening phases. In this study, the changes of confirmed cases, hospitalizations, and deaths were analyzed after reopening for 11 countries and 40 US states using an interrupted time series analysis. Additionally, the distribution of these categories was further analyzed by age due to the known increased risk in elderly patients. Reopening had varied effects on COVID-19 cases depending on the region. Recent increases in cases did not fully translate into increased deaths. Eight countries had increased cases after reopening while only two countries showed the same trend in deaths. In the US, 30 states had observed increases in cases while only seven observed increased deaths. In addition, we found that states with later reopening dates were more likely to have significant decreases in cases, hospitalizations, and deaths. Furthermore, age distributions through time were analyzed in relation to COVID-19 in the US. Younger age groups typically had an increased share of cases after reopening.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Weiqi Zhang", - "author_inst": "Merck Holding (China), Shanghai, China, a business of Merck KGaA, Darmstadt, Germany" - }, - { - "author_name": "Alina Oltean", - "author_inst": "MilliporeSigma, St. Louis, Missouri, a business of Merck KGaA, Darmstadt, Germany" - }, - { - "author_name": "Scott Nichols", - "author_inst": "MilliporeSigma, St. Louis, Missouri, a business of Merck KGaA, Darmstadt, Germany" - }, - { - "author_name": "Fuad Odeh", - "author_inst": "MilliporeSigma, St. Louis, Missouri, a business of Merck KGaA, Darmstadt, Germany" - }, - { - "author_name": "Fei Zhong", - "author_inst": "MilliporeSigma, St. Louis, Missouri, a business of Merck KGaA, Darmstadt, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.04.20167874", "rel_title": "Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing", @@ -1275166,6 +1275516,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.06.239798", + "rel_title": "IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection", + "rel_date": "2020-08-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.239798", + "rel_abs": "The novel virus SARS-CoV-2 has infected more than 14 million people worldwide resulting in the Coronavirus disease 2019 (COVID-19). Limited information on the underlying immune mechanisms that drive disease or protection during COVID-19 severely hamper development of therapeutics and vaccines. Thus, the establishment of relevant animal models that mimic the pathobiology of the disease is urgent. Rhesus macaques infected with SARS-CoV-2 exhibit disease pathobiology similar to human COVID-19, thus serving as a relevant animal model. In the current study, we have characterized the transcriptional signatures induced in the lungs of juvenile and old rhesus macaques following SARS-CoV-2 infection. We show that genes associated with Interferon (IFN) signaling, neutrophil degranulation and innate immune pathways are significantly induced in macaque infected lungs, while pathways associated with collagen formation are downregulated. In COVID-19, increasing age is a significant risk factor for poor prognosis and increased mortality. We demonstrate that Type I IFN and Notch signaling pathways are significantly upregulated in lungs of juvenile infected macaques when compared with old infected macaques. These results are corroborated with increased peripheral neutrophil counts and neutrophil lymphocyte ratio in older individuals with COVID-19 disease. In contrast, pathways involving VEGF are downregulated in lungs of old infected macaques. Using samples from humans with SARS-CoV-2 infection and COVID-19, we validate a subset of our findings. Finally, neutrophil degranulation, innate immune system and IFN gamma signaling pathways are upregulated in both tuberculosis and COVID-19, two pulmonary diseases where neutrophils are associated with increased severity. Together, our transcriptomic studies have delineated disease pathways to improve our understanding of the immunopathogenesis of COVID-19 to facilitate the design of new therapeutics for COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bruce A. Rosa", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Mushtaq Ahmed", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Dhiraj K. Singh", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jose Alberto Choreno-Parra", + "author_inst": "Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias" + }, + { + "author_name": "Journey Cole", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Armando Jimenez-Alvarez", + "author_inst": "Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias" + }, + { + "author_name": "Tatiana Sofia Rodriguez-Reyna", + "author_inst": "Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Medicas y Nutricion" + }, + { + "author_name": "Bindu Singh", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Olga Golzalez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Ricardo Carrion", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Larry S. Schlesinger", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "John Martin", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Joaquin Zuniga", + "author_inst": "Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional" + }, + { + "author_name": "Makedonka Mitreva", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Shabaana A Khader", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Deepak Kaushal", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.06.240333", "rel_title": "Computational Hot-Spot Analysis of the SARS-CoV-2 Receptor Binding Domain / ACE2 Complex", @@ -1275878,161 +1276307,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.08.05.238188", - "rel_title": "Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells", - "rel_date": "2020-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.05.238188", - "rel_abs": "Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) [1]. Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia [2]. We collected bronchoalveolar lavage fluid samples from 86 patients with SARS-CoV-2-induced respiratory failure and 252 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection at the onset of mechanical ventilation, the alveolar space is persistently enriched in alveolar macrophages and T cells without neutrophilia. Bulk and single cell transcriptomic profiling suggest SARS-CoV-2 infects alveolar macrophages that respond by recruiting T cells. These T cells release interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell recruitment. Our results suggest SARS-CoV-2 causes a slowly unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 transcripts and T cells form a positive feedback loop that drives progressive alveolar inflammation.\n\nThis manuscript is accompanied by an online resource: https://www.nupulmonary.org/covid-19/\n\nOne sentence summarySARS-CoV-2-infected alveolar macrophages form positive feedback loops with T cells in patients with severe COVID-19.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Rogan A Grant", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Luisa Morales-Nebreda", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Nikolay S Markov", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Suchitra Swaminathan", - "author_inst": "Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University; Robert H Lurie Comprehensive Cancer Research Center, Fei" - }, - { - "author_name": "Estefany R Guzman", - "author_inst": "Robert H Lurie Comprehensive Cancer Research Center, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Darryl A Abbott", - "author_inst": "Robert H Lurie Comprehensive Cancer Research Center, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Helen K Donnelly", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Alvaro Donayre", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Isaac A Goldberg", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Zasu M Klug", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Nicole Borkowski", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Ziyan Lu", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Hermon Kihshen", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Yuliya Politanska", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Lango Sichizya", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Mengjia Kang", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Ali Shilatifard", - "author_inst": "Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University; Simpson Querrey Center for Epigenetics, Feinberg School" - }, - { - "author_name": "Chao Qi", - "author_inst": "Department of Pathology, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "A Christine Argento", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Jacqueline M Kruser", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Elizabeth S Malsin", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Chiagozie O Pickens", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Sean Smith", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "James M Walter", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Anna E Pawlowski", - "author_inst": "Clinical and Translational Sciences Institute, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Daniel Schneider", - "author_inst": "Clinical and Translational Sciences Institute, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Prasanth Nannapaneni", - "author_inst": "Clinical and Translational Sciences Institute, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Hiam Abdala-Valencia", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Ankit Bharat", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University; Division of Thoracic Surgery, De" - }, - { - "author_name": "Cara J Gottardi", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "GR Scott Budinger", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Alexander V Misharin", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Benjamin D Singer", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University; Department of Biochemistry and M" - }, - { - "author_name": "Richard G Wunderink", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University; Simpson Querrey Center for Epige" - }, - { - "author_name": "- The NU SCRIPT Study Investigators", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.04.20165928", "rel_title": "Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation", @@ -1277088,6 +1277362,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.31.20163055", + "rel_title": "SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20163055", + "rel_abs": "ImportanceAntibody testing is important for understanding patterns of exposure and potential immunity to SARS-CoV-2. Prior data on seroprevalence have been subject to variations in selection of individuals and nature as well as timing of testing in relation to exposures.\n\nObjectiveWe sought to determine the extent of SARS-CoV-2 seroprevalance and the factors associated with seroprevelance across a diverse cohort of healthcare workers.\n\nDesignObservational cohort study of healthcare workers, including SARS-CoV-2 serology testing and participant questionaires.\n\nParticipantsA diverse and unselected population of adults (n=6,062) employed in a multi-site healthcare delivery system located in Los Angeles County, including individuals with direct patient contact and others with non-patient-oriented work functions.\n\nExposureExposure and infection with the SARS-CoV-2 virus, as determined by seropositivity.\n\nMain OutcomesUsing Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection.\n\nResultsWe observed a seroprevalence rate of 4.1%, with anosmia as the most prominently associated self-reported symptom in addition to fever, dry cough, anorexia, and myalgias. After adjusting for potential confounders, pre-existing medical conditions were not associated with antibody positivity. However, seroprevalence was associated with younger age, Hispanic ethnicity, and African-American race, as well as presence of either a personal or household member having a prior diagnosis of Covid-19. Importantly, African American race and Hispanic ethnicity were associated with antibody positivity even after adjusting for personal Covid-19 diagnosis status, suggesting the contribution of unmeasured structural or societally factors. Notably, number of people, or children, in the home was not associated with antibody positivity.\n\nConclusion and RelevanceThe demographic factors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace. The size and diversity of our study population, combined with robust survey and modeling techniques, provide a vibrant picture of the demographic factors, exposures, and symptoms that can identify individuals with susceptibility as well as potential to mount an immune response to Covid-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the SARS-CoV-2 IgG seroprevalence rate across a large and diverse healthcare worker population, and which clinical, envionrmental, and symptom-based measures are associated with seropositivity?\n\nFindingsWe observed a seroprevalence rate of 4.1%. Adjusting for potential confounders, seropositivity was associated with younger age, Hispanic ethnicity, African-American race, and the symptom of anosmia, while not significantly associated with any pre-existing medical conditions.\n\nMeaningFactors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Joseph Ebinger", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Gregory J. Botwin", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Christine M. Albert", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Mona Alotaibi", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Moshe Arditi", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Anders H. Berg", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Aleksandra Binek", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Patrick G. Botting", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Justyna Fert-Bober", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jane C. Figueiredo", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jonathan D. Grein", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Wohaib Hasan", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mir Henglin", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Shehnaz K. Hussain", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mohit Jain", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Sandy Joung", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Michael Karin", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Elizabeth H Kim", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Dalin Li", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Yunxian Liu", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Eric Luong", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Dermot P.B. McGovern", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Akil Merchant", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Noah M. Merin", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Peggy B. Miles", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Margo Minissian", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Trevor-Trung Nguyen", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Koen Raedschelders", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mohamad A. Rashid", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Celine E. Riera", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Richard V. Riggs", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Sonia Sharma", + "author_inst": "La Jolla Institute" + }, + { + "author_name": "Sarah Sternbach", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Nancy Sun", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Warren G. Tourtellotte", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jennifer E. Van Eyk", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Kimia Sobhani", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jonathan G. Braun", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Susan Cheng", + "author_inst": "Cedars-Sinai Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.31.20165738", "rel_title": "Early clinical characteristics of Covid-19: scoping review", @@ -1277948,37 +1278393,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.31.20166090", - "rel_title": "Land Use Change and Coronavirus Emergence Risk", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20166090", - "rel_abs": "Coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS) causing coronaviruses are mostly discovered in Asian horseshoe bats. It is still unclear how ongoing land use changes may facilitate SARS-related coronavirus transmission to humans. Here we use a multivariate hotspot analysis of high-resolution land-use data to show that regions of China populated by horseshoe bats are hotspots of forest fragmentation, livestock and human density. We also identify areas susceptible to new hotspot emergence in response to moderate expansion of urbanization, livestock production, or forest disturbance, thereby highlighting regions vulnerable to SARS-CoV spillover under future land-use change. In China population growth and increasing meat consumption associated with urbanization and economic development have expanded the footprint of agriculture, leading to human encroachment in wildlife habitat and increased livestock density in areas adjacent to fragmented forests. The reduced distance between horseshoe-bats and humans elevates the risk for SARS-related coronavirus transmission to humans.\n\nSentence summarizing manuscriptWildlife reservoirs for SARS-coronavirus-2 live in global hotspots of forest fragmentation, livestock, and human density in China", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Cristina Rulli", - "author_inst": "Politecnico di Milano" - }, - { - "author_name": "Paolo D'Odorico", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Nikolas Galli", - "author_inst": "Politecnico di Milano" - }, - { - "author_name": "David Hayman", - "author_inst": "Massey University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.01.20166173", "rel_title": "Comparison of media and standards for SARS-CoV-2 RT-qPCR without prior RNA preparation", @@ -1278818,6 +1279232,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.08.03.20167320", + "rel_title": "Retrospective SARS-CoV-2 Real-Time PCR Testing of Stored Bronchoalveolar Lavage Samples from February 2020", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167320", + "rel_abs": "Bronchoalveolar lavage samples (n=34) collected in February, 2020 prior to the wide availability of molecular testing for SARS-CoV-2 were retrospectively assayed for presence of viral RNA. None of these patients qualified for SARS-CoV-2 testing based on Centers for Disease Control criteria at the time. None of the samples tested positive for SARS-CoV-2, suggesting that the virus was not yet widespread in Minnesota at the time these samples were obtained.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Douglas W Challener", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Aditya Shah", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew Binnicker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John O'Horo", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.02.20166256", "rel_title": "Clinical characteristics and antibody response to SARS-CoV-2 spike 1 protein using the VITROS Anti-SARS-CoV-2 antibody tests in COVID-19 patients in Japan", @@ -1279338,41 +1279787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2020.08.02.20166793", - "rel_title": "Comparing the impact on COVID-19 mortality of self-imposed behavior change and of government regulations across 13 countries", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.02.20166793", - "rel_abs": "BackgroundCountries have adopted different approaches, at different times, to reduce the transmission of coronavirus disease 2019 (COVID-19). Cross-country comparison could indicate the relative efficacy of these approaches. We assess various non-pharmaceutical interventions (NPIs) over time, comparing the effects of self-imposed (i.e. voluntary) behavior change and of changes enforced via official regulations, by statistically examining their impacts on subsequent death rates in 13 European countries.\n\nMethods and findingsWe examine two types of NPI: the introduction of government-enforced closure policies over time; and self-imposed alteration of individual behaviors in response to awareness of the epidemic, in the period prior to regulations. Our proxy for the latter is Google mobility data, which captures voluntary behavior change when disease salience is sufficiently high. The primary outcome variable is the rate of change in COVID-19 fatalities per day, 16-20 days after interventions take place. Linear multivariate regression analysis is used to evaluate impacts. Voluntarily reduced mobility, occurring prior to government policies, decreases the percent change in deaths per day by 9.2 percentage points (95% CI 4.5-14.0 pp). Government closure policies decrease the percent change in deaths per day by 14.0 percentage points (95% CI 10.8-17.2 pp). Disaggregating government policies, the most beneficial are intercity travel restrictions, cancelling public events, and closing non-essential workplaces. Other sub-components, such as closing schools and imposing stay-at-home rules, show smaller and statistically insignificant impacts.\n\nConclusionsThis study shows that NPIs have substantially reduced fatalities arising from COVID-19. Importantly, the effect of voluntary behavior change is of the same order of magnitude as government-mandated regulations. These findings, including the substantial variation across dimensions of closure, have implications for the phased withdrawal of government policies as the epidemic recedes, and for the possible reimposition of regulations if a second wave occurs, especially given the substantial economic and human welfare consequences of maintaining lockdowns.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Julian Jamison", - "author_inst": "University of Exeter" - }, - { - "author_name": "Donald Bundy", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Dean Jamison", - "author_inst": "University of California at San Francisco" - }, - { - "author_name": "Jacob Spitz", - "author_inst": "independent researcher" - }, - { - "author_name": "Stephane Verguet", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.03.20167361", "rel_title": "Multisystem inflammatory syndrome in children (MIS-C) temporally associated with SARS-CoV-2 infection: a scoping review of the literature", @@ -1280380,6 +1280794,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.03.20165233", + "rel_title": "Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20165233", + "rel_abs": "Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4{degrees}C, room temperature ([~]19{degrees}C), and 30{degrees}C for prolonged periods and found limited evidence for viral replication in stored saliva samples. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Isabel M Ott", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Madison S Strine", + "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Anne E Watkins", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maikel Boot", + "author_inst": "Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Chaney C Kalinich", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Christina A Harden", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Arnau Casanovas-Massana", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Adam J Moore", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "M. Catherine Muenker", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maura Nakahata", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maria Tokuyama", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Allison Nelson", + "author_inst": "Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "John Fournier", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Santos Bermejo", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatrics, Division of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Rupak Datta", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "- the Yale IMPACT Research team", + "author_inst": "" + }, + { + "author_name": "Charles S Dela Cruz", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Shelli F Farhadian", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Medicine, Section of Infectious Diseases" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Anne Louise Wyllie", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.03.20167304", "rel_title": "Correlation between daily infections and fatality rate due to Covid-19 in Germany", @@ -1280992,41 +1281521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.04.20168039", - "rel_title": "The impact of the COVID-19 lockdown on maternal mental health and coping in the UK: Data from the COVID-19 New Mum Study", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168039", - "rel_abs": "BackgroundDepression and anxiety affect up to 20% of new and expectant mothers during the perinatal period; this rate may have increased due to COVID-19 and lockdown measures. This analysis aimed to assess how mothers are feeling and coping during lockdown, and to identify the potential pathways that can assist them.\n\nMethods1329 women living in the UK aged [≥]18 years with an infant [≤]12 months of age completed an anonymous online survey. Descriptive analysis of maternal mental health, coping, support received, activities undertaken and consequences of lockdown was conducted. Linear regression was used to predict maternal mental health and coping, using activities, support, and consequences of the lockdown as predictors, while adjusting for age, gestational age, ethnicity, income, marital status and number of children.\n\nResultsMore than half of the participants reported feeling down (56%), lonely (59%), irritable (62%) and worried (71%), to some or high extent since lockdown began. Despite this, 70% felt able to cope with the situation. Support with her own health (95% CI .004,235), contacting infant support groups (95% CI -.003, .252), and higher infant gestational age (95% CI .000, .063) predicted better mental health. Travelling for work (95% CI -.680, - .121), lockdown having a major impact on the ability to afford food (95% CI -1.202, -.177), and having an income lower than 30k (95% CI -.475, -.042) predicted poorer mental health. Support with her own health and more equal division of household chores were associated with better coping.\n\nConclusionDuring lockdown, a large proportion of new mothers experienced symptoms of poor mental health; mothers of infants with lower gestational age, with low income, and who are travelling to work were particularly at risk. However, greater support for maternal health and with household chores showed positive associations with maternal mental health and coping. These findings highlight the urgent need to assess maternal mental health, and to identify prevention strategies for mothers during different stages of lockdown.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sarah Dib", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Emeline Rougeaux", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Adriana V\u00e1zquez-V\u00e1zquez", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Jonathan CK Wells", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - }, - { - "author_name": "Mary Fewtrell", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.08.04.20167940", "rel_title": "SARS-CoV-2 antigens expressed in plants detect antibody responses in COVID-19 patients", @@ -1282222,6 +1282716,20 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.04.234880", + "rel_title": "SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing", + "rel_date": "2020-08-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.234880", + "rel_abs": "Here we provide technical data for amplifying the complete genome of SARS-CoV-2 from clinical samples using only seventeen pairs of primers. We demonstrate that the [C]V2000bp primer panel successfully produces genomes when used with the residual total RNA extracts from positive clinical samples following diagnostic RT-PCRs (with Ct in the range from 13 to 20). The library preparation method reported here includes genome amplification of ~1750-2000 bp fragments followed by ultrasonic fragmentation combined with the introduction of Illumina compatible adapters. Using the SCV2000bp panel, 25 complete SARS-CoV-2 virus genome sequences were sequenced from clinical samples of COVID-19 patients from Moscow obtained in late March - early April.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.08.04.236653", "rel_title": "Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2", @@ -1283002,49 +1283510,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.03.233866", - "rel_title": "SARS-CoV-2 genome sequences from late April in Stockholm, Sweden reveal a novel mutation in the spike protein", - "rel_date": "2020-08-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.03.233866", - "rel_abs": "Large research efforts are going into characterizing, mapping the spread, and studying the biology and clinical features of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we report four complete SARS-CoV-2 genome sequences obtained from patients confirmed to have the disease in Stockholm, Sweden, in late April. A variant at position 23463 was found for the first time in one genome. It changes an arginine (R) residue to histidine (H) at position 364 in the S1 subunit of the spike protein. The genomes belonged to two different genetic groups, previously reported as two of the three main genetic groups found in Sweden. Three of them are from group B.1/G, corresponding to the Italian outbreak, reported by the Public Health Agency of Sweden to have declined in prevalence by late April, and more investigation is needed in order to ensure that the spread of different types of SARS-CoV-2 is fully characterized.\n\nHighlightsO_LIFour near-complete genomes of SARS-CoV-2 were assembled from late April in Stockholm.\nC_LIO_LIA novel mutation in the spike protein were found.\nC_LIO_LIThe phylogeny of the strains were discussed.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tatiany Aparecida Teixeira Soratto", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Hamid Darban", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Annelie Bjerkner", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Maarten Coorens", - "author_inst": "Karolinska University Hospital" - }, - { - "author_name": "Jan Albert", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Tobias Allander", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Bjorn Andersson", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.08.02.233064", "rel_title": "Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery", @@ -1284392,6 +1284857,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.30.20163824", + "rel_title": "Clinical Utility of a Highly Sensitive Lateral Flow Immunoassay as determined by Titer Analysis for the Detection of anti-SARS-CoV-2 Antibodies at the Point-of-Care", + "rel_date": "2020-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20163824", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), became a pandemic in early 2020. Lateral flow immunoassays for antibody testing have been viewed as a cheap and rapidly deployable method for determining previous infection with SARS-CoV-2; however, these assays have shown unacceptably low sensitivity. We report on nine lateral flow immunoassays currently available and compare their titer sensitivity in serum to a best-practice enzyme-linked immunosorbent assay (ELISA) and viral neutralization assay. For a small group of PCR-positive, we found two lateral flow immunoassay devices with titer sensitivity roughly equal to the ELISA; these devices were positive for all PCR-positive patients harboring SARS-CoV-2 neutralizing antibodies. One of these devices was deployed in Northern Italy to test its sensitivity and specificity in a real-world clinical setting. Using the device with fingerstick blood on a cohort of 27 hospitalized PCR-positive patients and seven hospitalized controls, ROC curve analysis gave AUC values of 0.7646 for IgG. For comparison, this assay was also tested with saliva from the same patient population and showed reduced discrimination between cases and controls with AUC values of 0.6841 for IgG. Furthermore, during viral neutralization testing, one patient was discovered to harbor autoantibodies to ACE2, with implications for how immune responses are profiled. We show here through a proof-of-concept study that these lateral flow devices can be as analytically sensitive as ELISAs and adopted into hospital protocols; however, additional improvements to these devices remain necessary before their clinical deployment.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Amanda Haymond", + "author_inst": "George Mason University" + }, + { + "author_name": "Claudius Mueller", + "author_inst": "George Mason University" + }, + { + "author_name": "Hannah Steinberg", + "author_inst": "University of Illinois, Chicago" + }, + { + "author_name": "K. Alex Hodge", + "author_inst": "George Mason University" + }, + { + "author_name": "Caitlin W Lehman", + "author_inst": "George Mason University" + }, + { + "author_name": "Shih-Chao Lin", + "author_inst": "George Mason University" + }, + { + "author_name": "Lucia Collini", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Heather Branscome", + "author_inst": "George Mason University" + }, + { + "author_name": "Tuong Vi Nguyen", + "author_inst": "George Mason University" + }, + { + "author_name": "Sally Rucker", + "author_inst": "George Mason University" + }, + { + "author_name": "Lauren Panny", + "author_inst": "George Mason University" + }, + { + "author_name": "Rafaela Flor", + "author_inst": "George Mason University" + }, + { + "author_name": "Raouf Guirguis", + "author_inst": "George Mason University" + }, + { + "author_name": "Richard Hoefer", + "author_inst": "Sentara Dorothy G. Hoefer Comprehensive Breast Center" + }, + { + "author_name": "Giovanni Lorenzin", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Emanuel Petricoin", + "author_inst": "George Mason University" + }, + { + "author_name": "Fatah Kashanchi", + "author_inst": "George Mason University" + }, + { + "author_name": "Kylene Kehn-Hall", + "author_inst": "George Mason University" + }, + { + "author_name": "Paolo Lanzafame", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Lance Liotta", + "author_inst": "George Mason University" + }, + { + "author_name": "Alessandra Luchini", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.30.20114959", "rel_title": "Impact of tocilizumab administration on mortality in severe COVID-19", @@ -1285028,37 +1285592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.07.29.20164806", - "rel_title": "Comparative experimental evidence on compliance with social distancing during the COVID-19 pandemic", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164806", - "rel_abs": "Social distancing is a central public health measure in the fight against the COVID-19 pandemic, but individuals compliance cannot be taken for granted. We use a survey experiment to examine the prevalence of non-compliance with social distancing in nine countries and test pre-registered hypotheses about individual-level characteristics associated with less social distancing. Leveraging a list experiment to control for social desirability bias, we find large cross-national variation in adherence to social distancing guidelines. Compliance varies systematically with COVID-19 fatalities and the strictness of lockdown measures. We also find substantial heterogeneity in the role of individual-level predictors. While there is an ideological gap in social distancing in the US and New Zealand, this is not the case in European countries. Taken together, our results suggest caution when trying to model pandemic health policies on other countries experiences. Behavioral interventions targeted towards specific demographics that work in one context might fail in another.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Michael Becher", - "author_inst": "Institute for Advanced Study in Toulouse" - }, - { - "author_name": "Daniel Stegmueller", - "author_inst": "Duke University" - }, - { - "author_name": "Sylvain Brouard", - "author_inst": "CEVIPOF, Science Po, Paris" - }, - { - "author_name": "Eric Kerrouche", - "author_inst": "CEVIPOF, Science Po, Paris" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.07.30.20164368", "rel_title": "Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers", @@ -1286066,6 +1286599,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.31.231746", + "rel_title": "Engineered ACE2 receptor traps potently neutralize SARS-CoV-2", + "rel_date": "2020-08-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231746", + "rel_abs": "An essential mechanism for SARS-CoV-1 and -2 infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the 10-100 ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be pre-designed for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated or generated from convalescent patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anum Glasgow", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeff Edward Glasgow", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Daniel Limonta", + "author_inst": "University of Alberta" + }, + { + "author_name": "Paige Solomon", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Irene Lui", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yang Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A Nix", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nicholas J Rettko", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Shion A Lim", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Shoshana Zha", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rachel Yamin", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Kevin Kao", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Oren S Rosenberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeffrey V Ravetch", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Arun P Wiita", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin K Leung", + "author_inst": "UCSF" + }, + { + "author_name": "Xin X Zhou", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Tom C Hobman", + "author_inst": "University of Alberta" + }, + { + "author_name": "Tanja K Kortemme", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "James A. Wells", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.07.31.190454", "rel_title": "Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy", @@ -1286766,37 +1287394,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.30.20165191", - "rel_title": "Mathematical modeling of the transmission of SARS-CoV-2 '' Evaluating the impact of isolation in Sao Paulo State (Brazil) and lockdown in Spain associated with protective measures on the epidemic of covid-19", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165191", - "rel_abs": "Coronavirus disease 2019 (covid-19), with the fatality rate in elder (60 years old or more) being much higher than young (60 years old or less) patients, was declared a pandemic by the World Health Organization on March 11, 2020. Taking into account this age-dependent fatality rate, a mathematical model considering young and elder subpopulations was formulated based on the natural history of covid-19 to study the transmission of the SARS-CoV-2. This model can be applied to study the epidemiological scenario resulting from the adoption of isolation or lockdown in many countries to control the rapid propagation of covid-19. We chose as examples the isolation adopted in Sao Paulo State (Brazil) in the early phase but not at the beginning of the epidemic, and the lockdown implemented in Spain when the number of severe covid-19 cases was increasing rapidly. Based on the data collected from Sao Paulo State and Spain, the model parameters were evaluated and we obtained higher estimation for the basic reproduction number R0 (9.24 for Sao Paulo State, and 8 for Spain) compared to the currently accepted estimation of R0 around 3. The model allowed to explain the flattening of the epidemic curves by isolation in Sao Paulo State and lockdown in Spain when associated with the protective measures (face mask and social distancing) adopted by the population. However, a simplified mathematical model providing lower estimation for R0 did not explain the flattening of the epidemic curves. The implementation of the isolation in Sao Paulo State before the rapidly increasing phase of the epidemic enlarged the period of the first wave of the epidemic and delayed its peak, which are the desirable results of isolation to avoid the overloading in the health care system.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Hyun Mo Yang", - "author_inst": "State University of Campinas" - }, - { - "author_name": "Luis Pedro Lombardi Jr.", - "author_inst": "State University of Campinas" - }, - { - "author_name": "Fabio Fernandes Morato Castro", - "author_inst": "General Hospital of the Medicine School of University of Sao Paulo" - }, - { - "author_name": "Ariana Campos Yang", - "author_inst": "General Hospital of the Medicine School of University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.30.20165043", "rel_title": "A prospective study to identify rates of SARS-CoV-2 virus in the peritoneum and lower genital tract of patients having surgery", @@ -1287748,6 +1288345,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.31.231472", + "rel_title": "New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release", + "rel_date": "2020-07-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231472", + "rel_abs": "The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15,342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP 12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major {beta}-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tre Tomaszewski", + "author_inst": "University of Illinois" + }, + { + "author_name": "Ryan S DeVries", + "author_inst": "University of Illinois" + }, + { + "author_name": "Mengyi Dong", + "author_inst": "University of Illinois" + }, + { + "author_name": "Gitanshu Bhatia", + "author_inst": "University of Illinois" + }, + { + "author_name": "Miles D Norsworthy", + "author_inst": "University of Illinois" + }, + { + "author_name": "Xuying Zheng", + "author_inst": "University of Illinois" + }, + { + "author_name": "Gustavo Caetano-Anolles", + "author_inst": "University of Illinois" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.31.230730", "rel_title": "Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction", @@ -1288460,37 +1289100,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.07.28.20163964", - "rel_title": "Brazilian dental students and COVID-19: a survey on knowledge and perceptions", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163964", - "rel_abs": "This study evaluated the knowledge and perception of Brazilian dental students about COVID-19 and the undergraduate clinical practice during the outbreak by a self-administered web-based questionnaire. A social network campaign on Instagram was raised to approach the reach population. The survey covered demographic and academic profile, general knowledge, preventive measures, and perception about the COVID-19. Descriptive statistics were used to identify frequencies and distributions of variables, which were compared by type of institution and current year of enrollment using Chi-square or Fishers exact tests (=0.05). A total of 833 valid responses were received over 10 days. Students were able to identify the incubation period, main symptoms, and contagious routes of the disease but struggled in recognizing the name of the virus responsible for the pandemics. Hand washing before and after a dental appointment with a patient (97.7%) followed by use of barriers to protect mucosa (97.2%) were the more frequently recognized measures to prevent COVID-19 spread in the dental office. As for the perception of COVID-19, 73.2% of the dental students perceive the disease as severe, while only 11.1% of them think that COVID-19 is severe only for people presenting risk factors. Dental students knowledge and perception were associated with the type of institution and year of enrollment. In summary, the dental students demonstrated an acceptable general knowledge about COVID-19, but dental schools will need to address gaps in knowledge and control measures and perceptions to ensure a safer return to presential activities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Gerusa Brito Aragao", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Francisco Isaac Fernandes Gomes", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Leticia Pinho Maia Paixao de Melo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Silmara Aparecida Milori Corona", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2020.07.29.20164269", "rel_title": "The potential health and economic impact of dexamethasone treatment for patients with COVID-19", @@ -1289426,6 +1290035,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.28.20163816", + "rel_title": "Multimorbidity patterns among COVID-19 deaths: considerations for a better medical practice", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163816", + "rel_abs": "Medical care of individuals diagnosed with severe COVID-19 is complex, especially when patients are older adults with multimorbidity. The objective of this study was to describe patterns of multimorbidity among fatal cases of COVID-19. Data of Colombian confirmed deaths of COVID-19 until June 11, 2020, were included in this analysis (1488 deaths). Relationships between COVID-19, combinations of health conditions and age were explored using locally weighted polynomial regressions. Some multimorbidity patterns increase probability of death among older individuals, whereas other patterns are not age-related, or decreases the probability of death among older people. Consider multimorbidity in the medical management of COVID-19 patients is important to determine the more adequate medical interventions. In addition to the co-occurrence of COVID-19 with diseases of high prevalence in the world, in Colombia there are cases more complex with COVID-19 co-occur with endemic and orphan tropical diseases. In these cases, although its occurrence may be low, clinical management requires adjusting to its complex clinical condition.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Julian Alfredo Fernandez-Nino", + "author_inst": "Fundacion Universidad del Norte" + }, + { + "author_name": "Jhon A Guerra-Gomez", + "author_inst": "Northeastern University, Silicon Valle" + }, + { + "author_name": "Alvaro Javier Idrovo-Velandia", + "author_inst": "Universidad Industrial de Santander" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.28.20163980", "rel_title": "Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19", @@ -1289946,145 +1290582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.29.20162701", - "rel_title": "Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20162701", - "rel_abs": "BackgroundUnderstanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms.\n\nMethodsWe undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million.\n\nFindingsWe demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive.\n\nInterpretationSeroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response.\n\nFundingNIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Philippa M Wells", - "author_inst": "King's College London" - }, - { - "author_name": "Katie M Doores", - "author_inst": "King's College London" - }, - { - "author_name": "Simon Couvreur", - "author_inst": "KCL" - }, - { - "author_name": "Rocio Martin Martinez", - "author_inst": "King's College London" - }, - { - "author_name": "Jeffrey Seow", - "author_inst": "KCL" - }, - { - "author_name": "Carl Graham", - "author_inst": "KCL" - }, - { - "author_name": "Sam Acors", - "author_inst": "KCL" - }, - { - "author_name": "Neophytos Kouphou", - "author_inst": "KCL" - }, - { - "author_name": "Stuart Neil", - "author_inst": "KCL" - }, - { - "author_name": "Richard Tedder", - "author_inst": "Imperial" - }, - { - "author_name": "Pedro Matos", - "author_inst": "KCL" - }, - { - "author_name": "Kate Poulton", - "author_inst": "KCL" - }, - { - "author_name": "Maria Jose Lista", - "author_inst": "KCL" - }, - { - "author_name": "Ruth Dickenson", - "author_inst": "KCL" - }, - { - "author_name": "Helin Sertkaya", - "author_inst": "KCL" - }, - { - "author_name": "Thomas Maguire", - "author_inst": "KCL" - }, - { - "author_name": "Edward Scourfield", - "author_inst": "KCL" - }, - { - "author_name": "Ruth Bowyer", - "author_inst": "KCL" - }, - { - "author_name": "Deborah Hart", - "author_inst": "KCL" - }, - { - "author_name": "Aoife O'Byrne", - "author_inst": "KCL" - }, - { - "author_name": "Kathryn Steele", - "author_inst": "KCL" - }, - { - "author_name": "Oliver Hemmings", - "author_inst": "KCL" - }, - { - "author_name": "Carolina Rosadas", - "author_inst": "Imperial College London" - }, - { - "author_name": "Myra McClure", - "author_inst": "Imperial College London" - }, - { - "author_name": "Joan Capedevila-Pujol", - "author_inst": "KCL" - }, - { - "author_name": "Jonathan wolf", - "author_inst": "Zoe Global" - }, - { - "author_name": "Sebastien Ourseilin", - "author_inst": "Zoe Global" - }, - { - "author_name": "Matthew Brown", - "author_inst": "KCL" - }, - { - "author_name": "Michael Malim", - "author_inst": "KCL" - }, - { - "author_name": "Timothy Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Claire Steves", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.28.20163626", "rel_title": "Clinical validation of innovative, low cost, kit-free, RNA processing protocol for RT-PCR based COVID-19 testing.", @@ -1291156,6 +1291653,45 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.07.17.20156463", + "rel_title": "SARS-CoV-2 Infection and Stroke: Coincident or Causal?", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156463", + "rel_abs": "Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Data collected during peak of the Covid-19 pandemic from stroke centers in five states reveal few similarities to what has recently been published. Given the diversity in phenotype, we caution policymakers and health care providers when considering cerebrovascular complications from SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Melanie Walker", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Christopher C. Young", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Malveeka Sharma", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Michael R Levitt", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "David L Tirschwell", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "- WWAMI Stroke Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.07.23.20160887", "rel_title": "Divide in Vaccine Belief in COVID-19 Conversations: Implications for Immunization Plans", @@ -1291716,129 +1292252,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.27.20161836", - "rel_title": "A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20161836", - "rel_abs": "In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 minute gradient run with 100% specificity and 90.4 % sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Praveen Singh", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Rahul Chakraborty", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Robin Marwal", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Radhakrishan V S", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Akash Kumar Bhaskar", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Himanshu Vashisht", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Mahesh S Dhar", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Shalini Pradhan", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Gyan Ranjan", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Mohamed Imran", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Anurag Raj", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Uma Sharma", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Priyanka Singh", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Hemlata Lall", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Meena Dutta", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Parth Garg", - "author_inst": "Indraprastha Institute of Information Technology" - }, - { - "author_name": "Arjun Ray", - "author_inst": "Indraprastha Institute of Information Technology" - }, - { - "author_name": "Debasis Dash", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Sridhar Sivasubbu", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Hema Gogia", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Preeti Madan", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Sandhya Kabra", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Sujeet K Singh", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Anurag Agrawal", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Partha Rakhit", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Pramod Kumar", - "author_inst": "National Center for Disease Control" - }, - { - "author_name": "Shantanu Sengupta", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.26.20162255", "rel_title": "Magnetic bead-based ELISA allow inexpensive, rapid and quantitative detection of human antibodies against SARS-CoV-2", @@ -1292706,6 +1293119,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.27.20149757", + "rel_title": "Children with COVID-19 like symptoms in Italian Pediatric Surgeries: the dark side of the coin", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20149757", + "rel_abs": "BackgroundSymptoms of SARS-CoV-2 infection in children are nonspecific and shared with other common acute viral illnesses (fever, respiratory or gastrointestinal symptoms, and cutaneous signs), thus making clinical differential diagnosis tricky. In Italy, first line management of pediatric care is handed over to Primary Care Pediatricians (PCPs), who were not allowed to directly perform diagnostic tests during the recent COVID-19 outbreak. Without a confirmatory diagnosis, PCPs could only collect information on \"COVID-19 like symptoms\" rather than identify typical COVID-19 symptoms.\n\nAimTo evaluate the prevalence of COVID-19 like symptoms in outpatient children, during Italian lockdown. To provide PCPs a risk score to be used in clinical practice during the differential diagnosis process.\n\nMethodsA survey was submitted to 50 PCPs (assisting 47,500 children) from 7 different Italian regions between the 4th of March and the 23rd of May 2020 (total and partial lockdown period). COVID-19 like symptoms in the assisted children were recorded, as well as presence of confirmed/suspected cases in childrens families, which was taken as proxy of COVID-19. Multivariable logistic regression was accomplished to estimate the risk of having suspected/confirmed cases in families, considering symptoms as potential determinants.\n\nResults2,300 children (4.8% of overall survey population) fell ill with COVID-19 like symptoms, 3.1% and 1.7% during total and partial lockdown period respectively. The concurrent presence of fatigue, cough, and diarrhea in children, in absence of sore throat/earache and abnormal skin signs, represents the maximum risk level of having a suspected/confirmed case of COVID-19 at home.\n\nConclusionsThe percentage of children presenting COVID-19 like symptoms at home has been remarkable also during the total lockdown period. The present study identified a pattern of symptoms which could help, in a cost-effective perspective, PCPs in daily clinical practice to define priorities in addressing children to the proper diagnostic procedure.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gianfranco Trapani", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Sanremo (IM), Italy" + }, + { + "author_name": "Vassilios Fanos", + "author_inst": "Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy" + }, + { + "author_name": "Enrico Bertino", + "author_inst": "Neonatal Care Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Giulia Maiocco", + "author_inst": "Neonatal Care Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Osama Al Jamal", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Cagliari, Italy" + }, + { + "author_name": "Michele Fiore", + "author_inst": "Primary Care Pediatrician, Genoa, Italy" + }, + { + "author_name": "VIncenzo Bembo", + "author_inst": "Primary Care Pediatrician, Frosinone, Italy" + }, + { + "author_name": "Domenico Careddu", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Novara, Italy" + }, + { + "author_name": "Lando Barberio", + "author_inst": "Primary Care Pediatrician, Taggia (IM), Italy" + }, + { + "author_name": "Luisella Zanino", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Turin, Italy" + }, + { + "author_name": "Giuseppe Verlato", + "author_inst": "Unit of Epidemiology and Medical Statistics, Department of Diagnostics & Public Health, University of Verona, Verona, Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.27.20162057", "rel_title": "Predicting PPE use, post-traumatic stress, and physical symptoms during the early weeks of COVID-19 lockdowns in the USA", @@ -1293506,113 +1293978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.27.20161810", - "rel_title": "Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20161810", - "rel_abs": "BackgroundIdentification of risk factors for COVID-19-associated hospitalization is needed to guide prevention and clinical care.\n\nObjectiveTo examine if age, sex, race/ethnicity, and underlying medical conditions is independently associated with COVID-19-associated hospitalizations.\n\nDesignCross-sectional.\n\nSetting70 counties within 12 states participating in the Coronavirus Disease 2019-Associated Hospitalization Surveillance Network (COVID-NET) and a population-based sample of non-hospitalized adults residing in the COVID-NET catchment area from the Behavioral Risk Factor Surveillance System.\n\nParticipantsU.S. community-dwelling adults ([≥]18 years) with laboratory-confirmed COVID-19-associated hospitalizations, March 1- June 23, 2020.\n\nMeasurementsAdjusted rate ratios (aRR) of hospitalization by age, sex, race/ethnicity and underlying medical conditions (hypertension, coronary artery disease, history of stroke, diabetes, obesity [BMI [≥]30 kg/m2], severe obesity [BMI[≥]40 kg/m2], chronic kidney disease, asthma, and chronic obstructive pulmonary disease).\n\nResultsOur sample included 5,416 adults with COVID-19-associated hospitalizations. Adults with (versus without) severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7) had higher rates of hospitalization, after adjusting for age, sex, and race/ethnicity. In models adjusting for the presence of an individual underlying medical condition, higher hospitalization rates were observed for adults [≥]65 years, 45-64 years (versus 18-44 years), males (versus females), and non-Hispanic black and other race/ethnicities (versus non-Hispanic whites).\n\nLimitationsInterim analysis limited to hospitalizations with underlying medical condition data.\n\nConclusionOur findings elucidate groups with higher hospitalization risk that may benefit from targeted preventive and therapeutic interventions.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Jean Y. Ko", - "author_inst": "Centers for Disease Control and Prevention; U.S.Public Health Service" - }, - { - "author_name": "Melissa L. Danielson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Machell Town", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Gordana Derado", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Kurt J. Greenland", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Pam Daily Kirley", - "author_inst": "California Emerging Infections Program" - }, - { - "author_name": "Nisha B. Alden", - "author_inst": "Colorado Department of Public Health and Environment" - }, - { - "author_name": "Kimberly Yousey-Hindes", - "author_inst": "Connecticut Emerging Infections Program" - }, - { - "author_name": "Evan J. Anderson", - "author_inst": "Departments of Medicine and Pediatrics, Emory University School of Medicine; Emerging Infections Program, Georgia Department of Health; Atlanta Veterans Affairs" - }, - { - "author_name": "Patricia A. Ryan", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Sue Kim", - "author_inst": "Michigan Department of Health and Human Services" - }, - { - "author_name": "Ruth Lynfield", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Salina M. Torres", - "author_inst": "New Mexico Department of Health" - }, - { - "author_name": "Grant R. Barney", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Nancy M. Bennett", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Melissa Sutton", - "author_inst": "Oregon Health Authority" - }, - { - "author_name": "H. Keipp Talbot", - "author_inst": "Vanderbilt University School of Medicine" - }, - { - "author_name": "Mary Hill", - "author_inst": "Salt Lake County Health Department" - }, - { - "author_name": "Aron J. Hall", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Alicia M. Fry", - "author_inst": "Centers for Disease Control and Prevention; U.S. Public Health Service" - }, - { - "author_name": "Shikha Garg", - "author_inst": "Centers for Disease Control and Prevention; U.S. Public Health Service" - }, - { - "author_name": "Lindsay Kim", - "author_inst": "Centers for Disease Control and Prevention; U.S. Public Health Service" - }, - { - "author_name": "- COVID-NET Investigation Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.27.20163121", "rel_title": "Impact Assessment of Full and Partial Stay-at-Home Orders, Face Mask Usage, and Contact Tracing: An Agent-Based Simulation Study of COVID-19 for an Urban Region", @@ -1294748,6 +1295113,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.28.225581", + "rel_title": "Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis", + "rel_date": "2020-07-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.225581", + "rel_abs": "The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/225581v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@15ca5a6org.highwire.dtl.DTLVardef@17f455forg.highwire.dtl.DTLVardef@a39f50org.highwire.dtl.DTLVardef@306ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Mariana G. Ferrarini", + "author_inst": "University of Lyon, INSA-Lyon, INRAE, BF2I" + }, + { + "author_name": "Avantika Lal", + "author_inst": "NVIDIA" + }, + { + "author_name": "Rita Rebollo", + "author_inst": "University of Lyon, INSA-Lyon, INRAE, BF2I" + }, + { + "author_name": "Andreas Gruber", + "author_inst": "Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford" + }, + { + "author_name": "Andrea Guarracino", + "author_inst": "Centre for Molecular Bioinformatics, Department of Biology, University Of Rome Tor Vergata" + }, + { + "author_name": "Itziar Martinez Gonzalez", + "author_inst": "Netherlands\tAmsterdam UMC" + }, + { + "author_name": "Taylor Floyd", + "author_inst": "Center for Neurogenetics, Weill Cornell Medicine, Cornell University" + }, + { + "author_name": "Daniel Siqueira de Oliveira", + "author_inst": "Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, CNRS" + }, + { + "author_name": "Justin Shanklin", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Ethan Beausoleil", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Taneli Pusa", + "author_inst": "Luxembourg Centre for Systems Biomedicine" + }, + { + "author_name": "Brett Pickett", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Vanessa Aguiar-Pulido", + "author_inst": "Center for Neurogenetics, Weill Cornell Medicine, Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.29.227389", "rel_title": "On the molecular mechanism of SARS-CoV-2 retention in the upper respiratory tract", @@ -1295216,37 +1295648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.07.25.20159715", - "rel_title": "AutoSEIR: Accurate Forecasting from Real-time Epidemic Data Using Machine Learning", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20159715", - "rel_abs": "Since the SARS-CoV-2 virus outbreak has been recognized as a pandemic on March 11, 2020, several models have been proposed to forecast its evolution following the governments interventions. In particular, the need for fine-grained predictions, based on real-time and fluctuating data, has highlighted the limitations of traditional SEIR models and parameter fitting, encouraging the study of new models for greater accuracy. In this paper we propose a novel approach to epidemiological parameter fitting and epidemic forecasting, based on an extended version of the SEIR compartmental model and on an auto-differentiation technique for partially observable ODEs (Ordinary Differential Equations). The results on publicly available data show that the proposed model is able to fit the daily cases curve with greater accuracy, obtaining also a lower forecast error. Furthermore, the forecast accuracy allows to predict the peak with an error margin of less than one week, up to 50 days before the peak happens.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Stefano Giovanni Rizzo", - "author_inst": "Qatar Computing Reasearch Institute" - }, - { - "author_name": "Giovanna Vantini", - "author_inst": "Qatar Computing Research Institute" - }, - { - "author_name": "Mohamad Saad", - "author_inst": "Qatar Computing Research Institute" - }, - { - "author_name": "Sanjay Chawla", - "author_inst": "Qatar Computing Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.25.20161992", "rel_title": "Modeling Control, Lockdown & Exit Strategies for COVID-19 Pandemic in India", @@ -1296330,6 +1296731,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.28.224386", + "rel_title": "Comparative Analysis of Human Coronaviruses Focusing on Nucleotide Variability and Synonymous Codon Usage Pattern", + "rel_date": "2020-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.224386", + "rel_abs": "Prevailing pandemic across the world due to SARSCoV-2 drawing great attention towards discovering its evolutionary origin. We perform an exploratory study to understand the variability of the whole coding region of possible proximal evolutionary neighbours of SARSCoV-2. We consider seven (07) human coronavirus strains from six different species as a candidate for our study.\n\nFirst, we observe a good variability of nucleotides across candidate strains. We did not find a significant variation of GC content across the strains for codon position first and second. However, we interestingly see huge variability of GC-content in codon position 3rd (GC3), and pairwise mean GC-content (SARSCoV, MERSCoV), and (SARSCoV-2, hCoV229E) are quite closer. While observing the relative abundance of dinucleotide feature, we find a shared typical genetic pattern, i.e., high usage of GC and CT nucleotide pair at the first two positions (P12) of codons and the last two positions (P23) of codons, respectively. We also observe a low abundance of CG pair that might help in their evolution bio-process. Secondly, Considering RSCU score, we find a substantial similarity for mild class coronaviruses, i.e., hCoVOC43, hCoVHKU1, and hCoVNL63 based on their codon hit with high RSCU value ([≥] 1.5), and minim number of codons hit (count-9) is observed for MERSCoV. We see seven codons ATT, ACT, TCT, CCT, GTT, GCT and GGT with high RSCU value, which are common in all seven strains. These codons are mostly from Aliphatic and Hydroxyl amino acid group. A phylogenetic tree built using RSCU feature reveals proximity among hCoVOC43 and hCoV229E (mild). Thirdly, we perform linear regression analysis among GC content in different codon position and ENC value. We observe a strong correlation (significant p-value) between GC2 and GC3 for SARSCoV-2, hCoV229E and hCoVNL63, and between GC1 and GC3 for hCoV229E, hCoVNL63, SARSCoV. We believe that our findings will help in understanding the mechanism of human coronavirus.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jayanta Das", + "author_inst": "Johns Hopkins University, MD-21205, USA" + }, + { + "author_name": "Swarup Roy", + "author_inst": "Sikkim University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.22.20154542", "rel_title": "Prophylaxis with tetracyclines in ARDS: Potential therapy for COVID-19-induced ARDS?", @@ -1297058,65 +1297482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.25.20161869", - "rel_title": "Functional mapping of B-cell linear epitopes 1 of SARS-CoV-2 in COVID-19 convalescent population", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20161869", - "rel_abs": "Pandemic SARS-CoV-2 has infected over 10 million people and caused over 500,000 mortalities. Vaccine development is in urgent need to stop the pandemic. Despite great progresses on SARS-CoV-2 vaccine development, the efficacy of the vaccines remains to be determined. Deciphering the interactions of the viral epitopes with their elicited neutralizing antibodies in the convalescent COVID-19 population inspires the vaccine development. In this study, we devised a peptide array composed of 20-mer overlapped peptides of spike (S), membrane (M) and envelope (E) proteins, and performed a screening with 120 COVID-19 convalescent serums and 24 non-COVID-19 serums. We identified five SARS-CoV-2-specific dominant epitopes that reacted with above 40% COVID-19 convalescent serums. Epitopes in the receptor-binding domain (RBD) of S ill reacted with the convalescent serums. Of note, two peptides non-specifically interacted with most of the non-COVID-19 serums. Neutralization assay indicated that only five serums completely blocked viral infection at the dilution of 1:200. By using a peptide-compete neutralizing assay, we found that three dominant epitopes partially competed the neutralization activity of several convalescent serums, suggesting antibodies elicited by these epitopes played an important role in neutralizing viral infection. The epitopes we identified in this study may serve as vaccine candidates to elicit neutralizing antibodies in most vaccinated people or specific antigens for SARS-CoV-2 diagnosis.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zhigang Yi", - "author_inst": "Fudan University" - }, - { - "author_name": "Yun Ling", - "author_inst": "Shanghai public health clinical center, Fudan University" - }, - { - "author_name": "Xiaonan Zhang", - "author_inst": "Shanghai public health clinical center, Fudan University," - }, - { - "author_name": "Jieliang Chen", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University," - }, - { - "author_name": "Kongying Hu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Yuyan Wang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Wuhui Song", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Tianlei Ying", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Hongzou Lu", - "author_inst": "Shanghai public health clinical center, Fudan University" - }, - { - "author_name": "Zhenghong Yuan", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.23.20160747", "rel_title": "Associations of severe COVID-19 with polypharmacy in the REACT-SCOT case-control study", @@ -1298128,6 +1298493,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.27.223495", + "rel_title": "Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals", + "rel_date": "2020-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.223495", + "rel_abs": "The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Harsha Vardhan Doddapaneni", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Sara Javornik Cregeen", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Richard Sucgang", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Qingchang Meng", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Xiang Qing", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Vasanthi Avadhanula", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Hsu Chao", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Vipin Menon", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Erin Nicholson", + "author_inst": "Department of Molecular Virology and Microbiology, and Pediatrics , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "David Henke", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Felipe-Andres Piedra", + "author_inst": "Department of Molecular Virology and Microbiology , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Anubama Rajan", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Zeineen Momin", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Kavya Kottapalli", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Kristi L. Hoffman", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Ginger Metcalf", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Pedro A Piedra", + "author_inst": "Department of Molecular Virology and Microbiology and Pediatrics , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Donna M Muzny", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Joseph F Petrosino", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Richard A Gibbs", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.27.222836", "rel_title": "Targeting the endolysosomal host-SARS-CoV-2 interface by the clinically licensed antidepressant fluoxetine", @@ -1298732,73 +1299196,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.07.26.221861", - "rel_title": "Newcastle disease virus (NDV) expressing the spike protein of SARS-CoV-2 as vaccine candidate", - "rel_date": "2020-07-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.221861", - "rel_abs": "Due to the lack of protective immunity of humans towards the newly emerged SARS-CoV-2, this virus has caused a massive pandemic across the world resulting in hundreds of thousands of deaths. Thus, a vaccine is urgently needed to contain the spread of the virus. Here, we describe Newcastle disease virus (NDV) vector vaccines expressing the spike protein of SARS-CoV-2 in its wild type or a pre-fusion membrane anchored format. All described NDV vector vaccines grow to high titers in embryonated chicken eggs. In a proof of principle mouse study, we report that the NDV vector vaccines elicit high levels of antibodies that are neutralizing when the vaccine is given intramuscularly. Importantly, these COVID-19 vaccine candidates protect mice from a mouse-adapted SARS-CoV-2 challenge with no detectable viral titer and viral antigen in the lungs.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe spike (S) protein of the SARS-CoV-2 is the major antigen that notably induces neutralizing antibodies to block viral entry. Many COVID-19 vaccines are under development, among them viral vectors expressing the S protein of SARS-CoV-2 exhibit many benefits. Viral vector vaccines have the potential of being used as both live or inactivated vaccines and they can induce Th1 and Th2-based immune responses following different immunization regimens. Additionally, viral vector vaccines can be handled under BSL-2 conditions and they grow to high titers in cell cultures or other species restricted-hosts. For a SARS-CoV-2 vaccine, several viral vectors are being tested, such as adenovirus, measles virus and Modified vaccinia Ankara.\n\nAdded value of this studyThe NDV vector vaccine against SARS-CoV-2 described in this study has advantages similar to those of other viral vector vaccines. But the NDV vector can be amplified in embryonated chicken eggs, which allows for high yields and low costs per dose. Also, the NDV vector is not a human pathogen, therefore the delivery of the foreign antigen would not be compromised by any pre-existing immunity in humans. Finally, NDV has a very good safety record in humans, as it has been used in many oncolytic virus trials. This study provides an important option for a cost-effective SARS-CoV-2 vaccine.\n\nImplications of all the available evidenceThis study informs of the value of a viral vector vaccine against SARS-CoV-2. Specifically, for this NDV based SARS-CoV-2 vaccine, the existing egg-based influenza virus vaccine manufactures in the U.S. and worldwide would have the capacity to rapidly produce hundreds of millions of doses to mitigate the consequences of the ongoing COVID-19 pandemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Weina Sun", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sarah R Leist", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Stephen McCroskery", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Yonghong Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Stefan Slamanig", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Justine Oliva", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexandra Schaefer", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Kenneth Dinnon III", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Peter Palese", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.26.221572", "rel_title": "COVID-19 and Rheumatoid Arthritis share myeloid pathogenic and resolving pathways", @@ -1299866,6 +1300263,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.07.21.20156711", + "rel_title": "Healthcare Workers' Mental Health and Wellbeing During the COVID-19 Pandemic in the UK: Contrasting Guidelines with Experiences in Practice", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20156711", + "rel_abs": "BackgroundSubstantial evidence has highlighted the importance of considering healthcare workers (HCW) mental health during the COVID-19 pandemic, and several organisations have issued guidelines with recommendations. However, the definition of wellbeing and the evidence-base behind such guidelines remains unclear.\n\nObjectivesAssessing the applicability of wellbeing guidelines in practice; identifying unaddressed HCWs needs; and providing recommendations for supporting frontline staff during the current and future pandemics.\n\nMethods and DesignThis paper discusses the findings of a qualitative study based on interviews with frontline healthcare staff in the UK and examines them in relation to a rapid review of wellbeing guidelines developed in response to the COVID-19 pandemic.\n\nResults14 guidelines were included in the rapid review and 33 interviews with HCWs were conducted in the qualitative study. As a whole, the guidelines placed greater emphasis on wellbeing at an individual level, while HCWs placed greater emphasis on structural conditions at work, such as understaffing and the invaluable support of the community. This in turn had implications for the focus of wellbeing intervention strategies; staff reported an increased availability of formal mental health support, however, understaffing or clashing schedules prevented them from participating in these activities.\n\nConclusionHCWs expressed wellbeing needs which align with social-ecological conceptualisations of wellbeing related to quality of life. This approach to wellbeing has been highlighted in literature about HCWs support in previous health emergencies, yet it has not been monitored during this pandemic. Wellbeing guidelines should explore staffs needs and contextual characteristics affecting the implementation of recommendations.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Norha Vera San Juan", + "author_inst": "Insitute of Psychiatry, Psychology and Neuroscience. King's College London" + }, + { + "author_name": "David Aceituno", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience. King's College London" + }, + { + "author_name": "Nehla Djellouli", + "author_inst": "Institute for Global Health. University College London" + }, + { + "author_name": "Kirsi Sumray", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Nina Regenold", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Aron Syversen", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Sophie Mulcahy Symmons", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Anna Dowrick", + "author_inst": "Institute of Population Health and Science. Queen Mary University of London" + }, + { + "author_name": "Lucy Mitchinson", + "author_inst": "Marie Cuerie Pallatieve Care Research Department. University College London" + }, + { + "author_name": "Georgina Singleton", + "author_inst": "Health Services Research Centre. University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "Rapid Research, Evaluation and Appraisal Lab. University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.07.20.20157149", "rel_title": "Association of contact to small children with mild course of COVID-19", @@ -1301274,33 +1301730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20154575", - "rel_title": "Previous and active tuberculosis in COVID-19 patients increases risk of death and prolongs recovery", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20154575", - "rel_abs": "BackgroundThere is growing literature on the association of SARS-CoV-2 and other chronic respiratory conditions, such as COPD and asthma. However, little is known about the relationship between coinfection with tuberculosis (TB) and COVID-19. We aimed to compare the risk and survival time of death and recovery among COVID-19 patients with and without TB.\n\nMethodsWe created a 4:1 propensity score matched sample of COVID-19 patients without and with TB, using SARS-CoV-2 surveillance data in the Philippines. We conducted a longitudinal cohort analysis of matched COVID-19 patients as of May 17, 2020, following them until June 15, 2020. The primary analysis estimated the risk ratios of death and recovery comparing COVID-19 patients with and without TB. Kaplan-Meier curves described time-to-death and time-to-recovery stratified by TB status, and differences in survival were assessed using the Wilcoxon test. We also conducted the same analysis on a subsample of admitted COVID-19 patients only.\n\nResultsThe risk of death in COVID-19 patients with TB was 2.17 times greater compared to those without TB (95% CI: 1.40-3.37). The risk of recovery in TB patients was 25% less than the risk among those without TB (RR=0.75, 0.63-0.91). Similarly, time-to-death among COVID-19 patients with TB was significantly shorter (p=0.0031) and time-to-recovery in TB patients was significantly longer than patients without TB (p=0.0046).\n\nAmong those admitted, COVID-19 TB patients also had a similar significant increase in risk of death (RR=2.25, 95% CI: 1.35-3.75); however, the risk of recovery was not significantly less (RR=0.84, 95% CI: 0.68-1.06). Time-to-death among those with TB was also significantly longer (p=0.0031) than those without TB, but there was no difference in time-to-recovery (p=0.17).\n\nConclusionsOur findings show that coinfection with tuberculosis increases morbidity and mortality in COVID-19 patients. Our findings reiterate the need to prioritize routine and testing services for tuberculosis, even with increased disruptions to health systems during the SARS-CoV-2 pandemic. Additional research needs to focus on the interrelationship between TB and COVID-19 for appropriate planning and resource allocation, as SARS-CoV-2 continues to spread worldwide.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Karla Therese L. Sy", - "author_inst": "Boston University" - }, - { - "author_name": "Nel Jason Ladiao Haw", - "author_inst": "Ateneo de Manila University" - }, - { - "author_name": "Jhanna Uy", - "author_inst": "Philippine Institute for Development Studies" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.21.20136218", "rel_title": "Covid-19 serology in nephrology health care workers", @@ -1302096,6 +1302525,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.07.18.20156828", + "rel_title": "Local public health officials and COVID-19: Evidence from China", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156828", + "rel_abs": "Local public health authorities are at the forefront of fighting COVID-19. They monitor its spread in the local population and advise the local government on whether to close schools and businesses. Examining their role in battling COVID-19 will inform the public how best to prepare for a public health emergency. This study examined whether more competent local public health officials in China are more effective in fighting COVID-19, where competence was measured by the public health officials professional background. Only 38% of the heads of the public health departments of Chinese cities have a medical background. Cities with medical professionals as the head of public health departments had lower infection rates and death rates from COVID-19. The results were significant only at the start of the outbreak. Our results suggest that we should staff local public health authorities with competent professionals to better combat a pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "John Jiang", + "author_inst": "Michigan State University" + }, + { + "author_name": "Maobin Wang", + "author_inst": "The University of International Business and Economics" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.07.23.20158980", "rel_title": "Prevalence of mask wearing in northern Vermont in response to SARS-CoV-2", @@ -1302864,49 +1303316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.20.20158329", - "rel_title": "SARS-CoV-2 antibody prevalence in health care workers: Preliminary report of a single center study", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20158329", - "rel_abs": "SARS-CoV-2 has driven a pandemic crisis. Serological surveys have been conducted to establish prevalence for covid-19 antibody in various cohorts and communities. However, the prevalence among healthcare workers is still being analyzed. The present study reports on initial sero-surveillance conducted on healthcare workers at a regional hospital system in Orange County, California, during May and June, 2020.\n\nStudy participants were recruited from the entire hospital employee workforce and the independent medical staff. Data were collected for job title, location, covid-19 symptoms, a PCR test history, travel record since January 2020, and existence of household contacts with covid-19. A blood sample was collected from each subject for serum analysis for IgG antibodies to SARS- CoV-2.\n\nOf 3,013 tested individuals, a total 2,932 were included in the analysis due to some missing data. Observed prevalence of 1.06% (31 antibody positive cases), adjusted prevalence of 1.13% for test sensitivity and specificity were identified. Significant group differences between positive vs. negative were observed for age (z = 2.65, p = .008), race (p = .037), presence of fever (p < .001) and loss of smell (p < .001).\n\nPossible explanation for this low prevalence includes a relatively low local geographic community prevalence ([~]4.4%) at the time of testing, the hospitals timely procurement of personal protective equipment, rigorous employee education, patient triage and treatment protocol development and implementation. In addition, possible greater presence of cross- reactive adaptive T cell mediated immunity in healthcare workers vs. the general population may have contributed. Determining antibody prevalence in front-line workers, and duration of antibody presence may help stratify the workforce for risk, establish better health place policies and procedures, and potentially better mitigate transmission.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Michael Brant-Zawadzki", - "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian" - }, - { - "author_name": "Deborah Fridman", - "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian" - }, - { - "author_name": "Philip Robinson", - "author_inst": "Infection Prevention, Hoag Memorial Hospital Presbyterian" - }, - { - "author_name": "Matthew Zahn", - "author_inst": "Orange County Health Care Agency" - }, - { - "author_name": "Randy German", - "author_inst": "Laboratory Administrative Services, Hoag Memorial Hospital Presbyterian" - }, - { - "author_name": "Marcus Breit", - "author_inst": "Hoag Family Cancer Institute, Hoag Memorial Hospital Presbyterian" - }, - { - "author_name": "Junko Hara", - "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.20.20158386", "rel_title": "COVIDCare@Home: Lessons from a Family Medicine Led Remote Monitoring Program", @@ -1303746,6 +1304155,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.22.20159830", + "rel_title": "Clustering, diffusion and evolution of COVID19 infections during lock-down", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159830", + "rel_abs": "Epidemics such as the spreading of the SARS-CoV-2 virus are highly non linear, and therefore difficult to predict. In the present pandemic as time evolves, it appears more and more clearly that a clustered dynamics is a key element of description. This means that the disease rapidly evolves within spatially localized networks, that diffuse and eventually create new clusters. We improve upon the simplest possible compartmental model, the SIR model, by adding an additional compartment associated with the clustered individuals. The so-obtained SBIR model compares satisfactorily with results on the pandemic propagation in a number of European countries, during and immediately after lock-down. Especially, the decay exponent of the number of new cases after the first peak of the epidemic, is observed to be very similar for countries in which a strict lock-down was applied. We derive an analytical expression for the value of this exponent.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wouter Bos", + "author_inst": "CNRS" + }, + { + "author_name": "Jean-Pierre Bertoglio", + "author_inst": "CNRS" + }, + { + "author_name": "Louis Gostiaux", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.25.217158", "rel_title": "High neutralizing potency of swine glyco-humanized polyclonal antibodies against SARS-CoV-2", @@ -1304430,133 +1304866,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.21.20159178", - "rel_title": "SARS-CoV-2 infection induces sustained humoral immune responses in convalescent patients following symptomatic COVID-19", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159178", - "rel_abs": "Long-term antibody responses and neutralizing activities following SARS-CoV-2 infections have not yet been elucidated. We quantified immunoglobulin M (IgM) and G (IgG) antibodies recognizing the SARS-CoV-2 receptor-binding domain (RBD) of the spike (S) or the nucleocapsid (N) protein, and neutralizing antibodies during a period of six months following COVID-19 disease onset in 349 symptomatic COVID-19 patients, which were among the first world-wide being infected. The positivity rate and magnitude of IgM-S and IgG-N responses increased rapidly. High levels of IgM-S/N and IgG-S/N at 2-3 weeks after disease onset were associated with virus control and IgG-S titers correlated closely with the capacity to neutralize SARS-CoV-2. While specific IgM-S/N became undetectable 12 weeks after disease onset in most patients, IgG-S/N titers showed an intermediate contraction phase, but stabilized at relatively high levels over the six months observation period. At late time points the positivity rates for binding and neutralizing SARS-CoV-2-specific antibodies was still over 70%. Taken together, our data indicate sustained humoral immunity in recovered patients who suffer from symptomatic COVID-19, suggesting prolonged immunity.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Jun Wu", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Boyun Liang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Cunrong Chen", - "author_inst": "3 Department of ICU, Fujian Medical University Union Hospital, Fuzhou, 350001, China" - }, - { - "author_name": "Hua Wang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Yaohui Fang", - "author_inst": "4 State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China" - }, - { - "author_name": "Shu Shen", - "author_inst": "4 State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China" - }, - { - "author_name": "Xiaoli Yang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Baoju Wang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Liangkai Chen", - "author_inst": "5 Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan" - }, - { - "author_name": "Qi Chen", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China" - }, - { - "author_name": "Yang Wu", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China" - }, - { - "author_name": "Jia Liu", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Xuecheng Yang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Wei Li", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Bin Zhu", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Wenqing Zhou", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Huan Wang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Shumeng Li", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Sihong Lu", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Di Liu", - "author_inst": "7 Pritzker School of Medicine, University of Chicago, Chicago, USA" - }, - { - "author_name": "Huadong Li", - "author_inst": "Jin Yin-tan Hospital, Wuhan 430022, China" - }, - { - "author_name": "Adalbert Krawczyk", - "author_inst": "9 Department of Infectious Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen 45147, Germany." - }, - { - "author_name": "Mengji Lu", - "author_inst": "2 Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan,China;10 Institute for Virology, University Hos" - }, - { - "author_name": "Dongliang Yang", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - }, - { - "author_name": "Fei Deng", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China" - }, - { - "author_name": "Ulf Dittmer", - "author_inst": "2 Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan,China;10 Institute for Virology, University Hos" - }, - { - "author_name": "Mirko Trilling", - "author_inst": "2 Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan,China;10 Institute for Virology, University Hos" - }, - { - "author_name": "Xin Zheng", - "author_inst": "1 Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,China; 2 Joint International L" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.22.20159525", "rel_title": "Comparative Evaluation of 19 Reverse Transcription Loop-Mediated Isothermal Amplification Assays for Detection of SARS-CoV-2", @@ -1305344,6 +1305653,65 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.07.24.217562", + "rel_title": "Identification, Mapping and Relative Quantitation of SARS-Cov2 Spike Glycopeptides by Mass-Retention Time Fingerprinting", + "rel_date": "2020-07-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.24.217562", + "rel_abs": "We describe a novel analytical method for rapid and robust identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using any LC-TOF mass spectrometer, requires no specialised knowledge of glycan analysis and makes use of the differential resolving power of reversed phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. While this has previously been viewed as a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike. This database allows any ESI-TOF equipped lab to reliably identify and quantify spike glycans from a single overnight elastase protein digest in less than 90 minutes.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Rod Chalk", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "William Greenland", + "author_inst": "Agilent Technologies, Lakeside, Cheadle Royal Business Park, Cheadle, Cheshire, SK8 3GR, UK" + }, + { + "author_name": "Tiago Moreira", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Jesse Coker", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Shubhashish Mukhopadhyay", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Eleanor Williams", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Charlotte Manning", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Tina Bohstedt", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Rama McCrorie", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Alejandra Fernandez-Cid", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Nicola A Burgess-Brown", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.07.24.219139", "rel_title": "Tissue-specific and interferon-inducible expression of non-functional ACE2 through endogenous retrovirus co-option", @@ -1305744,41 +1306112,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.24.20161554", - "rel_title": "Concerns, quality of life, access to care and productivity of the general population during the first 8 weeks of the coronavirus lockdown in Belgium and the Netherlands", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161554", - "rel_abs": "BackgroundThe COVID-19 pandemic has a disruptive impact on our society. We therefore conducted a population survey to describe: 1) stress, concerns and quality of life 2) access to healthcare and cancelled/delayed healthcare and 3) productivity during the first 8 weeks of the coronavirus lockdown in the general population.\n\nMethodsAn online survey was conducted in a representative sample after 8 weeks of the coronavirus lockdown in Belgium and the Netherlands. The survey included questions about stress, concerns, quality of life delayed/cancelled medical care and productivity loss using validated questionnaires.\n\nResultsIn total, 2099 Belgian and 2058 Dutch respondents completed the survey with a mean age of 46.4 and 42.0 years, respectively. Half of the respondents were female in both countries. A small proportion tested positive for COVID-19, 1.4% vs 4.7%, respectively. The majority of respondents with a medical condition was worried about their current health state due to the pandemic (53%) vs (63%), respectively. Respondents experienced postponed/cancelled care (26%) and were concerned about the availability of medication (32%) for both countries. Productivity losses due to the COVID-19 restrictions were calculated in absenteeism (36%) and presenteeism (30%) for Belgium, and (19%) and (35%) for the Netherlands. Most concerns and productivity losses were reported by respondents with children <12 years, respondents aged 18-35 and respondents with an (expected) COVID-19 infection.\n\nConclusionsThis study describes stress, quality of life, medical resource loss and productivity losses in Belgium and the Netherlands after 8 weeks of coronavirus lockdown. The results underline the burden on society.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hanne van Ballegooijen", - "author_inst": "IQVIA" - }, - { - "author_name": "Lucas Goossens", - "author_inst": "Erasmus University Rotterdam, Erasmus School of Health Policy & Management" - }, - { - "author_name": "Ralph H Bruin", - "author_inst": "IQVIA" - }, - { - "author_name": "Renee Michels", - "author_inst": "IQVIA" - }, - { - "author_name": "Marieke Krol", - "author_inst": "IQVIA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.24.20161596", "rel_title": "The impact of COVID-19 on patients with asthma: A Big Data analysis", @@ -1306714,6 +1307047,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.23.20160564", + "rel_title": "Modelling Palliative and End of Life resource requirements during COVID-19: implications for quality care", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160564", + "rel_abs": "BackgroundThere were between 84,891 and 113,139 all-cause excess deaths in the United States (US) from February 1st to 25th May 2020. These deaths are widely attributed directly and indirectly to the COVID-19 pandemic. This surge in death necessitates a matched health system response to relieve serious health related suffering at the end of life (EoL) and achieve a dignified death, through timely and appropriate expertise, medication and equipment. Identifying the human and material resource needed relies on modelling resource and understanding anticipated surges in demand.\n\nMethodsA Discrete Event Simulation model designed in collaboration with health service funders, health providers, clinicians and modellers in the South West of England was created to estimate the resources required during the COVID-19 pandemic to care for deaths from COVID-19 in the community for a geographical area of nearly 1 million people. While our analysis focused on the UK setting, the model is flexible to changes in demand and setting.\n\nResultsThe model predicts that a mean of 11.97 hours (0.18 hours Standard Error (SE), up to a max of 28 hours) of additional community nurse time, up to 33 hours of care assistant time (mean 9.17 hours, 0.23 hours SE), and up to 30 hours additional care from care assistant night-sits (mean of 5.74 hours per day, 0.22 hours SE) will be required per day as a result of out of hospital COVID-19 deaths. Specialist palliative care demand is predicted to increase up to 19 hours per day (mean of 9.32 hours per day, 0.12 hours SE). An additional 286 anticipatory medicine bundles or just in case prescriptions per month will be necessary to alleviate physical symptoms at the EoL care for patients with COVID-19: an average additional 10.21 bundles (0.06 SE) of anticipatory medication per day. An average additional 9.35 syringe pumps (0.11 SE) could be needed to be in use per day (between 1 and 20 syringe pumps).\n\nConclusionModelling provides essential data to prepare, plan and deliver a palliative care pandemic response tailored to local work patterns and resource. The analysis for a large region in the South West of England shows the significant additional physical and human resource required to relieve suffering at the EoL as part of a pandemic response.\n\nWhy Was This Study Done?The resource required for the relief of suffering at the EoL in the community setting has been poorly described. The stark mortality resulting from the COVID-19 pandemic has highlighted the essential requirement to better understand the demand and available supply of EoL resource to prepare, plan and deliver a palliative care pandemic response.\n\nWhat Did the Researchers Do and Find?This manuscript describes the first open access model to describe EoL resource need during COVID-19 and presents an analysis based on a UK population of nearly 1 million people. The model identified a large increase in need for staff time, including registered community nurses, health care assistants and specialist palliative care nurses and doctors, as well as pressure on resources including syringe pumps and anticipatory medication (such as opioids) used at the EoL for symptom relief from breathlessness and delirium.\n\nWhat Do These Findings Mean?The model findings are critical in planning for a second wave of COVID-19. The open-access nature of the model allows researchers to tailor their analysis to low and middle income or high-income settings worldwide. The model ensures that EoL care is not an afterthought in pandemic planning, but an opportunity to ensure that the relief of suffering at the EoL is available to all.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Daniel Chalk", + "author_inst": "University of Exeter Medical School" + }, + { + "author_name": "Sara Robbins", + "author_inst": "University Hospitals Bristol and Weston NHS Foundation Trust" + }, + { + "author_name": "Rohan Kandasamy", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Kate Rush", + "author_inst": "Sirona Care and Health" + }, + { + "author_name": "Ajay Aggarwal", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Richard Sullivan", + "author_inst": "Kings College London" + }, + { + "author_name": "Charlotte Chamberlain", + "author_inst": "Bristol Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "palliative medicine" + }, { "rel_doi": "10.1101/2020.07.22.20160333", "rel_title": "The COVID-19 Pandemic Impact on Primary Health Care services: An Experience from Qatar", @@ -1307334,33 +1307710,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.23.20159897", - "rel_title": "What factors influence symptom reporting during an emerging infectious disease outbreak? A rapid review of the evidence", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20159897", - "rel_abs": "IntroductionDuring any emerging infectious disease outbreak, people with symptoms of the illness are often asked to report their symptoms to the health service in a timely manner, to facilitate contact tracing. Numerous factors may influence an individuals willingness to report these symptoms. Understanding these factors has become urgent during the COVID-19 pandemic.\n\nObjectiveTo determine which factors influence symptom reporting during an emerging infectious disease outbreak.\n\nMethodsWe conducted a rapid review of the evidence. We included papers based on primary research; published in a peer-reviewed journal; written in English; included factors associated with symptom reporting or accessing healthcare; and related to a major public health incident involving an infectious disease outbreak.\n\nMain resultsFive themes were identified as facilitators of symptom reporting or accessing healthcare: accurate and informative communication; symptom severity; concern about exposure; ease of access; and relationship with the healthcare provider. Seven themes were identified as barriers of symptom reporting or accessing healthcare: lack of knowledge; fear; stigmatization; invasion of privacy; low concern about symptoms; economics; and practicalities of attending a healthcare facility.\n\nDiscussion & ConclusionIf contract tracing services are to be effective, members of the public need to have the capability, opportunity and motivation to use them. The themes identified should be used to evaluate the information provided to the public about such a service, the routes of access, and the underlying policies relating to the service, in order to ensure that as many people as possible with relevant symptoms will make contact.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Patrice Carter", - "author_inst": "University College London" - }, - { - "author_name": "Odette Megnin-Viggars", - "author_inst": "University College London" - }, - { - "author_name": "Gideon James Rubin", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.22.20159962", "rel_title": "Mathematical model study of a pandemic: Graded lockdown approach", @@ -1307944,6 +1308293,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.17.20156075", + "rel_title": "A national consensus management pathway for Paediatric Inflammatory Multisystem Syndrome - Temporally associated with SARS-CoV-2 (PIMS-TS): The results of a national Delphi process", + "rel_date": "2020-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156075", + "rel_abs": "ObjectiveTo develop a consensus management pathway for children with Paediatric Inflammatory Multisystem Syndrome - Temporally associated with SARS-CoV-2 (PIMS-TS).\n\nDesignA three-phase online Delphi process and virtual consensus meeting sought consensus over the investigation, management and research priorities from 98 multidisciplinary participants caring for children with PIMS-TS. 46 participants (47%) completed all three phases. Participants were grouped into three panels and scored each statement from 1 (disagree) to 9 (strongly agree). In phase two participants were shown their panels scores, and in phase three all panels scores.\n\nConsensus agreement was defined as [≥]70% of participants in each panel scoring the statement 7-9, and <15% scoring 1-3, and consensus disagreement was the opposite of this. Statements which achieved consensus in 2/3 panels were discussed at the consensus meeting, and when [≥]70% participants agreed with the statement it achieved consensus.\n\nResults255 statements were assessed, with consensus agreement achieved for 111 (44%), consensus disagreement for 29 (11%), and no consensus for 115 (45%). The 140 consensus statements were used to derive the consensus management pathway.\n\nConclusionsA national consensus pathway has been developed for children suspected of having the novel syndrome PIMS-TS in a timely, cost-efficient manner, in the midst of a global pandemic. Use of a rapid online Delphi process has made this consensus process possible. Future evidence will inform updates to this guidance, which in the interim provides a solid framework to support clinicians caring for children with PIMS-TS.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Rachel Harwood", + "author_inst": "Department of Paediatric Surgery, Alder Hey Childrens Hospital, Eaton Road, Liverpool, L12 2AP" + }, + { + "author_name": "Benjamin Allin", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Health, University of Oxford, Old Road Campus, Oxford, OX3 9DU" + }, + { + "author_name": "Christine E Jones", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust and Faculty of Medicine and Ins" + }, + { + "author_name": "Elizabeth Whittaker", + "author_inst": "Department of Paediatrics, Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Padmanabhan Ramnarayan", + "author_inst": "Childrens Acute Transport Service, Great Ormond Street Hospital for Children, London, UK" + }, + { + "author_name": "Athimalaipet Ramanan", + "author_inst": "Bristol Royal Hospital for Children, Upper Maudlin Street Bristol, BS2 8BJ, UK" + }, + { + "author_name": "Musa Kaleem", + "author_inst": "Department of Paediatric Radiology, Alder Hey Childrens Hospital Eaton Road, Liverpool, L12 2AP, UK" + }, + { + "author_name": "Robert Tulloh", + "author_inst": "Bristol Royal Hospital for Children, Upper Maudlin Street Bristol, BS2 8BJ, UK" + }, + { + "author_name": "Mark J Peters", + "author_inst": "UCL Great Ormond St Institute of Child Health and Great Ormond St Hospital NHS Trust, NIHR Biomedical Research Centre, UK" + }, + { + "author_name": "Sarah Almond", + "author_inst": "Department of Paediatric Surgery, Alder Hey Childrens Hospital, Eaton Road, Liverpool, L12 2AP" + }, + { + "author_name": "Peter J Davis", + "author_inst": "Bristol Royal Hospital for Children, Upper Maudlin Street Bristol, BS2 8BJ, UK" + }, + { + "author_name": "Michael Levin", + "author_inst": "Department of Paediatrics, Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust and Faculty of Medicine and Ins" + }, + { + "author_name": "Marian Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Simon Kenny", + "author_inst": "NHS England/Improvement, PO Box 16738, Redditch, B97 9PT, UK" + }, + { + "author_name": "- PIMS-TS National Consensus Management Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.16.20155531", "rel_title": "Safety of Hydroxychloroquine among Outpatient Clinical Trial Participants for COVID-19", @@ -1308820,41 +1309248,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.23.217372", - "rel_title": "The new silicone N99 half-piece respirator, VJR-NMU N99: A novel and effective tool to prevent COVID-19", - "rel_date": "2020-07-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.23.217372", - "rel_abs": "Filter facepiece respirators (FFRs) are critical for preventing the transmission of respiratory tract infection disease, especially the dreadful coronavirus 2 (SARs-CoV-2). The N95 mask is a prototype, high-efficiency protective device that can effectively protect against airborne pathogens of less than 0.3 m. The N95 mask is tightly fitting and has high filtration capacity. The ongoing COVID-19 pandemic has led to a greater requirement for FFR. This rising demand greatly exceeds current production capabilities and stockpiles, resulting in shortages. To address this, our team has invented a new type of half-piece respirator made from silicone and assembled with HEPA or elastostatic filter. A variety of methods have been used to evaluate this new device, including a qualitative fit test with the Bitrex(R) test kit and filtration test. The preliminary results showed that the new N99 respirators pass the fit test. The filtration tests also confirmed the superiority of N99 over traditional N95 masks, with a mean performance of protection greater than 95%. For the filters, we used two types: SafeStar, which is a kind of HEPA filter; and CareStar, which is considered an elastostatic filler. CareStar was developed to filter virus and bacteria in the operating room, with a limit duration of use up to 24 h, while the safe star was designed for 72 h use and has the quality equivalent to a HEPA filter. Our study demonstrated superior filtration efficacy of both filters, more than 98% even after 24 h of use. CareStar has significantly more filtration efficacy than a safe star (p < 0.001). In conclusion, the development of our new N99 half-piece respirator should ultimately be applicable to healthcare workers with at least non-inferiority to the previously used N 95 respirators.. Currently, the adequate supply of such equipment is not feasible. The advent of the new protective device will help protect healthcare workers and replenish the shortage of N95 respirators during the COVID-19 pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thananda Trakarnvanich", - "author_inst": "Department of Medicine,Vajira hospital" - }, - { - "author_name": "Anan Manomaipiboon", - "author_inst": "Navamindradhiraj University" - }, - { - "author_name": "Sujaree Pupipatpab", - "author_inst": "Navamindradhiraj University" - }, - { - "author_name": "Pongsathorn Chomdee Chomdee", - "author_inst": "Navamindradhiraj University" - }, - { - "author_name": "Pathiporn Boonyapatkul", - "author_inst": "Navamindradhiraj University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2020.07.23.217331", "rel_title": "Development and validation of a clinical risk score to predict the risk of SARS-CoV-2 infection from administrative data: a population-based cohort study from Italy", @@ -1309906,6 +1310299,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20154955", + "rel_title": "The effect of border controls on the risk of COVID-19 reincursion from international arrivals", + "rel_date": "2020-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154955", + "rel_abs": "In an attempt to maintain elimination of COVID-19 in New Zealand, all international arrivals are required to spend 14 days in government-managed quarantine and to return a negative test result before being released. We model the testing, isolation and transmission of COVID-19 within quarantine facilities to estimate the risk of community outbreaks being seeded at the border. We use a simple branching process model for COVID-19 transmission that includes a time-dependent probability of a false negative test result. We show that the combination of 14-day quarantine with two tests reduces the risk of releasing an infectious case to around 0.1% per infected arrival. Shorter quarantine periods, or reliance on testing only with no quarantine, substantially increases this risk. We calculate the fraction of cases detected in the second week of their two week stay and show that this may be a useful indicator of the likelihood of transmission occurring within quarantine facilities. Frontline staff working at the border risk exposure to infected individuals and this has the potential to lead to a community outbreak. We use the model to test surveillance strategies and evaluate the likely size of the outbreak at the time it is first detected. We conclude with some recommendations for managing the risk of potential future outbreaks originating from the border.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicholas Steyn", + "author_inst": "University of Auckland" + }, + { + "author_name": "Michael J Plank", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Alex James", + "author_inst": "University of Canterbury, NZ" + }, + { + "author_name": "Rachelle N Binny", + "author_inst": "Manaaki Whenua" + }, + { + "author_name": "Shaun C Hendy", + "author_inst": "University of Auckland" + }, + { + "author_name": "Audrey Lustig", + "author_inst": "Manaaki Whenua" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.21.214759", "rel_title": "Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants", @@ -1310538,29 +1310970,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.07.18.20156745", - "rel_title": "Adaptive short term COVID-19 prediction for India", - "rel_date": "2020-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156745", - "rel_abs": "In this paper, a data-driven adaptive model for infection of COVID-19 is formulated to predict the confirmed total cases and active cases of an area over 4 weeks. The parameter of the model is always updated based on daily observations. It is found that the short term prediction of up to 3-4 weeks can be possible with good accuracy. Detailed analysis of predicted value and the actual value of confirmed total cases and active cases for India from 1st June to 3rd July is provided. Prediction over 7, 14, 21, 28 days has the accuracy about 0.73% {+/-} 1.97%, 1.92% {+/-} 2.95%, 4.34% {+/-} 3.91%, 6.40% {+/-} 9.26% of the actual value of confirmed total cases. Similarly, the 7, 14, 21, 28 days prediction has the accuracy about 1.24% {+/-} 6.57%, 3.04% {+/-} 10.00%, 6.33% {+/-} 16.12%, 10.20% {+/-} 24.14% of the actual value of confirmed active cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Shuvrangshu Jana", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Debasish Ghose", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.19.20157198", "rel_title": "High Community SARS-CoV-2 Antibody Seroprevalence in a Ski Resort Community, Blaine County, Idaho, US. Preliminary Results", @@ -1311412,6 +1311821,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.07.20.20157602", + "rel_title": "The COVID-19 outbreak in Sichuan, China: epidemiology and impact of interventions", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157602", + "rel_abs": "In January 2020, a COVID-19 outbreak was detected in Sichuan Province of China. The aim of this work is to characterize the epidemiology of the Sichuan outbreak and estimate the impact of the performed interventions. We analyzed patient records for all laboratory-confirmed cases reported in the province for the period of January 21 to March 16, 2020. To estimate the basic and daily reproduction numbers, we used a Bayesian framework. In addition, we estimate the number of cases averted by the implemented control strategies. The outbreak resulted in 539 confirmed cases, lasted less than two months, and no further local transmission was detected after February 27. The median age of local cases was 8 years older than that of imported cases. Severity of symptoms increased with age. We estimated R0 at 2.4 (95% CI: 1.6-3.7). The epidemic was self-sustained for about 3 weeks before going below the epidemic threshold 3 days after the declaration of a public health emergency by Sichuan authorities. Our findings indicate that, were the control measures be adopted four weeks later, the epidemic could have lasted 49 days longer (95%CI: 31-68 days), causing 9,216 (95%CI: 1,317-25,545) more cases and possibly overwhelming Sichuan healthcare system.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Quanhui Liu", + "author_inst": "Sichuan University, Chengdu, China" + }, + { + "author_name": "Ana I Bento", + "author_inst": "Indiana University" + }, + { + "author_name": "Kexin Yang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Hang Zhang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Xiaohan Yang", + "author_inst": "Department of Engineering and Computer Science, New York University Shanghai, Shanghai, China" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Jiancheng Lv", + "author_inst": "Sichuan University" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Tao Zhou", + "author_inst": "University of Electronic Science and Technology of China, Chengdu, China" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, IN, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.18.20156695", "rel_title": "A preliminary model to describe the transmission dynamics of Covid-19 between two neighboring cities or countries", @@ -1312032,89 +1312504,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.07.16.20155341", - "rel_title": "A global survey on changes in the supply, price and use of illicit drugs and alcohol, and related complications during the 2020 COVID-19 pandemic", - "rel_date": "2020-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155341", - "rel_abs": "Background and aimsCOVID-19 has infected more than 13 million people worldwide and impacted the lives of many more, with a particularly devastating impact on vulnerable populations, including people with substance use disorders (SUDs). Quarantines, travel bans, regulatory changes, social distancing and lockdown measures have affected drug and alcohol supply chains and subsequently their availability, price and use patterns, with possible downstream effects on presentations of SUDs and demand for treatment. Given the lack of multicentric epidemiologic studies, we conducted a rapid global survey within the International Society of Addiction Medicine (ISAM) network in order to understand the status of substance-use patterns during the current pandemic.\n\nDesignCross-sectional survey.\n\nSettingWorldwide.\n\nParticipantsStarting on April 4th, 2020 during a 5-week period, the survey received 185 responses from 77 countries.\n\nMeasurementsTo assess addiction medicine professionals perceived changes in drug and alcohol supply, price, use pattern and related complications during the COVID-19 pandemic.\n\nFindingsParticipants reported (among who answered \"decreased\" or \"increased\", percentage of those who were in majority is reported in the parenthesis) a decrease in drug supply (69.0%), and at the same time an increase in price (95.3%) globally. With respect to changes in use patterns, an increase in alcohol (71.7%), cannabis (63.0%), prescription opioids (70.9%), and sedative/hypnotics (84.6%) use was reported while the use of amphetamines (59.7%), cocaine (67.5%), and opiates (58.2%) was reported to decrease overall.\n\nConclusionsThe global report on changes in the availability, use patterns and complications of alcohol and drugs during the COVID-19 pandemic should be considered in making new policies and in developing mitigating measures and guidelines during the current pandemic (and probable future ones) in order to minimize risks to SUDs.\n\nCompeting interestAuthors claimed no competing interest", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ali Farhoudian", - "author_inst": "Substance Abuse and Dependence Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran; Department of Psychiatry, Tehran Univers" - }, - { - "author_name": "Seyed Ramin Radfar", - "author_inst": "UCLA Integrated Substance Abuse Programs" - }, - { - "author_name": "Hossein Mohaddes Ardabili", - "author_inst": "Psychiatry and Behavioral Sciences Research Center, Ibn-e-Sina Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran" - }, - { - "author_name": "Parnian Rafei", - "author_inst": "Department of Psychology, Faculty of Psychology and Education, University of Tehran, Iran" - }, - { - "author_name": "Mohsen Ebrahimy", - "author_inst": "Iranian National Center for Addiction Studies, Tehran University of Medical Sciences, Iran" - }, - { - "author_name": "Arash Khojasteh Zonoozi", - "author_inst": "Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran" - }, - { - "author_name": "Cornelis A J De Jong", - "author_inst": "Behavioral Science Institute, Radboud University, the Netherlands." - }, - { - "author_name": "Mehrnoosh Vahidi", - "author_inst": "Department of Psychiatry, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Masud Yunesian", - "author_inst": "School of Public Health, Tehran University of Medical Sciences, Iran" - }, - { - "author_name": "Christos Kouimtsidis", - "author_inst": "Surrey and Borders Partnership NHS Foundation Trust, UK" - }, - { - "author_name": "Shalini Arunogiri", - "author_inst": "Turning Point, Eastern Health, Box Hill, Australia" - }, - { - "author_name": "Helena Hansen", - "author_inst": "Departments of Anthropology and Psychiatry, New York University, USA" - }, - { - "author_name": "Kathleen T Brady", - "author_inst": "Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, USA." - }, - { - "author_name": "Marc N Potenza", - "author_inst": "Yale School of Medicine, Connecticut Council on Problem Gambling and Connecticut Mental Health Center, USA" - }, - { - "author_name": "- ISAM-PPIG Global Survey Consortium", - "author_inst": "-" - }, - { - "author_name": "Alexander Mario Baldacchino", - "author_inst": "Division of Population and Behaviour Sciences, Medical School, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom" - }, - { - "author_name": "Hamed Ekhtiari", - "author_inst": "Laureate Inst for Brain Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2020.07.21.214049", "rel_title": "Intranasal Immunization with a Lentiviral Vector Coding for SARS-CoV-2 Spike Protein Confers Vigorous Protection in Pre-Clinical Animal Models", @@ -1313150,6 +1313539,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.15.20154336", + "rel_title": "Epidemiological Profile and Transmission Dynamics of COVID-19 in the Philippines", + "rel_date": "2020-07-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154336", + "rel_abs": "The Philippines confirmed local transmission of COVID-19 on 7 March 2020. We described the characteristics and epidemiological time-to-event distributions for laboratory-confirmed cases in the Philippines. The median age of 8,212 cases was 46 years (IQR: 32-61), with 46.2% being female and 68.8% living in the National Capital Region. Health care workers represented 24.7% of all detected infections. Mean length of hospitalization for those who were discharged or died were 16.00 days (95% CI: 15.48, 16.54) and 7.27 days (95% CI: 6.59, 8.24). Mean duration of illness was 26.66 days (95% CI: 26.06, 27.28) and 12.61 days (95% CI: 11.88, 13.37) for those who recovered or died. Mean serial interval was 6.90 days (95% CI: 5.81, 8.41). Epidemic doubling time pre-quarantine (11 February and 19 March) was 4.86 days (95% CI: 4.67, 5.07) and the reproductive number was 2.41 (95% CI: 2.33, 2.48). During quarantine (March 20 to April 9), doubling time was 12.97 days (95% CI: 12.57, 13.39) and the reproductive number was 0.89 (95% CI: 0.78, 1.02).", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nel Jason Ladiao Haw", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Jhanna Uy", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Karla Therese L. Sy", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.18.20152256", "rel_title": "Providing breastfeeding support during the COVID-19 pandemic: Concerns of mothers who contacted the Australian Breastfeeding Association", @@ -1313870,97 +1314286,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.18.209270", - "rel_title": "Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome", - "rel_date": "2020-07-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.18.209270", - "rel_abs": "Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are beginning to target the viral RNA genome1, 2. The frameshift stimulation element (FSE) of the SARS-CoV-2 genome is required for balanced expression of essential viral proteins and is highly conserved, making it a potential candidate for antiviral targeting by small molecules and oligonucleotides3-6. To aid global efforts focusing on SARS-CoV-2 frameshifting, we report exploratory results from frameshifting and cellular replication experiments with locked nucleic acid (LNA) antisense oligonucleotides (ASOs), which support the FSE as a therapeutic target but highlight difficulties in achieving strong inactivation. To understand current limitations, we applied cryogenic electron microscopy (cryo-EM) and the Ribosolve7 pipeline to determine a three-dimensional structure of the SARS-CoV-2 FSE, validated through an RNA nanostructure tagging method. This is the smallest macromolecule (88 nt; 28 kDa) resolved by single-particle cryo-EM at subnanometer resolution to date. The tertiary structure model, defined to an estimated accuracy of 5.9 [A], presents a topologically complex fold in which the 5' end threads through a ring formed inside a three-stem pseudoknot. Our results suggest an updated model for SARS-CoV-2 frameshifting as well as binding sites that may be targeted by next generation ASOs and small molecules.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Kaiming Zhang", - "author_inst": "Stanford University" - }, - { - "author_name": "Ivan N. Zheludev", - "author_inst": "Stanford University" - }, - { - "author_name": "Rachel J. Hagey", - "author_inst": "Stanford University" - }, - { - "author_name": "Marie Teng-Pei Wu", - "author_inst": "Harvard University" - }, - { - "author_name": "Raphael Haslecker", - "author_inst": "Harvard University" - }, - { - "author_name": "Yixuan J. Hou", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Rachael Kretsch", - "author_inst": "Stanford University" - }, - { - "author_name": "Grigore D. Pintilie", - "author_inst": "Stanford University" - }, - { - "author_name": "Ramya Rangan", - "author_inst": "Stanford University" - }, - { - "author_name": "Wipapat Kladwang", - "author_inst": "Stanford University" - }, - { - "author_name": "Shanshan Li", - "author_inst": "Stanford University" - }, - { - "author_name": "Edward A. Pham", - "author_inst": "Stanford University" - }, - { - "author_name": "Claire Bernardin", - "author_inst": "Stanford University" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Timothy P. Sheahan", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Victoria Dsouza", - "author_inst": "Harvard University" - }, - { - "author_name": "Jeffrey S. Glenn", - "author_inst": "Stanford University" - }, - { - "author_name": "Wah Chiu", - "author_inst": "Stanford University" - }, - { - "author_name": "Rhiju Das", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.18.210013", "rel_title": "The folate antagonist methotrexate diminishes replication of the coronavirus SARS-CoV-2 and enhances the antiviral efficacy of remdesivir in cell culture models", @@ -1314656,6 +1314981,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.17.20156513", + "rel_title": "Large-scale Multi-omic Analysis of COVID-19 Severity", + "rel_date": "2020-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156513", + "rel_abs": "We performed RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive and negative patients with diverse disease severities. Over 17,000 transcripts, proteins, metabolites, and lipids were quantified and associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. We mapped 219 molecular features with high significance to COVID-19 status and severity, many involved in complement activation, dysregulated lipid transport, and neutrophil activation. We identified sets of covarying molecules, e.g., protein gelsolin and metabolite citrate or plasmalogens and apolipoproteins, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. We present a web-based tool (covid-omics.app) enabling interactive exploration of our compendium and illustrate its utility through a comparative analysis with published data and a machine learning approach for prediction of COVID-19 severity.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Katherine A Overmyer", + "author_inst": "Morgridge Institute for Research" + }, + { + "author_name": "Evgenia Shishkova", + "author_inst": "University of Wisconsin-Madison, Madison, WI USA" + }, + { + "author_name": "Ian Miller", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Joseph Balnis", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Matthew N. Bernstein", + "author_inst": "Morgridge Institute for Research" + }, + { + "author_name": "Trenton M. Peters-Clarke", + "author_inst": "University of Wisconsin-Madison, Madison, WI USA" + }, + { + "author_name": "Jesse G. Meyer", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Qiuwen Quan", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Laura K. Muehlbauer", + "author_inst": "University of Wisconsin-Madison, Madison, WI, USA" + }, + { + "author_name": "Edna A. Trujillo", + "author_inst": "University of Wisconsin-Madison, Madison, WI, USA" + }, + { + "author_name": "Yuchen He", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Amit Chopra", + "author_inst": "Albany Medical Center, Albany NY, USA" + }, + { + "author_name": "Hau Chieng", + "author_inst": "Albany Medical Center, Albany NY, USA" + }, + { + "author_name": "Anupama Tiwari", + "author_inst": "Albany Medical Center, Albany NY, USA" + }, + { + "author_name": "Marc A. Judson", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Brett Paulson", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Dain R. Brademan", + "author_inst": "University of Wisconsin-Madison, Madison, WI, USA" + }, + { + "author_name": "Yunyun Zhu", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Lia R. Serrano", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Vanessa Linke", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Lisa A. Drake", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Alejandro P. Adam", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Bradford S. Schwartz", + "author_inst": "Morgridge Institute for Research, Madison WI, USA" + }, + { + "author_name": "Harold A. Singer", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Scott Swanson", + "author_inst": "Morgridge Institute for Research, Madison WI, USA" + }, + { + "author_name": "Deane F. Mosher", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Ron Stewart", + "author_inst": "Morgridge Institute For Research, Madison WI, USA." + }, + { + "author_name": "Joshua J. Coon", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Ariel Jaitovich", + "author_inst": "Albany Medical College, Albany NY, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.17.20156539", "rel_title": "Quantifying SARS-CoV-2 infection risk within the Apple/Google exposure notification framework to inform quarantine recommendations", @@ -1315376,53 +1315832,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.15.20154286", - "rel_title": "A privacy-preserving Bayesian network model for personalised COVID19 risk assessment and contact tracing", - "rel_date": "2020-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154286", - "rel_abs": "Concerns about the practicality and effectiveness of using Contact Tracing Apps (CTA) to reduce the spread of COVID19 have been well documented and, in the UK, led to the abandonment of the NHS CTA shortly after its release in May 2020. One of the key non-technical obstacles to widespread adoption of CTA has been concerns about privacy. We present a causal probabilistic model (a Bayesian network) that provides the basis for a practical CTA solution that does not compromise privacy. Users of the model can provide as much or little personal information as they wish about relevant risk factors, symptoms, and recent social interactions. The model then provides them feedback about the likelihood of the presence of asymptotic, mild or severe COVID19 (past, present and projected). When the model is embedded in a smartphone app, it can be used to detect new outbreaks in a monitored population and identify outbreak locations as early as possible. For this purpose, the only data needed to be centrally collected is the probability the user has COVID19 and the GPS location.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Norman Fenton", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Scott McLachlan", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Peter Lucas", - "author_inst": "University of Twente, Netherlands" - }, - { - "author_name": "Kudakwashe Dube", - "author_inst": "Massey University, New Zealand" - }, - { - "author_name": "Graham Hitman", - "author_inst": "Blizard Institute, Queen Mary University of London" - }, - { - "author_name": "Magda Osman", - "author_inst": "Queen Mary University of London, United Kingdom" - }, - { - "author_name": "Evangelia Kyrimi", - "author_inst": "Queen Mary University" - }, - { - "author_name": "Martin Neil", - "author_inst": "Queen Mary, University of London and Agena Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.07.16.20155747", "rel_title": "Barriers to online learning in the time of COVID-19: A national survey of medical students in the Philippines", @@ -1316362,6 +1316771,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.16.20155630", + "rel_title": "Emerging Mental Health Challenges, Strategies and Opportunities in the context of the COVID-19 Pandemic: Perspectives from South American Decision-makers.", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155630", + "rel_abs": "BackgroundMental health awareness has increased during the COVID-19 pandemic. Although international guidelines address the mental health and psychosocial support (MHPSS) response to emergencies, regional recommendations on COVID-19 are still insufficient. We identified emerging mental health problems, strategies to address them, and opportunities to reform mental health systems during the COVID-19 pandemic in South America.\n\nMethodsAn anonymous online questionnaire was sent to mental health decision-makers of Ministries of Health in 10 South American countries in mid-April 2020. The semi-structured questionnaire had 12 questions clustered into 3 main sections: emerging challenges in mental health, current and potential strategies to face the pandemic, and, key elements for mental health reform. We identified keywords and themes for each section through summative content analysis.\n\nFindingsAn increasing mental health burden and emerging needs are arising as direct and indirect consequences of the pandemic among health care providers and the general population. National lockdowns challenge the delivery and access to mental health treatment and care. Strategies to meet these health needs rely heavily on timely and adequate responses by strengthened mental health governance and systems, availability of services, virtual platforms, and appropriate capacity building for service providers. Short- and medium-term strategies focused on bolstering community-based mental health networks and telemedicine for high-risk populations. Opportunities for long-term mental health reform entail strengthening legal frameworks, redistribution of financial resources and collaboration with local and international partners.\n\nInterpretationMental health and psychosocial support have been identified as a priority area by South American countries in the COVID-19 response. The pandemic has generated specific needs that require appropriate actions including: implementing virtual based interventions, orienting capacity building towards protection of users and health providers, strengthening evidence-driven decision making and integrating MHPSS in high-level mechanisms guiding the response to COVID-19.\n\nFundingNone.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe COVID-19 pandemic has affected mental health and wellbeing as well as its determinants. General population have reported anxiety and stress while health professionals fear, and bereavement. Mental health services have also been overburdened as the health needs increase as consequence of the pandemic and the isolation measures in place. The WHO General director has recognized mental health and psychological support (MHPPS) as a major pillar in the overall health response to the COVID-19 pandemic. Likewise, the Inter Agency Standing Committee (IASC) published a global briefing recommending eight MHPPS interventions to be implement during the crisis. Nonetheless, evidence to guide action at regional and sub-regional levels is still insufficient.\n\nAdded value of this studyThis study provides expert perspectives of decision-makers about mental health burden and actions during the COVID-19 in South America, currently the most serious hub of infection worldwide. Health services have reported an increase of anxiety, stress and fear among the general population emerging during the pandemic. The pandemic has generated specific needs that require appropriate actions including implementing virtual based interventions, bolstering community-based mental health networks, and integrating MHPSS in high-level mechanisms guiding the response to COVID-19. Decision-makers identified opportunities to seize for long-term mental health reform such as strengthening legal frameworks, redistribution of financial resources and collaboration with local and international partners.\n\nImplications of all the available evidenceThe importance of this research goes beyond documenting the status quo of mental health at country level, but implies fostering, enhancing and expanding collaborations in the Sub-region to strengthen the mental health response to the COVID-19 pandemic. Country-cooperation initiatives in mental health have been an important strategy to improve local mental health systems and services. Our findings are expected to better orient next steps in making decisions on mental health policies and services in South America, but also to inform public health key leaders and mental health experts within and beyond the Region of the Americas.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Daniel A Antiporta", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Andrea Bruni", + "author_inst": "Pan American Health Organization" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.16.20155572", "rel_title": "Probability of aerosol transmission of SARS-CoV-2", @@ -1317206,69 +1317638,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.14.20151159", - "rel_title": "Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20151159", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is a global pandemic with no licensed vaccine or specific antiviral agents for therapy. Little is known about the longitudinal dynamics of SARS-CoV-2-specific neutralizing antibodies (NAbs) in COVID-19 patients.\n\nMethodsBlood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines.\n\nResultsSARS-CoV-2-specific NAb titers were low for the first 7-10 d after symtom onset and increased after 2-3 weeks. The median peak time for NAbs was 33 d (IQR 24-59 d) after symptom onset. NAb titers in 93.3% (28/30) of the patients declined gradually over the 3-month study period, with a median decrease of 34.8% (IQR 19.6-42.4%). NAb titers increased over time in parallel with the rise in IgG antibody levels, correlating well at week 3 (r = 0.41, p < 0.05). The NAb titers also demonstrated a significant positive correlation with levels of plasma proinflammatory cytokines, including SCF, TRAIL, and M-CSF.\n\nConclusionsThese data provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Kai Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Quan-Xin Long", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Hai-Jun Deng", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Jie Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Qing-Zhu Gao", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Gui-Ji Zhang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Chang-Long He", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Lu-Yi Huang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Jie-Li Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Juan Chen", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ni Tang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ai-Long Huang", - "author_inst": "Chongqing Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.14.20153270", "rel_title": "Dynamics and future of SARS-CoV-2 in the human host", @@ -1318660,6 +1319029,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20153098", + "rel_title": "Public's perceived importance of non-pharmacological interventions for COVID-19 control in Greece: preliminary evidence from a cross-sectional study", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20153098", + "rel_abs": "BackgroundIn the early stages of coronavirus disease 2019 (COVID-19) pandemic, while effective pharmaceutical approaches are pending, COVID-19 management relies primarily on non-pharmaceutical interventions (NPIs), such as social distancing, which requirepublics engagement and behavioral adjustment. This study aims to evaluate publics perceived importance of the NPIs imposed for COVID-19 control in personal and public health protection in Greece.\n\nMethodsThis cross-sectional online study, enrolled 657 participants of the general Greek population in order to assess their beliefs and evaluate possible factors that influence their perceptions as regards NPI importance in personal and public health protection.\n\nResultsOverall, Greeks considered NPIs important for health protection. The participants who were less likely to consider NPIs important were men (OR versus females=1.64, 95% CI:1.15 to 2.36, p=0.007), people younger than 40 years old (OR between ages over 40 versus ages below 40=0.48, 95% CI:0.34 to 0.68, p<0.001), and people who did not chose the Hellenic National Public Health Organization (EODY) to get informed about COVID-19 (OR of EODY versus other sources of information = 0.65, 95% CI:0.46-0.92, p= 0.014).\n\nConclusionsThis study profiled Greek people who do and do not consider NPIs important, mainly as of their demographic features. Focused communicational strategies in certain population subgroups are recommended.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Eleni C. Boutsikari", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Anna Christakou", + "author_inst": "University of West Attica" + }, + { + "author_name": "Michail Elpidoforou", + "author_inst": "University of West Attica" + }, + { + "author_name": "Ioannis Kopsidas", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Nicholas Nikolovienis", + "author_inst": "University of West Attica" + }, + { + "author_name": "Despina Kardara", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Chrissoula C. Boutsikari", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Christos Triantafyllou", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.15.20147041", "rel_title": "A systematic review uncovers a wide-gap between COVID-19 in humans and animal models", @@ -1319296,41 +1319712,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, - { - "rel_doi": "10.1101/2020.07.16.20154229", - "rel_title": "Tele- Yoga therapy for Patients with Chronic Pain during Covid-19 Lockdown: A Prospective Nonrandomized Single Arm Clinical Trial", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20154229", - "rel_abs": "BackgroundPain management services and support programs have been closed during pandemic. Self-management options, particularly for chronic pain, is required which can be undertaken at ones own convenience and without leaving home.\n\nObjectivesTo evaluate the impact of tele-yoga therapy on patients suffering with chronic pain reducing pain intensity, disability, anxiety and depression.\n\nMaterial and methodsIn total 18 patients with different chronic pain diagnosis were recruited to individual yoga Therapy sessions twice a week at home (tele-yoga) using a videoconference app. Each participant followed set of practices every day at home. Main outcome measures included pain intensity, pain disability, anxiety and depression scores. Data were collected at baseline and after 6-weeks of intervention.\n\nResultsThere were significant improvement in pain intensity from Baseline to 6-weeks (P<0.001); also pain disability (P<0,001). Both scores of anxiety and depression reduced at the end of intervention period (P<0,001; P<0,001).\n\nConclusionsPilot results suggest that tele-yoga therapy may be an effective tool to self-manage chronic pain and related functional and psychological impacts. Further larger studies, randomized, controlled trials are needed to confirm the preliminary outcome.\n\nTrial RegistrationClinicalTrials.gov NCT04457388; https://clinicaltrials.gov/ct2/show/NCT04457388", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Neha Sharma", - "author_inst": "1Aarogyam (UK) CIC 143 Loughborough Road, Leicester, UK; LE4 5LR" - }, - { - "author_name": "Dipa Modi", - "author_inst": "East Park Medical Centre, 41-43 Doncaster Road, Leicester, LE4 6JL" - }, - { - "author_name": "Asha Nathwani", - "author_inst": "Aarogyam (UK) CIC 143 Loughborough Road, Leicester, UK; LE4 5LR" - }, - { - "author_name": "Bhavna Pandya", - "author_inst": "Aintree University Hospital, Liverpool University Hospitals NHS Foundation Trust, Lower Lane, Liverpool, Merseyside, L9 7AL" - }, - { - "author_name": "Jaydeep Joshi", - "author_inst": "1Aarogyam (UK) CIC 143 Loughborough Road, Leicester, UK; LE4 5LR" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pain medicine" - }, { "rel_doi": "10.1101/2020.07.16.20150292", "rel_title": "Continuity of services for patients with tuberculosis in China in the COVID-19 era", @@ -1320526,6 +1320907,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.17.20156117", + "rel_title": "Training and reployment of non-specialists is an effective solution for the shortage of health care workers in the COVID-19 pandemic", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156117", + "rel_abs": "ImportanceIn the COVID-19 pandemic many countries encounter problems arising from shortage of specialists. Short intensive training and reployment of non-specialists is an option but the effectiveness is unknown.\n\nObjectiveTo investigate whether there was difference in in-hospital mortality rates between COVID-19 patients managed by a mixed team (including non-specialists who had short intensive training and operated to a strict protocol) and those managed by a specialist team of health care workers.\n\nDesignCohort study, from January 26, 2020 to April 7, 2020, follow up to April 7, 2020.\n\nSettingMulticenter - Wuhan Hankou Hospital and Wuhan Xiehe Hospital, Wuhan, China.\n\nParticipants261 HCWs deployed to Wuhan from Guangdong emergency rescue team and the 269 COVID-19 patients they treated.\n\nExposureAmong 261 health care workers, 130 were in the specialist team and included 33 physicians, 32 of whom (97.0%) of whom were from relevant specialties. Each physician was in charge of 25-27 beds, with a 6-hour shift time. The mixed team included 131 health care workers, with 7 of the 28 physicians (25.0%) from relevant specialties. Each physician managed 12-13 beds, with a 4-hour shift time.\n\nNon-specialists received short-term intensive training and then followed strict management protocols. Specialists practiced as normal.\n\nMain Outcomes and MeasuresMain outcome was in-hospital mortality of COVID-19 patients. Another outcome was rate of SARS-CoV-2 infection in health care workers.\n\nResultsA total of 269 patients were included (144 male). In-hospital mortality rate of patients treated by the specialist teams and the mixed teams was 12.6% (20/159) and 12.7% (14/110) respectively (Difference = -0.1%, 95% CI -8.2% to 7.9%, p=.97). None of the health care workers were infected.\n\nConclusions and RelevanceTraining and reployment of non-specialists is an effective solution for the shortage of health care workers in the COVID-19 pandemic.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWas there difference in mortality rates between COVID-19 patients managed by a mixed team (including non-specialists who had short intensive training and operated to a strict protocol) and those managed by a specialist team of health care workers (HCWs)?\n\nFindingsIn-hospital mortality rate among patients managed by specialist team (130 HCWs, 159 patients) and mixed team (131 HCWs, 110 patients) was 12.6% (20/159) and 12.7% (14/110) respectively (Difference = -0.1%, 95% CI -8.2% to 7.9%, p=.97).\n\nMeaningWith shortage of specialist HCWs, training and reployment of non-specialists is an effective option in the management of COVID-19 patients.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ming Kuang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen Univeristy" + }, + { + "author_name": "Jianfeng Wu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yifeng Luo", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Han Xiao", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Ruiming Liang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Wenjie Hu", + "author_inst": "The First Affiliate Hospital of Sun Yat-sen University" + }, + { + "author_name": "Shouzhen Cheng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Qian Zhou", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Sui Peng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "KarKeung Cheng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Haipeng Xiao", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.17.20156158", "rel_title": "Multisectoral collaboration for pandemic response and operational support of critical care and emergency departments", @@ -1321354,105 +1321794,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.208439", - "rel_title": "SARS-CoV-2 RNA shedding in recovered COVID-19 cases and the presence of antibodies against SARS-CoV-2 in recovered COVID-19 cases and close contacts", - "rel_date": "2020-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.17.208439", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 emerged in December 2019 and has spread globally. Although Thailand has been effective at controlling the spread of COVID-19, disease surveillance and information on antibody responses in infected cases and close contacts are needed because there is still no specific treatment or vaccine available. We investigated 217 recovered COVID-19 cases to monitor their viral RNA shedding and production of antibodies against SARS-CoV-2. The presence of antibodies in blood samples from 308 close contacts of COVID-19 cases was also determined. Viral RNA was still detectable in 6.6 % of recovered COVID-19 cases. The most prolonged duration of viral RNA shedding detected in this study was 105 days. IgM, IgG, and IgA antibodies against SARS-CoV-2 were detected in 13.82, 88.48, and 83.41 % of the recovered cases 4-12 weeks after disease onset, respectively. Although the patients had recovered from their illness, the levels of antibodies detected showed association with their symptoms during their stay in hospital. Fifteen of the 308 contacts (4.87 %) of COVID-19 cases tested positive for IgG antibodies. The presence of antibodies against SARS-CoV-2 suggested that there was viral exposure among close contacts. Viral clearance and the pattern of antibody responses in infected individuals are both crucial for effectively combatting SARS-CoV-2. Our study provides additional information on the natural history of this newly emerging disease related to both natural host defenses and a strategy for vaccine development.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Chintana Chirathaworn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Manit Sripramote", - "author_inst": "Medical Service Department, Bangkok Metropolitan Administration" - }, - { - "author_name": "Piti Chalongviriyalert", - "author_inst": "Medical Service Department, Bangkok Metropolitan Administration" - }, - { - "author_name": "Supunee Jirajariyavej", - "author_inst": "Taksin Hospital" - }, - { - "author_name": "Phatharaporn Kiatpanabhikul", - "author_inst": "Charoenkrung Pracharak Hospital" - }, - { - "author_name": "Jatuporn Saiyarin", - "author_inst": "Klang General Hospital" - }, - { - "author_name": "Chulikorn Soudon", - "author_inst": "Sirindhorn Hospital" - }, - { - "author_name": "Orawan Thienfaidee", - "author_inst": "Ratchaphiphat Hospital" - }, - { - "author_name": "Thitisan Palakawong Na Ayuthaya", - "author_inst": "Public Health Center 28" - }, - { - "author_name": "Chantapat Brukesawan", - "author_inst": "Public Health Center 26" - }, - { - "author_name": "Dootchai Chaiwanichsiri", - "author_inst": "National Blood Center, Thai Red Cross Society" - }, - { - "author_name": "Duangnapa Intharasongkroh", - "author_inst": "National Blood Center, Thai Red Cross Society" - }, - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Jiratchaya Puenpa", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Ritthideach Yorsaeng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Arunee Thitithanyanont", - "author_inst": "Faculty of Science, Mahidol University" - }, - { - "author_name": "Rungrueng Kitphati", - "author_inst": "Shanxi Center for Disease Control and Prevention, Ministry of Public Health, Bangkok" - }, - { - "author_name": "Anek Mungaomklang", - "author_inst": "Institute for Urban Disease Control and Prevention, Ministry of Public Health, Bangkok" - }, - { - "author_name": "Pijaya Nagavajara", - "author_inst": "Office of the Permanent Secretary for the Bangkok Metropolitan Administration" - }, - { - "author_name": "Yong Poovorawan", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.17.208371", "rel_title": "Modeling the Impact of Lock-down on COVID-19 Spread in Malaysia", @@ -1322396,6 +1322737,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20154906", + "rel_title": "Higher Comorbidities and Early Death is Characteristic of Hospitalized African-American Patients with COVID-19", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154906", + "rel_abs": "BackgroundAfrican-Americans/Blacks have suffered higher morbidity and mortality from COVID-19 than all other racial groups. This study aims to identify the causes of this health disparity, determine prognostic indicators, and assess efficacy of treatment interventions.\n\nMethodWe performed a retrospective cohort study of clinical features and laboratory data of COVID-19 patients admitted over a five-week period at the height of the pandemic in the United States. This study was performed at an urban academic medical center in New York City, declared a COVID-only facility, serving a majority Black population\n\nResultOf the 1,070 consecutive patients who tested positive for COVID-19, 496 critically ill patients were hospitalized and included in the study. 88% of patients were Black; and a majority (53%) were 61-80 years old with a mean body mass index in the \"obese\" range. 97% had one or more comorbidities. Hypertension was the most common (84%) pre-existing condition followed by diabetes mellitus (57%) and chronic kidney disease (24%). Patients with chronic kidney disease and end-stage renal disease who received hemodialysis were found to have significantly lower mortality, then those who did not receive it, suggesting benefit from hemodialysis (11%, OR, 0.35, CI, 0.17 - 0.69 P=0.001). Age >60 years and coronary artery disease were independent predictors of mortality in multivariate analysis. Cox Proportional Hazards modeling for time to death demonstrated a significantly high ratio for COPD/Asthma, and favorable effects on outcomes for pre-admission ACE inhibitors and ARBs. CRP (180, 283 mg/L), LDH (551, 638 U/L), glucose (182, 163 mg/dL), procalcitonin (1.03, 1.68 ng/mL), and neutrophil / lymphocyte ratio (8.5, 10.0) were predictive of mortality on admission and at 48-96 hrs. Of the 496 inpatients, 48% died, one third of patients died within the first three days of admission. 54/488 patients received invasive mechanical ventilation, of which 87% died and of the remaining patients, 32% died.\n\nCONCLUSIONSCOVID-19 patients in our predominantly Black neighborhood had higher mortality, likely due to higher prevalence of comorbidities. Early dialysis and pre-admission intake of ACE inhibitors/ARBs improved patient outcomes. Early escalation of care based on comorbidities and key laboratory indicators is critical for improving outcomes in African-American patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Raavi Gupta", + "author_inst": "State University of New York, Downstate Medical Center" + }, + { + "author_name": "Raag Agrawal", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Zaheer Bukhari", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Absia Jabbar", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Donghai Wang", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "John Diks", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Mohamed Alshal", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Dokpe Yvonne Emechebe", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "F. Charles Brunicardi", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Jason M Lazar", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Robert Chamberlain", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Aaliya Burza", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "M. A. Haseeb", + "author_inst": "SUNY Downstate Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.15.20154971", "rel_title": "Time-dependent dynamic transmission potential and instantaneous reproduction number of COVID-19 pandemic in India.", @@ -1322820,41 +1323228,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.15.20154385", - "rel_title": "Interpreting Deep Ensemble Learning through Radiologist Annotations for COVID-19 Detection in Chest Radiographs", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154385", - "rel_abs": "Data-driven deep learning (DL) methods using convolutional neural networks (CNNs) demonstrate promising performance in natural image computer vision tasks. However, using these models in medical computer vision tasks suffers from several limitations, viz., (i) adapting to visual characteristics that are unlike natural images; (ii) modeling random noise during training due to stochastic optimization and backpropagation-based learning strategy; (iii) challenges in explaining DL black-box behavior to support clinical decision-making; and (iv) inter-reader variability in the ground truth (GT) annotations affecting learning and evaluation. This study proposes a systematic approach to address these limitations for COVID-19 detection using chest X-rays (CXRs). Specifically, our contribution benefits from (i) pretraining specific to CXRs in transferring and fine-tuning the learned knowledge toward improving COVID-19 detection performance; (ii) using ensembles of the fine-tuned models to further improve performance compared to individual constituent models; (iii) performing statistical analyses at various learning stages to validate our claims; (iv) interpreting learned individual and ensemble model behavior through class-selective relevance mapping (CRM)-based region of interest (ROI) localization; (v) analyzing inter-reader variability and ensemble localization performance using Simultaneous Truth and Performance Level Estimation (STAPLE) methods. We observe that: (i) ensemble approaches improved classification and localization performance; and, (ii) inter-reader variability and performance level assessment helped guide algorithm design and parameter optimization. To the best of our knowledge, this is the first study to construct ensembles, perform ensemble-based disease ROI localization, and analyze inter-reader variability and algorithm performance for COVID-19 detection in CXRs.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sivaramakrishnan Rajaraman", - "author_inst": "National Library of Medicine" - }, - { - "author_name": "Sudhir Sornapudi", - "author_inst": "Missouri University of Science and Technology" - }, - { - "author_name": "Philip O Alderson", - "author_inst": "School of Medicine, Saint Louis University" - }, - { - "author_name": "Les R Folio", - "author_inst": "Radiological and Imaging Sciences, Clinical Center, National Institutes of Health" - }, - { - "author_name": "Sameer K Antani", - "author_inst": "National Library of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.07.15.20154559", "rel_title": "Moderate to vigorous physical activity and sedentary behavior change in self-isolating adults during the COVID-19 pandemic in Brazil: A cross-sectional survey exploring correlates", @@ -1323830,6 +1324203,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.07.13.20152231", + "rel_title": "A Quantitative Lung Computed Tomography Image Feature for Multi-Center Severity Assessment of COVID-19", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152231", + "rel_abs": "The COVID-19 pandemic has affected millions and congested healthcare systems globally. Hence an objective severity assessment is crucial in making therapeutic decisions judiciously. Computed Tomography (CT)-scans can provide demarcating features to identify severity of pneumonia --commonly associated with COVID-19--in the affected lungs. Here, a quantitative severity assessing chest CT image feature is demonstrated for COVID-19 patients. An open-source multi-center Italian database1 was used, among which 60 cases were incorporated in the study (age 27-86, 71% males) from 27 CT imaging centers. Lesions in the form of opacifications, crazy-paving patterns, and consolidations were segmented. The severity determining feature --Lnorm was quantified and established to be statistically distinct for the three --mild, moderate, and severe classes (p-value<0.0001). The thresholds of Lnorm for a 3-class classification were determined based on the optimum sensitivity/specificity combination from Receiver Operating Characteristic (ROC) analyses. The feature Lnorm classified the cases in the three severity categories with 86.88% accuracy. Substantial to almost-perfect intra-rater and inter-rater agreements were achieved involving expert and non-expert based evaluations ({kappa}-score 0.79-0.97). We trained machine learning based classification models and showed Lnorm alone has a superior diagnostic accuracy over standard image intensity and texture features. Classification accuracy was further increased when Lnorm was used for 2-class classification i.e. to delineate the severe cases from non-severe ones with a high sensitivity (97.7%), and specificity (97.49%). Therefore, key highlights of this severity assessment feature are accuracy, lower dependency on expert availability, and wide utility across different imaging centers.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Biswajoy Ghosh", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Nikhil Kumar", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Nitisha Singh", + "author_inst": "National Institute of Technology Durgapur" + }, + { + "author_name": "Anup K Sadhu", + "author_inst": "EKO CT and MRI Scan Centre, Medical College and Hospitals Campus, Kolkata" + }, + { + "author_name": "Nirmalya Ghosh", + "author_inst": "Indian Institute of Technology Kharagur" + }, + { + "author_name": "Pabitra Mitra", + "author_inst": "Indian Institute of Technology Kharagur" + }, + { + "author_name": "Jyotirmoy Chatterjee", + "author_inst": "Indian Institute of Technology Kharagur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.07.13.20153130", "rel_title": "Asthma in COVID-19: An extra chain fitting around the neck?", @@ -1324434,105 +1324850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.13.20153148", - "rel_title": "Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153148", - "rel_abs": "BackgroundThe province of British Columbia (BC) has been recognized for successful SARS-CoV-2 control, with surveillance data showing amongst the lowest case and death rates in Canada. We estimate sero-prevalence for two periods flanking the start (March) and end (May) of first-wave mitigation measures in BC.\n\nMethodsSerial cross-sectional sampling was conducted using anonymized residual sera obtained from an outpatient laboratory network, including children and adults in the Greater Vancouver Area (population [~]3 million) where community attack rates were expected to be highest. Screening used two chemiluminescent immuno-assays for spike (S1) and nucleocapsid antibodies. Samples sero-positive on either screening assay were assessed by a third assay targeting the S1 receptor binding domain plus a neutralization assay. Age-standardized sero-prevalence estimates were based on dual-assay positivity. The May sero-prevalence estimate was extrapolated to the source population to assess surveillance under-ascertainment, quantified as the ratio of estimated infections versus reported cases.\n\nResultsSerum collection dates spanned March 5-13 and May 15-27, 2020. In March, two of 869 specimens were dual-assay positive, with age-standardized sero-prevalence of 0.28% (95%CI=0.03-0.95). Neither specimen had detectable neutralizing antibodies. In May, four of 885 specimens were dual-assay positive, with age-standardized sero-prevalence of 0.55% (95%CI=0.15-1.37%). All four specimens had detectable neutralizing antibodies. We estimate [~]8 times more infections than reported cases.\n\nConclusionsLess than 1% of British Columbians had been infected with SARS-CoV-2 when first-wave mitigation measures were relaxed in May 2020. Our findings indicate successful suppression of community transmission in BC, but also substantial residual susceptibility. Further sero-survey snapshots are planned as the pandemic unfolds.\n\nKey pointsCross-sectional sampling of anonymized residual sera at the start and end of first-wave mitigation measures in British Columbia, Canada shows SARS-CoV-2 sero-prevalence below 1% throughout the winter-spring 2020. Findings indicate successful suppression of community transmission but also substantial residual susceptibility.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Danuta M Skowronski", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Inna Sekirov", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Suzana Sabaiduc", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Macy Zou", - "author_inst": "BC Centre for Disease Control, Data and Analytic Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Muhammad Morshed", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "David Lawrence", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Kate Smolina", - "author_inst": "BC Centre for Disease Control, Data and Analytic Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "May A Ahmed", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Eleni Galanis", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Mieke Fraser", - "author_inst": "BC Centre for Disease Control, Data and Analytic Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Mayank Singal", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Monika Naus", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "David M Patrick", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Samantha Kaweski", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Christopher Mill", - "author_inst": "Public Health Agency of Canada, Health Security Infrastructure Branch, Canadian Public Health Service, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Romina C Reyes", - "author_inst": "LifeLabs, Department of Microbiology, Surrey, British Columbia, Canada" - }, - { - "author_name": "Michael T Kelly", - "author_inst": "LifeLabs, Department of Microbiology, Surrey, British Columbia, Canada" - }, - { - "author_name": "Paul N Levett", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Martin Petric", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Bonnie Henry", - "author_inst": "Office of the Provincial Health Officer, Ministry of Health, Victoria, British Columbia, Canada" - }, - { - "author_name": "Mel Krajden", - "author_inst": "BC Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.13.20153056", "rel_title": "Analysis of COVID-19 cases and associated ventilator requirement in Indian States", @@ -1325412,6 +1325729,33 @@ "type": "confirmatory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.15.176933", + "rel_title": "Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide", + "rel_date": "2020-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.176933", + "rel_abs": "A newly emerging novel coronavirus appeared and rapidly spread worldwide and World Health Organization declared a pandemic on March 11, 2020. The roles and characteristics of coronavirus have captured much attention due to its power of causing a wide variety of infectious diseases, from mild to severe on humans. The detection of the lethality of human coronavirus is key to estimate the viral toxicity and provide perspective for treatment. We developed alignment-free machine learning approaches for an ultra-fast and highly accurate prediction of the lethality of potential human-adapted coronavirus using genomic nucleotide. We performed extensive experiments through six different feature transformation and machine learning algorithms in combination with digital signal processing to infer the lethality of possible future novel coronaviruses using previous existing strains. The results tested on SARS-CoV, MERS-Cov and SARS-CoV-2 datasets show an average 96.7% prediction accuracy. We also provide preliminary analysis validating the effectiveness of our models through other human coronaviruses. Our study achieves high levels of prediction performance based on raw RNA sequences alone without genome annotations and specialized biological knowledge. The results demonstrate that, for any novel human coronavirus strains, this alignment-free machine learning-based approach can offer a reliable real-time estimation for its viral lethality.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rui YIN", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Zihan Luo", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Chee Keong Kwoh", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.14.203463", "rel_title": "Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations", @@ -1326160,45 +1326504,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.12.20152140", - "rel_title": "Complexity signatures in the COVID-19 epidemic: power law behaviour in the saturation regime of fatality curves", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20152140", - "rel_abs": "ABSTRACWe apply a versatile growth model, whose growth rate is given by a generalised beta distribution, to describe the complex behaviour of the fatality curves of the COVID-19 disease for several countries in Europe and North America. We show that the COVID-19 epidemic curves not only may present a subexponential early growth but can also exhibit a similar subexponential (power-law) behaviour in the saturation regime. We argue that the power-law exponent of the latter regime, which measures how quickly the curve approaches the plateau, is directly related to control measures, in the sense that the less strict the control, the smaller the exponent and hence the slower the diseases progresses to its end. The power-law saturation uncovered here is an important result, because it signals to policymakers and health authorities that it is important to keep control measures for as long as possible, so as to avoid a slow, power-law ending of the disease. The slower the approach to the plateau, the longer the virus lingers on in the population, and the greater not only the final death toll but also the risk of a resurgence of infections.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Giovani L. Vasconcelos", - "author_inst": "Universidade Federal do Paran\u00e1" - }, - { - "author_name": "Ant\u00f4nio M.S. Mac\u00eado", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Gerson C. Duarte-Filho", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Arthur A. Ara\u00fajo", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Raydonal Ospina", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Francisco A. G. Almeida", - "author_inst": "Universidade Federal de Sergipe" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.12.20151936", "rel_title": "Public Opinions towards COVID-19 in California and New York on Twitter", @@ -1327214,6 +1327519,73 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.14.202549", + "rel_title": "Targeting heparan sulfate proteoglycan-assisted endocytosis as a COVID-19 therapeutic option", + "rel_date": "2020-07-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.14.202549", + "rel_abs": "The cell entry of SARS-CoV-2 has emerged as an attractive drug repurposing target for COVID-19. Here we combine genetics and chemical perturbation to demonstrate that ACE2-mediated entry of SARS-CoV and CoV-2 requires the cell surface heparan sulfate (HS) as an assisting cofactor: ablation of genes involved in HS biosynthesis or incubating cells with a HS mimetic both inhibit Spike-mediated viral entry. We show that heparin/HS binds to Spike directly, facilitates the attachment of viral particles to the cell surface to promote cell entry. We screened approved drugs and identified two classes of inhibitors that act via distinct mechanisms to target this entry pathway. Among the drugs characterized, Mitoxantrone is a potent HS inhibitor, while Sunitinib and BNTX disrupt the actin network to indirectly abrogate HS-assisted viral entry. We further show that drugs of the two classes can be combined to generate a synergized activity against SARS-CoV-2-induced cytopathic effect. Altogether, our study establishes HS as an attachment factor that assists SARS coronavirus cell entry, and reveals drugs capable of targeting this important step in the viral life cycle.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Qi Zhang", + "author_inst": "NIH" + }, + { + "author_name": "Catherine Chen", + "author_inst": "NIH" + }, + { + "author_name": "Manju Swaroop", + "author_inst": "NIH" + }, + { + "author_name": "Miao Xu", + "author_inst": "NIH" + }, + { + "author_name": "Lihui Wang", + "author_inst": "NIH" + }, + { + "author_name": "Juhyung Lee", + "author_inst": "NIH" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "NIH" + }, + { + "author_name": "Min Shen", + "author_inst": "NIH" + }, + { + "author_name": "Zhiji Luo", + "author_inst": "NIH" + }, + { + "author_name": "Yue Xu", + "author_inst": "NIH" + }, + { + "author_name": "Wenwei Huang", + "author_inst": "NIH" + }, + { + "author_name": "Wei Zheng", + "author_inst": "NIH" + }, + { + "author_name": "Yihong Ye", + "author_inst": "NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.07.13.20152793", "rel_title": "At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data", @@ -1327866,57 +1328238,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.11.20151647", - "rel_title": "Social Disadvantage, Politics, and SARS-CoV-2 Trends: A County-Level Analysis of United States Data", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151647", - "rel_abs": "BackgroundUnderstanding the epidemiology of SARS-CoV-2 is essential for public health control efforts. Social, demographic, and political characteristics at the US county level might be associated with the trajectories of SARS-CoV-2 case incidence.\n\nObjectiveTo understand how underlying social, demographic, and political characteristics at the US county level might be associated with the trajectories of SARS-CoV-2 case incidence.\n\nDesignRetrospective analysis of the trajectory of reported SARS-CoV-2 case counts at the US county level during June 1, 2020 - June 30,2020 and social, demographic, and political characteristics of the county.\n\nSettingUnited States.\n\nParticipantsReported SARS-CoV-2 cases.\n\nExposuresMetropolitan designation, Social Deprivation Index (SDI), 2016 Republican Presidential Candidate Victory.\n\nMain Outcomes and MeasuresSARS-CoV-2 case incidence.\n\nResults1023/3142 US counties were included in the analysis. 678 (66.3%) had increasing SARS-CoV-2 case counts between June 1 - June 30, 2020. In univariate analysis, counties with increasing case counts had a significantly higher SDI (median 48, IQR 24 - 72) than counties with non-increasing case counts (median 40, IQR 19 - 66; p=0.009). In the multivariable model, metropolitan areas of 250,000 - 1 million population, higher percentage of Black residents and a 10-point or greater Republican victory were independently associated with increasing case counts.\n\nLimitationsThe data examines county-level voting patterns and does not account for individual voting behavior, subjecting this work to the potential for ecologic fallacy.\n\nConclusionIncreasing case counts of SARS-CoV-2 in the US are likely driven by a combination of social disadvantage, social networks, and behavioral factors. Addressing social disadvantage and differential belief systems that may correspond with political alignment will be essential for pandemic control.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ahmad Mourad", - "author_inst": "Duke University" - }, - { - "author_name": "Nicholas A Turner", - "author_inst": "Duke University" - }, - { - "author_name": "Arthur W Baker", - "author_inst": "Duke University" - }, - { - "author_name": "Nwora Lance Okeke", - "author_inst": "Duke University" - }, - { - "author_name": "Shanti Narayanasamy", - "author_inst": "Duke University" - }, - { - "author_name": "Robert Rolfe Jr.", - "author_inst": "Duke University" - }, - { - "author_name": "John J Engemann", - "author_inst": "Raleigh Infectious Diseases Associates" - }, - { - "author_name": "Gary M Cox", - "author_inst": "Duke University" - }, - { - "author_name": "Jason E Stout", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.11.20151308", "rel_title": "'Trained immunity' from Mycobacterium spp. exposure or BCG vaccination and COVID-19 outcomes", @@ -1328792,6 +1329113,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.13.20152355", + "rel_title": "State-level tracking of COVID-19 in the United States", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152355", + "rel_abs": "As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly modelled the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We used changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. Nationally, we estimated 3.7% [3.4%-4.0%] of the population had been infected by 1st June 2020, with wide variation between states, and approximately 0.01% of the population was infectious. We also demonstrated that good model forecasts of deaths for the next 3 weeks with low error and good coverage of our credible intervals.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "H Juliette T Unwin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Valerie C Bradley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Axel Gandy", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas A Mellan", + "author_inst": "Imperial College" + }, + { + "author_name": "Helen Coupland", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan Ish-Horowicz", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michaela Andrea Christine Vollmer", + "author_inst": "Imperial College London" + }, + { + "author_name": "Charles Whittaker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sarah L Filippi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Xiaoyue Xi", + "author_inst": "Imperial College London" + }, + { + "author_name": "M\u00e9lodie Monod", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Ratmann", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Hutchinson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fabian Valka", + "author_inst": "None" + }, + { + "author_name": "Harrison Zhu", + "author_inst": "Imperial College London" + }, + { + "author_name": "Iwona Hawryluk", + "author_inst": "Imperial College London" + }, + { + "author_name": "Philip Milton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kylie E C Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Adhiratha Boonyasiri", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nick F Brazeau", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lorenzo Cattarino", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zulma M Cucunub\u00e1", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gina Cuomo-Dannenburg", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ilaria Dorigatti", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver D Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jeffrey W Eaton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sabinee L van Elsland", + "author_inst": "Imperial College London" + }, + { + "author_name": "Richard G FitzJohn", + "author_inst": "Imperial College London" + }, + { + "author_name": "Katy A M Gaythorpe", + "author_inst": "Imperial College London" + }, + { + "author_name": "William Green", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wes Hinsley", + "author_inst": "Imperial College London" + }, + { + "author_name": "Benjamin Jeffrey", + "author_inst": "Imperial College London" + }, + { + "author_name": "Edward Knock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniel J Laydon", + "author_inst": "Imperial College London" + }, + { + "author_name": "John Lees", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gemma Nedjati-Gilani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Pierre Nouvellet", + "author_inst": "University of Sussex" + }, + { + "author_name": "Lucy C Okell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kris V Parag", + "author_inst": "Imperial College London" + }, + { + "author_name": "Igor Siveroni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hayley A Thompson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick Walker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lilith K Whittles", + "author_inst": "Imperial College London" + }, + { + "author_name": "Azra Ghani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Samir Bhatt", + "author_inst": "Imperial College London" + }, + { + "author_name": "Seth Flaxman", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.12.20152157", "rel_title": "Quantifying Respiratory Airborne Particle Dispersion Control Through Improvised Reusable Masks", @@ -1329240,69 +1329788,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.12.20100941", - "rel_title": "Covid-19 and dysregulated cerebral perfusion: observations with multimodal MRI", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20100941", - "rel_abs": "The pathogenesis of encephalopathy-associated Covid-19 is still unclear. Multimodal brain MRI in 25 Covid-19 patients with neurological symptoms revealed angiographic and brain perfusion changes suggesting an under-recognized dysregulated brain perfusion not identified by morphological neuroimaging alone. Endothelial dysfunction, a key pathomechanism of dysregulated brain perfusion, may contribute to central-nervous-system disturbances in Covid-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Marie-Cecile Henry Feugeas", - "author_inst": "Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard." - }, - { - "author_name": "Augustin Gaudemer", - "author_inst": "Service de Radiologie, Unite de Neuroradiologie, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France" - }, - { - "author_name": "Xavier Lescure", - "author_inst": "Service des Maladies infectieuses et Tropicales, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France; Infections Antimicrobials " - }, - { - "author_name": "Antoine Dossier", - "author_inst": "Service de Medecine Interne, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France, Universite Paris Diderot Paris, France" - }, - { - "author_name": "Romain Sonneville", - "author_inst": "Service de Reanimation medicale et des maladies infectieuses, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France, Inserm IAME U" - }, - { - "author_name": "Carsten Ehmer", - "author_inst": "Service de Radiologie, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France" - }, - { - "author_name": "Christophe Choquet", - "author_inst": "Service des Urgences, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France" - }, - { - "author_name": "theresa Israel", - "author_inst": "Service de Radiologie, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France" - }, - { - "author_name": "Agathe Raynaud-Simon", - "author_inst": "Service de Geriatrie, Assistance Publique-Hopitaux de Paris, Hopital Bichat-Claude Bernard, Paris, France, Universite Paris Diderot, Paris, France" - }, - { - "author_name": "Raphael Borie", - "author_inst": "Hopital Bichat" - }, - { - "author_name": "Pierre Amarenco", - "author_inst": "Service de Neurologie et des Accidents Vasculaires Cerebraux, APHP Nord, Hopital Bichat-Claude Bernard.INSERM Laboratory for Vascular Translational Science-Unit" - }, - { - "author_name": "Antoine Khalil", - "author_inst": "APHP Nord, Inserm UMR1152, Physiopathology and Epidemiology of Respiratory Diseases, Diderot Paris University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.07.13.20144907", "rel_title": "The National Early Warning Score (NEWS2) systematically underestimates the risk of in-hospital mortality in unplanned COVID-19 admissions to hospital.", @@ -1330238,6 +1330723,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.07.12.199364", + "rel_title": "Flexibility and mobility of SARS-CoV-2-related protein structures", + "rel_date": "2020-07-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.12.199364", + "rel_abs": "The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of SARS-CoV-2 drug targets, i.e. SARS-CoV-2 protein structures as deposited on the Protein Databank (PDB). We study their flexibility, rigidity and mobility, an important first step in trying to ascertain their dynamics for further drug-related docking studies. We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. For example, for the SARS-CoV-2 spike protein in the open configuration, our method identifies a possible further opening and closing of the S1 subunit through movement of SB domain. With full structural information of this process available, docking studies with possible drug structures are then possible in silico. In our study, we present full results for the more than 200 thus far published SARS-CoV-2-related protein structures in the PDB.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rudolf A Roemer", + "author_inst": "University of Warwick" + }, + { + "author_name": "Navodya Sophie Roemer", + "author_inst": "University of Lincoln" + }, + { + "author_name": "Anne Katrine Wallis", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.07.10.20150045", "rel_title": "Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka", @@ -1330890,25 +1331402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.09.20150029", - "rel_title": "A flexible COVID-19 model to assess mitigation, reopening, virus mutation and other changes", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20150029", - "rel_abs": "The COVID-19 epidemic which began in China last year has expanded worldwide. A flexible SEIRD epidemiological model with time-dependent parameters is applied to modeling the pandemic. The value of the effective reproduction ratio is varied to quantify the impact of quarantines and social distancing on the number of infections and deaths, on their daily changes. and on the maxima in these daily rates expected during the epidemic. The effect of changing Reff is substantial. It ought to inform policy decisions around resource allocation, mitigation strategies and their duration, and economic tradeoffs. The model can also calculate the impact of changes in infectiousness or morbidity as the virus mutates, or the expected effects of a new therapy or vaccine assumed to arrive at a future date. The paper concludes with a discussion of a potential endemic end of COVID-19, which might involve times of about 100 years.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sergio Bienstock", - "author_inst": "Retired" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.10.20150573", "rel_title": "Eurofins Covid-19 Sentinel TM Wastewater Test Provide Early Warning of a potential COVID-19 outbreak", @@ -1331768,6 +1332261,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.11.20151365", + "rel_title": "Decreased serum levels of inflammaging marker miR-146a are associated with clinical response to tocilizumab in COVID-19 patients", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151365", + "rel_abs": "BackgroundCurrent COVID-19 pandemic poses an unprecedented threat to global health and healthcare systems. At least in western countries, the most amount of the death toll is accounted by old people affected by age-related diseases. In this regard, we proposed that COVID-19 severity may be tightly related to inflammaging, i.e. the age-related onset of inflammation, which is responsible for age-related diseases. It has been reported that systemic hyper-inflammation may turn to be detrimental in COVID-19 patients.\n\nObjectiveHere, we exploited a recently closed clinical trial (NCT04315480) on the anti-IL-6 drug tocilizumab to assess whether microRNAs regulating inflammaging can be assessed as biomarkers of drug response and outcome.\n\nMethodsSerum levels of miR-146a-5p, -21-5p, and -126-3p were quantified by RT-PCR and Droplet Digital PCR by two independent laboratories on 30 patients with virologically confirmed COVID-19, characterized by multifocal interstitial pneumonia confirmed by CT-scan and requiring oxygen therapy, and 29 age- and gender-matched healthy control subjects. COVID-19 patients were treated with a single-dose intravenous infusion of 8 mg/kg tocilizumab and categorized into responders and non-responders.\n\nResultsWe showed that COVID-19 patients who did not respond to tocilizumab have lower serum levels of miR-146a-5p after the treatment (p=0.007). Moreover, among non-responders, those with the lowest serum levels of miR-146a-5p experienced the most adverse outcome (p=0.008).\n\nConclusionOur data show that blood-based biomarkers, such as miR-146a-5p, can provide a molecular link between inflammaging and COVID-19 clinical course, thus allowing to enlarge the drug armory against this worldwide health threat.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jacopo Sabbatinelli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Angelica Giuliani", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Giulia Matacchione", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Silvia Latini", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Noemi Laprovitera", + "author_inst": "University of Bologna" + }, + { + "author_name": "Giovanni Pomponio", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Alessia Ferrarini", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Silvia Svegliati Baroni", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Marianna Pavani", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Marco Moretti", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Armando Gabrielli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Antonio Domenico Procopio", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Manuela Ferracin", + "author_inst": "University of Bologna" + }, + { + "author_name": "Massimiliano Bonaf\u00e8", + "author_inst": "University of Bologna" + }, + { + "author_name": "Fabiola Olivieri", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.10.20150904", "rel_title": "Serological Tests for SARS-CoV-2 Coronavirus by Commercially Available Point-of-Care and Laboratory Diagnostics in Pre-COVID-19 Samples in Japan", @@ -1332288,61 +1332856,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.09.20149369", - "rel_title": "Pre-diagnostic circulating concentrations of insulin-like growth factor-1 and risk of COVID-19 mortality: results from UK Biobank", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149369", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) deteriorates suddenly primarily due to excessive inflammatory injury, and insulin-like growth factor-1 (IGF-1) is implicated in endocrine control of the immune system. However, the effect of IGF-1 levels on COVID-19 prognosis remains unknown.\n\nObjectiveTo investigate the association between circulating IGF-1 concentrations and mortality risk among COVID-19 patients.\n\nDesignProspective analysis.\n\nSettingUK Biobank.\n\nParticipants1425 COVID-19 patients who had pre-diagnostic serum IGF-1 measurements at baseline (2006-2010).\n\nMain outcome measuresCOVID-19 mortality (available death data updated to 22 May 2020). Unconditional logistic regression was performed to estimate the odds ratio (OR) and 95% confidence intervals (CIs) of mortality across the IGF-1 quartiles.\n\nResultsAmong 1425 COVID-19 patients, 365 deaths occurred due to COVID-19. Compared to the lowest quartile of IGF-1 concentrations, the highest quartile was associated with a 37% lower risk of mortality (OR: 0.63, 95% CI: 0.43-0.93, P-trend=0.03). The association was stronger in women and nonsmokers (both P-interaction=0.01).\n\nConclusionsHigher IGF-1 concentrations are associated with a lower risk of COVID-19 mortality. Further studies are required to determine whether and how targeting IGF-1 pathway might improve COVID-19 prognosis.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xikang Fan", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Cheng Yin", - "author_inst": "Jiangning Hospital Affiliated to Nanjing Medical University" - }, - { - "author_name": "Jiayu Wang", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Mingjia Yang", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Hongxia Ma", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Guangfu Jin", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Mingyang Song", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Zhibin Hu", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Hongbing Shen", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Dong Hang", - "author_inst": "Nanjing Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.09.20149682", "rel_title": "Undocumented infectives in the Covid-19 pandemic", @@ -1333422,6 +1333935,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.11.198770", + "rel_title": "ACE2-expressing endothelial cells in aging mouse brain", + "rel_date": "2020-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.11.198770", + "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is a key receptor mediating the entry of SARS-CoV-2 into the host cell. Through a systematic analysis of publicly available mouse brain sc/snRNA-seq data, we found that ACE2 is specifically expressed in small sub-populations of endothelial cells and mural cells, namely pericytes and vascular smooth muscle cells. Further, functional changes in viral mRNA transcription and replication, and impaired blood-brain barrier regulation were most prominently implicated in the aged, ACE2-expressing endothelial cells, when compared to the young adult mouse brains. Concordant EC transcriptomic changes were further found in normal aged human brains. Overall, this work reveals an outline of ACE2 distribution in the mouse brain and identify putative brain host cells that may underlie the selective susceptibility of the aging brain to viral infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "SU Bin Lim", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Valina L. Dawson", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Ted M. Dawson", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Sung-Ung Kang", + "author_inst": "Johns Hopkins University, School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2020.07.06.20147827", "rel_title": "Clinical Features of Hemodialysis (HD) patients confirmed with Coronavirus Disease 2019 (COVID-19): a Retrospective Case-Control Study", @@ -1334250,37 +1334794,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2020.07.09.20149435", - "rel_title": "Event-specific interventions to minimize COVID-19 transmission", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149435", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a global pandemic with over 11 million cases worldwide. Currently there is no treatment and no vaccine. Interventions such as hand washing, masks, social distancing, and \"social bubbles\" are used to limit community transmission, but it is challenging to choose the best interventions for a given activity. Here, we provide a quantitative framework to determine which interventions are likely to have the most impact in which settings. We introduce the concept of \"event R\", the expected number of new infections due to the presence of a single infected individual at an event. We obtain a fundamental relationship between event R and four parameters: transmission intensity, duration of exposure, the proximity of individuals, and the degree of mixing. We use reports of small outbreaks to establish event R and transmission intensity in a range of settings. We identify principles that guide whether physical distancing, masks and other barriers to transmission, or social bubbles will be most effective. We outline how this information can be obtained and used to re-open economies with principled measures to reduce COVID-19 transmission.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paul Tupper", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Madi Yerlanov", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Himani Boury", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University, Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.09.20141762", "rel_title": "Disentangling Increased Testing From Covid-19 Epidemic Spread", @@ -1335332,6 +1335845,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.08.20149146", + "rel_title": "Recurrent Neural Reinforcement Learning for Counterfactual Evaluation of Public Health Interventions on the Spread of Covid-19 in the world", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20149146", + "rel_abs": "As the Covid-19 pandemic soars around the world, there is urgent need to forecast the expected number of cases worldwide and the length of the pandemic before receding and implement public health interventions for significantly stopping the spread of Covid-19. Widely used statistical and computer methods for modeling and forecasting the trajectory of Covid-19 are epidemiological models. Although these epidemiological models are useful for estimating the dynamics of transmission of epidemics, their prediction accuracies are quite low. Alternative to the epidemiological models, the reinforcement learning (RL) and causal inference emerge as a powerful tool to select optimal interventions for worldwide containment of Covid-19. Therefore, we formulated real-time forecasting and evaluation of multiple public health intervention problems into off-policy evaluation (OPE) and counterfactual outcome forecasting problems and integrated RL and recurrent neural network (RNN) for exploring public health intervention strategies to slow down the spread of Covid-19 worldwide, given the historical data that may have been generated by different public health intervention policies. We applied the developed methods to real data collected from January 22, 2020 to July 30, 2020 for real-time forecasting the confirmed cases of Covid-19 across the world. We observed that the number of new cases of Covid-19 worldwide reached a peak (407,205) on July 24, 2020 and forecasted that the number of laboratory-confirmed cumulative cases of Covid-19 will pass 20 million as of August 22, 2020. The results showed that outbreak of Covid-19 worldwide has peaked and is on the decline", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Qiyang Ge", + "author_inst": "Fudan University" + }, + { + "author_name": "Zixin Hu", + "author_inst": "fudan University" + }, + { + "author_name": "Kai Zhang", + "author_inst": "University of Texas School of Public Health" + }, + { + "author_name": "Shudi Li", + "author_inst": "University of Texas School of Public Health" + }, + { + "author_name": "Wei Lin", + "author_inst": "Fudan University" + }, + { + "author_name": "Li Jin", + "author_inst": "Fudan University" + }, + { + "author_name": "Momiao Xiong", + "author_inst": "University of Texas School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.08.20148742", "rel_title": "Disproportionate incidence of COVID-19 in African Americans correlates with dynamic segregation", @@ -1336012,85 +1336568,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.10.197343", - "rel_title": "SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells.", - "rel_date": "2020-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.10.197343", - "rel_abs": "Several studies have analyzed antiviral immune pathways in late-stage severe COVID-19. However, the initial steps of SARS-CoV-2 antiviral immunity are poorly understood. Here, we have isolated primary SARS-CoV-2 viral strains, and studied their interaction with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. We show that pDC are not productively infected by SARS-CoV-2. However, they efficiently diversified into activated P1-, P2-, and P3-pDC effector subsets in response to viral stimulation. They expressed CD80, CD86, CCR7, and OX40 ligand at levels similar to influenza virus-induced activation. They rapidly produced high levels of interferon-, interferon-{lambda}1, IL-6, IP-10, and IL-8. All major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine. Mechanistically, SARS-CoV-2-induced pDC activation critically depended on IRAK4 and UNC93B1, as established using pDC from genetically deficient patients. Overall, our data indicate that human pDC are efficiently activated by SARS-CoV-2 particles and may thus contribute to type I IFN-dependent immunity against SARS-CoV-2 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Fanny Onodi", - "author_inst": "INSERM U976" - }, - { - "author_name": "Lucie Bonnet-Madin", - "author_inst": "INSERM" - }, - { - "author_name": "Laurent Meertens", - "author_inst": "INSERM" - }, - { - "author_name": "L\u00e9a Karpf", - "author_inst": "INSERM U976" - }, - { - "author_name": "Justine Poirot", - "author_inst": "INSERM U976" - }, - { - "author_name": "Shen-Ying Zhang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "capucine picard", - "author_inst": "APHP" - }, - { - "author_name": "Anne Puel", - "author_inst": "INSERM" - }, - { - "author_name": "Emmanuelle Jouanguy", - "author_inst": "INSERM" - }, - { - "author_name": "Qian Zhang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Jer\u00f4me LeGoff", - "author_inst": "Paris Diderot University and APHP - H\u00f4pital Saint-Louis" - }, - { - "author_name": "Jean-Michel Molina", - "author_inst": "Hopital Saint Louis" - }, - { - "author_name": "Constance Delaugerre", - "author_inst": "INSERM" - }, - { - "author_name": "Jean-Laurent Casanova", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Ali AMARA", - "author_inst": "INSERM" - }, - { - "author_name": "Vassili Soumelis", - "author_inst": "INSERM U976" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.09.196519", "rel_title": "Discriminating Mild from Critical COVID-19 by Innate and Adaptive Immune Single-cell Profiling of Bronchoalveolar Lavages", @@ -1337478,6 +1337955,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.09.194639", + "rel_title": "Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals", + "rel_date": "2020-07-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.194639", + "rel_abs": "In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to COVID-19 patients. The therapy has been deemed safe and several clinical trials assessing its efficacy are ongoing. While it remains to be formally proven, the presence of neutralizing antibodies is thought to play a positive role in the efficacy of this treatment. Indeed, neutralizing titers of [≥]1:160 have been recommended in some convalescent plasma trials for inclusion. Here we performed repeated analyses at one-month interval on 31 convalescent individuals to evaluate how the humoral responses against the SARS-CoV-2 Spike, including neutralization, evolve over time. We observed that receptor-binding domain (RBD)-specific IgG slightly decreased between six and ten weeks after symptoms onset but RBD-specific IgM decreased much more abruptly. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. If neutralization activity proves to be an important factor in the clinical efficacy of convalescent plasma transfer, our results suggest that plasma from convalescent donors should be recovered rapidly after symptoms resolution.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "Annemarie Laumaea", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Sai Priya Anand", + "author_inst": "CRCHUM / McGill" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Romain Gasser", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Guillaume Goyette", + "author_inst": "CRCHUM" + }, + { + "author_name": "Halima Medjahed", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jos\u00e9ee Perreault", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Tony Tremblay", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Antoine Lewin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Laurie Gokool", + "author_inst": "CRCHUM" + }, + { + "author_name": "Chantal Morrisseau", + "author_inst": "CRCHUM" + }, + { + "author_name": "Philippe B\u00e9gin", + "author_inst": "CHU Ste-Justine" + }, + { + "author_name": "Cecile Tremblay", + "author_inst": "CRCHUM" + }, + { + "author_name": "Val\u00e9rie Martel-Laferri\u00e8re", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jonathan Richard", + "author_inst": "Centre de Recherche du CHUM" + }, + { + "author_name": "Ren\u00e9e Bazin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.08.194456", "rel_title": "Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2", @@ -1338269,109 +1338833,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.07.20147884", - "rel_title": "SARS-CoV-2 Seroprevalence Rates of Children in Louisiana During the State Stay at Home Order.", - "rel_date": "2020-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20147884", - "rel_abs": "BACKGROUNDChildren ([≤]18 years) account for [~]20% of the US population but currently represent <2% of coronavirus disease 2019 (COVID-19) cases. Because infected children often have few or no symptoms and may not be tested, the extent of infection in children is poorly understood.\n\nMETHODSDuring the March 18th-May 15th 2020 Louisiana Stay At Home Order, 1690 blood samples from 812 individuals from a Childrens Hospital were tested for antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Demographics, COVID-19 testing, and clinical presentation abstracted from medical records were compared with local COVID-19 cases.\n\nRESULTSIn total, 62 subjects (7.6%) were found to be seropositive. The median age was 11 years with 50.4% female. The presenting complaint of seropositive patients was chronic illness (43.5%). Only 18.2% had a previous positive COVID-19 PCR or antibody test. Seropositivity was significantly associated with parish (counties), race, and residence in a low-income area. Importantly, seropositivity was linearly correlated with cumulative COVID-19 case number for all ages by parish.\n\nCONCLUSIONIn a large retrospective study, the seropositivity prevalence for SARS-CoV-2 in children in Louisiana during the mandated Stay At Home Order was 7.6%. Residence location, race, and lower socioeconomic factors were linked to more frequent seropositivity in children and correlated to regional COVID-19 case rates. Thus, a significant number of children in Louisiana had SARS-CoV-2 infections that went undetected and unreported and may have contributed to virus transmission.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Monika L Dietrich", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Elizabeth B Norton", - "author_inst": "Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Debra Elliott", - "author_inst": "Tulane University" - }, - { - "author_name": "Ashley R Smira", - "author_inst": "Tulane University" - }, - { - "author_name": "Julie A Rouelle", - "author_inst": "Tulane University" - }, - { - "author_name": "Nell G Bond", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Karen Aime-Marcelin", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Alisha Prystowsky", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Rebecca Kemnitz", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Arunava Sarma", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Sarah Talia Himmelfarb", - "author_inst": "Internal Medicine and Pediatrics, Tulane University, New Orleans, LA USA" - }, - { - "author_name": "Neha Sharma", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Addison E Stone", - "author_inst": "Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Randall Craver", - "author_inst": "Childrens Hospital of New Orleans, New Orleans, LA USA" - }, - { - "author_name": "Alyssa R Lindrose", - "author_inst": "Department of Psychiatry and Behavioral Sciences, Tulane University, LA USA" - }, - { - "author_name": "Leslie A Smitley", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Robert B Uddo", - "author_inst": "Childrens Hospital of New Orleans, New Orleans, LA USA" - }, - { - "author_name": "Leann Myers", - "author_inst": "Department of Biostatistics & Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Stacy S Drury", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA, Department of Psychiatry and Behavioral Sciences, Tulane University, LA USA" - }, - { - "author_name": "John S Schieffelin", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "James E Robinson", - "author_inst": "Department of Pediatrics, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Kevin J Zwezdaryk", - "author_inst": "Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.06.20146712", "rel_title": "Risk of Transmission of infection to Healthcare Workers delivering Supportive Care for Coronavirus Pneumonia;A Rapid GRADE Review", @@ -1339399,6 +1339860,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.07.20148304", + "rel_title": "COVID-19 Mortality Risk Assessment: An International Multi-Center Study", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148304", + "rel_abs": "BackgroundTimely identification of COVID-19 patients at high risk of mortality can significantly improve patient management and resource allocation within hospitals. This study seeks to develop and validate a data-driven personalized mortality risk calculator for hospitalized COVID-19 patients.\n\nMethodsDe-identified data was obtained for 3,927 COVID-19 positive patients from six independent centers, comprising 33 different hospitals. Demographic, clinical, and laboratory variables were collected at hospital admission. The COVID-19 Mortality Risk (CMR) tool was developed using the XGBoost algorithm to predict mortality. Its discrimination performance was subsequently evaluated on three validation cohorts.\n\nFindingsThe derivation cohort of 3,062 patients has an observed mortality rate of 26.84%. Increased age, decreased oxygen saturation ([≤] 93%), elevated levels of C-reactive protein ([≥] 130 mg/L), blood urea nitrogen ([≥] 18 mg/dL), and blood creatinine ([≥] 1.2 mg/dL) were identified as primary risk factors, validating clinical findings. The model obtains out-of-sample AUCs of 0.90 (95% CI, 0.87-0.94) on the derivation cohort. In the validation cohorts, the model obtains AUCs of 0.92 (95% CI, 0.88-0.95) on Seville patients, 0.87 (95% CI, 0.84-0.91) on Hellenic COVID-19 Study Group patients, and 0.81 (95% CI, 0.76-0.85) on Hartford Hospital patients. The CMR tool is available as an online application at covidanalytics.io/mortality_calculator and is currently in clinical use.\n\nInterpretationThe CMR model leverages machine learning to generate accurate mortality predictions using commonly available clinical features. This is the first risk score trained and validated on a cohort of COVID-19 patients from Europe and the United States.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, BioRxiv, MedRxiv, arXiv, and SSRN for peer-reviewed articles, preprints, and research reports in English from inception to March 25th, 2020 focusing on disease severity and mortality risk scores for patients that had been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Earlier investigations showed promise at predicting COVID-19 disease severity using data at admission. However, existing work was limited by its data scope, either relying on a single center with rich clinical information or broader cohort with sparse clinical information. No analysis has leveraged Electronic Health Records data from an international multi-center cohort from both Europe and the United States.\n\nAdded value of this studyWe present the first multi-center COVID-19 mortality risk study that uses Electronic Health Records data from 3,062 patients across four different countries, including Greece, Italy, Spain, and the United States, encompassing 33 hospitals. We employed state-of-the-art machine learning techniques to develop a personalized COVID-19 mortality risk (CMR) score for hospitalized patients upon admission based on clinical features including vitals, lab results, and comorbidities. The model validates clinical findings of mortality risk factors and exhibits strong performance, with AUCs ranging from 0.81 to 0.92 across external validation cohorts. The model identifies increased age as a primary mortality predictor, consistent with observed disease trends and subsequent public health guidelines. Additionally, among the vital and lab values collected at admission, decreased oxygen saturation ([≤] 93%) and elevated levels of C-reactive protein ([≥] 130 mg/L), blood urea nitrogen ([≥] 18 mg/dL), blood creatinine ([≥] 1.2 mg/dL), and blood glucose ([≥]180 mg/dL) are highlighted as key biomarkers of mortality risk. These findings corroborate previous studies that link COVID-19 severity to hypoxemia, impaired kidney function, and diabetes. These features are also consistent with risk factors used in severity risk scores for related respiratory conditions such as community-acquired pneumonia.\n\nImplications of all the available evidenceOur work presents the development and validation of a personalized mortality risk score. We take a data-driven approach to derive insights from Electronic Health Records data spanning Europe and the United States. While many existing papers on COVID-19 clinical characteristics and risk factors are based on Chinese hospital data, the similarities in our findings suggest consistency in the disease characteristics across international cohorts. Additionally, our machine learning model offers a novel approach to understanding the disease and its risk factors. By creating a single comprehensive risk score that integrates various admission data components, the calculator offers a streamlined way of evaluating COVID-19 patients upon admission to augment clinical expertise. The CMR model provides a valuable clinical decision support tool for patient triage and care management, improving risk estimation early within admission, that can significantly affect the daily practice of physicians.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Dimitris Bertsimas", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Galit Lukin", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Luca Mingardi", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Omid Nohadani", + "author_inst": "Benefits Science Technologies" + }, + { + "author_name": "Agni Orfanoudaki", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Bartolomeo Stellato", + "author_inst": "Princeton University" + }, + { + "author_name": "Holly Wiberg", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Sara Gonzalez-Garcia", + "author_inst": "Institute of Biomedicine of Seville (IBIS), Virgen del Rocio University Hospital, CSIC, University of Seville" + }, + { + "author_name": "Carlos Luis Parra-Calderon", + "author_inst": "Institute of Biomedicine of Seville (IBIS), Virgen del Rocio University Hospital, CSIC, University of Seville" + }, + { + "author_name": "- The Hellenic COVID-19 Study Group", + "author_inst": "" + }, + { + "author_name": "Kenneth Robinson", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Michelle Schneider", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Barry Stein", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Alberto Estirado", + "author_inst": "HM Hospitals" + }, + { + "author_name": "Lia a Beccara", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Rosario Canino", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Martina Dal Bello", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Federica Pezzetti", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Angelo Pan", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.07.20148213", "rel_title": "No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS).", @@ -1340123,93 +1340675,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.07.08.191072", - "rel_title": "Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures", - "rel_date": "2020-07-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.08.191072", - "rel_abs": "With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Roberto Melero", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Carlos Oscar S Sorzano", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Brent Foster", - "author_inst": "Dept. of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA" - }, - { - "author_name": "Jose Luis Vilas", - "author_inst": "Dept. of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA" - }, - { - "author_name": "Marta Martinez", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Roberto Marabini", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Erney Ramirez-Aportela", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Ruben Sanchez-Garcia", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "David Herreros", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Laura del Cano", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Patricia Losana", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Yunior C. Fonseca-Reyna", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Pablo Conesa", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - }, - { - "author_name": "Daniel Wrapp", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA" - }, - { - "author_name": "Pablo Chacon", - "author_inst": "Instituto Rocasolano-CSIC, c/Serrano, 119, 28006, Madrid, Spain" - }, - { - "author_name": "Jason S. McLellan", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA" - }, - { - "author_name": "Hemant D. Tagare", - "author_inst": "Dept. of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06520, USA" - }, - { - "author_name": "Jose Maria Carazo", - "author_inst": "Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.07.192732", "rel_title": "In vivo structural characterization of the whole SARS-CoV-2 RNA genome identifies host cell target proteins vulnerable to re-purposed drugs", @@ -1341057,6 +1341522,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.06.182972", + "rel_title": "Unique transcriptional changes in coagulation cascade genes in SARS-CoV-2-infected lung epithelial cells: A potential factor in COVID-19 coagulopathies", + "rel_date": "2020-07-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.182972", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic. In addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients. Currently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. While there are many theories for the cause of this pathology, including hyper inflammation and excess tissue damage, the cellular and molecular underpinnings are not yet clear. By analyzing transcriptomic data sets from experimental and clinical research teams, we determined that changes in the gene expression of genes important in the extrinsic coagulation cascade in the lung epithelium may be important triggers for COVID-19 coagulopathy. This regulation of the extrinsic blood coagulation cascade is not seen with influenza A virus (IAV)-infected NHBEs suggesting that the lung epithelial derived coagulopathies are specific to SARS-Cov-2 infection. This study is the first to identify potential lung epithelial cell derived factors contributing to COVID-19 associated coagulopathy.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC=\"FIGDIR/small/182972v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@93cfb7org.highwire.dtl.DTLVardef@2a23c9org.highwire.dtl.DTLVardef@93623borg.highwire.dtl.DTLVardef@161e25_HPS_FORMAT_FIGEXP M_FIG C_FIG AUTHOR SUMMARYO_ST_ABSWhy was this study done?C_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic.\nC_LIO_LIIn addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients.\nC_LIO_LICurrently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. Understanding the molecular basis of dysregulated blood coagulation during SARS-CoV-2 infection may help promote new therapeutic strategies to mitigate these complications in COVID-19 patients.\nC_LI\n\nWhat did the researchers do and find?O_LIWe analyzed three publicly available RNA sequencing datasets to identify possible molecular etiologies of COVID-19 associated coagulopathies. These data sets include sequencing libraries from clinically isolated samples of bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMCs) from SARS-CoV-2 positive patients and healthy controls. We also analyzed a publicly available RNA sequencing dataset derived from in vitro SARS-CoV-2 infected primary normal human bronchial epithelial (NHBE) cells and mock infected samples.\nC_LIO_LIPathway analysis of both NHBE and BALF differential gene expression gene sets. We found that SARS-CoV-2 infection induces the activation of the extrinsic blood coagulation cascade and suppression of the plasminogen activation system in both NHBEs and cells isolated from the BALF. PBMCs did not differentially express genes regulating blood coagulation.\nC_LIO_LIComparison with influenza A virus (IAV)-infected NHBEs revealed that the regulation of the extrinsic blood coagulation cascade is unique to SARS-CoV-2, and not seen with IAV infection.\nC_LI\n\nWhat do these findings mean?O_LIThe hyper-activation of the extrinsic blood coagulation cascade and the suppression of the plasminogen activation system in SARS-CoV-2 infected epithelial cells may drive diverse coagulopathies in the lung and distal organ systems.\nC_LIO_LIThe gene transcription pattern in SARS-CoV-2 infected epithelial cells is distinct from IAV infected epithelial cells with regards to the regulation of blood coagulation.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ethan S. FitzGerald", + "author_inst": "Brown University" + }, + { + "author_name": "Amanda M. Jamieson", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.07.07.192005", "rel_title": "A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex", @@ -1341589,25 +1342077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.25.20140459", - "rel_title": "The socioeconomic determinants of COVID-19: A spatial analysis of German county level data", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140459", - "rel_abs": "The study explores the influence of socio-economic variables on case and death rates of the COVID-19 pandemic in Germany until mid-June 2020. It covers Germanys 401 counties by multivariate spatial models that can take into account regional interrelationships and possible spillover effects. The case and death rates are, for example, significantly positively associated with early cases from the beginning of the epidemic, the average age, the population density and the number of people employed in elderly care. By contrast, they are significantly negatively associated with the density of schoolchildren and infant care as well as the density of doctors. In addition, for certain variables significant spillover effects on the case numbers of neighbouring regions could be identified, which have a different sign than the overall effects and thus give cause for further analyses of the mechanisms of action of COVID-19 infections. The results complement the knowledge about COVID-19 infection beyond the clinical risk factors discussed so far by a socio-economic perspective. The findings can contribute to the targeted derivation of political measures and their review, as is currently being discussed in particular for the tourism and education sectors.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andree Ehlert", - "author_inst": "HWWI" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.07.05.20146787", "rel_title": "Racial segregation, testing sites access, and COVID-19 incidence rate in Massachusetts, USA", @@ -1342299,6 +1342768,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.07.06.20147751", + "rel_title": "COVID-19 presenting as anosmia and dysgeusia in New York City emergency departments, March - April, 2020", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147751", + "rel_abs": "BackgroundIncreasing evidence has been emerging of anosmia and dysgeusia as frequently reported symptoms in COVID-19. Improving our understanding of these presenting symptoms may facilitate the prompt recognition of the disease in emergency departments and prevent further transmission.\n\nMethodsWe examined a cross-sectional cohort using New York City emergency department syndromic surveillance data for March and April 2020. Emergency department visits for anosmia and/or dysgeusia were identified and subsequently matched to the Electronic Clinical Laboratory Reporting System to determine testing results for SARS-CoV-2.\n\nResultsOf the 683 patients with anosmia and/or dysgeusia included, SARS-CoV-2 testing was performed for 232 (34%) and 168 (72%) were found to be positive. Median age of all patients presenting with anosmia and/or dysgeusia symptoms was 38, and 54% were female. Anosmia and/or dysgeusia was the sole complaint of 158 (23%) patients, of whom 35 were tested for SARS-CoV-2 and 23 (66%) were positive. While the remaining patients presented with at least one other symptom, nearly half of all patients (n=334, 49%) and more than a third of those who tested positive (n=62, 37%) did not have any of the CDC-established symptoms used for screening of COVID-19 such as fever, cough, shortness of breath, or sore throat.\n\nConclusions and RelevanceAnosmia and/or dysgeusia have been frequent complaints among patients presenting to emergency departments during the COVID-19 pandemic, and, while only a small proportion of patients ultimately underwent testing for SARS-CoV-19, the majority of patients tested have been positive. Anosmia and dysgeusia likely represent underrecognized symptoms of COVID-19 but may have important future implications in disease diagnosis and surveillance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tina Z. Wang", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jessica Sell", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Don Weiss", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Ramona Lall", + "author_inst": "New York City Department of Health and Mental Hygiene" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.06.20147702", "rel_title": "COVID-19 screening strategies that permit the safe re-opening of college campuses", @@ -1342767,49 +1343267,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.06.20147090", - "rel_title": "Examining the protection efficacy of face shields against cough aerosol droplets using water sensitive papers", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147090", - "rel_abs": "Simple plastic face shields have many advantages compared to regular medical masks. They are easily cleaned for reuse and comfortable to wear. In light of the spreading COVID-19 pandemic, the potential of face shields as a substitution for medical masks, as a recommendation to the general population, was tested. Testing the efficacy of the protective equipment utilized a cough simulator that was carefully tuned to replicate human cough in terms of droplet size distribution and outlet velocity. The tested protective equipment was worn on a manikin head simulating human breathing. An Aerodynamic Particle Sizer (APS) was used to analyze the concentration and size distribution of small particles that reach the manikin head respiration pathways. Additionally, Water sensitive papers were taped over and under the tested protective equipment, and were subsequently photographed and analyzed. For droplets larger than 3m by diameter, the efficiency of shields to block cough droplets was found to be comparable to that of regular medical masks, with enhanced protection on face parts the mask does not cover. Additionally, for finer particles, of the order 0.3 to few microns, a shield was found to perform even better, blocking about 10 times more fine particles than the medical mask. This implies that for the general population that is not intendedly exposed to confirmed infected individuals, recommending the use of face shields as an alternative to medical masks should be considered.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ayala Ronen", - "author_inst": "Isreal Isntitute for Biological Research, Department of Environmental Physics" - }, - { - "author_name": "Hadar Rotter", - "author_inst": "Isreal Isntitute for Biological Research, Department of Physical Chemistry" - }, - { - "author_name": "Shmuel Elisha", - "author_inst": "Isreal Isntitute for Biological Research, Department of Environmental Physics" - }, - { - "author_name": "Sagi Sevilia", - "author_inst": "Israel Institute for Biological Research, Department of Environmental Physics" - }, - { - "author_name": "Batya Parizer", - "author_inst": "Isreal Isntitute for Biological Research, Department of Environmental Physics" - }, - { - "author_name": "Nir Hafif", - "author_inst": "Israel Institute for Biological Research, Department of Physical Chemistry" - }, - { - "author_name": "Alon Manor", - "author_inst": "Israel Institute for Biological Research, Department of Environmental Physics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.06.20141333", "rel_title": "Passive Monitoring of Physiological Data and Self-reported Symptoms to Detect Clusters of People with COVID-19", @@ -1343721,6 +1344178,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.03.20145797", + "rel_title": "Dengue antibodies can cross-react with SARS-CoV-2 and vice versa-Antibody detection kits can give false-positive results for both viruses in regions where both COVID-19 and Dengue co-exist", + "rel_date": "2020-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145797", + "rel_abs": "Five of thirteen Dengue antibody-positive serum samples, dated 2017 (pre-dating the COVID-19 outbreak) produced false-positive results in SARS-CoV-2 IgG/IgM rapid strip tests. Our results emphasize the importance of NAT and/or virus antigen tests to complement sero-surveillance for definitive diagnosis of COVID-19/Dengue in regions where both viruses are co-endemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Himadri Nath", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Abinash Mallick", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Subrata Roy", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Soumi Sukla", + "author_inst": "NIPER, Kolkata" + }, + { + "author_name": "Keya Basu", + "author_inst": "IPGMER, Kolkata (Department of Pathology)" + }, + { + "author_name": "Abhishek De", + "author_inst": "Calcutta National Medical College, Kolkata (Department of Dermatology)" + }, + { + "author_name": "Subhajit Biswas", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.29.20131367", "rel_title": "Evaluation of Viasure SARS-CoV-2 RT-qPCR kit (CerTest Biotec) using CDC FDA EUA RT-qPCR kit as a gold standard.", @@ -1344209,49 +1344709,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.06.190413", - "rel_title": "Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3", - "rel_date": "2020-07-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.190413", - "rel_abs": "Small molecules that bind the SARS-CoV-2 non-structural protein 3 Mac1 domain in place of ADP-ribose could be useful as molecular probes or scaffolds for COVID-19 antiviral drug discovery because Mac1 has been linked to coronavirus ability to evade cellular detection. A high-throughput assay based on differential scanning fluorimetry (DSF) was therefore optimized and used to identify possible Mac1 ligands in small libraries of drugs and drug-like compounds. Numerous promising compounds included nucleotides, steroids, beta-lactams, and benzimidazoles. The main drawback to this approach was that a high percentage of compounds in some libraries were found to influence the observed Mac1 melting temperature. To prioritize DSF screening hits, the shapes of the observed melting curves and initial assay fluorescence were examined, and the results were compared with virtual screens performed using Autodock VINA. The molecular basis for alternate ligand binding was also examined by determining a structure of one of the hits, cyclic adenosine monophosphate, with atomic resolution.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rajdeep S Virdi", - "author_inst": "University of Wisconsin- Milwaukee" - }, - { - "author_name": "Robert V Bavisotto", - "author_inst": "University of Wisconsin- Milwaukee" - }, - { - "author_name": "Nicholas C Hopper", - "author_inst": "University of Wisconsin- Milwaukee" - }, - { - "author_name": "Nemanja Vuksanovic", - "author_inst": "The University of Wisconsin- Milwaukee" - }, - { - "author_name": "Trevor R Melkonian", - "author_inst": "The University of Wisconsin- Milwaukee" - }, - { - "author_name": "Nicholas R Silvaggi", - "author_inst": "The University of Wisconsin- Milwaukee" - }, - { - "author_name": "David Frick", - "author_inst": "University of Wisconsin- Milwaukee" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.06.190207", "rel_title": "Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets", @@ -1344927,6 +1345384,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20143032", + "rel_title": "Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients", + "rel_date": "2020-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20143032", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear.\n\nMethodBetween January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined.\n\nFindingsNotably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission.\n\nInterpretationOur findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2.\n\nFundingNational Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Huanzi Zhong", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China. Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denma" + }, + { + "author_name": "Yanqun Wang", + "author_inst": "Guangzhou Institute of Respiratory Health" + }, + { + "author_name": "Zhun Shi", + "author_inst": "BGI-Shenzhen,Shenzhen 518083,China" + }, + { + "author_name": "Lu Zhang", + "author_inst": "Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China 510060." + }, + { + "author_name": "Huahui Ren", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Weiqun He", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Zhaoyong Zhang", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Airu Zhu", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Jingxian Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Fei Xiao", + "author_inst": "Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imag" + }, + { + "author_name": "Fangming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Tianzhu Liang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Feng Ye", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Bei Zhong", + "author_inst": "The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong, China" + }, + { + "author_name": "Shicong Ruan", + "author_inst": "Yangjiang People's Hospital, Yangjiang, Guangdong, China" + }, + { + "author_name": "Mian Gan", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Jiahui Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Fang Li", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Fuqiang Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Daxi Wang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Jiandong Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Peidi Ren", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Shida Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Huanming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Jian Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Karsten Kristiansen", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Hein M Tun", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China." + }, + { + "author_name": "Weijun Chen", + "author_inst": "BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China." + }, + { + "author_name": "Nanshan Zhong", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-shenzhen" + }, + { + "author_name": "Yi-min Li", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Junhua LI", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.20145052", "rel_title": "Modeling COVID-19 for lifting non-pharmaceutical interventions", @@ -1345507,25 +1346111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.07.02.20145425", - "rel_title": "How was the Mental Health of Colombian people on March during Pandemics Covid19?", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145425", - "rel_abs": "Actual pandemic started with first cases in China and fast spread in Europe, Asia and the next continents became a global concern from March, so the most of countries ordered a lockdown to decrease infection rate forced people to stay at home. The first confirmed case was on March 6, during the next days more cases were confirmed by Minster of Health, the first death was on March 21, one day after of the announcement of lockdown in Colombia. During this period of waiting for what is going to happen people can develop mental stress as fear, sleep disorders so to analyze how was the behaviour on the population the present study is conducted using a Social Network as Twitter, Natural Language algorithms and Data Mining criterions. The findings confirmed the interest of covid19 was increasing daily, people was experimenting fear, anxiety, mental stress.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Josimar E. Chire Saire", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.07.03.20145748", "rel_title": "Are Our COVID Warriors Cared-for Enough?A Nationwide Survey on Stress Among Doctors During the COVID-19 Pandemic", @@ -1346349,6 +1346934,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.03.20145672", + "rel_title": "A Novel Approach for Estimating the Final Outcome of Global Diseases Like COVID-19", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145672", + "rel_abs": "The existence of a universal law which maps the bell curve of daily cases to a sigmoid curve for cumulative ones is used for making robust estimations about the final outcome of a disease. Computations of real time effective reproduction rate are presented and its limited usefulness is derived. After using methods ESE & EDE we are able to find the inflection point of the cumulative curve under consideration and study its time evolution. Since mortality processes tend to follow a Gompertz distribution, we apply the properties of it and introduce novel estimations for both the time remaining after inflection time and the capacity of the curve. Special properties of sigmoid curves are used for assessing the quality of estimation and as indices for the cycle completion. Application is presented for COVID-19 evolution for most affected countries and the World.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Demetris T Christopoulos", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.03.20146167", "rel_title": "Serial interval, basic reproduction number and prediction of COVID-19 epidemic size in Jodhpur, India", @@ -1346933,61 +1347537,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.02.20144964", - "rel_title": "A systematic review of the smartphone applications available for coronavirus disease 2019 (COVID19) and their assessment using the mobile app rating scale (MARS)", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20144964", - "rel_abs": "The global impact of COVID-19 pandemic has increased the need to rapidly develop and improve utilization of mobile applications across the healthcare continuum to address rising barriers of access to care due to social distancing challenges and allow continuity in sharing of health information, assist with COVID-19 activities including contact tracing, and providing useful information as needed. Here we provide an overview of mobile applications being currently utilized for COVID-19 related activities. We performed a systematic review of the literature and mobile platforms to assess mobile applications been currently utilized for COVID-19, and quality assessment of these applications using the Mobile Application Rating Scale (MARS) for overall quality, Engagement, Functionality, Aesthetics, and Information. Finally, we provide an overview of the key salient features that should be included in mobile applications being developed for future use. Our search identified 63 apps that are currently being used for COVID-19. Of these, 25 were selected from the Google play store and Apple App store in India, and 19 each from the UK and US. 18 apps were developed for sharing up to date information on COVID-19, and 8 were used for contact tracing while 9 apps showed features of both. On MARS Scale, overall scores ranged from 2.4 to 4.8 with apps scoring high in areas of functionality and lower in Engagement. Future steps should involve developing and testing of mobile applications using assessment tools like the MARS scale and the study of their impact on health behaviors and outcomes.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Samira Davalbhakta", - "author_inst": "BJGMC Pune and Sassoon General Hospitals" - }, - { - "author_name": "Shailesh Advani", - "author_inst": "Social Behavioural Research Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA" - }, - { - "author_name": "Shobhit Kumar", - "author_inst": "King George's Medical University Lucknow, India" - }, - { - "author_name": "Vishwesh Agarwal", - "author_inst": "Mahatma Gandhi Missions Medical College" - }, - { - "author_name": "Samruddhi Bhoyar", - "author_inst": "University of Massachusetts, Amherst, Massachusetts, USA" - }, - { - "author_name": "Elizabeth Fedirko", - "author_inst": "University of Massachusetts, Amherst, Massachusetts, USA" - }, - { - "author_name": "Durga Misra", - "author_inst": "Department of Clinical Immunology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India" - }, - { - "author_name": "Ashish Goel", - "author_inst": "Department of Medicine, University College of Medical Sciences, New Delhi, India" - }, - { - "author_name": "Latika Gupta", - "author_inst": "SGPGI" - }, - { - "author_name": "Vikas Agarwal", - "author_inst": "Department of Clinical Immunology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.02.20144873", "rel_title": "Clinical Characteristics of Recurrent-positive Coronavirus Disease 2019 after Curative Discharge: a retrospective analysis of 15 cases in Wuhan China", @@ -1347915,6 +1348464,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.01.20129882", + "rel_title": "Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies", + "rel_date": "2020-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20129882", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a potentially life-threatening respiratory infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), for which numerous serologic assays are available. In a CLIA laboratory setting, we used a retrospective sample set (n = 457) to evaluate two lateral flow immunoassays (LFIAs; two iterations of Rapid Response COVID-19 Test Cassette, BTNX Inc.) and a subset of to evaluate SARS-COV-2 IgG/IgM Rapid Test, ACON Laboratories (n = 200); and Standard Q COVID-19 IgM/IgG Duo, SD BIOSENSOR (n = 155) for their capacity to detect of SARS-CoV-2 IgG. In a cohort of primarily hospitalized patients with RT-PCR confirmed COVID-19, the BTNX assays demonstrated 95% and 92% agreement with the Abbott SARS-CoV-2 IgG assay and sensitivity was highest at [≥] 14 days from symptom onset [BTNX kit 1, 95%; BTNX kit 2, 91%]. ACON and SD assays demonstrated 99% and 100% agreement with the Abbott assay at [≥] 14 days from symptom onset. Specificity was measured using 74 specimens collected prior to SARS-CoV-2 circulation in the United States and 31 \"cross-reactivity challenge\" specimens, including those from patients with a history of seasonal coronavirus infection and was 98% for BTNX kit 1 and ACON and 100% for BTNX kit 2 and SD. Taken with data from EUA assays, these results suggest that LFIAs may provide adequate results for rapid detection of SARS-CoV-2. Replicating these results in fingerstick blood in outpatient populations, would further support the possibility that LFIAs may be useful to increase access to serologic testing", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kathrine McAulay", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Bryan", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Francisca Grill", + "author_inst": "Arizona State University" + }, + { + "author_name": "Douglas F. Lake", + "author_inst": "Arizona State University" + }, + { + "author_name": "Erin J. Kaleta", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Thomas E Grys", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144667", "rel_title": "Numerical Analysis of Disastrous Effect of Reopening Too Soon in Georgia, USA", @@ -1348395,41 +1348987,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.06.29.20142836", - "rel_title": "Sample pooling on triplets to speed up SARS-CoV-2 diagnosis using CDC FDA EUA RT-qPCR kit.", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142836", - "rel_abs": "The CDC designed \"FDA Emergeny Use Autorization\" 2019-nCoV CDC RT-qPCR kit uses 3 different FAM probes for SARS-CoV-2 diagnosis so 3 reactions per sample are needed. We herein describe a sample pooling protocol: 3 RNA extractions are combined into a single PCR reaction. The sensitivity for this protocol is 100% as no shift on Ct values for N1 or N2 probes were observed. For a typical 96-well plate, triplet assay allows 96 samples processing, speeding up diagnosis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Byron Freire-Paspuel", - "author_inst": "Universidad de Las Americas" - }, - { - "author_name": "Patricio Alejandro Vega-Marino", - "author_inst": "Agencia de Regulacion y Control de la Bioseguridad y Cuarentena para Galapagos" - }, - { - "author_name": "Alberto Velez", - "author_inst": "Agencia de Regulacion y Control de la Bioseguridad y Cuarentena para Galapagos" - }, - { - "author_name": "Marilyn Cruz", - "author_inst": "Agencia de Regulacion y Control de la Bioseguridad y Cuarentena para Galapagos" - }, - { - "author_name": "Miguel Angel Garcia Bereguiain", - "author_inst": "Universidad de Las Americas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.03.186296", "rel_title": "The major genetic risk factor for severe COVID-19 is inherited from Neandertals", @@ -1349469,6 +1350026,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.30.20143651", + "rel_title": "Identifying main and interaction effects of risk factors to predict intensive care admission in patients hospitalized with COVID-19: a retrospective cohort study in Hong Kong", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143651", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) has become a pandemic, placing significant burdens on the healthcare systems. In this study, we tested the hypothesis that a machine learning approach incorporating hidden nonlinear interactions can improve prediction for Intensive care unit (ICU) admission.\n\nMethodsConsecutive patients admitted to public hospitals between 1st January and 24th May 2020 in Hong Kong with COVID-19 diagnosed by RT-PCR were included. The primary endpoint was ICU admission.\n\nResultsThis study included 1043 patients (median age 35 (IQR: 32-37; 54% male). Nineteen patients were admitted to ICU (median hospital length of stay (LOS): 30 days, median ICU LOS: 16 days). ICU patients were more likely to be prescribed angiotensin converting enzyme inhibitors/angiotensin receptor blockers, anti-retroviral drugs lopinavir/ritonavir and remdesivir, ribavirin, steroids, interferon-beta and hydroxychloroquine. Significant predictors of ICU admission were older age, male sex, prior coronary artery disease, respiratory diseases, diabetes, hypertension and chronic kidney disease, and activated partial thromboplastin time, red cell count, white cell count, albumin and serum sodium. A tree-based machine learning model identified most informative characteristics and hidden interactions that can predict ICU admission. These were: low red cells with 1) male, 2) older age, 3) low albumin, 4) low sodium or 5) prolonged APTT. A five-fold cross validation confirms superior performance of this model over baseline models including XGBoost, LightGBM, random forests, and multivariate logistic regression.\n\nConclusionsA machine learning model including baseline risk factors and their hidden interactions can accurately predict ICU admission in COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jiandong Zhou", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Gary Tse", + "author_inst": "Tianjin Medical University" + }, + { + "author_name": "Sharen Lee", + "author_inst": "Laboratory of Cardiovascular Physiology" + }, + { + "author_name": "Tong Liu", + "author_inst": "Tianjin Medical University" + }, + { + "author_name": "William KK Wu", + "author_inst": "LKS Institute of Health Sciences" + }, + { + "author_name": "zhidong cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Dajun Zeng", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Ian CK Wong", + "author_inst": "HKU" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Bernard MY Cheung", + "author_inst": "HKU" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144030", "rel_title": "Broad phenotypic alterations and potential dysfunctions of lymphocytes in COVID-19 recovered individuals", @@ -1350001,57 +1350613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.01.20144402", - "rel_title": "ESTIMATING UNDERDIAGNOSIS OF COVID-19 WITH NOWCASTING AND MACHINE LEARNING: EXPERIENCE FROM BRAZIL", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144402", - "rel_abs": "BackgroundBrazil has the second largest COVID-19 number of cases, worldly. Even so, underdiagnosis in the country is massive. Nowcasting techniques have helped to overcome the underdiagnosis. Recent advances in machine learning techniques offer opportunities to refine the nowcasting. This study aimed to analyze the underdiagnosis of COVID-19, through nowcasting with machine learning, in a South of Brazil capital.\n\nMethodsThe study has an observational ecological design. It used data from 3916 notified cases of COVID-19, from April 14th to June 02nd, 2020, in Florianopolis, Santa Catarina, Brazil. We used machine-learning algorithm to classify cases which had no diagnosis yet, producing the nowcast. To analyze the underdiagnosis, we compared the difference between the data without nowcasting and the median of the nowcasted projections for the entire period and for the six days from the date of onset of symptoms to diagnosis at the moment of data extraction.\n\nResultsThe number of new cases throughout the entire period, without nowcasting, was 389. With nowcasting, it was 694 (UI95 496-897,025). At the six days period, the number without nowcasting was 19 and 104 (95% UI 60-142) with. The underdiagnosis was 37.29% in the entire period and 81.73% at the six days period.\n\nConclusionsThe underdiagnosis was more critical in six days from the date of onset of symptoms to diagnosis before the data collection than in the entire period. The use of nowcasting with machine learning techniques can help to estimate the number of new cases of the disease.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Leandro Pereira Garcia", - "author_inst": "Public Health Department of Florianopolis" - }, - { - "author_name": "Andre Vinicius Goncalves", - "author_inst": "Universidade Federal de Santa Catarina and Instituto Federal do Norte de Minas Gerais" - }, - { - "author_name": "Matheus Pacheco de Andrade", - "author_inst": "Public Health Department of Florianopolis" - }, - { - "author_name": "Lucas Alexandre Pedebos", - "author_inst": "Public Health Department of Florianopolis" - }, - { - "author_name": "Ana Cristina Vidor", - "author_inst": "Public Health Department of Florianopolis" - }, - { - "author_name": "Roberto Zaina", - "author_inst": "Universidade Federal de Santa Catarina" - }, - { - "author_name": "Graziela de Luca Canto", - "author_inst": "Universidade Federal de Santa Catarina" - }, - { - "author_name": "Gustavo Medeiros de Araujo", - "author_inst": "Universidade Federal de Santa Catarina" - }, - { - "author_name": "Fernanda Vargas Amaral", - "author_inst": "Universidad de Malaga" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.01.20144188", "rel_title": "Differential COVID-19 case positivity in New York City neighborhoods: socioeconomic factors and mobility", @@ -1351031,6 +1351592,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.23.20132522", + "rel_title": "The advantages of the simplest pandemic models", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20132522", + "rel_abs": "As a pandemic of coronavirus spreads across the globe, people debate policies to mitigate its severity. Many complex, highly detailed models have been developed to help policy setters make better decisions. However, the basis of these models is unlikely to be understood by non-experts.\n\nWe describe the advantages of simple models for covid-19. We say a model is \"simple\" if its only parameter is the rate of contact between people in the population. This contact rate can vary over time, depending on choices by policy setters. Such models can be understood by a broad audience, and thus can be helpful in explaining the policy decisions to the public. They can be used to evaluate outcomes of different policy strategies. However, simple models have a disadvantage when dealing with inhomogeneous populations.\n\nTo augment the power of a simple model to evaluate complicated situations, we add what we call \"satellite\" equations that do not change the original model. For example, with the help of a satellite equation, one could know what his/her chance is of remaining uninfected through the end of epidemic. Satellite equations can model the effect of the epidemic on high-risk individuals, or death rates, or on nursing homes, and other isolated populations.\n\nTo compare simple models with complex models, we introduce our \"slightly complex\" Model J. We find the conclusions of simple and complex models can be quite similar. But, for each added complexity, a modeler may have to choose additional parameter values describing who will infect whom under what conditions, choices for which there is often little rationale but that can have a big impact on predictions. Our simulations suggest that the added complexity offers little predictive advantage.\n\nAuthor SummaryThere is a large variety of available data about the coronavirus pandemic, but we still lack data about some important factors. Who is likely to infect whom and under what conditions and how long after becoming infected? These factors are the essence of transmission dynamics. Two groups using identical complex models can be expected to make different predictions simply because they make different choices for such transmission parameters in the model. The audience has no way to choose between their predictions. We explain how simple models can be used to answer complex questions by adding what we call satellite equations, addressing questions involving age groups, death rates, and likelihood of transmission to nursing homes and to uninfected, isolated populations. Simple models are ideal for seeing what kinds of interventions are needed to achieve goals of policy setters.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sana Jahedi", + "author_inst": "University of New Brunswick" + }, + { + "author_name": "James Yorke", + "author_inst": "University of Maryland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.24.20138644", "rel_title": "Strong Correlation Between Prevalence of Severe Vitamin D Deficiency and Population Mortality Rate from COVID-19 in Europe", @@ -1351791,57 +1352375,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.28.20142000", - "rel_title": "Cluster analysis of epidemiological characteristic features of confirmed cases with the novel coronavirus (COVID-19) outside China: a descriptive study", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20142000", - "rel_abs": "BackgroundNovel coronavirus COVID-19 has caused significant global outbreaks outside China. Many countries have closed their borders with China and performed obligate protective procedures, however, this disease was still rising worldwide. In this report, we aim to identify transmission patterns from China to other countries, along with describing the disease control situation of countries.\n\nMethodsWe retrospectively collected information about infected cases with COVID-19 from WHO situation reports, official notification websites of health ministries and reliable local newspapers from each country. Descriptive and cluster analysis was performed to describe the transmission characteristics while the logistic regression test was used to estimate the risk factors for the occurrence of an infected individual with an unknown source.\n\nResultsA total of 446 infected cases were recorded from 24 countries outside China until 12 February 2020, with the number of reported infected cases were doubled every 3.08 {+/-} 0.35 days (range from 2.6 to 3.9). Besides the spread from China, the transmission was originated from sub-endemic countries (Japan, Thailand, Singapore, Malaysia, France, German). Out of 6 countries got occurrence of an infected individual with unknown source and possible potential factors contributed to this occurrence was a time of epidemic circulating, number of patients and number of clusters when the occurrence still has not happened, and notably, the unreported situation of Chinese tourists information.\n\nConclusionsThe situational reports of each country about COVID-19 should be more detailed mentioning the transmissions routes with keeping contact tracing of the unknown cases to increase the control of this disease.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Minh-Duc Nguyen-Tran", - "author_inst": "Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam" - }, - { - "author_name": "Ali Ahmed-Fouad Abozaid", - "author_inst": "Faculty of Medicine, Ain Shams University, Cairo 11843, Egypt" - }, - { - "author_name": "Luu Lam Thang Tai", - "author_inst": "Department of Emergency, City childrens hospital, Ho Chi Minh City, 700000, Vietnam" - }, - { - "author_name": "Le Huu Nhat Minh", - "author_inst": "Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam" - }, - { - "author_name": "Quang-Loc Le", - "author_inst": "Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam" - }, - { - "author_name": "Hoang-Dung Nguyen", - "author_inst": "Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam" - }, - { - "author_name": "Khanh-Linh Dao", - "author_inst": "Faculty of Medicine, Haiphong University of Medicine and Pharmacy, Hai Phong City , Vietnam." - }, - { - "author_name": "Huu-Hoai Le", - "author_inst": "Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam" - }, - { - "author_name": "Nguyen Tien Huy", - "author_inst": "Institute of Tropical Medicine, Nagasaki University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.29.20140111", "rel_title": "Cost-effectiveness of public health strategies for COVID-19 epidemic control in South Africa", @@ -1352833,6 +1353366,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.30.181297", + "rel_title": "If the link missed\uff1aCould inflammatory skin disorders with barrier dysfunction increase the risk of COVID-19?", + "rel_date": "2020-07-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.181297", + "rel_abs": "Since the end of 2019, COVID-19 pandemic caused by the SARS-CoV-2 emerged globally. The angiotensin-converting enzyme 2 (ACE2) on the cell surface is crucial for SARS-COV-2 entering into the cells. We use SARS-COV-2 pseudo virus and humanized ACE2 mice to mimic the possible transmitting of SARS-COV-2 through skin based on the data we found that skin ACE2 level is associated with skin pre-existing cutaneous conditions in human and mouse models and inflammatory skin disorders with barrier dysfunction increased the penetration of topical FITC conjugated spike protein into the skin. Our study indicated the possibility that the pre-existing cutaneous conditions could increase the risk for SARS-COV-2 infection.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC=\"FIGDIR/small/181297v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (33K):\norg.highwire.dtl.DTLVardef@14cef60org.highwire.dtl.DTLVardef@1f78c65org.highwire.dtl.DTLVardef@1224834org.highwire.dtl.DTLVardef@1b27475_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qiannan Xu", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Lihong Chen", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Li Zhang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Mengyan Hu", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Xiaopan Wang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Qi Yang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Yunchen Le", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Feng Xue", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Xia Li", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Jie Zheng", + "author_inst": "Shanghai Ruijin Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.06.24.20134288", "rel_title": "A retrospective study evaluating efficacy and safety of compassionate use of tocilizumab in 13 patients with severe-to-critically ill COVID-19: analysis of well-responding cases and rapidly-worsening cases after tocilizumab administration", @@ -1353753,61 +1354341,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.29.178343", - "rel_title": "Structure of the full SARS-CoV-2 RNA genome in infected cells", - "rel_date": "2020-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.178343", - "rel_abs": "SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on native RNA structures in SARS-CoV-2 and most putative regulatory sequences are functionally uncharacterized. Here we report secondary structure ensembles of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and the algorithm detection of RNA folding ensembles using expectation-maximization clustering (DREEM). Our results reveal previously undescribed alternative RNA conformations across the genome, including structures of the frameshift stimulating element (FSE), a major drug target, that are drastically different from prevailing in vitro population average models. Importantly, we find that this structural ensemble promotes frameshifting rates (~40%) similar to in vivo ribosome profiling studies and much higher than the canonical minimal FSE (~20%). Overall, our result highlight the value of studying RNA folding in its native, dynamic and cellular context. The genomic structures detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tammy C.T. Lan", - "author_inst": "Whitehead Institute for Biomedical Research" - }, - { - "author_name": "Matthew F. Allan", - "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology" - }, - { - "author_name": "Lauren Malsick", - "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University School of Medicine" - }, - { - "author_name": "Stuti Khandwala", - "author_inst": "Whitehead Institute for Biomedical Research" - }, - { - "author_name": "Sherry S.Y. Nyeo", - "author_inst": "Whitehead Institute for Biomedical Research" - }, - { - "author_name": "Yu Sun", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA" - }, - { - "author_name": "Junjie U. Guo", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA" - }, - { - "author_name": "Mark Bathe", - "author_inst": "Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology" - }, - { - "author_name": "Anthony Griffiths", - "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University School of Medicine" - }, - { - "author_name": "Silvi Rouskin", - "author_inst": "Whitehead Institute for Biomedical Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.30.180380", "rel_title": "A High Content Screen for Mucin-1-Reducing Compounds Identifies Fostamatinib as a Candidate for Rapid Repurposing for Acute Lung Injury during the COVID-19 pandemic", @@ -1354863,6 +1355396,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20140129", + "rel_title": "Assessment of a Diagnostic Strategy Based on Chest Computed Tomography in Patients Hospitalized for COVID-19 Pneumonia: an observational study", + "rel_date": "2020-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20140129", + "rel_abs": "ObjectivesTo assess the relevance of a diagnostic strategy for COVID-19 based on chest computed tomography (CT) in patients with hospitalization criteria.\n\nSettingObservational study with retrospective analysis in a French emergency department (ED).\n\nParticipants and interventionFrom March 3 to April 2, 2020, 385 adult patients presenting to the ED for suspected COVID-19 underwent an evaluation that included history, physical examination, blood tests, real-time reverse transcription-polymerase chain reaction (RT-PCR) and chest CT. When the time-interval between chest CT and RT-PCR assays was longer than 7 days, patients were excluded from the study. Only patients with hospitalization criteria were included. Diagnosis accuracy was assessed using the sensitivity and specificity of RT-PCR.\n\nOutcomesSensitivity and specificity of RT-PCR, chest CT (also accompanied by lymphopenia) were measured and were also analyzed by subgroups of age and sex.\n\nResultsAmong 377 included subjects, RT-PCR was positive in 36%, while chest CT was compatible with a COVID-19 diagnosis in 59%. In the population with positive RT-PCR, there were more men (55% vs 37%, p=0.015), a higher frequency of reticular and, or, interlobular septal thickening (53% vs 31%, p=0.02) as well as a higher frequency of bilateral lesion distribution (98% vs 86%, p=0.01) compared to the population with negative RT-PCR. The proportion of lymphopenia was higher in men vs women (47% vs 39%, p=0.03) and varies between patients >80 versus 50-80 and p<0.001).\n\nUsing CT as reference, RT-PCR obtained a sensitivity of 61%, specificity of 93%. There was a significant difference between CT and RT-PCR diagnosis performance (p<0.001). When CT was accompanied by lymphopenia, sensitivity and specificity of RT-PCR were respectively 71% and 94%. CT abnormalities and lymphopenia provided diagnosis in 29% of patients with negative PCR.\n\nConclusionsChest CT had a superior yield than RT-PCR in COVID-19 hospitalized patients, especially when accompanied by lymphopenia.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Marine Thieux", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + }, + { + "author_name": "Anne Charlotte Kalenderian", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Aurelie Chabrol", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Laurent Gendt", + "author_inst": "Medipole Hopital Mutualiste Eurofins CBM 69" + }, + { + "author_name": "Emma Giraudier", + "author_inst": "Lyon 2 University Masters Degree in Medical Translation and Scientific Writing" + }, + { + "author_name": "Herve Lelievre", + "author_inst": "Medipole Hopital Mutualiste Eurofins CBM 69" + }, + { + "author_name": "Samir Lounis", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Yves Mataix", + "author_inst": "Medipole Hopital Mutualiste Department of Medicine" + }, + { + "author_name": "Emeline Moderni", + "author_inst": "Lyon 2 University Masters Degree in Medical Translation and Scientific Writing" + }, + { + "author_name": "Laetitia Paradisi", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + }, + { + "author_name": "Guillaume Ranchon", + "author_inst": "Medipole Hopital Mutualiste Emergency Department" + }, + { + "author_name": "Carlos El Khoury", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.28.20141838", "rel_title": "SARS-CoV-2 serological testing using electrochemiluminescence reveals arapid onset of seroconversion in severe COVID-19 patients", @@ -1355855,49 +1356451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.24.20121905", - "rel_title": "The therapeutic effectiveness of Convalescent plasma therapy on treating COVID-19 patients residing in respiratory care units in hospitals in Baghdad, Iraq", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20121905", - "rel_abs": "ObjectivesThe current COVID-19 pandemic needs unconventional therapies to tackle the resulted high morbidity and mortality. Convalescent plasma is one of the therapeutic approaches that might be of benefit.\n\nMethodsForty nine early-stage critically-ill COVID-19 patients residing in RCU of three hospitals in Baghdad, Iraq were included, 21 received convalescent plasma while 28 did not receive, namely control group. Recovery or death, length of stay in hospital, and improvement in the clinical course of the disease were monitored clinically along with laboratory monitoring through SARS-CoV-2 RNA detection via PCR, and SARS-CoV-2 IgG and IgM serological monitoring.\n\nResultsPatients received convalescent plasma showed reduced duration of infection in about 4 days, and showed less death rate, 1/21 versus 8/28 in control group. In, addition, all of the patients received convalescent plasma showed high levels of SARS-CoV-2 IgG and IgM 3 days after plasma transfusion. Plasma from donors with high levels of SARS-CoV-2 IgG and donors with positive SRAS-CoV-2 IgM showed better therapeutic results than other donors.\n\nConclusionsConvalescent plasma therapy is an effective mode of therapy if donors with high level of SARS-Cov2 antibodies are selected and if recipients were at their early stage of critical illness, being no more than 3 days in RCU.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Anwar M. Rasheed", - "author_inst": "Baghdad-Alkarkh general Directorate of Health" - }, - { - "author_name": "Dhurgham F. Ftak", - "author_inst": "Baghdad-Alkarkh general Directorate of Health" - }, - { - "author_name": "Hashim A. Hashim", - "author_inst": "Alkarkh Hospital" - }, - { - "author_name": "Mohammed F. Maulood", - "author_inst": "Alforat hospital" - }, - { - "author_name": "Khulood K Kabah", - "author_inst": "Baghdad-Alkarkh general Directorate of Health" - }, - { - "author_name": "Yaqoob A. Almusawi", - "author_inst": "National Center of Blood Donation, Bab Madhim, Baghdad, Iraq" - }, - { - "author_name": "Ahmed S. Abdulamir", - "author_inst": "College of Medicine, Alnahrain University, Baghdad, Iraq" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.29.20142331", "rel_title": "SARS-CoV-2 seroprevalence in the municipality of Sao Paulo, Brazil, ten weeks after the first reported case", @@ -1356841,6 +1357394,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.06.27.20141689", + "rel_title": "Estimating the infection fatality risk of COVID-19 in New York City, March 1-May 16, 2020", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141689", + "rel_abs": "During March 1-May 16, 2020, 191,392 laboratory-confirmed COVID-19 cases were diagnosed and reported and 20,141 confirmed and probable COVID-19 deaths occurred among New York City (NYC) residents. We applied a network model-inference system developed to support the Citys pandemic response to estimate underlying SARS-CoV-2 infection rates. Based on these estimates, we further estimated the infection fatality risk (IFR) for 5 age groups (i.e. <25, 25-44, 45-64, 65-74, and 75+ years) and all ages overall, during March 1-May 16, 2020. We estimated an overall IFR of 1.45% (95% Credible Interval: 1.09-1.87%) in NYC. In particular, weekly IFR was estimated as high as 6.1% for 65-74 year-olds and 17.0% for 75+ year-olds. These results are based on more complete ascertainment of COVID-19-related deaths in NYC and thus likely more accurately reflect the true, higher burden of death due to COVID-19 than previously reported elsewhere. It is thus crucial that officials account for and closely monitor the infection rate and population health outcomes and enact prompt public health responses accordingly as the pandemic unfolds.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wan Yang", + "author_inst": "Columbia University" + }, + { + "author_name": "Sasikiran Kandula", + "author_inst": "Columbia University" + }, + { + "author_name": "Mary Huynh", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Sharon K Greene", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Gretchen Van Wye", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Wenhui Li", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Hiu Tai Chan", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Emily McGibbon", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Alice Yeung", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Don Olson", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Anne Fine", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.26.20131144", "rel_title": "The scale and dynamics of COVID-19 epidemics across Europe", @@ -1357501,45 +1358117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.27.20141754", - "rel_title": "Higher pharyngeal epithelial gene expression of Angiotensin-Converting Enzyme-2 in upper respiratory infection patients", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141754", - "rel_abs": "We analyzed the expression of ACE2 in pharyngeal epithelium and examined its relationship with clinical features and serological parameters in the upper respiratory infection (URI) patients. The expression of ACE2 were significantly higher in URI patients than in healthy controls individuals, and positively correlated with age and body temperature.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mingjiao Zhang", - "author_inst": "Department of Laboratory Medicine, The Third Affiliated Hospital, Southern Medical University" - }, - { - "author_name": "Lingyan Du", - "author_inst": "Department of Laboratory Medicine, The Third Affiliated Hospital, Southern Medical University" - }, - { - "author_name": "Oluwasijibomi Damola Faleti", - "author_inst": "Department of laboratory medicine, The Third Affiliated Hospital, Southern Medical University" - }, - { - "author_name": "Jing Huang", - "author_inst": "Department of laboratory medicine, The Third Affiliated Hospital, Southern Medical University" - }, - { - "author_name": "Gang Xiao", - "author_inst": "Department of laboratory medicine, The Third Affiliated Hospital, Southern Medical University" - }, - { - "author_name": "Xiaoming Lyu", - "author_inst": "The Third Affiliated Hospital, Southern Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.27.20105429", "rel_title": "Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review", @@ -1358315,6 +1358892,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20142281", + "rel_title": "Early Hemoglobin kinetics in response to ribavirin: Safety lesson learned from Hepatitis C to CoVID-19 therapy", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142281", + "rel_abs": "BackgroundRibavirin (RBV) is been used for SARS-CoV-2 infection. This drug is associated with a wide range of side effects, mainly anemia, so its use in patients with potential respiratory affectation could not be appropriate. The evidences of adverse events associated with RBV-use has mainly been derived in the context of hepatitis C (HCV) treatment, however the possible use of RBV in CoVID-19 patients could be limited to 14 days.\n\nMethodsLongitudinal study including HIV/HCV coinfected patients. We evaluate the hemoglobin dynamics and reductions as well as evaluate the development rate of anemia during the first 2 weeks of therapy in HCV infected patients.\n\nResults189 patients were included in the study. The median hemoglobin levels were 14.6 g/dL (IQR: 13.2-15.6 g/dL) and 13.5 g/dL (IQR: 12.3-14.5 g/dL) at weeks 1 and 2 of therapy, respectively. A cumulative number of 27 (14.2%) patients developed anemia (23 grade 1 [12.1%] and 4 grade 2 [2.1%]). We identify a baseline hemoglobin levels of 14 g/dL as the better cut-off to identify those patients with a high chance to develop anemia. Of the 132 patients with baseline hemoglobin level >14 g/dL, 8 developed anemia (6.1%) compared with 19 of 57 (33.3%) with hemoglobin levels lower than 14 g/dL (p < 0.001).\n\nConclusionsOur study shows valuable information about the early hemoglobin kinetic timing in patients on RBV-therapy, that could be useful to tailor CoVID-19 treatment if RBV use is considered.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Antonio Rivero-Juarez", + "author_inst": "IMIBIC" + }, + { + "author_name": "Mario Frias", + "author_inst": "IMIBIC" + }, + { + "author_name": "Isabel Machuca", + "author_inst": "IMIBIC" + }, + { + "author_name": "Marina Gallo", + "author_inst": "IMIBIC" + }, + { + "author_name": "Pedro Lopez-Lopez", + "author_inst": "IMIBIC" + }, + { + "author_name": "Angela Camacho", + "author_inst": "IMIBIC" + }, + { + "author_name": "Antonio Rivero", + "author_inst": "IMIBIC" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "toxicology" + }, { "rel_doi": "10.1101/2020.06.28.20141960", "rel_title": "Data presented by the UK government as lockdown was eased shows the transmission of COVID-19 had already increased.", @@ -1358855,61 +1359475,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.29.177238", - "rel_title": "Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline", - "rel_date": "2020-06-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.177238", - "rel_abs": "In order to explore nonsynonymous mutations and deletions in the spike (S) protein of SARS-CoV-2, we comprehensively analyzed 35,750 complete S protein gene sequences from across six continents and five climate zones around the world, as documented in the GISAID database as of June 24th, 2020. Through a custom Python-based pipeline for analyzing mutations, we identified 27,801 (77.77 % of spike sequences) mutated strains compared to Wuhan-Hu-1 strain. 84.40% of these strains had only single amino-acid (aa) substitution mutations, but an outlier strain from Bosnia and Herzegovina (EPI_ISL_463893) was found to possess six aa substitutions. The D614G variant of the major G clade was found to be predominant across circulating strains in all climates. We also identified 988 unique aa substitution mutations distributed across 660 positions within the spike protein, with eleven sites showing high variability - these sites had four types of aa variations at each position. Besides, 17 in-frame deletions at four major regions (three in N-terminal domain and one just downstream of the RBD) may have possible impact on attenuation. Moreover, the mutational frequency differed significantly (p= 0.003, Kruskal-Wallis test) among the SARS-CoV-2 strains worldwide. This study presents a fast and accurate pipeline for identifying nonsynonymous mutations and deletions from large dataset for any particular protein coding sequence and presents this S protein data as representative analysis. By using separate multi-sequence alignment with MAFFT, removing ambiguous sequences and in-frame stop codons, and utilizing pairwise alignment, this method can derive nonsynonymus mutations (Reference:Position:Strain). We believe this will aid in the surveillance of any proteins encoded by SARS-CoV-2, and will prove to be crucial in tracking the ever-increasing variation of many other divergent RNA viruses in the future.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "M. Shaminur Rahman", - "author_inst": "Department of Microbiology, University of Dhaka" - }, - { - "author_name": "Md. Rafiul Islam", - "author_inst": "University of Dhaka" - }, - { - "author_name": "M. Nazmul Hoque", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Agricultural University Gazipur-1706, Bangladesh" - }, - { - "author_name": "A. S. M. Rubayet Ul Alam", - "author_inst": "Department of Microbiology, University of Dhaka" - }, - { - "author_name": "Masuda Akther", - "author_inst": "Department of Microbiology, University of Dhaka" - }, - { - "author_name": "J. Akter Puspo", - "author_inst": "Department of Microbiology, University of Dhaka" - }, - { - "author_name": "Salma Akter", - "author_inst": "Department of Microbiology, University of Dhaka" - }, - { - "author_name": "Azraf Anwar", - "author_inst": "British Columbia University, Vancouver, Canada" - }, - { - "author_name": "Munawar Sultana", - "author_inst": "Department of Microbiology, University of Dhaka" - }, - { - "author_name": "Md. Anwar Hossain", - "author_inst": "University of Dhaka" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.06.27.20141671", "rel_title": "Estimating the state of the Covid-19 epidemic in France using a non-Markovian model", @@ -1359705,6 +1360270,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.26.20140616", + "rel_title": "The impact of SARS-CoV-2 transmission fear and COVID-19 pandemic on the mental health of patients with primary immunodeficiency disorders, severe asthma, and other high-risk groups", + "rel_date": "2020-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140616", + "rel_abs": "BackgroundThe adverse effects of COVID-19 pandemic on the mental health of high-risk group patients for morbidity and mortality and its impact on public health in the long term have not been clearly determined.\n\nObjectiveTo determine the level of COVID-19 related transmission fear and anxiety in healthcare workers and patients with primary immunodeficiency disorder (PID), severe asthma, and the ones with other comorbidities.\n\nMethodsThe healthcare workers and patients with PID, severe asthma (all patients receiving biological agent treatment), malignancy, cardiovascular disease, hypertension (90% of patients receiving ACEI or ARB therapy), diabetes mellitus (42 % of patients receiving DPP-4 inhibitor therapy) were included in the study. A total of 560 participants, 80 individuals in each group, were provided. The hospital anxiety and depression scale (HADS) and Fear of illness and virus evaluation (FIVE) scales were applied to the groups with face to face interview methods.\n\nResultsThe mean age was 49.30 {+/-} 13.74 years and 306 (55 %) were female. The FIVE Scale and HADS-A scale scores of health care workers were significantly higher than other groups scores (p = 0.001 and 0.006). The second-highest scores belonged to patients with PID. There was no significant difference between the groups for the HADS-D score (p=0.07). The lowest score in all scales was observed in patients with hypertension.\n\nConclusionsThis study demonstrated that in the pandemic process, patients with primary immunodeficiency, asthma patients, and other comorbid patients, especially healthcare workers, should be referred to the centers for the detection and treatment of mental health conditions.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Fatih Colkesen", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine," + }, + { + "author_name": "Oguzhan Kilincel", + "author_inst": "Department of Psychiatry, Sakarya Yenikent State Hospital" + }, + { + "author_name": "Mehmet Sozen", + "author_inst": "Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine" + }, + { + "author_name": "Eray Yildiz", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine" + }, + { + "author_name": "Sengul Beyaz", + "author_inst": "Division of Clinical Immunology and Allergy, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University" + }, + { + "author_name": "Fatma Colkesen", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Konya Training and Research Hospital" + }, + { + "author_name": "Gokhan Aytekin", + "author_inst": "Department of Clinical Immunology and Allergy, University of Health Sciences, Konya Training and Research Hospital" + }, + { + "author_name": "Mehmet Zahit Kocak", + "author_inst": "Department of Medical Oncology, Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Yakup Alsancak", + "author_inst": "Department of Cardiology , Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Murat Araz", + "author_inst": "Department of Medical Oncology, Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Sevket Arslan", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.25.20139907", "rel_title": "Teach, and teach and teach: does the average citizen use masks correctly during daily activities? Results from an observational study with more than 12,000 participants", @@ -1360377,37 +1361001,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.06.26.174698", - "rel_title": "A facile Q-RT-PCR assay for monitoring SARS-CoV-2 growth in cell culture", - "rel_date": "2020-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.174698", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the ongoing COVID-19 pandemic, has infected millions within just a few months and is continuing to spread around the globe causing immense respiratory disease and mortality. Assays to monitor SARS-CoV-2 growth depend on time-consuming and costly RNA extraction steps, hampering progress in basic research and drug development efforts. Here we developed a facile Q-RT-PCR assay that bypasses viral RNA extraction steps and can monitor SARS-CoV-2 replication kinetics from a small amount of cell culture supernatants. Using this assay, we screened the activities of a number of entry, SARS-CoV-2- and HIV-1-specific inhibitors in a proof of concept study. In line with previous studies which has shown that processing of the viral Spike protein by cellular proteases and endosomal fusion are required for entry, we found that E64D and apilimod potently decreased the amount of SARS-CoV-2 RNA in cell culture supernatants with minimal cytotoxicity. Surprisingly, we found that macropinocytosis inhibitor EIPA similarly decreased viral RNA in supernatants suggesting that entry may additionally be mediated by an alternative pathway. HIV-1-specific inhibitors nevirapine (an NNRTI), amprenavir (a protease inhibitor), and ALLINI-2 (an allosteric integrase inhibitor) modestly inhibited SARS-CoV-2 replication, albeit the IC50 values were much higher than that required for HIV-1. Taken together, this facile assay will undoubtedly expedite basic SARS-CoV-2 research, be amenable to mid-throughput screens to identify chemical inhibitors of SARS-CoV-2, and be applicable to a broad number of RNA and DNA viruses.\n\nImportanceSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the COVID-19 pandemic, has quickly become a major global health problem causing immense respiratory disease and social and economic disruptions. Conventional assays that monitor SARS-CoV-2 growth in cell culture rely on costly and time-consuming RNA extraction procedures, hampering progress in basic SARS-CoV-2 research and development of effective therapeutics. Here we developed a facile Q-RT-PCR assay to monitor SARS-CoV-2 growth in cell culture supernatants that does not necessitate RNA extraction, and is as accurate and sensitive as existing methods. In a proof-of-concept screen, we found that E64D, apilimod, EIPA and remdesivir can substantially impede SARS-Cov-2 replication providing novel insight into viral entry and replication mechanisms. This facile approach will undoubtedly expedite basic SARS-CoV-2 research, be amenable to screening platforms to identify therapeutics against SARS-CoV-2 and can be adapted to numerous other RNA and DNA viruses.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Christian Shema Mugisha", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Hung R. Vuong", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Maritza Puray-Chavez", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sebla Bulent Kutluay", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.24.170324", "rel_title": "Saliva sampling is an excellent option to increase the number of SARS CoV2 diagnostic tests in settings with supplies shortages", @@ -1361315,6 +1361908,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.23.20138222", + "rel_title": "Phylogenomics and phylodynamics of SARS-CoV-2 retrieved genomes from India", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138222", + "rel_abs": "The ongoing SARS-CoV-2 pandemic is one of the biggest outbreaks after the Spanish flu of 1918. Understanding the epidemiology of viral outbreaks is the first step towards vaccine development programs. This is the first phylodynamics study attempted on of SARS-CoV-2 genomes from India to infer its current evolution in the context of an ongoing pandemic. Out of 286 retrieved SARS-CoV-2 whole genomes from India, 138 haplotypes were generated and analyzed. Median-joining network was built to investigate the relatedness of SARS-CoV-2 haplotypes in India. The BDSIR package of BEAST2 was used to calculate the reproduction number (R0) and the infectious rate of the virus. Past and current population trend was investigated using the stamp date method in coalescent Bayesian skyline plot, implemented in BEAST2 and by exponential growth prior in BEAST 1.10.4. Median-joining network reveals two distinct ancestral clusters A and B showing genetic affinities with Wuhan outbreak sample. The network also illustrates the autochthonous development of isolates in a few instances. High basic reproduction number of SARS-nCoV-2 in India points towards the phase of active community transmission. The Bayesian skyline plot revel exponential rise in the effective population size (Ne) of Indian isolates from the first week of January to the first week of April 2020. More genome sequencing and analyses of the virus will be required in coming days to monitor COVID19 after the upliftment of lock down in India.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sameera Farah", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, Amravati-444604-India; Department " + }, + { + "author_name": "Ashwin Atkulwar", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, VMV Road, Amravati-444604-Indial; " + }, + { + "author_name": "Manas Ranjan Praharaj", + "author_inst": "National Institute of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana-500032-India." + }, + { + "author_name": "Raja Khan", + "author_inst": "Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P - 243122, India." + }, + { + "author_name": "Ravikumar Gandham", + "author_inst": "National Institute of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana-500032-India." + }, + { + "author_name": "Mumtaz Baig", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, Amravati-444604-India; Department " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.22.20134130", "rel_title": "Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island", @@ -1361871,25 +1362503,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.06.25.20139840", - "rel_title": "The effect of reopening policy on COVID-19 related cases and deaths", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20139840", - "rel_abs": "By May 29, 2020, all 50 states in the United States had reopened their economies to some extent after the coronavirus lockdown. Although there are many debates about whether states reopened their economies too early, no study has examined this effect quantitatively. This paper takes advantage of the daily cases, deaths, and test data at the state level, and uses the synthetic control method to address this question. I find that reopening the economy caused an additional 2000 deaths in the 6 states (Alabama, Colorado, Georgia, Mississippi, Tennessee, and Texas) that reopened before May 1st by three weeks after reopening. It also increased daily confirmed cases by 40%, 52%, and 53% after the first, second, and third week of reopening, respectively. Moreover, contrary to scientists prescription that expanding tests is a necessary condition for reopening, these states witnessed a decline in daily tests by 17%, 47%, and 31% after the first, second, and third week of reopening, respectively.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Qiyao Zhou", - "author_inst": "University of Maryland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.06.24.20139642", "rel_title": "Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): A retrospective observational analysis of 193 confirmed cases in Thailand", @@ -1362609,6 +1363222,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20139329", + "rel_title": "A Decision Analytic Approach for Social Distancing Policies During the COVID-19 Pandemic", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139329", + "rel_abs": "The COVID-19 pandemic has become a crucial public health issue in many countries including the United States. In the absence of the right vaccine strain and sufficient antiviral stockpiles on hand, non-pharmaceutical interventions have become valuable public health tools at the early stages of the pandemic and they are employed by many countries across the globe. These interventions are designed to increase social distancing between individuals to reduce the transmission of the virus and eventually dampen the burden on the healthcare system. The virus transmissibility is a function of the average number of contacts individuals have in their communities and it is highly dependent on population density and daily mobility patterns, along with other social factors. These show significant variation across the United States. In this article, we study the effectiveness of social distancing measures in communities with different population density. Specifically, first we show how the empirical estimation of reproduction number differs for two completely different states, thus the experience of the COVID-19 outbreak is drastically different, suggesting different outbreak growth rates in practice. Second, we develop an age-structured compartmental model for simulating the disease spread in order to demonstrate the variation in the observed outbreak characteristics. We find that early trigger and late trigger options present a trade-off between the peak magnitude and the overall death toll of the outbreak which may also vary across different populations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Zeynep Ertem", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ozgur Araz", + "author_inst": "University of Nebraska" + }, + { + "author_name": "Maytee Cruz-Aponte", + "author_inst": "University of Puerto Rico" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.25.20140384", "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in Six Sites in the United States, March 23-May 3, 2020", @@ -1363521,37 +1364161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.26.20140525", - "rel_title": "Hypoferremia predicts hospitalization and oxygen demand in COVID-19 patients", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140525", - "rel_abs": "BackgroundIron metabolism might play a crucial role in cytokine release syndrome in COVID-19 patients. Therefore we assessed iron metabolism markers in COVID-19 patients for their ability to predict disease severity.\n\nMethodsCOVID-19 patients referred to the Heidelberg University Hospital were retrospectively analyzed. Patients were divided into outpatients (cohort A, n=204), inpatients (cohort B, n=81), and outpatients later admitted to hospital because of health deterioration (cohort C, n=23).\n\nResultsIron metabolism parameters were severely altered in patients of cohort B and C compared to cohort A. In multivariate regression analysis including age, gender, CRP and iron-related parameters only serum iron and ferritin were significantly associated with hospitalization. ROC analysis revealed an AUC for serum iron of 0.894 and an iron concentration <6{micro}mol/l as the best cutoff-point predicting hospitalization with a sensitivity of 94.7% and a specificity of 67.9%. When stratifying inpatients in a low- and high oxygen demand group serum iron levels differed significantly between these two groups and showed a high negative correlation with the inflammatory parameters IL-6, procalcitonin, and CRP. Unexpectedly, serum iron levels poorly correlate with hepcidin.\n\nConclusionWe conclude that measurement of serum iron can help predicting the severity of COVID-19. The differences in serum iron availability observed between the low and high oxygen demand group suggest that disturbed iron metabolism likely plays a causal role in the pathophysiology leading to lung injury.\n\nKEY POINTSO_LIIron metabolism parameters are severely altered in COVID-19 patients.\nC_LIO_LIMeasurement of serum iron can help predicting the severity of COVID-19.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Theresa Hippchen", - "author_inst": "Department of Internal Medicine IV, University Hospital Heidelberg" - }, - { - "author_name": "Sandro Altamura", - "author_inst": "Pediatric Oncology, Hematology & Immunology, University Hospital Heidelberg" - }, - { - "author_name": "Martina U. Muckenthaler", - "author_inst": "Pediatric Oncology, Hematology & Immunology, University Hospital Heidelberg" - }, - { - "author_name": "Uta Merle", - "author_inst": "Department of Internal Medicine IV, University Hospital Heidelberg" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.26.20140590", "rel_title": "A Metapopulation Network Model for the Spreading of SARS-CoV-2: Case Study for Ireland", @@ -1364299,6 +1364908,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20138982", + "rel_title": "Modeling the Covid-19 Pandemic Response of the US States", + "rel_date": "2020-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138982", + "rel_abs": "BackgroundThe United States of America (USA) has been the country worst affected, in absolute terms, by the Covid-19 pandemic. The country comprises 50 states under a federal system. The impact of the pandemic has resulted in different responses at the state level, which are driven by differing intervention policies, demographics, connectedness and other factors. Understanding the dynamics of the Covid-19 pandemic at the state level is essential in predicting its future evolution.\n\nObjectiveOur objective is to identify and characterize multiple waves of the pandemic by analyzing the reported infected population curve in each of the 50 US states. Based on the intensity of the waves, characterized by declining, stationary, or increasing strengths, each states response can be inferred and quantified.\n\nMethodsWe apply a recently proposed multiple-wave model to fit the infected population data for each state in USA, and use the proposed Pandemic Response Index to quantify their response to the Covid-19 pandemic.\n\nResultsWe have analyzed reported infected cases from each one of the 50 USA states and the District of Columbia, based on the multiple-wave model, and present the relevant parameters. Multiple waves have been identified and this model is found to describe the data better. Each of the states can be classified into one of three distinct classes characterized by declining, increasing, or stationary strength of the waves following the initial one. The effectiveness of intervention measures can be inferred by the peak intensities of the waves, and states with similar population characteristics can be directly compared. We estimate how much lower the number of infections might have been, if early and strict intervention measures had been imposed to stop the disease spread at the first wave, as was the case for certain states. Based on our models results, we compute the value of the Pandemic Response Index, a recently introduced metric for quantifying in an objective manner the response to the pandemic.\n\nConclusionsOur results reveal a series of epidemic waves, characterizing USAs pandemic response at the state level, and also infer to what extent the imposition of early intervention measures could have had on the spread and impact of the disease. As of June 11, 2020, only 19 states and the District of Columbia (40% of the total) clearly exhibit declining trends in the numbers of reported infected cases, while 13 states exhibit stationary and 18 states increasing trends in the numbers of reported cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Georgios Neofotistos", + "author_inst": "Institute for Applied Computational Science (IACS), John A. Paulson School of Engineering and Applied Sciences, Harvard University" + }, + { + "author_name": "Efthimios Kaxiras", + "author_inst": "Institute for Applied Computational Science (IACS), John A. Paulson School of Engineering and Applied Sciences, Harvard University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20139196", "rel_title": "How Many Lives Has Lockdown Saved in the UK?", @@ -1364730,57 +1365362,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.24.150326", - "rel_title": "Antiviral Drug Screen of Kinase inhibitors Identifies Cellular Signaling Pathways Critical for SARS-CoV-2 Replication", - "rel_date": "2020-06-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.150326", - "rel_abs": "Emergence of a highly contagious novel coronavirus, SARS-CoV-2 that causes COVID-19, has precipitated the current global health crisis with over 479,000 deaths and more than 9.3 million confirmed cases. Currently, our knowledge of the mechanisms of COVID-19 disease pathogenesis is very limited which has hampered attempts to develop targeted antiviral strategies. Therefore, we urgently need an effective therapy for this unmet medical need. Viruses hijack and dysregulate cellular machineries in order for them to replicate and infect more cells. Thus, identifying and targeting dysregulated signaling pathways that have been taken over by viruses is one strategy for developing an effective antiviral therapy. We have developed a high-throughput drug screening system to identify potential antiviral drugs targeting SARS-CoV-2. We utilized a small molecule library of 430 protein kinase inhibitors, which are in various stages of clinical trials. Most of the tested kinase antagonists are ATP competitive inhibitors, a class of nucleoside analogs, which have been shown to have potent antiviral activity. From the primary screen, we have identified 34 compounds capable of inhibiting viral cytopathic effect in epithelial cells. Network of drug and protein relations showed that these compounds specifically targeted a limited number of cellular kinases. More importantly, we have identified mTOR-PI3K-AKT, ABL-BCR/MAPK, and DNA-Damage Response (DDR) pathways as key cellular signaling pathways critical for SARS-CoV-2 infection. Subsequently, a secondary screen confirmed compounds such as Berzosertib (VE-822), Vistusertib (AZD2014), and Nilotinib with anti SARS-CoV-2 activity. Finally, we found that Berzosertib, an ATR kinase inhibitor in the DDR pathway, demonstrated potent antiviral activity in a human epithelial cell line and human induced pluripotent stem cell (hIPSC)-derived cardiomyocytes. These inhibitors are already in clinical trials of phase 2 or 3 for cancer treatment, and can be repurposed as promising drug candidates for a host-directed therapy of SARS-CoV-2 infection. In conclusion, we have identified small molecule inhibitors exhibiting anti SARS-CoV-2 activity by blocking key cellular kinases, which gives insight on important mechanism of host-pathogen interaction. These compounds can be further evaluated for the treatment of COVID-19 patients following additional in vivo safety and efficacy studies.\n\nDisclosuresNone declared.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Gustavo Garcia Jr.", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Arun Sharma", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Arunachalam Ramaiah", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Chandani Sen", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Donald Kohn", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Brigitte Gomperts", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Clive N Svendsen", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Robert D Damoiseaux", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Vaithilingaraja Arumugaswami", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.24.170332", "rel_title": "Comparison of 12 molecular detection assays for SARS-CoV-2", @@ -1365940,6 +1366521,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.24.168534", + "rel_title": "Lung expression of genes encoding SARS-CoV-2 cell entry molecules and antiviral restriction factors: interindividual differences are associated with age and germline variants", + "rel_date": "2020-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.168534", + "rel_abs": "Germline variants in genes involved in SARS-CoV-2 cell entry (i.e. ACE2 and TMPRSS2) may influence the susceptibility to infection, as may polymorphisms in genes involved in the innate host response to viruses (e.g. APOBEC3 family). We searched for polymorphisms acting, in lung tissue, as expression quantitative trait loci (eQTLs) for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. No significant eQTLs were identified for ACE2 and TMPRSS2 genes, whose expression levels did not associate with either sex or age of the 408 patients whose non-diseased lung tissue was analyzed. Instead, we identified seven cis-eQTLs (FDR<0.05) for APOBEC3D and APOBEC3G (rs139296, rs9611092, rs139331, rs8177832, rs17537581, rs61362448, and rs738469). The genetic control of the expression of APOBEC3 genes, which encode enzymes that interfere with virus replication, may explain interindividual differences in risk or severity of viral infections. Future studies should investigate the role of host genetics in COVID-19 patients using a genome-wide approach, to identify other genes whose expression levels are associated with susceptibility to SARS-CoV-2 infection or COVID-19 severity.\n\nAuthor summaryIdentification of expression quantitative trait loci (eQTLs) has become commonplace in functional studies on the role of individual genetic variants in susceptibility to diseases. In COVID-19, it has been proposed that individual variants in SARS-CoV-2 cell entry and innate host response genes may influence the susceptibility to infection. We searched for polymorphisms acting, in non-diseased lung tissue of 408 patients, as eQTLs for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. Seven cis-eQTLs were detected for APOBEC3D and APOBEC3G genes, which encode enzymes that interfere with virus replication. No significant eQTLs were identified for ACE2 and TMPRSS2 genes. Therefore, the identified eQTLs may represent candidate loci modulating interindividual differences in risk or severity of SARS-CoV-2 virus infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chiara E. Cotroneo", + "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" + }, + { + "author_name": "Nunzia Mangano", + "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" + }, + { + "author_name": "Tommaso A. Dragani", + "author_inst": "Fondazione IRCCS Istituto Nazionale Tumori" + }, + { + "author_name": "Francesca Colombo", + "author_inst": "Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.06.23.167791", "rel_title": "N-glycosylation network construction and analysis to modify glycans on the spike S glycoprotein of SARS-CoV-2.", @@ -1366496,77 +1367108,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.24.20138875", - "rel_title": "Seroprevalence of SARS-CoV-2 IgG significantly varies with age: results from a mass population screening (SARS-2-SCREEN-CdA).", - "rel_date": "2020-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138875", - "rel_abs": "ObjectivesCastiglione DAdda is one of the municipalities more precociously and severely affected by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) epidemic in Lombardy. With our study we aimed to understand the diffusion of the infection by mass seroprevalence screening.\n\nMethodsWe searched for SARS-CoV-2 IgGs in the entire voluntary population using lateral flow immune-cromatographic tests on capillary blood (rapid tests). We then performed chemioluminescent serological assays (CLIA) and naso-pharyngeal swabs in a randomized representative sample of 562 subjects and in every subject with a positive rapid test.\n\nResultsBased on CLIA serologies on the representative random sample (509 subjects), we estimated a 23% IgG seroprevalence. We also found a strong correlation between age and prevalence, with the elderly showing the highest probability of a positive serological test.\n\nConclusionsIn an area of unrestricted viral circulation less than one-fourth of the population tested positive for SARS-CoV-2 IgG. Seroprevalence increased with increasing age, possibly suggesting differences in susceptibility to the infection.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gabriele Pagani", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Federico Conti", - "author_inst": "Universita' Degli Studi Di Milano" - }, - { - "author_name": "Andrea Giacomelli", - "author_inst": "ASST-FBF-Sacco, University of Milan" - }, - { - "author_name": "Dario Bernacchia", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Rossana Rondanin", - "author_inst": "Medispa" - }, - { - "author_name": "Andrea Prina", - "author_inst": "Medispa" - }, - { - "author_name": "Vittore Scolari", - "author_inst": "Institut Curie - Sorbonne Universite'" - }, - { - "author_name": "Cecilia Eugenia Gandolfi", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Silvana Castaldi", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Giuseppe Marano", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Cosimo Ottomano", - "author_inst": "Synlab Italia" - }, - { - "author_name": "Patrizia Boracchi", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Elia Mario Biganzoli", - "author_inst": "Universita' degli Studi di Milano" - }, - { - "author_name": "Massimo Galli", - "author_inst": "Universita' degli Studi di Milano" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.23.20138693", "rel_title": "Forecasting COVID-19 and Analyzing the Effect of Government Interventions", @@ -1367165,6 +1367706,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20117747", + "rel_title": "SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20117747", + "rel_abs": "Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we use longitudinal wastewater analysis to track SARS-CoV-2 dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. Viral titers in wastewater increased exponentially from mid-March to mid-April, after which they began to decline. Viral titers in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4-10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral titers as a convolution of back-dated new clinical cases with the viral shedding function of an individual. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. Finally, we found that wastewater viral titers at the neighborhood level correlate better with demographic variables than with population size. This work suggests that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and may shed light on infection characteristics that are difficult to capture in clinical investigations, such as early viral shedding dynamics.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Fuqing Wu", + "author_inst": "MIT" + }, + { + "author_name": "Amy Xiao", + "author_inst": "MIT" + }, + { + "author_name": "Jianbo Zhang", + "author_inst": "MIT" + }, + { + "author_name": "Katya Moniz", + "author_inst": "MIT" + }, + { + "author_name": "Noriko Endo", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Federica Armas", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Richard Bonneau", + "author_inst": "New York University" + }, + { + "author_name": "Megan A Brown", + "author_inst": "New York University" + }, + { + "author_name": "Mary Bushman", + "author_inst": "Harvard University" + }, + { + "author_name": "Peter R Chai", + "author_inst": "Harvard University" + }, + { + "author_name": "Claire Duvallet", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Timothy B Erickson", + "author_inst": "Harvard University" + }, + { + "author_name": "Katelyn Foppe", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Newsha Ghaeli", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Xiaoqiong Gu", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "William P Hanage", + "author_inst": "Harvard University" + }, + { + "author_name": "Katherine H Huang", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Wei Lin Lee", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Mariana Matus", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Kyle A McElroy", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Jonathan Nagler", + "author_inst": "Center for Data Science NYU" + }, + { + "author_name": "Steven F Rhode", + "author_inst": "Massachusetts Water Resources Authority, Boston, MA" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Harvard University" + }, + { + "author_name": "Joshua A Tucker", + "author_inst": "Center for Data Science NYU" + }, + { + "author_name": "Stefan Wuertz", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Shijie Zhao", + "author_inst": "MIT" + }, + { + "author_name": "Janelle Thompson", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Eric J Alm", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.22.20132910", "rel_title": "Insufficient social distancing may be related to a future COVID-19 outbreak in Ijui-Brazil: Predictions of further social interventions.", @@ -1367753,37 +1368421,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.20.20136382", - "rel_title": "Behavioral changes before lockdown, and decreased retail and recreation mobility during lockdown, contributed most to the successful control of the COVID-19 epidemic in 35 Western countries", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20136382", - "rel_abs": "The COVID-19 pandemic has prompted a lockdown in many countries to control the exponential spread of the SARS-CoV-2 virus (1, 2). This resulted in curbing the epidemic by reducing the time-varying basic reproduction number (Rt) to below one (3, 4). Governments are looking for evidence to balance the demand of their citizens to ease some of the restriction, against the fear of a second peak in infections. More details on the specific circumstances that promote exponential spread (i.e. Rt > 1) and the measures that contributed most to a reduction in Rt are needed. Here we show that in 33 of 35 Western countries (32 European, plus Israel, USA and Canada), Rt fell to around or below one during lockdown (March - May 2020). One third of the effect happened already on average 6 days before the lockdown, with lockdown itself causing another major drop in transmission. Country-wide compulsory usage of masks was implemented only in Slovakia 10 days into lockdown, and on its own reduced transmission by half. During lockdown, decreased mobility in retail and recreation was an independent predictor of lower Rt during lockdown, while changes in other types of mobility were not. These results are consistent with anecdotal evidence that large recreational gatherings are super-spreading events (5, 6), and may even suggest that infections during day-to-day contact at work are not sufficient to spark exponential growth. Our data suggest measures that will contribute to avoiding a second peak include a tight control on circumstances that facilitate massive spread such as large gatherings especially indoors, physical distancing, and mask use.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Koen Deforche", - "author_inst": "Emweb bv" - }, - { - "author_name": "Jurgen Vercauteren", - "author_inst": "KULeuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for " - }, - { - "author_name": "Viktor M\u00fcller", - "author_inst": "Insitute of Biology, E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, Hungary" - }, - { - "author_name": "Anne-Mieke Vandamme", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.21.20136705", "rel_title": "Healthcare workers experiences of working on the frontline and views about support during COVID-19 and comparable pandemics: A rapid review and meta-synthesis", @@ -1368531,6 +1369168,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.21.20136937", + "rel_title": "A Statistical and Dynamical Model for Forecasting COVID-19 Deaths based on a Hybrid Asymmetric Gaussian and SEIR Construct", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136937", + "rel_abs": "BackgroundThe limitations of forecasting (real-time statistical) and predictive (dynamic epidemiological) models have become apparent as COVID-19 has progressed from a rapid exponential ascent to a slower decent, which is dependent on unknowable parameters such as extent of social distancing and easing. We present a means to optimize a forecasting model by functionalizing our previously reported Asymmetric Gaussian model with SEIR-like parameters. Conversely, SEIR models can be adapted to better incorporate real-time data.\n\nMethodsOur previously reported asymmetric Gaussian model was shown to greatly improve on forecasting accuracy relative to use of symmetric functions, such as Gaussian and error functions for death rates and cumulative deaths, respectively. However, the reported asymmetric Gaussian implementation, which fitted well to the ascent and much of the recovery side of the real death rate data, was not agile enough to respond to changing social behavior that is resulting in persistence of infections and deaths in the later stage of recovery. We have introduced a time-dependent {sigma}(t) parameter to account for transmission rate variability due to the effects of behavioral changes such as social distancing and subsequent social easing. The {sigma}(t) parameter is analogous to the basic reproduction number R0 (infection factor) that is evidently not a constant during the progression of COVID-19 for a particular population. The popularly used SEIR model and its many variants are also incorporating a time dependent R0(t) to better describe the effects of social distancing and social easing to improve predictive capability when extrapolating from real-time data.\n\nResultsComparisons are given for the previously reported Asymmetric Gaussian model and to the revised, what we call, SEIR Gaussian model. We also have developed an analogous model based on R0(t) that we call SEIR Statistical model to show the correspondence that can be attained. It is shown that these two models can replicate each other and therefore provide similar forecasts based on fitting to the same real-time data. We show the results for reported U.S. death rates up to June 12, 2020 at which time the cumulative death count was 113,820. The forecasted cumulative deaths for these two models and compared to the University of Washington (UW) IHME model are 140,440, 139,272, and 149,690 (for 8/4/20) and 147,819, 148, 912, and 201,129 (for 10/1/20), respectively. We also show how the SEIR asymmetric Gaussian model can also account for various scenarios of social distancing, social easing, and even re-bound outbreaks where the death and case rates begin climbing again.\n\nConclusionsForecasting models, based on real-time data, are essential for guiding policy and human behavior to minimize the deadly impact of COVID-19 while balancing the need to socialize and energize the economy. It is becoming clear that changing social behavior from isolation to easing requires models that can adapt to the changing transmission rate in order to more accurately forecast death and case rates. We believe our asymmetric Gaussian approach has advantages over modified SEIR models in offering simpler governing equations that are dependent on fewer variables.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jack A. Syage", + "author_inst": "ImmunogenX" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.21.20136929", "rel_title": "Derivation and Validation of Clinical Prediction Rule for COVID-19 Mortality in Ontario, Canada", @@ -1369143,61 +1369799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.22.20137380", - "rel_title": "The timing and effectiveness of implementing mild interventions of COVID-19 in large industrial cities", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137380", - "rel_abs": "The outbreak of novel coronavirus disease (COVID-19) has spread around the world since it was detected in December 2019. The Chinese government executed a series of interventions to curb the pandemic. The \"battle\" against COVID-19 in Shenzhen, China is valuable because populated industrial cities are the epic centres of COVID-19 in many regions. We made use of synthetic control methods to create a reference population matching specific characteristics of Shenzhen. With both the synthetic and observed data, we introduced an epidemic compartmental model to compare the spread of COVID-19 between Shenzhen and its counterpart regions in the United States that didnt implement interventions for policy evaluation. Once the effects of policy interventions adopted in Shenzhen were estimated, the delay effects of those interventions were referred to provide the further control degree of interventions. Thus, the hypothetical epidemic situations in Shenzhen were inferred by using time-varying reproduction numbers in the proposed SIHR (Susceptible, Infectious, Hospitalized, Removed) model and considering if the interventions were delayed by 0 day to 5 days. The expected cumulative confirmed cases would be 1546, which is 5.75 times of the observed cumulative confirmed cases of 269 in Shenzhen on February 3, 2020, based on the data from the counterpart counties (mainly from Broward, New York, Santa Clara, Pinellas, and Westchester) in the United States. If the interventions were delayed by 5 days from the day when the interventions started, the expected cumulative confirmed cases of COVID-19 in Shenzhen on February 3, 2020 would be 676 with 95% credible interval (303,1959). Early implementation of mild interventions can subdue the epidemic of COVID-19. The later the interventions were implemented, the more severe the epidemic was in the hard-hit areas. Mild interventions are less damaging to the society but can be effective when implemented early.\n\nAMS 2000 O_SCPLOWSUBJECTC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWCLASSIFICATIONSC_SCPLOW: Primary 00K00, 00K01; secondary 00K02.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ting Tian", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Wenxiang Luo", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Jianbin Tan", - "author_inst": "Sun Yat-Sen University" - }, - { - "author_name": "Yukang Jiang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Minqiong Chen", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Wenliang Pan", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Songpan Yang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Jiashu Zhao", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xueqin Wang", - "author_inst": "University of Science and Technology of China" - }, - { - "author_name": "Heping Zhang", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.21.20134882", "rel_title": "3d Virtual Patho-Histology of Lung Tissue from Covid-19 Patients based on Phase Contrast X-ray Tomography", @@ -1370009,6 +1370610,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.23.20137596", + "rel_title": "Platelets can contain SARS-CoV-2 RNA and are hyperactivated in COVID-19", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137596", + "rel_abs": "RationaleIn addition to the overwhelming lung inflammation that prevails in COVID-19, hypercoagulation and thrombosis contribute to the lethality of subjects infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Platelets are chiefly implicated in thrombosis. Moreover, they can interact with viruses and are an important source of inflammatory mediators. While a lower platelet count is associated with severity and mortality, little is known about platelet function during COVID-19.\n\nObjectiveTo evaluate the contribution of platelets to inflammation and thrombosis in COVID-19 patients.\n\nMethods and ResultsWe document the presence of SARS-CoV-2 RNA in platelets of COVID-19 patients. Exhaustive assessment of cytokines in plasma and in platelets revealed the modulation of platelet-associated cytokine levels in COVID-19, pointing to a direct contribution of platelets to the plasmatic cytokine load. Moreover, we demonstrate that platelets release their alpha- and dense-granule contents and phosphatidylserine-exposing extracellular vesicles. Functionally, platelets were hyperactivated in COVID-19 subjects, with aggregation occurring at suboptimal thrombin concentrations. Furthermore, platelets adhered more efficiently onto collagen-coated surfaces under flow conditions.\n\nConclusionsThese data suggest that platelets could participate in the dissemination of SARS-CoV-2 and in the overwhelming thrombo-inflammation observed in COVID-19. Thus, blockade of platelet activation pathways may improve outcomes in this disease.\n\nKEY POINTSPlatelets are a source of inflammatory cytokines and degranulate in COVID-19 Platelets contain SARS-CoV-2 RNA molecules and are prone to activation in COVID-19\n\nSubject termsInfectious diseases/Emerging infectious diseases, SARS-CoV-2, COVID-19, Hematology, Platelets", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Younes Zaid", + "author_inst": "Cheikh Zaid Hospital; Mohammed V University" + }, + { + "author_name": "Florian Puhm", + "author_inst": "Universite Laval" + }, + { + "author_name": "Isabelle Allaeys", + "author_inst": "Universite Laval" + }, + { + "author_name": "Abdallah Naya", + "author_inst": "Hassan II University" + }, + { + "author_name": "Mounia Oudghiri", + "author_inst": "Hassan II University" + }, + { + "author_name": "Loubna Khalki", + "author_inst": "Mohammed VI University of Health Sciences (UM6SS)" + }, + { + "author_name": "Youness Limami", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Nabil Zaid", + "author_inst": "Mohammed V University" + }, + { + "author_name": "Khalid Sadki", + "author_inst": "Mohammed V University" + }, + { + "author_name": "Rafiqua Ben El Haj", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Wissal Maher", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Lamiae Belayachi", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Bouchra Belefquih", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Amina Benouda", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Amine Cheikh", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Yahia Cherrah", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Louis Flamand", + "author_inst": "Universite Laval" + }, + { + "author_name": "Fadila Guessous", + "author_inst": "Mohammed VI University of Health Sciences (UM6SS); University of Virginia" + }, + { + "author_name": "Eric Boilard", + "author_inst": "Universite Laval" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.23.20137521", "rel_title": "SARS CoV-2 Serosurvey in Addis Ababa, Ethiopia", @@ -1370717,81 +1371409,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.23.167098", - "rel_title": "RAAS blockade, kidney disease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells", - "rel_date": "2020-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.23.167098", - "rel_abs": "SARS-CoV-2, the coronavirus that causes COVID-19, binds to angiotensin-converting enzyme 2 (ACE2) on human cells. Beyond the lung, COVID-19 impacts diverse tissues including the kidney. ACE2 is a key member of the Renin-Angiotensin-Aldosterone System (RAAS) which regulates blood pressure, largely through its effects on the kidney. RAAS blockers such as ACE inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs) are widely used therapies for hypertension, cardiovascular and chronic kidney diseases, and therefore, there is intense interest in their effect on ACE2 expression and its implications for SARS-CoV-2 pathogenicity. Here, we analyzed single-cell and single-nucleus RNA-seq of human kidney to interrogate the association of ACEi/ARB use with ACE2 expression in specific cell types. First, we performed an integrated analysis aggregating 176,421 cells across 49 donors, 8 studies and 8 centers, and adjusting for sex, age, donor and center effects, to assess the relationship of ACE2 with age and sex at baseline. We observed a statistically significant increase in ACE2 expression in tubular epithelial cells of the thin loop of Henle (tLoH) in males relative to females at younger ages, the trend reversing, and losing significance with older ages. ACE2 expression in tLoH increases with age in females, with an opposite, weak effect in males. In an independent cohort, we detected a statistically significant increase in ACE2 expression with ACEi/ARB use in epithelial cells of the proximal tubule and thick ascending limb, and endothelial cells, but the association was confounded in this small cohort by the underlying disease. Our study illuminates the dynamics of ACE2 expression in specific kidney cells, with implications for SARS-CoV-2 entry and pathogenicity.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Ayshwarya Subramanian", - "author_inst": "Broad Institute" - }, - { - "author_name": "Katherine Vernon", - "author_inst": "Broad Institute" - }, - { - "author_name": "Michal Slyper", - "author_inst": "Broad Institute" - }, - { - "author_name": "Julia Waldman", - "author_inst": "Broad Institute" - }, - { - "author_name": "Malte D Luecken", - "author_inst": "Helmholtz Zentrum Munchen" - }, - { - "author_name": "Kirk Gosik", - "author_inst": "Broad Institute" - }, - { - "author_name": "Dan Dubinsky", - "author_inst": "Broad Institute" - }, - { - "author_name": "Michael S Cuoco", - "author_inst": "Broad Institute" - }, - { - "author_name": "Jason Purnell", - "author_inst": "Broad Institute" - }, - { - "author_name": "Lan Nguyen", - "author_inst": "Broad Institute" - }, - { - "author_name": "Danielle Dionne", - "author_inst": "Broad Institute" - }, - { - "author_name": "Orit Rozenblatt-Rosen", - "author_inst": "Broad Institute" - }, - { - "author_name": "- Human Cell Atlas Lung Biological Network", - "author_inst": "-" - }, - { - "author_name": "Aviv Regev", - "author_inst": "Broad Institute" - }, - { - "author_name": "Anna Greka", - "author_inst": "Broad Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.23.167064", "rel_title": "SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography", @@ -1371587,6 +1372204,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.20.20134387", + "rel_title": "A systematic review and meta-analysis reveals long and dispersive incubation period of COVID-19", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20134387", + "rel_abs": "BackgroundThe incubation period of SARS-CoV-2 remains uncertain, which has important implications for estimating transmission potential, forecasting epidemic trends, and decision-making in prevention and control.\n\nPurposeTo estimate the central tendency and dispersion for incubation period of COVID-19 and, in turn, assess the effect of a certain length of quarantine for close contacts in active monitoring.\n\nData SourcesPubMed, Embase, medRxiv, bioRxiv, and arXiv, searched up to April 26, 2020\n\nStudy SelectionCOVID-19 studies that described either individual-level incubation period data or summarized statistics for central tendency and dispersion measures of incubation period were recruited.\n\nData ExtractionFrom each recruited study, either individual-level incubation period data or summarized statistics for central tendency and dispersion measures were extracted, as well as population characteristics including sample size, average age, and male proportion.\n\nData SynthesisFifty-six studies encompassing 4 095 cases were included in this meta-analysis. The estimated median incubation period for general transmissions was 5.8 days [95% confidence interval (95%CI), 5.3 to 6.2 d]. Median and dispersion were higher for SARS-CoV-2 incubation compared to other viral respiratory infections. Furthermore, about 20 in 10 000 contacts in active monitoring would develop symptoms after 14 days, or below 1 in 10 000 for young-age infections or asymptomatic transmissions.\n\nLimitationSmall sample sizes for subgroups; some data were possibly used repeatedly in different studies; limited studies for outside mainland China; non-negligible intra-study heterogeneity.\n\nConclusionThe long, dispersive incubation period of SARS-CoV-2 contributes to the global spread of COVID-19. Yet, a 14-day quarantine period is sufficient to trace and identify symptomatic infections, which while could be justified according to a better understanding of the crucial parameters.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yongyue Wei", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Liangmin Wei", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yihan Liu", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Lihong Huang", + "author_inst": "Zhongshan Hospital Fudan University" + }, + { + "author_name": "Sipeng Shen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Ruyang Zhang", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Jiajin Chen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yang Zhao", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Hongbing Shen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Feng Chen", + "author_inst": "Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.18.20132571", "rel_title": "Transcriptomic profiling of disease severity in patients with COVID-19 reveals role of blood clotting and vasculature related genes", @@ -1372047,41 +1372719,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.20.20134817", - "rel_title": "Type and frequency of ocular and other known symptoms experienced by people who self diagnosed as suffering from COVID-19 in the UK", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20134817", - "rel_abs": "BackgroundRecent literature suggests that ocular manifestations present in people suffering from COVID-19. However, the prevalence and the type of ocular symptoms varies substantially, and most studies report retrospective data from patients suffering from more serious versions of the disease. Little is known of exactly which ocular symptoms manifest in people with milder forms of COVID-19.\n\nMethodsAn online questionnaire obtained self-report data from people in the community, who reported to be inflicted with COVID-19. The type and frequency of different symptoms suffered during COVID-19 were obtained. Details of any pre-existing ocular conditions and the duration of symptoms of COVID-19 were ascertained.\n\nResultsData from 132 participants showed that the four most reported COVID-19 symptoms were Dry Cough (63%), Fever (67%), Fatigue (83%), and loss of Smell/Taste (63%). 56% of the participants reported to having experienced an eye symptom, 46% reported to having a new or different eye symptom compared to pre-COVID-19 state. Three ocular symptoms (watery eyes, sore eyes, sensitivity to light) were significantly different from Pre-COVID-19 state (p<0.05). Logistic regression showed a significant association of eye symptoms with Fever (p=0.035).\n\nConclusionNearly half of the sample of people studied experienced ocular symptoms. The significant ocular symptoms, indicative of viral conjunctivitis, might have been missed in patients with more serious manifestations of the disease. It is also important to differentiate between the types of ocular manifestation, as symptoms of bacterial conjunctivitis (i.e. mucous discharge, gritty eyes) were not significant. Possible mechanisms for SARS-CoV-2 infection within the eye are discussed.\n\nKey messageTo date, there are no studies on ocular symptoms experienced by people who self-reported as suffering from mild case of COVID-19. In the absence of population -wide testing in the UK, our study shows that nearly half of the population reported to having experienced an eye symptom. It is likely that the significant ocular symptoms, indicative of viral conjunctivitis, might have been overlooked in the light of other more serious and critical manifestations of COVID-19. The data are important, especially in countries that rely on self -report of COVID-19 symptoms when confirmative tests for COVID-19 are not available.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shahina Pardhan", - "author_inst": "Anglia Ruskin University" - }, - { - "author_name": "Megan Vaughan", - "author_inst": "Anglia Ruskin University" - }, - { - "author_name": "Jufen Zhang", - "author_inst": "Anglia Ruskin University" - }, - { - "author_name": "Lee Smith", - "author_inst": "Anglia Ruskin University" - }, - { - "author_name": "Havovi Chichger", - "author_inst": "Anglia Ruskin University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2020.06.18.20135152", "rel_title": "Polymorphisms in the ACE2 Locus Associate with Severity of COVID-19 Infection", @@ -1372944,6 +1373581,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.21.162396", + "rel_title": "Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis", + "rel_date": "2020-06-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.21.162396", + "rel_abs": "COVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Chee Keng Mok", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Yan Ling Ng", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Bintou Ahmadou Ahidjo", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Regina Ching Hua Lee", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Marcus Wing Choy Loe", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jing Liu", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Kai Sen Tan", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Parveen Kaur", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Wee Joo Chng", + "author_inst": "National University of Singapore" + }, + { + "author_name": "John Eu Li Wong", + "author_inst": "National University of Singapore" + }, + { + "author_name": "De Yun Wang", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Er Wei Hao", + "author_inst": "Guangxi University of Chinese Medicine, China" + }, + { + "author_name": "Xiaotao Hao", + "author_inst": "Guangxi University of Chinese Medicine" + }, + { + "author_name": "Yong Wah Tan", + "author_inst": "Agency for Science, Technology and Research, Singapore" + }, + { + "author_name": "Tze Minn Mak", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Cui Lin", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Raymond V.T.P Lin", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Paul A Tambyah", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jiagang Deng", + "author_inst": "Guangxi University of Chinese Medicine, China" + }, + { + "author_name": "Justin Jang Hann Chu", + "author_inst": "National University of Singapore" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.22.133355", "rel_title": "Companion vaccine Bioinformatic design tool reveals limited functional genomic variability of SARS-Cov-2 Spike Receptor Binding Domain", @@ -1373732,49 +1374464,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.06.21.163444", - "rel_title": "Characterization of 100 sequential SARS-CoV-2 convalescent plasma donations", - "rel_date": "2020-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.21.163444", - "rel_abs": "Transfusion of SARS-CoV-2 convalescent plasma is a promising treatment for severe COVID-19 cases, with success of the intervention based on neutralizing antibody content. Measurement by serological correlates without biocontainment needs, and an understanding of donor characteristics that may allow for targeting of more potent donors would greatly facilitate effective collection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Christof Jungbauer", - "author_inst": "Austrian Red Cross, Blood Service for Vienna, Lower Austria and Burgenland" - }, - { - "author_name": "Lukas Weseslindtner", - "author_inst": "Center for Virology, Medical University of Vienna" - }, - { - "author_name": "Lisa Weidner", - "author_inst": "Austrian Red Cross, Blood Service for Vienna, Lower Austria and Burgenland" - }, - { - "author_name": "Simon Gaensdorfer", - "author_inst": "Austrian Red Cross, Blood Service for Vienna, Lower Austria and Burgenland" - }, - { - "author_name": "Maria R. Farcet", - "author_inst": "Baxter AG, a Takeda company" - }, - { - "author_name": "Eva Gschaider-Reichhart", - "author_inst": "Baxter AG, a Takeda company" - }, - { - "author_name": "Thomas R. Kreil", - "author_inst": "Baxter AG, a Takeda company" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.06.17.158527", "rel_title": "SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients", @@ -1374818,6 +1375507,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.20.162560", + "rel_title": "Multi-Omics and Integrated Network Approach to Unveil Evolutionary Patterns, Mutational Hotspots, Functional Crosstalk and Regulatory Interactions in SARS-CoV-2", + "rel_date": "2020-06-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.162560", + "rel_abs": "SARS-CoV-2 pandemic resulted in 92 million cases in a span of one year. The study focuses on understanding population specific variations attributing its high rate of infections in specific geographical regions particularly in USA. Rigorous phylogenomic network analysis of complete SARS-CoV-2 genomes (245) inferred five central clades named a (ancestral), b, c, d and e (subtype e1 & e2). The clade d & e2 were found exclusively comprising of USA. Clades were distinguished by 10 co-mutational combinations in Nsp3, ORF8, Nsp13, S, Nsp12, Nsp2 and Nsp6. Our analysis revealed that only 67.46% of SNP mutations were at amino acid level. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except 6 strains which were marked as ancestral type; whereas co-mutation (P409L & Y446C) in Nsp13 were found in 64 genomes from USA highlighting its 100% co-occurrence. Docking highlighted mutation (D614G) caused reduction in binding of Spike proteins with ACE2, but it also showed better interaction with TMPRSS2 receptor contributing to high transmissibility among USA strains. We also found host proteins, MYO5A, MYO5B, MYO5C had maximum interaction with viral proteins (N, S, M). Thus, blocking the internalization pathway by inhibiting MYO5 proteins which could be an effective target for COVID-19 treatment. The functional annotations of the HPI network were found to be closely associated with hypoxia and thrombotic conditions confirming the vulnerability and severity of infection. We also screened CpG islands in Nsp1 & N conferring ability of SARS-CoV-2 to enter and trigger ZAP activity inside host cell.\n\nImportanceIn the current study we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic. This is hitherto the most comprehensive comparative genomics analysis of full-length genomes for co-mutations at different geographical regions specially in USA strains. Compositional structural biology results suggested that mutations have balance of contrary forces effect on pathogenicity suggesting only few mutations to effective at translation level but not all. Novel HPI analysis and CpG predictions elucidates the proof of concept of hypoxia and thrombotic conditions in several patients. Thus, the current study focuses the understanding of population specific variations attributing high rate of SARS-CoV-2 infections in specific geographical regions which may eventually be vital for the most severely affected countries and regions for sharp development of custom-made vindication strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Vipin Gupta", + "author_inst": "PHIXGEN PVT. LTD" + }, + { + "author_name": "Shazia Haider", + "author_inst": "Jaypee Institute of Information Technology, Noida" + }, + { + "author_name": "Mansi Verma", + "author_inst": "Sri Venkateswara College, University of Delhi" + }, + { + "author_name": "Nirjara Singhvi", + "author_inst": "University of Delhi" + }, + { + "author_name": "Kalaiarasan Ponnusamy", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Md. Zubbair Malik", + "author_inst": "Jawaharlal Nehru University, New Delhi, India." + }, + { + "author_name": "Helianthous Verma", + "author_inst": "Ramjas College, University of Delhi" + }, + { + "author_name": "Roshan Kumar", + "author_inst": "Magadh University, Bodh Gaya, Bihar" + }, + { + "author_name": "Utkarsh Sood", + "author_inst": "The Energy and Resources Institute" + }, + { + "author_name": "Princy Hira", + "author_inst": "Maitreyi College, University of Delhi." + }, + { + "author_name": "Shiva Satija", + "author_inst": "Sri Venkateswara College, University of Delhi" + }, + { + "author_name": "Rup Lal", + "author_inst": "The Energy and Resources Institute" + }, + { + "author_name": "Yogendra Singh", + "author_inst": "University of Delhi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.20135996", "rel_title": "The support needs of Australian primary health care nurses during the COVID-19 pandemic", @@ -1375446,29 +1376202,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.06.20.20136150", - "rel_title": "Critical care demand and intensive care supply for patients in Japan with COVID-19 at the time of the state of emergency declaration in April 2020: a descriptive analysis.", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20136150", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic, due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), threatened to overwhelm Japans intensive care capacity due to the rising numbers of infected patients. This study aimed to determine the number of critically ill patients with COVID-19 who required intensive care, including mechanical ventilation and extracorporeal membrane oxygenation (ECMO), during the pandemic and to compare these patient numbers with Japans overall intensive care capacity.\n\nMethodsJapanese Society of Intensive Care Medicine datasets were used to obtain the number of confirmed patients with COVID-19 who had undergone mechanical ventilation and ECMO between February 15 and June 4 2020, to determine and compare intensive care unit (ICU) and attending bed needs for patients with COVID-19, and to estimate peak ICU demands in Japan.\n\nResultsIn total, 17968 ICU days, 15171 mechanical ventilation days, and 2797 ECMO days were attributable to patients with COVID-19. There was a median (interquartile range) 143 (63-255) patients in ICU, 124 (51-225) patients on mechanical ventilation, and 18 (15-36) patients on ECMO machines. During the epidemic peak in late April, 11443 patients (1.03 per 10000 adults) had been infected, 373 patients (0.034 per 10000 adults) were in ICU, 312 patients (0.028 per 10000 adults) were receiving mechanical ventilation, and 62 patients (0.0056 per 10000 adults) were on ECMO machines per day. The number of infected patients at the peak of the epidemic was 651% of total designated beds and the number of patients requiring intensive care at the peak of the epidemic was 6.0% of total ICU beds in Japan, 19.1% of total board-certified intensivists in Japan and 106% of total designated medical institutions for Category II infectious diseases in Japan, respectively.\n\nConclusionsFollowing the state of emergency declaration on April 7 2020, the number of patients with COVID-19 and the number of critically ill patients continued to rise, exceeding the number of designated beds but not exceeding ICU capacity. Urgent nationwide and regional planning is needed to prevent an overwhelming burden on ICUs in relation to critically ill patients with COVID-19 in Japan.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yosuke Fujii", - "author_inst": "Kansai Medical University" - }, - { - "author_name": "Kiichi Hirota", - "author_inst": "Institute of Biomedical Science, Kansai Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.06.19.20135475", "rel_title": "Chloroquine, but not hydroxychlorquine, prolongs the QT interval in a primary care population", @@ -1376224,6 +1376957,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.18.20134700", + "rel_title": "Predictable county-level estimates of R0 for COVID-19 needed for public health planning in the USA", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134700", + "rel_abs": "The basic reproduction number, R0, determines the rate of spread of a communicable disease and therefore gives fundamental information needed to plan public health interventions. Estimated R0 values are only useful, however, if they accurately predict the future potential rate of spread. Using mortality records, we estimated the rate of spread of COVID-19 among 160 counties and county-aggregates in the USA. Most of the high among-county variance in the rate of spread was explained by four factors: the timing of the county-level outbreak (partial R2 = 0.093), population size (partial R2 = 0.34), population density (partial R2 = 0.13), and spatial location (partial R2 = 0.42). Of these, the effect of timing is explained by early steps that people and governments took to reduce transmission, and population size is explained by the sample size of deaths that affects the statistical ability to estimate R0. For predictions of future spread, population density is important, likely because it scales the average contact rate among people. To generate support for a possible explanation for the importance of spatial location, we show that SARS-CoV-2 strains containing the G614 mutation to the spike gene are associated with higher rates of spread (P = 0.016). The high predictability of R0 based on population density and spatial location allowed us to extend estimates to all 3109 counties in the lower 48 States. The high variation of R0 among counties argues for public health policies that are enacted at the county level for controlling COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anthony R Ives", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Claudio Bozzuto", + "author_inst": "Wildlife Analysis GmbH, Zurich, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.18.20134346", "rel_title": "The Relationship between the Global Burden of Influenza from 2017-2019 and COVID-19", @@ -1377060,133 +1377816,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.06.19.20133991", - "rel_title": "The clinical spectrum of encephalitis in COVID-19 disease: the ENCOVID multicentre study", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20133991", - "rel_abs": "ImportanceSeveral preclinical and clinical investigations have argued for nervous system involvement in SARS-CoV-2 infection. Some sparse case reports have described various forms of encephalitis in COVID-19 disease, but very few data have focused on clinical presentations, clinical course, response to treatment and outcomes yet.\n\nObjectiveto describe the clinical phenotype, laboratory and neuroimaging findings of encephalitis associated with SARS-CoV-2 infection, their relationship with respiratory function and inflammatory parameters and their clinical course and response to treatment.\n\nDesignThe ENCOVID multicentre study was carried out in 13 centres in northern Italy between February 20th and May 31st, 2020. Only patients with altered mental status and at least two supportive criteria for encephalitis with full infectious screening, CSF, EEG, MRI data and a confirmed diagnosis of SARS-CoV-2 infection were included. Clinical presentation and laboratory markers, severity of COVID-19 disease, response to treatment and outcomes were recorded.\n\nResultsOut of 45 cases screened, twenty-five cases of encephalitis positive for SARS-CoV-2 infection with full available data were included. The most common symptoms at onset were delirium (68%), aphasia/dysarthria (24%) and seizures (24%). CSF showed hyperproteinorrachia and/or pleocytosis in 68% of cases whereas SARS-CoV-2 RNA by RT-PCR resulted negative. Based on MRI, cases were classified as ADEM (n=3), limbic encephalitis (LE, n=2), encephalitis with normal imaging (n=13) and encephalitis with MRI alterations (n=7). ADEM and LE cases showed a delayed onset compared to the other encephalitis (p=0.001) and were associated with previous more severe COVID-19 respiratory involvement. Patients with MRI alterations exhibited worse response to treatment and final outcomes compared to other encephalitis.\n\nConclusions and relevanceWe found a wide clinical spectrum of encephalitis associated with COVID19 infection, underlying different pathophysiological mechanisms. Response to treatment and final outcome strongly depended on specific CNS-manifestations.\n\nQuestionwhat are the phenotypes of encephalitis associated to SARS-CoV-2 infection?\n\nFindings25 cases of encephalitis in SARS-CoV-2 infection were included in a prospective observational multi-centre study. Encephalitis cases in COVID-19 exhibited a wide heterogeneity in terms of clinical features, CSF, MRI findings, response to treatment and outcomes with 13 cases with normal MRI, 7 with heterogeneous MRI alterations and rarer ADEM/limbic encephalitis cases.\n\nMeaningheterogeneity of presentation, response to treatment and outcomes of encephalitis of COVID-19 underlines different pathophysiological mechanisms", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Andrea Pilotto", - "author_inst": "University of Brescia" - }, - { - "author_name": "Stefano Masciocchi", - "author_inst": "Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Italy" - }, - { - "author_name": "Irene Volonghi", - "author_inst": "Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Italy" - }, - { - "author_name": "Elisabetta del Zotto", - "author_inst": "Neurology Unit, Poliambulanza Hospital, Brescia, Italy" - }, - { - "author_name": "Eugenio Magni", - "author_inst": "Neurology Unit, Poliambulanza Hospital, Brescia, Italy" - }, - { - "author_name": "Valeria De Giuli", - "author_inst": "Neurology Unit, Istituti Ospedalieri, ASST Cremona, Cremona, Italy" - }, - { - "author_name": "Francesca Caprioli", - "author_inst": "Neurology Unit, Istituti Ospedalieri, ASST Cremona, Cremona, Italy" - }, - { - "author_name": "Nicola Rifino", - "author_inst": "Department of Neurology, Papa Giovanni XXIII Hospital, ASST Papa Giovanni XXII, Bergamo, Italy" - }, - { - "author_name": "Maria Sessa", - "author_inst": "Department of Neurology, Papa Giovanni XXIII Hospital, ASST Papa Giovanni XXII, Bergamo, Italy" - }, - { - "author_name": "Michele Gennuso", - "author_inst": "Neurology Unit, Crema Hospital, Crema, Italy" - }, - { - "author_name": "Maria Sofia Cotelli", - "author_inst": "Neurology Unit, ASST Valcamonica, Esine, Brescia, Italy" - }, - { - "author_name": "Marinella Turla", - "author_inst": "Neurology Unit, ASST Valcamonica, Esine, Brescia, Italy" - }, - { - "author_name": "Ubaldo Balducci", - "author_inst": "Neurology Unit, ASST Chiari, Chiari, Italy" - }, - { - "author_name": "Sara Mariotto", - "author_inst": "Neurology Unit, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy" - }, - { - "author_name": "Sergio Ferrari", - "author_inst": "Neurology Unit, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy" - }, - { - "author_name": "Alfonso Ciccone", - "author_inst": "Department of Neurology and Stroke Unit, Carlo Poma Hospital, ASST Mantova, Mantova, Italy" - }, - { - "author_name": "Fabrizio Fiacco", - "author_inst": "Neurology Unit, ASST Bergamo Est, Seriate, Italy" - }, - { - "author_name": "Alberto Imarisio", - "author_inst": "Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Italy" - }, - { - "author_name": "Barbara Risi", - "author_inst": "Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Italy" - }, - { - "author_name": "Alberto Benussi", - "author_inst": "University of Brescia" - }, - { - "author_name": "Emanuele Foca'", - "author_inst": "University Division of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy" - }, - { - "author_name": "Francesca Caccuri", - "author_inst": "Microbiology Unit, Department of Molecular and Translational Medicine, University" - }, - { - "author_name": "Matilde Leonardi", - "author_inst": "Neurology, Public Health, Disability Unit - IRCCS Neurology Institute Besta, Milan, Italy" - }, - { - "author_name": "Roberto Gasparotti", - "author_inst": "Neuroradiology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia and ASST Spedali Civili Hosp" - }, - { - "author_name": "Francesco Castelli", - "author_inst": "University Division of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy" - }, - { - "author_name": "Gianluigi Zanusso", - "author_inst": "Neurology Unit, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy" - }, - { - "author_name": "Alessandro Pezzini", - "author_inst": "University of Brescia" - }, - { - "author_name": "Alessandro Padovani", - "author_inst": "Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Italy" - } - ], - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.06.18.20134353", "rel_title": "IL-13 Predicts the Need for Mechanical Ventilation in COVID-19 Patients", @@ -1378550,6 +1379179,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.19.161687", + "rel_title": "Cytosine deamination in SARS-CoV-2 leads to progressive CpG depletion.", + "rel_date": "2020-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.161687", + "rel_abs": "RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. In an attempt to address this we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5'-UCG-3' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mukhtar Sadykov", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Tobias Mourier", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Qingtian Guan", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Arnab Pain", + "author_inst": "King Abdullah University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.158717", "rel_title": "No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia.", @@ -1379390,65 +1380050,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.06.16.20128660", - "rel_title": "Potential involvement of monoamine oxidase activity in SARS-COV2 infection and delirium onset", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20128660", - "rel_abs": "Delirium is an acute change in attention and cognition occurring in ~65% of severe SARS-CoV-2 cases. It is also common following surgery and an indicator of brain vulnerability and risk for the development of dementia. In this work we analyzed the underlying role of metabolism in delirium-susceptibility in the postoperative setting using metabolomic profiling of cerebrospinal fluid and blood taken from the same patients prior to planned orthopaedic surgery. Significant concentration differences in several amino acids, acylcarnitines and polyamines were found in delirium-prone patients leading us to a hypothesis about the significance of monoamine oxidase B (MAOB) in predisposition to delirium. Subsequent computational structural comparison between MAOB and angiotensin converting enzyme 2 as well as protein-protein docking analysis showed possibly strong binding of SARS-CoV-2 spike protein to MAOB resulting in a hypothesis that SARS-CoV-2 influences MAOB activity possibly lead to many observed neurological and platelet-based complications of SARS-CoV-2 infection. This proposition is possibly of significance for diagnosis, treatment and prevention of vulnerabilities causing delirium, dementias and severe COVID-19 response.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Miroslava Cuperlovic-Culf", - "author_inst": "National Research Council" - }, - { - "author_name": "Emma L Cunningham", - "author_inst": "2Centre for Public Health, Queens University Belfast, Block B, Institute of Clinical Sciences, Royal Victoria Hospital site, Grosvenor Road, Belfast, BT12 6BA, " - }, - { - "author_name": "Anuradha Surendra", - "author_inst": "National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada" - }, - { - "author_name": "Xiaobei Pan", - "author_inst": "Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, 8 Malone Road, Belfast, BT9 5BN, Northern Ireland" - }, - { - "author_name": "Steffany A.L. Bennett", - "author_inst": "Neural Regeneration Laboratory, Ottawa Institute of Systems Biology, Brain and Mind Research Institute, Department of Biochemistry, Microbiology, and Immunology" - }, - { - "author_name": "Mijin Jung", - "author_inst": "3Institute for GlobaFood Security, School of Biological Sciences, Queens University Belfast, 8 Malone Road, Belfast, BT9 5BN, Northern Ireland" - }, - { - "author_name": "Bernadette McGuiness", - "author_inst": "Centre for Public Health, Queens University Belfast, Block B, Institute of Clinical Sciences, Royal Victoria Hospital site, Grosvenor Road, Belfast, BT12 6BA, N" - }, - { - "author_name": "Anthony Peter Passmore", - "author_inst": "Centre for Public Health, Queens University Belfast, Block B, Institute of Clinical Sciences, Royal Victoria Hospital site, Grosvenor Road, Belfast, BT12 6BA, N" - }, - { - "author_name": "Danny McAuley", - "author_inst": "Centre for Experimental Medicine, Queens University Belfast, Wellcome-Wolfson Institute for Experimental Medicine, 97 Lisburn Road, Belfast, BT9 7BL" - }, - { - "author_name": "David Beverland", - "author_inst": "Outcomes Assessment Unit, Musgrave Park Hospital, Stockmans Lane, Belfast, BT9 7JB, Northern Ireland" - }, - { - "author_name": "Brian D. Green", - "author_inst": "Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, 8 Malone Road, Belfast, BT9 5BN, Northern Ireland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.06.16.20130914", "rel_title": "A longitudinal study of immune cells in severe COVID-19 patients.", @@ -1380048,6 +1380649,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.16.20132423", + "rel_title": "Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132423", + "rel_abs": "ObjectivesPopulation screening for IgG and IgM against SARS-CoV-2 was initiated on March 25 and was open to all residents of Wuhan who were symptom-free. All ages with no fever, headache or other symptoms of COVID-19 among residents in Wuhan were included.\n\nMethodsThis study adopted a cross-sectional study. Pearson Chi-square test, T-test, and Mann-Whitney test were used in comparison between different groups. To correct the effects of gender and age, the seroprevalence of IgM positivity, IgG positivity, and IgM and/or IgG positivity were standardized according to the gender and age-specific population of Wuhan in 2017.\n\nResultsThe seroprevalence of IgG and IgM standardized for age and gender in Wuhan showed a downward trend. No significant correlation was observed between the seroprevalence of IgG and the different age groups. The seroprevalence was significantly higher for females than males (x2 =35.702, p < 0.001), with an odds ratio of 1.36 (95% CI: 1.24-1.48). A significant difference was seen in the seroprevalence of IgG among people from different geographic areas and different types of workplaces (respectively, x2 = 42.871, p < 0.001 and x2 = 202.43, p < 0.001). The IgG antibody-positive cases had a greater number of abnormalities in CT imaging than IgG-negative cases (30.7% vs 19.7%).\n\nConclusionsOur work found the reported number of confirmed patients in Wuhan only represents a small proportion of the total number of infections. There was a significant aggregation of asymptomatic infections in individuals from some occupations, and based on CT and laboratory findings, some damage may have occurred in asymptomatic individuals positive for IgG antibody.\n\nO_LSTStrengths and limitations of this studyC_LSTO_LIThis study has the important feature of having been designed as repeated five-day serosurveys, which allowed for the monitoring of seroprevalence progression.\nC_LIO_LIThis study applied scientific statistical methods accounting for the demographic structure of the general population and imperfect diagnostic tests to estimate seroprevalence in the overall population.\nC_LIO_LIThis study had selection bias since the analyzed medical records were based on examinees directed by their work units.\nC_LIO_LIPeople under the age of 19 and over age 65 were too few to be fully covered in analyses.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ruijie Ling", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Yihan Yu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Jiayu He", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Jixian Zhang", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Sha Xu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Renrong Sun", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Wangcai Zhu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Mingfeng Chen", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Tao Li", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Honglong Ji", + "author_inst": "Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas, USA" + }, + { + "author_name": "Huanqiang Wang", + "author_inst": "National Institute of Occupational Health and Poisons Control,Chinese CDC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.16.20133207", "rel_title": "Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis", @@ -1380672,41 +1381332,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.17.20133868", - "rel_title": "The impact of the Covid-19 lockdown on the experiences and feeding practices of new mothers in the UK: Preliminary data from the COVID-19 New Mum Study", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133868", - "rel_abs": "BackgroundThe COVID-19 New Mum Study is recording maternal experiences and infant feeding during the period of UK lockdown. This report from week 1 of the survey aims to (1) provide information relevant for those supporting this population; (2) identify groups currently under-represented in the survey.\n\nMethodsWomen living in the UK aged [≥]18 years with an infant [≤]12 months of age completed an anonymous online survey (https://is.gd/covid19newmumstudy). Information/links are shared via websites, social media and existing contacts.\n\nResultsBetween May 27th and June 3rd 2020, 1365 women provided data (94% white, 95% married/with partner, 66% degree/higher qualification, 86% living in house; 1049 (77%) delivered before lockdown (BL) and 316 (23%) during lockdown (DL). Delivery mode, skin-to-skin contact and breastfeeding initiation did not differ between groups. DL women had shorter hospital stays (p<0.001) and 39% reported changes to their birth plan. Reflecting younger infant age, 59% of DL infants were exclusively breast-fed or mixed fed versus 39% of BL (p<0.05). Thirteen % reported a change in feeding; often related to lack of breastfeeding support, especially with practical problems. Important sources of feeding support were the partner (60%), health professional (50%) and online groups (47%). 45% of DL women reported insufficient support with feeding. Among BL women, 57% and 69% reported decreased feeding support and childcare, respectively. 40% BL/45% DL women reported insufficient support with their own health, 8%/9% contacted a mental health professional and 11% reported their mental health was affected. 9% highlighted lack of contact and support from family and distress that they had missed seeing the baby.\n\nConclusionLockdown has had an impact on maternal experiences, resulting in distress for many women. Survey participants are currently not representative of the population; notably, groups at greater risk are under-represented. Increasing the diversity of participants is a priority.\n\nSurvey fundingNone. All research at Great Ormond Street Hospital NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health is made possible by the NIHR Great Ormond Street Hospital Biomedical Research Centre. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Adriana Vazquez-Vazquez", - "author_inst": "UCL Great Ormond Street Institute of Child Health, London, UK" - }, - { - "author_name": "Sarah Dib", - "author_inst": "UCL Great Ormond Street Institute of Child Health, London, UK" - }, - { - "author_name": "Emeline Rougeaux", - "author_inst": "UCL Great Ormond Street Institute of Child Health, London, UK" - }, - { - "author_name": "Jonathan C Wells", - "author_inst": "UCL Great Ormond Street Institute of Child Health, London, UK" - }, - { - "author_name": "Mary Fewtrell", - "author_inst": "UCL Great Ormond Street Institute of Child Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.06.17.20133587", "rel_title": "Essential epidemiological parameters of COVID-19 for clinical and mathematical modeling purposes: a rapid review and meta-analysis", @@ -1381558,6 +1382183,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.06.17.20133611", + "rel_title": "Knowledge, Attitudes, and Fear of COVID-19 during the Rapid Rise Period in Bangladesh", + "rel_date": "2020-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133611", + "rel_abs": "ObjectivesTo determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of Fear towards COVID-19 in subjects living in Bangladesh.\n\nDesignProspective, cross-sectional survey of (n= 2157) male and female subjects, 13-90 years of age, living in Bangladesh.\n\nMethodsEthical Approval and Trial registration were obtained prior to the commencement of the study. Subjects who volunteered to participate and signed the informed consent were enrolled in the study and completed the \"Fear of COVID-19 Scale\" (FCS).\n\nResultsTwenty-eight percent (28.69%) of subjects reported one or more COVID-19 symptoms and 21.4% of subjects reported one or more comorbidities. Knowledge scores were slightly higher in males (8.75{+/-} 1.58) than females (8.66{+/-} 1.70). Knowledge was significantly correlated with age (p<.005), an education level (p<.001), Attitude (p<.001), and urban location (p=<.001). Knowledge scores showed an inverse correlation with Fear scores (p=<.001). Eighty-three percent (83.7%) of subjects with COVID-19 symptoms reported wearing a mask in public and 75.4% of subjects reported staying away from crowded places. Subjects with one or more symptoms reported higher Fear compared to subjects without (18.73{+/-} 4.6; 18.45{+/-} 5.1).\n\nConclusionsOverall, Bangladeshis reported a high prevalence of self-isolation, positive preventive health behaviors related to COVID-19, and moderate to high fear levels. Higher Knowledge and Practice were found in males, higher education levels, older age, and urban location. \"Fear\" of COVID-19 was more prevalent in female and elderly subjects. Positive \"Attitude\" was reported for the majority of subjects, reflecting the belief that COVID-19 was controllable and containable.\n\nEthical approvalEthical permission obtained from the Institutional review board (BPA-IPRR/IRB/29/03/2020/021) of Institute of Physiotherapy, Rehabilitation, and Research (IPRR), the academic organization of the Bangladesh Physiotherapy Association.\n\nWHO Trial registryThe trial registration obtained prospectively from a primary trial registry of WHO (CTRI/2020/04/024413).\n\nData AvailabilityThe data are available regarding this study and can be viewed upon request", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mohammad Anwar Hossain", + "author_inst": "Centre for the Rehabilitation of the Paralysed" + }, + { + "author_name": "K M Amran Hossain", + "author_inst": "Bangladesh Health Professions Institute" + }, + { + "author_name": "Lori Maria Walton", + "author_inst": "University of Scranton" + }, + { + "author_name": "Zakir Uddin", + "author_inst": "McGill University" + }, + { + "author_name": "Md. Obaidul Haque", + "author_inst": "Bangladesh Health Professions Institute" + }, + { + "author_name": "Md. Feroz Kabir", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "S. M. Yasir Arafat", + "author_inst": "Enam Medical College & Hospital" + }, + { + "author_name": "Mohamed Sakel", + "author_inst": "East Kent University NHS Hospital" + }, + { + "author_name": "Rafey Faruqui", + "author_inst": "Kent & Medway NHS and Social care Partnership Trust" + }, + { + "author_name": "Ikbal Kabir Jahid", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Zahid Hossain", + "author_inst": "Bangladesh Health Professions Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.16.20133215", "rel_title": "The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2", @@ -1382370,45 +1383054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.20133181", - "rel_title": "Limited Role for Antibiotics in COVID-19: Scarce Evidence of Bacterial Coinfection", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133181", - "rel_abs": "BackgroundThere is currently a paucity of data describing bacterial coinfections, related antibiotic prescribing patterns, and the potential role of antimicrobial stewardship in the care of patients infected with SARS-CoV-2.\n\nMethodsThis prospective, observational study was conducted from March 10, 2020 to April 21, 2020 in admitted patients with confirmed COVID-19. Patients were included if [≥] 18 years old and admitted to the hospital for further treatment. Data was collected via chart review from the enterprise electronic health record database. Data collected include factors driving antibiotic choice, indication, and duration of therapy as well as microbiological data.\n\nFindingsAntibiotics were initiated on admission in 87/147 (59%) patients. Of these, 85/87 (98%) prescriptions were empiric. The most common indication for empiric antibiotics was concern for community-acquired pneumonia (76/85, 89%) with the most prescribed antibiotics being ceftriaxone and azithromycin. The median duration of antibiotic therapy was two days (interquartile range 1-5). No patients had a community-acquired bacterial respiratory coinfection, but 10/147 (7%) of patients were found to have concurrent bacterial infections from a non-respiratory source, and one patient was diagnosed with active pulmonary tuberculosis at the time of admission for COVID-19.\n\nInterpretationBacterial coinfection in patients with COVID-19 was infrequent. Antibiotics are likely unnecessary in patients with mild symptoms. There is little role for broad-spectrum antibiotics to empirically treat multidrug resistant organisms in patients with COVID-19, regardless of disease severity. Antimicrobial stewardship remains important in patients infected with SARS-CoV-2.\n\nFundingThe authors received no funding for this work.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wenjing Wei", - "author_inst": "Parkland Health & Hospital System" - }, - { - "author_name": "Jessica K Ortwine", - "author_inst": "Parkland Health & Hospital System" - }, - { - "author_name": "Norman S Mang", - "author_inst": "Parkland Health & Hospital System" - }, - { - "author_name": "Christopher Joseph", - "author_inst": "UT Southwestern Medical Center" - }, - { - "author_name": "Brenton C Hall", - "author_inst": "Parkland Health & Hospital System" - }, - { - "author_name": "Bonnie Chase Prokesch", - "author_inst": "UT Southwestern" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.16.20132746", "rel_title": "Time Course of COVID-19 epidemic in Algeria: Retrospective estimate of the actual burden", @@ -1383432,6 +1384077,25 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.06.16.154559", + "rel_title": "in-silica Analysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA", + "rel_date": "2020-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154559", + "rel_abs": "The recent pandemic of COVID19 that has struck the world is yet to be battled by a potential cure. Countless lives have been claimed due to the existing pandemic and the societal normalcy has been damaged permanently. As a result, it becomes crucial for academic researchers in the field of bioinformatics to combat the existing pandemic. The study involved collecting the virulent strain sequence of SARS-nCoV19 for the country USA against human host through publically available bioinformatics databases. Using in-silica analysis and reverse vaccinology, two leader proteins were identified to be potential vaccine candidates for development of a multi-epitope drug. The results of this study can provide further researchers better aspects and direction on developing vaccine and immune responses against COVID19. This work also aims at promoting the use of existing bioinformatics tools to faster streamline the pipeline of vaccine development.\n\nThe Situation of COVID19A new infection respiratory disease was first observed in the month of December 2019, in Wuhan, situated in the Hubei province, China. Studies have indicated that the reason of this disease was the emergence of a genetically-novel coronavirus closely related to SARS-CoV. This coronavirus, now named as nCoV-19, is the reason behind the spread of this fatal respiratory disease, now named as COVID-19. The initial group of infections is supposedly linked with the Huanan seafood market, most likely due to animal contact. Eventually, human-to-human interaction occurred and resulted in the transmission of the virus to humans. [13].\n\nSince then, nCoV-19 has been rapidly spreading within China and other parts of World. At the time of writing this article (mid-March 2020), COVID-19 has spread across 146 countries. A count of 164,837 cases have been confirmed of being diagnosed with COVID-19, and a total of 6470 deaths have occurred. The cumulative cases have been depicting a rising trend and the numbers are just increasing. WHO has declared COVID-19 to be a \"global health emergency\". [14].\n\nCurrent Scenario and ObjectivesCurrently, research is being conducted on a massive level to understand the immunology and genetic characteristics of the disease. However, no cure or vaccine of nCoV-19 has been developed at the time of writing this article.\n\nThough, nCoV-19 and SARS-CoV are almost genetically similar, the respiratory syndrome caused by both of them, COVID-19 and SARS respectively, are completely different. Studies have indicated that -\n\n\"SARS was more deadly but much less infectious than COVID-19\".\n\n-World Health Organization", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ajay Agarwal", + "author_inst": "DIT University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.15.20130328", "rel_title": "Can we trust the prediction model? Demonstrating the importance of external validation by investigating the COVID-19 Vulnerability (C-19) Index across an international network of observational healthcare datasets", @@ -1384156,101 +1384820,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2020.06.15.20131722", - "rel_title": "Delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131722", - "rel_abs": "BackgroundFrailty, increased vulnerability to physiological stressors, is associated with adverse outcomes. COVID-19 exhibits a more severe disease course in older, co-morbid adults. Awareness of atypical presentations is critical to facilitate early identification.\n\nObjectiveTo assess how frailty affects presenting COVID-19 symptoms in older adults.\n\nDesignObservational cohort study of hospitalised older patients and self-report data for community-based older adults.\n\nSettingAdmissions to St Thomas Hospital, London with laboratory-confirmed COVID-19. Community-based data for 535 older adults using the COVID Symptom Study mobile application.\n\nSubjectsHospital cohort: patients aged 65 and over (n=322); unscheduled hospital admission between March 1st, 2020-May 5th, 2020; COVID-19 confirmed by RT-PCR of nasopharyngeal swab. Community-based cohort: participants aged 65 and over enrolled in the COVID Symptom Study (n=535); reported test-positive for COVID-19 from March 24th (application launch)-May 8th, 2020.\n\nMethodsMultivariate logistic regression analysis performed on age-matched samples from hospital and community-based cohorts to ascertain association of frailty with symptoms of confirmed COVID-19.\n\nResultsHospital cohort: significantly higher prevalence of delirium in the frail sample, with no difference in fever or cough. Community-based cohort :significantly higher prevalence of probable delirium in frailer, older adults, and fatigue and shortness of breath.\n\nConclusionsThis is the first study demonstrating higher prevalence of delirium as a COVID-19 symptom in older adults with frailty compared to other older adults. This emphasises need for systematic frailty assessment and screening for delirium in acutely ill older patients in hospital and community settings. Clinicians should suspect COVID-19 in frail adults with delirium.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Maria Beatrice Zazzara", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Gerontology, Neuroscience and O" - }, - { - "author_name": "Rose S. Penfold", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Amy L. Roberts", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Karla Lee", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Hannah Dooley", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Carole H. Sudre", - "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK" - }, - { - "author_name": "Carly Welch", - "author_inst": "Institute of Inflammation and Ageing, University of Birmingham, B15 2TT" - }, - { - "author_name": "Ruth C. E. Bowyer", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Alessia Visconti", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Massimo Mangino", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; NIHR Biomedical Research Centre at Guy's and " - }, - { - "author_name": "Maxim B. Freydin", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Julia S. El-Sayed Moustafa", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Kerrin Small", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK" - }, - { - "author_name": "Marc Modat", - "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK" - }, - { - "author_name": "Finbarr C. Martin", - "author_inst": "Population Health Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK" - }, - { - "author_name": "Claire J. Steves", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - }, - { - "author_name": "Mary Ni Lochlainn", - "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2020.06.15.20131987", "rel_title": "Can the protection be among us? Previous viral contacts and prevalent HLA alleles could be avoiding an even more disseminated COVID-19 pandemic.", @@ -1385094,6 +1385663,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.16.151555", + "rel_title": "Decoding of persistent multiscale structures in complex biological networks", + "rel_date": "2020-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.151555", + "rel_abs": "In any omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here we use the concept of \"persistent homology\", drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fan Zheng", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "She Zhang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Christopher Churas", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Dexter Pratt", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Ivet Bahar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Trey Ideker", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.06.17.157982", "rel_title": "Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding", @@ -1385930,65 +1386538,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.06.14.20103754", - "rel_title": "Development and validation of a knowledge-driven risk calculator for critical illness in COVID-19 patients", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20103754", - "rel_abs": "Facing the rapidly spreading novel coronavirus disease (COVID-19), evidence to inform decision-making at both the clinical and policy-making level is highly needed. Based on the results of a study by Petrilli et al, we have developed a calculator using patient data at admission to predict the risk of critical illness (intensive care unit admission, use of mechanical ventilation, discharge to hospice, or death).\n\nWe report a retrospective validation of the risk calculator on 145 consecutive patients admitted with COVID-19 to a single hospital in Israel. Of the 18 patients with critical illness, 17 were correctly identified by the model(sensitivity: 94.4%, 95% CI, 72.7% to 99.9%; specificity: 81.9%, 95% CI, 74.1% to 88.2%). Of the 127 patients with non-critical illness, 104 were correctly identified. This, despite considerable differences between the original and validation study populations.\n\nOur results show that data from published knowledge can be used to provide reliable, patient level, automated risk assessment, potentially reducing the cognitive burden on physicians and helping policy makers better prepare for future needs.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Amos Cahan", - "author_inst": "Kahun Medical" - }, - { - "author_name": "Tamar Gottesman", - "author_inst": "Hasharon campus, Rabin Medical Center, Petach Tikva, Israel." - }, - { - "author_name": "Michal Tzuchman Katz", - "author_inst": "Kahun Medical Ltd" - }, - { - "author_name": "Roee Masad", - "author_inst": "Kahun Medical Ltd" - }, - { - "author_name": "Gal Azulay", - "author_inst": "Kahun Medical Ltd." - }, - { - "author_name": "Dror Dicker", - "author_inst": "Hasharon campus, Rabin Medical Center, Petach Tikva, Israel." - }, - { - "author_name": "Aliza Zeidman", - "author_inst": "Hasharon campus, Rabin Medical Center, Petach Tikva, Israel." - }, - { - "author_name": "Evgeny Berkov", - "author_inst": "Hasharon campus, Rabin Medical Center, Petach Tikva, Israel." - }, - { - "author_name": "Gal Sahaf Levin", - "author_inst": "The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Boaz Tadmor", - "author_inst": "Research Authority, Rabin Medical Center, Petach Tikva, Israel" - }, - { - "author_name": "Shaul Lev", - "author_inst": "General Intensive Care Unit, HasHasharon Hospital, Rabin Medical Center, Petach Tikva, Israel; The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, I" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.14.20123315", "rel_title": "Risk of death by age and gender from CoVID-19 in Peru, March-May, 2020", @@ -1386908,6 +1387457,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.13.20130062", + "rel_title": "Guillain Barr e syndrome in COVID-19:A scoping review", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130062", + "rel_abs": "IntroductionThe novel corona virus (COVID19) can result in several neurological complications. Guillain-Barre Syndrome (GBS) is one of them and has been reported from different parts of the world in this pandemic. It is an acute post infectious polyneuropathy. The review aims to summarize the demographic features, clinical presentation, diagnostics workup, and management strategies of COVID-19 associated GBS reported in literature.\n\nMaterial and methodWe searched Medline, PubMed Central, SCOPUS and Google Scholar using pre-defined keywords, with no time limits and in English language only. We aimed to include all kind of manuscripts. Last search was done on 18th May 2020.\n\nDemographics, clinical features, diagnostic workup, management, and outcomes were documented in the data sheet.\n\nResultsWe identified 24 cases of COVID-19 associated GBS. Most of the cases were reported from Italy followed by USA. Majority were males (18 /24) The age ranged from 23 -84 years. The clinical presentation was typical sensory-motor GBS in most. Nine patients had facial palsy of which five had bilateral involvement. Two patients had bilateral abducent nerve palsy while two presented as paraparetic GBS variant with autonomic dysfunction. Electrodiagnostics was performed in 17 patients only and 12 had typical features of acute inflammatory demyelinating polyneuropathy.. Intravenous immunoglobulins were the preferred mode of treatment in most of the patient. There was one death, and most were discharged to rehabilitation or home.\n\nConclusionGBS is a frequent neurological complication associated with COVID-19. There is no clear causative relationship between GBS, and COVID-19 at present and more data are needed to establish the casualty. However, most cases have a post-infectious onset with male preponderance. Most of the cases have a typical presentation but some may present in an atypical way. Prognosis is generally good.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Imran Ahmad", + "author_inst": "Bahria University Medical and Dental College" + }, + { + "author_name": "Farooq Azam Rathore", + "author_inst": "Bahria University Medical and Dental College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.06.13.20130310", "rel_title": "COVID-19: a crash test for biomedical publishing?", @@ -1387308,49 +1387880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.14.20130740", - "rel_title": "Air Quality and COVID-19 Prevalence/Fatality", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130740", - "rel_abs": "To investigate the association of real-time/observed ozone/PM2.5 levels with COVID-19 prevalence/fatality, meta-regression of data from the Northeast megalopolis was conducted. Daily Air Quality Index (AQI) values based on available ozone/PM2.5 data in these counties/cities (3/15/2020-5/31/2020) were extracted from US Environmental Protection Agency and World Air Quality Project. In each county/city, total confirmed COVID-19 cases/deaths (5/31/2020) were available from Johns Hopkins Coronavirus Resource Center, and total population was extracted from US Census Bureau. Random-effects meta-regression was performed using OpenMetaAnalyst. A meta-regression graph depicted COVID-19 prevalence and fatality (plotted as logarithm-transformed prevalence/fatality on the y-axis) as a function of mean ozone/PM2.5 AQI (plotted on the x-axis). Coefficients were not statistically significant for ozone (P = 0.212/0.814 for prevalence/fatality) and PM2.5 (P = 0.986/0.499). Although multivariable analysis had been planned, it was not performed because of non-significant covariates of interest in the univariable model. In conclusion, ozone/PM2.5 may be unassociated with COVID-19 prevalence/fatality.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hisato Takagi", - "author_inst": "Shizuoka Medical Center, Shizuoka, Japan; Kitasato University School of Medicine, Sagamihara, Japan" - }, - { - "author_name": "Toshiki Kuno", - "author_inst": "Mount Sinai Beth Israel Medical Center, New York, NY, USA" - }, - { - "author_name": "Yujiro Yokoyama", - "author_inst": "Easton Hospital, Easton, PA, USA" - }, - { - "author_name": "Hiroki Ueyama", - "author_inst": "Mount Sinai Beth Israel Medical Center, New York, NY, USA" - }, - { - "author_name": "Takuya Matsushiro", - "author_inst": "Shizuoka Medical Center, Shizuoka, Japan; Kitasato University School of Medicine, Sagamihara, Japan" - }, - { - "author_name": "Yosuke Hari", - "author_inst": "Shizuoka Medical Center, Shizuoka, Japan; Kitasato University School of Medicine, Sagamihara, Japan" - }, - { - "author_name": "Tomo Ando", - "author_inst": "New York Presbyterian Hospital/Columbia University Medical Center, New York, NY, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.14.20130765", "rel_title": "Risk factors for critical-ill events of patients with COVID-19 in Wuhan, China: a retrospective cohort study", @@ -1388014,6 +1388543,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.13.20130617", + "rel_title": "Is tracking and modeling Covid-19 infection dynamics for Bangladesh using daily data feasible?", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130617", + "rel_abs": "Given the low Covid-19 testing coverage in the country, this study tested whether the daily change in the number of new Covid-19 cases is due to increase (or decrease) in the number of tests done daily. We performed Granger causality test based on vector autoregressive models on Bangladeshs case and test numbers between 8 March and 5 June 2020, using publicly available data. The test results show that the daily number of tests Granger-cause the number of new cases (p <0.001), meaning the daily number of new cases is perhaps due to an increase in test capacity rather than a change in the infection rates. From the results of this test we can infer that if the number of daily tests does not increase substantially, data on new infections will not give much information for understanding covid-19 infection dynamics in Bangladesh.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Karar Zunaid Ahsan", + "author_inst": "Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, NC, USA" + }, + { + "author_name": "Rashida Ijdi", + "author_inst": "Carolina Population Center, University of North Carolina at Chapel Hill, NC, USA" + }, + { + "author_name": "Peter Kim Streatfield", + "author_inst": "Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.13.20130088", "rel_title": "Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia. When late administration is too late.", @@ -1388698,89 +1389254,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.15.20131029", - "rel_title": "Complement and tissue factor-enriched neutrophil extracellular traps are key drivers in COVID-19 immunothrombosis", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131029", - "rel_abs": "Emerging data indicate that complement and neutrophils are involved in the maladaptive host immune response that fuels hyper-inflammation and thrombotic microangiopathy increasing the mortality rate in coronavirus disease 2019 (COVID-19). Here, we investigated the interaction between complement and the platelet/neutrophil extracellular traps (NETs)/thrombin axis, using COVID-19 clinical samples, cell-based inhibition studies and NETs/human aortic endothelial cell (HAEC) co-cultures. Increased plasma levels of NETs, TF activity and sC5b-9 were detected in patients. Neutrophils yielded high tissue factor (TF) expression and released NETs carrying functionally active TF. Confirming our ex vivo findings, treatment of control neutrophils with COVID-19 platelet-rich plasma generated TF-bearing NETs that induced thrombotic activity of HAEC. Thrombin or NETosis inhibition or C5aR1 blockade attenuated platelet-mediated NET-driven thrombogenicity. Serum isolated from COVID-19 patients induces complement activation in vitro, which is consistent with high complement activity in clinical samples. Complement inhibition at the level of C3 with compstatin Cp40 disrupted TF expression in neutrophils. In conclusion, we provide a mechanistic basis that reveals the pivotal role of complement and NETs in COVID-19 immmunothrombosis. This study supports emerging strategies against SARS-CoV-2 infection that exploit complement therapeutics or NETosis inhibition.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Panagiotis Skendros", - "author_inst": "First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandro" - }, - { - "author_name": "Alexandros Mitsios", - "author_inst": "Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Akrivi Chrysanthopoulou", - "author_inst": "Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Dimitrios C Mastellos", - "author_inst": "National Center for Scientific Research Demokritos, Aghia Paraskevi, Athens, Greece." - }, - { - "author_name": "Simeon Metallidis", - "author_inst": "First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece." - }, - { - "author_name": "Petros Rafailidis", - "author_inst": "Second Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Maria Ntinopoulou", - "author_inst": "Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Eleni Sertaridou", - "author_inst": "Intensive Care Unit, University Hospital of Alexandroupolis, Alexandroupolis, Greece." - }, - { - "author_name": "Victoria Tsironidou", - "author_inst": "Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Christina Tsigalou", - "author_inst": "Laboratory of Microbiology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Maria Tektonidou", - "author_inst": "First Department of Propaedeutic Internal Medicine, National and Kapodistrian University of Athens, Greece" - }, - { - "author_name": "Theocharis Konstantinidis", - "author_inst": "Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece." - }, - { - "author_name": "Charalampos Papagoras", - "author_inst": "First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandro" - }, - { - "author_name": "Ioannis Mitroulis", - "author_inst": "First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandro" - }, - { - "author_name": "Georgios Germanidis", - "author_inst": "First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece." - }, - { - "author_name": "John D Lambris", - "author_inst": "Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA." - }, - { - "author_name": "Konstantinos Ritis", - "author_inst": "First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandro" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.06.14.20125997", "rel_title": "Impact of Chronic Comorbidities on Progression and Prognosis in Patients with COVID-19: A Retrospective Cohort Study in 1031 Hospitalized Cases in Wuhan, China", @@ -1389812,6 +1390285,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.15.153692", + "rel_title": "Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases", + "rel_date": "2020-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.153692", + "rel_abs": "The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as gene on-tology and protein-protein interaction (PPI) networks from other closely related species presents a vital approach to infer the molecular impact of a new species. In this paper, we propose the transferred multi-relational embedding model Bio-JOIE to capture the knowledge of gene ontology and PPI networks, which demonstrates superb capability in modeling the SARS-CoV-2-human protein interactions. Bio-JOIE jointly trains two model components. The knowledge model encodes the relational facts from the protein and GO domains into separated embedding spaces, using a hierarchy-aware encoding technique employed for the GO terms. On top of that, the transfer model learns a non-linear transformation to transfer the knowledge of PPIs and gene ontology annotations across their embedding spaces. By leveraging only structured knowledge, Bio-JOIE significantly outperforms existing state-of-the-art methods in PPI type prediction on multiple species. Furthermore, we also demonstrate the potential of leveraging the learned representations on clustering proteins with enzymatic function into enzyme commission families. Finally, we show that Bio-JOIE can accurately identify PPIs between the SARS-CoV-2 proteins and human proteins, providing valuable insights for advancing research on this new disease.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Junheng Hao", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chelsea Jui-Ting Ju", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Muhao Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yizhou Sun", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Carlo Zaniolo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Wei Wang", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.16.153403", "rel_title": "Oral drug repositioning candidates and synergistic remdesivir combinations for the prophylaxis and treatment of COVID-19", @@ -1390472,101 +1390984,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.16.154286", - "rel_title": "Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154286", - "rel_abs": "Genomic surveillance has a key role in tracking the ongoing COVID-19 pandemic, but information on how different sequencing library preparation approaches affect the data produced are lacking. We compared three library preparation methods using both tagmentation (Nextera XT and Nextera Flex) and ligation-based (KAPA HyperPrep) approaches on both positive and negative samples to provide insights into any methodological differences between the methods, and validate their use in SARS-CoV-2 amplicon sequencing. We show that all three library preparation methods allow us to recover near-complete SARS-CoV-2 genomes with identical SNP calls. The Nextera Flex and KAPA library preparation methods gave better coverage than libraries prepared with Nextera XT, which required more reads to call the same number of genomic positions. The KAPA ligation-based approach shows the lowest levels of human contamination, but contaminating reads had no effect on the downstream analysis. We found some examples of library preparation-specific differences in minority variant calling. Overall our data shows that the choice of Illumina library preparation method has minimal effects on consensus base calling and downstream phylogenetic analysis, and suggests that all methods would be suitable for use if specific reagents are difficult to obtain.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Elizabeth M Batty", - "author_inst": "Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand and Centre for Tropical Medicine and Global " - }, - { - "author_name": "Theerarat Kochakarn", - "author_inst": "Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand and" - }, - { - "author_name": "Arporn Wangwiwatsin", - "author_inst": "Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand" - }, - { - "author_name": "Khajohn Joonlasak", - "author_inst": "Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand" - }, - { - "author_name": "Angkana T. Huang", - "author_inst": "Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand" - }, - { - "author_name": "Bhakbhoom Panthan", - "author_inst": "Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Poramate Jiaranai", - "author_inst": "Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Krittikorn K\u00fcmpornsin", - "author_inst": "Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK" - }, - { - "author_name": "Namfon Kotanan", - "author_inst": "Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Wudtichai Manasatienkij", - "author_inst": "Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand" - }, - { - "author_name": "Treewat Watthanachockchai", - "author_inst": "Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Kingkan Rakmanee", - "author_inst": "Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Anthony R Jones", - "author_inst": "Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand" - }, - { - "author_name": "Stefan Fernandez", - "author_inst": "Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand" - }, - { - "author_name": "Insee Sensorn", - "author_inst": "Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Somnuek Sungkanuparph", - "author_inst": "Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand" - }, - { - "author_name": "Ekawat Pasomsub", - "author_inst": "Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Chonticha Klungthong", - "author_inst": "Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand" - }, - { - "author_name": "Thanat Chookajorn", - "author_inst": "Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Wasun Chantratita", - "author_inst": "Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.12.20128298", "rel_title": "Self-reported taste and smell disorders in patients with COVID-19: distinct features in China", @@ -1391654,6 +1392071,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128330", + "rel_title": "Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador.", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128330", + "rel_abs": "SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador.\n\nIMPORTANCECOVID-19, an infectious disease caused by SARS-CoV-2, has spread globally including Latin American countries including Ecuador. The first strain of SARS-CoV-2 sequenced was from Wuhan, which is considered as the reference strain. There were no data about the SARS-CoV-2 lineages in Ecuador, and the purpose of this study was to find out the origin of the different lineages circulating in the population. We also were interested in the mutations present in these genomes as they can influence virulence, transmission and infectivity.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sully Marquez", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Belen Prado-Vivar", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Juan Jose Guadalupe", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnologia Vegetal" + }, + { + "author_name": "Bernardo Gutierrez Granja", + "author_inst": "Department of Zoology, University of Oxford" + }, + { + "author_name": "Manuel Jibaja", + "author_inst": "Hospital Eugenio Espejo, Quito" + }, + { + "author_name": "Milton Tobar", + "author_inst": "Hospital Eugenio Espejo, Quito" + }, + { + "author_name": "Francisco Mora", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Juan Gaviria", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Maria Garcia", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Edison Ligna", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Franklin Espinosa", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Jorge Reyes", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Veronica Barragan", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Patricio Rojas-Silva", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Gabriel Trueba", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Michelle Grunauer", + "author_inst": "Universidad San Francisco de Quito, Escuela de Medicina, COCSA" + }, + { + "author_name": "Paul Cardenas", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129098", "rel_title": "Laboratory Testing Implications of Risk-Stratification and Management for Improving Clinical Outcomes of COVID-19 Patients", @@ -1392374,85 +1392874,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.06.13.150250", - "rel_title": "SARS-CoV-2 Neutralizing Antibody Responses Are More Robust in Patients with Severe Disease", - "rel_date": "2020-06-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.13.150250", - "rel_abs": "We studied plasma antibody responses of 35 patients about 1 month after SARS-CoV-2 infection. Titers of antibodies binding to the viral nucleocapsid and spike proteins were significantly higher in patients with severe disease. Likewise, mean antibody neutralization titers against SARS-CoV-2 pseudovirus and live virus were higher in the sicker patients, by ~5-fold and ~7-fold, respectively. These findings have important implications for those pursuing plasma therapy, isolation of neutralizing monoclonal antibodies, and determinants of immunity.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Pengfei Wang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Manoj S. Nair", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Michael T. Yin", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Yang Luo", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Qian Wang", - "author_inst": "Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School" - }, - { - "author_name": "Ting Yuan", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Kanako Mori", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Axel Guzman Solis", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Masahiro Yamashita", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Lawrence J. Purpura", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Justin C. Laracy", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Jian Yu", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Joseph Sodroski", - "author_inst": "Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "David D. Ho", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.14.150458", "rel_title": "Calreticulin co-expression supports high level production of a recombinant SARS-CoV-2 spike mimetic in Nicotiana benthamiana", @@ -1393164,6 +1393585,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20127241", + "rel_title": "Critical Questions when Interpreting Coronavirus PCR Diagnostics", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127241", + "rel_abs": "The results of PCR measurements are regarded as unquestionable. This statement must be put into perspective. This relativization is particularly important in connection with the interpretation of SARS-CoV-2 results. Members of the critical infrastructure, such as nurses, may be quarantined although this is not necessary and are therefore missing from patient care. With our small but impressive comparison of methods and transport media for SARS-CoV-2, we not only show the different sensitivity of common routine systems and media in laboratory medicine. Further, we would like to inform clinically working physicians, who are not familiar with the technical weaknesses of the PCR investigation, about gaps and present solutions for their daily work.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Juergen Durner", + "author_inst": "Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig- Maximilians-" + }, + { + "author_name": "Siegfried Burggraf", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Ludwig Czibere", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Tobias Fleige", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Michael Spannagl", + "author_inst": "Haemophilia Treatment Centre, Ludwig-Maximilians-University of Munich" + }, + { + "author_name": "David Watts", + "author_inst": "School of Medical Sciences and Photon Science Institute, University of Manchester, UK" + }, + { + "author_name": "Marc Becker", + "author_inst": "Laboratory Becker & Colleagues" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.11.20128991", "rel_title": "Transformed time series analysis of first-wave COVID-19: universal similarities found in the Group of Twenty (G20) Countries", @@ -1393816,73 +1394280,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.12.149229", - "rel_title": "Cystal structure of inhibitor-bound human MSPL/TMPRSS13 that can activate high pathogenic avian influenza", - "rel_date": "2020-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.149229", - "rel_abs": "Infection of certain influenza viruses is triggered when its hemagglutinin (HA) is cleaved by host cell proteases such as proprotein convertases and type II transmembrane serine proteases (TTSP). HA with a monobasic motif is cleaved by trypsin-like proteases, including TMPRSS2 and HAT, while the multibasic motif found in high pathogenicity avian influenza HA is cleaved by furin, PC5/6, or MSPL. MSPL belongs to the TMPRSS family and preferentially cleaves [R/K]-K-K-R{downarrow} sequences. Here, we solved the crystal structure of the extracellular region of human MSPL in complex with an irreversible substrate-analog inhibitor. The structure revealed three domains clustered around the C-terminal -helix of the SPD. The inhibitor structure and its putative model show that the P1-Arg inserts into the S1 pocket, whereas the P2-Lys and P4-Arg interacts with the Asp/Glu-rich 99-loop that is unique to MSPL. Based on the structure of MSPL, we also constructed a homology model of TMPRSS2, which is essential for the activation of the SARS-CoV-2 spike protein and infection. The model may provide the structural insight for the drug development for COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ayako Ohno", - "author_inst": "Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School" - }, - { - "author_name": "Nobuo Maita", - "author_inst": "Division of Disease Proteomics, Institute of Advanced Medical Sciences, Tokushima University" - }, - { - "author_name": "Takanori Tabata", - "author_inst": "Laboratory for Pharmacology, Pharmaceutical Research Center, Asahikasei Pharma" - }, - { - "author_name": "Hikaru Nagano", - "author_inst": "Department of Nutrition, Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University" - }, - { - "author_name": "Kyohei Arita", - "author_inst": "Graduate School of Medical Life Science, Yokohama City University" - }, - { - "author_name": "Mariko Ariyoshi", - "author_inst": "Graduate School of Frontier Biosciences, Osaka University" - }, - { - "author_name": "Takayuki Uchida", - "author_inst": "Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School" - }, - { - "author_name": "Reiko Nakao", - "author_inst": "Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School" - }, - { - "author_name": "Anayt Ulla", - "author_inst": "Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School" - }, - { - "author_name": "Kosuke Sugiura", - "author_inst": "Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School Graduate School" - }, - { - "author_name": "Koji Kishimoto", - "author_inst": "Graduate School of Technology, Industrial and Social Sciences, Tokushima University" - }, - { - "author_name": "Shigetada Teshima-Kondo", - "author_inst": "Department of Nutrition, Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University" - }, - { - "author_name": "Takeshi Nikawa", - "author_inst": "Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.06.12.148296", "rel_title": "DeepEMhacer: a deep learning solution for cryo-EM volume post-processing", @@ -1394510,6 +1394907,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20107086", + "rel_title": "COVID-19: Comparison between 8-days and extended 4-weeks outbreak periods through socioeconomic and natural factors", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20107086", + "rel_abs": "Since mid-March 2020, global COVID-19 pandemic has experienced an exponential growth in process from sporadic to sudden outbreaks. This paper selects the 8-day surge data of daily cases, death and recovery rates (March 19-26, 2020) from 18 countries with severe pandemic situation to discuss the impact of 9 factors of both socioeconomic and natural on the pathogen outbreak. Moreover, the paper also elaborates analysis and comparison of relatively slow 4-week (February 1-29, 2020) data of Chinas surge cases to determine the relationship between social and natural factors and on the spread of pandemic, which provides an effective reference for delaying and controlling the pandemic development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Sana Ullah", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Jianghua ZHENG", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China" + }, + { + "author_name": "Zhengkang ZUO", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Feizhou ZHANG", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Ke SHANG", + "author_inst": "School of Geophysics and Information Technology, China University of Geosciences, Beijing, 100083, China." + }, + { + "author_name": "Wenjie YU", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China." + }, + { + "author_name": "Yu FU", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Chuqiao HAN", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China." + }, + { + "author_name": "Yi LIN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Kaiwen JIANG", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Shanlin SUN", + "author_inst": "College of Electronic Information and Automation, Guilin University of Aerospace Technology, Guilin 541004, Guangxi Province China." + }, + { + "author_name": "Yiyuan SUN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Shoujiang ZHAO", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Lei YAN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.09.20120139", "rel_title": "Prevalence and Predictors of General Psychiatric Disorders and Loneliness during COVID-19 in the United Kingdom: Results from the Understanding Society UKHLS", @@ -1395134,45 +1395602,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.06.10.20122275", - "rel_title": "Predictors of household food insecurity in the United States during the COVID-19 pandemic", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20122275", - "rel_abs": "ObjectiveTo examine associations between sociodemographic and mental health characteristics with household food insecurity as a result of the COVID-19 outbreak.\n\nDesignCross-sectional online survey analyzed using univariable tests and a multivariable logistic regression model.\n\nSettingThe United States during the week of March 30, 2020.\n\nParticipantsConvenience sample of 1,965 American adults using Amazons Mechanical Turk (MTurk) platform. Participants reporting household food insecurity prior to the pandemic were excluded from analyses.\n\nResults1,517 participants reported household food security before the COVID-19 outbreak. Among this subset, 30% reported food insecurity after the COVID-19 outbreak, 53% were women and 72% were white. On multivariable analysis, race, income, relationship status, anxiety, and depression were significantly associated with incident household food insecurity. Black respondents, Hispanic/Latino respondents, and respondents with annual income less than $100,000 were significantly more likely to experience incident household food insecurity. Individuals experiencing incident household food insecurity were 2.09 (95% CI 1.58-2.83) times more likely to screen positively for anxiety and 1.88 (95% CI 1.37-2.52) times more likely to screen positively for depression.\n\nConclusionsFood insecurity due to the COVID-19 pandemic is common, and certain populations are particularly vulnerable. There are strong associations between food insecurity and anxiety/depression. Public health interventions to increase the accessibility of healthful foods, especially for Black and Hispanic/Latino communities, are crucial to relieving the economic stress of this pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Brianna N Lauren", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Elisabeth R Silver", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Adam S Faye", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Jennifer A Woo Baidal", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Elissa M Ozanne", - "author_inst": "University of Utah School of Medicine" - }, - { - "author_name": "Chin Hur", - "author_inst": "Columbia University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2020.06.09.20124719", "rel_title": "Kinetics of the humoral immune response to SARS-CoV-2: comparative analytical performance of seven commercial serology tests", @@ -1395860,6 +1396289,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.09.20126086", + "rel_title": "Private Health Sector in India: Ready and willing, yet underutilized in the Covid-19 pandemic.", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126086", + "rel_abs": "BackgroundThe private medical sector is a resource that must be estimated for efficient inclusion into public healthcare during pandemics.\n\nMethodsA survey was conducted among private healthcare workers to ascertain their views on the potential resources that can be accessed from the private sector and methods to do the same.\n\nResultsThere were 213 respondents, 80% of them being doctors. Nearly half (47.4%) felt that the contribution from the private medical sector has been suboptimal. Areas suggested for improved contributions by the private sector related to patient care (71.8%) and provision of equipment (62.4%), with fewer expectations (39.9%) on the research front. Another area of deemed support was maintaining continuity of care for non-COVID patients using virtual consultation services (77.4%), tele-consultation being the preferred option (60%). 58.2% felt that the Government had not involved the private sector adequately; and 45.1% felt they should be part of policy-making.\n\nConclusionA streamlined pathway to facilitate the private sector to join hands with the public sector for a national cause is the need of the hour. Through our study, we have identified gaps in the current contribution by the private sector and identified areas in which they could contribute, by their own admission.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Samira Davalbhakta", + "author_inst": "Byramjee Jeejeebhoy Government Medical College and Sassoon General Hospitals" + }, + { + "author_name": "Supriya Sharma", + "author_inst": "Department of Surgical Gastroenterology Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Shefali Gupta", + "author_inst": "Department of Microbiology Maharishi Markandeshwar Institute of Medical Sciences and Research (MMIMSR) Haryana, India" + }, + { + "author_name": "Vishwesh Agarwal", + "author_inst": "Mahatma Gandhi Missions Medical College" + }, + { + "author_name": "Gaurav Pandey", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Durga Prasanna Misra", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Bijaya Nanda Naik", + "author_inst": "Dept of Community Medicine NAMO Medical Education and Research Institute, Silvassa, DNH" + }, + { + "author_name": "Ashish Goel", + "author_inst": "University College Of Medical Sciences, New Delhi" + }, + { + "author_name": "Latika Gupta", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Vikas Agarwal", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.10.20127266", "rel_title": "Resource requirements for reintroducing elective surgery in England during the COVID-19 pandemic: a modelling study", @@ -1396540,49 +1397024,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.10.20127621", - "rel_title": "Ethnicity and outcomes in patients hospitalised with COVID-19 infection in East London: an observational cohort study", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127621", - "rel_abs": "BackgroundPreliminary studies suggest that people from Black, Asian and Minority Ethnic (BAME) backgrounds experience higher mortality from COVID-19 but the underlying reasons remain unclear.\n\nMethodsProspective analysis of registry data describing patients admitted to five acute NHS Hospitals in east London, UK for COVID-19. Emergency hospital admissions with confirmed SARS-CoV-2 aged 16 years or over were included. Data, including ethnicity, social deprivation, frailty, patient care and detailed risk factors for mortality, were extracted from hospital electronic records. Multivariable survival analysis was used to assess associations between ethnic group and mortality accounting for the effects of age, sex and various other risk factors. Results are presented as hazard ratios (HR) or odds ratios (OR) with 95% confidence intervals.\n\nFindings1996 adult patients were admitted between 1st March and 13th May 2020. After excluding 259 patients with missing ethnicity data, 1737 were included in our analysis of whom 511 had died by day 30 (29%). 538 (31%) were from Asian, 340 (20%) Black and 707 (40%) white backgrounds. Compared to White patients, those from BAME backgrounds were younger, with differing co-morbidity profiles and less frailty. Asian and Black patients were more likely to be admitted to intensive care and to receive invasive ventilation (OR 1{middle dot}54, [1{middle dot}06-2{middle dot}23]; p=0{middle dot}023 and 1{middle dot}80 [1{middle dot}20-2{middle dot}71]; p=0{middle dot}005, respectively). After adjustment for age and sex, patients from Asian (HR 1{middle dot}49 [1{middle dot}19-1{middle dot}86]; p<0{middle dot}001) and Black (HR 1{middle dot}30 [1{middle dot}02-1{middle dot}65]; p=0{middle dot}036) backgrounds were more likely to die. These findings persisted across a range of risk-factor adjusted analyses.\n\nInterpretationPatients from Asian and Black backgrounds are more likely to die from COVID-19 infection despite controlling for all previously identified confounders. Higher rates of invasive ventilation in intensive care indicate greater acute disease severity. Our analyses suggest that patients of Asian and Black backgrounds suffered disproportionate rates of premature death from COVID-19.\n\nFundingNone\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Google Scholar, Medrxiv, Trip Medical Database and internet search engines from inception to May 10th 2020, using the terms \"(COVID-19 or 2019-nCoV or SARS-CoV-2) AND (ethnicity)\", with no language restrictions, for research articles, editorials and commentaries. We identified 25 articles. Ten were international opinion pieces, fifteen were research articles reporting analyses of national and cohort datasets, predominantly in the United Kingdom (UK) and United States (US). Each of these studies indicated an increased risk of adverse outcomes in people from BAME backgrounds; either in terms of COVID-19 acquisition, disease severity or mortality. However, the underlying causes were unclear. Aggregated US data determined the relative risk of death for those of Black ethnicity compared to White ethnic groups to be 3.57. Three UK biobank cohort studies, limited by low BAME representation, described ethnicity as an independent risk factor of COVID-19 infection, partially attenuated by socio-economic status (SES). Analysis of a London hospital cohort of 520; experiencing 144 deaths, revealed an age and co-morbidity adjusted mortality odds ratio of 1.72 in Black populations of borderline significance. Age and geographical region-adjusted standardised mortality ratios, derived from UK composite hospital data, emphasised ethnic differences; being 2.41 for Bangladeshis and 3.24 for Black Africans. The impact of gender and deprivation was not explored. Another study of 5683 in-hospital deaths (England alone; 629 (11%) BAME) confirmed increased mortality risks in people from Black and Asian groups only partially attributable to social deprivation and co-morbidity but did not adjust for other vulnerability factors. There remained a need for a more detailed analysis of outcomes across different ethnic groups in a large, high acuity dataset, adjusting for broader clinical and laboratory prognostic factors, alongside SES, smoking status, age, body mass index (BMI) and sex.\n\nAdded value of this studyWe conducted a large observational cohort study of COVID-19 hospital admissions within an area which experienced the highest rates of COVID-19 infection and mortality in the UK. It offers detailed insight into a majority (60%) ethnically diverse cohort and adds substantial evidence that ethnicity is a predictor of poor outcomes for COVID-19 patients at, and beyond, 30 days. Using robust multivariable survival analyses we have quantified and described the impact on this association of a number of additional prognostic factors such as frailty score and markers of inflammation alongside age, sex, deprivation, co-morbidity, BMI and smoking status. Those of Asian and Black ethnicities were consistently found to have an increased risk of 30 and 90 day mortality and an increased risk of requiring mechanical ventilation as compared to those of White ethnicity. The peak CRP and D-dimer levels in those of Black ethnicity were significantly higher than those of other ethnicities suggesting that these biological differences may accompany greater disease severity and increased risk of adverse outcomes.\n\nImplications of all the available evidenceIt is clear that ethnicity is a predictor of a positive SARS-CoV2 result, disease severity and mortality, regardless of age, sex, geographical location, deprivation, smoking status, BMI, co-morbidities and frailty. The association appears to be underpinned by a combination of factors including SES, pre-existing health conditions, biological risk factors such as D-dimers, environmental and structural determinants of health; but their relative contribution is unclear. Understanding these drivers is critical to designing interventions and refining clinical and Public Health policies. The evidence also emphasises the need for robust surveillance of ethnicity in health care research.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vanessa J Apea", - "author_inst": "Department of Infection and Immunity, Royal London Hospital, Barts Health NHS Trust; Blizard Institute, Queen Mary University of London" - }, - { - "author_name": "Yize I Wan", - "author_inst": "William Harvey Research Institute, Queen Mary University of London" - }, - { - "author_name": "Rageshri Dhairyawan", - "author_inst": "Department of Infection and Immunity, Royal London Hospital, Barts Health NHS Trust; Blizard Institute, Queen Mary University of London" - }, - { - "author_name": "Zudin A Puthucheary", - "author_inst": "William Harvey Research Institute, Queen Mary University of London" - }, - { - "author_name": "Rupert M Pearse", - "author_inst": "William Harvey Research Institute, Queen Mary University of London" - }, - { - "author_name": "Chloe M Orkin", - "author_inst": "Department of Infection and Immunity, Royal London Hospital, Barts Health NHS Trust; Blizard Institute, Queen Mary University of London" - }, - { - "author_name": "John R Prowle", - "author_inst": "William Harvey Research Institute, Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.10.20127530", "rel_title": "State heterogeneity of human mobility and COVID-19 epidemics in the European Union", @@ -1397386,6 +1397827,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20127894", + "rel_title": "A scenario modeling pipeline for COVID-19 emergency planning", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127894", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused strain on health systems worldwide due to its high mortality rate and the large portion of cases requiring critical care and mechanical ventilation. During these uncertain times, public health decision makers, from city health departments to federal agencies, sought the use of epidemiological models for decision support in allocating resources, developing non-pharmaceutical interventions, and characterizing the dynamics of COVID-19 in their jurisdictions. In response, we developed a flexible scenario modeling pipeline that could quickly tailor models for decision makers seeking to compare projections of epidemic trajectories and healthcare impacts from multiple intervention scenarios in different locations. Here, we present the components and configurable features of the COVID Scenario Pipeline, with a vignette detailing its current use. We also present model limitations and active areas of development to meet ever-changing decision maker needs.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Joseph Chadi Lemaitre", + "author_inst": "EPFL" + }, + { + "author_name": "Kyra H Grantz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joshua Kaminsky", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Hannah R Meredith", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Shaun A Truelove", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Stephen A Lauer", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lindsay T Keegan", + "author_inst": "University of Utah" + }, + { + "author_name": "Sam Shah", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Josh Wills", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Kathryn Kaminsky", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Javier Perez-Saez", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.10.20127589", "rel_title": "Effect of social distancing on COVID-19 incidence and mortality in the US", @@ -1397958,29 +1398466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20128173", - "rel_title": "Optimizing the COVID-19 Intervention Policy in Scotland and the Case for Testing and Tracing", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128173", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWUnlike other European countries the UK has abandoned widespread testing and tracing of known SARS-CoV-2 carriers in mid-March. The reason given was that the pandemic was out of control and with wide community based spread it would not be possible to contain it by tracing any longer. Like other countries the UK has since relied on a lockdown as the main measure to contain the virus (or more precisely the reproduction number[R] ) at significant economic and social cost. It is clear that this level of lockdown cannot be sustained until a vaccine is available, yet it is not clear what an exit strategy would look like that avoids the danger of a second (or subsequent waves).\n\nIn this paper we argue that, when used within a portfolio of intervention strategies, widespread testing and tracing leads to significant cost savings compared to using lockdown measures alone. While the effect is most pronounced if a large proportion of the infectious population can be identified and their contacts traced, under reasonable assumptions there are still significant savings even if the fraction of infectious people found by tracing is small.\n\nWe also present a policy optimization model that finds, for given assumptions on the disease parameters, the best intervention strategy to contain the virus by varying the degree of tracing and lockdown measure (and vaccination once that option is available) over time. We run the model on data fitted to the published COVID-19 outbreak figures for Scotland. The model suggests an intervention strategy that keeps the number of COVID-19 deaths low using a combination of tracing and lockdown. This strategy would only require lockdown measures equivalent to a reduction of[R] to about 1.8-2.0 if lockdown was used alone, at acceptable economic cost, while the model finds no such strategy without tracing enabled.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andreas Grothey", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Kenneth I.M. McKinnon", - "author_inst": "School of Mathematics, University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20128710", "rel_title": "Rotational Thromboelastometry predicts care level in Covid-19", @@ -1398760,6 +1399245,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128389", + "rel_title": "Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128389", + "rel_abs": "BackgroundTesting is one of the commendable preventive measures against coronavirus disease (COVID-19), and needs to be done using both most appropriate specimen and an accurate diagnostic test like real time reverse transcription polymerase chain reaction (qRT-PCR). However, the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from different clinical specimens after onset of symptoms is not yet well established. For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted.\n\nMethodsThe systematic search was done using PubMed/MEDLINE, Science direct, Google Scholar, among others. The search included studies on laboratory diagnosis of SARS-CoV-2 from different clinical specimens using PCR. Data extraction was done using Microsoft Excel spread sheet 2010 and reported according to PRISMA-P guidelines. Using Open Meta Analyst software, DerSimonian-Laird random effects analysis was performed to determine a summary estimate (positive rate [PR]/proportions) and their 95% confidence interval (95%CI).\n\nResultsA total of 8136 different clinical specimens were analyzed to detect SARS-CoV-2, with majority being nasopharyngeal swabs (69.6%). Lower respiratory tract (LRT) specimens had a PR of 71.3% (95%CI:60.3%-82.3%) while no virus was detected from the urinogenital specimens. Bronchoalveolar lavage fluid (BLF) specimen had the PR of 91.8% (95%CI:79.9-103.7%), followed by rectal swabs, 87.8 % (95%CI:78.6%-96.9%) then sputum, 68.1% (95%CI:56.9%-79.4%). Low PR was observed in oropharyngeal swabs, 7.6% (95%CI:5.7%-9.6%) and blood samples, 1.0% (95%CI: -0.1%-2.1%), whilst no SARS-CoV-2 was detected in urine samples. Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95%CI:31.2%-59.7%).\n\nConclusionIn this study, SARS-CoV-2 was highly detected in lower respiratory tract specimens while there was no detected virus in urinogenital specimens. Regarding the type of clinical specimens, bronchoalveolar lavage fluid had the highest positive rate followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had a moderate detection rate. Low positive rate was recorded in oropharyngeal swab and blood sample while no virus was found in urine samples. More importantly, the virus was detected in feces, suggesting SARS-CoV-2 transmission by the fecal route.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "George M. Bwire", + "author_inst": "School of Pharmacy, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania." + }, + { + "author_name": "Mtebe V. Majigo", + "author_inst": "School of Medicine, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + }, + { + "author_name": "Belinda J. Njiro", + "author_inst": "School of Medicine, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + }, + { + "author_name": "Akili Mawazo", + "author_inst": "Institute of Allied Health Sciences, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.11.20128165", "rel_title": "Easing social distancing index after COVID-19 pandemic", @@ -1399284,37 +1399800,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.11.20128652", - "rel_title": "Coronavirus and birth in Italy: results of a national population-based cohort study", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128652", - "rel_abs": "IntroductionThe study was implemented to provide guidance to decision-makers and clinicians by describing hospital care offered to women who gave birth with confirmed COVID-19 infection.\n\nMaterials and methodsNational population-based prospective cohort study involving all women with confirmed COVID-19 who gave birth between February 25 and April 22, 2020 in any Italian hospital.\n\nResultsThe incidence rate of confirmed SARS-CoV-2 infection in women who gave birth was 2.1 per 1000 maternities at a national level and 6.9/1000 in the Lombardy Region. Overall one third of the women developed a pneumonia and 49.7% assumed at least one drug. Caesarean section rate was 32.9%, no mothers nor newborns died. Six percent of the infants tested positive for SARS - CoV-2 at birth.\n\nConclusionsClinical features and outcomes of COVID-19 in women who gave birth are similar to those described for the general population, most women developing mild to moderate illness.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alice Maraschini", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Edoardo Corsi", - "author_inst": "University of Rome Tor Vergata" - }, - { - "author_name": "Michele Antonio Salvatore", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Serena Donati", - "author_inst": "Istituto Superiore di Sanita" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.06.11.20128702", "rel_title": "Emotional health concerns of oncology physicians in the United States: fallout during the COVID-19 pandemic", @@ -1400646,6 +1401131,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.10.20127175", + "rel_title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "rel_abs": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Amitava Banerjee", + "author_inst": "University College London" + }, + { + "author_name": "Suliang Chen", + "author_inst": "University College London" + }, + { + "author_name": "Laura Pasea", + "author_inst": "University College London" + }, + { + "author_name": "Alvina Lai", + "author_inst": "University College London" + }, + { + "author_name": "Michail Katsoulis", + "author_inst": "UCL" + }, + { + "author_name": "Spiros Denaxas", + "author_inst": "University College London" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Bryan Williams", + "author_inst": "UCL" + }, + { + "author_name": "Wai Keong Wong", + "author_inst": "University College London Hospitals NHS Trust" + }, + { + "author_name": "Ameet Bakhai", + "author_inst": "Royal Free Hospitals NHS Trust" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Deenan Pillay", + "author_inst": "UCL" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "UCL" + }, + { + "author_name": "Honghan Wu", + "author_inst": "UCL" + }, + { + "author_name": "Nilesh Pareek", + "author_inst": "King's College Hospital" + }, + { + "author_name": "Daniel Bromage", + "author_inst": "Kings College London" + }, + { + "author_name": "Theresa Mcdonagh", + "author_inst": "Kings College London" + }, + { + "author_name": "Jonathan Byrne", + "author_inst": "Kings London NHS Trust" + }, + { + "author_name": "James T Teo", + "author_inst": "Kings College Hospital NHS Foundation Trust" + }, + { + "author_name": "Ajay Shah", + "author_inst": "King's College London" + }, + { + "author_name": "Ben Humberstone", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Liang V Tang", + "author_inst": "Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Anoop SV Shah", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Andrea Rubboli", + "author_inst": "Ospedale S. Maria delle Croci, Ravenna, Italy" + }, + { + "author_name": "Yutao Guo", + "author_inst": "PLA General Hospital, Beijing, China." + }, + { + "author_name": "Yu Hu", + "author_inst": "Huazhong University of Science and Technology, Wuhan, China." + }, + { + "author_name": "Cathie LM Sudlow", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Gregory YH Lip", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Harry Hemingway", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.10.20127258", "rel_title": "Knowledge, attitudes, and practices among the general population during COVID-19 outbreak in Iran: A national cross-sectional survey", @@ -1401346,33 +1401962,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.09.20126862", - "rel_title": "Bayesian investigation of SARS-CoV-2-related mortality in France", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126862", - "rel_abs": "The SARS-CoV-2 epidemic in France has focused a lot of attention as it has had one of the largest death tolls in Europe. It provides an opportunity to examine the effect of the lockdown and of other events on the dynamics of the epidemic. In particular, it has been suggested that municipal elections held just before lockdown was ordered may have helped spread the virus. In this manuscript we use Bayesian models of the number of deaths through time to study the epidemic in 13 regions of France. We found that the models accurately predict the number of deaths 2 to 3 weeks in advance, and recover estimates that are in agreement with recent models that rely on a different structure and different input data. In particular, the lockdown reduced the viral reproduction number by {approx} 80%. However, using a mixture model, we found that the lockdown had had different effectiveness depending on the region, and that it had been slightly more effective in decreasing the reproduction number in denser regions. The mixture model predicts that 2.08 (95% CI: 1.85-2.47) million people had been infected by May 11, and that there were 2567 (95% CI: 1781-5182) new infections on May 10. We found no evidence that the reproduction numbers differ between week-ends and week days, and no evidence that the reproduction numbers increased on the election day. Finally, we evaluated counterfactual scenarios showing that ordering the lockdown 1 to 7 days sooner would have resulted in 19% to 76% fewer deaths, but that ordering it 1 to 7 days later would have resulted in 21% to 266% more deaths. Overall, the predictions of the model indicate that holding the elections on March 15 did not have a detectable impact on the total number of deaths, unless it motivated a delay in imposing the lockdown.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Louis Duchemin", - "author_inst": "Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France" - }, - { - "author_name": "Philippe Veber", - "author_inst": "Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France" - }, - { - "author_name": "Bastien Boussau", - "author_inst": "Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.09.20126805", "rel_title": "What does and does not correlate with COVID-19 death rates", @@ -1402204,6 +1402793,73 @@ "type": "confirmatory results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.06.10.144816", + "rel_title": "Remdesivir but not famotidine inhibits SARS-CoV-2 replication in human pluripotent stem cell-derived intestinal organoids", + "rel_date": "2020-06-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144816", + "rel_abs": "Gastrointestinal symptoms in COVID-19 are associated with prolonged symptoms and increased severity. We employed human intestinal organoids derived from pluripotent stem cells (PSC-HIOs) to analyze SARS-CoV-2 pathogenesis and to validate efficacy of specific drugs in the gut. Certain, but not all cell types in PSC-HIOs express SARS-CoV-2 entry factors ACE2 and TMPRSS2, rendering them susceptible to SARS-CoV-2 infection. Remdesivir, a promising drug to treat COVID-19, effectively suppressed SARS-CoV-2 infection of PSC-HIOs. In contrast, the histamine-2-blocker famotidine showed no effect. Thus, PSC-HIOs provide an interesting platform to study SARS-CoV-2 infection and to identify or validate drugs.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jan Krueger", + "author_inst": "Ulm University" + }, + { + "author_name": "Ruediger Gross", + "author_inst": "Ulm University" + }, + { + "author_name": "Carina Conzelmann", + "author_inst": "Ulm University" + }, + { + "author_name": "Janis A Mueller", + "author_inst": "Ulm University" + }, + { + "author_name": "Lennart Koepke", + "author_inst": "Ulm University" + }, + { + "author_name": "Konstantin Sparrer", + "author_inst": "Ulm University" + }, + { + "author_name": "Desiree Schuetz", + "author_inst": "Ulm University" + }, + { + "author_name": "Thomas Seufferlein", + "author_inst": "Ulm University" + }, + { + "author_name": "Thomas F.E. Barth", + "author_inst": "Ulm University" + }, + { + "author_name": "Steffen Stenger", + "author_inst": "Ulm University" + }, + { + "author_name": "Sandra Heller", + "author_inst": "Ulm University" + }, + { + "author_name": "Alexander Kleger", + "author_inst": "Ulm University" + }, + { + "author_name": "Jan Muench", + "author_inst": "Ulm University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.11.140285", "rel_title": "ROBOCOV: An affordable open-source robotic platform for COVID-19 testing by RT-qPCR", @@ -1403104,45 +1403760,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.09.141101", - "rel_title": "SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins", - "rel_date": "2020-06-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.09.141101", - "rel_abs": "Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and may assemble within viral factories, dynamic compartments formed within the host cells. Here, we examine the possibility that the multivalent RNA-binding nucleocapsid protein (N) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) compacts RNA via protein-RNA liquid-liquid phase separation (LLPS) and that N interactions with host RNA-binding proteins are mediated by phase separation. To this end, we created a construct expressing recombinant N fused to a N-terminal maltose binding protein tag which helps keep the oligomeric N soluble for purification. Using in vitro phase separation assays, we find that N is assembly-prone and phase separates avidly. Phase separation is modulated by addition of RNA and changes in pH and is disfavored at high concentrations of salt. Furthermore, N enters into in vitro phase separated condensates of full-length human hnRNPs (TDP-43, FUS, and hnRNPA2) and their low complexity domains (LCs). However, N partitioning into the LC of FUS, but not TDP-43 or hnRNPA2, requires cleavage of the solubilizing MBP fusion. Hence, LLPS may be an essential mechanism used for SARS-CoV-2 and other RNA viral genome packing and host protein co-opting, functions necessary for viral replication and hence infectivity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Theodora Myrto Perdikari", - "author_inst": "Center for Biomedical Engineering, Brown University" - }, - { - "author_name": "Anastasia C Murthy", - "author_inst": "Molecular Biology, Cell Biology & Biochemistry Graduate Program, Brown University" - }, - { - "author_name": "Veronica H Ryan", - "author_inst": "Neuroscience Graduate Program, Brown University" - }, - { - "author_name": "Scott Watters", - "author_inst": "Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University" - }, - { - "author_name": "Mandar T Naik", - "author_inst": "Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University" - }, - { - "author_name": "Nicolas L Fawzi", - "author_inst": "Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.10.144188", "rel_title": "Age-dependent progression of SARS-CoV-2 infection in Syrian hamsters", @@ -1404046,6 +1404663,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.08.20125658", + "rel_title": "Temporal evolution of COVID-19 in the states of India using SIQR Model", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125658", + "rel_abs": "COVID 19 entered during the last week of April 2020 in India has caused 3,546 deaths with 1,13,321 number of reported cases. Indian government has taken many proactive steps, including strict lockdown of the entire nation for more than 50 days, identification of hotspots, app-based tracking of citizens to track infected. This paper investigated the evolution of COVID 19 in five states of India (Maharashtra, UP, Gujrat, Tamil Nadu, and Delhi) from 1st April 2020 to 20th May 2020. Variation of doubling rate and reproduction number (from SIQR) with time is used to analyse the performance of the majorly affected Indian states. It has been determined that Uttar Pradesh is one of the best performers among five states with the doubling rate crossing 18 days as of 20th May. Tamil Nadu has witnessed the second wave of infections during the second week of May. Maharashtra is continuously improving at a steady rate with its doubling rate reaching to 12.67 days. Also these two states are performing below the national average in terms of infection doubling rate. Gujrat and Delhi have reported the doubling rate of 16.42 days and 15.49 days respectively. Comparison of these states has also been performed based on time-dependent reproduction number. Recovery rate of India has reached to 40 % as the day paper is written.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "ALOK TIWARI", + "author_inst": "IIT BOMBAY" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20125062", "rel_title": "Principles and Practice of SARS-CoV-2 Decontamination of N95 Masks with UV-C", @@ -1404670,69 +1405306,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.08.20125989", - "rel_title": "Longitudinal Surveillance for SARS-CoV-2 RNA Among Asymptomatic Staff in Five Colorado Skilled Nursing Facilities: Epidemiologic, Virologic and Sequence Analysis.", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125989", - "rel_abs": "SARS-CoV-2 emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 also has been notable due to its impacts on individuals residing within skilled nursing facilities (SNFs) such as rehabilitation centers and nursing homes. SNF residents tend to possess several risk factors for the most severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of multiple comorbidities. Indeed, residents of long-term care facilities represent approximately 40 percent of US SARS-CoV-2 deaths. To assess the prevalence and incidence of SARS-CoV-2 among SNF workers, determine the extent of asymptomatic infection by SARS-CoV-2, and provide information on the genomic epidemiology of the virus within these unique care settings, we sampled workers weekly at five SNFs in Colorado using nasopharyngeal swabs, determined the presence of viral RNA and infectious virus among these workers, and sequenced 48 nearly complete genomes. This manuscript reports results from the first five to six weeks of observation. Our data reveal a strikingly high degree of asymptomatic infection, a strong correlation between RNA detection and the presence of infectious virus in NP swabs, persistent RNA in a subset of individuals, and declining incidence over time. Our data suggests that asymptomatic individuals infected by SARS-CoV-2 may contribute to virus transmission within the workplace.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Kendra Quicke", - "author_inst": "Colorado State University" - }, - { - "author_name": "Emily Gallichote", - "author_inst": "CSU" - }, - { - "author_name": "Nicole Sexton", - "author_inst": "CSU" - }, - { - "author_name": "Emily Fitzmeyer", - "author_inst": "CSU" - }, - { - "author_name": "Michael Young", - "author_inst": "CSU" - }, - { - "author_name": "Ashley Janich", - "author_inst": "CSU" - }, - { - "author_name": "Karen Dobos", - "author_inst": "CSU" - }, - { - "author_name": "Kristy Pabilonia", - "author_inst": "CSU" - }, - { - "author_name": "Gregory Gahm", - "author_inst": "Vivage Senior Living" - }, - { - "author_name": "Elizabeth J Carlton", - "author_inst": "University of Colorado, Colorado School of Public Health" - }, - { - "author_name": "Gregory D Ebel", - "author_inst": "Colorado State University" - }, - { - "author_name": "Nicole Ehrhart", - "author_inst": "CSU, Columbine Health Systems Center for Healthy Aging" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.08.20125484", "rel_title": "An analysis of SARS-CoV-2 viral load by patient age", @@ -1405999,6 +1406572,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.08.139477", + "rel_title": "An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance", + "rel_date": "2020-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.139477", + "rel_abs": "With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jayeshkumar Narsibhai Davda", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Keith Frank", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Sivakumar Prakash", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Gunjan Purohit", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Devi Prasad Vijayashankar", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Dhiviya Vedagiri", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Karthik Bharadwaj Tallapaka", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Krishnan Harinivas Harshan", + "author_inst": "CSIR-Centre for Cellular and Molecular Biollgy" + }, + { + "author_name": "Archana Bharadwaj Siva", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Rakesh Kumar Mishra", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Jyotsna Dhawan", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Imran Siddiqi", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.07.20121939", "rel_title": "Mortality Analysis of COVID-19 Confirmed cases in Pakistan", @@ -1406819,65 +1407455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.08.20115683", - "rel_title": "Adverse Outcomes and Mortality in Users of Non-Steroidal Anti-Inflammatory Drugs tested positive for SARS-CoV-2: A Danish Nationwide Cohort Study", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20115683", - "rel_abs": "BackgroundConcerns over the safety of non-steroidal anti-inflammatory drug (NSAID) use during SARS-CoV-2 infection have been raised.\n\nObjectivesTo study whether use of NSAIDs is associated with adverse outcomes and mortality during SARS-CoV-2 infection.\n\nDesignPopulation based cohort study\n\nSettingDanish administrative and health registries.\n\nParticipants Individuals tested positive for SARS-CoV-2 during Feb 27, 2020 to Apr 29, 2020. Treated individuals (defined as a filled NSAID prescription up to 30 days before the SARS-CoV-2 test) were matched to up to 4 non-treated individuals on propensity scores based on age, sex, relevant comorbidities and prescription fills.\n\nOutcome measuresThe main outcome was 30-day mortality and treated individuals were compared to untreated individuals using risk ratios (RR) and risk differences (RD). Secondary outcomes included hospitalisation, intensive care unit (ICU) admission, mechanical ventilation and acute renal replacement therapy.\n\nResultsA total of 9236 SARS-CoV-2 PCR positive individuals were eligible for inclusion. Of these, 248 (2.7%) had filled a prescription for NSAIDs and 535 (5.8%) died within 30 days. In the matched analyses, treatment with NSAIDs was not associated with 30-day mortality (RR 1.02, 95% CI 0.57 to 1.82; RD 0.1%, -3.5% to 3.7%), increased risk of hospitalisation (RR 1.16, 0.87 to 1.53; RD 3.3%, -3.4% to 10%), ICU-admission (RR 1.04, 0.54 to 2.02; RD 0.2%, -3.0% to 3.4%), mechanical ventilation (RR 1.14, 0.56 to 2.30; RD 0.5%, - 2.5% to 3.6%), or renal replacement therapy (RR 0.86, 0.24 to 3.09; RD -0.2%, -2.0% to 1.6%).\n\nConclusionUse of NSAIDs was not associated with 30-day mortality, hospitalisation, ICU-admission, mechanical ventilation or renal replacement therapy in Danish individuals tested positive for SARS-CoV-2.\n\nRegistrationThe European Union electronic Register of Post-Authorisation Studies, EUPAS-34734 (http://www.encepp.eu/encepp/viewResource.htm?id=34735)", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lars Christian Lund", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Kasper Bruun Kristensen", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Mette Reilev", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Steffen Christensen", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Reimar W. Thomsen", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Christian F. Christiansen", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Henrik Stoevring", - "author_inst": "Aarhus University" - }, - { - "author_name": "Nanna Borup Johansen", - "author_inst": "Danish Medicines Agency" - }, - { - "author_name": "Nikolai Brun", - "author_inst": "Danish Medicines Agency" - }, - { - "author_name": "Jesper Hallas", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Anton Pottegaard", - "author_inst": "University of Southern Denmark" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.08.140152", "rel_title": "D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly", @@ -1407849,6 +1408426,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.08.20125377", + "rel_title": "Weather variables impact on COVID-19 incidence", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125377", + "rel_abs": "We test the hypothesis of COVID-19 contagion being influenced by meteorological parameters such as temperature or humidity. We analysed data at high spatial resolution (regions in Italy and counties in the USA) and found that while at low resolution this might seem the case, at higher resolution no correlation is found. Our results are consistent with a poor outdoors transmission of the disease. However, a possible indirect correlation between good weather and a decrease in disease spread may occur, as people spend longer time outdoors.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Javier G. Corripio", + "author_inst": "meteoexploration.com" + }, + { + "author_name": "Lorna Raso", + "author_inst": "meteoexploration.com" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.08.20124305", "rel_title": "Time-series plasma cell-free DNA analysis reveals disease severity of COVID-19 patients", @@ -1408397,33 +1408997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.06.08.20125583", - "rel_title": "An optimal lockdown relaxation strategy for minimizing the economic effects of covid-19 outbreak in Sri Lanka", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125583", - "rel_abs": "In order to recover the damage to the economy by the ongoing covid-19 pandemic, many countries consider the transition from strict lockdowns to partial lockdowns through relaxation of preventive measures. In this work, we propose an optimal lockdown relaxation strategy, which is aimed at minimizing the damage to the economy, while confining the covid-19 incidence to a level endurable by the available healthcare facilities in the country. In order to capture the transmission dynamics, we adopt the compartment models and develop the relevant optimization model, which turns out to be non-linear. We generate approximate solutions to the problem, whereas our experimentation is based on the data on the covid-19 outbreak in Sri Lanka.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anuradha C Mahasinghe", - "author_inst": "University of Colombo, Sri Lanka" - }, - { - "author_name": "Hasitha Erandi", - "author_inst": "University of Colombo, Sri Lanka" - }, - { - "author_name": "Sanjeewa Perera", - "author_inst": "University of Colombo, Sri Lanka" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.06.08.20124990", "rel_title": "An Aberration Detection-Based Approach for Sentinel Syndromic Surveillance of COVID-19 and Other Novel Influenza-Like Illnesses", @@ -1409231,6 +1409804,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.06.20124149", + "rel_title": "Hawkes process modeling of COVID-19 with mobility leading indicators and spatial covariates", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124149", + "rel_abs": "Hawkes processes are used in machine learning for event clustering and causal inference, while they also can be viewed as stochastic versions of popular compartmental models used in epidemiology. Here we show how to develop accurate models of COVID-19 transmission using Hawkes processes with spatial-temporal covariates. We model the conditional intensity of new COVID-19 cases and deaths in the U.S. at the county level, estimating the dynamic reproduction number of the virus within an EM algorithm through a regression on Google mobility indices and demographic covariates in the maximization step. We validate the approach on short-term forecasting tasks, showing that the Hawkes process outperforms several benchmark models currently used to track the pandemic, including an ensemble approach and a SEIR-variant. We also investigate which covariates and mobility indices are most important for building forecasts of COVID-19 in the U.S.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wen-Hao Chiang", + "author_inst": "Indiana University-Purdue University Indianapolis" + }, + { + "author_name": "Xueying Liu", + "author_inst": "Indiana University-Purdue University Indianapolis" + }, + { + "author_name": "George Mohler", + "author_inst": "Indiana University-Purdue University Indianapolis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.04.20122325", "rel_title": "Sub-weekly cycle uncovers the hidden link of 1atmospheric pollution to Kawasaki Disease", @@ -1409927,25 +1410527,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.06.20124529", - "rel_title": "A Machine Learning Explanation of Incidence Inequalities of SARS-CoV-2 Across 88 Days in 157 Countries", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124529", - "rel_abs": "Because the SARS-CoV-2 (COVID-19) pandemic viral outbreaks will likely continue until effective vaccines are widely administered, (1) new capabilities to accurately predict incidence rates by location and time to know in advance the disease burden and specific needs for any given population are valuable to minimize morbidity and mortality. In this study, a random forest of 9,250 regression trees was applied to 6,941 observations of 13 statistically significant predictor variables targeting SARS-CoV-2 incidence rates per 100,000 across 88 days in 157 countries. One key finding is an algorithm that can predict the incidence rate per day of a SARS-CoV-2 epidemic cycle with a pseudo-R2 accuracy of 98.5% and explain 97.4% of the variances. Another key finding is the relative importance of 13 demographic, economic, environmental, and public health modulators to the SARS-CoV-2 incidence rate. Four factors proposed in earlier research as potential modulators have no statistically significant relationship with incidence rates (2)(3). These findings give leaders new capabilities for improved capacity planning and targeting stay-at-home interventions and prioritizing programming by knowing the atypical social determinants that are the root causes of SARS-CoV-2 incidence variance. This work also proves that machine learning can accurately and quickly explain disease dynamics for zoonoses with pandemic potential.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Eric Luellen", - "author_inst": "Bioinformatix" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.06.20124313", "rel_title": "Closed form solution of the SIR model for the COVID-19 outbreak in Italy", @@ -1411053,6 +1411634,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.06.05.20123117", + "rel_title": "Serology confirms SARS-CoV-2 infection in PCR-negative children presenting with Paediatric Inflammatory Multi-System Syndrome", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123117", + "rel_abs": "BackgroundDuring the COVID-19 outbreak, reports have surfaced of children who present with features of a multisystem inflammatory syndrome with overlapping features of Kawasaki disease and toxic shock syndrome - Paediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 pandemic (PIMS-TS). Initial reports find that many of the children are PCR-negative for SARS-CoV-2, so it is difficult to confirm whether this syndrome is a late complication of viral infection in an age group largely spared the worst consequences of this infection, or if this syndrome reflects enhanced surveillance.\n\nMethodsChildren hospitalised for symptoms consistent with PIMS-TS between 28 April and 8 May 2020, and who were PCR-negative for SARS-CoV-2, were tested for antibodies to viral spike glycoprotein using an ELISA test.\n\nResultsEight patients (age range 7-14 years, 63% male) fulfilled case-definition for PIMS-TS during the study period. Six of the eight patients required admission to intensive care. All patients exhibited significant IgG and IgA responses to viral spike glycoprotein. Further assessment showed that the IgG isotypes detected in children with PIMS-TS were of the IgGl and lgG3 subclasses, a distribution similar to that observed in samples from hospitalised adult COVID-19 patients. In contrast, lgG2 and lgG4 were not detected in children or adults. IgM was not detected in children, which contrasts with adult hospitalised adult COVID-19 patients of whom all had positive IgM responses.\n\nConclusionsStrong IgG antibody responses can be detected in PCR-negative children with PIMS-TS. The low detection rate of IgM in these patients is consistent with infection having occurred weeks previously and that the syndrome onset occurs well after the control of SARS-CoV-2 viral load. This implies that the disease is largely immune-mediated. Lastly, this indicates that serology can be an appropriate diagnostic tool in select patient groups.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Marisol Perez-Toledo", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sian E. Faustini", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sian E. Jossi", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Adrian Shields", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Hari Krishnan Kanthimathinathan", + "author_inst": "Birmingham Women and Children's NHS Foundation Trust" + }, + { + "author_name": "Joel D. Allen", + "author_inst": "University of Southampton" + }, + { + "author_name": "Yasunori Watanabe", + "author_inst": "University of Southampton" + }, + { + "author_name": "Margaret Goodall", + "author_inst": "University of Birmingham" + }, + { + "author_name": "David C. Wraith", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tonny V. Veenith", + "author_inst": "University Hospitals Birmingham NHS Trust" + }, + { + "author_name": "Mark T. Drayson", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Deepthi Jyothish", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Eslam Al-Abadi", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Ashish Chikermane", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Steven Welch", + "author_inst": "University Hospitals Birmingham" + }, + { + "author_name": "Kavitha Masilamani", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Scott Hackett", + "author_inst": "University Hospitals Birmingham" + }, + { + "author_name": "Max Crispin", + "author_inst": "University of Southampton" + }, + { + "author_name": "Barnaby Scholefield", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Adam F. Cunningham", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Alex G. Richter", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.05.20123745", "rel_title": "Combined oropharyngeal/nasal swab is equivalent to nasopharyngeal sampling for SARS-CoV-2 diagnostic PCR", @@ -1411509,33 +1412189,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.05.20123547", - "rel_title": "Multiscale dynamics of COVID-19 and model-based recommendations for 105 countries", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123547", - "rel_abs": "We analyse the dynamics of COVID-19 using computational modelling at multiple scales. For large scale analysis, we propose a 2-scale lattice extension of the classical SIR-type compartmental model with spatial interactions called the Lattice-SIRQL model. Computational simulations show that global quantifiers are not completely representative of the actual dynamics of the disease especially when mitigation measures such as quarantine and lockdown are applied. Furthermore, using real data of confirmed COVID-19 cases, we calibrate the Lattice-SIRQL model for 105 countries. The calibrated model is used to make country specific recommendations for lockdown relaxation and lockdown continuation. Finally, using an agent-based model we analyse the influence of cluster level relaxation rate and lockdown duration on disease spreading.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jithender J. Timothy", - "author_inst": "Ruhr University Bochum" - }, - { - "author_name": "Vijaya Holla", - "author_inst": "Ruhr University Bochum" - }, - { - "author_name": "Guenther Meschke", - "author_inst": "Ruhr University Bochum" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.04.20122812", "rel_title": "'Drawing on Wisdom to Cope with Adversity:' A Systematic Review Protocol of Older Adults' Mental and Psychosocial Health During Acute Respiratory Disease Propagated-Type Epidemics and Pandemics (COVID-19, SARS-CoV, MERS, and Influenza).", @@ -1412231,6 +1412884,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.04.20122317", + "rel_title": "Heart Disease Deaths during the Covid-19 Pandemic", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122317", + "rel_abs": "The SARS-CoV-2 pandemic is associated with a reduction in hospitalization for an acute cardiovascular conditions. In a major health system in Massachusetts, there was a 43% reduction in these types of hospitalizations in March 2020 compared with March 2019.4 Whether mortality rates from heart disease have changed over this period is unknown.\n\nWe assembled information from the National Center for Health Statistics (Centers for Disease Control and Prevention) for 118,356,533 person-weeks from Week 1 (ending January 4) through Week 17 (ending April 25) of 2020 for the state of Massachusetts. We found that heart disease deaths are unchanged during the Covid-19 pandemic period as compared to the corresponding period of 2019. This is despite reports that admissions for acute myocardial infarction have fallen during this time.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jeremy Faust", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Zhenqiu Lin", + "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" + }, + { + "author_name": "Harlan Krumholz", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.07.137802", "rel_title": "Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system", @@ -1412959,37 +1413639,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.03.20120337", - "rel_title": "Belief of Previous COVID-19 Infection and Unclear Government Policy are Associated with Reduced Willingness to Participate in App-Based Contact Tracing: A UK-Wide Observational Study of 13,000 Patients", - "rel_date": "2020-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120337", - "rel_abs": "BackgroundContact tracing and lockdown are health policies being used worldwide to combat the coronavirus (COVID-19). While easing lockdown, the UK National Health Service (NHS) launched its Track and Trace Service at the end of May 2020, and aims by end of June 2020 also to include app-based notification and advice to self-isolate for those who have been in contact with a person known to have COVID-19. To be successful, such an app will require high uptake, the determinants and willingness for which are unclear but essential to understand for effective public health benefit.\n\nObjectivesTo measure the determinants of willingness to participate in an NHS app-based contact tracing programme using a questionnaire within the Care Information Exchange (CIE) - the largest patient-facing electronic health record in the NHS.\n\nMethodsObservational study of 47,708 registered NHS users of the CIE, 27% of whom completed a novel questionnaire asking about willingness to participate in app-based contact tracing, understanding of government advice, mental and physical wellbeing and their healthcare utilisation -- related or not to COVID-19. Descriptive statistics are reported alongside univariate and multivariable logistic regression models, with positive or negative responses to a question on app-based contact tracing as the dependent variable.\n\nResults26.1% of all CIE participants were included in the analysis (N = 12,434, 43.0% male, mean age 55.2). 60.3% of respondents were willing to participate in app-based contact tracing. Out of those who responded no, 67.2% stated that this was due to privacy concerns. In univariate analysis, worsening mood, fear and anxiety in relation to changes in government rules around lockdown were associated with lower willingness to participate. Multivariable analysis showed that difficulty understanding government rules was associated with a decreased inclination to download the app, with those scoring 1-2 and 3-4 in their understanding of the new government rules being 45% and 27% less inclined to download the contact tracing app, respectively; when compared to those who rated their understanding as 5-6/10 (OR for 1-2/10 = 0.57 [CI 0.48 - 0.67]; OR for 3-4/10 = 0.744 [CI 0.64 - 0.87]), whereas scores of 7-8 and 9-10 showed a 43% and 31% respective increase. Those reporting an unconfirmed belief of having previously had and recovered from COVID-19 were 27% less likely to be willing to download the app; belief of previous recovery from COVID-19 infection OR 0.727 [0.585 - 0.908]).\n\nConclusionsIn this large UK-wide questionnaire of wellbeing in lockdown, a willingness for app-based contact tracing is 60% - close to the estimated 56% population uptake, and substantially less than the smartphone-user uptake considered necessary for an app-based contact-tracing to be an effective intervention to help suppress an epidemic. Given this marginal level of support over an appropriate age range, the impacts of difficulty comprehending government advice and a policy of not testing to confirm self-reported COVID-19 infection during lockdown indicate that uncertainty in communication and diagnosis in adopted public health policies will negatively impact the effectiveness of a government contact tracing app.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Patrik Bachtiger", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alexander Adamson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jennifer K Quint", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nicholas S Peters", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.26.20114009", "rel_title": "How Should Clinicians Interpret Imprecise Trials Assessing Drugs for COVID-19 Patients?", @@ -1414253,6 +1414902,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20117499", + "rel_title": "Emergency calls are early indicators of ICU bed requirement during the COVID-19 epidemic", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20117499", + "rel_abs": "BackgroundAlthough the number of intensive care unit (ICU) beds is crucial during the COVID-19 epidemic caring for the most critically ill infected patients, there is no recognized early indicator to anticipate ICU bed requirements.\n\nMethodsIn the Ile-de-France region, from February 20 to May 5, 2020, emergency medical service (EMS) calls and the response provided (ambulances) together the percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, general practitioner (GP) and emergency department (ED) visits, and hospital admissions of COVID-19 patients were recorded daily and compared to the number of COVID-19 ICU patients. Correlation curve analysis was performed to determine the best correlation coefficient (R), depending on the number of days the indicator has been shifted. A delay [≥]7 days was considered as an early alert, and a delay [≥]14 days a very early alert.\n\nFindingsEMS calls, percentage of positive RT-PCR tests, ambulances used, ED and GP visits of COVID-19 patients were strongly associated with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipate ICU bed requirement.\n\nInterpretationThe daily number of COVID19-related telephone calls received by the EMS and corresponding dispatch ambulances, and the proportion of positive RT-PCR tests were the earliest indicators of the number of COVID19 patients requiring ICU care during the epidemic crisis in the Ile-de-France region, rapidly followed by ED and GP visits. This information may help health authorities to anticipate a future epidemic, including a second wave of COVID19 or decide additional social measures.\n\nFundingOnly institutional funding was provided.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed and preprint archives for articles published up to May 17, 2020, that contained information about the anticipation of intensive care unit (ICU) bed requirement during the COVID-19 outbreak using the terms \"coronavirus\", \"2009-nCOV\", \"COVID-19\", SARS-CoV2\", \"prediction\" \"resource\" and \"intensive care\". We also reviewed relevant references in retrieved articles and the publicly available publication list of the COVID-19 living systematic review.22 This list contains studies on covid-19 published on PubMed and Embase through Ovid, bioRxiv, and medRxiv, and is continuously updated. Although many studies estimated the number of patients who would have severe COVID-19 requiring ICU, very few contained assessment for early signals (from internet or social media), and we retrieved no study whose data came from suspected or infected patients.\n\nAdded values of this studyDuring the COVID-19 epidemic, emergency medical system (EMS) calls, percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, ambulance dispatch, emergency department (ED) and general practitioner (GP) visits of COVID-19 patients were strongly associated with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipated COVID-19 ICU bed requirement.\n\nImplication of all available evidenceEMS calls and ambulance dispatch, percent of positive RT-PCR, and ED and GP visits could be valuable tools as daily alert signals to set up plan to face the burden of ICU bed requirement during the initial wave of the COVID-19 epidemic, and may possibly also help anticipating a second wave. These results are important since mortality has been reported being correlated to health care resources.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- The COVID-19 APHP-Universities-INRIA-INSERM Group", + "author_inst": "" + }, + { + "author_name": "Bruno Riou", + "author_inst": "Sorbonne Universite and Assistance Publique-Hopitaux de Paris, Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.06.01.20119560", "rel_title": "Covid-19 Epidemiological Factor Analysis: Identifying Principal Factors with Machine Learning", @@ -1414733,25 +1415405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.02.20119883", - "rel_title": "A simplified model for the analysis of COVID-19 evolution during the lockdown period in Italy", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20119883", - "rel_abs": "A simplified model applied to COVID-19 cases detected and officially published by the italian government [1], seems to fit quite well the time evolution of the disease in Italy during the period feb-24th - may-19th 2020.\n\nThe hypothesis behind the model is based on the fact that in the lockdown period the infection cannot be transmitted due to social isolation and, more generally, due to the strong protection measures in place during the observation period. In this case a compartment model is used and the interactions between the different compartments are simplified. The sample of cases detected is intended as a set of individuals susceptible to infection which, after being exposed and undergoing the infection, were isolated ( treated) in such a way they can no longer spread the infection.\n\nThe values obtained are to be considered indicative.\n\nThe same model has been applied both to the data relating to Italy and to some regions of Italy (Lombardia, Piemonte, Lazio, Campania, Calabria, Sicilia, Sardegna), generally finding a good response and indicatively interesting values (see chap. 5).\n\nThe only tuning parameter is the incubation period{tau} that, together with the calculated growth rate{kappa} of the exponential curve used to approximate the early stage data, in this modelization, are in strong relationship with the compartments transfer rates.\n\nIn particular[R] 0 and the numerical value of{kappa} (dimensionless) in this model are linked by the relation:[R] 0 = 1/{kappa}2\n\nRevision HistoryO_ST_ABSRevision # 1C_ST_ABSO_LIErrata corrige in section 1 (Introduction): the equations that summarize the relationship between the parameters were wrong. This revised version contains the correct equations at page 2.\nC_LIO_LIThe synchronization criteria is updated. No need to use a threshold different to the one used to determine the growth coefficient. The results are now updated with the synchronization point near to the 20% of the maximum value of the cases detected per day: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD\nC_LIO_LIModifications in section 4 (Model results for Italy). It is appropriate to use an exponential function instead of a logistic function to find the growth rate in the initial phase. Section 4 and the results are now updated.\nC_LIO_LISome non-substantial corrections in the descriptive part.\nC_LI\n\nRevision # 2O_LIErrata corrige in the system differential equation 6: in the the derivative of S were reported a wrong additional term N. Now the equation 6 is correct.\nC_LI", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Roberto Simeone", - "author_inst": "None" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.03.20120576", "rel_title": "A RELAXATION VIEWPOINT TO COVID-19 INFECTION", @@ -1415595,6 +1416248,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.03.20121590", + "rel_title": "Deep Learning and Holt-Trend Algorithms for predicting COVID-19 pandemic", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121590", + "rel_abs": "According to WHO, more than one million individuals are infected with COVID-19, and around 20000 people have died because of this infectious disease around the world. In addition, COVID-19 epidemic poses serious public health threat to the world where people with little or no pre-existing human immunity can be more vulnerable to the effects of the effects of the coronavirus. Thus, developing surveillance systems for predicting COVID-19 pandemic in an early stage saves millions of lives. In this study, the deep learning algorithm and Holt-trend model is proposed to predict coronavirus. The Long-Short Term Memory (LSTM) algorithm and Holt-trend were applied to predict confirmed numbers and death cases. The real time data have been collected from the World Health Organization (WHO). In the proposed research, we have considered three countries to test the proposed model namely Saudi Arabia, Spain and Italy. The results suggest that the LSTM models showed better performance in predicting the cases of coronavirus patients. Standard measure performance MSE, RMSE, Mean error and correlation are employed to estimate the results of the proposed models. The empirical results of the LSTM by using correlation metric are 99.94%, 99.94% and 99.91 to predict number of confirmed cases on COVID-19 in three countries. Regarding the prediction results of LSTM model to predict the number of death on COVID-19 are 99.86%, 98.876% and 99.16 with respect to the Saudi Arabia, Italy and Spain respectively. Similarly the experimented results of Holt-Trend to predict the number of confirmed cases on COVID-19 by using correlation metrics are 99.06%, 99.96% and 99.94, whereas the results of Holt-Trend to predict the number of death cases are 99.80%, 99.96 and 99.94 with respect to the Saudi Arabia, Italy and Spain respectively. The empirical results indicate the efficient performance of the presented model in predicting the number of confirmed and death cases of COVID-19 in these countries. Such findings provide better insights about the future of COVID-19 in general. The results were obtained by applying the time series models which needs to be considered for the sake of saving the lives of many people.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Theyazn H.H Aldhyani", + "author_inst": "Department of Computer Science and Information at king faisal University, Kingdom of Saudi Arabia" + }, + { + "author_name": "Melfi Alrasheed Sr.", + "author_inst": "Department of Quantitative Methods, School of Business, King Faisal University. Saudi" + }, + { + "author_name": "Ahmed i Abdullah Alqarn Sr.", + "author_inst": "Department of Computer Sciences and Information Technology, Albaha University," + }, + { + "author_name": "Mohammed Y. Alzahrani", + "author_inst": "Department of Computer Sciences and Information Technology, Albaha University" + }, + { + "author_name": "Ahmed H., Alahmadi", + "author_inst": "Department of Computer Science and Information at Taibah University," + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.04.20121848", "rel_title": "An Agent Based Model methodology for assessing spread and health systems burden for Covid-19 using a synthetic population from India", @@ -1416431,29 +1417119,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.03.132134", - "rel_title": "Detection dogs as a help in the detection of COVID-19: Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples? Proof-of-concept study", - "rel_date": "2020-06-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.132134", - "rel_abs": "The aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount of positive samples sniffing ranging from four to ten. For this proof of concept, we kept 8 dogs of the initial group (explosive detection dogs and colon cancer detection dogs), who performed a total of 368 trials, and will include the other dogs in our future studies as their adaptation to samples scenting takes more time.The percentages of success of the dogs to find the positive sample in a line containing several other negative samples or mocks (2 to 6) were 100p100 for 4 dogs, and respectively 83p100, 84p100, 90p100 and 94p100 for the others, all significantly different from the percentage of success that would be obtained by chance alone.We conclude that there is a very high evidence that the armpits sweat odour of COVID-19+ persons is different, and that dogs can detect a person infected by the SARS-CoV-2 virus.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Riad Sarkis", - "author_inst": "University Saint Joseph Beirout Lebanon" - }, - { - "author_name": "Jean-Pierre Tourtier", - "author_inst": "HIA Begin Saint Mande France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2020.06.04.20121947", "rel_title": "Extended use or re-use of single-use surgical masks and filtering facepiece respirators: A rapid evidence review", @@ -1417752,6 +1418417,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.06.04.20122846", + "rel_title": "A tertiary center experience of multiple myeloma patients with COVID-19: lessons learned and the path forward", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122846", + "rel_abs": "BackgroundThe COVID-19 pandemic, caused by SARS-CoV-2 virus, has resulted in over 100,000 deaths in the United States. Our institution has treated over 2,000 COVID-19 patients during the pandemic in New York City. The pandemic directly impacted cancer patients and the organization of cancer care. Mount Sinai Hospital has a large and diverse multiple myeloma (MM) population. Herein, we report the characteristics of COVID-19 infection and serological response in MM patients in a large tertiary care institution in New York.\n\nMethodsWe performed a retrospective study on a cohort of 58 patients with a plasma-cell disorder (54 MM, 4 smoldering MM) who developed COVID-19 between March 1, 2020 and April 30, 2020. We report epidemiological, clinical and laboratory characteristics including persistence of viral detection by polymerase chain reaction (PCR) and anti-SARS-CoV-2 antibody testing, treatments initiated, and outcomes.\n\nResultsOf the 58 patients diagnosed with COVID-19, 36 were hospitalized and 22 were managed at home. The median age was 67 years; 52% of patients were male and 63% were non-white. Hypertension (64%), hyperlipidemia (62%), obesity (37%), diabetes mellitus (28%), chronic kidney disease (24%) and lung disease (21%) were the most common comorbidities. In the total cohort, 14 patients (24%) died. Older age (>70 years), male sex, cardiovascular risk, and patients not in complete remission (CR) or stringent CR were significantly (p<0.05) associated with hospitalization. Among hospitalized patients, laboratory findings demonstrated elevation of traditional inflammatory markers (CRP, ferritin, D-dimer) and a significant (p<0.05) association between elevated inflammatory markers, severe hypogammaglobulinemia, non-white race, and mortality. Ninety-six percent (22/23) of patients developed antibodies to SARS-CoV-2 at a median of 32 days after initial diagnosis. Median time to PCR negativity was 43 (range 19-68) days from initial positive PCR.\n\nConclusionsDrug exposure and MM disease status at the time of contracting COVID-19 had no bearing on mortality. Mounting a severe inflammatory response to SARS-CoV-2 and severe hypogammaglobulinemia were associated with higher mortality. The majority of patients mounted an antibody response to SARS-CoV-2. These findings pave a path to identification of vulnerable MM patients who need early intervention to improve outcome in future outbreaks of COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Bo Wang", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Oliver Van Oekelen", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Tarek Mouhieddine", + "author_inst": "Mount Sinai Hospital" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Joshua Richter", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Hearn Jay Cho", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Shambavi Richard", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Ajai Chari", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sundar Jagannath", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Samir Parekh", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Deepu Madduri", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.06.04.20122564", "rel_title": "Adverse effects of COVID-19 related lockdown on pain, physical activity and psychological wellbeing in people with chronic pain", @@ -1418192,45 +1418924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.04.20121830", - "rel_title": "Effect of gamma sterilization on filtering efficiency of various respiratory face-masks", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20121830", - "rel_abs": "Three types of respiratory masks viz N95, nonwoven fabric and double layer cotton cloth are being used as an essential inhalation protective measure against COVID-19 by suppressing the entry of respiratory droplets. The filtering efficiency of these masks were tested before and after sterilisation using gamma radiation for the two flow rate conditions corresponding normal breath rate (20lpm) and during sneezing/coughing (90lpm).Sterilisation is carried out using a gamma irradiator containing Co-60 source for the two dose exposures viz. 15kGy and 25kGy.The filtering efficiency for surgical (nonwoven fabric) and double layer cotton cloth mask is found to vary from 18% to 22% for the cumulative particle of size [≥] 0.3{micro}m in both un-irradiated and irradiated condition. The filtration efficiency of N95 mask is found to be reduced to 70% for the most penetrating particle size (0.3 {micro}m) with the flow rate of 20lpm and further reduced for particles in the range of 0.1 and 0.2{micro}m with flow rate of 90 lpm. The reduction in efficiency after gamma sterilization is associated with reduction of electrostatic interaction of filter medium with particles laden in the air stream. Even with reduced filtering efficiency due to gamma sterilisation, the N95 masks are much superior than the surgical and cloth masks. Instead of disposing N95 mask after single use, they can be reused a few times as N70 mask during this pandemic crisis after sterilisation using gamma radiation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Amit Kumar", - "author_inst": "Indira Gandhi Centre for Atomic Research" - }, - { - "author_name": "D. N. Saneetha", - "author_inst": "Indira Gandhi Centre for Atomic Research" - }, - { - "author_name": "Ramani Yuvaraj", - "author_inst": "Indira Gandhi Centre for Atomic Research" - }, - { - "author_name": "M. Menaka", - "author_inst": "Indira Gandhi Centre for Atomic Research" - }, - { - "author_name": "V. Subramanian", - "author_inst": "Indira Gandhi Centre for Atomic Research" - }, - { - "author_name": "B. Venkatraman", - "author_inst": "Indira Gandhi Centre for Atomic Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.04.20122473", "rel_title": "FAST: a Feasible, Accurate and Speedy Test Strategy for COVID-19", @@ -1419062,6 +1419755,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.03.132639", + "rel_title": "Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors", + "rel_date": "2020-06-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.132639", + "rel_abs": "Development of an anti-SARS-CoV-2 therapeutic is hindered by the lack of physiologically relevant model systems that can recapitulate host-viral interactions in human cell types, specifically the epithelium of the lung. Here, we compare induced pluripotent stem cell (iPSC)-derived alveolar and airway epithelial cells to primary lung epithelial cell controls, focusing on expression levels of genes relevant for COVID-19 disease modeling. iPSC-derived alveolar epithelial type II-like cells (iAT2s) and iPSC-derived airway epithelial lineages express key transcripts associated with lung identity in the majority of cells produced in culture. They express ACE2 and TMPRSS2, transcripts encoding essential host factors required for SARS-CoV-2 infection, in a minor subset of each cell sub-lineage, similar to frequencies observed in primary cells. In order to prepare human culture systems that are amenable to modeling viral infection of both the proximal and distal lung epithelium, we adapt iPSC-derived alveolar and airway epithelial cells to two-dimensional air-liquid interface cultures. These engineered human lung cell systems represent sharable, physiologically relevant platforms for SARS-CoV-2 infection modeling and may therefore expedite the development of an effective pharmacologic intervention for COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Kristine M Abo", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Liang Ma", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Taylor Matte", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Jessie Huang", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Konstantinos D Alysandratos", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Rhiannon B Werder", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Aditya Mithal", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Mary Lou Beermann", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Jonathan Lindstrom-Vautrin", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Gustavo Mostoslavsky", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Laertis Ikonomou", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Darrell N Kotton", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Finn Hawkins", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Andrew Wilson", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Carlos Villacorta-Martin", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.04.135012", "rel_title": "Olfactory transmucosal SARS-CoV-2 invasion as port of Central Nervous System entry in COVID-19 patients", @@ -1419878,109 +1420646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.02.20120477", - "rel_title": "Detection of asymptomatic SARS-CoV-2 exposed individuals by a sensitive S-based ELISA.", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120477", - "rel_abs": "The current SARS-CoV-2 pandemic has highlighted a need for easy and safe blood sampling in combination with accurate serological methodology. Venipuncture is usually performed by trained staff at health care centers. Long travel distances may introduce a bias of testing towards relatively large communities with close access to health care centers. Rural regions may thus be overlooked. Here, we demonstrate a sensitive method to measure antibodies to the S-protein of SARS-CoV-2. We adapted and optimized this assay for clinical use together with capillary blood sampling to meet the geographical challenges of serosurveillance. Finally, we tested remote at-home capillary blood sampling together with centralized assessment of S-specific IgG in a rural region of northern Scandinavia that encompasses 55,185 sq kilometers. We conclude that serological assessment from capillary blood sampling gives comparable results as analysis of venous blood. Importantly, at-home sampling enabled citizens living in remote rural areas access to centralized and sensitive laboratory antibody tests.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Julia Wigren", - "author_inst": "Umea University" - }, - { - "author_name": "Linnea Vikstrom", - "author_inst": "Umea University" - }, - { - "author_name": "Ebba Rosendal", - "author_inst": "Umea University" - }, - { - "author_name": "Remigius Groening", - "author_inst": "Umea University" - }, - { - "author_name": "Kwon Yongdae", - "author_inst": "Umea University" - }, - { - "author_name": "Emma Nilsson", - "author_inst": "Umea University" - }, - { - "author_name": "Atin Sharma", - "author_inst": "Umea University" - }, - { - "author_name": "akbar espaillat", - "author_inst": "Umea University" - }, - { - "author_name": "Leo Hanke", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Gerald McInerney", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Andrea Puhar", - "author_inst": "Umea University" - }, - { - "author_name": "Felipe Cava", - "author_inst": "Umea University" - }, - { - "author_name": "Gunilla B Karlsson Hedestam", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Therese Thunberg", - "author_inst": "Umea University" - }, - { - "author_name": "Tor Monsen", - "author_inst": "Umea University" - }, - { - "author_name": "Fredrik Elgh", - "author_inst": "Umea University" - }, - { - "author_name": "Magnus Evander", - "author_inst": "Umea University" - }, - { - "author_name": "Anders Johansson", - "author_inst": "Umea University" - }, - { - "author_name": "Anna K Overby", - "author_inst": "Umea University" - }, - { - "author_name": "Clas Ahlm", - "author_inst": "Umea University" - }, - { - "author_name": "Johan Normark", - "author_inst": "Umea University" - }, - { - "author_name": "Mattias Forsell", - "author_inst": "Umea University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.02.20120865", "rel_title": "Decreased plasma levels of the survival factor renalase are associated with worse outcomes in COVID-19", @@ -1420684,6 +1421349,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.01.20119347", + "rel_title": "COVID-19 Public Sentiment Insights and MachineLearning for Tweets Classification", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119347", + "rel_abs": "Along with the Coronavirus pandemic, another crisis has manifested itself in the form of mass fear and panic phenomena, fueled by incomplete and often inaccurate information. There is therefore a tremendous need to address and better understand COVID-19s informational crisis and gauge public sentiment, so that appropriate messaging and policy decisions can be implemented. In this research article, we identify public sentiment associated with the pandemic using Coronavirus specific Tweets and R statistical software, along with its sentiment analysis packages. We demonstrate insights into the progress of fear-sentiment over time as COVID-19 approached peak levels in the United States, using descriptive textual analytics supported by necessary textual data visualizations. Furthermore, we provide a methodological overview of two essential machine learning (ML) classification methods, in the context of textual analytics, and compare their effectiveness in classifying Coronavirus Tweets of varying lengths. We observe a strong classification accuracy of 91% for short Tweets, with the Naive Bayes method. We also observe that the logistic regression classification method provides a reasonable accuracy of 74% with shorter Tweets, and both methods showed relatively weaker performance for longer Tweets. This research provides insights into Coronavirus fear sentiment progression, and outlines associated methods, implications, limitations and opportunities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jim Samuel", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Ali G. G. Md. Nawaz", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Md Mokhlesur Rahman", + "author_inst": "University of North Carolina at Charlotte, Charlotte, NC; Khulna University of Engineering & Technology (KUET), Khulna, Bangladesh" + }, + { + "author_name": "Ek Esawi", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Yana Samuel", + "author_inst": "Northeastern University, Boston, MA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.29.20117143", "rel_title": "Detection of lung hypoperfusion in Covid-19 patients during recovery by digital imaging quantification", @@ -1421180,81 +1421880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.30.20117945", - "rel_title": "COVID-SGIS: A smart tool for dynamic monitoring and temporal forecasting of Covid-19", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117945", - "rel_abs": "ObjectiveThe new kind of coronavirus SARS-Cov2 spread to countries in all continents in the World. The coronavirus disease 2019 (Covid-19) causes fever, cough, sore throat, and in severe cases shortness of breath and death. To evaluate strategies, it is necessary to forecast the number of cases and deaths, in order to aid the stakeholders in the process of making decisions against the disease. We propose a system for real-time forecast of the cumulative cases of Covid-19 in Brazil.\n\nStudy DesignMonitoring of all Brazilian cities using oficial information from the National Notification System, from March to May 2020, concentrated on Brazil.io databases. Training and evaluation of ARIMA and other machine learning algorithms for temporal forecasting using correlation indexes (Pearsons, Spearmans, and Kendalls) and RMSE(%). Validation from the relative errors of the following six days.\n\nMethodsOur developed software, COVID-SGIS, captures information from the 26 states and the Distrito Federal at the Brazil.io database. From these data, ARIMA models are created for the accumulation of confirmed cases and death cases by Covid-19. Finally, six-day forecasts graphs are available for Brazil and for each of its federative units, separately, with a 95% CI. In addition to these predictions, the worst and best scenarios are also presented.\n\nResultsARIMA models were generated for Brazil and its 27 federative units. The states of Bahia, Maranhao, Piaui, Rio Grande do Norte and Amapa, Rondonia every day of the predictions were in the projection interval. The same happened to the states of Espirito Santo, Minas Gerais, Parana and Santa Catarina. In Brazil, the percentage error between the predicted values and the actual values varied between 2.56% and 6.50%. For the days when the forecasts outside the prediction interval, the percentage errors in relation to the worst case scenario were below 5%. The states of Bahia, Maranhao, Piaui, Rio Grande do Norte, Amapa, and Rondonia every day of the predictions were in the projection interval. The same happened to the states of Espirito Santo, Minas Gerais, Parana and Santa Catarina.\n\nConclusionThe proposed method for dynamic forecasting may be used to guide social policies and plan direct interventions in a robust, flexible and fast way. Since it is based on information from multiple databases, it can be adapted to the different realities, becoming an important tool to guide the course of politics and action against Covid-19 pandemic worldwide.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Clarisse Lins de Lima", - "author_inst": "Escola Politecnica da Universidade de Pernambuco" - }, - { - "author_name": "Cecilia Cordeiro da Silva", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Ana Clara Gomes da Silva", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Eduardo Luiz Silva", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Gabriel Souza Marques", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Lucas Job Brito de Araujo", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Luiz Antonio Albuquerque Junior", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Samuel Barbosa Jatoba de Souza", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Maira Araujo de Santana", - "author_inst": "Escola Politecnica de Universidade de Pernambuco" - }, - { - "author_name": "Juliana Carneiro Gomes", - "author_inst": "Escola Politecnica da Universidade de Pernambuco" - }, - { - "author_name": "Valter Augusto de Freitas Barbosa", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Anwar Musah", - "author_inst": "University College London" - }, - { - "author_name": "Patty Kostkova", - "author_inst": "University College London" - }, - { - "author_name": "Wellington Pinheiro dos Santos", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Abel Guilhermino da Silva Filho", - "author_inst": "Universidade Federal de Pernambuco" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.30.20117770", "rel_title": "COVID-19 apparent reproductive number dropped during Spain's nationwide dropdown, then spiked at lower-incidence regions", @@ -1421870,6 +1422495,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.30.20117853", + "rel_title": "Evaluating the Efficacy of Stay-At-Home Orders: Does Timing Matter?", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117853", + "rel_abs": "BACKGROUNDThe many economic, psychological, and social consequences of pandemics and social distancing measures create an urgent need to determine the efficacy of non-pharmaceutical interventions (NPIs), and especially those considered most stringent, such as stay-at-home and self-isolation mandates. This study focuses specifically on the efficacy of stay-at-home orders, both nationally and internationally, in the control of COVID-19.\n\nMETHODSWe conducted an observational analysis from April to May 2020 and included countries and US states with known stay-at-home orders. Our primary exposure was the time between the date of the first reported case of COVID-19 to an implemented stay-at-home mandate for each region. Our primary outcomes were the time from the first reported case to the highest number of daily cases and daily deaths. We conducted simple linear regression analyses, controlling for the case rate of the outbreak.\n\nRESULTSFor US states and countries, a larger number of days between the first reported case and stay-at-home mandates was associated with a longer time to reach the peak daily case and death counts. The largest effect was among regions classified as the latest 10% to implement a mandate, which in the US, predicted an extra 35.3 days to the peak number of cases (95 % CI: 18.2, 52.5), and 38.3 days to the peak number of deaths (95 % CI: 23.6, 53.0).\n\nCONCLUSIONSOur study supports the potential beneficial effect of earlier stay-at-home mandates, by shortening the time to peak case and death counts for US states and countries. Regions in which mandates were implemented late experienced a prolonged duration to reaching both peak daily case and death counts.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alexandra Medline, MPH", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Lamar Hayes, MPH", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Farnoosh Vahedi", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Katia Valdez", + "author_inst": "Fielding School of Public Health, University of California Los Angeles" + }, + { + "author_name": "Jake Sonnenberg", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Will Capell", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Ami Hayashi", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Zoe Glick", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Jeffrey D. Klausner, MD, MPH", + "author_inst": "UCLA David Geffen School of Medicine and Fielding School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.31.20118315", "rel_title": "Cytokine biomarkers of COVID-19", @@ -1422438,41 +1423114,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.31.20118059", - "rel_title": "The Chest CT Features of Coronavirus Disease 2019 (COVID-19) in China: A Meta-analysis of 19 Trials", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118059", - "rel_abs": "ObjectiveThis study aimed to summarize the characteristics of chest CT imaging in Chinese patients with Coronavirus Disease 2019 (COVID-19) to provide reliable evidence for further guiding clinical routine.\n\nMethodsPubMed, Embase and Web of Science databases were thoroughly searched to identified relevant articles involving the features of chest CT imaging in Chinese patients with COVID-19. All data were analyzed utilizing R software version i386 4.0.0. Random-effects models were employed to calculate pooled mean differences.\n\nResults19 trials incorporating 1332 cases were included in the study. The results demonstrated that the incidence of ground-glass opacities (GGO) was 0.79, consolidation was 0.34; mixed GGO and consolidation was 0.46; air bronchogram sign was 0.41; crazy paving pattern was 0.32; interlobular septal thickening was 0.55; reticulation was 0.30; bronchial wall thickening was 0.24; vascular enlargement was 0.74. subpleural linear opacity was 0.28; intrathoracic lymph node enlargement was 0.03; pleural effusions was 0.03. The distribution in lung: the incidence of central was 0.05; peripheral was 0.74; peripheral involving central was 0.38; diffuse was 0.19; unifocal involvement was 0.09; multifocal involvement was 0.57; unilateral was 0.16; bilateral was 0.83; The incidence of lobes involved (>2) was 0.70; lobes involved ([less double equals]2) was 0.35.\n\nConclusionGGO, vascular enlargement, interlobular septal thickening more frequently occurred in patients with COVID-19. Peripheral, bilateral, involved lobes >2 might be the features of COVID-19 in the distribution aspect. Therefore, based on the aboved features of COVID-19 in chest CT imaging, it might be a promising means for identifying COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Haitao Yang", - "author_inst": "Department of pulmonary and critical care medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital" - }, - { - "author_name": "lan yuzhu", - "author_inst": "Department of pulmonary and critical care medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital" - }, - { - "author_name": "Xiujuan Yao", - "author_inst": "Department of pulmonary and critical care medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital" - }, - { - "author_name": "Sheng Lin", - "author_inst": "Department of pulmonary and critical care medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital" - }, - { - "author_name": "Baosong Xie", - "author_inst": "Department of pulmonary and critical care medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.06.01.20118869", "rel_title": "It's the very time to learn a pandemic lesson: why have predictive techniques been ineffective when describing long-term events?", @@ -1423152,6 +1423793,37 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.03.129817", + "rel_title": "Closing coronavirus spike glycoproteins by structure-guided design", + "rel_date": "2020-06-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.129817", + "rel_abs": "The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface, determining host and tissue tropism, and fusion of the viral and host membranes. Although SARS-CoV- 2 S is the main target of neutralizing antibodies and the focus of vaccine design, its stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a prefusion SARS-CoV-2 S ectodomain trimer construct covalently stabilized in the closed conformation. Structural and antigenicity analysis showed we successfully shut S in the closed state without otherwise altering its architecture. Finally, we show that this engineering strategy is applicable to other {beta}-coronavirus S glycoproteins and might become an important tool for vaccine design, structural biology, serology and immunology studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Matthew McCallum", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.02.130955", "rel_title": "Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations", @@ -1423636,73 +1424308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.01.20112334", - "rel_title": "A cohort study to evaluate the effect of combination Vitamin D, Magnesium and Vitamin B12 (DMB) on progression to severe outcome in older COVID-19 patients.", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20112334", - "rel_abs": "ObjectiveTo determine the clinical outcomes of older COVID-19 patients who received DMB compared to those who did not. We hypothesized that fewer patients administered DMB would require oxygen therapy and/or intensive care support than those who did not.\n\nMethodologyCohort observational study of all consecutive hospitalized COVID-19 patients aged 50 and above in a tertiary academic hospital who received DMB compared to a recent cohort who did not. Patients were administered oral vitamin D3 1000 IU OD, magnesium 150mg OD and vitamin B12 500mcg OD (DMB) upon admission if they did not require oxygen therapy. Primary outcome was deterioration post-DMB administration leading to any form of oxygen therapy and/or intensive care support.\n\nResultsBetween 15 January and 15 April 2020, 43 consecutive COVID-19 patients aged [≥]50 were identified. 17 patients received DMB and 26 patients did not. Baseline demographic characteristics between the two groups was significantly different in age. In univariate analysis, age and hypertension showed significant influence on outcome while DMB retained protective significance after adjusting for age or hypertension separately in multivariate analysis. Fewer DMB patients than controls required initiation of oxygen therapy during their hospitalization (17.6% vs 61.5%, P=0.006). DMB exposure was associated with odds ratios of 0.13 (95% CI: 0.03 - 0.59) and 0.20 (95% CI: 0.04 - 0.93) for oxygen therapy and/or intensive care support on univariate and multivariate analyses respectively.\n\nConclusionsDMB combination in older COVID-19 patients was associated with a significant reduction in proportion of patients with clinical deterioration requiring oxygen support and/or intensive care support. This study supports further larger randomized control trials to ascertain the full benefit of DMB in ameliorating COVID-19 severity.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Chuen Wen Tan", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Liam Pock Ho", - "author_inst": "Singapore general hospital" - }, - { - "author_name": "Shirin Kalimuddin", - "author_inst": "SIngapore General Hospital" - }, - { - "author_name": "Benjamin Pei Zhi Cherng", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Yii Ean Teh", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Siew Yee Thien", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Hei Man Wong", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Paul Jie Wen Tern", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Jason Wai Mun Chay", - "author_inst": "Sengkang General Hospital" - }, - { - "author_name": "Chandramouli Nagarajan", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Rehena Sultana", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Jenny Guek Hong Low", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Heng Joo Ng", - "author_inst": "Singapore General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.30.20111393", "rel_title": "Antibody profiling of COVID-19 patients in an urban low-incidence region in Northern Germany", @@ -1424802,6 +1425407,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.01.20118612", + "rel_title": "Modeling the Covid-19 Epidemic using Time Series Econometrics", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118612", + "rel_abs": "The classic logistic model has provided a realistic model of the behavior of Covid-19 in China and many East Asian countries. Once these countries passed the peak, the daily case count fell back, mirroring its initial climb in a symmetric way, just as the classic model predicts. However, in Italy and Spain, and now the UK and many other Western countries, the experience has been very different. The daily count has fallen back gradually from the peak but remained stubbornly high. The reason for the divergence from the classical model remain unclear. We take an empirical stance on this issue and develop a model that is based upon the statistical characteristics of the time series. With the possible exception of China, the workhorse logistic model is decisively rejected against more flexible alternatives.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Peter D. Spencer", + "author_inst": "University of York" + }, + { + "author_name": "Adam Golinski", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.01.20118505", "rel_title": "Pulmonary Thromboembolic Disease in Patients with COVID-19 Undergoing Computed Tomography Pulmonary Angiography (CTPA): Incidence and Relationship with Pulmonary Parenchymal Abnormalities", @@ -1425346,101 +1425974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.29.20114223", - "rel_title": "Efficacy and Safety of Leflunomide for Refractory COVID-19: An Open-label Controlled Study", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20114223", - "rel_abs": "OBJECTIVETo evaluate the safety and efficacy of leflunomide for the treatment of refractory COVID-19 in adult patients.\n\nDESIGNOpen-label controlled study\n\nSETTINGA designated hospital for patients with refractory COVID-19 in Wuhan, China.\n\nPARTICIPANTS27 hospitalized adult patients ([≥]18 years of age) with radiologically confirmed pneumonia and SARS-CoV-2 positive for more than 28 days despite standard care were assigned to receive standard of care (SOC, grp I) or leflunomide + SOC (grp 2). After 2 weeks, grp 1 and grp 2 patients who continued to be SARS-CoV-2-positive received leflunomide for 14 days while continuing SOC.\n\nMAIN OUTCOME MEASURESThe primary outcomes were the rate of and time to SARS-CoV-2 clearance and the 14-day and 30-day hospital discharge rate.\n\nRESULTSTwelve patients enrolled in grp 1 and 15 patients were in grp 2. The 14 days SARS-CoV-2 viral clearance rate was 80.0% (12/15) for grp 2 patients receiving leflunomide versus 16.7% for grp 1 patients (2/12) (P=0.002). By day 14, the median time to SARS-CoV-2 clearance was 6.0 days (range 1-12, IQR 1-12) for grp 2 patients. In grp 1, two patients converted to viral negative on days 1 and 6 (P=0.002). The 14-day discharge rate was 73.3% (11/15) for the grp 2 versus 8.3% (1/12) for grp 1 (P=0.001). The 30-day discharge rate was 100% (15/15) for the grp 2 versus 66.7% (8/12) for grp 1. No severe adverse events or deaths were reported.\n\nCONCLUSIONLeflunomide is effective in enhancing SARS-CoV-2 clearance and hospital discharge in refractory COVID-19 patients. The addition of leflunomide to SOC did not increase adverse events versus SOC. These preliminary observations underscore a need for a randomized clinical study of leflunomide in SARS-CoV-2 infection.\n\nWHAT IS ALREADY KNOWN ON THIS TOPICBased on the large numbers of global infected patients of SARS-CoV-2, there will be many patients on persist viral positive which is named refractory covid-19. Specific medication for the treatment of the refractory covid-19 has been approved.\n\nLeflunomide has been widely used in rheumatoid arthritis and psoriatic arthritis with good safety and tolerance. Recently, it is found an activity of anti-SARS-CoV-2 in vitro and the effective concentration of leflunomide is within the recognized therapeutic level for rheumatoid arthritis.\n\nWHAT THIS STUDY ADDSLeflunomide is effective in enhancing SARS-CoV-2 clearance and hospital discharge in refractory COVID-19 patients. The safety and tolerability of the 14-28-day course of treatment with leflunomide is acceptable.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Qiang Wang", - "author_inst": "Department of Nephrology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Haipeng Guo", - "author_inst": "Department of Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yu Li", - "author_inst": "Department of Respirology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Xiangdong Jian", - "author_inst": "Department of Emergency Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Xinguo Hou", - "author_inst": "Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Ning Zhong", - "author_inst": "Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Jianchun Fei", - "author_inst": "Department of Anesthesiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Dezhen Su", - "author_inst": "Department of Psychiatry, Renmin Hospital of Wuhan University" - }, - { - "author_name": "Zhouyan Bian", - "author_inst": "Department of Cardiology, Renmin Hospital of Wuhan University" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Department of Respirology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yingying Hu", - "author_inst": "Department of Quality control, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yan Sun", - "author_inst": "Department of Nephropathy, Shandong Provincial Third Hospital Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Xueyan Yu", - "author_inst": "Department of Nephrology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yuan Li", - "author_inst": "Department of Critical Care Medicine, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Bei Jiang", - "author_inst": "Department of Nephrology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yan Li", - "author_inst": "Department of Nephrology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Fengping Qin", - "author_inst": "Department of Nephrology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yingying Wu", - "author_inst": "Department of Nephrology, Qilu Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Yanxia Gao", - "author_inst": "Department of Nephrology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Zhao Hu", - "author_inst": "Qilu Hospital, Cheeloo College of Medicine, Shandong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.01.20119602", "rel_title": "High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay", @@ -1426268,6 +1426801,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.29.20114751", + "rel_title": "Syncope at SARS-CoV-2 onset due to impaired baroreflex response", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20114751", + "rel_abs": "We describe clinical and laboratory findings in 35 consecutive patients tested positive for SARS-CoV-2 by reverse transcriptase-polymerase chain reaction on nasopharyngeal swab that presented one or multiple syncopal events at disease onset. Neurological examination and electrocardiographic findings were normal. Chest computed tomography showed findings consistent with interstitial pneumonia. Arterial blood gas analysis showed low pO2, pCO2, and P/F ratio indicating hypocapnic hypoxemia, while patients did not show the expected compensatory heart rate increase. Such mechanism could have led to syncope. We speculate that SARS-CoV-2 could have caused angiotensin-converting enzyme-2 (ACE2) receptor internalization in the nucleus of the solitary tract (NTS), thus altering the baroreflex response and inhibiting the compensatory tachycardia during acute hypocapnic hypoxemia.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ciro Canetta", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Silvia Accordino", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Elisabetta Buscarini", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Gianpaolo Benelli", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Giuseppe La Piana", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Alessandro Scartabellati", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Giovanni Vigano'", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Roberto Assandri", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Alberto Astengo", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Chiara Benzoni", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Gianfranco Gaudiano", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Daniele Cazzato", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Sebastiano Davide Rossi", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Susanna Usai", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Irene Tramacere", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Giuseppe Lauria", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy; Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.29.20114199", "rel_title": "Effect of Dry Heat and Autoclave Decontamination Cycles on N95 FFRs", @@ -1427472,85 +1428084,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.05.29.20115253", - "rel_title": "The COVID-19 Critical Care Consortium observational study: Design and rationale of a prospective, international, multicenter, observational study", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20115253", - "rel_abs": "ImportanceThere is a paucity of data that can be used to guide the management of critically ill patients with coronavirus disease 2019 (COVID-19). Global collaboration offers the best chance of obtaining these data, at scale and in time. In the absence of effective therapies, insights derived from real-time observational data will be a crucial means of improving outcomes.\n\nObjectiveIn response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, a research and data-sharing collaborative has been assembled to harness the cumulative experience of intensive care units (ICUs) worldwide. The resulting observational study provides a platform to rapidly disseminate detailed data and insights.\n\nDesignThe COVID-19 Critical Care Consortium observational study is an international, multicenter, prospective, observational study of patients with confirmed or suspected SARSCoV-2 infection admitted to ICUs.\n\nSettingThis is an evolving, open-ended study that commenced on January 1st, 2020 and currently includes more than 350 sites in over 48 countries. The study enrolls patients at the time of ICU admission and follows them to the time of death, hospital discharge, or 28 days post-ICU admission, whichever occurs last.\n\nParticipantsAll subjects, without age limit, requiring admission to an ICU for SARS-CoV-2 infection, confirmed by real-time polymerase chain reaction (PCR) and/or next-generation sequencing or with high clinical suspicion of the infection. Patients admitted to an ICU for any other reason are excluded.\n\nMain outcomes and measuresKey data, collected via an electronic case report form devised in collaboration with the ISARIC/SPRINT-SARI networks, include: patient demographic data and risk factors, clinical features, severity of illness and respiratory failure, need for non-invasive and/or mechanical ventilation and/or extracorporeal membrane COVID-19 CCC observational study protocol oxygenation (ECMO), and associated complications, as well as data on adjunctive therapies. Final outcomes of in-hospital death, discharge or continuing admissions at 28 days.\n\nDiscussionThis large-scale, observational study of COVID-19 in the critically ill will provide rapid international characterization. Open-ended accrual will increase the power to answer hypothesis-led questions over time. Several sub-studies have already been initiated, examining hemostasis, neurological, cardiac, and long-term outcomes.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Gianluigi Li Bassi", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Jacky Suen", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Adrian G Barnett", - "author_inst": "Queensland University of Technology, Brisbane, Australia" - }, - { - "author_name": "Amanda Corley", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Jonathan E. Millar", - "author_inst": "Roslin Institute, University of Edinburgh, Scotland" - }, - { - "author_name": "Jonathon P Fanning", - "author_inst": "University of Queensland" - }, - { - "author_name": "India Lye", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Sebastiano Colombo", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Karin Wildi", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Samantha Livingstone", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Gabriella Abbate", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - }, - { - "author_name": "Samuel Hinton", - "author_inst": "University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Benoit Liquet", - "author_inst": "University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Sally Shrapnel", - "author_inst": "University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Heidi J Dalton", - "author_inst": "INOVA Fairfax Medical Center, Heart and Vascular Institute, Falls Church VA, USA" - }, - { - "author_name": "John F Fraser", - "author_inst": "Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.28.20116152", "rel_title": "Early CPAP reduced mortality in covid-19 patients. Audit results from Wrightington, Wigan and Leigh Teaching Hospitals NHS Foundation Trust.", @@ -1428454,6 +1428987,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.01.20100461", + "rel_title": "Determining the optimal strategy for reopening schools, work and society in the UK: balancing earlier opening and the impact of test and trace strategies with the risk of occurrence of a secondary COVID-19 pandemic wave", + "rel_date": "2020-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20100461", + "rel_abs": "BackgroundIn order to slow down the spread of SARS-CoV-2, the virus causing the COVID-19 pandemic, the UK government has imposed strict physical distancing ( lockdown) measures including school dismissals since 23 March 2020. As evidence is emerging that these measures may have slowed the spread of the pandemic, it is important to assess the impact of any changes in strategy, including scenarios for school reopening and broader relaxation of social distancing. This work uses an individual-based model to predict the impact of a suite of possible strategies to reopen schools in the UK, including that currently proposed by the UK government.\n\nMethodsWe use Covasim, a stochastic agent-based model for transmission of COVID-19, calibrated to the UK epidemic. The model describes individuals contact networks stratified as household, school, work and community layers, and uses demographic and epidemiological data from the UK. We simulate a range of different school reopening strategies with a society-wide relaxation of lockdown measures and in the presence of different non-pharmaceutical interventions, to estimate the number of new infections, cumulative cases and deaths, as well as the effective reproduction number with different strategies. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages.\n\nFindingsWe found that with increased levels of testing of people (between 25% and 72% of symptomatic people tested at some point during an active COVID-19 infection depending on scenarios) and effective contact-tracing and isolation for infected individuals, an epidemic rebound may be prevented across all reopening scenarios, with the effective reproduction number (R) remaining below one and the cumulative number of new infections and deaths significantly lower than they would be if testing did not increase. If UK schools reopen in phases from June 2020, prevention of a second wave would require testing 51% of symptomatic infections, tracing of 40% of their contacts, and isolation of symptomatic and diagnosed cases. However, without such measures, reopening of schools together with gradual relaxing of the lockdown measures are likely to induce a secondary pandemic wave, as are other scenarios for reopening. When infectiousness of <20 year olds was varied from 100% to 50% of that of older ages, our findings remained unchanged.\n\nInterpretationTo prevent a secondary COVID-19 wave, relaxation of social distancing including reopening schools in the UK must be implemented alongside an active large-scale population-wide testing of symptomatic individuals and effective tracing of their contacts, followed by isolation of symptomatic and diagnosed individuals. Such combined measures have a greater likelihood of controlling the transmission of SARS-CoV-2 and preventing a large number of COVID-19 deaths than reopening schools and society with the current level of implementation of testing and isolation of infected individuals.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSSince the onset of COVID-19 pandemic, mathematical modelling has been at the heart of informing decision-making, including the imposing of the lockdown in the UK. As countries are now starting to plan modification of these measures, it is important to assess the impact of different lockdown exit strategies including whether and how to reopen schools and relax other social distancing measures.\n\nAdded value of this studyUsing mathematical modelling, we explored the impact of strategies to reopen schools and society in the UK, including that currently proposed by the UK government. We assessed the impact of opening all schools fully or in a phased way with only some school years going back, with a society-wide relaxation of lockdown measures and in the presence of a different levels of implementation of test-trace-isolate strategies. We projected the number of new COVID-19 infections, cumulative cases and deaths, as well as the temporal distribution in the effective reproduction number (R) across different strategies. Our study is the first to provide quantification of the amount of testing and tracing that would be needed to prevent a second wave of COVID-19 in the UK under different reopening scenarios. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages.\n\nImplications of all the available evidenceEvidence to date points to the need for additional testing, contact tracing, and isolation of individuals who have either been diagnosed with COVID-19, or who are considered to be at high risk of carrying infection due to their contact history or symptoms. Our study supports these conclusions and provides additional quantification of the amount of testing and tracing that would be needed to prevent a second wave of COVID-19 in the UK under different lockdown exit strategies. Reopening schools and society alongside active testing of the symptomatic population (between 25% and 72% of people with symptomatic COVID-19 infection depending on scenarios) and with an effective contact-tracing and rapid isolation of symptomatic and diagnosed individuals, will not only prevent a secondary pandemic wave, but is also likely to be able to control the transmission of SARS-CoV-2, via keeping the R value below 1, thus preventing a large number of COVID-19 cases and deaths. However, in the absence of fully implemented large-scale testing, contact-tracing and isolation strategy, plans for reopening schools, including those currently proposed by the UK government, and the associated increase in work and community contacts, are likely to induce a secondary pandemic wave of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "UCL" + }, + { + "author_name": "Cliff Kerr", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Robyn Margaret Stuart", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Dina Mistry", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Daniel Klein", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Russell M Viner", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Chris Bonell", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.01.20118885", "rel_title": "Modelling testing frequencies required for early detection of a SARS-CoV-2 outbreak on a university campus", @@ -1429030,73 +1429606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20104539", - "rel_title": "Pediatric COVID-19 in Southern California: clinical features and viral genetic diversity", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20104539", - "rel_abs": "As the pandemic enters its fifth month, information regarding COVID-19 in children is rapidly evolving. Here, we explore clinical features and SARS-CoV-2 genetic variation in children presenting with COVID-19. We observed diverse clinical presentations and identified association between disease severity, viral load and age. SARS-CoV-2 genomes from the patients showed limited number of variations and an evolutionary rate comparable to other RNA viruses. We did not identify correlation between disease severity and viral genetic variations. Epidemiological investigation revealed multiple introductions of virus into Southern California.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Utsav Pandey", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Rebecca Yee", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Mimi Precit", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Moiz Bootwalla", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Alex Ryutov", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Lishuang Shen", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Dennis T Maglinte", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Dejerianne Ostrow", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Jaclyn A Biegel", - "author_inst": "Children's Hospital Los Angeles; University of California, Keck School of Medicine" - }, - { - "author_name": "Alexander R Judkins", - "author_inst": "Children's Hospital Los Angeles; University of California, Keck School of Medicine" - }, - { - "author_name": "Jeffrey M Bender", - "author_inst": "Children's Hospital Los Angeles; University of California, Keck School of Medicine" - }, - { - "author_name": "Xiaowu Gai", - "author_inst": "Children's Hospital Los Angeles; University of California, Keck School of Medicine" - }, - { - "author_name": "Jennifer Dien Bard", - "author_inst": "Children's Hospital Los Angeles; University of California, Keck School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.29.20102913", "rel_title": "The Neutrophil Lymphocyte Ratio (NLR), Platelet Lymphocyte Ratio (PLR) and routine hematological parameters of COVID-19 Patient : A perspective of the Indian scenario from a frontline pilot study of 32 COVID-19 cases in a Tertiary Care Institute of North India", @@ -1429875,6 +1430384,81 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.31.116061", + "rel_title": "Origin and cross-species transmission of bat coronaviruses in China", + "rel_date": "2020-05-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.31.116061", + "rel_abs": "Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and across more distantly related host taxa in alpha-than beta-CoVs, and more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Alice Latinne", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Ben Hu", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Kevin J Olival", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Guangjian Zhu", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Libiao Zhang", + "author_inst": "Guangdong Institute of Applied Biological Resources" + }, + { + "author_name": "Hongying Li", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Aleksei A Chmura", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Hume E Field", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Carlos Zambrana-Torrelio", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Jonathan H Epstein", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Bei Li", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Duke-NUS Graduate Medical School" + }, + { + "author_name": "Zhengli Shi", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Peter Daszak", + "author_inst": "EcoHealth Alliance" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.31.126136", "rel_title": "A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates", @@ -1430367,109 +1430951,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.05.30.125484", - "rel_title": "Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes", - "rel_date": "2020-05-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.30.125484", - "rel_abs": "The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to [~]10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 [A]-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Ching-Lin Hsieh", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jory A Goldsmith", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jeffrey M Schaub", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Andrea M DiVenere", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Hung-Che Kuo", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kamyab Javanmardi", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kevin C Le", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Daniel Wrapp", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Alison Gene-Wei Lee", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Yutong Liu", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Chia-Wei Chou", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Patrick O Byrne", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Christy K Hjorth", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Nicole V Johnson", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "John Ludes-Meyers", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Annalee W Nguyen", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Juyeon Park", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Nianshuang Wang", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Amengor Dzifa", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jennifier A Maynard", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Ilya J Finkelstein", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jason S McLellan", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.29.124776", "rel_title": "Validation and Performance Comparison of Three SARS-CoV-2 Antibody Assays", @@ -1431469,6 +1431950,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.28.20115584", + "rel_title": "Prognostic value of visual quantification of lesion severity at initial chest CT in confirmed Covid-19 infection: a retrospective analysis on 216 patients", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115584", + "rel_abs": "Rationale and ObjectivesStudies suggest an association between chest CT findings assessed with semi-quantitative CT score and gravity of Covid-19. The objective of this work is to analyze potential correlation between visual quantification of lesion severity at initial chest CT and clinical outcome in confirmed Covid-19 patients.\n\nMaterials and MethodsFrom March 5th to March 21st, 2020, all consecutive patients that underwent chest CT for clinical suspicion of Covid-19 at a single tertiary center were retrospectively evaluated for inclusion. Patients with lung parenchyma lesions compatible with Covid-19 and positive RT-PCR were included.\n\nGlobal extensiveness of abnormal lung parenchyma was visually estimated and classified independently by 2 readers, following the European Society of Thoracic Imaging Guidelines. Death and/or mechanical ventilation within 30 days following the initial chest CT was chosen as the primary hard endpoint.\n\nResults216 patients (124 men, 62 years-old {+/-} 16.5, range 22 - 94 yo) corresponding to 216 chest CT were included. Correlation between lesion severity and percentage of patients that met the primary endpoint was high, with a coefficient {rho} of 0.87 (p = 0.05).\n\nA greater than 25% involvement was significantly associated with a higher risk of mechanical ventilation or death at 30 days, with a Risk Ratio of 5.00 (95% CI [3.59-6.99]).\n\nConclusionThis retrospective cohort confirms a correlation between visual evaluation of lesions severity at initial chest CT and the 30 days clinical outcome of Covid-19 patients and suggests using a threshold of greater than 25% involvement to identify patients at risk.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Elias Taieb", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Aissam Labani", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Yvon Ruch", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Francois Danion", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Mathieu Oberlin", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Pascal Bilbault", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Pierre Leyendecker", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Catherine Roy", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Mickael Ohana", + "author_inst": "Hopitaux Universitaires de Strasbourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.29.20116376", "rel_title": "Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report", @@ -1432189,37 +1432721,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.05.29.20117333", - "rel_title": "Monitoring the post-containment COVID-19 crisis in Guadeloupe: Early-warning signals of destabilisation through bootstrapped probability density functions", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20117333", - "rel_abs": "We propose a method to detect early-warning information in relation with subtle changes occurring in the trend of evolution in data time series of the COVID-19 epidemic spread (e.g. daily new cases). The method is simple and easy to implement on laptop computers. It is designed to be able to provide reliable results even with very small amounts of data (i.e. {approx} 10 - 20). The results are given as compact graphics easy to interpret. The data are separated into two subsets: the old data used as control points to statistically define a \"trend\" and the recent data that are tested to evaluate their conformity with this trend. The trend is characterised by bootstrapping in order to obtain probability density functions of the expected misfit of each data point. The probability densities are used to compute distance matrices where data clusters and outliers are easily visually recognised. In addition to be able to detect very subtle changes in trend, the method is also able to detect outliers. A simulated case is analysed where R0 is slowly augmented (i.e. from 1.5 to 2.0 in 20 days) to pass from a stable damped control of the epidemic spread to an exponentially diverging situation. The method is able to give an early warning signal as soon as the very beginning of the R0 variation. Application to the data of Guadeloupe shows that a small destabilising event occurred in the data near April 30, 2020. This may be due to an increase of R0 0.7 around April 13-15, 2020.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Meriem ALLALI", - "author_inst": "CHU POINTE-A-PITRE" - }, - { - "author_name": "Patrick Portecop", - "author_inst": "CHU POINTE-A-PITRE" - }, - { - "author_name": "Michel Carles", - "author_inst": "CHU POINTE-A-PITRE" - }, - { - "author_name": "Dominique Gibert", - "author_inst": "Univ Lyon, Univ Lyon 1, ENSL, CNRS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.28.20116095", "rel_title": "Mortality rate and estimate of fraction of undiagnosed COVID-19 cases in the US in March and April 2020", @@ -1432999,6 +1433500,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.29.20116921", + "rel_title": "Time courses of COVID-19 infection and local variation in socioeconomic and health disparities in England", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116921", + "rel_abs": "ObjectiveTo identify factors associated with local variation in the time course of COVID-19 case burden in England.\n\nMethodsWe analyzed laboratory-confirmed COVID-19 case data for 150 upper tier local authorities, from the period from January 30 to May 6, 2020, as reported by Public Health England. Using methods suitable for time-series data, we identified clusters of local authorities with distinct trajectories of daily cases, after adjusting for population size. We then tested for differences in sociodemographic, economic, and health disparity factors between these clusters.\n\nResultsTwo clusters of local authorities were identified: a higher case trajectory that rose faster over time to reach higher peak infection levels, and a lower case trajectory cluster that emerged more slowly, and had a lower peak. The higher case trajectory cluster (79 local authorities) had higher population density (p<0.001), higher proportion of Black and Asian residents (p=0.03; p=0.02), higher multiple deprivation scores (p<0.001), a lower proportions of older adults (p=0.005), and higher preventable mortality rates (p=0.03). Local authorities with higher proportions of Black residents were more likely to belong to the high case trajectory cluster, even after adjusting for population density, deprivation, proportion of older adults and preventable mortality (p=0.04).\n\nConclusionAreas belonging to the trajectory with significantly higher COVID-19 case burden were more deprived, and had higher proportions of ethnic minority residents. A higher proportion of Black residents in regions belonging to the high trajectory cluster was not fully explained by differences in population density, deprivation, and other overall health disparities between the clusters.\n\nWhat is already known on this subject?Emerging evidence suggests that the burden of COVID-19 infection is falling unequally across England, with provisional data suggesting higher overall infection and mortality rates for Black, Asian, and mixed race/ethnicity individuals.\n\nWhat does this study add?We found that regions with greater socioeconomic deprivation and poorer population health measures showed a faster rise in COVID-19 cases, and reached higher peak case levels. Areas with a higher proportion of Black residents were more likely to show this kind of time course, even after adjusting for multiple co-occurring factors, including population density. This finding merits further investigation in terms of the intersecting vulnerability factors Black and other minority ethnic individuals face in England (e.g. proportion of people working in service and caring roles, and the role of structural discrimination), and has implications for the ongoing allocation of public health resources, in order to better mitigate such inequalities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shelley H. Liu", + "author_inst": "Icahn School of Medicine at Mount SInai" + }, + { + "author_name": "Bian Liu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Yan Li", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Agnes Norbury", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.29.20116657", "rel_title": "Loneliness during lockdown: trajectories and predictors during the COVID-19 pandemic in 35,712 adults in the UK", @@ -1433459,33 +1433991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.27.20107656", - "rel_title": "The expediency of local modelling to aid national responses to SARS-CoV-2.", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20107656", - "rel_abs": "BackgroundWith the SARS-CoV-2 pandemic gripping most of the globe, healthcare and economic recovery strategies are being explored currently as a matter of urgency. The underpinning rationale of this paper is that we believe that health and care services are provided locally, therefore, local implications of national policy need to be reflected when informing national responses to the SARS-CoV-2 pandemic.\n\nMethodsWe adopted the assumptions underlying the United Kingdom governments national epidemiological model which influences the national policy response to the SARS-CoV-2 pandemic. We used these in a local context and show projections in terms of presentations of symptomatic patients differ in a variety of settings. Setting: North of England, United Kingdom, population modelled at four local constituent levels which aggregated gives a total population of 3.2m.\n\nResultsWe clearly demonstrate that there is significant difference in the way the national modelling outputs are replicated at local levels. Specifically, in terms of projected increased levels of demand for services on the local health and care systems.\n\nConclusionsWe present significant evidence of differing timelines specifically in terms of subsequent projected peak demands. Additionally, it clearly indicates varying levels of such demand throughout the four modelled localities. These idiosyncrasies are masked by both regional and national approaches to modelling. We urge readers to ensure that any national policy is appropriately adopted through the use of complementary bottom up approach, to suit local health and care systems. Finally, we share our methodology to ensure other professionals could replicate this study elsewhere.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Bernard M Groen", - "author_inst": "Durham University" - }, - { - "author_name": "Paul Turner", - "author_inst": "University of Lincoln" - }, - { - "author_name": "Peter Lacey", - "author_inst": "Whole System Partnership" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20115477", "rel_title": "Study of the Sudanese perceptions of COVID-19: Applying the Health Belief Model.", @@ -1434169,6 +1434674,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.27.20114819", + "rel_title": "Distinctive trajectories of COVID-19 epidemic by age and gender: a retrospective modeling of the epidemic in South Korea", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114819", + "rel_abs": "ObjectivesElderly people had suffered disproportional burden of COVID-19. We hypothesized that males and females in different age groups might have different epidemic trajectories.\n\nMethodsUsing publicly available data from South Korea, daily new COVID-19 cases were fitted with generalized additive models, assuming Poisson and negative binomial distributions. Epidemic dynamics by age and gender groups were explored with interactions between smoothed time terms and age and gender.\n\nResultsA negative binomial distribution fitted the daily case counts best. Interaction between the dynamic patterns of daily new cases and age groups was statistically significant (p<0.001), but not with gender group. People aged 20-39 years led the epidemic processes in the society with two peaks: one major peak around March 1 and a smaller peak around April 7, 2020. The epidemic process among people aged 60 or above was trailing behind that of younger people with smaller magnitude. After March 15, there was a consistent decline of daily new cases among elderly people, despite large fluctuations of case counts among young adults.\n\nConclusionsAlthough young people drove the COVID-19 epidemic in the whole society with multiple rebounds, elderly people could still be protected from virus infection after the peak of epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xinhua Yu", + "author_inst": "University of Memphis" + }, + { + "author_name": "Jiasong Duan", + "author_inst": "University of Memphis" + }, + { + "author_name": "Yu Jiang", + "author_inst": "University of Memphis" + }, + { + "author_name": "Hongmei Zhang", + "author_inst": "University of Memphis" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.27.20114728", "rel_title": "Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19", @@ -1434721,89 +1435257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.26.20113373", - "rel_title": "Mortality reduction in 46 severe Covid-19 patients treated with hyperimmune plasma. A proof of concept single arm multicenter interventional trial", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113373", - "rel_abs": "BACKGROUNDHyperimmune plasma from Covid-19 convalescent is a potential treatment for severe Covid-19.\n\nMETHODSWe conducted a multicenter one arm proof of concept interventional study. Patients with Covid-19 disease with moderate-to-severe Acute Respiratory Distress Syndrome, elevated C-reactive Protein and need for mechanical ventilation and/or CPAP were enrolled. One to three 250-300 ml unit of hyperimmune plasma (neutralizing antibodies titer [≥]1:160) were administered. Primary outcome was 7-days hospital mortality. Secondary outcomes were PaO2/FiO2, laboratory and radiologic changes, as well as weaning from mechanical ventilation and safety.\n\nRESULTSThe study observed 46 patients from March, 25 to April, 21 2020. Patients were aged 63, 61% male, 30 on CPAP and 7 intubated. PaO2/FiO2 was 128 (SD 47). Symptoms and ARDS duration were 14 (SD 7) and 6 days (SD 3). Three patients (6.5%) died within 7 days. The upper one-sided 90%CI was 13.9%, allowing to reject the null hypothesis of a 15% mortality. PaO2/FiO2 increased by 112 units (95%CI 82 to142) in survivors, the chest radiogram severity decreased in 23% (95%CI 5% to 42%); CRP, Ferritin and LDH decreased by 60, 36 and 20% respectively. Weaning from CPAP was obtained in 26/30 patients and 3/7 were extubated. Five serious adverse events occurred in 4 patients (2 likely, 2 possible treatment related).\n\nCONCLUSIONSHyperimmune plasma in Covid-19 shows promising benefits, to be confirmed in a randomized controlled trial. This proof of concept study could open to future developments including hyperimmune plasma banking, development of standardized pharmaceutical products and monoclonal antibodies.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Cesare Perotti", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia" - }, - { - "author_name": "Fausto Baldanti", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia & University of Pavia" - }, - { - "author_name": "Raffaele Bruno", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia & University of Pavia" - }, - { - "author_name": "Claudia Delfante", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia" - }, - { - "author_name": "Elena Seminari", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia" - }, - { - "author_name": "Salvatore Casari", - "author_inst": "Calo Poma Hospital, ASST Mantova" - }, - { - "author_name": "Elena Percivalle", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia" - }, - { - "author_name": "Claudia Glingani", - "author_inst": "Carlo Poma Hospital, ASST Mantova" - }, - { - "author_name": "Valeria Musella", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia" - }, - { - "author_name": "Mirko Belliato", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia" - }, - { - "author_name": "Martina Garuti", - "author_inst": "Carlo Poma Hospital, ASST Mantova" - }, - { - "author_name": "Federica Meloni", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia & University of Pavia" - }, - { - "author_name": "Marilena Frigato", - "author_inst": "Carlo Poma Hospital, ASST Mantova" - }, - { - "author_name": "Antonio Di Sabatino", - "author_inst": "Fondazione IRCCS Policlinico SanMatteo, Pavia & University of Pavia" - }, - { - "author_name": "Catherine Klersy", - "author_inst": "Fondazione IRCCS Policlinco San Matteo" - }, - { - "author_name": "Giuseppe De Donno", - "author_inst": "Carlo Poma Hospital, ASST Mantova" - }, - { - "author_name": "Massimo Franchini", - "author_inst": "Carlo Poma Hospital, ASST Mantova" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20113167", "rel_title": "A pilot study to investigate the fecal dissemination of SARS-CoV-2 virus genome in COVID-19 patients in Odisha, India", @@ -1435443,6 +1435896,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.29.20117069", + "rel_title": "Regression Analysis of COVID-19 Spread in India and its Different States", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20117069", + "rel_abs": "Linear and polynomial regression model has been used to investigate the COVID-19 outbreak in India and its different states using time series epidemiological data up to 26th May 2020. The data driven analysis shows that the case fatality rate (CFR) for India (3.14% with 95% confidence interval of 3.12% to 3.16%) is half of the global fatality rate, while higher than the CFR of the immediate neighbors i.e. Bangladesh, Pakistan and Sri Lanka. Among Indian states, CFR of West Bengal (8.70%, CI: 8.21-9.18%) and Gujrat (6.05%, CI: 4.90-7.19%) is estimated to be higher than national rate, whereas CFR of Bihar, Odisha and Tamil Nadu is less than 1%. The polynomial regression model for India and its different states is trained with data from 21st March 2020 to 19th May 2020 (60 days). The performance of the model is estimated using test data of 7 days from 20th May 2020 to 26th May 2020 by calculating RMSE and % error. The model is then used to predict number of patients in India and its different states up to 16th June 2020 (21 days). Based on the polynomial regression analysis, Maharashtra, Gujrat, Delhi and Tamil Nadu are continue to remain most affected states in India.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Poonam Chauhan", + "author_inst": "Central University of Punjab, Bathinda" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Central University of Punjab" + }, + { + "author_name": "Pooja Jamdagni", + "author_inst": "Himachal Pradesh University, Shimla" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.28.121533", "rel_title": "Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies", @@ -1436031,45 +1436511,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.05.27.20114017", - "rel_title": "Modelling the SARS-CoV-2 first epidemic wave in Greece: social contact patterns and impact assessment of social distancing interventions.", - "rel_date": "2020-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114017", - "rel_abs": "In Greece, a nationwide lockdown to mitigate the transmission of SARS-CoV-2 was imposed on March 23, 2020. As by the end of April the first epidemic wave is waning, it is important to assess the infection attack rate and quantify the impact of physical distancing. We implemented a survey to assess social mixing patterns before the epidemic and during lockdown. We estimated R0 from surveillance data and assessed its decline as a result of physical distancing based on social contacts data. We applied a Susceptible-Exposed-Infectious-Recovered model to estimate the infection attack rate and the infection fatality ratio (IFR). As multiple social distancing measures were implemented simultaneously (schools/work/leisure), we assessed their overall impact as well as their relative contribution. R0 was estimated 2{middle dot}38 (95%CI: 2{middle dot}01,2{middle dot}80). By April 26th, the infection attack rate was 0{middle dot}12% (95%CrI: 0{middle dot}06%,0{middle dot}26%) and the IFR 1{middle dot}12% (95%CrI: 0{middle dot}55%,2{middle dot}31%). During lockdown, daily contacts were reduced by 86{middle dot}9% and the effective reproduction number reached 0{middle dot}46 (95%CrI: 0{middle dot}35,0{middle dot}57). The reduction in R0 attributed to lockdown was 81{middle dot}0% (95%CrI: 71{middle dot}8%,86{middle dot}0%) whereas the reduction attributed to each measure separately ranged between 10%-24%. We assessed scenarios with less disruptive social distancing measures as well as scenarios where measures are partially lifted after lockdown. This is the first impact assessment of the first wave of SARS-CoV-2 in a European country. It suggests that only multiple measures implemented simultaneously could reduce R0 below 1. Measuring social mixing patterns can be a tool for real-time monitoring of the epidemic potential.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Vana Sypsa", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Sotirios Roussos", - "author_inst": "National and Kapodistrian University of Athens, Greece" - }, - { - "author_name": "Dimitrios Paraskevis", - "author_inst": "National and Kapodistrian University of Athens, Greece" - }, - { - "author_name": "Theodore Lytras", - "author_inst": "National Public Health Organization" - }, - { - "author_name": "Sotirios Tsiodras", - "author_inst": "National and Kapodistrian University of Athens, Greece" - }, - { - "author_name": "Angelos Hatzakis", - "author_inst": "National and Kapodistrian University of Athens, Greece" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20114124", "rel_title": "Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak", @@ -1436997,6 +1437438,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.24.20101238", + "rel_title": "Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20101238", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused over 220,000 deaths so far and is still an ongoing global health problem. However, the immunopathological changes of key types of immune cells during and after virus infection remain unclear. Here, we enriched CD3+ and CD19+ lymphocytes from peripheral blood mononuclear cells of COVID-19 patients (severe patients and recovered patients at early or late stages) and healthy people (SARS-CoV-2 negative) and revealed transcriptional profiles and changes in these lymphocytes by comprehensive single-cell transcriptome and V(D)J recombination analyses. We found that although the T lymphocytes were decreased in the blood of patients with virus infection, the remaining T cells still highly expressed inflammatory genes and persisted for a while after recovery in patients. We also observed the potential transition from effector CD8 T cells to central memory T cells in recovered patients at the late stage. Among B lymphocytes, we analyzed the expansion trajectory of a subtype of plasma cells in severe COVID-19 patients and traced the source as atypical memory B cells (AMBCs). Additional BCR and TCR analyses revealed a high level of clonal expansion in patients with severe COVID-19, especially of B lymphocytes, and the clonally expanded B cells highly expressed genes related to inflammatory responses and lymphocyte activation. V-J gene usage and clonal types of higher frequency in COVID-19 patients were also summarized. Taken together, our results provide crucial insights into the immune response against patients with severe COVID-19 and recovered patients and valuable information for the development of vaccines and therapeutic strategies.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xiaoying Fan", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Xiangyang Chi", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Wenji Ma", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Suijuan Zhong", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Yunzhu Dong", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Wei Zhou", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Wenyu Ding", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Hongyan Fan", + "author_inst": "Department of Clinical Laboratory, The 940th Hospital of PLA Joint Logistics Support Forces" + }, + { + "author_name": "Chonghai Yin", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhentao Zuo", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yilong Yang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Mengyao Zhang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Qiang Ma", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Jianwei Liu", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Ting Fang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Qian Wu", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Wei Chen", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Xiaoqun Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20111120", "rel_title": "THE LOW-HARM SCORE FOR PREDICTING MORTALITY IN PATIENTS DIAGNOSED WITH COVID-19: A MULTICENTRIC VALIDATION STUDY", @@ -1437421,37 +1437949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.25.20113084", - "rel_title": "A chest radiography-based artificial intelligence deep-learning model to predict severe Covid-19 patient outcomes: the CAPE (Covid-19 AI Predictive Engine) Model", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20113084", - "rel_abs": "BackgroundChest radiography may be used together with deep-learning models to prognosticate COVID-19 patient outcomes\n\nPurposeT o evaluate the performance of a deep-learning model for the prediction of severe patient outcomes from COVID-19 pneumonia on chest radiographs.\n\nMethodsA deep-learning model (CAPE: Covid-19 AI Predictive Engine) was trained on 2337 CXR images including 2103 used only for validation while training. The prospective test set consisted of CXR images (n=70) obtained from RT-PCR confirmed COVID-19 pneumonia patients between 1 January and 30 April 2020 in a single center. The radiographs were analyzed by the AI model. Model performance was obtained by receiver operating characteristic curve analysis.\n\nResultsIn the prospective test set, the mean age of the patients was 46 (+/-16.2) years (84.2% male). The deep-learning model accurately predicted outcomes of ICU admission/mortality from COVID-19 pneumonia with an AUC of 0.79 (95% CI 0.79-0.96). Compared to traditional risk scoring systems for pneumonia based upon laboratory and clinical parameters, the model matched the EWS and MulBTSA risk scoring systems and outperformed CURB-65.\n\nConclusionsA deep-learning model was able to predict severe patient outcomes (ICU admission and mortality) from COVID-19 on chest radiographs.\n\nKey ResultsA deep-learning model was able to predict severe patient outcomes (ICU admission and mortality) from COVID-19 from chest radiographs with an AUC of 0.79, which is comparable to traditional risk scoring systems for pneumonia.\n\nSummary StatementThis is a chest radiography-based AI model to prognosticate the risk of severe COVID-19 pneumonia outcomes.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Charlene Liew", - "author_inst": "SingHealth" - }, - { - "author_name": "Jessica Quah", - "author_inst": "SingHealth" - }, - { - "author_name": "Han Leong Goh", - "author_inst": "IHIS" - }, - { - "author_name": "Narayan Venkataraman", - "author_inst": "SingHealth" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.25.20112615", "rel_title": "Thermal Disinfection Inactivates SARS-CoV-2 in N95 Respirators while Maintaining Their Protective Function", @@ -1438499,6 +1438996,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.27.119610", + "rel_title": "Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection", + "rel_date": "2020-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.119610", + "rel_abs": "BackgroundCOVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID-19 infection. To evaluate the probable reasons behind the excessive susceptibility and fatality of lung cancer patients to COVID-19 infection, we targeted two most crucial biomarkers of COVID-19, ACE2 and CXCL10. ACE2 plays a vital role in the SARS CoV-2 entry into the host cell while CXCL10 is a cytokine mainly responsible for the lung cell damage involving in a cytokine storm.\n\nMethodsFirstly, we used the TIMER, UALCAN and GEPIA2 databases to analyze the expression and correlation of ACE2 and CXCL10 in LUAD and LUSC. After that, using the cBioPortal database, we performed an analytical study to determine the genetic changes in ACE2 and CXCL10 protein sequences that are responsible for lung cancer development. Finally, we analyzed different functional approaches of ACE2, CXCL10 and their co-expressed genes associated with lung cancer and COVID-19 development by using the PANTHER database.\n\nResultsInitially, we observed that ACE2 and CXCL10 are mostly overexpressed in LUAD and LUSC. We also found the functional significance of ACE2 and CXCL10 in lung cancer development by determining the genetic alteration frequency in their amino acid sequences. Lastly, by doing the functional assessment of the targeted genes, we identified that ACE2 and CXCL10 along with their commonly co-expressed genes are respectively involved in the binding activity and immune responses in case of lung cancer and COVID-19 infection.\n\nConclusionsFinally, on the basis of this systemic analysis, we came to the conclusion that ACE2 and CXCL10 are possible biomarkers responsible for the higher susceptibility and fatality of lung cancer patients towards the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tousif Bin Mahmood", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Afrin Sultana Chowdhury", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Mehedee Hasan", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Md. Mezbah-Ul-Islam Aakil", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Mohammad Imran Hossan", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.26.20109595", "rel_title": "Efficacy and harms of remdesivir for the treatment of COVID-19: a systematic review and meta-analysis", @@ -1439147,33 +1439679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.26.20113464", - "rel_title": "The Potential Impact of Intensified Community Hand Hygiene Interventions on Respiratory tract Infections: A Modelling Study", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113464", - "rel_abs": "Increased hand hygiene amongst the general public has been widely promoted as one of the most important non-pharmaceutical interventions for reducing transmission during the ongoing COVID-19 pandemic and is likely to continue to play a key role in long-term efforts to suppress transmission before a vaccine can be deployed. For other respiratory tract infections community hand hygiene interventions are supported by evidence from randomised trials, but information on how effectiveness in reducing transmission scales with achieved changes in hand hygiene behaviour is lacking. This information is of critical importance when considering the potential value of substantially enhancing community hand hygiene frequency to help suppress COVID-19. Here, we developed a simple model-based framework for understanding the key determinants of the effectiveness of changes in hand hygiene behaviour in reducing transmission and use it to explore the potential impact of interventions aimed at achieving large-scale population-wide changes in hand hygiene behaviour. Our analyses show that the effect of hand hygiene is highly dependent on the duration of viral persistence on hands and that hand washing needs to be performed very frequently or immediately after hand contamination events in order to substantially reduce the probability of infection. Hand washing at a lower frequency, such as every 30 minutes or with a delay of 15 minutes after contamination events, may be adequate to reduce the probability of infection when viral survival on hands is longer, such as when hands are contaminated with mucus. Immediate hand washing after contamination is more effective than hand washing at fixed-time intervals even when the total number of hand washing events is similar. This event-prompted hand washing strategy is consistently more effective than fixed-time strategy regardless of hand contamination rates and should be highlighted in hand hygiene campaigns.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Thi Mui Pham", - "author_inst": "Julius Center for Health Sciences and Primary Care of the UMC Utrecht" - }, - { - "author_name": "Yin Mo", - "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Ben Cooper", - "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20113696", "rel_title": "Application of pooled testing in screening and estimating the prevalence of Covid-19", @@ -1439997,6 +1440502,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.26.20104497", + "rel_title": "Knowledge and attitude towards COVID-19 in Bangladesh: Population-level estimation and a comparison of data obtained by phone and online survey methods", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20104497", + "rel_abs": "Peoples adherence to the guidelines and measures suggested in fighting the ongoing COVID-19 pandemic is partly determined by the Knowledge, Attitude, and Practices (KAP) of the population. In this cross-sectional study, we primarily addressed two key issues. First, we tried to determine whether there is a significant difference in the estimated COVID-19 knowledge level from the online and phone survey methods. Second, we tried to quantify the knowledge and attitude of COVID-19 in Bangladeshi adult population. Data were collected through phone calls (April 14-23, 2020) and online survey (April 18-19, 2020) in Bangladesh. The questionnaire had 20 knowledge questions with each correct response getting one point and incorrect/dont know response getting no point (maximum total knowledge score 20). Participants scoring >17 were categorized as having good knowledge. The percentages of good knowledge holders were 57.6%, 75.1%, and 95.8% in the phone (n=1426), online non-medical (n=1097), and online medical participants (n=382), respectively. Comparison between phone and online survey showed that, overall, online survey might overestimate knowledge level than that of phone survey, although there was no difference for elderly, poor, and rural people. Male gender, higher education, living in town/urban areas, good financial condition, and use of internet were positively associated with good knowledge. However, higher knowledge was associated with having less confidence in the final control of COVID-19. Our adult population-level estimates showed that only 32.6% (95% CI 30.1-35.2%) had good knowledge. This study provides crucial information that could be useful for the researchers and policymakers to develop effective strategies.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Anwarul Karim", + "author_inst": "Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Mastura Akter", + "author_inst": "Department of Biomedical Sciences, City University of Hong Kong, Hong Kong" + }, + { + "author_name": "AHM Thafikul Mazid", + "author_inst": "Department of Medicine, Dhaka Medical College and Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Orindom Shing Pulock", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Tasmiah Tahera Aziz", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Samira Hayee", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Nowrin Tamanna", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "GS Chuwdhury", + "author_inst": "Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Afsana Haque", + "author_inst": "Department of Urban Planning and Design, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Farhana Yeasmin", + "author_inst": "Department of Applied Food Science and Nutrition, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh" + }, + { + "author_name": "Mashkura Akter Mitu", + "author_inst": "Faculty of Agriculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh" + }, + { + "author_name": "Farjana Yeasmin", + "author_inst": "Department of Zoology, Government Hazi Mohammad Mohsin College, National University, Bangladesh" + }, + { + "author_name": "Humayun Rashid", + "author_inst": "Chattogram International Medical College, Chattogram, Bangladesh" + }, + { + "author_name": "Ashish Kumar Kuri", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Arni Das", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Koushik Majumder", + "author_inst": "Chittagong Medical College and Hospital, Chattogram, Bangladesh" + }, + { + "author_name": "Dipen Barua", + "author_inst": "Centre of Buddhist Studies, Faculty of Arts, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Md Mahabubur Rahaman", + "author_inst": "Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Sanjida Akter", + "author_inst": "Department of Social and Preventive Medicine, Faculty of Medicine, University Malaya, Malaysia" + }, + { + "author_name": "Nashid Niaz Munia", + "author_inst": "Chattogram International Medical College, Chattogram, Bangladesh" + }, + { + "author_name": "Jabin Sultana", + "author_inst": "Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangl" + }, + { + "author_name": "Faeeqa Usaila", + "author_inst": "Department of Biomedical Sciences, City University of Hong Kong, Hong Kong" + }, + { + "author_name": "Sabrina Sifat", + "author_inst": "Shaheed Suhrawardy Medical College and Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Nishat Anjum Nourin", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Md Forhad Uddin", + "author_inst": "Independent Researcher, Chattogram, Bangladesh" + }, + { + "author_name": "Mrinmoy Bhowmik", + "author_inst": "Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh" + }, + { + "author_name": "Tanvir Ahammed", + "author_inst": "Department of Statistics, Shahjalal University of Science and Technology, Sylhet, Bangladesh" + }, + { + "author_name": "Nabil Sharik", + "author_inst": "Upzila Health and Family Planning Office, Sadar, Gopalganj, Bangladesh" + }, + { + "author_name": "Quddus Mehnaz", + "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Md Nur Hossain Bhuiyan", + "author_inst": "Department of Surgery, Chittagong Medical College and Hospital, Chattogram, Bangladesh" + }, + { + "author_name": "Tahmina Banu", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.19.20106492", "rel_title": "A modified SEIR Model with Confinement and Lockdown of COVID-19 for Costa Rica", @@ -1440489,45 +1441133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20106518", - "rel_title": "Using Artificial Intelligence for COVID-19 Chest X-ray Diagnosis", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20106518", - "rel_abs": "Coronavirus disease-19 (COVID-19), caused by a novel member of the coronavirus family, is a respiratory disease that rapidly reached pandemic proportions with high morbidity and mortality. It has had a dramatic impact on society and world economies in only a few months. COVID-19 presents numerous challenges to all aspects of healthcare, including reliable methods for diagnosis, treatment, and prevention. Initial efforts to contain the spread of the virus were hampered by the time required to develop reliable diagnostic methods. Artificial intelligence (AI) is a rapidly growing field of computer science with many applications to healthcare. Machine learning is a subset of AI that employs deep learning with neural network algorithms. It can recognize patterns and achieve complex computational tasks often far quicker and with increased precision than humans. In this manuscript, we explore the potential for a simple and widely available test as a chest x-ray (CXR) to be utilized with AI to diagnose COVID-19 reliably. Microsoft CustomVision is an automated image classification and object detection system that is a part of Microsoft Azure Cognitive Services. We utilized publicly available CXR images for patients with COVID-19 pneumonia, pneumonia from other etiologies, and normal CXRs as a dataset to train Microsoft CustomVision. Our trained model overall demonstrated 92.9% sensitivity (recall) and positive predictive value (precision), with results for each label showing sensitivity and positive predictive value at 94.8% and 98.9% for COVID-19 pneumonia, 89% and 91.8% for non-COVID-19 pneumonia, 95% and 88.8% for normal lung. We then validated the program using CXRs of patients from our institution with confirmed COVID-19 diagnoses along with non-COVID-19 pneumonia and normal CXRs. Our model performed with 100% sensitivity, 95% specificity, 97% accuracy, 91% positive predictive value, and 100% negative predictive value. Finally, we developed and described a publicly available website to demonstrate how this technology can be made readily available in the future.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Andrew A Borkowski", - "author_inst": "James A. Haley Veterans' Hospital and the University of South Florida Morsani College of Medicine, Tampa, FL" - }, - { - "author_name": "Narayan A Viswanadham", - "author_inst": "James A. Haley Veterans' Hospital, Tampa, FL" - }, - { - "author_name": "L Brannon Thomas", - "author_inst": "James A. Haley Veterans' Hospital and the University of South Florida Morsani College of Medicine, Tampa, FL" - }, - { - "author_name": "Rodney D Guzman", - "author_inst": "InterKnowlogy, LLC, Carlsbad, CA" - }, - { - "author_name": "Lauren A Deland", - "author_inst": "James A. Haley Veterans' Hospital, Tampa, FL" - }, - { - "author_name": "Stephen M Mastorides", - "author_inst": "James A. Haley Veterans' Hospital and the University of South Florida Morsani College of Medicine, Tampa, FL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20105486", "rel_title": "SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus", @@ -1441567,6 +1442172,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2020.05.19.20107532", + "rel_title": "COVID-19 Datasets: A Survey and Future Challenges", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107532", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIn December 2019, a novel virus named COVID-19 emerged in the city of Wuhan, China. In early 2020, the COVID-19 virus spread in all continents of the world except Antarctica causing widespread infections and deaths due to its contagious characteristics and no medically proven treatment. The COVID-19 pandemic has been termed as the most consequential global crisis after the World Wars. The first line of defense against the COVID-19 spread are the non-pharmaceutical measures like social distancing and personal hygiene. The great pandemic affecting billions of lives economically and socially has motivated the scientific community to come up with solutions based on computer-aided digital technologies for diagnosis, prevention, and estimation of COVID-19. Some of these efforts focus on statistical and Artificial Intelligence-based analysis of the available data concerning COVID-19. All of these scientific efforts necessitate that the data brought to service for the analysis should be open source to promote the extension, validation, and collaboration of the work in the fight against the global pandemic. Our survey is motivated by the open source efforts that can be mainly categorized as (a) COVID-19 diagnosis from CT scans, X-ray images, and cough sounds, (b) COVID-19 case reporting, transmission estimation, and prognosis from epidemiological, demographic, and mobility data, (c) COVID-19 emotional and sentiment analysis from social media, and (d) knowledge-based discovery and semantic analysis from the collection of scholarly articles covering COVID-19. We survey and compare research works in these directions that are accompanied by open source data and code. Future research directions for data-driven COVID-19 research are also debated. We hope that the article will provide the scientific community with an initiative to start open source extensible and transparent research in the collective fight against the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junaid Shuja", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Eisa Alanazi", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Waleed Alasmary", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Abdulaziz Alashaikh", + "author_inst": "University of Jeddah" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.24.20107193", "rel_title": "Using HoloLens\u2122 to reduce staff exposure to aerosol generating procedures during a global pandemic", @@ -1442071,53 +1442707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.05.19.20106856", - "rel_title": "Currently prescribed drugs in the UK that could up or downregulate ACE2 in COVID-19 disease: A systematic review", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106856", - "rel_abs": "ObjectiveTo review evidence on routinely prescribed drugs in the UK that could up or downregulate Angiotensin Converting Enzyme 2 (ACE2) and potentially affect COVID-19 disease\n\nDesignSystematic review\n\nData sourceMEDLINE, EMBASE, CINAHL, the Cochrane Library and Web of Science\n\nStudy selectionAny design with animal or human models examining a currently prescribed UK drug compared to a control, placebo or sham group, and reporting an effect on ACE2 level, activity or gene expression.\n\nData extraction and synthesisMEDLINE, EMBASE, CINAHL, the Cochrane Library, Web of Science and OpenGrey from inception to 1st April 2020. Methodological quality was assessed using the SYRCLEs risk of bias tool for animal studies and Cochrane risk of bias tool for human studies.\n\nResultsWe screened 3,360 titles and included 112 studies with 21 different drug classes identified as influencing ACE2 activity. Ten studies were in humans and 102 were in animal models None examined ACE2 in human lungs. The most frequently examined drugs were Angiotensin Receptor Blockers (ARBs) (n= 55) and Angiotensin-Converting Enzyme-Inhibitors (ACE-I) (n= 22). More studies reported upregulation than downregulation with ACE-I (n=22), ARBs (n=55), insulin (n=8), thiazolidinedione (n=7) aldosterone agonists (n=3), statins (n=5), oestrogens (n=5) calcium channel-blockers (n=3) GLP-1 agonists (n=2) and NSAIDs (n=2).\n\nConclusionsThere is an abundance of academic literature and media reports on the potential of drugs that could attenuate or exacerbate COVID-19 disease. This is leading to trials of repurposed drugs and uncertainty amongst patients and clinicians concerning continuation or cessation of prescribed medications. Our review indicates that the impact of currently prescribed drugs on ACE2 has been poorly studied in-vivo, particularly in human lungs where the SARS-CoV-2 virus appears to enact its pathogenic effects. We found no convincing evidence to justify starting or stopping currently prescribed drugs to influence outcomes of COVID-19 disease.\n\nO_LSTStrengths and limitationsC_LSTO_LIThis review addresses a high priority patient and clinician concern\nC_LIO_LIGiven the limited evidence on the subject, we included human and animal models both in vivo and in vitro for a comprehensive review\nC_LIO_LIThis is the first systematic review specifically focussed on UK prescribed drugs that could alter ACE2 in COVID-19 disease\nC_LIO_LIThe heterogeneity across study designs and models meant meta-analysis was not suitable\nC_LIO_LIGiven the rapidly changing evidence as the pandemic progresses, it is possible that new studies have since been published.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hajira Dambha-Miller", - "author_inst": "University of Southampton" - }, - { - "author_name": "Ali Albasri", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sam Hodgson", - "author_inst": "University of Southampton" - }, - { - "author_name": "Christopher R Wilcox", - "author_inst": "University of Southampton" - }, - { - "author_name": "Shareen Khan", - "author_inst": "Oxford Health Foundation Trust" - }, - { - "author_name": "Nazrul Nazrul Islam", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul Little", - "author_inst": "University of Southampton" - }, - { - "author_name": "Simon J Griffin", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.21.20108704", "rel_title": "COVID-19 in Bangladesh: Measuring differences in individual precautionary behaviors among young adults", @@ -1442993,6 +1443582,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.20.20107755", + "rel_title": "BCG vaccination and socioeconomic variables vs Covid-19 global features: clearing up a controversial issue", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107755", + "rel_abs": "BackgroundThe Covid-19 pandemic is characterized by extreme variability in the outcome distribution and mortality rates across different countries. Some recent studies suggested an inverse correlation with BCG vaccination at population level, while others denied this hypothesis. In order to address this controversial issue, we performed a strict epidemiological study collecting data available on a global scale, considering additional variables such as cultural-political factors and adherence to other vaccination coverages.\n\nMethodsData on 121 countries, accounting for about 99% of Covid-19 cases and deaths globally, were from Johns Hopkins Coronavirus Resource Center, World Bank, International Monetary Fund, United Nations, Human Freedom Report, and BCG Atlas. Statistical models used were Ordinary Least Squares, Tobit and Fractional Probit, implemented on Stata/MP16 software.\n\nResultsBased on our results, countries where BCG vaccination is or has been mandated in the last decades have seen a drastic reduction in Covid-19 diffusion (-80% on average) and mortality (-50% on average), even controlling for relative wealth of countries and their governmental health expenditure. A significant contribution to this reduction (respectively -50% and -13% on average) was also associated to the outbreak onset during summer, suggesting a possible influence of seasonality. Other variables turned out to be associated, though to a lesser extent.\n\nConclusionsRelying on a very large dataset and a wide array of control variables, our study confirms a strong and robust association between Covid-19 diffusion and mortality with BCG vaccination and a set socio-economic factors, opening new perspectives for clinical speculations and public health policies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luigi Ventura", + "author_inst": "Department of Economy and Law, Sapienza University of Rome, Rome, Italy" + }, + { + "author_name": "Matteo Vitali", + "author_inst": "Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy" + }, + { + "author_name": "Vincenzo Romano Spica", + "author_inst": "Department of Movement, Human and Health Sciences, University of Rome \u201cForo Italico\u201d, Rome Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.25.20109470", "rel_title": "Seroprevalence of antibodies against SARS-CoV-2 among public community and health-care workers in Alzintan City of Libya", @@ -1443745,37 +1444361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.05.23.20111559", - "rel_title": "Estimating Household Transmission of SARS-CoV-2", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111559", - "rel_abs": "Introduction and GoalsSARS-CoV-2 is transmitted both in the community and within households. Social distancing and lockdowns reduce community transmission but do not directly address household transmission. We provide quantitative measures of household transmission based on empirical data, and estimate the contribution of households to overall spread. We highlight policy implications from our analysis of household transmission, and more generally, of changes in contact patterns under social distancing.\n\nMethodsWe investigate the household secondary attack rate (SAR) for SARS-CoV-2, as well as Rh, which is the average number of within-household infections caused by a single index case. We identify previous works that estimated the SAR. We correct these estimates based on the false-negative rate of PCR testing and the failure to test asymptomatics. Results are pooled by a hierarchical Bayesian random-effects model to provide a meta-analysis estimate of the SAR. We estimate Rh using results from population testing in Vo, Italy and contact tracing data that we curate from Singapore. The code and data behind our analysis are publicly available1.\n\nResultsWe identified nine studies of the household secondary attack rate. Our modeling suggests the SAR is heterogeneous across studies. The pooled central estimate of the SAR is 30% but with a posterior 95% credible interval of (0%, 67%) reflecting this heterogeneity. This corresponds to a posterior mean for the SAR of 30% (18%, 43%) and a standard deviation of 15% (9%, 27%). If results are not corrected for false negatives and asymptomatics, the pooled central estimate for the SAR is 20% (0%, 43%). From the same nine studies, we estimate Rh to be 0.47 (0.13, 0.77). Using contact tracing data from Singapore, we infer an Rh value of 0.32 (0.22, 0.42). Population testing data from Vo yields an Rh estimate of 0.37 (0.34, 0.40) after correcting for false negatives and asymptomatics.\n\nInterpretationOur estimates of Rh suggest that household transmission was a small fraction (5%-35%) of R before social distancing but a large fraction after (30%-55%). This suggests that household transmission may be an effective target for interventions. A remaining uncertainty is whether household infections actually contribute to further community transmission or are contained within households. This can be estimated given high-quality contact tracing data.\n\nMore broadly, our study points to emerging contact patterns (i.e., increased time at home relative to the community) playing a role in transmission of SARS-CoV-2. We briefly highlight another instance of this phenomenon (differences in contact between essential workers and the rest of the population), provide coarse estimates of its effect on transmission, and discuss how future data could enable a more reliable estimate.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mihaela Curmei", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Andrew Ilyas", - "author_inst": "MIT" - }, - { - "author_name": "Owain Evans", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jacob Steinhardt", - "author_inst": "UC Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.23.20110189", "rel_title": "Explainable machine learning models to understand determinants of COVID-19 mortality in the United States", @@ -1444723,6 +1445308,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.05.23.20111310", + "rel_title": "No evidence for allelic association between Covid-19 and ACE2 genetic variants by direct exome sequencing in 99 SARS-CoV-2 positive patients", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111310", + "rel_abs": "BackgroundCoronaviruses (CoV) are a large family of viruses that are common in people and many animal species. Animal coronaviruses rarely infect humans with the exceptions of the Middle East Respiratory Syndrome (MERS-CoV), the Severe acute respiratory syndrome coronavirus (SARS-CoV), and now SARS-CoV-2, which is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19). Many studies suggested that genetic variants in ACE2 gene may influence the host susceptibility/resistance to SARS-CoV-2 virus according to the functional role of ACE2 in human pathophysiology. However, all these studies have been conducted in silico based on epidemiological and population data. We therefore investigated the occurrence of ACE2 variants in a cohort of 99 Italian unrelated individuals clinically diagnosed with coronavirus disease 19 (COVID-19) to experimental demonstrate allelic association with disease severity.\n\nMethodsBy whole-exome sequencing we analysed 99 DNA samples of severely and extremely severely COVID-19 patients hospitalized at the University Hospital of Rome \"Tor Vergata\" and Bambino Gesu Hospital in Rome.\n\nResultsWe identified three different germline variants, one intronic (c.439+4G>A) and two missense (c.2158A>G, p.Asn720Asp; c.1888G>C, p.Asp630His), in 26 patients with a similar frequency between male and female and a not statistically different frequency, except for c.1888G>C, (p.Asp630His) with the ethnically matched populations (EUR).\n\nConclusionsOur results suggest that there is not any ACE2 exonic allelic association with disease severity. It is possible that rare susceptibility alleles are located in the non-coding region of the gene able to control ACE2 gene activity. It is therefore of interest, to explore the existence of ACE2 susceptibility alleles to SARS-Co-V2 in these regulatory regions. In addition, we found no significant evidence that ACE2 alleles is associated with disease severity/sex bias in the Italian population.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Antonio Novelli", + "author_inst": "Laboratory of Medical Genetics, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Michela Biancolella", + "author_inst": "Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy" + }, + { + "author_name": "Paola Borgiani", + "author_inst": "Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy" + }, + { + "author_name": "Dario Cocciadiferro", + "author_inst": "Laboratory of Medical Genetics, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Vito Luigi Colona", + "author_inst": "Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy" + }, + { + "author_name": "Maria Rosaria D'Apice", + "author_inst": "Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy" + }, + { + "author_name": "Paola Rogliani", + "author_inst": "Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome \"Tor Vergata\", Rome, Italy" + }, + { + "author_name": "Salvatore Zaffina", + "author_inst": "Occupational Medicine, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Francesca Leonardis", + "author_inst": "Intensive Care Unit, Tor Vergata University Hospital, Rome, Italy" + }, + { + "author_name": "Andrea Campana", + "author_inst": "Department of Pediatrics, IRCCS Bambino Ges\u00f9 Children's Hospital, Rome, Italy" + }, + { + "author_name": "Massimiliano Raponi", + "author_inst": "Medical Directorate, IRCCS Bambino Ges\u00f9 Children's Hospital, Rome, Italy" + }, + { + "author_name": "Massimo Andreoni", + "author_inst": "Infectious Diseases Clinic, Policlinico Tor Vergata, Rome, Italy" + }, + { + "author_name": "Sandro Grelli", + "author_inst": "Dept. of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Italy" + }, + { + "author_name": "Giuseppe Novelli", + "author_inst": "Tor Vergata University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.05.25.20112938", "rel_title": "What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?", @@ -1445067,73 +1445723,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.26.20113233", - "rel_title": "Knowledge, attitude, practice and fear of COVID-19: A cross-cultural study", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113233", - "rel_abs": "BackgroundKnowledge, Attitude and Practice (KAP), and Fear toward COVID-19 are an important issue when designing public health approaches to control the spread of this highly contagious disease like COVID-19 during the global pandemic period. Studies with KAP and fear measures are limited only regional or country level, not yet with global or cross-cultural populations. The study is aimed to measure KAP and fear level towards COVID-19 and explore its cross-cultural variances in knowledge by socio-demographic factors among the general population of 8 different countries over 5 continents.\n\nMethodA cross-sectional online survey was conducted in April 2020 among 1296 participants using the Google form platform. Considering the social distancing formula and pandemic situation, we collect data using popular social media networks. Univariate and bivariate analyses were used to explore the collected data on KAP, fear, and sociodemographic factors.\n\nResultOverall knowledge score was 9.7 (out of 12) and gender differences (female vs male: 9.8 vs 9.5) were significant (p=0.008) in the bivariate analysis. Knowledge score variances found significant in some regions by gender, marital status and education qualification. The highest and lowest mean knowledge scores were recorded in the Middle East (10.0) and Europe (9.3). Despite having a high fear score (22.5 out of 35), 78.35% of respondents were in a positive attitude and 81.7% in good practice level. Fear score rankings: Middle East (1st; 23.8), Europe (2nd; 23.2); Africa (3rd; 22.7); South Asia (4th; 22.1); Oceania (5th; 21.9); and North America (6th; 21.7). We didnt find a correlation between fear and knowledge.\n\nLimitationDue to the nature of the online survey, aged and rural populations are under-representing (e.g. more than half of the responders are 16-29 age group).\n\nConclusionKAP and fear variation exist among geographical regions. Gender, marital status and education qualification are factors in knowledge variances for some regions. KAP and fear measures can assist health education programs considering some sociodemographic factors and regions during an outbreak of highly contagious disease and, which can uplift a positive attitude and good practice.\n\nHighlightsO_LICross-cultural KAP and fear toward COVID-19 are evaluated\nC_LIO_LIRespondents from Europe scored less knowledge on COVID 19 but had more good knowledge level\nC_LIO_LIAbout 80% participants had positive attitude and good practice behavior.\nC_LIO_LIInterestingly, Participants in Oceania avoided more crowded places whereas, in Europe worn more masks during outing as a measure of prevention\nC_LIO_LIParticipants in Middle East had the highest score in fear, and fear was independent of knowledge\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mohammad Ali", - "author_inst": "Uttara Adhunik Medical College Hospital, Dhaka, Bangladesh" - }, - { - "author_name": "Zakir Uddin", - "author_inst": "McMaster University" - }, - { - "author_name": "Palash Chandra Banik", - "author_inst": "Bangladesh University of Health Sciences, Bangladesh" - }, - { - "author_name": "Fatema A Hegazy", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Shamita Zaman", - "author_inst": "Macquarie University" - }, - { - "author_name": "Abu Sleh Mohammed Ambia", - "author_inst": "Royal Borough of Windsor & Maidenhead, UK" - }, - { - "author_name": "Md. Kaoser Bin Siddique", - "author_inst": "Disabled Rehabilitation and Research Association, Bangladesh" - }, - { - "author_name": "Rezoana Islam", - "author_inst": "University of Toronto" - }, - { - "author_name": "Fatema Khanam", - "author_inst": "Widerstromska Gymnesiet, Huddinge Municipality, Sweden" - }, - { - "author_name": "Sayed Mohammad Bahalul", - "author_inst": "Sundsvall Hospital, Sundsvall, Sweden" - }, - { - "author_name": "Md Ahiduzzaman Sharkar", - "author_inst": "Division of Public Health, Manitoba Health, MB Government, Canada" - }, - { - "author_name": "F M Akram Hossain", - "author_inst": "Department of Physical Therapy, Citi medical services, New York, USA" - }, - { - "author_name": "Gias Uddin Ahsan", - "author_inst": "North South University, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.23.20111435", "rel_title": "Enveloped Virus Inactivation on Personal Protective Equipment by Exposure to Ozone", @@ -1445857,6 +1446446,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.23.112284", + "rel_title": "SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search", + "rel_date": "2020-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.112284", + "rel_abs": "The COVID-19 pandemic has sparked unprecedented mobilization of scientists, generating a deluge of papers that makes it hard for researchers to keep track and explore new directions. Search engines are designed for targeted queries, not for discovery of connections across a corpus. In this paper, we present SciSight, a system for exploratory search of COVID-19 research integrating two key capabilities: first, exploring associations between biomedical facets automatically extracted from papers (e.g., genes, drugs, diseases, patient outcomes); second, combining textual and network information to search and visualize groups of researchers and their ties. SciSight1 has so far served over 15K users with over 42K page views and 13% returns.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tom Hope", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Jason Portenoy", + "author_inst": "University of Washington" + }, + { + "author_name": "Kishore Vasan", + "author_inst": "University of Washington" + }, + { + "author_name": "Jonathan Borchardt", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Eric Horvitz", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Daniel S. Weld", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Marti A. Hearst", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Jevin West", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.23.20111443", "rel_title": "COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance.", @@ -1446429,45 +1447065,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.23.20093484", - "rel_title": "Fevers Are Rarest in the Morning: Could We Be Missing Infectious Disease Cases by Screening for Fever Then?", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20093484", - "rel_abs": "We retrospectively studied US emergency department visits (n=295,406), including nationally representative results. Patients were less likely to have detectable fevers during mornings, with especially large morning-evening differences during influenza outbreaks (national RR=0.56, 95%CI=0.47-0.66). This suggests morning screenings could miss otherwise-detectable cases. Twice-daily screenings could be a simple solution. However, similar COVID-19 research is needed.\n\nArticle Summary LineFevers were about half as common in the morning as in the evening during influenza outbreaks, suggesting that mornings may be a bad time to perform once-daily fever screenings for infectious diseases, and that twice-daily screenings could be preferable.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Charles Harding", - "author_inst": "Independent Statistical Analyst, Seattle, WA, USA" - }, - { - "author_name": "Francesco Pompei", - "author_inst": "Exergen, Corp., Watertown, MA, USA" - }, - { - "author_name": "Samantha F Bordonaro", - "author_inst": "Professional Emergency Services, Gates Vascular Institute, Buffalo, NY, USA" - }, - { - "author_name": "Daniel C McGillicuddy", - "author_inst": "Departments of Emergency Medicine, Saint Joseph Mercy Hospital & University of Michigan, Ann Arbor, MI, USA" - }, - { - "author_name": "Dmitriy Burmistrov", - "author_inst": "Independent Statistical Analyst, MA, USA" - }, - { - "author_name": "Leon D Sanchez", - "author_inst": "Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.116780", "rel_title": "Study of cell to cell transmission of SARS CoV 2 virus particle using gene network from micro array data", @@ -1447291,6 +1447888,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20104414", + "rel_title": "Risk of infection and hospitalization by Covid-19 in Mexico: a case-control study", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20104414", + "rel_abs": "ObjectiveDuring the onset of a novel epidemic, there are public health priorities that need to be estimated, such as risk factors for infection, hospitalization, and clinical severity to allocate resources and issue health policies. In this work we calculate the risk of infection and hospitalization by Covid-19 conferred by demographic, lifestyle, and co-morbidity factors.\n\nMaterial and methodsThis is a case-control study including the tested individuals for SARS-Cov-2 by RT-PCR officially reported by the Health Secretary of Mexico from January 01 to May 8, 2020 (102,875 subjects). Demographic (sex, age, foreign and immigrant status, native speaking, place of residence), life-style (smoking), and co-morbidities [diabetes, obesity, high blood pressure (HBP), asthma, immunosuppression, chronic obstructive pulmonary disease (COPD), cardiovascular disease other than HBP, chronic kidney disease (CKD), and other not specified diseases (other diseases)] variables were included in this study. The risk of infection and hospitalization conferred by each variable was calculated with univariate (ULR) and multivariate (MLR) logistic regression models.\n\nResultsThe place of residence (OR=4.91 living in Tijuana City), followed by advanced age (OR=6.71 in 61-70 years-old), suffering from diabetes (OR=1.87) or obesity (OR=1.61), being male (OR=1.55), having HBP (OR=1.52), and notoriously being indigenous (OR=1.49) conferred a higher risk of becoming infected by SARS-CoV-2 in Mexico. Unexpectedly, we found that having asthma (OR=0.63), immunosuppression (OR=0.65) or smoking (OR=0.85) are protective factors against infection, while suffering from COPD does not increase the risk for SARS-CoV-2 infection. In contrast, advanced age (OR=11.6 in [≥] 70 years-old) is the main factor for hospitalization due to Covid-19, followed by some co-morbidities, mainly diabetes (OR=3.69) and HBP (OR=2.79), being indigenous (OR=1.89), male sex (OR=1.67) and the place of residence (OR=4.22 for living in Juarez City). Unlike the protective risk against infection, immunosuppression (OR=2.69) and COPD (OR=3.63), contribute to the risk of being hospitalized, while having asthma (OR=0.7) also provides protection against hospitalization.\n\nConclusionsIn addition to confirming that older age, diabetes, HBP and obesity are the main risk of infection and hospitalization by Covid-19, we found that being indigenous, immunosuppression, smoking and asthma protect against infection, and the latter also against hospitalization.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jaime Berumen", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Max Schmulson", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Jesus Alegre", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Guadalupe Guerrero", + "author_inst": "Hospital General de Mexico, Dr. Eduardo Liceaga, Mexico City, Mexico" + }, + { + "author_name": "Gustavo Olaiz", + "author_inst": "Centro de Investigacion en politicas, poblacion y salud, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Rosa M. Wong-Chew", + "author_inst": "Division de Investigacion, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Jorge Larriva-Sahd", + "author_inst": "Instituto de Neurobiologia, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Queretaro Mexico" + }, + { + "author_name": "Carlos Cantu-Brito", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Ana Ochoa-Guzman", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Adrian Garcilazo-Avila", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Carlos Gonzalez-Carballo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Erwin Chiquete", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20102525", "rel_title": "Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients", @@ -1447783,25 +1448443,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.22.20110254", - "rel_title": "Flattening the COVID 19 curve in susceptible forest indigenous tribes using SIR model", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110254", - "rel_abs": "COVID 19 is a global threat and globally spreading. The international cooperation involving indigenous peoples and local communities is urgently required in joint prevention to control the epidemic. Currently, many indigenous populations are continuing to face COVID 19. This study is concerned about the dynamic of COVID 19 pandemic among indigenous populations living in the remote Amazon rainforest enclaves. Using the Susceptible Infectious Recovered (SIR) model, the spread of the COVID 19 under 3 intervention scenarios (low, moderate, high) is simulated and predicted in indigenous tribe populations. The SIR model forecasts that without intervention, the epidemic peak may reach within 1020 days. Nonetheless the peak can be reduced with strict interventions. Under low intervention, the COVID 19 cases are reduced to 73% and 56% of the total populations. While, in the scenario of high intervention, the COVID 19 peaks can be reduced to values ranging from 53% to 15%. To conclude, the simulated interventions tested by SIR model have reduced the pandemic peak and flattened the COVID 19 curve in indigenous populations. Nonetheless, it is mandatory to strengthen all mitigation efforts, reduce exposures, and decrease transmission rate as possible for COVID 19 containment.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andrio Adwibowo", - "author_inst": "University of Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.21.20108910", "rel_title": "Global Infodemiology of COVID-19: Focus on Google web searches and Instagram hashtags", @@ -1448509,6 +1449150,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.19.20107425", + "rel_title": "A Modelling Analysis of Strategies for Relaxing COVID-19 Social Distancing", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107425", + "rel_abs": "BackgroundThe ability of countries to contain and control COVID-19 virus transmission via social distancing is critical in the absence of a vaccine. Early activation of robust measures has been shown to control the daily infection rate, and consequential pressure on the health care system. As countries begin to control COVID-19 spread an understanding of how to ease social distancing measures to prevent a rebound in cases and deaths is required.\n\nMethodsUsing COVID-19 transmission data from the outbreak source in Hubei Province, China prior to activation of containment measures, we adapted an established individual-based simulation model of the city of Newcastle, Australia. Simulation of virus transmission in this model, with and without, social distancing measures activated permitted us to quantify social distancing effectiveness. Optimal strategies for relaxing social distancing were determined under two settings: with high numbers of daily cases, as in New York; and where early social distancing activation resulted in limited ongoing transmission, as in Perth, Australia.\n\nFindingsIn countries where strong social distancing measures were activated after the COVID-19 virus had spread widely, our study found these measures are required to be maintained for significant periods before being eased, to return to a situation where daily case numbers become low. In countries where early responses to the COVID-19 pandemic have been highly successful, as in Australia, we show that a staged relaxation of social distancing prevents a rebound in cases.\n\nInterpretationModelling studies and direct observation have shown that robust and timely social distancing have the most effect in containing the spread of the COVID-19 virus. Questions arise as to the duration of strong social distancing measures, given they are highly disruptive to society and economic activity. This study demonstrates the necessity of holding robust social distancing in place until COVID-19 virus transmission has significantly decreased, and how they may then be safely eased.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "George J Milne", + "author_inst": "University of Western Australia" + }, + { + "author_name": "Simon Xie", + "author_inst": "the University of Western Australia" + }, + { + "author_name": "Dana Poklepovich", + "author_inst": "University of Western Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.20.20107573", "rel_title": "Modelling information-dependent social behaviors in response to lockdowns: the case of COVID-19 epidemic in Italy", @@ -1449381,29 +1450049,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.24.20112193", - "rel_title": "Covid19 Surveillance in Peru on April using Text Mining", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112193", - "rel_abs": "The present outbreak as consequence by coronavirus covid19 has generated an big impact over the world. South American countries had their own limitations, challengues and pandemic has highlighted what needs to improve. Peru is a country with good start with quarantine, social distancing policies but the policies was not enough during the weeks. So, the analysis over April is performed through infoveillance using posts from different cities to analyze what population was living or worried during this month. Results presents a high concern about international context, and national situation, besides Economy and Politics are issues to solve. By constrast, Religion and Transport are not very important for peruvian citizens.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Josimar E. Chire Saire", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Jimmy Oblitas", - "author_inst": "Universidad Privada del Norte" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.24.20112136", "rel_title": "Spatiotemporal Analysis of Medical Resource Deficiencies in the U.S. under COVID-19 Pandemic", @@ -1450187,6 +1450832,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.22.20109959", + "rel_title": "CLINICAL CHARACTERISTICS AND PROGNOSTIC FACTORS FOR ICU ADMISSION OF PATIENTS WITH COVID-19 USING MACHINE LEARNING AND NATURAL LANGUAGE PROCESSING", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109959", + "rel_abs": "There remain many unknowns regarding the onset and clinical course of the ongoing COVID-19 pandemic. We used a combination of classic epidemiological methods, natural language processing (NLP), and machine learning (for predictive modeling), to analyse the electronic health records (EHRs) of patients with COVID-19.\n\nWe explored the unstructured free text in the EHRs within the SESCAM Healthcare Network (Castilla La-Mancha, Spain) from the entire population with available EHRs (1,364,924 patients) from January 1st to March 29th, 2020. We extracted related clinical information upon diagnosis, progression and outcome for all COVID-19 cases, focusing in those requiring ICU admission.\n\nA total of 10,504 patients with a clinical or PCR-confirmed diagnosis of COVID-19 were identified, 52.5% males, with age of 58.2{+/-}19.7 years. Upon admission, the most common symptoms were cough, fever, and dyspnoea, but all in less than half of cases. Overall, 6% of hospitalized patients required ICU admission. Using a machine-learning, data-driven algorithm we identified that a combination of age, fever, and tachypnoea was the most parsimonious predictor of ICU admission: those younger than 56 years, without tachypnoea, and temperature <39{degrees}C, (or >39{degrees}C without respiratory crackles), were free of ICU admission. On the contrary, COVID-19 patients aged 40 to 79 years were likely to be admitted to the ICU if they had tachypnoea and delayed their visit to the ER after being seen in primary care.\n\nOur results show that a combination of easily obtainable clinical variables (age, fever, and tachypnoea with/without respiratory crackles) predicts which COVID-19 patients require ICU admission.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jose Luis Izquierdo", + "author_inst": "Hospital Universitario de Guadalajara, Guadalajara, Spain" + }, + { + "author_name": "Julio Ancochea", + "author_inst": "Hospital Universitario de La Princesa, Madrid, Spain" + }, + { + "author_name": "- Savana COVID-19 Research Group", + "author_inst": "" + }, + { + "author_name": "Joan B Soriano", + "author_inst": "Hospital Universitario de La Princesa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.05.21.20108969", "rel_title": "ASSESSMENT OF WORKERS PERSONAL VULNERABILITY TO COVID-19 USING COVID-AGE", @@ -1450907,81 +1451583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.22.20110718", - "rel_title": "Occupational Exposures and Programmatic Response to COVID-19 Pandemic: An Emergency Medical Services Experience", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110718", - "rel_abs": "BackgroundRigorous assessment of occupational COVID-19 risk and personal protective equipment (PPE) use are not well-described. We evaluated 9-1-1 emergency medical services (EMS) encounters for patients with COVID-19 to assess occupational exposure, programmatic strategies to reduce exposure, and PPE use.\n\nMethodsWe conducted a retrospective cohort investigation of lab-confirmed COVID-19 patients in King County, WA who received 9-1-1 EMS responses from February 14, 2020 to March 26, 2020. We reviewed dispatch, EMS, and public health surveillance records to evaluate the temporal relationship between exposure and programmatic changes to EMS operations designed to identify high-risk patients, protect the workforce, and conserve PPE.\n\nResultsThere were 274 EMS encounters for 220 unique COVID-19 patients involving 700 unique EMS providers with 988 EMS person-encounters. Use of \"full\" PPE including mask, eye protection, gown and gloves (MEGG) was 67%. There were 151 person-exposures among 129 individuals, who required 981 quarantine days. Of the 700 EMS providers, 3 (0.4%) tested positive within 14 days of encounter. Programmatic changes were associated with a temporal reduction in exposures. When stratified at the study encounters midpoint, 94% (142/151) of exposures occurred during the first 137 EMS encounters compared to 6% (9/151) during the second 137 EMS encounters (p<0.01). By the investigations final week, EMS deployed MEGG PPE in 34% (3579/10,468) of all EMS person-encounters.\n\nConclusionLess than 0.5% of EMS providers experienced COVID-19 illness within 14 days of occupational encounter. Programmatic strategies were associated with a reduction in exposures, while achieving a measured use of PPE.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "David L Murphy", - "author_inst": "Department of Emergency Medicine, University of Washington, Seattle WA" - }, - { - "author_name": "Leslie M Barnard", - "author_inst": "Division of Emergency Medical Services, Public Health - Seattle & King County WA" - }, - { - "author_name": "Christopher J Drucker", - "author_inst": "Division of Emergency Medical Services Public Health - Seattle & King County WA" - }, - { - "author_name": "Betty Y Yang", - "author_inst": "Department of Emergency Medicine, University of Washington, Seattle WA" - }, - { - "author_name": "Jamie M Emert", - "author_inst": "Division of Emergency Medical Services Public Health - Seattle & King County WA" - }, - { - "author_name": "Leilani Schwarcz", - "author_inst": "Division of Emergency Medical Services Public Health - Seattle & King County WA" - }, - { - "author_name": "Catherine R Counts", - "author_inst": "Department of Emergency Medicine, University of Washington, Seattle WA" - }, - { - "author_name": "Tracie Y Jacinto", - "author_inst": "Division of Emergency Medical Services Public Health - Seattle & King County WA" - }, - { - "author_name": "Andrew M McCoy", - "author_inst": "Department of Emergency Medicine, University of Washington, Seattle WA; American Medical Response Puget Sound, Seattle WA" - }, - { - "author_name": "Tyler A Morgan", - "author_inst": "Tri-Med Ambulance, Kent WA" - }, - { - "author_name": "Jim E Whitney", - "author_inst": "Redmond Fire Department, Redmond WA" - }, - { - "author_name": "Joel V Bodenman", - "author_inst": "Kirkland Fire Department, Kirkland WA" - }, - { - "author_name": "Jeffrey S Duchin", - "author_inst": "Public Health - Seattle & King County WA; Department of Medicine, University of Washington, Seattle WA" - }, - { - "author_name": "Michael R Sayre", - "author_inst": "Department of Emergency Medicine, University of Washington, Seattle WA; Seattle Fire Department, Seattle WA" - }, - { - "author_name": "Thomas D Rea", - "author_inst": "Division of Emergency Medical Services Public Health - Seattle & King County WA; Department of Medicine, University of Washington, Seattle WA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.05.22.20110403", "rel_title": "Why are most COVID-19 infection curves linear?", @@ -1451625,6 +1452226,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.22.20110502", + "rel_title": "Conditions for a second wave of COVID-19 due to interactions between disease dynamics and social processes", + "rel_date": "2020-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110502", + "rel_abs": "In May 2020, many jurisdictions around the world began lifting physical distancing restrictions against the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), giving rise to concerns about a possible second wave of coronavirus disease 2019 (COVID-19). These restrictions were imposed as a collective population response to the presence of COVID-19 in communities. However, lifting restrictions is also a population response to their socio-economic impacts, and is expected to increase COVID-19 cases, in turn. This suggests that the COVID-19 pandemic exemplifies a coupled behaviour-disease system. Here we develop a minimal mathematical model of the interaction between social support for school and workplace closure and the transmission dynamics of SARS-CoV-2. We find that a second wave of COVID-19 occurs across a broad range of plausible model input parameters, on account of instabilities generated by behaviour-disease interactions. We conclude that second waves of COVID-19-should they materialize-can be interpreted as the outcomes of nonlinear interactions between disease dynamics and population behaviour.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sansao A Pedro", + "author_inst": "Universidade Eduardo Mondlane, Departamento de Matematica e Informatica, Maputo, Mozambique" + }, + { + "author_name": "Frank T Ndjomatchoua", + "author_inst": "International Rice Research Institute, Sustainable Impact Platform, Geospatial Science and Modelling cluster, DAPO Box 7777-1301, Metro Manila, Philippines" + }, + { + "author_name": "Peter Jentsch", + "author_inst": "University of Guelph, School of Environmental Sciences, Guelph, N1G 2W1, Canada and University of Waterloo, Department of Applied Mathematics, Waterloo, N2L 3G1" + }, + { + "author_name": "Jean M Tcheunche", + "author_inst": "Avenir Health, Glastonbury, CT, USA" + }, + { + "author_name": "Madhur Anand", + "author_inst": "University of Guelph, School of Environmental Sciences, Guelph, N1G 2W1, Canada" + }, + { + "author_name": "Chris T Bauch", + "author_inst": "University of Waterloo, Department of Applied Mathematics, Waterloo, N2L 3G1, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20110551", "rel_title": "Anti-SARS-CoV-2 IgG antibodies are associated with reduced viral load", @@ -1452157,45 +1452797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20108951", - "rel_title": "Effective Screening of SARS-CoV-2 Neutralizing Antibodies in Patient Serum using Lentivirus Particles Pseudotyped with SARS-CoV-2 Spike Glycoprotein", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108951", - "rel_abs": "Pseuodotyped particles have significant importance and use in virology as tools for studying the biology of highly pathogenic viruses in a lower biosafety environment. The biological, chemical, and serological studies of the recently emerged SARS-CoV-2 will be greatly aided by the development and optimization of a suitable pseudotyping system. Here, we pseudotyped the SARS-CoV-2 Spike glycoprotein (SPG) on a retroviral (MMLV) as well as a third generation lentiviral (pLV) vector and tested the transduction efficiency in several mammalian cell lines expressing SARS-CoV-2 receptor hACE2. While MMLV pseudotyped the vesicular stomatitis virus G glycoprotein (VSV-G) efficiently, it could not pseudotype SPG. In contrast, pLV pseudotyped both glycoproteins efficiently; however, much higher titers of pLV-G particles were produced. Among all the tested mammalian cells, 293Ts expressing hACE2 were most efficiently transduced using the pLV-S system. The pLV-S particles were efficiently neutralized by diluted serum (>:640) from a recently recovered COVID-19 patient who showed high SARS-CoV-2 specific IgM and IgG levels. In summary, pLV-S pseudotyped virus provides a valid screening tool for the presence of anti SARS-CoV-2 specific neutralizing antibodies in convalescent patient serum.\n\nSignificance StatementSARS-CoV-2 has emerged as one of the biggest threats in the history of humankind and is comparable to medieval plague, 1918 Spanish Flu, as well as world wars. Investigations into the biology of SARS-CoV-2 are partially hindered by the highly transmissible and pathogenic nature of this virus, which requires biosafety level 3 containment in a laboratory for investigation. The study here describes a pseudotyping system which mimics the surface properties of SARS-CoV-2 and can be used in lower biosafety level laboratory for the purpose of vaccine studies, drug inhibition studies, and serological screening to determine the status of herd immunity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ritesh Tandon", - "author_inst": "University of Mississippi Medical Center" - }, - { - "author_name": "Dipanwita Mitra", - "author_inst": "University of Mississippi Medical Center" - }, - { - "author_name": "Poonam Sharma", - "author_inst": "University of Mississippi Medical Center" - }, - { - "author_name": "Stephan J Stray", - "author_inst": "University of Mississippi Medical Center" - }, - { - "author_name": "John T Bates", - "author_inst": "University of Mississippi Medical Center" - }, - { - "author_name": "Gailen D Marshall", - "author_inst": "University of Mississippi Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20108639", "rel_title": "Validation of the Kuwait Progression Indicator Score for predicting progression of severity in COVID19", @@ -1453019,6 +1453620,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.23.107334", + "rel_title": "Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID-19", + "rel_date": "2020-05-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.107334", + "rel_abs": "SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna A. Valyaeva", + "author_inst": "Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University" + }, + { + "author_name": "Anastasia A. Zharikova", + "author_inst": "Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University" + }, + { + "author_name": "Artem S. Kasianov", + "author_inst": "The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute)" + }, + { + "author_name": "Yegor S. Vassetzky", + "author_inst": "CNRS, UMR 9018, Universite Paris-Saclay, Institut Gustave Roussy" + }, + { + "author_name": "Eugene V. Sheval", + "author_inst": "Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.05.21.109322", "rel_title": "The emergence of SARS-CoV-2 in Europe and the US", @@ -1453851,101 +1454487,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20109074", - "rel_title": "Repurposing Existing Medications for Coronavirus Disease 2019: Protocol for a Rapid and Living Systematic Review", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109074", - "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) has no known specific treatments. However, there might be in vitro and early clinical data as well as evidence from Severe Acute Respiratory Syndrome and Middle Eastern Respiratory Syndrome that could inform clinicians and researchers. This systematic review aims to create priorities for future research of drugs repurposed for COVID-19.\n\nMethodsThis systematic review will include in vitro, animal, and clinical studies evaluating the efficacy of a list of 34 specific compounds and four groups of drugs identified in a previous scoping review. Studies will be identified both from traditional literature databases and pre-print servers. Outcomes assessed will include time to clinical improvement, time to viral clearance, mortality, length of hospital stay, and proportions transferred to the intensive care unit and intubated, respectively. We will use the GRADE methodology to assess the quality of the evidence.\n\nDiscussionThe challenge posed by COVID-19 requires not just a rapid review of drugs that can be repurposed but also a sustained effort to integrate new evidence into a living systematic review.\n\nSystematic review registrationPROSPERO 2020 CRD42020175648", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Benjamin P. Geisler", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Lara Zahabi", - "author_inst": "McGill University" - }, - { - "author_name": "Adam E. Lang", - "author_inst": "McDonald Army Health Center" - }, - { - "author_name": "Naomi Eastwood", - "author_inst": "Wirral University Teaching Hospital NHS Foundation Trust" - }, - { - "author_name": "Elaine Tennant", - "author_inst": "Royal North Shore Hospital" - }, - { - "author_name": "Ljiljan Lukic", - "author_inst": "University Hospital for Infectious Disease Zagreb \"Dr. Fran Mihaljevic\"" - }, - { - "author_name": "Elad Sharon", - "author_inst": "National Cancer Institute" - }, - { - "author_name": "Hai-Hua Chuang", - "author_inst": "Chang Gung Memorial Hospital" - }, - { - "author_name": "Chang-Berm Kang", - "author_inst": "Proof Biotechnologies" - }, - { - "author_name": "Knakita Clayton-Johnson", - "author_inst": "Portmore Hospital Complex" - }, - { - "author_name": "Ahmed Aljaberi", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Haining Yu", - "author_inst": "University of California San Francisco Medical Center" - }, - { - "author_name": "Chinh Bui", - "author_inst": "Massachusetts Institute for Technology" - }, - { - "author_name": "Tuan Le Mau", - "author_inst": "Institute of High Performance Computing" - }, - { - "author_name": "Wen-Cheng Li", - "author_inst": "Chang Gung Memorial Hospital" - }, - { - "author_name": "Debbie Teodorescu", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Ludwig Christian Hinske", - "author_inst": "Ludwig Maximilian University" - }, - { - "author_name": "Dennis L. Sun", - "author_inst": "California Polytechnic State University" - }, - { - "author_name": "Farrin A. Manian", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Adam G. Dunn", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20109439", "rel_title": "Longitudinal laboratory testing tied to PCR diagnostics in COVID-19 patients reveals temporal evolution of distinctive coagulopathy signatures", @@ -1454633,6 +1455174,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.18.20105874", + "rel_title": "Early experiences with antibody testing in a Flemish nursing home during an acute COVID-19 outbreak: a retrospective cohort study.", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105874", + "rel_abs": "objectivesto assess the prevalence of COVID-19 (PCR-test) in residents and staff of a nursing home. To examine the presence of IgM and IgG antibodies in the sample and the relation between PCR and antibody test results.\n\ndesigncross-sectional and (retrospective) cohort study\n\nsettinga nursing home for the elderly Bessemerberg in Lanaken (Belgium) with up to 130 beds. Lanaken is situated in the Belgian province with the highest COVID-19 prevalence.\n\nparticipantsresidents (N=108) and staff members (N=93) of the nursing home\n\noutcomesPCR, IgM and IgG\n\nresultsthe prevalence of COVID-19, based on PCR test was 34% (N=40) for residents and 13% (N=11) for staff members, respectively. Of the residents, 13% showed positive IgM results and 15% positive IgG results. In 17% of the residents, at least one of the antibodies was positive. In total 13% of the staff members had positive IgM and 16% had a positive IgG. In 20% of the staff members at least one of these antibody tests was positive. In PCR positive residents, the percentage of IgM positive, IgG positive, and at least one of both was 28%, 34%, and 41%. In PCR positive staff, we found 30%, 60%, and 60%. Additional antibody tests were performed in nine residents between day 11 and 14 after the positive PCR test. Of those, 7 (78%) tested positive on at least one antibody. When retesting three weeks later, all remaining residents also tested positive.\n\nconclusionsRecently it was reported that in Belgium antibodies are present in 3-4% of the general population. Although, the prevalence in our residents is higher, the number is largely insufficient for herd immunity. In staff members of the regional hospital the prevalence of antibodies was 6%. The higher prevalence in nursing home staff (21%) may be related to the complete absence of good quality protection in the first weeks of the outbreak.\n\nArticle summaryO_LSTStrengths and limitations of this studyC_LST- This is the first study in Belgium examining the prevalence of COVID-19 and the presence of antibodies in residents and staff members of a nursing home\n- The internal procedural control was positive -with one exception- in all tests, which suggests good quality sampling and testing.\n- Some degree of selection bias should be assumed in residents, since some residents were absent; mostly from hospitalisation or death which can be related to the presence of COVID-related disease.\n- The study was set up in one nursing home and is consequently not representative for the whole of the Flemish community", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Frank Buntinx", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Peter Claes", + "author_inst": "Woonzorgcentrum Bessemerberg, Lanaken, Belgium." + }, + { + "author_name": "Marjo Gulikers", + "author_inst": "Woonzorgcentrum Bessemerberg, Lanaken, Belgium." + }, + { + "author_name": "Jan Y Verbakel", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Jan De Lepeleire", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Michael Van der Elst", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Marc Van Ranst", + "author_inst": "University of Leuven, Laboratory of Clinical and Epidemiological Virology (Rega Institute), Leuven, Belgium" + }, + { + "author_name": "Pieter Vermeersch", + "author_inst": "Department of cardiovascular Sciences, KU Leuven, Leuven Belgium" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.18.20104703", "rel_title": "COVID-19 in China: Risk Factors and R0 Revisited", @@ -1455221,41 +1455809,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.05.18.20105866", - "rel_title": "Acute cardiac injury in patients with COVID-19", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105866", - "rel_abs": "IntroductionCardiac complications of COVID-19 are potentially life-threatening. The occurrence of myocardial injury in the context of COVID-19 is multifactorial and has generated increasing interest.\n\nMethodsA systematic review with meta-analysis of the literature was performed. MEDLINE and EMBASE were searched. Two independente reviewers evaluated the selected manuscripts for the outcome \"myocardial injury\", defined by troponin elevation above the 99th percentile. Study heterogeneity and risk of bias were evaluated.\n\nResultsEight studies, with a total of 1229 patients, were included. The frequency of myocardial injury was 16% (95% CI: 9% - 27%). The heterogeneity among studies was high (93%). Conclusions: Myocardial injury may occur in patients with COVID-19, with a frequency of 16% among current studies. Continuous research is needed to update these findings, as the pandemic evolves, and to define the implications of myocardial injury in the context of this infection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrea De Lorenzo", - "author_inst": "Instituto Nacional de Cardiologia" - }, - { - "author_name": "Daniel Kasal", - "author_inst": "Instituto Nacional de Cardiologia" - }, - { - "author_name": "Bernardo Tura", - "author_inst": "Instituto Nacional de Cardiologia" - }, - { - "author_name": "Cristiane Lamas", - "author_inst": "Instituto Nacional de Cardiologia" - }, - { - "author_name": "Helena Rey", - "author_inst": "Instituto Nacional de Cardiologia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.18.20106013", "rel_title": "Exploring the spread dynamics of COVID-19 inMorocco", @@ -1456203,6 +1456756,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.21.109280", + "rel_title": "A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic", + "rel_date": "2020-05-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109280", + "rel_abs": "Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Chase W. Nelson", + "author_inst": "American Museum of Natural History" + }, + { + "author_name": "Zachary Ardern", + "author_inst": "Chair for Microbial Ecology, Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Tony L. Goldberg", + "author_inst": "Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI" + }, + { + "author_name": "Chen Meng", + "author_inst": "Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Chen-Hao Kuo", + "author_inst": "Biodiversity Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Christina Ludwig", + "author_inst": "Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Sergios-Orestis Kolokotronis", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY" + }, + { + "author_name": "Xinzhu Wei", + "author_inst": "Departments of Integrative Biology and Statistics, University of California, Berkeley, CA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.21.109298", "rel_title": "Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping", @@ -1456943,53 +1457543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.19.20103168", - "rel_title": "Multifocal transient cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20103168", - "rel_abs": "We report four cases of subacute encephalopathy occurring in patients with SARS-CoV-2 infection. All patients have been intubated in the first week from onset of ARDS and presented neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. The MRI picture and the clinical features are described. MRI lesions characteristics are unusual but demonstrate a highly consistent pattern through all the four patients with similar neurological symptoms. They do not fulfill any typical criteria for a definite neuroradiological entity. Their predominantly parieto-occipital distribution recalls posterior reversible encephalopathy syndrome (PRES), although the prevalent cortical involvement and diffusion MRI pattern are not typical of PRES. We speculate that this pattern may be related to a possible transient dysregulation of vasomotor reactivity.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nicoletta Anzalone", - "author_inst": "Department of Neuroradiology, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Antonella Castellano", - "author_inst": "Department of Neuroradiology, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Roberta Scotti", - "author_inst": "Department of Neuroradiology, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Anna Mara Scandroglio", - "author_inst": "Department of Anesthesia and Intensive Care, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Massimo Filippi", - "author_inst": "Department of Neurology, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Fabio Ciceri", - "author_inst": "Department of Hematology and Stem Cell Transplantation, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Moreno Tresoldi", - "author_inst": "Unit of General Medicine and Advanced Care, IRCCS San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Andrea Falini", - "author_inst": "Department of Neuroradiology, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.05.17.20104562", "rel_title": "COVID 19 in Bangladesh: Assumption of possible infection and death", @@ -1457901,6 +1458454,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.17.20104687", + "rel_title": "A DISSYMMETRY IN THE FIGURES RELATED TO THE COVID-19 PANDEMIC IN THE WORLD: WHAT FACTORS EXPLAIN THE DIFFERENCE BETWEEN AFRICA AND THE REST OF THE WORLD?", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104687", + "rel_abs": "Humanity has experienced outbreaks for millennia, from epidemics limited to pandemics that have claimed many victims and changed the course of civilizations. The advent of vaccines has eradicated some of the serious pathogens and reduced many others. However, pandemics are still part of our modern world, as we continue to have pandemics as devastating as HIV and as alarming as severe acute respiratory syndrome, Ebola and the Middle East respiratory syndrome. The Covid-19 epidemic with 0-exponential contamination curves reaching 3 million confirmed cases should not have come as a surprise, nor should it have been the last pandemic in the world. In this article, we try to summarize the lost opportunities as well as the lessons learned, hoping that we can do better in the future. The objective of this study is to relate the situation of Covid-19 in African countries with those of the countries most affected by the pandemic. It also allows us to verify how, according to the observed situation, the African ecosystem seems to be much more resilient compared to that of other continents where the number of deaths is in the thousands. To verify this, the diagnosed morbidity and mortality reported for different states of the world are compared to the ages of life and the average annual temperature of these states. The results show that the less dramatic balance of the African continent compared to other continents is partly linked to the relatively high temperatures on the continent but also to the relatively young character of its population.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cheikh Faye Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + }, + { + "author_name": "CheikhTidiane Wade Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + }, + { + "author_name": "Ibrahima Demba Dione Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.20.20103200", "rel_title": "The Hybrid Forecasting Method SVR-ESAR forCovid-19", @@ -1458405,105 +1458985,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.21.109157", - "rel_title": "Trimeric SARS-CoV-2 Spike interacts with dimeric ACE2 with limited intra-Spike avidity", - "rel_date": "2020-05-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109157", - "rel_abs": "A serious public health crisis is currently unfolding due to the SARS-CoV-2 pandemic. SARS-CoV-2 viral entry depends on an interaction between the receptor binding domain of the trimeric viral Spike protein (Spike-RBD) and the dimeric human angiotensin converting enzyme 2 (ACE2) receptor. While it is clear that strategies to block the Spike/ACE2 interaction are promising as anti-SARS-CoV-2 therapeutics, our current understanding is insufficient for the rational design of maximally effective therapeutic molecules. Here, we investigated the mechanism of Spike/ACE2 interaction by characterizing the binding affinity and kinetics of different multimeric forms of recombinant ACE2 and Spike-RBD domain. We also engineered ACE2 into a split Nanoluciferase-based reporter system to probe the conformational landscape of Spike-RBDs in the context of the Spike trimer. Interestingly, a dimeric form of ACE2, but not monomeric ACE2, binds with high affinity to Spike and blocks viral entry in pseudotyped virus and live SARS-CoV-2 virus neutralization assays. We show that dimeric ACE2 interacts with an RBD on Spike with limited intra-Spike avidity, which nonetheless contributes to the affinity of this interaction. Additionally, we demonstrate that a proportion of Spike can simultaneously interact with multiple ACE2 dimers, indicating that more than one RBD domain in a Spike trimer can adopt an ACE2-accessible \"up\" conformation. Our findings have significant implications on the design strategies of therapeutic molecules that block the Spike/ACE2 interaction. The constructs we describe are freely available to the research community as molecular tools to further our understanding of SARS-CoV-2 biology.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Irene Lui", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Xin X Zhou", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Shion A Lim", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Susanna Elledge", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Paige Solomon", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Nicholas J Rettko", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Beth Shoshana Zha", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lisa L Kirkemo", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Josef A Gramespacher", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jia Liu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Julio Cesar Cetrulo Lorenzi", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Yiska Weisblum", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Davide F Robbiani", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Michel C Nussenzweig", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Paul D Bieniasz", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Oren Rosenberg", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kevin K Leung", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "James A. Wells", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.21.108506", "rel_title": "No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2", @@ -1459323,6 +1459804,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.17.20104968", + "rel_title": "Fuzzy Autocatalytic analysis of Covid-19 outbreak in Malaysia", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104968", + "rel_abs": "The objective of this research is to demonstrate a mathematical technique to analyze the Covid-19 outbreak, particularly with respect to Malaysia. The technique is able to accommodate scarcity, quantity, and availability of the data set. The obtained results can offer descriptive insight for reflecting and strategizing actions in combating the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tahir Ahmad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Azmirul Ashaari", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Siti Rahmah Awang", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Siti Salwana Mamat", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Wan Munirah Wan Mohamad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Amirul Aizad Ahmad Fuad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Nurfarhana Hassan", + "author_inst": "Universiti Teknologi Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.18.20105155", "rel_title": "The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19", @@ -1459999,57 +1460523,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.05.21.108381", - "rel_title": "Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2", - "rel_date": "2020-05-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.108381", - "rel_abs": "The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay details and primer sequences become widely known, many laboratories could perform diagnostic tests using methods such as RT-PCR or isothermal RT-LAMP amplification. A key advantage of RT-LAMP based approaches compared to RT-PCR is that RT-LAMP is known to be robust in detecting targets from unprocessed samples. In addition, RT-LAMP assays are performed at a constant temperature enabling speed, simplicity, and point-of-use testing. Here, we provide the details of an RT-LAMP isothermal assay for the detection of SARS-CoV-2 virus with performance comparable to currently approved tests using RT-PCR. We characterize the assay by introducing swabs in virus spiked synthetic nasal fluids, moving the swab to viral transport medium (VTM), and using a volume of that VTM for performing the amplification without an RNA extraction kit. The assay has a Limit-of-Detection (LOD) of 50 RNA copies/L in the VTM solution within 20 minutes, and LOD of 5000 RNA copies/L in the nasal solution. Additionally, we show the utility of this assay for real-time point-of-use testing by demonstrating detection of SARS-CoV-2 virus in less than 40 minutes using an additively manufactured cartridge and a smartphone-based reader. Finally, we explore the speed and cost advantages by comparing the required resources and workflows with RT-PCR. This work could accelerate the development and availability of SARS-CoV-2 diagnostics by proving alternatives to conventional laboratory benchtop tests.\n\nSignificance StatementAn important limitation of the current assays for the detection of SARS-CoV-2 stem from their reliance on time- and labor-intensive and laboratory-based protocols for viral isolation, lysis, and removal of inhibiting materials. While RT-PCR remains the gold standard for performing clinical diagnostics to amplify the RNA sequences, there is an urgent need for alternative portable platforms that can provide rapid and accurate diagnosis, potentially at the point-of-use. Here, we present the details of an isothermal amplification-based detection of SARS-CoV-2, including the demonstration of a smartphone-based point-of-care device that can be used at the point of sample collection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Anurup Ganguli", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Ariana Mostafa", - "author_inst": "University of Illinois at urbana champaign" - }, - { - "author_name": "Jacob Berger", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Mehmet Aydin", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Fu Sun", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Enrique Valera", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Brian T. Cunningham", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "William P. King", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Rashid Bashir", - "author_inst": "University of Illinois at Urbana Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.05.21.107565", "rel_title": "Immunization with the receptor-binding domain of SARS-CoV-2 elicits antibodies cross-neutralizing SARS-CoV-2 and SARS-CoV without antibody-dependent enhancement", @@ -1460881,6 +1461354,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.18.20103283", + "rel_title": "Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20103283", + "rel_abs": "Objectivedetermine the percentage of healthcare workers (HCW) carrying SARS-CoV-2 in high exposure areas of the hospital.\n\nDesigncross-sectional study during April 15-24th in Hospital Costa del Sol (Marbella, Spain), excluding HCW with previous COVID19.\n\nSettinghospital based, focused on patient care areas COVID19.\n\nParticipants498 subjects, 80% women. Participation was offered to all the HCW of Emergencies, Intensive Care and Anesthesia, Internal Medicine and Pneumology. Other units not directly involved in the care of these patients were offered to participate.\n\nInterventionnaso and oropharyngeal PCR determination was performed together with IgG and IgM antibody determination by immunochromatography. On the day of sampling, a health questionnaire was answered, reporting symptoms on the same day and in the previous fourteen days.\n\nMain outcome measurespercentage of HCW with positive PCR for SARS-CoV-2, percentage of HCW with positive IgG for SARS-CoV-2.\n\nResultsTwo individuals were detected with PCR for SARS-CoV-2 positive (0.4%). Both were asymptomatic on the day of sampling, but one of them had had a CoVID-19 compatible picture in the previous two weeks and had positive IgG and IgM; therefore, only one subject was truly asymptomatic carrier (0.2%). 9 workers with positive IgG (1.8%) were detected.\n\nConclusionsthe prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This type of strategy can be one more tool in controlling the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julian Olalla", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol" + }, + { + "author_name": "Ana M Correa", + "author_inst": "Unidad de Microbiologia. Hospital Costa del Sol." + }, + { + "author_name": "Maria Dolores Martin-Escalante", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol." + }, + { + "author_name": "Maria Luisa Hortas", + "author_inst": "Area de Laboratorio. Hospital Costa del Sol." + }, + { + "author_name": "Maria Jesus Martin-Sendarrubias", + "author_inst": "Salud Laboral. Hospital Costa del Sol." + }, + { + "author_name": "Victor Fuentes", + "author_inst": "Medicina Preventiva. Hospital Costa del Sol." + }, + { + "author_name": "Gabriel Sena", + "author_inst": "Unidad de Microbiologia. Hospital Costa del Sol." + }, + { + "author_name": "Javier Garcia-Alegria", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol." + }, + { + "author_name": "ROBLE Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.15.20103531", "rel_title": "IL6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections", @@ -1461269,41 +1461793,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.16.20103820", - "rel_title": "Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103820", - "rel_abs": "The NHS Pathways triage system collates data on enquiries to 111 and 999 services in England. Since the 18th of March 2020, these data have been made publically available for potential COVID-19 symptoms self-reported by members of the public. Trends in such reports over time are likely to reflect behaviour of the ongoing epidemic within the wider community, potentially capturing valuable information across a broader severity profile of cases than hospital admission data. We present a fully reproducible analysis of temporal trends in NHS Pathways reports until 14th May 2020, nationally and regionally, and demonstrate that rates of growth/decline and effective reproduction number estimated from these data may be useful in monitoring transmission. This is a particularly pressing issue as lockdown restrictions begin to be lifted and evidence of disease resurgence must be constantly reassessed. We further assess the correlation between NHS Pathways reports and a publicly available NHS dataset of COVID-19-associated deaths in England, finding that enquiries to 111/999 were strongly associated with daily deaths reported 16 days later. Our results highlight the potential of NHS Pathways as the basis of an early warning system. However, this dataset relies on self-reported symptoms, which are at risk of being severely biased. Further detailed work is therefore necessary to investigate potential behavioural issues which might otherwise explain our conclusions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Quentin J Leclerc", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Emily Nightingale", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Thibaut Jombart", - "author_inst": "London School of Hygiene and Tropical Medicine (LSHTM)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.20103747", "rel_title": "Evaluate the timing of resumption of business for the states of New York, New Jersey and California via a pre-symptomatic and asymptomatic transmission model of COVID-19", @@ -1462159,6 +1462648,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.19.105445", + "rel_title": "Clinical And Analytical Performance Of An Automated Serological Test That Identifies S1/S2 Neutralizing IgG In Covid-19 Patients Semiquantitatively.", + "rel_date": "2020-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.105445", + "rel_abs": "BACKGROUNDIn the Covid-19 pandemic, highly selective serological testing is essential to define exposure to SARS-CoV-2 virus. Many tests have been developed, yet with variable speed to first result, and of unknown quality, particularly when considering the prediction of neutralizing capacity.\n\nOBJECTIVES/METHODSThe LIAISON(R) SARS-CoV-2 S1/S2 IgG assay was designed to measure antibodies against the SARS-CoV-2 native S1/S2 proteins in a standardized automated chemiluminescent assay. Clinical and analytical performance of the test were validated in an observational study using residual samples (>1500) with positive or negative Covid-19 diagnosis.\n\nRESULTSThe LIAISON(R) SARS-CoV-2 S1/S2 IgG assay proved highly selective and specific, and offers semiquantitative measures of serum or plasma levels of anti-S1/S2 IgG with neutralizing activity. The diagnostic sensitivity was 91.3% and 95.7% at >5 or [≥]15 days from diagnosis respectively, and 100% when assessed against a neutralizing assay. The specificity ranged between 97% and 98.5%. The average imprecision of the assay was <5 % coefficient of variation. Assay performance at 2 different cut-offs was evaluated to optimize predictive values in settings with different % disease prevalence. CONCLUSIONS. The automated LIAISON(R) SARS-CoV-2 S1/S2 IgG assay brings efficient, sensitive, specific, and precise serological testing to the laboratory, with the capacity to test large amounts of samples per day: first results are available within 35 minutes with a throughput of 170 tests/hour. The test also provides a semiquantitative measure to identify samples with neutralizing antibodies, useful also for a large scale screening of convalescent plasma for safe therapeutic use.\n\nIMPORTANCEWith the worldwide advance of the COVID-19 pandemic, efficient, reliable and accessible diagnostic tools are needed to support public health officials and healthcare providers in their efforts to deliver optimal medical care, and articulate sound demographic policy. DiaSorin has developed an automated serology based assay for the measurement of IgG specific to SARS CoV-2 Spike protein, and tested its clinical performance in collaboration with Italian health care professionals who provided access to large numbers of samples from infected and non-infected individuals. The assay delivers excellent sensitivity and specificity, and is able to identify samples with high levels of neutralizing antibodies. This will provide guidance in assessing the true immune status of subjects, as well as meeting the pressing need to screen donors for high titer convalescent sera for subsequent therapeutic and prophylactic use.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Fabrizio Bonelli", + "author_inst": "DiaSorin" + }, + { + "author_name": "Antonella Sarasini", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Claudia Zierold", + "author_inst": "DiaSorin" + }, + { + "author_name": "Mariella Calleri", + "author_inst": "DiaSorin" + }, + { + "author_name": "Alice Bonetti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Frank A Blocki", + "author_inst": "DiaSorin" + }, + { + "author_name": "Luca Pallavicini", + "author_inst": "DiaSorin" + }, + { + "author_name": "Alberto Chinali", + "author_inst": "DiaSorin" + }, + { + "author_name": "Daniela Campisi", + "author_inst": "ASST Niguarda Hospital" + }, + { + "author_name": "Elena Percivalle", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Anna Pia DiNapoli", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Carlo Federico Perno", + "author_inst": "University of Milan" + }, + { + "author_name": "Fausto Balldanti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.20.105247", "rel_title": "A replication-competent vesicular stomatitis virus for studies of SARS-CoV-2 spike-mediated cell entry and its inhibition", @@ -1462839,53 +1463395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.14.20102418", - "rel_title": "Preventive behavior of Vietnamese people in response to the COVID-19 pandemic", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102418", - "rel_abs": "We sought to evaluate the adherence of Vietnamese adults to COVID-19 preventive measures, and gain insight into the effects of the epidemic on the daily lives of Vietnamese people. An online questionnaire survey was organized from March 31 to April 6, 2020. The questionnaire assessed preventive behavior using multiple-answer responses to indicate the extent of adherence. In total, 2175 respondents completed the questionnaire (age range: 18-69 years). The mean adherence scores for personal and community preventive measures were 7.23 {+/-} 1.63 (range 1-9) and 9.57 {+/-} 1.12 (range 1-11), respectively. Perceived adaptation of the community to lockdown ({beta}=2.64, 95% CI 1.25-4.03), fears/worries concerning ones health ({beta}=2.87, 95% CI 0.04-5.70), residing in large cities ({beta}=19.40, 95% CI 13.78-25.03), access to official COVID-19 information sources ({beta}=16.45, 95% CI 6.82-26.08), and belonging to the healthcare sector ({beta}=22.53, 95% CI 16.00-29.07) were associated with a higher adherence score to anti-COVID instructions. The study indicates excellent preventive behavior of the Vietnamese population which explains the low number of COVID-19 infections and zero recorded mortality up to the first week of May 2020. Further monitoring is recommended to assess the sustainability of COVID-19 prevention via behavior change in the medium and long-term.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thang Van Thang", - "author_inst": "Institute for Community Health Research" - }, - { - "author_name": "Nhan Phuc Thanh Nguyen", - "author_inst": "Institute for Community Health Research, University of Medicine and Pharmacy, Hue University, Vietnam" - }, - { - "author_name": "Tuyen Dinh Hoang", - "author_inst": "Faculty of Public Health, University of Medicine and Pharmacy, Hue University, Vietnam" - }, - { - "author_name": "Vi Thao Tran", - "author_inst": "Institute for Community Health Research, University of Medicine and Pharmacy, Hue University, Vietnam" - }, - { - "author_name": "Cuc Thi Vu", - "author_inst": "Institute for Community Health Research, University of Medicine and Pharmacy, Hue University, Vietnam" - }, - { - "author_name": "Joseph Nelson Siewe", - "author_inst": "Global Health Institute, University of Antwerp, Belgium" - }, - { - "author_name": "Robert Colebunders", - "author_inst": "Global Health Institute, University of Antwerp, Belgium" - }, - { - "author_name": "Michael Dunne", - "author_inst": "Faculty of Health, Queensland University of Technology, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.14.20102517", "rel_title": "Assessment of dispersion of airborne particles of oral/nasal fluid by high flow nasal cannula therapy", @@ -1463549,6 +1464058,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.18.20101501", + "rel_title": "The impact of physical distancing measures against COVID-19 transmission on contacts and mixing patterns in the Netherlands: repeated cross-sectional surveys", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20101501", + "rel_abs": "BackgroundDuring the current pandemic of coronavirus (COVID-19) many countries have taken drastic measures to reduce transmission of SARS-CoV2. The measures often include physical distancing that aims to reduce the number of contacts in the population. Little is known about the actual reduction in number of contacts as a consequence of physical distancing measures.\n\nMethodsIn the Netherlands, a cross-sectional survey was carried out in 2016/2017 in which 8179 participants retrospectively reported the number, age and gender of different persons they had contacted (spoken to in person or touched) during the previous day. The survey was repeated among 2830 of the original participants, using the same questionnaire, in March and April 2020 after physical distancing measures had been implemented.\n\nResultsThe average number of contacts in the community was reduced from on average 12.5 (interquartile range: 2-17) to 3.7 (interquartile range: 0-4) different persons per participant, a reduction of 71% (95% confidence interval: 71-71). The reduction in the number of community contacts was highest for children and adolescents (between 5 and 20 years) and smallest for elderly persons of 80 years and older. The reduction in the effective number of total contacts, measured as the largest eigenvalue of the matrix with community and household contacts, was 62% (95% confidence interval: 48 - 72).\n\nConclusionThe substantial reduction in contacts has contributed greatly in halting the COVID-19 epidemic. This reduction was unevenly distributed over age groups, household sizes and occupations. These findings offer guidance for the lifting of age-group targeted measures.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jantien A. Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Liesbeth Mollema", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Eric R. A. Vos", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Don Klinkenberg", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Fiona R.M. van der Klis", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Hester E. de Melker", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.15.20103077", "rel_title": "Mathematical Modeling and Simulation of SIR Model for COVID-2019 Epidemic Outbreak: A Case Study of India", @@ -1464013,37 +1464569,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20099044", - "rel_title": "Forecasting the COVID-19 Pandemic with Climate Variables for Top Five Burdening and Three South Asian Countries", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099044", - "rel_abs": "BackgroundThe novel coronavirus (COVID-19) is now in a horrific situation around the world. Prediction about the number of infected and death cases may help to take immediate action to prevent the epidemic as well as control the situation of a country. The ongoing debate about the climate factors may need more validation with more studies. The climate factors of the top-five affected countries and three south Asian countries have considered in this study to have a real-time forecast and robust validation about the impact of climate variables.\n\nMethodsThe ARIMA model have included to model the univariate cumulative confirmed and death cases separately. The MLP, ELM and likelihood-based GLM count time series also considered as they consider the external variables as exogenous regressors. As the death count includes zero itself, zero-inflated count time series model has included instead of likelihood-based GLM. The better fitting of the ARIMA model will validate the under-whelm of meteorological factors was the initial hypothesis. The best model has identified through the application and comparison with the real data points.\n\nResultsThe results depict that there is an influence of meteorological variables like temperature and humidity mostly for all the selected countries cumulative confirm cases excluding Italy and Sri-Lanka. However, the best models for deaths count of each country also identify the impact of meteorological variables for each country.\n\nConclusionThe authors make the sixty days ahead forecast for each country which will be beneficial for the policymakers.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Md. Karimuzzaman", - "author_inst": "Jahangirnagar University" - }, - { - "author_name": "Sabrina Afroz", - "author_inst": "Jahangirnagar University" - }, - { - "author_name": "Md. Moyazzem Hossain", - "author_inst": "Newcastle University" - }, - { - "author_name": "Azizur Rahman", - "author_inst": "Charles Sturt University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.12.20098962", "rel_title": "Experience of quantitative SARS-CoV-2 antibody screening of health-care workers in the southern part of Kyoto city during COVID-19 peri-pandemic period", @@ -1465043,6 +1465568,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20100495", + "rel_title": "Risk factors for adverse clinical outcomes in patients with COVID-19: A systematic review and meta-analysis", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100495", + "rel_abs": "ImportanceCOVID-19 is a clinically heterogeneous disease of varying severity and prognosis. Clinical characteristics that impact disease course could offer guidance for clinical decision making and future research endeavors and unveil disease pathways.\n\nObjectiveTo examine risk factors associated with adverse clinical outcomes in patients with COVID-19.\n\nData sourcesWe performed a systematic review in PubMed from January 1 until April 19, 2020.\n\nStudy selectionObservational studies that examined the association of any clinical characteristic with an adverse clinical outcome were considered eligible. We scrutinized studies for potential overlap.\n\nData extraction and synthesisInformation on the effect of clinical factors on clinical endpoints of patients with COVID-19 was independently extracted by two researchers. When an effect size was not reported, crude odds ratios were calculated based on the available information from the eligible articles. Study-specific effect sizes from non-overlapping studies were synthesized applying the random-effects model.\n\nMain outcome and measureThe examined outcomes were severity and progression of disease, admission to ICU, need for mechanical ventilation, mortality, or a composite outcome.\n\nResultsWe identified 88 eligible articles, and we performed a total of 256 meta-analyses on the association of 98 unique risk factors with five clinical outcomes. Seven meta-analyses presented the strongest epidemiological evidence in terms of statistical significance (P-value <0.005), between-study heterogeneity (I2 <50%), sample size (more than 1000 COVID-19 patients), 95% prediction interval excluded the null value, and absence of small-study effects. Elevated C-reactive protein (OR, 6.46; 95% CI, 4.85 - 8.60), decreased lymphocyte count (OR, 4.16; 95% CI, 3.17 - 5.45), cerebrovascular disease (OR, 2.84; 95% CI, 1.55 - 5.20), chronic obstructive pulmonary disease (OR, 4.44; 95% CI, 2.46 - 8.02), diabetes mellitus (OR, 2.04; 95% CI, 1.54 - 2.70), hemoptysis (OR, 7.03; 95% CI, 4.57 - 10.81), and male sex (OR, 1.51; 95% CI, 1.30 - 1.75) were associated with risk of severe COVID-19.\n\nConclusions and relevanceOur results highlight factors that could be useful for prognostic model building, help guide patients selection for randomized clinical trials, as well as provide alternative treatment targets by shedding light to disease pathophysiology.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vanesa Bellou", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Ioanna Tzoulaki", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Evangelos Evangelou", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Lazaros Belbasis", + "author_inst": "University of Ioannina Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20100404", "rel_title": "Clinical characteristics and early outcomes in patients with COVID-19 treated with tocilizumab at a United States academic center", @@ -1465615,53 +1466171,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.14.20101931", - "rel_title": "Development of a Predictive Score for COVID-19 Diagnosis based on Demographics and Symptoms in Patients Attended at a Dedicated Screening Unit", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101931", - "rel_abs": "BackgroundThe diagnosis of COVID-19 based on clinical evaluation is difficult because symptoms often overlap with other respiratory diseases. A clinical score predictive of COVID-19 based on readily assessed variables may be useful in settings with restricted or no access to molecular diagnostic tests.\n\nMethodsA score based on demographics and symptoms was developed in a cross-sectional study including patients attended in a dedicated COVID-19 screening unit. A backward stepwise logistic regression model was constructed and values for each variable were assigned according to their {beta} coefficient values in the final model. Receiver operating characteristic (ROC) curve was constructed and its area under the curve (AUC) was calculated.\n\nResultsA total of 464 patients were included: 98 (21.1%) COVID-19 and 366 (78.9%) non-COVID-19 patients. The score included variables independently associated with COVID-19 in the final model: age [≥]60 years (2 points), fever (2), dyspnea (1), fatigue (1 point) and coryza (-1). Score values were significantly higher in COVID-19 than non-COVID-19 patients: median (Interquartile Range), 3 (2-4), and 1 (0-2), respectively; P<0.001. The score had an AUC of 0.80 (95% Confidence Interval [CI], 0.76-0.86). The specificity of scores [≥]4 and [≥]5 points were 90.4 (95%CI, 87.0-93.3) and 96.2 (95%CI, 93.7-97.9), respectively.\n\nConclusionsThis preliminary score based on patients symptoms is a feasible tool that may be useful in setting with restricted or no access to molecular tests in a pandemic period, owing to the high specificity. Further studies are required to validate the score in other populations.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alexandre P Zavascki", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Marcelo B Gazzana", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Joao Pedro Bidart", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Patricia S Fernandes", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Aline Galiotto", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Cristiane T Kawski", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Luiz A Nasi", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Diego R Falci", - "author_inst": "Hospital Moinhos de Vento" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.14.20101378", "rel_title": "COVID-19 FATALITY RISK: WHY IS AUSTRALIA LOWER THAN SOUTH KOREA?", @@ -1466205,6 +1466714,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.14.20101824", + "rel_title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101824", + "rel_abs": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.\n\nOne sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hamish Gibbs", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl AB Pearson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Chris Grundy", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Billy J Quilty", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Charlie Diamond", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.14.20101873", "rel_title": "COVID Faster R-CNN: A Novel Framework to Diagnose Novel Coronavirus Disease (COVID-19) in X-Ray Images", @@ -1466821,25 +1467377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.19.104281", - "rel_title": "Isolation of and Characterization of Neutralizing Antibodies to Covid-19 from a Large Human Nai\u0308ve scFv Phage Display Library", - "rel_date": "2020-05-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.104281", - "rel_abs": "SARS-CoV-2 (Covid-19) has caused currently ongoing global plague and imposed great challenges to health managing systems all over the world, with millions of infections and hundreds of thousands of deaths. In addition to racing to develop vaccines, neutralizing antibodies (nAbs) to this virus have been extensively sought and are expected to provide another prevention and therapy tool against this frantic pandemic. To offer fast isolation and shortened early development, a large human naive phage display antibody library, was built and used to screen specific nAbs to the receptor-binding domain, RBD, the key for Covid-19 virus entry through a human receptor, ACE2. The obtained RBD-specific antibodies were characterized by epitope mapping, FACS and neutralization assay. Some of the antibodies demonstrated spike-neutralizing property and ACE2-competitiveness. Our work proved that RBD-specific neutralizing binders from human naive antibody phage display library are promising candidates to for further Covid-19 therapeutics development.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andy Qingan Yuan", - "author_inst": "Excyte LLC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.19.100214", "rel_title": "log(x+1)* and log(1+x)", @@ -1467883,6 +1468420,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.18.101493", + "rel_title": "SARS-CoV2 infection in farmed mink, Netherlands, April 2020", + "rel_date": "2020-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.101493", + "rel_abs": "In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Nadia Oreshkova", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Robert-Jan Molenaar", + "author_inst": "GD Animal Health, Deventer, The Netherlands" + }, + { + "author_name": "Sandra Vreman", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Frank Harders", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands WBVR" + }, + { + "author_name": "Bas B. Oude Munnink", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Renate W. Hakze-vd Honing", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Nora Gerhards", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Paulien Tolsma", + "author_inst": "Regional Public Health Service Brabant-Zuid-Oost, Eindhoven, The Netherlands" + }, + { + "author_name": "Ruth Bouwstra", + "author_inst": "GD Animal Health, Deventer, The Netherlands" + }, + { + "author_name": "Reina Sikkema", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Mirriam Tacken", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Myrna M.T. de Rooij", + "author_inst": "Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Eefke Weesendorp", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Marc Engelsma", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Christianne Bruschke", + "author_inst": "Ministry of Agriculture, Nature and Food Quality, The Hague, The Netherlands" + }, + { + "author_name": "Lidwien A.M. Smit", + "author_inst": "Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Wim H.M. van der Poel", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "JA Stegeman", + "author_inst": "Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, The Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.18.102038", "rel_title": "Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.", @@ -1468539,61 +1469167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.05.16.20103408", - "rel_title": "Interpretable Artificial Intelligence for COVID-19 Diagnosis from Chest CT Reveals Specificity of Ground-Glass Opacities", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103408", - "rel_abs": "11.1 BackgroundThe use of CT imaging enhanced by artificial intelligence to effectively diagnose COVID-19, instead of or in addition to reverse transcription-polymerase chain reaction (RT-PCR), can improve widespread COVID-19 detection and resource allocation.\n\n1.2 Methods904 axial lung window CT slices from 338 patients in 17 countries were collected and labeled. The data included 606 images from COVID-19 positive patients (confirmed via RT-PCR), 224 images of a variety of other pulmonary diseases including viral pneumonias, and 74 images of normal patients. We developed, trained, validated, and tested an object detection model which detects features in three categories: ground-glass opacities (GGOs) for COVID-19, GGOs for non-COVID-19 diseases, and features that are inconsistent with a COVID-19 diagnosis. These collected features are passed into an interpretable decision tree model to make a suggested diagnosis.\n\n1.3 ResultsOn an independent test of 219 images from COVID-19 positive, a variety of pneumonia, and healthy patients, the model predicted COVID-19 diagnoses with an accuracy of 96.80 % (95% confidence interval [CI], 96.75 to 96.86), AUC-ROC of 0.9664 (95% CI, 0.9659 to 0.9671), sensitivity of 98.33% (95% CI, 98.29 to 98.40), precision of 95.93% (95% CI, 95.83 to 95.99), and specificity of 94.95% (95% CI, 94.84 to 95.05). On an independent test of 34 images from asymptomatic COVID-19 positive patients, our model achieved an accuracy of 97.06% (95% CI, 96.81 to 97.06) and a sensitivity of 96.97% (95% CI, 96.71 to 96.97). Similarly high performance was also obtained for out-of-sample countries, and no significant performance difference was obtained between genders.\n\n1.4 ConclusionWe present an interpretable artificial intelligence CT analysis tool to diagnose COVID-19 in both symptomatic and asymptomatic patients. Further, our model is able to differentiate COVID-19 GGOs from similar pathologies suggesting that GGOs can be disease-specific.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Anmol Warman", - "author_inst": "Duke University" - }, - { - "author_name": "Pranav Warman", - "author_inst": "Duke University" - }, - { - "author_name": "Ayushman Sharma", - "author_inst": "Morsani College of Medicine, James A. Haley VA Hospital" - }, - { - "author_name": "Puja Parikh", - "author_inst": "Morsani College of Medicine, James A. Haley VA Hospital" - }, - { - "author_name": "Roshan Warman", - "author_inst": "Yale University" - }, - { - "author_name": "Narayan Viswanadhan", - "author_inst": "James A. Haley VA Hospital" - }, - { - "author_name": "Lu Chen", - "author_inst": "Morsani College of Medicine" - }, - { - "author_name": "Subhra Mohapatra", - "author_inst": "Morsani College of Medicine, James A. Haley VA Hospital" - }, - { - "author_name": "Shyam Mohapatra", - "author_inst": "Morsani College of Medicine, James A. Haley VA Hospital" - }, - { - "author_name": "Guillermo Sapiro", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.13.20092510", "rel_title": "A citizen science initiative for open data and visualization of COVID-19 outbreak in Kerala, India", @@ -1469833,6 +1470406,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.14.20096602", + "rel_title": "Decline in Emergent and Urgent Care during the COVID-19 Pandemic", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20096602", + "rel_abs": "Due to the ongoing coronavirus disease (COVID-19) pandemic, there are concerns that patients may be avoiding care for emergent and urgent health conditions due to fear of contagion or as an unintentional consequence of government orders to postpone \"non-essential\" services. We therefore sought to evaluate the effect of the COVID-19 pandemic on the number of patient encounters for select emergent or urgent diagnoses at a large tertiary-care academic medical center in Boston. Inpatient diagnoses included acute myocardial infarction (MI) and stroke, and outpatient but urgent diagnoses included new referrals for breast and hematologic malignancies. For each condition, we used a \"difference-in-differences\" approach to estimate the proportional change in number of encounters during the pandemic (March - April 2020) compared with earlier in the same year (January - February 2020), using equivalent periods in 2019 as a control. After the onset of the pandemic, we observed significant reductions in hospitalizations for MI (difference-in-differences estimate, 0.67; 95%CI, 0.46-0.96; P=0.04) and stroke (difference-in-differences estimate, 0.42; 95%CI, 0.28-0.65; P<0.001) (Table). In the ambulatory setting, there was a reduction in referrals for breast cancer and hematologic cancers, but this did not reach statistical significance until the month after the onset of the pandemic. Our findings suggest an urgent need for public health messaging to ensure that patients continue to seek care for acute emergencies. In addition, decisions by health systems regarding when to reinitiate non-emergent care should carefully factor in the harms of delayed diagnosis and treatment occurring during the COVID-19 pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Dhruv S Kazi", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Rishi K Wadhera", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Changyu Shen", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Kalon K.L. Ho", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Rushad Patell", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Magdy H. Selim", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "John H. Urwin", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Mark L. Zeidel", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Peter Zimetbaum", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Kevin Tabb", + "author_inst": "Beth Israel Lahey Health, Cambridge, MA" + }, + { + "author_name": "Robert W. Yeh", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.05.11.20098053", "rel_title": "Parasites and their protection against COVID-19- Ecology or Immunology?", @@ -1470413,37 +1471045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.12.20096792", - "rel_title": "On the heterogeneity of infections, containment measures and the preliminary forecast of COVID-19 epidemic", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20096792", - "rel_abs": "BackgroundAs of May 1, 2020, there had been over three million of officially confirmed cases of novel coronavirus (COVID-19) infections reported worldwide. The pandemic originated from a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus similar to severe acute respiratory syndrome (SARS). The dynamics of the pathogen incurred the incidence of the unidentified cases that were potentially substantial in magnitude. Unparalleled extensive measures, either in terms of medical quarantine or non-medical containment, were taken to deplete the growth of infected population and thereafter settle down the outbreak. We aimed to estimate the gap in sizes and peak dates between the confirmed and unconfirmed, and how containment measures impacted the dynamic trajectory of the COVID-19 in Japan. We performed simulations and desired to provide meaningful insight for the upcoming responses to the outbreak, for which much still remained to be unknown.\n\nMethodsTo examine the differentiation between identified and unidentified cases, and how heterogeneity of medical quarantine and non-medical control were associated with the advancement of the outbreak dynamics, we employed the susceptible-infected-removed-contained (SIR-C) model that derived from the basic SIR concept where the target population was divided into three differentiated compartments: (S)usceptibles (be subject to infections), (I)nfected (confirmed infections) and (R)emoved (not in the procedure of transmission due to the reason of either recovered or died). By applying the transmission model to the latest outbreak data in Japan, we established the least-squares fitted estimates parameters and the epidemiological trajectory of the COVID-19 pandemic. In compliance with the estimated framework, we simulated the ongoing trend of outbreak in Japan by calibrating the potential changes in measures ceteris paribus starting April 7, the date when the state of emergency was declared. We assumed a variety of settings and simulated how the heterogeneity in containment shifted the subsequent advancement of the outbreak.\n\nFindingsThe epidemiologically estimated outcomes with least-squares fitting indicated a gap between the confirmed and unconfirmed cases in terms of size and peak dates. The saturation size of the reported infections was comparative to the unidentified infections in magnitude contingent on the duration of infection (DOI). However, peak dates for the former delayed by nearly two-and-half months. The declaration of state of emergency incurred changed patterns in social behaviors and sub-exponential growth of the outbreak. Medical and non-medical measures were effective in controlling the outbreak of COVID-19. By assuming a changed pattern of containment measures since April 7, a diminishing growth of infections and reduced saturation of cases were to be observed, accompanied by an earlier arrival of peak dates. However, the modelled effects of quarantine and control measures vary with the unclear infectiousness and the attributes of containment.\n\nInterpretationAs the number of infected cases, especially of those asymptomatic, mild symptomatic and infection-route-unknown cases, was growing over time, it was of importance to verify the assumption of the potential existence of the gap in size between those already identified and those not. Our analysis reinforced this by quantifying this magnitude. The trend curve of reported cases differentiated from unidentified cases with a time-lagged effect. Containment measures, if followed effectually, would probably help reduce the spread of epidemic. Our simulations suggested that 1% of growth in rate of non-medical containment could approximately predate the peak by 18 days and reduce the peak size by one-thirds. Commensurate level of containment effect was to be reached when the rate of medical quarantine was increased ten-folds. We thus projected that changes in interventions could lead to an earlier peak date but reduced peak size, which could be flattened by calibrating the interventions gradually. Limitations of our research include the uncertainties in the estimates of duration of infection and the reproduction number.\n\nFundingPhilosophy and Social Sciences Association in FuJian, Science and Technology Development Center of the Ministry of Education.\n\nResearch in contextO_ST_ABSEvidence before this researchC_ST_ABSCOVID-19 pandemic was reported to emerge in late 2019 and cases were reported ever since. China adopted multiple options of efforts including medical quarantine and non-medical measures, such as isolation of cases, physical distancing, contact tracing, school closure and workplace shutdown, at a national level to break down the spread of COVID-19. By significantly decreasing the likelihood of close proximity person-to-person contact, these measures took effect and by the end of March 2020 the reported cases lowered dramatically. Japan identified its first case of COVID-19 on Jan 22, 2020 and dynamic exponential-like growth of cases was observed since. The investigation of epidemiological feature for containment measures in other countries attracted much attention; in contrast, the trajectory for Japan remained to be unclear. We searched web of science and science direct for research published in English from 2019 up to May 6, 2020, with the terms \" coronavirus control or containment measures\" in combination with \"Japan\" and identified 6 and 5 results respectively. Relatively little was known about the gap in size and in peak time between the confirmed and unconfirmed in Japan; how containment measures influenced its trajectory of COVID-19 since the state of emergency was declared; and how the shift of the pandemic was influenced by the containment.\n\nAdded value of this studyThe measures studied were divided into two broad ranges in Japan: medical quarantine and non-medical containment. Medical quarantine typically corresponded to cases with severe symptoms that need urgent care; in comparison, non-medical measures consisted of a wider variety of control by complementing the effect of quarantine and corresponded to cases such as asymptomatic, pre-symptomatic, mild symptomatic patients and the susceptibles. We found that the declaration of state of emergency incurred social behaviors change and was in connection with subsequent sub-exponential growth of cases. Our study implied the essential existence of gap, subsequently quantified its asymptotic size and its peak timing between the identified and the unidentified. Time-delaying effect in saturation was meaningful in that it provided the information to understand the intrinsic intra-correlation of an epidemic like COVID-19. The outcomes of simulation implied that early containment measures which linked to a reduced and predated peak, were crucial to control further spread. A dynamic transmission model was employed to assess the potential trajectory starting the point of emergency declaration.\n\nImplications of all the available evidenceThe efficacy of containment has been identified in China and induced changes of behaviors in individuals responsive to the pandemic where asymptomatic, mildly symptomatic and infection-route-unknown cases were not to be ascertained. This might be of great importance for developing control strategies for currently yet to be convergent communities or possibly subsequent cyclical outbreaks of COVID-19. It was of difficulty to estimate the accurate gap in practice; however, asymptotic measures could deliver information that tended to be ignored. Medical quarantine and non-medical measures were at work during the COVID-19 outbreak and the test of heterogeneity on its quantitative and qualitative efficacy in different countries might assist to uncover more on the unknown of this pathogen. Parameter-fitted simulations could provide decision makers with scenarios not reflected in the available information and thus the insights on timely and prioritized decisions even in the uncertainties such as COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ichiro Nakamoto", - "author_inst": "Fujian University of Technology" - }, - { - "author_name": "Weiqing Zhuang", - "author_inst": "Fujian University of Technology" - }, - { - "author_name": "Sheng Wang", - "author_inst": "Fujian University of Technology" - }, - { - "author_name": "Yan Guo", - "author_inst": "Fujian University of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.10.20096974", "rel_title": "Study of Non-Pharmacological Interventions on COVID-19 Spread", @@ -1471035,6 +1471636,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.05.11.20098392", + "rel_title": "Forecasting Covid-19 dynamics in Brazil: a data driven approach", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098392", + "rel_abs": "This paper has a twofold contribution. The first is a data driven approach for predicting the Covid-19 pandemic dynamics, based on data from more advanced countries. The second is to report and discuss the results obtained with this approach for Brazilian states, as of May 4th, 2020. We start by presenting preliminary results obtained by training an LSTM-SAE network, which are somewhat disappointing. Then, our main approach consists in an initial clustering of the world regions for which data is available and where the pandemic is at an advanced stage, based on a set of manually engineered features representing a countrys response to the early spread of the pandemic. A Modified Auto-Encoder network is then trained from these clusters and learns to predict future data for Brazilian states. These predictions are used to estimate important statistics about the disease, such as peaks. Finally, curve fitting is carried out on the predictions in order to find the distribution that best fits the outputs of the MAE, and to refine the estimates of the peaks of the pandemic. Results indicate that the pandemic is still growing in Brazil, with most states peaks of infection estimated between the 25th of April and the 19th of May 2020. Predicted numbers reach a total of 240 thousand infected Brazilians, distributed among the different states, with Sao Paulo leading with almost 65 thousand estimated, confirmed cases. The estimated end of the pandemics (with 97% of cases reaching an outcome) starts as of May 28th for some states and rests through August 14th, 2020.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Igor Gadelha Pereira", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Joris M Guerin", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Andouglas Goncalves Silva Jr.", + "author_inst": "Instituto Federal do Rio Grande do Norte" + }, + { + "author_name": "Cosimo Distante", + "author_inst": "CNR" + }, + { + "author_name": "Gabriel Santos Garcia", + "author_inst": "Universidade de Brasilia" + }, + { + "author_name": "Luiz M.G. Goncalves", + "author_inst": "Universidade Federal do Rio Grande do Norte" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.11.20098459", "rel_title": "Distinct systems serology features in children, elderly and COVID patients", @@ -1471599,25 +1472239,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.11.20098418", - "rel_title": "Spread of the Novel Coronavirus (SARS-CoV-2): Modeling and Simulation of Control Strategies", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098418", - "rel_abs": "The coronavirus disease 2019 (COVID-19) is spreading throughout the world and all healthcare systems are loaded beyond its capacity. The virus is named as SARS-CoV-2. In this situation, rational decisions need to be made on how the care is provided for patients with COVID-19. The Incidence report, general symptoms and readily available testing kits, different control strategies, the basic compartmental model, and some of the current research on the epidemiology of the disease are discussed and previously published models are reviewed. Modeling this disease helps in understanding the spread, and predict its future to evaluate different control strategies (Social Distancing, Contact Tracing and Hospitalization). Compartmental modeling framework is used in this work. The non-linear equations are formulated and fitted to the cumulative case and mortality data. Analytical analysis along with uncertainty analysis and sensitivity analysis is performed, and the conditions to achieve disease free equilibrium is evaluated. Finally, Different control strategies are simulated to show their importance. This paper aims to shows the advantage of mathematical modeling and their simulations in times like now, during which the COVID-19 spreading like wildfire. It also includes Pre-symptomatic and asymptomatic individuals in the modeling. The simulations are performed for the model fit to Cumulative Case and Mortality data in the United States of America. The Reproduction number is found to be 2.71914.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Harishankar Prabhakaran", - "author_inst": "Arizona State University, Tempe" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.11.20098517", "rel_title": "An SEIARD epidemic model for COVID-19 in Mexico: mathematical analysis and state-level forecast", @@ -1472333,6 +1472954,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.18.099507", + "rel_title": "Afucosylated immunoglobulin G responses are a hallmark of enveloped virus infections and show an exacerbated phenotype in COVID-19", + "rel_date": "2020-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.099507", + "rel_abs": "IgG antibodies are crucial for protection against invading pathogens. A highly conserved N-linked glycan within the IgG-Fc-tail, essential for IgG function, shows variable composition in humans. Afucosylated IgG variants are already used in anti-cancer therapeutic antibodies for their elevated binding and killing activity through Fc receptors (Fc{gamma}RIIIa). Here, we report that afucosylated IgG which are of minor abundance in humans ([~]6% of total IgG) are specifically formed against surface epitopes of enveloped viruses after natural infections or immunization with attenuated viruses, while protein subunit immunization does not elicit this low fucose response. This can give beneficial strong responses, but can also go awry, resulting in a cytokine-storm and immune-mediated pathologies. In the case of COVID-19, the critically ill show aggravated afucosylated-IgG responses against the viral spike protein. In contrast, those clearing the infection unaided show higher fucosylation levels of the anti-spike protein IgG. Our findings indicate antibody glycosylation as a potential factor in inflammation and protection in enveloped virus infections including COVID-19.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mads D. Larsen", + "author_inst": "Sanquin Reseach" + }, + { + "author_name": "Erik L de Graaf", + "author_inst": "Sanquin Reseach" + }, + { + "author_name": "Myrthe E. Sonneveld", + "author_inst": "Sanquin Research" + }, + { + "author_name": "H. Rosina Plomp", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Federica Linty", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Remco Visser", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Maximilian Brinkhaus", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Tonci Sustic", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Steven W. deTaeye", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Arthur E.H. Bentlage", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Jan Nouta", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Suvi Natunen", + "author_inst": "Finnish Red Cross Blood Service" + }, + { + "author_name": "Carolien A.M. Koeleman", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Susanna Sainio", + "author_inst": "Finnish Red Cross Blood Service" + }, + { + "author_name": "Neeltje A. Kootstra", + "author_inst": "University of Amsterdam" + }, + { + "author_name": "Philip J.M. Brouwer", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Rogier W. Sanders", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Marit J. van Gils", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Sanne de Bruin", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Alexander P.J. Vlaar", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Amsterdam UMC COVID-19 biobank study group", + "author_inst": "" + }, + { + "author_name": "Hans L. Zaaijer", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Manfred Wuhrer", + "author_inst": "Leiden University Medical Center," + }, + { + "author_name": "C. Ellen van der Schoot", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Gestur Vidarsson", + "author_inst": "Sanquin Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.12.20099085", "rel_title": "Understanding the indoor pre-symptomatic transmission mechanism of COVID-19", @@ -1472853,57 +1473589,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.17.099143", - "rel_title": "Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel", - "rel_date": "2020-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.17.099143", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease that is of public health emergency of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 has high homology with that of severe acute respiratory syndrome coronavirus. (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Our results suggest that the pentameric E protein promotes the penetration of monovalent ions through the channel. Analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore demonstrated a clear wetting/dewetting transition with monovalent cation selectivity under transmembrane voltage, which indicates that it is a hydrophobic voltage-dependent channel. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yipeng Cao", - "author_inst": "1. Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060 P.R. China 2. National Supercomputer " - }, - { - "author_name": "Rui Yang", - "author_inst": "Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital. 190, Jieyuan Road, Hongqiao District, Tianjin, 300031" - }, - { - "author_name": "Wei Wang", - "author_inst": "Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060 P.R. China" - }, - { - "author_name": "Imshik Lee", - "author_inst": "College of Physics, Nankai University, Tianjin, 300071 P.R. China" - }, - { - "author_name": "Ruiping Zhang", - "author_inst": "Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060 P.R. China" - }, - { - "author_name": "Wenwen Zhang", - "author_inst": "Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060 P.R. China" - }, - { - "author_name": "Jiana Sun", - "author_inst": "Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060 P.R. China" - }, - { - "author_name": "Bo Xu", - "author_inst": "1,Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060 P.R. China. 2, Center for Intelligent " - }, - { - "author_name": "Xiangfei Meng", - "author_inst": "National Supercomputer Center in Tianjin, 300457 P.R. China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.05.17.100685", "rel_title": "Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein", @@ -1473527,6 +1474212,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.14.20102483", + "rel_title": "Early and massive testing saves lives: COVID-19 related infections and deaths in the United States during March of 2020", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102483", + "rel_abs": "To optimize epidemiologic interventions, predictors of mortality should be identified. The US COVID-19 epidemic data -reported up to 3-31-2020- were analyzed using kernel regularized least squares regression. Six potential predictors of mortality were investigated: (i) the number of diagnostic tests performed in testing week I; (ii) the proportion of all tests conducted during week I of testing; (iii) the cumulative number of (test-positive) cases through 3-31-2020, (iv) the number of tests performed/million citizens; (v) the cumulative number of citizens tested; and (vi) the apparent prevalence rate, defined as the number of cases/million citizens. Two metrics estimated mortality: the number of deaths and the number of deaths/million citizens. While both expressions of mortality were predicted by the case count and the apparent prevalence rate, the number of deaths/million citizens was {approx}3.5 times better predicted by the apparent prevalence rate than the number of cases. In eighteen states, early testing/million citizens/population density was inversely associated with the cumulative mortality reported by 31 March, 2020. Findings support the hypothesis that early and massive testing saves lives. Other factors -e.g., population density-may also influence outcomes. To optimize national and local policies, the creation and dissemination of high-resolution geo-referenced, epidemic data is recommended.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "James B. Hittner", + "author_inst": "Department of Psychology, College of Charleston, Charleston, South Carolina, United States of America" + }, + { + "author_name": "Folorunso O. Fasina", + "author_inst": "Food and Agriculture Organization, Dar es Salam, Tanzania" + }, + { + "author_name": "Almira L. Hoogesteijn", + "author_inst": "Human Ecology, Centro de Investigacion y de Estudios Avanzados (CINVESTAV), Merida, Mexico" + }, + { + "author_name": "Renata Piccinini", + "author_inst": "Department of Veterinary Medicine, University of Milan, Milan, Italy" + }, + { + "author_name": "Prakasha Kempaiah", + "author_inst": "Loyola University Chicaco Stritch School of Medicine, Chicago, USA" + }, + { + "author_name": "Stephen D. Smith", + "author_inst": "Institute for Resource Information Science, College of Agriculture, Cornell University, Ithaca, United States of America" + }, + { + "author_name": "Ariel L. Rivas", + "author_inst": "Center for Global Health, Department of Internal Medicine, Medical School, University of New Mexico, Albuquerque, New Mexico, United States of America" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20099614", "rel_title": "Dynamic liver function indexes monitoring and clinical characteristics in three types of COVID-19 patients", @@ -1474043,45 +1474771,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.12.20099804", - "rel_title": "Environmental indicator for effective control of COVID-19 spreading", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099804", - "rel_abs": "Recently, a novel coronavirus (COVID-19) has caused viral pneumonia worldwide, spreading to more than 200 countries, posing a major threat to international health. To prevent the spread of COVID-19, in this study, we report that the city lockdown measure was an effective way to reduce the number of new cases, and the nitrogen dioxide (NO2) concentration can be adopted as an environmental lockdown indicator. In China, after strict city lockdown, the average NO2 concentration decreased 55.7% (95% confidence interval (CI): 51.5-59.6%) and the total number of newly confirmed cases decreased significantly. Our results also indicate that the global airborne NO2 concentration steeply decreased over the vast majority of COVID-19-hit areas based on satellite measurements. We found that the total number of newly confirmed cases reached an inflection point about two weeks after the lockdown. The total number of newly confirmed cases can be reduced by about 50% within 30 days of the lockdown. The stricter lockdown will help newly confirmed cases to decline earlier and more rapidly. Italy, Germany and France are good examples. Our results suggest that NO2 satellite measurement can help decision makers effectively monitor control regulations to reduce the spread of COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Xinbo Lian", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Jianping Huang Sr.", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Li Zhang", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Chuwei Liu", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Xiaoyue Liu", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Lina Wang", - "author_inst": "Gansu Province Environmental Monitoring Center" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.12.20099945", "rel_title": "SARS pandemic exposure impaired early childhood development: A lesson for COVID-19", @@ -1474925,6 +1475614,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20100370", + "rel_title": "Derivation and validation of a prognostic model for predicting in-hospital mortality in patients admitted with COVID-19 in Wuhan, China: the PLANS (Platelet Lymphocyte Age Neutrophil Sex) model", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100370", + "rel_abs": "OBJECTIVETo develop and validate a prognostic model for in-hospital mortality in COVID-19 patients using routinely collected demographic and clinical characteristics.\n\nDESIGNMulticenter, retrospective cohort study.\n\nSETTINGJinyintan Hospital, Union Hospital, and Tongji Hosptial in Wuhan, China.\n\nPARTICIPANTSA pooled derivation cohort of 1008 COVID-19 patients from Jinyintan Hospital, Union Hospital in Wuhan and an external validation cohort of 1031 patients from Tongji Hospital in Wuhan, China.\n\nMAIN OUTCOME MEASURESOutcome of interest was in-hospital mortality, treating discharged alive from hospital as the competing event. Fine-Gray models, using backward elimination for inclusion of predictor variables and allowing non-linear effects of continuous variables, were used to derive a prognostic model for predicting in-hospital mortality among COVID-19 patients. Internal validation was implemented to check model overfitting using bootstrap approach. External validation to a separate hospital was implemented to evaluate the generalizability of the model.\n\nRESULTSThe derivation cohort was a case-mix of mild-to-severe hospitalized COVID-19 patients (n=1008, 43.6% females, median age 55). The final model (PLANS), including five predictor variables of platelet count, lymphocyte count, age, neutrophil count, and sex, had an excellent predictive performance (optimism-adjusted C-index: 0.85, 95% CI: 0.83 to 0.87; averaged calibration slope: 0.95, 95% CI: 0.82 to 1.08). Internal validation showed little overfitting. External validation using an independent cohort (n=1031, 47.8% female, median age 63) demonstrated excellent predictive performance (C-index: 0.87, 95% CI: 0.85 to 0.89; calibration slope: 1.02, 95% CI: 0.92 to 1.12). The averaged predicted survival curves were close to the observed survival curves across patients with different risk profiles.\n\nCONCLUSIONSThe PLANS model based on the five routinely collected demographic and clinical characteristics (platelet count, lymphocyte count, age, neutrophil count, and sex) showed excellent discriminative and calibration accuracy in predicting in-hospital mortality in COVID-19 patients. This prognostic model would assist clinicians in better triaging patients and allocating healthcare resources to reduce COVID-19 fatality.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jiong Li", + "author_inst": "Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Yuntao Chen", + "author_inst": "Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Shujing Chen", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Sihua Wang", + "author_inst": "Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Dingyu Zhang", + "author_inst": "Department of Tuberculosis and Respiratory Disease, Jinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Junfeng Wang", + "author_inst": "Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Douwe Postmus", + "author_inst": "Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Hesong Zeng", + "author_inst": "Department of Cardiology, Tongji Hospital, School of Medicine, Huazhong University of Science and Technology, Wuhan, China." + }, + { + "author_name": "Guoyou Qin", + "author_inst": "Department of Biostatistics, School of Public Health, and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China" + }, + { + "author_name": "Yin Shen", + "author_inst": "Eye Center, Medical Research Institute, Wuhan University Renmin Hospital, Wuhan University, Wuhan, China" + }, + { + "author_name": "Jinjun Jiang", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Yongfu Yu", + "author_inst": "Department of Biostatistics, School of Public Health, and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20101006", "rel_title": "Loss of Taste and Smell as Distinguishing Symptoms of COVID-19", @@ -1475593,41 +1476345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.10.20076414", - "rel_title": "The impact of isolation measures due to COVID-19 on energy intake and physical activity levels in Australian university students", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20076414", - "rel_abs": "BackgroundThe pandemic inflicted by coronavirus disease 2019 (COVID-19) resulted in physical isolation measures in many parts of the world. In Australia, nationwide restrictions included staying at home, unless seeking medical care, providing care, purchasing food, undertaking exercise, or attending work in an essential service. All undergraduate university classes transitioned to online, mostly home-based learning. This disruption to daily life may have consequences for eating and physical activity patterns.\n\nMethodsIn this observational study, we examined the effect of isolation measures, during the early phase of the COVID-19 pandemic in Australia (March/April), on diet (24-hour diet recall, ASA-24) and physical activity (Active Australia Survey) patterns among third-year biomedical students in Brisbane, Australia. Findings were compared to students enrolled in the same course in the previous two years.\n\nResultsIn females, energy intake was ~20% greater in 2020 compared with 2018 and 2019, and the frequency of snacking and energy density of consumed snacks were also increased. In males, there was no difference in energy intake or snacking behaviour. Physical activity was impacted for both sexes, whereby fewer students undertook any walking activity and, of those that did, time spent doing so was less compared with 2018 and 2019. The proportion of students reporting any vigorous activity was not different for males or females but, among males who participated in this level of activity, the duration was less in 2020 compared with previous years. The proportion of male and female students achieving sufficient levels of activity, defined by at least 150 mins over at least 5 sessions, was ~30% less in 2020. Indeed, the majority of students reported as having undertaken less physical activity than usual.\n\nConclusionsIncreased energy intake for females and reduced physical activity for males and females demonstrate impacts of isolation measures that may have deleterious consequences for physical and mental wellbeing, with the potential to affect long-term nutrition and activity patterns.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Linda A Gallo", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Tania F Gallo", - "author_inst": "North Melbourne Football Club" - }, - { - "author_name": "Sophia L Young", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Karen M Moritz", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Lisa K Akison", - "author_inst": "The Univeristy of Queensland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2020.05.11.20082396", "rel_title": "Virtual health care for community management of patients with COVID-19.", @@ -1476671,6 +1477388,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.11.20095158", + "rel_title": "SARS-CoV-2 antibody seroprevalence in industry workers in Split-Dalmatia and Sibenik-Knin County, Croatia", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20095158", + "rel_abs": "BACKGROUNDAs a result of global spread, COVID-19 has also affected the Republic of Croatia in the last week of February. Although official data show that the number of newly infected is declining, it is still unknown what proportion of the population has been affected by the disease.\n\nAIMTo examine seroprevalence of SARS-CoV-2 antibodies in industry workers population sample.\n\nMETHODSFrom 23 to 28 April 2020, we conducted serological testing for antibodies (IgG and IgM) on 1494 factory employees living in the Split-Dalmatia and [S]ibenik-Knin County (Croatia). We analysed antibody seroprevalence on the level of the company, county, and separately for employees living at the factory premises with limited mobility during the lockdown measures.\n\nRESULTSIn a total sample of tested company employees, we detected antibodies in 1.27% of participants (95% CI 0.77-1.98%). In Split facility 13/1316 (0.99%, 95% CI 0.53-1.68%) of participants were tested positive, of which 13/1079 (1.20%, 95% CI 0.64-2.05%) of those living outside the facility and 0/237 (0%, 95% CI 0-1.26%) of those living inside the facility. In Knin facility, 6/178 (3.37%, 95% CI 1.25-7.19%) participants were tested positive for antibodies. The difference between Split (no mobility restrictions) and Knin, was not statistically significant ({chi}2 = 3.47, P = 0.062).\n\nCONCLUSIONSThe study showed relatively small SARS-CoV-2 antibody seroprevalence in the DIV Group population sample. When the study findings are interpreted on the county levels, they could indicate that most of the counties population was not exposed to the virus.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ivan Jerkovic", + "author_inst": "University Department of Forensic Sciences University of Split" + }, + { + "author_name": "Toni Ljubic", + "author_inst": "University Department of Forensic Sciences University of Split" + }, + { + "author_name": "Zeljana Basic", + "author_inst": "University Department of Forensic Sciences" + }, + { + "author_name": "Ivana Kruzic", + "author_inst": "University Deparment ofForensic Sciences" + }, + { + "author_name": "Nenad Kunac", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Josko Bezic", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Arijana Vuko", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Alemka Markotic", + "author_inst": "Dr. Fran Mihaljevic University Hospital for Infectious Diseases, Zagreb, Croatia; Catholic University of Croatia, Zagreb, Croatia; University of Rijeka School o" + }, + { + "author_name": "Simun Andjelinovic", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split, Split, Croatia; University of Split, School of Medicine, Sp" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.10.20097543", "rel_title": "Estimating the extent of true asymptomatic COVID-19 and its potential for community transmission: systematic review and meta-analysis", @@ -1477178,125 +1477946,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.10.20097469", - "rel_title": "Covasim: an agent-based model of COVID-19 dynamics and interventions", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097469", - "rel_abs": "The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), an open-source model developed to help address these questions. Covasim includes country-specific demographic information on age structure and population size; realistic transmission networks in different social layers, including households, schools, workplaces, long-term care facilities, and communities; age-specific disease outcomes; and intrahost viral dynamics, including viral-load-based transmissibility. Covasim also supports an extensive set of interventions, including non-pharmaceutical interventions, such as physical distancing and protective equipment; pharmaceutical interventions, including vaccination; and testing interventions, such as symptomatic and asymptomatic testing, isolation, contact tracing, and quarantine. These interventions can incorporate the effects of delays, loss-to-follow-up, micro-targeting, and other factors. Implemented in pure Python, Covasim has been designed with equal emphasis on performance, ease of use, and flexibility: realistic and highly customized scenarios can be run on a standard laptop in under a minute. In collaboration with local health agencies and policymakers, Covasim has already been applied to examine epidemic dynamics and inform policy decisions in more than a dozen countries in Africa, Asia-Pacific, Europe, and North America.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Cliff C. Kerr", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Robyn M. Stuart", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Dina Mistry", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Romesh G. Abeysuriya", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Katherine Rosenfeld", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Gregory R. Hart", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Rafael C. Nunez", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Jamie A. Cohen", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Prashanth Selvaraj", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Brittany Hagedorn", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Lauren George", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Michal Jastrzebski", - "author_inst": "GitHub, Inc." - }, - { - "author_name": "Amanda Izzo", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Greer Fowler", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Anna Palmer", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Dominic Delport", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Nick Scott", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Sherrie Kelly", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Caroline S Bennette", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Bradley Wagner", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Stewart Chang", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Assaf P. Oron", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Edward Wenger", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Jasmina Panovska-Griffiths", - "author_inst": "University College London" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Daniel J. Klein", - "author_inst": "Institute for Disease Modeling" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.10.20096446", "rel_title": "Strategic release of lockdowns in a COVID infection model", @@ -1478268,6 +1478917,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.14.097204", + "rel_title": "Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats", + "rel_date": "2020-05-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.097204", + "rel_abs": "Objective Patients with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibit not only respiratory symptoms but also symptoms of chemo-sensitive disorders and kidney failure. Cellular entry of SARS-CoV-2 depends on the binding of its spike protein to a cellular receptor named angiotensin-converting enzyme 2 (ACE2), and the subsequent spike protein-priming by host cell proteases, including transmembrane protease serine 2 (TMPRSS2). Thus, high expression of ACE2 and TMPRSS2 are considered to enhance the invading capacity of SARS-CoV-2.Methods To elucidate the underlying histological mechanisms of the aerodigestive disorders caused by SARS-CoV-2, we investigated the expression of ACE2 and TMPRSS2 proteins in the aerodigestive tracts of the tongue, hard palate with partial nasal tissue, larynx with hypopharynx, trachea, esophagus, lung, and kidney of rats through immunohistochemistry.Results Strong co-expression of ACE2 and TMPRSS2 proteins was observed in the nasal respiratory epithelium, trachea, bronchioles, alveoli, kidney, and taste buds of the tongue. Remarkably, TMPRSS2 expression was much stronger in the peripheral alveoli than in the central alveoli. These results coincide with the reported clinical symptoms of COVID-19, such as the loss of taste, loss of olfaction, respiratory dysfunction, and acute nephropathy.Conclusions A wide range of organs have been speculated to be affected by SARS-CoV-2 depending on the expression levels of ACE2 and TMPRSS2. Differential distribution of TMPRSS2 in the lung indicated the COVID-19 symptoms to possibly be exacerbated by TMPRSS2 expression. This study might provide potential clues for further investigation of the pathogenesis of COVID-19.Level of Evidence NACompeting Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rumi Ueha", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Taku Sato", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Takao Goto", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Akihito Yamauchi", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Kenji Kondo", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Tatsuya Yamasoba", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.15.097501", "rel_title": "Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells", @@ -1479192,73 +1479880,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.05.15.098079", - "rel_title": "Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1) Formulated with Alum Induces Protective Immunity and Reduces Immune Enhancement", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.098079", - "rel_abs": "We developed a severe acute respiratory syndrome (SARS) subunit recombinant protein vaccine candidate based on a high-yielding, yeast-engineered, receptor-binding domain (RBD219-N1) of the SARS beta-coronavirus (SARS-CoV) spike (S) protein. When formulated with Alhydrogel\u00ae, RBD219-N1 induced high-level neutralizing antibodies against both pseudotyped virus and a clinical (mouse-adapted) isolate of SARS-CoV. Here, we report that mice immunized with RBD219-N1/Alhydrogel\u00ae were fully protected from lethal SARS-CoV challenge (0% mortality), compared to \u223c 30% mortality in mice when immunized with the SARS S protein formulated with Alhydrogel\u00ae, and 100% mortality in negative controls. An RBD219-N1 formulation Alhydrogel\u00ae was also superior to the S protein, unadjuvanted RBD, and AddaVax (MF59-like adjuvant)-formulated RBD in inducing specific antibodies and preventing cellular infiltrates in the lungs upon SARS-CoV challenge. Specifically, a formulation with a 1:25 ratio of RBD219-N1 to Alhydrogel\u00ae provided high neutralizing antibody titers, 100% protection with non-detectable viral loads with minimal or no eosinophilic pulmonary infiltrates. As a result, this vaccine formulation is under consideration for further development against SARS-CoV and potentially other emerging and re-emerging beta-CoVs such as SARS-CoV-2.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Wen-Hsiang Chen", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Xinrong Tao", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Anurodh Agrawal", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Abdullah Algaissi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Bi-Hung Peng", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jeroen Pollet", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Ulrich Strych", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Maria Elena Bottazzi", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Peter J Hotez", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Sara Lustigman", - "author_inst": "Lindsley F Kimball Research Institute, New York Blood Center" - }, - { - "author_name": "Lanying Du", - "author_inst": "Lindsley F Kimball Research Institute, New York Blood Center" - }, - { - "author_name": "Shibo Jiang", - "author_inst": "Lindsley F Kimball Research Institute, New York Blood Center" - }, - { - "author_name": "Chien-Te K Tseng", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.15.098616", "rel_title": "SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics.", @@ -1480246,6 +1480867,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.14.096081", + "rel_title": "Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes", + "rel_date": "2020-05-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.096081", + "rel_abs": "Among 15 nonstructural proteins (Nsps), the newly emerging SARS-CoV-2 encodes a large, multidomain Nsp3. One of its units is ADP-ribose phosphatase domain (ADRP, also known as macrodomain) which is believed to interfere with the host immune response. Such a function appears to be linked to the proteins ability to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remains unknown. Here, we have determined five, high resolution (1.07 - 2.01 [A]) crystal structures corresponding to the apo form of the protein and complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr. We show that the protein undergoes conformational changes to adapt to the ligand in a manner previously observed before for in close homologs from other viruses. We also identify a conserved water molecule that may participate in hydrolysis. This work builds foundations for future structure-based research of the ADRP, including search for potential antiviral therapeutics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Karolina Michalska", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Youngchang Kim", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Robert Jedrzejczak", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Natalia I. Maltseva", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Lucy Stols", + "author_inst": "University of Chicago" + }, + { + "author_name": "Michael Endres", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Andrzej Joachimiak", + "author_inst": "Argonne National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.05.14.092767", "rel_title": "ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study", @@ -1480702,97 +1481366,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.12.092056", - "rel_title": "Tracing two causative SNPs reveals SARS-CoV-2 transmission in North America population", - "rel_date": "2020-05-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.092056", - "rel_abs": "During the COVID-19 pandemic, precisely tracing the route of the SARS-CoV-2 transmission in human population remains challenging. Because this RNA virus can mutate massively without a specifically tracing maker. Herein, using a geographic stratified genome-wide association study (GWAS) of 2599 full-genome sequences, we identified that two SNPs (i.e., 1059.C>T and 25563.G>T) of linkage disequilibrium were presented in approximately half of North America SARS-CoV-2 population (p = 2.44 x 10-212 and p = 2.98 x 10-261), resulting two missense mutations (i.e., Thr 265 Ile and Gln 57 His) in ORF1ab and ORF3a, respectively. Interestingly, these two SNPs exclusively occurred in the North America dominated clade 1, accumulated during mid to late March, 2020. We did not find any of these two SNPs by retrospectively tracing the two SNPs in bat and pangolin related SARS-CoV-2 and human SARS-CoV-2 from the first epicenter Wuhan or other regions of China mainland. This suggested that the SARS-CoV-2 population of Chinese mainland were different from the prevalent strains of North America. Time-dependently, we found that these two SNPs first occurred in Europe SARS-CoV-2 (26-Feb-2020) which was 3 days early than the occurring date of North America isolates and 17 days early for Asia isolates (Taiwan China dominated). Collectively, this population genetic analysis highlights a well-confidential transmission route of the North America isolates and the two SNPs we newly identified are possibly novel diagnosable or druggable targets for surveillance and treatment.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Xumin Ou", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Zhishuang Yang", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Dekang Zhu", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Sai Mao", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Mingshu Wang", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Renyong Jia", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Shun Chen", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Mafeng Liu", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Qiao Yang", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Ying Wu", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Xinxin Zhao", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Shaqiu Zhang", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Juan Huang", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Qun Gao", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Yunya Liu", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Ling Zhang", - "author_inst": "Sichuan Agricultural University" - }, - { - "author_name": "Maikel Peopplenbosch", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Qiuwei Pan", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "An-chun Cheng", - "author_inst": "Sichuan Agricultural University" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.13.094490", "rel_title": "A rapid, point of care red blood cell agglutination assay for detecting antibodies against SARS-CoV-2", @@ -1481624,6 +1482197,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.10.20097154", + "rel_title": "The Estimated Time-Varying Reproduction Numbers during the Ongoing Pandemic of the Coronavirus Disease 2019 (COVID-19) in 12 Selected Countries outside China", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097154", + "rel_abs": "BackgroundHow can we anticipate the progression of the ongoing pandemic of the coronavirus disease 2019 (COVID-19)? As a measure of transmissibility, we aimed to estimate concurrently the time-varying reproduction number, R0(t), over time during the COVID-19 pandemic for each of the following 12 heavily-attacked countries: Singapore, South Korea, Japan, Iran, Italy, Spain, Germany, France, Belgium, United Kingdom, the United States of America, and South Africa.\n\nMethodsWe downloaded the publicly available COVID-19 pandemic data from the WHO COVID-19 Dashboard website (https://covid19.who.int/) for the duration of January 11, 2020 and May 1, 2020. Then, we specified two plausible distributions of serial interval to apply the novel estimation method implemented in the incidence and EpiEstim packages to the data of daily new confirmed cases for robustly estimating R0(t) in the R software.\n\nResultsWe plotted the epidemic curves of daily new confirmed cases for the 12 selected countries. A clear peak of the epidemic curve appeared in 10 of the 12 selected countries at various time points, and then the epidemic curve declined gradually. However, the United States of America and South Africa happened to have two or more peaks and their epidemic curves either reached a plateau or still climbed up. Almost all curves of the estimated R0(t) monotonically went down to be less than or close to 1.0 up to April 30, 2020 except Singapore, South Korea, Japan, Iran, and South Africa, of which the curves surprisingly went up and down at various time periods during the COVID-19 pandemic. Finally, the United States of America and South Africa were the two countries with the approximate R0(t) [≥] 1.0 at the end of April, and thus they were now facing the harshest battles against the coronavirus among the 12 selected countries. By contrast, Spain, Germany, and France with smaller values of the estimated R0(t) were relatively better than the other 9 countries.\n\nConclusionSeeing the estimated R0(t) going downhill speedily is more informative than looking for the drops in the daily number of new confirmed cases during an ongoing epidemic of infectious disease. We urge public health authorities and scientists to estimate R0(t) routinely during an epidemic of infectious disease and to report R0(t) daily to the public until the end of the epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Fu-Chang Hu", + "author_inst": "National Taiwan University, College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.12.091314", "rel_title": "Meta-analysis of transcriptomes of SARS-Cov2 infected human lung epithelial cells identifies transmembrane serine proteases co-expressed with ACE2 and biological processes related to viral entry, immunity, inflammation and cellular stress.", @@ -1482280,161 +1482872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.08.20095471", - "rel_title": "Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095471", - "rel_abs": "BackgroundCOVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for more than 100 years.\n\nMethodsPatients (n=25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28 - April 14, 2020. Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 post-transfusion. Clinical improvement was assessed based on a modified World Health Organization 6-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains.\n\nResultsAt baseline, all patients were receiving supportive care, including anti-inflammatory and anti-viral treatments, and all patients were on oxygen support. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. By day 14 post-transfusion, 19 (76%) patients had at least a 1-point improvement in clinical status and 11 were discharged. No adverse events as a result of plasma transfusion were observed. The whole genome sequencing data did not identify a strain genotype-disease severity correlation.\n\nConclusionsThe data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Randomized, controlled trials are needed to determine its efficacy.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Eric Salazar", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Katherine K. Perez", - "author_inst": "Department of Pharmacy, Houston Methodist Hospital" - }, - { - "author_name": "Madiha Ashraf", - "author_inst": "Department of Clinical Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Jian Chen", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Brian Castillo", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Paul A. Christensen", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Taryn Eubank", - "author_inst": "Department of Pharmacy, Houston Methodist Hospital" - }, - { - "author_name": "David W. Bernard", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Todd N. Eagar", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "S. Wesley Long", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Sishir Subedi", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Randall J. Olsen", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Christopher Leveque", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Mary R. Schwartz", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Monisha Dey", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Cheryl Chavez-East", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "John Rogers", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Ahmed Shehabeldin", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "David Joseph", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Guy Williams", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Karen Thomas", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - }, - { - "author_name": "Faisal Masud", - "author_inst": "Department of Anesthesiology and Critical Care, Houston Methodist Hospital" - }, - { - "author_name": "Christina Talley", - "author_inst": "Academic Office of Clinical Trials, Houston Methodist Research Institute" - }, - { - "author_name": "Katharine G. Dlouhy", - "author_inst": "Academic Office of Clinical Trials, Houston Methodist Research Institute" - }, - { - "author_name": "Bevin Valdez Lopez", - "author_inst": "Academic Office of Clinical Trials, Houston Methodist Research Institute" - }, - { - "author_name": "Curt Hampton", - "author_inst": "Academic Office of Clinical Trials, Houston Methodist Research Institute" - }, - { - "author_name": "Jason Lavinder", - "author_inst": "Department of Molecular Biosciences, University of Texas at Austin" - }, - { - "author_name": "Jimmy D. Gollihar", - "author_inst": "CCDC Army Research Laboratory-South, University of Texas at Austin" - }, - { - "author_name": "Andre C. Maranhao", - "author_inst": "Department of Molecular Biosciences, University of Texas at Austin" - }, - { - "author_name": "Gregory C. Ippolito", - "author_inst": "Department of Molecular Biosciences, University of Texas at Austin" - }, - { - "author_name": "Matthew Ojeda Saavedra", - "author_inst": "Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute" - }, - { - "author_name": "Concepcion C. Cantu", - "author_inst": "Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute" - }, - { - "author_name": "Prasanti Yerramilli", - "author_inst": "Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute" - }, - { - "author_name": "Layne Pruitt", - "author_inst": "Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute" - }, - { - "author_name": "James M. Musser", - "author_inst": "Department of Pathology and Genomic Medicine, Houston Methodist Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.05.08.20095745", "rel_title": "On the Front (Phone) Lines: Results of a COVID-19 Hotline in Northeast Ohio", @@ -1483062,6 +1483499,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.09.20096420", + "rel_title": "Timing of non-pharmaceutical interventions to mitigate COVID-19 transmission and their effects on mobility: A cross-country analysis", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096420", + "rel_abs": "Non-pharmaceutical interventions (NPIs) that encourage physical distancing can decrease and delay the transmission of COVID-19. They have been implemented globally during the pandemic, however, the specific NPIs implemented and the timing of interventions has varied widely. We validated two published datasets on the implementation of NPIs globally. The health and socioeconomic factors associated with delay in implementation of NPIs was analyzed using fractional logit and probit models, and beta regression models. The probability of timely NPI implementation by a country was analyzed using a probit model. The effects of these interventions on mobility changes using Google social mobility reports, were analyzed with propensity score matching methods. Three NPIs were analyzed: national school closure, national lockdown, and global travel ban. Countries with higher incomes, larger populations, and better health preparedness measures had greater delays in implementation. Countries with greater population density, more democratic political systems, lower case detection capacity, and later arrival of first cases were more likely to implement NPIs. Implementation of lockdowns significantly reduced physical mobility. Mobility was further reduced when lockdowns were enforced with curfews or fines, or were more strictly defined. National school closures did not significantly change mobility. The implementation of NPIs is a global public good during pandemics, and the international community needs to address constraints and design incentives so countries implement NPIs in a timely manner. Further analysis is needed on the effect of NPI variations on mobility and transmission, and their associated costs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Amit Summan", + "author_inst": "Center for Disease Dynamics, Economics, and Policy" + }, + { + "author_name": "Arindam Nandi", + "author_inst": "The Center for Disease Dynamics, Economics & Policy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.09.20096099", "rel_title": "Healthcare workers preparedness for COVID-19 pandemic in the occupied Palestinian territory: a cross-sectional survey", @@ -1483566,25 +1484026,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.09.20096735", - "rel_title": "Modelling the evolution of COVID-19 in high-incidence European countries and regions: estimated number of infections and impact of past and future intervention measures", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096735", - "rel_abs": "A previously developed mechanistic model of COVID-19 transmission has been adapted and applied here to study the evolution of the disease and the effect of intervention measures in some European countries and territories where the disease had major impact. A clear impact of the major intervention measures on the reproduction number (Rt) has been found in all studied countries and territories, as already suggested by the drop in the number of deaths over time. Interestingly, the impact of such major intervention measures seems to be the same in most of these countries. The model has also provided realistic estimates of the total number of infections, active cases and future outcome. While the predictive capabilities of the model are much more uncertain before the peak of the outbreak, we could still reliably predict the evolution of the disease after a major intervention by assuming the afterwards reproduction number from current study. More challenging is to foresee the long-term impact of softer intervention measures, but this model can estimate the outcome of different scenarios and help planning changes in the implementation of control measures in a given country or region.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Juan Fernandez-Recio", - "author_inst": "ICVV-CSIC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.09.20096636", "rel_title": "The Coronavirus 2019 pandemic in Canada: the impact of public health interventions on the course of the outbreak in Alberta and other provinces", @@ -1484680,6 +1485121,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.12.092163", + "rel_title": "A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data", + "rel_date": "2020-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.092163", + "rel_abs": "In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms, and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input, and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction, and other pre-processing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid SARS-CoV-2 identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, MERS, and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shifu Chen", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Changshou He", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Yingqiang Li", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Zhicheng Li", + "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Charles E Melancon III", + "author_inst": "HaploX Biotechnology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.13.092577", "rel_title": "Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection", @@ -1485136,89 +1485612,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20094599", - "rel_title": "Early outcomes of tocilizumab in adults hospitalized with severe COVID19. An initial report from the Vall dHebron COVID19 prospective cohort study.", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094599", - "rel_abs": "BackgroundModulation of the immune system to prevent lung injury is being widely used against the new coronavirus disease (COVID-19) despite the scarcity of evidence.\n\nMethodsWe report the preliminary results from the Vall dHebron prospective cohort study at Vall dHebron University Hospital, in Barcelona (Spain), including all consecutive patients who had a confirmed infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and who were treated with tocilizumab until March 25th. The primary endpoint was mortality at 7 days after tocilizumab administration. Secondary endpoints were admission to the intensive care unit, development of ARDS and respiratory insufficiency among others.\n\nResults82 patients with COVID-19 received at least one dose of tocilizumab. The mean ({+/-} SD) age was 59.1 (19.8) years, 63% were male, 22% were of non-Spanish ancestry, and the median (IQR) age-adjusted Charlson index at baseline was 3 (1-4) points. Respiratory failure and ARDS developed in 62 (75.6%) and 45 (54.9%) patients, respectively. Median time from symptom onset to ARDS development was 8 (5-11) days. The median time from symptom onset to the first dose of tocilizumab was 9 (7-11) days. Mortality at 7 days was 26.8%. Hazard ratio for mortality was 3.3; 95% CI, 1.3 to 8.5 (age-adjusted hazard ratio for mortality 2.1; 95% CI, 0.8 to 5.8) if tocilizumab was administered after the onset of ARDS.\n\nConclusionTime from lung injury onset to tocilizumab administration may be critical to patient recovery. Our preliminary data could inform bedside decisions until more data from clinical trials becomes available.\n\nSummary of the articles main pointIn patient with COVID-19 and lung injury, time from lung injury onset to tocilizumab administration may be critical to patient recovery. Early administration of host-directed therapies may improve patient outcome.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Adrian Sanchez-Montalva", - "author_inst": "Vall d'Hebron University Hospital, Infectious Diseases Department, Global Health and Tuberculosis Unit, National Referral Center for Tropical Diseases" - }, - { - "author_name": "Julia Selares-Nadal", - "author_inst": "Vall d'Hebron University Hospital, Internal Medicine and Infectious Diseases" - }, - { - "author_name": "Juan Espinosa-Pereiro", - "author_inst": "Vall d'Hebron University Hospital, Infectious Diseases Department, Global Health and Tuberculosis Unit, National Referral Center for Tropical Diseases" - }, - { - "author_name": "Nuria Fernandez-Hidalgo", - "author_inst": "Vall d'Hebron University Hospital, Infectious Diseases Department, Cardiovascular Infections Unit" - }, - { - "author_name": "Santiago Perez-Hoyos", - "author_inst": "Vall d'HebronResearch Institute, Statistics and Bioinformatics Unit" - }, - { - "author_name": "Fernando Salvador", - "author_inst": "Vall d'Hebron University Hospital, Infectious Diseases Department, Global Health and Tuberculosis Unit, National Referral Center for Tropical Diseases" - }, - { - "author_name": "Xavier Dura-Miralles", - "author_inst": "Vall d'Hebron University Hospital, Internal Medicine and Infectious Diseases" - }, - { - "author_name": "Marta Miarons", - "author_inst": "Vall d'Hebron University Hospital, Hospital Pharmacy" - }, - { - "author_name": "Andres Anton", - "author_inst": "Vall d'Hebron University Hospital, Micriobiology Depratment" - }, - { - "author_name": "Simeon Eremiev", - "author_inst": "Vall d'Hebron University Hospital Internal Medicine and Infectious Diseases" - }, - { - "author_name": "Abiu Sempere-Gonzalez", - "author_inst": "Vall d'Hebron University Hospital, Internal Medicine and Infectious Diseases" - }, - { - "author_name": "Pau Bosch-Nicolau", - "author_inst": "Vall d'Hebron University Hospital, Infectious Diseases Department, Global Health and Tuberculosis Unit, National Referral Center for Tropical Diseases" - }, - { - "author_name": "Arnau Monforte-Pallares", - "author_inst": "Vall d'Hebron University Hospital, Internal Medicine and Infectious Diseases" - }, - { - "author_name": "Salvador Augustin", - "author_inst": "Vall d'Hebron University Hospital, Hepatology Department" - }, - { - "author_name": "Julia Sampol", - "author_inst": "Vall d'Hebron University Hospital, Pneumology Department" - }, - { - "author_name": "Alfredo Guillen-del-Castillo", - "author_inst": "Vall d'Hebron University Hospital, Internal Medicine, Systemic Diseases Division" - }, - { - "author_name": "Benito Almirante", - "author_inst": "Vall d'Hebron University Hospital, Infectious Diseases Depratment" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.08.20095018", "rel_title": "Clinical Course and Risk Factors for Recurrence of Positive SARS-CoV-2 RNA: A Retrospective Cohort Study from Wuhan, China", @@ -1485974,6 +1486367,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.05.08.20095463", + "rel_title": "Using epidemic simulators for monitoring an ongoing epidemic", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095463", + "rel_abs": "Prediction of infection trends, estimating the efficacy of contact tracing, testing or impact of influx of infected are of vital importance for administration during an ongoing epidemic. Most effective methods currently are empirical in nature and their relation to parameters of interest to administrators are not evident. We thus propose a modified SEIRD model that is capable of modeling effect of interventions and in migrations on the progress of an epidemic. The tunable parameters of this model bear relevance to monitoring of an epidemic. This model was used to show that some of the commonly seen features of cumulative infections in real data can be explained by piece wise constant changes in interventions and population influx. We also show that the data of cumulative infections from twelve Indian states between mid March and mid April 2020 can be generated from the model by applying interventions according to a set of heuristic rules. Prediction for the next ten days based on this model, reproduced real data very well. In addition, our model also reproduced the time series of recoveries and deaths. Our work constitutes an important first step towards an effective dashboard for the monitoring of epidemic by the administration, especially in an Indian context.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mohan Raghavan", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Kousik Sarathy Sridharan", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Yashaswini M R", + "author_inst": "Indian Institute of Technology Hyderabad" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.08.20093229", "rel_title": "Placental pathology in COVID-19", @@ -1486761,57 +1487181,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.05.07.082768", - "rel_title": "Mutation landscape of SARS-CoV-2 reveals three mutually exclusive clusters of leading and trailing single nucleotide substitutions", - "rel_date": "2020-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.07.082768", - "rel_abs": "The COVID-19 pandemic has spread across the globe at an alarming rate. However, unlike any of the previous global outbreaks the availability of a large number of SARS-CoV-2 sequences provides us with a unique opportunity to understand viral evolution in real time. We analysed 1448 full-length (>29000 nt) sequences available and identified 40 single-nucleotide substitutions occurring in >1% of the genomes. Majority of the substitutions were C to T or G to A. We identify C/Gs with an upstream TTT trinucleotide motif as hotspots for mutations in the SARS-CoV-2 genome. Interestingly, three of the 40 substitutions occur within highly conserved secondary structures in the 5 and 3 regions of the genomic RNA that are critical for the virus life cycle. Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. Of note, we observed several co-occurring mutations that almost never occur individually. We define five mutually exclusive lineages (A1, B1, C1, D1 and E1) of SARS-CoV-2 which account for about three quarters of the genomes analysed. We identify lineage-defining leading mutations in the SARS-CoV-2 genome which precede the occurrence of sub-lineage defining trailing mutations. The identification of mutually exclusive lineage-defining mutations with geographically restricted patterns of distribution has potential implications for diagnosis, pathogenesis and vaccine design. Our work provides novel insights on the temporal evolution of SARS-CoV-2.\n\nImportanceThe SARS-CoV-2 / COVID-19 pandemic has spread far and wide with high infectivity. However, the severeness of the infection as well as the mortality rates differ greatly across different geographic areas. Here we report high frequency mutations in the SARS-CoV-2 genomes which show the presence of linage-defining, leading and trailing mutations. Moreover, we propose for the first time, five mutually exclusive clusters of SARS-CoV-2 which account for 75% of the genomes analysed. This will have implications in diagnosis, pathogenesis and vaccine design", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Akhilesh Mishra", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Ashutosh Kumar Pandey", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Parul Gupta", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Prashant Pradhan", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Sonam Dhamija", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "James Gomes", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Bishwajit Kundu", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Perumal Vivekanandan", - "author_inst": "Indian Institute of Technology, New Delhi" - }, - { - "author_name": "Manoj B. Menon", - "author_inst": "Indian Institute of Technology, New Delhi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.12.090035", "rel_title": "Comparative analysis of antiviral efficacy of FDA-approved drugs against SARS-CoV-2 in human lung cells: Nafamostat is the most potent antiviral drug candidate", @@ -1487563,6 +1487932,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.06.20093419", + "rel_title": "Evidence of Protective Role of Ultraviolet-B (UVB) Radiation in Reducing COVID-19 Deaths", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093419", + "rel_abs": "BackgroundResearch is ongoing to identify an effective way to prevent or treat COVID-19, but thus far these efforts have not yet identified a possible solution. Prior studies indicate the protective role of Ultraviolet-B (UVB) radiation in human health, mediated by vitamin D synthesis. In this study, we empirically outline a negative association of UVB radiation as measured by ultraviolet index (UVI) with the number of deaths attributed to COVID-19 (COVID- 19 deaths).\n\nMethodsWe carry out an observational study, applying a fixed-effect log-linear regression model to a panel dataset of 152 countries over a period of 108 days (n=6524). We use the cumulative number of COVID-19 deaths and case-fatality rate (CFR) as the main dependent variables to test our hypothesis and isolate UVI effect from potential confounding factors such as underlying time trends, country-specific time-constant and time-varying factors such as weather.\n\nFindingsAfter controlling for time-constant and time-varying factors, we find that a permanent unit increase in UVI is associated with a 1.2 percentage points decline in daily growth rates of cumulative COVID-19 deaths [p < 0.01] as well as a 1.0 percentage points decline in the daily growth rates of CFR [p < 0.05]. These results represent a significant percentage reduction in terms of the daily growth rates of cumulative COVID-19 deaths (-11.88%) and CFR (-38.46%). Our results are consistent across different model specifications.\n\nInterpretationWe find a significant negative association between UVI and COVID-19 deaths, indicating evidence of the protective role of UVB in mitigating COVID-19 deaths. If confirmed via clinical studies, then the possibility of mitigating COVID-19 deaths via sensible sunlight exposure or vitamin D intervention will be very attractive because it is cost-effective and widely available.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rahul Kalippurayil Moozhipurath", + "author_inst": "Goethe University Frankfurt am Main" + }, + { + "author_name": "Lennart Kraft", + "author_inst": "Goethe University Frankfurt am Main" + }, + { + "author_name": "Bernd Skiera", + "author_inst": "Goethe University Frankfurt am Main" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.07.20094888", "rel_title": "SARS-CoV-2 Infection Associated Hemophagocytic Lymphohistiocytosis: An autopsy series with clinical and laboratory correlation.", @@ -1488255,93 +1488651,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.05.20077610", - "rel_title": "Celebrex adjuvant therapy on COVID-19: An experimental study", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20077610", - "rel_abs": "BackgroundThe world is under serious threat with the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19). However, there is no effective drug for the treatment of COVID-19. Based on analyses of available data, we deduced that the excessive prostaglandins E2 (PGE2) accumulation mediated by cyclooxygenase-2 (COX-2) was the key pathological basis of COVID-19.\n\nMethodsThe urine PGE2 levels were measured by mass spectrometry. An experimental study about Celebrex to treat COVID-19 was conducted based on routine treatment. A total of 44 confirmed COVID-19 patients were enrolled (Experimental group n=37, Control group n=7). Patients in experimental group were given Celebrex once or twice a day (0.2 g/time) for 7-14 days. The dosage or duration was modified for individuals. Clinical outcomes of Celebrex adjuvant therapy were evaluated by vital signs, laboratory tests, and computed tomography upon the discontinuance of Celebrex.\n\nResultsWe found that the concentrations of PGE2 in urine samples of COVID-19 patients were significantly higher than that of healthy individuals (mean value is 170 ng/ml vs 18.8 ng/ml, p<0.01) and positively correlated with the progression of COVID-19. Among the experimental group (ordinary n=29, severe n=7, critical n=1), 25 cases were treated with full dose and 11 cases with half dose of Celebrex, and 1 case with Ibuprofen. The remission rate were 100%, 82% and 57% in full dose, half dose and control group respectively. Celebrex significantly reduced the PGE2 levels and promoted recovery of ordinary or severe COVID-19.\n\nConclusionOur study suggests that Celebrex adjuvant treatment may be helpful for the therapy of COVID-19.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Wenxin Hong", - "author_inst": "The Eighth People's Hospital of Guangzhou, Guangzhou 510060, China" - }, - { - "author_name": "Yan Chen", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Kai You", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Shenglin Tan", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Feima Wu", - "author_inst": "The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China" - }, - { - "author_name": "Jiawang Tao", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Xudan Chen", - "author_inst": "The Eighth People's Hospital of Guangzhou, Guangzhou 510060, China" - }, - { - "author_name": "Jiaye Zhang", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Yue Xiong", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Fang Yuan", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Zhen Yang", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Tingting Chen", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Xinwen Chen", - "author_inst": "Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China" - }, - { - "author_name": "Ping Peng", - "author_inst": "The Eighth People's Hospital of Guangzhou, Guangzhou 510060, China" - }, - { - "author_name": "Qiang Tai", - "author_inst": "The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China" - }, - { - "author_name": "Jian Wang", - "author_inst": "The Eighth People's Hospital of Guangzhou, Guangzhou 510060, China" - }, - { - "author_name": "Fuchun Zhang", - "author_inst": "The Eighth People's Hospital of Guangzhou, Guangzhou 510060, China" - }, - { - "author_name": "Yinxiong Li", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.07.20084087", "rel_title": "Concerns about disease management and psychological stress in SAPHO patients during the COVID-19 epidemic", @@ -1489237,6 +1489546,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20092445", + "rel_title": "Smoking and the risk of COVID-19 infection in the UK Biobank Prospective Study", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092445", + "rel_abs": "Several studies suggest a lower prevalence of smoking than expected among adults with coronavirus disease (COVID-19). We conducted logistic regression analyses of the UK Biobank prospective study of 0.5 million adults followed for an average of 11 years. Compared to women, men were more likely to be tested and to test positive. In sex-stratified analyses, current smokers had higher adjusted Odds Ratios (OR) for being tested (male OR 1.60, 95%CI 1.32-1.95 and female OR 1.50,1.21-.1.86). Current smokers were more slightly more likely than never smokers to test positive for COVID-19. Further examination of smoking as a risk factor for COVID-19 is required. These must take into account reverse causality, where smokers quit to avoid disease as well as prior diseases.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Eo Rin Cho", + "author_inst": "Centre for Global Health Research, St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Arthur S Slutsky", + "author_inst": "Centre for Global Health Research, St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Prabhat Jha", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20092957", "rel_title": "Associations with covid-19 hospitalisation amongst 406,793 adults: the UK Biobank prospective cohort study", @@ -1489805,73 +1490141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20093542", - "rel_title": "Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20093542", - "rel_abs": "Rapid, reliable, and widespread testing is required to curtail the ongoing COVID-19 pandemic. Current gold standard nucleic acid tests are hampered by supply shortages in critical reagents including nasal swabs, RNA extraction kits, personal protective equipment (PPE), instrumentation, and labor. Here we present an approach to overcome these challenges with the development of a rapid colorimetric assay using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) optimized on human saliva samples without an RNA purification step. We describe our optimizations of the LAMP reaction and saliva pretreatment protocols that enabled rapid and sensitive detection of < 102 viral genomes per reaction in contrived saliva controls. Moreover, our saliva pretreatment protocol enabled sensitive viral detection by conventional quantitative reverse transcription polymerase chain reaction (qRT-PCR) without RNA extraction. We validated the high performance of these assays on clinical samples and demonstrate a promising approach to overcome the current bottlenecks limiting widespread testing.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Matthew A Lalli", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "S Joshua Langmade", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Xuhua Chen", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Catrina C Fronick", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Christopher S Sawyer", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Lauren C Burcea", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Michael N Wilkinson", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Robert S Fulton", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Michael Heinz", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "William J Buchser", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Richard D Head", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Robi D Mitra", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Jeffrey Milbrandt", - "author_inst": "Washington University in St Louis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.08.20031666", "rel_title": "Psychological morbidities and fatigue in patients with confirmed COVID-19 during disease outbreak: prevalence and associated biopsychosocial risk factors", @@ -1490867,6 +1491136,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.07.20094177", + "rel_title": "Clinical and behavioural characteristics of self-isolating healthcare workers during the COVID-19 pandemic: a single-centre observational study", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094177", + "rel_abs": "ObjectivesTo describe a cohort of self-isolating healthcare workers (HCWs) with presumed COVID-19.\n\nDesignA cross-sectional, single-centre study.\n\nSettingA large, teaching hospital based in Central London with tertiary infection services.\n\nParticipants236 HCWs completed a survey distributed by internal staff email bulletin. 167 were female and 65\n\nMeasuresInformation on symptomatology, exposures and health-seeking behaviour were collected from participants by self-report.\n\nResultsThe 236 respondents reported illness compatible with COVID-19 and there was an increase in illness reporting during March 2020. Diagnostic swabs were not routinely performed.. Cough (n=179, 75.8%), fever (n=138, 58.5%), breathlessness (n=84, 35.6%) were reported. Anosmia was reported in 42.2%. Fever generally settled within 1 week (n=110, 88%). Several respondents remained at home and did not seek formal medical attention despite reporting severe breathlessness and measuring hypoxia (n=5/9, 55.6%). 2 patients required hospital admission but recovered following oxygen therapy. 84 respondents (41.2%) required greater than the obligated 7 days off work and 9 required greater than 3 weeks off.\n\nConclusionThere was a significant increase in staff reporting illness compatible with possible COVID-19 during March 2020. Conclusions cannot be drawn about exact numbers of confirmed cases due to lack of diagnostic swabbing. There were significant numbers of respondents reporting anosmia; as well as early non-specific illness prior to onset of cough and fever. This may represent pre-symptomatic HCWs who are likely to be infectious and thus criteria for isolation and swabbing should be broadened. The study also revealed concerning lack of healthcare seeking in respondents with significant red flag symptoms (severe breathlessness, hypoxia). This should be addressed urgently to reduce risk of severe disease being detected late. Finally, this study should inform trusts that HCWs may require longer than 7 days off work to recover from illness.\n\nO_LSTStrengths and limitations of this studyC_LSTO_LITo the authors knowledge, this study presents one of the first descriptive data analysis of self-reported healthcare worker (HCW) COVID-19 exposures and symptomatology in the UK.\nC_LIO_LIStudy respondents represented a broad range of job roles, including both frontline clinical and non-patient facing staff.\nC_LIO_LIThe inclusion of questions focusing on health-seeking behaviour allows results to be used to inform human resource management in the developing pandemic, and provides concerning but important data around late healthcare seeking in HCWs\nC_LIO_LIData were self-reported, cross-sectional and retrospective, which may be subject to recall bias, and the lack of diagnostic swabbing in the majority of respondents limits interpretation of the data\nC_LIO_LIFull demographic data were not collected on participants and certain staff groups may have been over-represented in the sample, which may introduce sampling bias.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Angus de Wilton", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Eliz Kilich", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Zain Chaudhry", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Lucy CK Bell", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Joshua Gahir", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Jane Cadman", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Robert A Lever", + "author_inst": "Hospital of Tropical Diseases, London; University College London" + }, + { + "author_name": "Sarah Logan", + "author_inst": "Hospital of Tropical Diseases, London; COVID-19 Response Team, University College London Hospitals NHS Foundation Trust;" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20094276", "rel_title": "Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy", @@ -1491419,73 +1491735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.07.20094557", - "rel_title": "Early impact of the COVID-19 pandemic and social distancing measures on routine childhood vaccinations in England, January to April 2020", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094557", - "rel_abs": "Electronic health records were used to assess the early impact of COVID-19 on routine childhood vaccination in England to 26 April 2020.\n\nMMR vaccination counts fell from February 2020, and in the three weeks after introduction of social distancing measures were 19.8% lower (95% CI -20.7 to -18.9%) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated on introduction of social distancing.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Medicine and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation" - }, - { - "author_name": "Elise Tessier", - "author_inst": "Public Health England" - }, - { - "author_name": "Joanne M White", - "author_inst": "Public Health England" - }, - { - "author_name": "Matthew Woodruff", - "author_inst": "TPP (Leeds) Ltd" - }, - { - "author_name": "Charlotte Knowles", - "author_inst": "TPP (Leeds) Ltd" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP (Leeds) Ltd" - }, - { - "author_name": "John Parry", - "author_inst": "TPP (Leeds) Ltd" - }, - { - "author_name": "Jemma L Walker", - "author_inst": "London School of Hygiene and Tropical Medicine; Public Health England; NIHR Health Protection Research Unit (HPRU) in Immunisation" - }, - { - "author_name": "J Anthony Scott", - "author_inst": "London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit (HPRU) in Immunisation" - }, - { - "author_name": "Joanne Yarwood", - "author_inst": "Public Health England" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "Public Health England; NIHR Health Protection Research Unit (HPRU) in Immunisation" - }, - { - "author_name": "Michael Edelstein", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.08.20095679", "rel_title": "Negative nasopharyngeal SARS-CoV-2 PCR conversion in Response to different therapeutic interventions", @@ -1492293,6 +1492542,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.06.20093492", + "rel_title": "Metapopulation modeling of COVID-19 advancing into the countryside: an analysis of mitigation strategies for Brazil", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093492", + "rel_abs": "Since the first case of COVID-19 was confirmed in Brazil on 19 February 2020, this epidemic has spread throughout all states and at least 2142 of 5570 municipalities up to 30 April 2020. In order to understand this spreading, we investigate a stochastic epidemic model using a metapopulation approach. Simulations are supplied with real data for mobility, demography, and confirmed cases of COVID-19 extracted from public sources. Contagion follows a compartmental epidemic model for each municipality; the latter, in turn, interact with each other through recurrent mobility. Considering the number of municipalities with confirmed COVID-19 cases, simulations can infer the level of mitigation (strong, moderate, or none) that each state is effectively adopting. Properties of the epidemic curves such as time and value of epidemic peak and outbreak duration have very broad distributions across different geographical locations. This outbreak variability is observed on several scales from state, passing through intermediate, immediate down to municipality levels. The epidemic waves start from several foci concentrated in highly populated regions and propagate towards the countryside. Correlations between delay of the epidemic outbreak and distance from the respective capital cities are strong in several states, showing propagation towards the countryside, and weak in others, signaling strong influences of multiple centers, not necessarily within the same state. Our take home message is that the responses of different regions to the same mitigation protocol can vary enormously such that the policies of combating COVID-19, such as quarantine or lockdown, must be engineered according to the region specificity but integrated with the overall situation. Even though we restricted our study to Brazil, we believe that these ideas can be generalized to other countries with continental scales and heterogeneous demographic distributions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Guilherme S Costa", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil" + }, + { + "author_name": "Wesley Cota", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil" + }, + { + "author_name": "Silvio C Ferreira", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil and National Institute of Science and Technology for Complex Systems, Rio d" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20093476", "rel_title": "Sensitivity and specificity of a rapid test for assessment of exposure to SARS-CoV-2 in a community-based setting in Brazil", @@ -1492789,41 +1493065,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.08.085506", - "rel_title": "Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity", - "rel_date": "2020-05-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.085506", - "rel_abs": "As the current SARS-CoV-2 pandemic continues, serological assays are urgently needed for rapid diagnosis, contact tracing and for epidemiological studies. So far, there is little data on how commercially available tests perform with real patient samples and if detected IgG antibodies provide protective immunity. Focusing on IgG antibodies, we demonstrate the performance of two ELISA assays (Euroimmun SARS-CoV-2 IgG & Vircell COVID-19 ELISA IgG) in comparison to one lateral flow assay ((LFA) FaStep COVID-19 IgG/IgM Rapid Test Device) and two in-house developed assays (immunofluorescence assay (IFA) and plaque reduction neutralization test (PRNT)). We tested follow up serum/plasma samples of individuals PCR-diagnosed with COVID-19. Most of the SARS-CoV-2 samples were from individuals with moderate to severe clinical course, who required an in-patient hospital stay.\n\nFor all examined assays, the sensitivity ranged from 58.8 to 76.5% for the early phase of infection (days 5-9) and from 93.8 to 100% for the later period (days 10-18) after PCR-diagnosed with COVID-19. With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. Regarding specificity, there was evidence that samples of endemic coronavirus (HCoV-OC43, HCoV-229E) and Epstein Barr virus (EBV) infected individuals cross-reacted in the ELISA assays and IFA, in one case generating a false positive result (may giving a false sense of security). This need to be further investigated.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Niko Kohmer", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Sandra Westhaus", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Cornelia Ruehl", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Holger F Rabenau", - "author_inst": "Goethe University Frankfurt" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.06.20069872", "rel_title": "Characterisation of Acute Kidney Injury in Critically Ill Patients with Severe Coronavirus Disease-2019 (COVID-19)", @@ -1494079,6 +1494320,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.05.20092122", + "rel_title": "Indian communitys Knowledge, Attitude & Practice towards COVID-19", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092122", + "rel_abs": "As COVID-19 pandemic has caused unprecedented human health consequences. Knowledge, attitude, perception of general population of India towards the transmission and prevention plays vital role for effective control measures. The study was conducted to assess the knowledge, attitude and practice of the general public of India on COVID-19. In this study, a web-based cross-sectional survey was conducted between 10th March to 18th April 2020. A 19-item questionnaire was generated, Cronbachs alpha was used to measure the internal consistency of the questionnaire & randomly distributed among the public using Google forms through social media networks. The chi-square test or Fischer exact test was used to compare categorical data and multiple linear regression was used to identify factor influencing KAP. Among 7978 participants, the overall knowledge, attitude and practice score was 80.64%, 97.33% and 93.8% consecutively. Majority of Indian population demonstrated preceded good knowledge, positive attitude and good practice regarding COVID-19 pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Balvir Singh Tomar", + "author_inst": "Institute of Gastroenterology Hepatology & Transplant" + }, + { + "author_name": "Pratima Singh", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur India" + }, + { + "author_name": "Deepak Nathiya", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan Jaipur India" + }, + { + "author_name": "Supriya Suman", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur India" + }, + { + "author_name": "Preeti Raj", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur, India" + }, + { + "author_name": "Sandeep Tripathi", + "author_inst": "National Institute of Medical Sciences & Research, Nims University Rajasthan, Jaipur, India" + }, + { + "author_name": "Dushyant Singh Chauhan", + "author_inst": "Institute of Advance Sciences, Nims University Rajasthan, Jaipur, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.05.20092254", "rel_title": "County-level factors influence the trajectory of Covid-19 incidence", @@ -1494595,73 +1494879,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20092296", - "rel_title": "Ethnicity and risk of death in patients hospitalised for COVID-19 infection: an observational cohort study in an urban catchment area", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092296", - "rel_abs": "BackgroundStudies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients.\n\nMethodsPatients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10th March 2020-17th April 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching.\n\nResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2-1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)).\n\nConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Elizabeth Sapey", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Suzy Gallier", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Chris Mainey", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Peter Nightingale", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "David McNulty", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Hannah Crothers", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Felicity Evison", - "author_inst": "University Hospitals Birmingham NHS FoundationTrust" - }, - { - "author_name": "Katharine Reeves", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Domenico Pagano", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Alastair K Denniston", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Krishnarajah Nirantharakumar", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Peter Diggle", - "author_inst": "University of Lancaster" - }, - { - "author_name": "Simon Ball", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20092288", "rel_title": "Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing", @@ -1495561,6 +1495778,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20091637", + "rel_title": "Application-oriented mathematical algorithms for group testing", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091637", + "rel_abs": "Group testing is a widely used protocol which aims to test a small group of people to identify whether at least one of them is infected. It is particularly efficient if the infection rate is low, because it only requires a single test if everybody in the group is negative. The most efficient use of group testing is a complex mathematical question. However, the answer highly depends on practical parameters and restrictions, which are partially ignored by the mathematical literature. This paper aims to offer practically efficient group testing algorithms, focusing on the current COVID-19 epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Endre Csoka", + "author_inst": "Alfred Renyi Institute of Mathematics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.08.083816", "rel_title": "Intra-genome variability in the dinucleotide composition of SARS-CoV-2", @@ -1495933,29 +1496169,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.03.20052779", - "rel_title": "Estimative of real number of infections by COVID-19 on Brazil and possible scenarios", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20052779", - "rel_abs": "This paper attempts to provide methods to estimate the real scenario of the novel coronavirus pandemic crisis on Brazil and the states of Sao Paulo, Pernambuco, Espirito Santo, Amazonas and Distrito Federal. By the use of a SEIRD mathematical model with age division, we predict the infection and death curve, stating the peak date for Brazil and these states. We also carry out a prediction for the ICU demand on these states for a visualization of the size of a possible collapse on the local health system. By the end, we establish some future scenarios including the stopping of social isolation and the introduction of vaccines and efficient medicine against the virus.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pedro Henrique Pinheiro Cintra", - "author_inst": "University of Brasilia, Physics Institute" - }, - { - "author_name": "Felipe Fontinele Nunes", - "author_inst": "University of Brasilia, Physics Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.05.20075275", "rel_title": "Covid-19 prevalence estimation by random sampling in the wider population - Optimal sample pooling under varying assumptions about true prevalence", @@ -1497283,6 +1497496,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.05.04.20090316", + "rel_title": "Early postmortem brain MRI findings in COVID-19 non-survivors", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090316", + "rel_abs": "ImportanceThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to have potential neuro-invasiveness that might lead to acute brain disorders or contribute to respiratory distress in patients with coronavirus disease 2019 (COVID-19). Brain magnetic resonance imaging (MRI) data in COVID-19 patients are scarce due to difficulties to obtain such examination in infected unstable patients during the COVID-19 outbreak.\n\nObjectiveTo investigate the occurrence of structural brain abnormalities in non-survivors of COVID-19 in a virtopsy framework.\n\nDesignProspective, case series study with postmortem brain MRI obtained early (<24h) after death.\n\nSettingMonocentric study.\n\nParticipantsFrom 31/03/2020 to 24/04/2020, consecutive decedents who fulfilled the following inclusion criteria were included: death <24 hours, SARS-CoV-2 detection on nasopharyngeal swab specimen, chest computerized tomographic (CT) scan suggestive of COVID-19, absence of known focal brain lesion, and MRI compatibility.\n\nMain Outcome(s) andMeasure(s)Signs of acute brain injury and MRI signal abnormalities along the olfactory tract and brainstem were searched independently by 3 neuroradiologists, then reviewed with neurologists and clinicians.\n\nResultsAmong the 62 patients who died from COVID-19 during the inclusion period, 19 decedents fulfilled inclusion criteria. Subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent) were observed. Asymmetric olfactory bulbs were found in 4 other decedents without downstream olfactory tract abnormalities. No brainstem MRI signal abnormality.\n\nConclusions and RelevancePostmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by the virus-induced endothelial disturbances. SARS-CoV-2-related olfactory impairment seems to be limited to olfactory bulbs. The absence of brainstem MRI abnormalities does not support a brain-related contribution to respiratory distress in COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs there common brain MRI abnormalities patterns in non-survivors of coronavirus disease 2019 ?\n\nFindingsIn a case series of 19 non-survivors of severe COVID-19 disease, early postmortem brain MRI demonstrated patterns evocative of intracranial vasculopathy in 4 decedents: subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent). Asymmetric olfactory bulbs were found in 4 other decedents but without downstream olfactory tract abnormalities.\n\nMeaningPostmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by virus-induced endothelial disturbances.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tim Coolen", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Valentina Lolli", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Niloufar Sadeghi", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Antonin Rovai", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Nicola Trotta", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Fabio S Taccone", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Jacques Creteur", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Sophie Henrard", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Jean-Christophe Goffard", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Olivier Dewitte", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Gilles Naeije", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Serge Goldman", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Xavier De Tiege", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.04.20091041", "rel_title": "The Social and Economic Factors Underlying the Impact of COVID-19 Cases and Deaths in US Counties", @@ -1498307,45 +1498587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20091827", - "rel_title": "A Noel Intervention Recurrent autoencoder for real time forecasting and non-pharmaceutical intervention selection to curb the spread of Covid-19 in the world", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091827", - "rel_abs": "As the Covid-19 pandemic soars around the world, there is urgent need to forecast the number of cases worldwide at its peak, the length of the pandemic before receding and implement public health interventions to significantly stop the spread of Covid-19. Widely used statistical and computer methods for modeling and forecasting the trajectory of Covid-19 are epidemiological models. Although these epidemiological models are useful for estimating the dynamics of transmission od epidemics, their prediction accuracies are quite low. To overcome this limitation, we formulated the real-time forecasting and evaluating multiple public health intervention problem into forecasting treatment response problem and developed recurrent neural network (RNN) for modeling the transmission dynamics of the epidemics and Counterfactual-RNN (CRNN) for evaluating and exploring public health intervention strategies to slow down the spread of Covid-19 worldwide. We applied the developed methods to the real data collected from January 22, 2020 to May 8, 2020 for real-time forecasting the confirmed cases of Covid-19 across the world.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Qiyang Ge", - "author_inst": "Fu Dan University, Shanghai" - }, - { - "author_name": "Zhixin Hu", - "author_inst": "Fudan University, Shanghai" - }, - { - "author_name": "Shudi Li", - "author_inst": "The University of Texas Health Science Center at Houston, Houston" - }, - { - "author_name": "Wei Lin", - "author_inst": "Fudan University, Shanghai" - }, - { - "author_name": "Li Jin", - "author_inst": "Fudan University, Shanghai" - }, - { - "author_name": "Momiao Xiong", - "author_inst": "University of Texas School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.05.20091645", "rel_title": "The First Wave of COVID-19 in Israel - Initial Analysis of Publicly Available Data", @@ -1499141,6 +1499382,61 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.08.084061", + "rel_title": "Comparison of SARS-CoV-2 spike protein binding to human, pet, farm animals, and putative intermediate hosts ACE2 and ACE2 receptors", + "rel_date": "2020-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.084061", + "rel_abs": "The emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used recently released X-ray structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins known to serve or not serve as receptor allows to define residues important for binding. From the 20 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery of the binding site, while changes of the invariable residues prevent S-binding or infection of the respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites located near the S-interface. Of note, pigs and dogs which are not or not effectively infected, respectively, have only a few changes in the binding site have relatively low levels of ACE2 in the respiratory tract. Comparison of the RBD of S of SARS-CoV-2 with viruses from bat and pangolin revealed that the latter contains only one substitution, whereas the bat virus exhibits five. However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new insight into the receptor usage and animal source/origin of SARS-COV-2.\n\nIMPORTANCESARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the species barrier might be low. However, the lower expression of ACE2 in the upper respiratory tract of some pets and livestock means more research and monitoring should be done to explore the animal source of infection and the risk of potential cross-species transmission. Finally, the analysis also showed that SARS-CoV-2 may not specifically adapted to any of its putative intermediate hosts.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xiaofeng Zhai", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jiumeng Sun", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Ziqing Yan", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jie Zhang", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jin Zhao", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Zongzheng Zhao", + "author_inst": "Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China." + }, + { + "author_name": "Qi Gao", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Wan-Ting He", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Michael Veit", + "author_inst": "Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany." + }, + { + "author_name": "Shuo Su", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.08.084384", "rel_title": "ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity", @@ -1499641,29 +1499937,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.07.082297", - "rel_title": "Lung biopsy cells transcriptional landscape from COVID-19 patient stratified lung injury in SARS-CoV-2 infection through impaired pulmonary surfactant metabolism", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.07.082297", - "rel_abs": "Clinical management of COVID-19 is still complicated due to the lack of therapeutic interventions to reduce the breathing problems, respiratory complications and acute lung injury - which are the major complications of most of the mild to critically affected patients and the molecular mechanisms behind these clinical features are still largely unknown. In this study, we have used the RNA-seq gene expression pattern in the COVID-19 affected lung biopsy cells and compared it with the effects observed in typical cell lines infected with SARS-CoV-2 and SARS-CoV. We performed functional overrepresentation analyses using these differentially expressed genes to signify the processes/pathways which could be deregulated during SARS-CoV-2 infection resulting in the symptomatic impairments observed in COVID-19. Our results showed that the significantly altered processes include inflammatory responses, antiviral cytokine signaling, interferon responses, and interleukin signaling etc. along with downmodulated processes related to lungs functionality like-responses to hypoxia, lung development, respiratory processes, cholesterol biosynthesis and surfactant metabolism. We also found that the viral protein interacting hosts proteins involved in similar pathways like: respiratory failure, lung diseases, asthma, and hypoxia responses etc., suggesting viral proteins might be deregulating the processes related to acute lung injury/breathing complications in COVID-19 patients. Protein-protein interaction networks of these processes and map of gene expression of deregulated genes revealed that several viral proteins can directly or indirectly modulate the host genes/proteins of those lung related processes along with several host transcription factors and miRNAs. Surfactant proteins and their regulators SPD, SPC, TTF1 etc. which maintains the stability of the pulmonary tissue are found to be downregulated through viral NSP5, NSP12 that could lead to deficient gaseous exchange by the surface films. Mitochondrial dysfunction owing to the aberration of NDUFA10, NDUFAF5, SAMM50 etc. by NSP12; abnormal thrombosis in lungs through atypical PLAT, EGR1 functions by viral ORF8, NSP12; dulled hypoxia responses due to unusual shift in HIF-1 downstream signaling might be the causative elements behind the acute lung injury in COVID-19 patients. Our study put forward a distinct mechanism of probable virus induced lung damage apart from cytokine storm and advocate the need of further research for alternate therapy in this direction.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Abul B.M.M.K. Islam", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" - }, - { - "author_name": "Md. Abdullah-Al-Kamran Khan", - "author_inst": "Department of Mathematics and Natural Sciences, BRAC University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.03.20089508", "rel_title": "A seven-day cycle in COVID-19 infection and mortality rates: Are inter-generational social interactions on the weekends killing susceptible people?", @@ -1500615,6 +1500888,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2020.05.04.20090076", + "rel_title": "Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090076", + "rel_abs": "The world faces an unprecedented SARS-CoV2 pandemic where many critical factors still remain unknown. The case fatality rates (CFR) reported in the context of the SARS-CoV-2 pandemic substantially differ between countries. For SARS-CoV-2 infection with its broad clinical spectrum from asymptomatic to severe disease courses, the infection fatality rate (IFR) is the more reliable parameter to predict the consequences of the pandemic. Here we combined virus RT-PCR testing and assessment for SARS-CoV2 antibodies to determine the total number of individuals with SARS-CoV-2 infections in a given population.\n\nMethodsA sero-epidemiological GCP- and GEP-compliant study was performed in a small German town which was exposed to a super-spreading event (carnival festivities) followed by strict social distancing measures causing a transient wave of infections. Questionnaire-based information and biomaterials were collected from a random, household-based study population within a seven-day period, six weeks after the outbreak. The number of present and past infections was determined by integrating results from anti-SARS-CoV-2 IgG analyses in blood, PCR testing for viral RNA in pharyngeal swabs and reported previous positive PCR tests.\n\nResultsOf the 919 individuals with evaluable infection status (out of 1,007; 405 households) 15.5% (95% CI: [12.3%; 19.0%]) were infected. This is 5-fold higher than the number of officially reported cases for this community (3.1%). Infection was associated with characteristic symptoms such as loss of smell and taste. 22.2% of all infected individuals were asymptomatic. With the seven SARS-CoV-2-associated reported deaths the estimated IFR was 0.36% [0.29%; 0.45%]. Age and sex were not found to be associated with the infection rate. Participation in carnival festivities increased both the infection rate (21.3% vs. 9.5%, p<0.001) and the number of symptoms in the infected (estimated relative mean increase 1.6, p=0.007). The risk of a person being infected was not found to be associated with the number of study participants in the household this person lived in. The secondary infection risk for study participants living in the same household increased from 15.5% to 43.6%, to 35.5% and to 18.3% for households with two, three or four people respectively (p<0.001).\n\nConclusionsWhile the number of infections in this high prevalence community is not representative for other parts of the world, the IFR calculated on the basis of the infection rate in this community can be utilized to estimate the percentage of infected based on the number of reported fatalities in other places with similar population characteristics. Whether the specific circumstances of a super-spreading event not only have an impact on the infection rate and number of symptoms but also on the IFR requires further investigation. The unexpectedly low secondary infection risk among persons living in the same household has important implications for measures installed to contain the SARS-CoV-2 virus pandemic.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Hendrik Streeck", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Bianca Schulte", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Beate Kuemmerer", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Enrico Richter", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Tobias Hoeller", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Christine Fuhrmann", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Eva Bartok", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Ramona Dolscheid", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Moritz Berger", + "author_inst": "Institute for Medical Biometry, Informatics and Epidemiology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Lukas Wessendorf", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Monika Eschbach-Bludau", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Angelika Kellings", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Astrid Schwaiger", + "author_inst": "Biobank Core Unit, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Martin Coenen", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Per Hoffmann", + "author_inst": "Institute of Human Genetics, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Markus Noethen", + "author_inst": "Institute of Human Genetics, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Anna-Maria Eis-Huebinger", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Martin Exner", + "author_inst": "Institute for Hygiene and Public Health, University Hospital, University of Bonn" + }, + { + "author_name": "Ricarda Schmithausen", + "author_inst": "Institute for Hygiene and Public Health, University Hospital, University of Bonn" + }, + { + "author_name": "Matthias Schmid", + "author_inst": "Institute for Medical Biometry, Informatics and Epidemiology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Gunther Hartmann", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany; German Center for Infection Research (DZIF), partne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.04.20090555", "rel_title": "Laboratory findings associated with mechanical ventilation requirement and mortality among hospitalized individuals with Covid-19 in Eastern Massachusetts", @@ -1501231,41 +1501603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.02.20088559", - "rel_title": "Efficacy of remdesivir in COVID-19 patients with a simulated two-arm controlled study", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088559", - "rel_abs": "While the recent study on the compassionate use of remdesivir for COVID-19 patients has shown a 68% clinical improvement7 it is a one-arm study that renders the evaluation of the efficacy in reducing death and the length of stay of hospitalization intractable due to a lacking of the control group. We came up with a two-arm controlled study design to simulate the treated and the untreated (control group) group by applying two respective transition models to the empirical data on dynamics of the disease severity (Figure 2 of the original article7) that are classified into low- (no and low oxygen supplement), medium- (non-invasive ventilator and high oxygen supplement), and high-(ECMO and invasive ventilator) from enrolment until discharge, death or the end of follow-up. By using a simulated two-arm controlled study, the remdesivir treatment group as opposed to the control group led to a statistically significantly 29% (95% CI: 22-35%) reduction of death from COVID-19. The treated group also revealed a 33% (95% CI 28-38%) significantly higher odds of discharge than the control group. The median time to discharge for the treated group (5.5 days, 16.5 days, and 29.5 days for low-, medium-, and high-risk state, respectively) was around half of those of the control arm. Our results with a simulated two-arm controlled study have not only corroborated the efficacy of remdesivir but also made great contribution to designing a further large-scale randomized controlled trial. They have significant implications for reducing transmission probability and infectious time of COVID-19 patients when contacting with susceptible health care workers during hospitalization.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/20088559v1_fig2.gif\" ALT=\"Figure 2\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@1c9a456org.highwire.dtl.DTLVardef@1442cdeorg.highwire.dtl.DTLVardef@ddd9d6org.highwire.dtl.DTLVardef@10895f9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Cumulative rate of discharge and death by treatments\n\nC_FIG Key PointsO_ST_ABSQuestionC_ST_ABSWhat is the efficacy of remdesivir in reducing advanced disease state or death from COVID-19 and the length of stay of hospitalization?\n\nFindingsRemdesivir treatment results in a 33% significantly higher odds of discharge, a 29% significantly lower risk of death, and a 39% significantly lower risk for the combined endpoint of severe status and death. The median time to discharge for the remdesivir treated group was around half of the median time-to-discharge compared with the control arm.\n\nMeaningRemdesivir is effective in treating COVID-19 patients in terms of enhancing recovery and accelerating discharge.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chen-Yang Hsu", - "author_inst": "Dachung Hospital, Miaoli, Taiwan." - }, - { - "author_name": "Chao-Chih Lai", - "author_inst": "Emergency Department of Taipei City Hospital, Ren-Ai Branch, Taiwan" - }, - { - "author_name": "Amy Ming-Fang Yen", - "author_inst": "School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan" - }, - { - "author_name": "Sam Li-She Chen", - "author_inst": "School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan" - }, - { - "author_name": "Hsiu-Hsi Chen", - "author_inst": "Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20088104", "rel_title": "IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", @@ -1502365,6 +1502702,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.06.20092858", + "rel_title": "Spatial Network based model forecasting transmission and control of COVID-19", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092858", + "rel_abs": "The SARS-CoV-2 driven infectious novel coronavirus disease (COVID-19) has been declared a pandemic by virtue of its brutal impact on the world in terms of loss on human life, health, economy, and other crucial resources. With the aim to explore more about its aspects, we adopted the SEIQRD (Susceptible-Exposed-Infected-Quarantine-Recovered-Death) pandemic spread with a time delay on the heterogeneous population and geography in this work. Focusing on the spatial heterogeneity, the entire population of interest in a region is divided into small distinct geographical sub regions, which interact by means of migration networks across boundaries. Utilizing the estimations of the time delay differential equations based model, we analyzed the spread dynamics of disease in a region and its sub regions. The model based numerical outcomes are validated from real time available data for India. We computed the approximate peak infection in forward time and relative timespan when disease outspread halts. To further evaluate the influence of the delay on the long term system dynamics, the sensitivity analysis is performed on time delay. The most crucial parameter, basic reproduction number R0 and its time-dependent generalization, has been estimated at both regional and sub regional levels. The impact of the most significant lockdown measure that has been implemented in India to contain the pandemic spread has been extensively studied by considering no lockdown scenario. A suggestion based on outcomes, for a bit relaxed lockdown, followed by an extended period of strict social distancing as one of the most effective control measures to manage COVID-19 spread is provided for India.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Arvind Kumar Gupta", + "author_inst": "Indian Institute of Technology Ropar" + }, + { + "author_name": "Natasha Sharma", + "author_inst": "Kanya Maha Vidyalaya, Jalandhar" + }, + { + "author_name": "Atul Kumar Verma", + "author_inst": "Indian Institute of Technology, Ropar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089938", "rel_title": "Protocol for a systematic review of qualitative and quantitative effects of cardiovascular disease risk communication using heart age concepts", @@ -1502837,45 +1503201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.04.20090092", - "rel_title": "The intensity of COVID-19 outbreaks is modulated by SARS-CoV-2 free-living survival and environmental transmission", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090092", - "rel_abs": "Variation in free-living, microparasite survival can have a meaningful impact on the ecological dynamics of established and emerging infectious diseases. Nevertheless, resolving the importance of environmental transmission in the ecology of epidemics remains a persistent challenge, requires accurate measuring the free-living survival of pathogens across reservoirs of various kinds, and quantifying the extent to which interaction between hosts and reservoirs generates new infections. These questions are especially salient for emerging pathogens, where sparse and noisy data can obfuscate the relative contribution of different infection routes. In this study, we develop a mechanistic, mathematical model that permits both direct (host-to-host) and indirect (environmental) transmission and then fit this model to empirical data from 17 countries affected by an emerging virus (SARS-CoV-2). From an ecological perspective, our model highlights the potential for environmental transmission to drive complex, non-linear dynamics during infectious disease outbreaks. Summarizing, we propose that fitting such models with environmental transmission to real outbreak data from SARS-CoV-2 transmission highlights that variation in environmental transmission is an underappreciated aspect of the ecology of infectious disease, and an incomplete understanding of its role has consequences for public health interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "C. Brandon Ogbunugafor", - "author_inst": "Brown University" - }, - { - "author_name": "Miles D. Miller-Dickson", - "author_inst": "Brown University" - }, - { - "author_name": "Victor A. Meszaros", - "author_inst": "Brown University" - }, - { - "author_name": "Lourdes M. Gomez", - "author_inst": "Brown University" - }, - { - "author_name": "Anarina L. Murillo", - "author_inst": "Brown University" - }, - { - "author_name": "Samuel V. Scarpino", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.03.20089698", "rel_title": "Social determinants of COVID-19 mortality at the county level", @@ -1503838,6 +1504163,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.06.074039", + "rel_title": "The heterogeneous landscape and early evolution of pathogen-associated CpG and UpA dinucleotides in SARS CoV-2", + "rel_date": "2020-05-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.074039", + "rel_abs": "COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We find that the CpG content, which we characterize by a force parameter that accounts for statistical constraints acting on the genome at the nucleotidic and amino-acid levels, is, on average, low compared to other pathogenic betacoronaviruses. However, the CpG force widely fluctuates along the genome, with a particularly low value, comparable to the circulating seasonal HKU1, in the spike coding region and a greater value, comparable to SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the Zinc finger Anti-viral Protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias and the pressure to lower CpG content.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrea Di Gioacchino", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + }, + { + "author_name": "Petr Sulc", + "author_inst": "Arizona State University" + }, + { + "author_name": "Anastassia V Komarova", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Benjamin D Greenbaum", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Remi Monasson", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + }, + { + "author_name": "Simona Cocco", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.07.082487", "rel_title": "COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection.", @@ -1504494,25 +1504858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20088617", - "rel_title": "A mathematical model to investigate the transmission of COVID-19 in the Kingdom of Saudi Arabia", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088617", - "rel_abs": "Since the first confirmed case of SARS-CoV-2 coronavirus (COVID-19) in the 2nd day of March, Saudi Arabia has not report a quite rapid COVD-19 spread compared to America and many European countries. Possible causes include the spread of asymptomatic cases. To characterize the transmission of COVID-19 in Saudi Arabia, this paper applies a susceptible, exposed, symptomatic, asymptomatic, hospitalized, and recovered dynamical model, along with the official COVID-19 reported data by the Ministry of Health in Saudi Arabia. The basic reproduction number R0 is estimated to range from 2.87 to 4.9.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Fehaid Salem Alshammari", - "author_inst": "Imam Mohammad Ibn Saud Islamic University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.01.20088021", "rel_title": "COVID-19 in Children with Brain-Based Developmental Disabilities: A Rapid Review", @@ -1505208,6 +1505553,109 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.06.080119", + "rel_title": "Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix", + "rel_date": "2020-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.080119", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019 the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of the 21th of April, 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Gabor Kemenesi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Safia Zeghbib", + "author_inst": "University of Pecs" + }, + { + "author_name": "Balazs Somogyi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Gabor E Toth", + "author_inst": "University of Pecs" + }, + { + "author_name": "Krisztian Banyai", + "author_inst": "Centre for Agricultural Research, Hungary" + }, + { + "author_name": "Norbert Solymosi", + "author_inst": "University of Veterinary Medicine Budapest" + }, + { + "author_name": "Peter M Szabo", + "author_inst": "Stromal Biology, Bristol-Myers Squibb, Princeton" + }, + { + "author_name": "Istvan Szabo", + "author_inst": "National Food Safety Office, Budapest" + }, + { + "author_name": "Adam Balint", + "author_inst": "National Food Safety Office, Budapest" + }, + { + "author_name": "Peter Urban", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Robert Herczeg", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Attila Gyenesei", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Agnes Nagy", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Csaba I Pereszlenyi", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gergely Babinszky", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gabor Dudas", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gabriella Terhes", + "author_inst": "Institute of Clinical Microbiology, University of Szeged" + }, + { + "author_name": "Viktor Zoldi", + "author_inst": "Independent researcher, Vantaa, Finland" + }, + { + "author_name": "Robert Lovas", + "author_inst": "Institute for Computer Science and Control, Hungarian Academy of Sciences" + }, + { + "author_name": "Szabolcs Tenczer", + "author_inst": "Institute for Computer Science and Control, Hungarian Academy of Sciences" + }, + { + "author_name": "Laszlo Kornya", + "author_inst": "Central Hospital of Southern Pest, Budapest" + }, + { + "author_name": "Ferenc Jakab", + "author_inst": "University of Pecs" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.05.079202", "rel_title": "Neutralization of SARS-CoV-2 by destruction of the prefusion Spike", @@ -1505812,77 +1506260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.02.20088666", - "rel_title": "Urine Proteome of COVID-19 Patients", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088666", - "rel_abs": "The atypical pneumonia (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic and a serious threat to global public health. The COVID-19 patients with severe symptoms account for a majority of mortality of this disease. However, early detection and effective prediction of patients with mild to severe symptoms remains challenging. In this study, we performed proteomic profiling of urine samples from 32 healthy control individuals and 6 COVID-19 positive patients (3 mild and 3 severe). We found that urine proteome samples from the mild and severe COVID-19 patients with comorbidities can be clearly differentiated from healthy proteome samples based on the clustering analysis. Multiple pathways have been compromised after the COVID-19 infection, including the dysregulation of immune response, complement activation, platelet degranulation, lipoprotein metabolic process and response to hypoxia. We further validated our finding by directly comparing the same patients urine proteome after recovery. This study demonstrates the COVID-19 pathophysiology related molecular alterations could be detected in the urine and the potential application of urinary proteome in auxiliary diagnosis, severity determination and therapy development of COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Yanchang Li", - "author_inst": "Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Yihao Wang", - "author_inst": "Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Huiying Liu", - "author_inst": "The Fifth Medical Center of PLA General Hospital" - }, - { - "author_name": "Wei Sun", - "author_inst": "Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Baoqing Ding", - "author_inst": "Department of Ecology and Evolutionary Biology, University of Connecticut" - }, - { - "author_name": "Yinghua Zhao", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Peiru Chen", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Li Zhu", - "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology" - }, - { - "author_name": "Zhaodi Li", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Naikang Li", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Lei Chang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - }, - { - "author_name": "Hengliang Wang", - "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology" - }, - { - "author_name": "Changqing Bai", - "author_inst": "The Fifth Medical Center of PLA General Hospital" - }, - { - "author_name": "Ping Xu", - "author_inst": "Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.03.20089417", "rel_title": "First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey", @@ -1506778,6 +1507155,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.01.20086801", + "rel_title": "Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20086801", + "rel_abs": "Extensive virological testing is central to SARS-CoV-2 containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combine a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence, and to ratify losses in sensitivity against the time course of individual infections. Using this framework, we show that prevalence can be accurately estimated across four orders of magnitude using only a few dozen pooled tests without the need for individual identification. We then exhaustively evaluate the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many positives compared to individual testing with a given budget. We illustrate how pooling affects sensitivity and overall detection capacity during an epidemic and on each day post infection, finding that sensitivity loss is mainly attributed to individuals sampled at the end of infection when detection for public health containment has minimal benefit. Crucially, we confirm that our theoretical results can be accurately translated into practice using pooled human nasopharyngeal specimens. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect epidemiologically relevant infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brian Cleary", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "James A Hay", + "author_inst": "Harvard T H Chan School of Public Health" + }, + { + "author_name": "Brendan Blumenstiel", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Maegan Harden", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Michelle Cipicchio", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jon Bezney", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Brooke Simonton", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "David Hong", + "author_inst": "Wharton Statistics, University of Pennsylvania" + }, + { + "author_name": "Madikay Senghore", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Abdul K Sesay", + "author_inst": "MRC Unit The Gambia at London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stacey Gabriel", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Aviv Regev", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Michael J Mina", + "author_inst": "Harvard School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20084947", "rel_title": "Voluntary Cyclical Distancing: A potential alternative to constant level mandatory social distancing, relying on an 'infection weather report'", @@ -1507350,25 +1507794,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.01.20087197", - "rel_title": "National and state wise estimate of time varying reproduction number for COVID-19 in India during the nationwide lockdown.", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087197", - "rel_abs": "To understand the effect of nationwide lockdown on transmissibilty of SARS-CoV-2 in India, time varying reproduction number during the first weeks of April, 2020 was estimated. The time varying reproduction number was estimated using EpiEstim package in R programming language. The reproduction number has come down significantly during the lockdown period both at national level and in most states but it wasnt reduced to less than 1. This calls for urgent need for more effective control measures in addition to lockdown to stop the epidemic spread of the virus.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Padmanaban Venkatesan", - "author_inst": "Christian Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.01.20087320", "rel_title": "Correlating Covid-19 mortality and infection levels", @@ -1507980,6 +1508405,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20087833", + "rel_title": "Early Evidence of Disparities in COVID-19 Testing in US Cities", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087833", + "rel_abs": "BackgroundPreliminary evidence has shown inequities in COVID-19 related cases and deaths in the US.\n\nObjectiveWe explored the emergence of spatial inequities in COVID-19 testing, positivity, confirmed cases, and mortality in New York City, Philadelphia, and Chicago during the first six months of the pandemic.\n\nDesignEcological, observational study at the zip code tabulation area (ZCTA) level from March to September 2020.\n\nSettingChicago, New York City and Philadelphia.\n\nParticipantsAll populated ZCTAs in the three cities.\n\nMeasuresOutcomes were ZCTA-level COVID-19 testing, positivity, confirmed cases, and mortality cumulatively through the end of September. Predictors were the CDC social vulnerability index and its four domains, obtained from the 2014-2018 American Community Survey. We examined the spatial autocorrelation of COVID-19 outcomes using global and local Morans I and estimated associations using spatial conditional autoregressive negative binomial models.\n\nResultsWe found spatial clusters of high and low positivity, confirmed cases and mortality, co-located with clusters of low and high social vulnerability. We also found evidence for the existence of spatial inequities in testing, positivity, confirmed cases and mortality for the three cities. Specifically, neighborhoods with higher social vulnerability had lower testing rates, higher positivity ratios, confirmed case rates and mortality rates.\n\nLimitationsZCTAs are imperfect and heterogeneous geographical units of analysis. We rely on surveillance data, which may be incomplete.\n\nConclusionWe found spatial inequities in COVID-19 testing, positivity, confirmed cases, and mortality in three large cities of the US.\n\nRegistrationN/A\n\nFunding sourceNIH (DP5OD26429) and RWJF (77644)", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Usama Bilal", + "author_inst": "Drexel University" + }, + { + "author_name": "Loni P Tabb", + "author_inst": "Drexel University" + }, + { + "author_name": "Sharrelle Barber", + "author_inst": "Drexel University" + }, + { + "author_name": "Ana V Diez-Roux", + "author_inst": "Drexel University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20087460", "rel_title": "Prediction of Spreads of COVID-19 in India from Current Trend", @@ -1508588,105 +1509044,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.02.20087924", - "rel_title": "A strategy for finding people infected with SARS-CoV-2: optimizing pooled testing at low prevalence", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20087924", - "rel_abs": "Suppressing SARS-CoV-2 will likely require the rapid identification and isolation of infected individuals, on an ongoing basis. RT-PCR (reverse transcription polymerase chain reaction) tests are accurate but costly, making regular testing of every individual expensive. The costs are a challenge for all countries and particularly for developing countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups. We propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, uniquely identifies infected individuals in a small number of tests. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof of concept experiments in which a positive subsample was detected even when diluted a hundred-fold with negative subsamples. Using these methods, the costs of mass testing could be reduced by a large factor. If infected individuals are quickly and effectively quarantined, the prevalence will fall and so will the cost of regular, mass testing. Such a strategy provides a possible pathway to the longterm elimination of SARS-CoV-2. Field trials of our approach are now under way in Rwanda.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Leon Mutesa", - "author_inst": "Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda" - }, - { - "author_name": "Pacifique Ndishimye", - "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" - }, - { - "author_name": "Yvan Butera", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Jacob Souopgui", - "author_inst": "Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda" - }, - { - "author_name": "Annette Uwineza", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Robert Rutayisire", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Emile Musoni", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Nadine Rujeni", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Thierry Nyatanyi", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Edouard Ntagwabira", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Muhammed Semakula", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Clarisse Musanabaganwa", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Daniel Nyamwasa", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Maurice Ndashimye", - "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" - }, - { - "author_name": "Eva Ujeneza", - "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" - }, - { - "author_name": "Ivan Emile Mwikarago", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Claude Mambo Muvunyi", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Jean Baptiste Mazarati", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Sabin Nsanzimana", - "author_inst": "Rwanda Joint Task Force COVID-19, Kigali, Rwanda" - }, - { - "author_name": "Neil Turok", - "author_inst": "Perimeter Institute for Theoretical Physics" - }, - { - "author_name": "Wilfred Ndifon", - "author_inst": "African Institute for Mathematical Sciences, Kigali, Rwanda" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.02.20086876", "rel_title": "Ultra-fast and onsite interrogation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in environmental specimens via surface enhanced Raman scattering (SERS)", @@ -1509522,6 +1509879,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084376", + "rel_title": "A novel deterministic forecast model for COVID-19 epidemic based on a single ordinary integro-differential equation", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084376", + "rel_abs": "In this paper we present a new approach to deterministic modelling of COVID-19 epidemic. Our model dynamics is expressed by a single prognostic variable which satisfies an integro-differential equation. All unknown parameters are described with a single, time-dependent variable R(t). We show that our model has similarities to classic compartmental models, such as SIR, and that the variable R(t) can be interpreted as a generalized effective reproduction number. The advantages of our approach are the simplicity of having only one equation, the numerical stability due to an integral formulation and the reliability since the model is formulated in terms of the most trustable statistical data variable: the number of cumulative diagnosed positive cases of COVID-19. Once this dynamic variable is calculated, other non-dynamic variables, such as the number of heavy cases (hospital beds), the number of intensive-care cases (ICUs) and the fatalities, can be derived from it using a similarly stable, integral approach. The formulation with a single equation allows us to calculate from real data the values of the sample effective reproduction number, which can then be fitted. Extrapolated values of R(t) can be used in the model to make reliable forecasts, though under the assumption that measures for reducing infections are maintained. We have applied our model to more than 15 countries and the ongoing results are available on a web-based platform [1]. In this paper, we focus on the data for two exemplary countries, Italy and Germany, and show that the model is capable of reproducing the course of the epidemic in the past and forecasting its course for a period of four to five weeks with a reasonable numerical stability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Felix Koehler-Rieper", + "author_inst": "Goethe-Universtitaet Frankfurt, Germany" + }, + { + "author_name": "Claudius H. F. Roehl", + "author_inst": "Universitaet Leipzig, Germany" + }, + { + "author_name": "Enrico De Micheli", + "author_inst": "IBF - Consiglio Nazionale Delle Ricerche, Genova, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20084384", "rel_title": "A Susceptible-Infected-Removed (SIR) model of COVID-19 epidemic trend in Malaysia under Movement Control Order (MCO) using a data fitting approach", @@ -1510206,49 +1510590,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.01.20086421", - "rel_title": "Characteristics of lymphocyte subsets and their predicting values for the severity of COVID-19 patients", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20086421", - "rel_abs": "Severe COVID-19 patients showed worse clinical outcomes compared to mild and moderate patients. However, effective indicators are still lacking to predict the severity of the disease. In the present study, we retrospectively analyzed the clinical and laboratory data of 16 COVID-19 patients and found that the absolute counts of three T-cells (CD3+, CD4+, and CD8+) were significantly lower in the moderate and severe patients than those in mild patients and were significantly lower in severe patients than in moderate patients on admission. With the recovery of the COVID-19, serum levels of inflammatory biomarkers (CRP, PCT, and IL6) of moderate and severe patients gradually decreased. In contrast, the counts of lymphocytes and their subsets including CD3+, CD4+, and CD8+ T cells gradually increased in severe patients, and eventually showed comparable levels with moderate patients. ROC analysis showed that the counts of CD3+, CD4+, and CD8+ T-cells with AUC > 0.9 have potential values for predicting the severity of COVID-19 patients. In conclusion, the reduction of CD3+, CD4+, and CD8+ T-cells is related to the severity of COVID-19 and dynamic detection of these T-lymphocyte subsets may help predict the outcome of the patients.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jingrong Wang", - "author_inst": "First People's Hospital of Yunnan Province" - }, - { - "author_name": "Xingqi Dong", - "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" - }, - { - "author_name": "Boting Zhang", - "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" - }, - { - "author_name": "Xinping Yang", - "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" - }, - { - "author_name": "Zhi Li", - "author_inst": "First People's Hospital of Yunnan Province" - }, - { - "author_name": "Xicheng Wang", - "author_inst": "Yunnan Provincial Hospital of Infectious Diseases" - }, - { - "author_name": "Shuguang Zuo", - "author_inst": "Kaifeng Kangbien Medical Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.30.20086082", "rel_title": "Probable causes and risk factors for positive SARS-CoV-2 test in recovered patients: Evidence from Brunei Darussalam", @@ -1511080,6 +1511421,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2020.04.30.20086462", + "rel_title": "Kidney Allograft Recipients Diagnosed with Coronavirus Disease-2019: A Single Center Report", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086462", + "rel_abs": "BackgroundOrgan graft recipients receiving immunosuppressive therapy are likely to be at heightened risk for the Coronavirus Disease 2019 (Covid-19) and adverse outcomes including death. It is therefore important to characterize the clinical course and outcome of Covid-19 in this vulnerable population and identify therapeutic strategies that are safe.\n\nMethodsWe performed a retrospective chart review of 54 adult kidney transplant patients diagnosed with Covid-19 and all managed in New York State, the epicenter of Covid-19 pandemic. All 54 patients were evaluated by video visits, or phone interviews, and referred to our Fever Clinic or Emergency Room for respiratory illness symptoms consistent with Covid-19 and admitted if deemed necessary from March 13, 2020 to April 20, 2020. Characteristics of the patients were stratified by hospitalization status and disease severity. Clinical course including alterations in immunosuppressive therapy were retrieved from their electronic medical records. Primary outcomes included recovery from Covid-19 symptoms, acute kidney injury, graft failure, and case fatality rate.\n\nResultsOf the 54 SARS-Cov-2 positive kidney transplant recipients, 39 with moderate to severe symptoms were admitted and 15 with mild symptoms were managed at home. Hospitalized patients compared to non-hospitalized patients were more likely to be male, of Hispanic ethnicity, and to have cardiovascular disease. At baseline, all but 2 were receiving tacrolimus, mycophenolate mofetil (MMF) and 32 were on a steroid free immunosuppression regimen. Tacrolimus dosage was reduced in 46% of hospitalized patients and maintained at baseline level in the non-hospitalized cohort. Mycophenolate mofetil (MMF) dosage was maintained at the baseline dosage in 11% of hospitalized patients and 64% of non-hospitalized patients and was stopped in 61% hospitalized patients and 0% in the non-hospitalized cohort. Azithromycin or doxycycline were prescribed at a similar rate among hospitalized and non-hospitalized patients (38% vs. 40%). In addition, 50% of hospitalized patients were treated for concurrent bacterial infections including pneumonia, urinary tract infections and sepsis. Hydroxychloroquine was prescribed in 79% of hospitalized patients and only one of 15 non-hospitalized patients. Acute kidney injury occurred in 51% of hospitalized patients. Patients with severe disease were more likely to have elevations in inflammatory biomarkers at presentation. At a median of 21 days follow up, 67% of patients have had their symptoms resolved or improved and 33% have persistent symptoms. Graft failure requiring hemodialysis occurred in 3 of 39 hospitalized patients (8%). Three of 39 (8%) hospitalized patients expired and none of the 15 non-hospitalized patients expired.\n\nConclusionsClinical presentation of Covid-19 in kidney transplant recipients was similar to what has been described in the general population. The case fatality rate in our entire cohort of 54 kidney transplant recipients was reassuringly low and patients with mild symptomology could be successfully managed at home. Data from the our study suggest that a strategy of systematic screening and triage to outpatient or inpatient care, close monitoring, early management of concurrent bacterial infections and judicious use of immunosuppressive drugs rather than cessation is beneficial.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michelle Lubetzky", + "author_inst": "New York Presbyterian, Weill Cornell" + }, + { + "author_name": "Meredith Aull", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Rebecca Craig-Shapiro", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Jun Lee", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "John Lee", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Samuel Sultan", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Jehon Marku-Podvorica", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Laura Gingras", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Rosy Priya Kodiyanplakkal", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Choli Hartono", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "Stuart Saal", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "Thangamani Muthukumar", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Sandip Kapur", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Manikkam Suthanthiran", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Darshana Dadhania", + "author_inst": "New York Presbyterian-Weill Cornell" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.04.30.20086447", "rel_title": "Evaluation of effects of public health interventions on COVID-19 transmission for Pakistan: A mathematical simulation study", @@ -1511548,29 +1511964,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.30.20086496", - "rel_title": "Higher virulence of COVID-19 in the air-polluted regions of eight severely affected countries", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086496", - "rel_abs": "COVID-19 has spread in all continents in a span of just over three months, escalating into a pandemic that poses several humanitarian as well as scientific challenges. We here investigated the geographical character of the infection and correlate it with several annual satellite and ground indexes of air quality in: China, the United States, Italy, Iran, France, Spain, Germany, and the United Kingdom. Controlling for population size, we found more viral infections in those areas afflicted by high PM 2.5 and Nitrogen Dioxide values. Higher mortality was also correlated with relatively poor air quality. In Italy, the correspondence between the Po valley pollution and SARS-CoV-2 infections and induced mortality was the starkest, originating right in the most polluted European area. Air pollution appears to be for this disease a risk factor similar to smoking. This suggests the detrimental impact climate change will have on the trajectory of future respiratory epidemics.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Riccardo Pansini", - "author_inst": "Yunnan University of Finance and Economics" - }, - { - "author_name": "Davide Fornacca", - "author_inst": "Dali University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.30.20086884", "rel_title": "Modeling the COVID-19 outbreak in the United States", @@ -1512262,6 +1512655,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.20081828", + "rel_title": "Modeling COVID-19 on a network: super-spreaders, testing and containment", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20081828", + "rel_abs": "To model COVID-19 spread, we use an SEIR agent-based model on a graph, which takes into account several important real-life attributes of COVID-19: super-spreaders, realistic epidemiological parameters of the disease, testing and quarantine policies. We find that mass-testing is much less effective than testing the symptomatic and contact tracing, and some blend of these with social distancing is required to achieve suppression. We also find that the fat tail of the degree distribution matters a lot for epidemic growth, and many standard models do not account for this. Additionally, the average reproduction number for individuals, equivalent in many models to R0, is not an upper bound for the effective reproduction number, R. Even with an expectation of less than one new case per person, our model shows that exponential spread is possible. The parameter which closely predicts growth rate is the ratio between 2nd to 1st moments of the degree distribution. We provide mathematical arguments to argue that certain results of our simulations hold in more general settings.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ofir Reich", + "author_inst": "Google" + }, + { + "author_name": "Guy Shalev", + "author_inst": "Google" + }, + { + "author_name": "Tom Kalvari", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20077594", "rel_title": "Early transmission dynamics and control of COVID-19 in a southern hemisphere setting: Lima-Peru, February 29th-March 30th, 2020 .", @@ -1512990,37 +1513410,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "anesthesia" }, - { - "rel_doi": "10.1101/2020.04.29.20083485", - "rel_title": "Global prediction of unreported SARS-CoV2 infection from observed COVID-19 cases", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20083485", - "rel_abs": "Estimation of infectiousness and fatality of the SARS-CoV-2 virus in the COVID-19 global pandemic is complicated by ascertainment bias resulting from incomplete and non-representative samples of infected individuals. We developed a strategy for overcoming this bias to obtain more plausible estimates of the true values of key epidemiological variables. We fit mechanistic Bayesian latent-variable SIR models to confirmed COVID-19 cases, deaths, and recoveries, for all regions (countries and US states) independently. Bayesian averaging over models, we find that the raw infection incidence rate underestimates the true rate by a factor, the case ascertainment ratio CARt that depends upon region and time. At the regional onset of COVID-19, the predicted global median was 13 infections unreported for each case confirmed (CARt = 0.07 C.I. (0.02, 0.4)). As the infection spread, the median CARt rose to 9 unreported cases for every one diagnosed as of April 15, 2020 (CARt = 0.1 C.I. (0.02, 0.5)). We also estimate that the median global initial reproduction number R0 is 3.3 (C.I (1.5, 8.3)) and the total infection fatality rate near the onset is 0.17% (C.I. (0.05%, 0.9%)). However the time-dependent reproduction number Rt and infection fatality rate as of April 15 were 1.2 (C.I. (0.6, 2.5)) and 0.8% (C.I. (0.2%,4%)), respectively. We find that there is great variability between country- and state-level values. Our estimates are consistent with recent serological estimates of cumulative infections for the state of New York, but inconsistent with claims that very large fractions of the population have already been infected in most other regions. For most regions, our estimates imply a great deal of uncertainty about the current state and trajectory of the epidemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Carson C Chow", - "author_inst": "NIDDK, National Institutes of Health" - }, - { - "author_name": "Joshua C Chang", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Richard C Gerkin", - "author_inst": "Arizona State University" - }, - { - "author_name": "Shashaank Vattikuti", - "author_inst": "NIDDK, National Institutes of Healthj" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.28.20083782", "rel_title": "A Method to Identify the Missing COVID-19 Cases in the U.S. and Results for mid-April 2020", @@ -1513924,6 +1514313,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084244", + "rel_title": "Are COVID-19 infected children with gastrointestinal symptoms different from those without symptoms? A comparative study of the clinical characteristics and epidemiological trend of 244 pediatric cases from Wuhan", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084244", + "rel_abs": "ObjectiveCOVID-19 patients presenting with gastrointestinal (GI) symptoms occur in both adults and children. To date, however, no large sample size study focusing on gastrointestinal symptoms in pediatric cases has been published. We analyzed COVID-19 infected children in Wuhan who presented with initial GI symptoms to determine the GI characteristics and epidemiological trend of the disease.\n\nDesignWe retrospectively analyzed 244 children patients confirmed with COVID-19 at Wuhan Childrens Hospital from 21 Jan to 20 Mar 2020. Symptomatic cases were divided into two groups according to whether the patients presented with or without GI symptoms on admission. Demographic, epidemiological, symptoms, and laboratory data were compared. We also analyzed the respective trends of case number changes of GI cases and asymptomatic cases.\n\nResults34 out of 193 symptomatic children had GI symptoms. They had lower median age and weight, a higher rate of fever, a longer length of stay and more hematological and biochemical abnormalities than patients without GI symptoms. There was no significant difference in chest CT findings or stool SARS-CoV-2 test positive percentages between the two groups. The number of patients admitted with GI symptoms showed an overall downward trend with time. At the time of writing, 242 patients were discharged, one died, and one critically ill patient was still in the intensive care unit.\n\nConclusionCOVID-19 infected children with GI symptoms are prone to presenting with more clinical and laboratory abnormalities than patients without GI symptoms. More attention and timely hospital admission are needed for these patients.\n\nSignificance of this studyO_LSTWhat is already known on this subject?C_LSTO_LICOVID-19 is now a pandemic with more than 1.6 million people infected worldwide\nC_LIO_LIAlthough attacking the respiratory tract mostly, both adult and children infected with COVID-19 can present with GI symptoms\nC_LI\n\nO_LSTWhat are the new findings?C_LSTO_LIInfants younger than two years old and presence of fever are the two risk factors of presenting with GI symptoms\nC_LIO_LIA high proportion of patients without GI symptoms and asymptomatic patients will have positive RT-PCR for the virus in stool\nC_LIO_LIEarlier testing through contact screening of family members means more COVID-19 infected children are diagnosed when completely asymptomatic\nC_LI\n\nO_LSTHow might it impact on clinical practice in the foreseeable future?C_LSTO_LIThe presence of COVID-19 in stool in infected children will have a major implication for parents and carers of young infants\nC_LIO_LIIncreasing number of asymptomatic COVID-19 patients who are detected through screening could provide a useful lesson for other countries still experiencing the rise and peak of the pandemic\nC_LI", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Xiaoli Xiong", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Kenenth Kak-Yuen Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Shuiqing Chi", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Aifen Zhou", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Jianqiao Tang", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Lishan Zhou", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Patrick Ho-yu Chung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Gilbert Chua", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Keith TS Tung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ian CK Wong", + "author_inst": "The Univeristy of Hong Kong" + }, + { + "author_name": "Celine SL Chui", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Xue Li", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Mike Yat-wah Kwan", + "author_inst": "Princess Margaret Hospital, Hong Kong" + }, + { + "author_name": "Wilfred HS Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Marco Hok-kung Ho", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Godfrey CF Chan", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Guoqing Cao", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Kang Li", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Patrick Ip", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Peng Chen", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Shaotao Tang", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Paul KH Tam", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.04.30.20083881", "rel_title": "Associations between psychiatric disorders, COVID-19 testing probability and COVID-19 testing results: Findings from a population-based study", @@ -1514536,49 +1515028,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.28.20075523", - "rel_title": "Detection of SARS-CoV-2 in Human Breast Milk", - "rel_date": "2020-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20075523", - "rel_abs": "SARS-CoV-2 (CoV-2) is mainly transmitted in the human population during close contact and respiratory droplets. It is currently unclear, however, whether CoV-2 is shed into milk and may also be transmitted from infected mothers to newborns trough breast feeding. Two recent reviews on the topic (1,2) did not find evidence for CoV-2 in human milk. However, the number of breast milk samples analyzed so far is small and samples were taken only once from each mother (2).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "R\u00fcdiger Gro\u00df", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Carina Conzelmann", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Janis M\u00fcller", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Steffen Stenger", - "author_inst": "Institute for Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Karin Steinhart", - "author_inst": "Administrative District Heidenheim, Public Health Office, Heidenheim, Germany" - }, - { - "author_name": "Frank Kirchhoff", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - }, - { - "author_name": "Jan M\u00fcnch", - "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20077602", "rel_title": "Commercial stocks of SARS-CoV-2 RNA may report low concentration values, leading to artificially increased apparent sensitivity of diagnostic assays", @@ -1515670,6 +1516119,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.03.073080", + "rel_title": "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication", + "rel_date": "2020-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.073080", + "rel_abs": "The COVID-19 pandemic, attributed to the SARS-CoV-2 coronavirus infection, resulted in millions infected worldwide and an immediate need for antiviral treatments. The main protease (Mpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide and subsequent viral replication. Feline infectious peritonitis, a fatal infection in cats caused by a coronavirus, was successfully treated previously with a dipeptide-based protease inhibitor. Here we show this drug, GC376, and its analog GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of the SARS-CoV and SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 in cell culture, with EC50 values near one micromolar and little to no toxicity. These protease inhibitors are soluble, non-toxic, and bind reversibly. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals (cats). The work here lays the framework for their use in human trials for the treatment of COVID-19.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wayne Vuong", + "author_inst": "University of Alberta" + }, + { + "author_name": "Muhammad Bashir Khan", + "author_inst": "University of Alberta" + }, + { + "author_name": "Conrad Fischer", + "author_inst": "University of Alberta" + }, + { + "author_name": "Elena Arutyunova", + "author_inst": "University of Alberta" + }, + { + "author_name": "Tess Lamer", + "author_inst": "University of Alberta" + }, + { + "author_name": "Justin Shields", + "author_inst": "University of Alberta" + }, + { + "author_name": "Holly A Saffran", + "author_inst": "University of Alberta" + }, + { + "author_name": "Ryan T McKay", + "author_inst": "University of Alberta" + }, + { + "author_name": "Marco J van Belkum", + "author_inst": "University of Alberta" + }, + { + "author_name": "Michael Joyce", + "author_inst": "University of Alberta" + }, + { + "author_name": "Howard S Young", + "author_inst": "University of Alberta" + }, + { + "author_name": "D. Lorne Tyrrell", + "author_inst": "University of Alberta" + }, + { + "author_name": "John C Vederas", + "author_inst": "University of Alberta" + }, + { + "author_name": "M Joanne Lemieux", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.05.02.043554", "rel_title": "Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease", @@ -1516446,29 +1516966,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20081398", - "rel_title": "Estimation of SARS-CoV-2 emissions from non-symptomatic cases", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081398", - "rel_abs": "ImportanceCases of the coronavirus disease 2019 (COVID-19) with no or mild symptoms were reported to frequently transmit the disease even without direct contact. The severe acute respiratory syndrome virus (SARS-COV-2) was found at very high concentrations in swab and sputum of such cases.\n\nObjectiveWe aimed to estimate in a mathematical modeling study the virus release from such cases into different aerosol sizes by normal breathing and coughing, and what exposure can result from this in a room shared with such as case.\n\nData Sources and ModelWe combined the size-distribution of exhaled breath microdroplets for coughing and normal breathing with viral sputum concentrations as approximation for lung lining liquid to obtain an estimate of emitted virus levels. The resulting emission data fed a single-compartment model of airborne concentrations in a room of 50 m3, the size of a small office or medical exam room.\n\nResultsThe estimated viral load in microdroplets emitted by simulated patients while breathing normally was on typical 0.0000049 copies/cm3 and could go up to 0.637 copies/cm3. The corresponding numbers for coughing simulated patients were 0.277 copies/cm3 and 36,030/cm3, respectively, per cough. The resulting concentrations in a room with a coughing emitter were always very high, up to 7.44 million copies/m3. However, also regular breathing microdroplets from high emitters was modelled to lead to 1248 copies/m3.\n\nConclusions and RelevanceIn this modelling study, breathing and coughing were estimated to release large numbers of viruses, ranging from thousands to millions of virus copies/m3 in a room with an emitter having a high viral load, depending on ventilation and microdroplet formation process. These findings suggest that strict respiratory protection may be needed when there is a chance to be in the same room with a patient - whether symptomatic or not - especially for a prolonged time.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow much SARS-CoV-2 virus is released from a case by breathing and coughing, and what is the resulting concentration in a room?\n\nFindingIn this mathematical modelling study, both, breathing and coughing were estimated to release large numbers of viruses, which can lead to millions of virus copies/m3 in a poorly ventilated room with a coughing emitter.\n\nMeaningThese results may explain the important rate of transmissions and implies the need for strict respiratory protection when people are in the same room with a case with COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Michael Riediker", - "author_inst": "Swiss Centre for Occupational and Environmental Health" - }, - { - "author_name": "Dai-Hua Tsai", - "author_inst": "Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.04.27.20081372", "rel_title": "How Social Media and 3D Printing Tackles the PPE Shortage during Covid - 19 Pandemic", @@ -1517384,6 +1517881,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.04.27.20081794", + "rel_title": "Predicting community mortality risk due to CoVID-19 using machine learning and development of a prediction tool", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081794", + "rel_abs": "BackgroundThe recent pandemic of CoVID-19 has emerged as a threat to global health security. There are a very few prognostic models on CoVID-19 using machine learning.\n\nObjectivesTo predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making.\n\nMaterials and methodsMortality for confirmed CoVID-19 patients (n=3,299) between January 20, 2020 and April 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). Performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool.\n\nResultsThe random forest algorithm was the best performer in terms of predictive ability (accuracy=0.981), discrimination (area under ROC curve=0.886), calibration (Matthews Correlation Coefficient=0.459; Brier Score=0.063) and. The best performer algorithm (random forest) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP (https://ashis-das.shinyapps.io/CoCoMoRP/).\n\nConclusionsWe describe the development and deployment of an open-source machine learning tool to predict mortality risk among CoVID-19 confirmed patients using publicly available surveillance data. This tool can be utilized by potential stakeholders such as health providers and policy makers to triage patients at the community level in addition to other approaches.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "ASHIS DAS", + "author_inst": "The World Bank" + }, + { + "author_name": "Shiba Mishra", + "author_inst": "Credit Suisse Private Limited" + }, + { + "author_name": "Saji Saraswathy Gopalan", + "author_inst": "The World Bank Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.27.20081539", "rel_title": "An ARIMA Model to Forecast the Spread and the Final Size of COVID-2019 Epidemic in Italy", @@ -1518472,25 +1518996,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20081752", - "rel_title": "Variation among states in rate of coronavirus spread", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081752", - "rel_abs": "The corona virus, COVID-19, has been spreading rapidly across the USA since early March, but at a decreasing rate, where the rate r is defined as the exponential increase. I modeled the way the rate of increase y = log(exp(r)-1) has declined through time in each of the 51 states with the goal of determining whether state-at-home orders correlate with reductions in the rate of spread of the virus. A piecewise linear regression was used, with a single break point. This model can identify whether there was a change in the rate of decline, when the change happened, and which states have shown the greatest improvement in reducing the spread of COVID-19. The piecewise model identified a significant breakpoint on 24 Mar for all states combined, and all states had nearly the same breakpoint. Prior to 24 Mar, the average change in y was -0.013 per day, meaning a reduction in the rate of spread from 23.5 pct. per day to 19.5 pct. per day; after 24 Mar, the average change in y was -0.070 per day, a reduction from 19.5 pct. per day to 7.5 pct. per day. Prior to 24 Mar there was no significant variation among states in the decline in y, but after 24 Mar there was substantial variation, and the date on which states issued stay at home orders correlated with that variation. Montana, Idaho, and Vermont showed the greatest improvement, while Nebraska, South Dakota, and Iowa the least. The improvement as measured by the reduction after 24 Mar did not correlate with case density in a state, nor state population.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Richard Condit", - "author_inst": "Retired" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.27.20081737", "rel_title": "COVID-19 spreading in Rio de Janeiro, Brazil: do the policies of social isolation really work?", @@ -1519258,6 +1519763,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20081893", + "rel_title": "Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081893", + "rel_abs": "Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as \"frailty variation\". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being critical to protect vulnerable individuals from severe outcomes as the virus becomes endemic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC=\"FIGDIR/small/20081893v5_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@aeb87forg.highwire.dtl.DTLVardef@d2c441org.highwire.dtl.DTLVardef@152aeceorg.highwire.dtl.DTLVardef@1526779_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVariation in susceptibility/exposure responds to selection by natural infection\nC_LIO_LISelection on susceptibility/exposure flattens epidemic curves\nC_LIO_LIModels with incomplete heterogeneity overestimate intervention impacts\nC_LIO_LIIndividual variation lowered the natural herd immunity threshold for SARS-CoV-2\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "M. Gabriela M. Gomes", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Marcelo U. Ferreira", + "author_inst": "Universidade de Sao Paulo, Brazil" + }, + { + "author_name": "Rodrigo M. Corder", + "author_inst": "Universidade de Sao Paulo, Brazil" + }, + { + "author_name": "Jessica G. King", + "author_inst": "University of Edinburgh, UK" + }, + { + "author_name": "Caetano Souto-Maior", + "author_inst": "National Institutes of Health, USA" + }, + { + "author_name": "Carlos Penha-Goncalves", + "author_inst": "Instituto Gulbenkian de Ciencia, Portugal" + }, + { + "author_name": "Guilherme Goncalves", + "author_inst": "Universidade do Porto, Portugal" + }, + { + "author_name": "Maria Chikina", + "author_inst": "University of Pittsburgh, USA" + }, + { + "author_name": "Wesley Pegden", + "author_inst": "Carnegie Mellon University, USA" + }, + { + "author_name": "Ricardo Aguas", + "author_inst": "University of Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20074849", "rel_title": "Performance verification of detecting COVID-19 specific antibody by using four chemiluminescence immunoassay systems", @@ -1519874,37 +1520434,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.04.28.20083667", - "rel_title": "Geographical identification of the vulnerable groups during COVID-19 crisis: the typhoon eye effect and its boundary conditions", - "rel_date": "2020-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083667", - "rel_abs": "AimAlthough some studies suggest the coronavirus disease (COVID-19) is associated with negative consequences on physical health, our knowledge about the detrimental effects of COVID-19 on peoples mental health is still nascent. This study uses typhoon eye theory to offer insights in helping clinical psychiatrists to screen people with well-being issues during COVID-19 outbreak.\n\nMethodsWe collected survey data from working adults across different geographical areas in China on 20 and 21 February 2020 during the outbreak of COVID-19. The sample contains 308 working adults, who were in various parts of China, with varying distance to the epicenter of Wuhan.\n\nResultsIndividual adults distance to the epicenter was negatively associated with life satisfaction ({beta} = -0.235, 95% CI -0.450 to -0.020, p = 0.032). This association between distance and life satisfaction was significant only for adults who were young or had smaller family sizes. For example, the negative relationship was strongest when the individuals were in the age bracket of 20 years old (15.7%; {beta} = -0.703, 95% CI -1.098 to -0.307; p = 0.001) and single (32.3%; {beta} = -0.767, 95% CI -1.125 to -0.408; p < 0.001).\n\nConclusionOur results that peoples well-being deteriorates by the distance from the epicenter for specific groups of people help guide mental healthcare providers towards the regions that are further away from the epicenter in the ongoing COVID-19 outbreak. Meanwhile, our results indicate the practitioners should be cautious of using typhoon eye effect for individuals who were older or had a larger family size.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Pok Man Tang", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Stephen X. Zhang", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Chi Hon Li", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Feng Wei", - "author_inst": "Tongji University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.29.20084798", "rel_title": "Act early, save lives: managing COVID-19 in Greece", @@ -1520836,6 +1521365,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.28.20083089", + "rel_title": "A possible role of immunopathogenesis in COVID-19 progression", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083089", + "rel_abs": "BackgroundThe role of cellular immunity in pathogenesis of COVID-19 is unclear and conflicting data points to insufficient or pathogenic immunity as drivers of COVID-19 progression. Here we aimed to delineate the phenotype and function of the immune system in patients with moderate, severe, and critical COVID-19.\n\nMethodsIn this prospective study, we included 53 patients with moderate (n=21), severe (n=18), and critical (n=14) COVID-19 manifestations. Using multiparametric flow cytometry we compared quantitative, phenotypic, and functional characteristics of circulating immune cells, SARS-CoV-2 antigen-reactive T-cells, and humoral immunity.\n\nResultsDeep phenotypic profiling revealed a depletion of circulating bulk CD8+ T-cells, CD4+ and CD8+ T-cell subsets with activated memory/effector T-cells expressing CD57+, HLA-DR+, and the key activation and migration molecule CD11a++ in critical COVID-19. Importantly, survival from acute respiratory distress syndrome was accompanied by a recovery of the depleted CD11++ T-cell subsets including T-cells expressing CD28, CD57, HLA-DR activation/effector molecules. We further observed a stronger response of S-protein specific T-cells producing inflammatory cytokines in critical COVID-19 cases. This seemingly contradictory observation is in fact confirmation of the underlying immunopathogenesis in patients with critical COVID-19.\n\nConclusionOur findings suggest a CD11a-based immune signature as a possible prognostic marker for disease development. Our data further reveal that increased rather than decreased SARS-CoV-2 specific T cell immunity is associated with adverse outcome in COVID-19. Tissue migration of activated effectors T-cells may constitute a crucial cornerstone in the immunopathogenesis of SARS-CoV-2 associated tissue injury.\n\nTrial registrationThis is a prospective observational study without a trial registration number.\n\nFundingThis work was supported by grants from Mercator Foundation, the BMBF e:KID (01ZX1612A), and BMBF NoChro (FKZ 13GW0338B).\n\n25 Word summaryStronger S-protein reactivity and decreased frequency of activated memory/effector T-cells expressing CD11a++ suggests immunopathogenesis in critical COVID-19 mediated by tissue migration of activated effector T-cells.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Moritz Anft", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Krystallenia Paniskaki", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Arturo Blazquez-Navarro", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Adrian Atila Nicolas Doevelaar", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Felix Seibert", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Bodo Hoelzer", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Sarah Skrzypczyk", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Eva Kohut", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Julia Kurek", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Jan Zapka", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Patrizia Wehler", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Sviatlana Kaliszczyk", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Sharon Bajda", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Constantin Thieme", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Toralf Roch", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Margarethe Justine Konik", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Thorsten Brenner", + "author_inst": "Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Clemens Tempfer", + "author_inst": "Department of Gynecology and Obstetrics, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Hoelkeskampring 40, 44625 Herne, Germany" + }, + { + "author_name": "Carsten Watzl", + "author_inst": "Department of Immunology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund (IfADo), Ardeystrasse 67, 44139" + }, + { + "author_name": "Sebastian Dolff", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Ulf Dittmer", + "author_inst": "Germany Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Timm Westhoff", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Oliver Witzke", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Ulrik Stervbo", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Nina Babel", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.04.26.20080341", "rel_title": "How the COVID-19 pandemic is favoring the adoption of digital technologies in healthcare: a rapid literature review", @@ -1521536,97 +1522180,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.04.26.20073569", - "rel_title": "Regressing SARS-CoV-2 sewage measurements onto COVID-19 burden in the population: a proof-of-concept for quantitative environmental surveillance", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20073569", - "rel_abs": "SARS-CoV-2 is an RNA virus, a member of the coronavirus family of respiratory viruses that includes SARS-CoV-1 and MERS. COVID-19, the clinical syndrome caused by SARSCoV-2, has evolved into a global pandemic with more than 2,900,000 people infected. It has had an acute and dramatic impact on health care systems, economies, and societies of affected countries within these few months. Widespread testing and tracing efforts are employed in many countries in order to contain and mitigate this pandemic. Recent data has indicated that fecal shedding of SARS-CoV-2 is common, and that the virus can be detected in wastewater. This indicates that wastewater monitoring is a potentially efficient tool for epidemiological surveillance of SARS-CoV-2 infection in large populations at relevant scales. Collecting raw sewage data, representing specific districts, and crosslinking this data with the number of infected people from each location, will enable us to derive and provide quantitative surveillance tools. In particular, this will provide important means to (i) estimate the extent of outbreaks and their spatial distributions, based primarily on in-sewer measurements (ii) manage the early-warning system quantitatively and efficiently (and similarly, verify disease elimination). Here we report the development of a virus concentration method using PEG or alum, providing an important a tool for detection of SARS-CoV-2 RNA in sewage and relating it to the local populations and geographic information. This will provide a proof of concept for the use of sewage associated virus data as a reliable epidemiological tool.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Itay Bar Or", - "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" - }, - { - "author_name": "Karin Yaniv", - "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel." - }, - { - "author_name": "Marilou Shagan", - "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel." - }, - { - "author_name": "Eden Ozer", - "author_inst": "Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel" - }, - { - "author_name": "Oran Erster", - "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel and School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, " - }, - { - "author_name": "Batya Mannasse", - "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" - }, - { - "author_name": "Rachel Shirazi", - "author_inst": "Central virology lab, Ministry of health, Sheba medical center, Israel" - }, - { - "author_name": "Esti Kramarsky-Winter", - "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel." - }, - { - "author_name": "Oded Nir", - "author_inst": "Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boker, 84990, Israel" - }, - { - "author_name": "Hala Abu-Ali", - "author_inst": "Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boker, 84990, Israel" - }, - { - "author_name": "Zeev Ronen", - "author_inst": "Zuckerberg Institute for Water Research (ZIWR), Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boker, 84990, Israel" - }, - { - "author_name": "Ehud Rinott", - "author_inst": "Faculty of Health Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel" - }, - { - "author_name": "Yair E. Lewis", - "author_inst": "Faculty of Medicine, Technion-Israel Institute of Technology, Israel" - }, - { - "author_name": "Eran Friedler Friedler", - "author_inst": "Faculty of Civ. and Env. Eng., Technion-Israel Inst. of Technology; Haifa 32000, Israel" - }, - { - "author_name": "Yossi Paitan", - "author_inst": "Clinical Microbiology Laboratory, Meir Medical Center, 44282, Kfar Saba, Israel and Department of Clinical Microbiology and Immunology, Sackler Faculty of Medic" - }, - { - "author_name": "Eden Bitkover", - "author_inst": "Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel" - }, - { - "author_name": "Yakir Berchenko", - "author_inst": "Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel" - }, - { - "author_name": "Ariel Kushmaro", - "author_inst": "Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel and The Ilse Katz Center for M" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.27.20070466", "rel_title": "Correlation analysis of risk factors and GSI score of a medical team assisting Wuhan city during the epidemic of COVID-19 in China -A cohort study", @@ -1522406,6 +1522959,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.26.20080770", + "rel_title": "A first study on the impact of containment measure on COVID-19 spread in Morocco", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080770", + "rel_abs": "BackgroundSince the appearance of the first case of COVID-19 in Morocco, the cumulative number of reported infectious cases continues to increase and, consequently, the government imposed the containment measure within the country. Our aim is to predict the impact of the compulsory containment on COVID-19 spread. Earlier knowledge of the epidemic characteristics of COVID-19 transmission related to Morocco will be of great interest to establish an optimal plan-of-action to control the epidemic.\n\nMethodUsing a Susceptible-Asymptomatic-Infectious model and the data of reported cumulative confirmed cases in Morocco from March 2nd to April 9, 2020, we determined the basic and control reproduction numbers and we estimated the model parameter values. Furthermore, simulations of different scenarios of containment are performed.\n\nResultsEpidemic characteristics are predicted according to different rates of containment. The basic reproduction number is estimated to be 2.9949, with CI(2.6729-3.1485). Furthermore, a threshold value of containment rate, below which the epidemic duration is postponed, is determined.\n\nConclusionOur findings show that the basic reproduction number reflects a high speed of spread of the epidemic. Furthermore, the compulsory containment can be efficient if more than 73% of population are confined. However, even with 90% of containment, the end-time is estimated to happen on July 4th which can be harmful and lead to consequent social-economic damages. Thus, containment need to be accompanied by other measures such as mass testing to reduce the size of asymptomatic population. Indeed, our sensitivity analysis investigation shows that the COVID-19 dynamics depends strongly on the asymptomatic duration as well as the contact and containment rates. Our results can help the Moroccan government to anticipate the spread of COVID-19 and avoid human loses and consequent social-economic damages as well.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Aayah Hammoumi", + "author_inst": "Cadi Ayyad University" + }, + { + "author_name": "Redouane Qesmi", + "author_inst": "USMBA University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20076000", "rel_title": "The effect of a national lockdown in response to COVID-19 pandemic on the prevalence of clinical symptoms in the population", @@ -1522910,57 +1523486,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.28.20080671", - "rel_title": "Protective elements of mental health status during the COVID-19 outbreak in the Portuguese population", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20080671", - "rel_abs": "The outbreak of COVID-19 might produce dramatic psychological effects on the individuals life. In this study, we aimed to explore the elements that may reduce the negative effects on mental health of the quarantine period imposed by most governments during this worldwide crisis. We conducted an online survey to evaluate demographic, lifestyle and mental health variables in the Portuguese population. We observed that factors related with living conditions, maintaining the work either online or in the workplace, frequency of exercise and absence of a previous psychological or physic disorders are protective features of psychological well-being (anxiety, depression, stress and obsessive-compulsive symptoms). Finally, the individuals previously receiving psychotherapeutic support exhibited better psychological indicators if they did not interrupt the process as a consequence of the outbreak. Our results indicate that the practice of physical exercise, reduced consumption of COVID-19 information and the implementation of remote mental healthcare measures might prevent larger impacts on mental health during the COVID-19 outbreak.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Pedro Silva Moreira", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho. Psychological Neuroscience Lab, CIPsi, School of Psychology, Unive" - }, - { - "author_name": "Sonia Ferreira", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Beatriz Couto", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Mafalda Machado-Sousa", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Marcos Fernandez", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Catarina Raposo-Lima", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Nuno Sousa", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Maria Pico-Perez", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - }, - { - "author_name": "Pedro Morgado", - "author_inst": "Life and Health Sciences Research Institute (ICVS), School of Medicine - University of Minho" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.26.20080614", "rel_title": "Spread of virus during soccer matches", @@ -1523652,6 +1524177,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.069922", + "rel_title": "Broad-spectrum antiviral activity of naproxen: from Influenza A to SARS-CoV-2 Coronavirus", + "rel_date": "2020-05-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.069922", + "rel_abs": "There is an urgent need for specific antiviral drugs directed against SARS-CoV-2 both to prevent the most severe forms of COVID-19 and to reduce viral excretion and subsequent virus dissemination; in the present pandemic context, drug repurposing is a priority. Targeting the nucleoprotein N of the SARS-CoV-2 coronavirus in order to inhibit its association with viral RNA could be a strategy to impeding viral replication and possibly other essential functions associated with viral N. The antiviral properties of naproxen, belonging to the NSAID family, previously demonstrated against Influenza A virus, were evaluated against SARS-CoV-2. Naproxen binding to the nucleoprotein of SARS-CoV2 was shown by molecular modeling. In VeroE6 cells and reconstituted human primary respiratory epithelium models of SARS-CoV-2 infection, naproxen inhibited viral replication and protected the bronchial epithelia against SARS-CoV-2 induced-damage. The benefit of naproxen addition to the standard of care is tested in an on-going clinical study.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Olivier Terrier", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Sebastien Dilly", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Mario-Andres Pizzorno", + "author_inst": "Lyon I University, CIRI, INSERM 1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Julien Henri", + "author_inst": "Institut de Biologie Physico-Chimique CNRS UMR 8226" + }, + { + "author_name": "Francis Berenbaum", + "author_inst": "Sorbonne University, INSERM, CRSA UMR S_938, AP-HP" + }, + { + "author_name": "Bruno Lina", + "author_inst": "Lyon I University, CIRI, INSERM U 1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Bruno Feve", + "author_inst": "INSERM and Sorbonne Universitu CRSA UMR S_938, AP-HP, ICAN" + }, + { + "author_name": "Frederic Adnet", + "author_inst": "AP-HP, SAMU, Avicenne Hospital" + }, + { + "author_name": "Michele Sabbah", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Manuel Rosa-Calavatra", + "author_inst": "University Lyon I, CIRI, INSERM U1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Vincent Marechal", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Anny Slama-Schwok", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.30.071175", "rel_title": "Electrostatic Characteristics of SARS-CoV-2 Spike and Human ACE2 Protein Variations Predict Mutable Binding Efficacy", @@ -1524300,25 +1524888,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.01.072330", - "rel_title": "Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses - causes and consequences for their short and long evolutionary trajectories", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.072330", - "rel_abs": "The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3x10-4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5U/A and 3U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts.\n\nImportanceThe evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Peter Simmonds", - "author_inst": "Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK." - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.28.20083055", "rel_title": "A comparison of health care worker-collected foam and polyester nasal swabs in convalescent COVID-19 patients", @@ -1525150,6 +1525719,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.27.20078329", + "rel_title": "Population-scale testing can suppress the spread of COVID-19", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20078329", + "rel_abs": "We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) self-quarantine of infected individuals. Using a standard epidemiological model (SIR), we show here that by identification and isolation of the majority of infectious individuals, including those who may be asymptomatic, the reproduction number R0 of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. We replicate these observations in a more complex stochastic dynamic model on a social network graph. We also find that the testing regime would be additive to other interventions, and be effective at any level of prevalence. If adopted as a policy, any industrial society could sustain the regime for as long as it takes to find a safe and effective cure or vaccine. Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Testing at the required scale would be feasible if existing qPCR-based methods are scaled up and multiplexed. A mass produced, low throughput field test kit could also be carried out at home. Economic analysis also supports the feasibility of the approach: current reagent costs for tests are in the range of a dollar or less, and the estimated benefits for population-scale testing are so large that the policy would be cost-effective even if the costs were larger by more than two orders of magnitude. To identify both active and previous infections, both viral RNA and antibodies could be tested. All technologies to build such test kits, and to produce them in the scale required to test the entire worlds population exist already. Integrating them, scaling up production, and implementing the testing regime will require resources and planning, but at a scale that is very small compared to the effort that every nation would devote to defending itself against a more traditional foe.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jussi Taipale", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Paul Romer", + "author_inst": "New York University" + }, + { + "author_name": "Sten Linnarsson", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.24.20078717", "rel_title": "Full lockdown policies in Western Europe countries have no evident impacts on the COVID-19 epidemic.", @@ -1525694,37 +1526290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20079673", - "rel_title": "COVID-19 Control Strategies and Intervention Effects in Resource Limited Settings: A Modeling Study", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20079673", - "rel_abs": "BackgroundMany countries with weaker health systems are struggling to put together a coherent strategy against the COVID-19 epidemic. We explored COVID-19 control strategies that could offer the greatest benefit in resource limited settings.\n\nMethodsUsing an age-structured SEIR model, we explored the effects of COVID-19 control interventions--a lockdown, physical distancing measures, and active case finding (testing and isolation, contact tracing and quarantine)-- implemented individually and in combination to control a hypothetical COVID-19 epidemic in Kathmandu (population 2.6 million), Nepal.\n\nResultsA month-long lockdown that is currently in place in Nepal will delay peak demand for hospital beds by 36 days, as compared to a base scenario of no interventions (peak demand at 108 days (Inter-Quartile Range IQR 97-119); a 2 month long lockdown will delay it by 74 days, without any difference in annual mortality, or healthcare demand volume. Year-long physical distancing measures will reduce peak demand to 36% (IQR 23%-46%) and annual morality to 67% (IQR 48%-77%) of base scenario. Following a month long lockdown with ongoing physical distancing measures and an active case finding intervention that detects 5% of the daily infection burden could reduce projected morality and peak demand by more than 99%.\n\nInterpretationLimited resources settings are best served by a combination of early and aggressive case finding with ongoing physical distancing measures to control the COVID-19 epidemic. A lockdown may be helpful until combination interventions can be put in place but is unlikely to reduce annual mortality or healthcare demand.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kiran Raj Pandey", - "author_inst": "Hospital for Advanced Medicine and Surgery" - }, - { - "author_name": "Anup Subedee", - "author_inst": "Hospital for Advanced Medicine and Surgery" - }, - { - "author_name": "Bishesh Khanal", - "author_inst": "Nepal Applied Mathematics and Informatics Institute for Research" - }, - { - "author_name": "Bhagawan Koirala", - "author_inst": "Hospital for Advanced Medicine and Surgery" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.25.20079905", "rel_title": "Informative Ranking of Stand Out Collections of Symptoms: A New Data-Driven Approach to Identify the Strong Warning Signs of COVID 19", @@ -1526352,6 +1526917,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.29.069054", + "rel_title": "Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2", + "rel_date": "2020-04-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.069054", + "rel_abs": "We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "S. Gnana Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Heyjin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Werner Abfalterer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Brian Foley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Elena E Giorgi", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Tanmoy Bhattacharya", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Matthew D Parker", + "author_inst": "The University of Sheffield" + }, + { + "author_name": "David G Partridge", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Cariad M Evans", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Thushan de Silva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Celia C LaBranche", + "author_inst": "Duke Univerisity" + }, + { + "author_name": "David C Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "- Sheffield COVID-19 Genomics Group", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.04.30.029736", "rel_title": "Susceptibility of tree shrew to SARS-CoV-2 infection", @@ -1527016,29 +1527660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.24.20077966", - "rel_title": "Sequential informed pooling approach to detect SARS-CoV2 infection", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20077966", - "rel_abs": "The alarming spread of the pandemic coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus is requiring several measures to reduce the risk of contagion. Every successful strategy in controlling SARS-CoV2 infection depends on the timely viral diagnosis which should include asymptomatic carriers. Consequently, strategies to increase the throughput for clinical laboratories to conduct large-scale diagnostic testing are urgently needed. Here we support the hypothesis that standard diagnostic protocol for SARS-CoV-2 virus could be conveniently applied to pooled samples obtained from different subjects. We suggest that a two-step sequential pooling procedure could identify positive subjects, ensuring at the same time significant benefits of costs and time. Simulation data are used to assess the efficiency, in terms of number of required tests, both for random assignment of the subjects to the pools and for situations when epidemiological and clinical data are used to create an \"informed\" version of the pooling. Different scenarios are examined in the simulations to measure the effect of different pool sizes and different values for the virus frequency. Our results allow to customize the pooling strategy according to the specific characteristics of the cohort to be tested.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Renato Millioni", - "author_inst": "University of Padova" - }, - { - "author_name": "Cinzia Mortarino", - "author_inst": "University of Padova" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20077891", "rel_title": "COVID-19 in Africa -- outbreak despite interventions?", @@ -1527694,6 +1528315,29 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.04.24.20078824", + "rel_title": "Estimating COVID-19 Antibody Seroprevalence in Santa Clara County, California. A re-analysis of Bendavid et al.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078824", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWA recent study by Bendavid et al. claimed that the rate of infection of COVID-19 in Santa Clara county was between 2.49% and 4.16%, 50-85 times higher than the number of officially confirmed cases. The statistical methodology used in that study overestimates of rate of infection given the available data. We jointly estimate the sensitivity and specificity of the test kit along with rate of infection with a simple Bayesian model, arriving at lower estimates of the rate of COVID-19 in Santa Clara county. Re-analyzing their data, we find that the rate of infection was likely between 0.27% and 3.21%.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Stephen T Bennett", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Mark Steyvers", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.24.20078808", "rel_title": "Reacting to outbreaks at neighboring localities", @@ -1528110,37 +1528754,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.24.20079046", - "rel_title": "Gender-Based Disparities in COVID-19: Clinical Characteristics and Propensity-matched Analysis of Outcomes", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20079046", - "rel_abs": "COVID-19 epidemiological data show higher mortality among males as compared to females. However, it remains unclear if this disparity is due to gender differences in high-risk characteristics. Our study, including a large cohort of male and female patients, showed that males have a higher risk for mortality, hospitalization and mechanical ventilation even when compared to a matched cohort of females with similar age, high-risk behavior, and comorbidities. This gender-based risk of poor outcomes among COVID-19 patients is especially more pronounced in advanced age. High-risk characteristics only partially explain the gender disparity, and further research is needed to understand the causes of this disparity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Shailendra Singh", - "author_inst": "Charleston Area Medical Center, Charleston WV" - }, - { - "author_name": "Monica Chowdhry", - "author_inst": "West Virginia University Health Sciences Center Charleston Division, Charleston, WV" - }, - { - "author_name": "Arka Chatterjee", - "author_inst": "Division of Cardiovascular Disease, University of Alabama at Birmingham" - }, - { - "author_name": "Ahmad Khan", - "author_inst": "Department of Medicine, West Virginia University Health Sciences Center Charleston Division, Charleston, WV" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.24.20078782", "rel_title": "Clinical Laboratory Parameters Associated with Severe or Critical Novel Coronavirus Disease 2019 (COVID-19): A Systematic Review and Meta-analysis", @@ -1529132,6 +1529745,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20078774", + "rel_title": "State-by-State prediction of likely COVID-19 scenarios in the United States and assessment of the role of testing and control measures", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078774", + "rel_abs": "Due to the heterogeneity among the States in the US, predicting COVID-19 trends and quantitatively assessing the effects of government testing capability and control measures need to be done via a State-by-State approach. We develop a comprehensive model for COVID-19 incorporating time delays and population movements. With key parameter values determined by empirical data, the model enables the most likely epidemic scenarios to be predicted for each State, which are indicative of whether testing services and control measures are vigorous enough to contain the disease. We find that government control measures play a more important role than testing in suppressing the epidemic. The vast disparities in the epidemic trends among the States imply the need for long-term placement of control measures to fully contain COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Zheng-Meng Zhai", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yong-Shang Long", + "author_inst": "East China Normal University" + }, + { + "author_name": "Jie Kang", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yi-Lin Li", + "author_inst": "East China Normal University" + }, + { + "author_name": "Lang Zeng", + "author_inst": "East China Normal University" + }, + { + "author_name": "Li-Lei Han", + "author_inst": "East China Normal University" + }, + { + "author_name": "Zhao-Hua Lin", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yin-Qi Zeng", + "author_inst": "East China Normal University" + }, + { + "author_name": "Da-Yu Wu", + "author_inst": "East China Normal University" + }, + { + "author_name": "Ming Tang", + "author_inst": "East China Normal University" + }, + { + "author_name": "Di Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zonghua Liu", + "author_inst": "East China Normal University" + }, + { + "author_name": "Ying-Cheng Lai", + "author_inst": "Arizona State University - Tempe Campus" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.28.066977", "rel_title": "Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world", @@ -1529696,33 +1530376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.25.20079475", - "rel_title": "Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079475", - "rel_abs": "World Health Organization (WHO) declared COVID-19 as a pandemic disease on March 11, 2020. Comparison of genome sequences from diverse locations allows us to identify the genetic diversity among viruses which would help in ascertaining viral virulence, disease pathogenicity, origin and spread of the SARS-CoV-2 between countries. The aim of this study is to ascertain the genetic diversity among Indian SARS-CoV-2 isolates. Initial examination of the phylogenetic data of SARS-CoV-2 genomes (n=3123) from different continents deposited at GISAID (Global Initiative on Sharing All Influenza Data) revealed multiple origin for Indian isolates. An in-depth analysis of 449 viral genomes derived from samples representing countries from USA, Europe, China, East Asia, South Asia, Oceania, Middle East regions and India revealed that most Indian samples are divided into two clusters (A and B) with cluster A showing more similarity to samples from Oceania and Kuwait and the cluster B grouping with countries from Europe, Middle East and South Asia. Diversity analysis of viral clades, which are characterized by specific non-synonymous mutations in viral proteins, discovered that the cluster A Indian samples belong to I clade (V378I in ORF1ab), which is an Oceania clade with samples having Iran connections and the cluster B Indian samples belong to G clade (D614G in Spike protein), which is an European clade. Thus our study identifies that the Indian SARS-CoV-2 viruses belong to I and G clades with potential origin to be countries mainly from Oceania, Europe, Middle East and South Asia regions, which strongly implying the spread of virus through most travelled countries. The study also emphasizes the importance of pathogen genomics through phylogenetic analysis to discover viral genetic diversity and understand the viral transmission dynamics with eventual grasp on viral virulence and disease pathogenesis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kumaravel Somasundaram", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Mainak Mondal", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Ankita Lawarde", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.04.25.20079509", "rel_title": "Pregnancy and breastfeeding during COVID-19 pandemic: A systematic review of published pregnancy cases", @@ -1530590,6 +1531243,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20077230", + "rel_title": "Analysis of national and international guidelines on respiratory protection equipment for COVID-19 in healthcare settings.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077230", + "rel_abs": "BackgroundConsistent guidelines on respiratory protection for healthcare professionals combined with improved global supply chains are critical to prevent COVID-19. We analysed the guidelines published by national and international societies/organizations on facemasks and respirators to prevent COVID-19 in healthcare settings.\n\nMethodsFrom the 1st January to the 2nd April 2020, guidelines published in four countries (France, Germany, United States, United Kingdom), and two international organizations (US and European Centre for Diseases Control, and World Health Organization) were reviewed to analyse the mask and respirators recommended for healthcare settings during the COVID-19 outbreak. The aerosol generating procedures (AGP) definitions and the strategy recommended for optimizing supplies and overcoming shortages were collected.\n\nFindingsThe recommendation of respirator was universally recommended for AGP across countries, although the type of respirators and what constituted an AGP was variable. Some guidance maintained the use of N95/99 for all contact with confirmed COVID-19 cases (i.e. Germany) whereas others, recommended a surgical mask (i.e. WHO, UK, France). Most guidelines were published in March with either downgraded (US and European CDC), relatively stable (WHO, Germany, and UK), or a mixing of high and low level equipment (France). The strategies to overcome shortage of respiratory protection equipment were based on minimizing the need and rationalizing the use, but also prolonging their use, reusing them after cleaning/sterilization, or using cloth masks.\n\nInterpretationsIn a crisis context, stable and consistent guidelines clearly detailing the respiratory protection type, and their indications, may prevent the confusion and anxiety among frontline staff, and avoid shortage.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gabriel Birgand", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nico T. Mutters", + "author_inst": "Heidelberg University Hospital" + }, + { + "author_name": "Jonathan Otter", + "author_inst": "Imperial College London" + }, + { + "author_name": "Vanessa M. Eichel", + "author_inst": "Heidelberg University Hospital" + }, + { + "author_name": "Didier Lepelletier", + "author_inst": "CHU de Nantes" + }, + { + "author_name": "Daniel J. Morgan", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Jean Christophe Lucet", + "author_inst": "AP-HP, Hopital Bichat Claude Bernard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20074856", "rel_title": "Test performance evaluation of SARS-CoV-2 serological assays", @@ -1531250,37 +1531946,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20077123", - "rel_title": "Significantly Improved COVID-19 Outcomes in Countries with Higher BCG Vaccination Coverage: A Multivariable Analysis", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077123", - "rel_abs": "COVID-19 has spread to 210 countries within 3 months. We tested the hypothesis that the vaccination with BCG correlates with a better outcome for COVID-19 patients. Our analysis covers 55 countries, complying with predetermined thresholds on population size and deaths per million (DPM). We found a strong negative correlation between the years of BCG administration and a lower DPM along with the pandemic progression in time. The results from multivariable regression tests with 22 economical, demographic, and health-related quantitative properties for each country substantiate the dominant contribution of BCG administration years to the COVID-19 outcomes. Analyzing countries according to an age-group partition reveals that the strongest correlation is attributed to the coverage in BCG vaccination of the young population and mostly to recent years immunization. We propose that BCG immunization coverage, especially among the most recently vaccinated contributes to attenuation of the spread and severity of the COVID-19 pandemic.\n\nOne Sentence SummaryBCG vaccination regimes and COVID-19 outcomes", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Danielle Klinger", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Ido Blass", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Nadav Rappoport", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Michal Linial", - "author_inst": "The Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20077065", "rel_title": "Estimation of COVID-19 spread curves integrating global data and borrowing information", @@ -1531956,6 +1532621,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.26.20073411", + "rel_title": "Machine Learning to Predict Mortality and Critical Events in COVID-19 Positive New York City Patients", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20073411", + "rel_abs": "Coronavirus 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become the deadliest pandemic in modern history, reaching nearly every country worldwide and overwhelming healthcare institutions. As of April 20, there have been more than 2.4 million confirmed cases with over 160,000 deaths. Extreme case surges coupled with challenges in forecasting the clinical course of affected patients have necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods for achieving this are lacking. In this paper, we use electronic health records from over 3,055 New York City confirmed COVID-19 positive patients across five hospitals in the Mount Sinai Health System and present a decision tree-based machine learning model for predicting in-hospital mortality and critical events. This model is first trained on patients from a single hospital and then externally validated on patients from four other hospitals. We achieve strong performance, notably predicting mortality at 1 week with an AUC-ROC of 0.84. Finally, we establish model interpretability by calculating SHAP scores to identify decisive features, including age, inflammatory markers (procalcitonin and LDH), and coagulation parameters (PT, PTT, D-Dimer). To our knowledge, this is one of the first models with external validation to both predict outcomes in COVID-19 patients with strong validation performance and identify key contributors in outcome prediction that may assist clinicians in making effective patient management decisions.\n\nOne-Sentence SummaryWe identify clinical features that robustly predict mortality and critical events in a large cohort of COVID-19 positive patients in New York City.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Akhil Vaid", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sulaiman Somani", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam J Russak", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica K De Freitas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fayzan F Chaudhry", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ishan Paranjpe", + "author_inst": "Ican School of Medicine at Mount Sinai" + }, + { + "author_name": "Kipp W Johnson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Samuel J Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Riccardo Miotto", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shan Zhao", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Noam Beckmann", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nidhi Naik", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kodi Arfer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Arash Kia", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Prem Timsina", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anuradha Lala", + "author_inst": "Icahn School of Medicine Mount Sinai" + }, + { + "author_name": "Manish Paranjpe", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Patricia Glowe", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eddye Golden", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matteo Danieletto", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Manbir Singh", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dara Meyer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Paul F O'Reilly", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Laura H Huckins", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Joseph Finkelstein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert M Freeman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar Argulian", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrew Kasarskis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bethany Percha", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Judith A Aberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emilia Bagiella", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carol R Horowitz", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Barbara Murphy", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric J Nestler", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric E Schadt", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Judy H Cho", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carlos Cordon-Cardo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Valentin Fuster", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dennis S Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "David L Reich", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Erwin P Bottinger", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matthew A Levin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jagat Narula", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zahi A Fayad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Allan Just", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander W Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish N Nadkarni", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benjamin S Glicksberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.22.20074351", "rel_title": "Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation", @@ -1532764,33 +1533640,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.22.20075697", - "rel_title": "Evaluation of WHO listed COVID-19 qPCR primers and probe in silico with 375 SERS-CoV-2 full genome sequences", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075697", - "rel_abs": "Quantitative reverse-transcription PCR (qRT-PCR) assays remains the gold standard for detection of the SARS-CoV-2 virus because of its sensitivity and specificity. However, successful design of qRT-PCR assays requires accurate viral genome sequences. With mutations accumulating as the virus is transmitted globally, we sought to compare current assays recommended by the World Health Organization with available SARS-CoV-2 genomic sequences in silico. While most sequences were conserved, there were notable mismatches, particularly in assays developed using early sequences when compared to more recent isolates. We recommend that any assay being evaluated for diagnostic tests be compared with prevalent sequence data from the region of proposed testing and that continued publicly accessible sequence information continue to be provided by the research community.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Derek Toms", - "author_inst": "University of Calgary" - }, - { - "author_name": "Julang Li", - "author_inst": "University of Guelph" - }, - { - "author_name": "Hugh Y Cai", - "author_inst": "University of Guelph" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.24.20075291", "rel_title": "Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors", @@ -1533586,6 +1534435,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.28.066761", + "rel_title": "Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin.", + "rel_date": "2020-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.28.066761", + "rel_abs": "The dependence of the host on the interaction of hundreds of extracellular proteins with the cell surface glycosaminoglycan heparan sulphate (HS) for the regulation of homeostasis is exploited by many microbial pathogens as a means of adherence and invasion. The closely related polysaccharide heparin, the widely used anticoagulant drug, which is structurally similar to HS and is a common experimental proxy, can be expected to mimic the properties of HS. Heparin prevents infection by a range of viruses if added exogenously, including S-associated coronavirus strain HSR1. Heparin prevents infection by a range of viruses if added exogenously, including S-associated coronavirus strain HSR1. Here, we show that the addition of heparin to Vero cells between 6.25 - 200 g.ml-1, which spans the concentration of heparin in therapeutic use, and inhibits invasion by SARS-CoV-2 at between 44 and 80%. We also demonstrate that heparin binds to the Spike (S1) protein receptor binding domain and induces a conformational change, illustrated by surface plasmon resonance and circular dichroism spectroscopy studies. The structural features of heparin on which this interaction depends were investigated using a library of heparin derivatives and size-defined fragments. Binding is more strongly dependent on the presence of 2-O or 6-O sulphation, and the consequent conformational consequences in the heparin structure, than on N-sulphation. A hexasaccharide is required for conformational changes to be induced in the secondary structure that are comparable to those that arise from heparin binding. Enoxaparin, a low molecular weight clinical anticoagulant, also binds the S1 RBD protein and induces conformational change. These findings have implications for the rapid development of a first-line therapeutic by repurposing heparin as well as for next-generation, tailor-made, GAG-based antiviral agents against SARS-CoV-2 and other members of the Coronaviridae.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Courtney Mycroft-West", + "author_inst": "Keele University" + }, + { + "author_name": "Dunhao Su", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Isabel Pagani", + "author_inst": "IRCCS San Raffaele Scientific Institute" + }, + { + "author_name": "Timothy Rudd", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Stefano Elli", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Scott Guimond", + "author_inst": "Keele University" + }, + { + "author_name": "Gavin Miller", + "author_inst": "Keele University" + }, + { + "author_name": "Maria Meneghetti", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Helena Nader", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Yong Li", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Quentin Nunes", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Patricia Procter", + "author_inst": "Keele University" + }, + { + "author_name": "Nicasio Mancini", + "author_inst": "Universita Vita-Salute San Raffaele" + }, + { + "author_name": "Massimo Clementi", + "author_inst": "Universita Vita-Salute San Raffaele" + }, + { + "author_name": "Antonella Bisio", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Nicholas Forsyth", + "author_inst": "Keele University" + }, + { + "author_name": "Jeremy Turnbull", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marco Guerrini", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "David Fernig", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Elisa Vicenzi", + "author_inst": "San Raffaele Scientific Institute" + }, + { + "author_name": "Edwin Yates", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marcelo Lima", + "author_inst": "Keele University" + }, + { + "author_name": "Mark A Skidmore", + "author_inst": "Keele University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.27.064139", "rel_title": "A Modular Framework for Multiscale Spatial Modeling of Viral Infection and Immune Response in Epithelial Tissue", @@ -1534074,81 +1535030,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.04.22.20072389", - "rel_title": "SARS-CoV-2 On-the-Spot Virus Detection Directly From Patients", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20072389", - "rel_abs": "Many countries are currently in a lockdown state due to the SARS-CoV-2 pandemic. One key aspect to transition safely out of lockdown is to continuously test the population for infected subjects. Currently, detection is performed at points of care using quantitative reverse-transcription PCR (RT-qPCR), and requires dedicated professionals and equipment. Here, we developed a protocol based on Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP) for detection of SARS-CoV-2. This protocol is applied directly on SARS-CoV-2 nose and throat swabs, with no RNA purification step required. We tested this protocol on over 180 suspected patients, and compared its results to the standard method. We further succeeded to apply the protocol on self-sampled saliva from confirmed cases. Since the proposed protocol provides results on-the-spot, and can detect SARS-CoV-2 from saliva, it can allow simple and continuous surveillance of the community.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Nadav Ben-Assa", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Rawi Naddaf", - "author_inst": "Technion-Israel Institute of Technology" - }, - { - "author_name": "Tal Gefen", - "author_inst": "Technion-Israel Institute of Technology" - }, - { - "author_name": "Tal Capucha", - "author_inst": "Technion-Israel Institute of Technology" - }, - { - "author_name": "Haitham Hajjo", - "author_inst": "Technion-Israel Institute of Technology" - }, - { - "author_name": "Noa Mandelbaum", - "author_inst": "Technion-Israel Institute of Technology" - }, - { - "author_name": "Lilach Elbaum", - "author_inst": "Technion-Israel Institute of Technology" - }, - { - "author_name": "Peter Rogov", - "author_inst": "311 cross st, Winchester MA 01890" - }, - { - "author_name": "Daniel A. King", - "author_inst": "Meir Medical Center" - }, - { - "author_name": "Shai Kaplan", - "author_inst": ". Robiotec ltd 9 Aharonwitz st. Rehovot, Israel, 7634709" - }, - { - "author_name": "Assaf Rotem", - "author_inst": "47 Bow Rd, Newton MA 02459" - }, - { - "author_name": "Michal Chowers", - "author_inst": "Tel-Aviv University" - }, - { - "author_name": "Moran Szwarcwort-Cohen", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Mical Paul", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Naama Geva-Zatorsky", - "author_inst": "Technion - Israel Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.27.064774", "rel_title": "A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains", @@ -1535000,6 +1535881,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20074450", + "rel_title": "The dynamics of Covid-19: weather, demographics and infection timeline", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074450", + "rel_abs": "We study the effects of temperature, absolute humidity, population density and when country/U.S. state reached 100 cases on early pace of Covid-19 expansion, for all 50 U.S. states and 110 countries with enough data. For U.S. states, weather variables show opposite effects when compared to the case of countries: higher temperature or absolute humidity imply faster early outbreak. The higher the population density or the earlier the date when state reached 100th case, the faster the pace of outbreak. When all variables are considered, only population density and the timeline variable show statistical significance. Discounting the effect of the timeline variable, we obtain an estimate for the initial growth rate of Covid-19, which can be also used to estimate the basic reproduction number for a region, in terms of population density. This has policy implications regarding how to control the pace of Covid-10 outbreak in a particular area, and we discuss some of them. In the case of countries, for which we did not have demographic information, weather variables lose statistical significance once the timeline variable is added. Relaxing CI requirements, absolute humidity contributes mildly to the reduction of growth rate of cases for the countries studied. Our results suggest that population density should be employed as a control variable and that analysis should have a local character, for subregions and countries separately, in studies involving the dynamics of Covid-19 and similar infectious diseases.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Renato H.L. Pedrosa", + "author_inst": "Unicamp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.22.20075762", "rel_title": "Proactive social distancing mitigates COVID-19 outbreaks within a month across 58 mainland China cities", @@ -1535460,25 +1536360,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.21.20068478", - "rel_title": "Bringing accountability to the peak of the pandemic using linear response theory", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20068478", - "rel_abs": "The peak of the daily new infections in COVID-19 remained qualitative in description and elusive in arrival. Because of the lack of clarity in what to expect from the peak, apart from the hope that one day the peak will be reached, there has been no metric to describe the success of the implemented strategies. We propose a way of predicting the number of infections that can be expected after a lockdown, assuming they come from the asymptomatic cases prior to the lockdown and using linear response theory. These predictions for several western countries faithfully follow the observed infections for several weeks after the lockdown, suggesting universalities in the recovery pattern of several countries. At the same time, the gap between the quantitative predictions of the recovery patterns for New York and Milan and the observations is striking. These gaps which arise even while emulating the recovery patterns of other western countries raise the possibility of an audit of the success of the implemented strategies, and the potential newer sources of infection.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Meher K Prakash", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20071043", "rel_title": "Contact Tracing: a game of big numbers in the time of COVID-19", @@ -1536018,6 +1536899,53 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.26.062406", + "rel_title": "How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography", + "rel_date": "2020-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.26.062406", + "rel_abs": "SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mukesh Thakur", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Abhishek Singh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Bheem Dutt Joshi", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Avijit Ghosh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Sujeet Kumar Singh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Neha Singh", + "author_inst": "University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Lalit Kumar Sharma", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Kailash Chandra", + "author_inst": "Zoological Survey of India, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.23.20076612", "rel_title": "A systematic review of Anakinra, Tocilizumab, Sarilumab and Siltuximab for coronavirus-related infections", @@ -1536618,37 +1537546,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.22.055327", - "rel_title": "Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2", - "rel_date": "2020-04-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.055327", - "rel_abs": "The SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. This study compared two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2 to the Roche cobas SARS-CoV-2 assay. A total of 113 nasopharyngeal swabs were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. These findings highlight an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance of ID Now for direct swabs.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Marie C Smithgall", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Ioana Scherberkova", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Susan Whittier", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Daniel Green", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.25.060350", "rel_title": "SARS-CoV-2 Productively Infects Human Gut Enterocytes", @@ -1537704,6 +1538601,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20074641", + "rel_title": "Association between rRT-PCR test results upon admission and outcome in hospitalized chest CT-Positive COVID-19 patients; a provincial retrospective cohort with active follow-up", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074641", + "rel_abs": "BackgroundThe Covid-19 pandemic imposed the most devastating challenge on healthcare systems worldwide. Iran was among the first countries that had to confront serious shortages in RT-PCR testing for SARS-CoV-2 and ventilators availabilities throughout the COVID-19 outbreak. This study aimed to investigate the clinical course of hospitalized COVID-19 patients with different rRT-PCR test results during the first 3 weeks of the outbreak in Qazvin province, Iran.\n\nMethodsFor this retrospective cohort study, data of hospitalized patients primarily diagnosed as having COVID-19 in all 12 centers across the whole Qazvin province during Feb 20-Mar 11, 2020 was analyzed. A multivariate logistic regression model was applied to assess the independent associates of death among COVID-19 patients.\n\nResults998 patients (57% male, median age 54 years) with positive chest CT-scan changes were included in this study. Among them, 558 patients were examined with rRT-PCR test and 73{middle dot}8% tested positive. Case fatality rate was 20{middle dot}68% and 7{middle dot}53% among test-positive and test negative hospitalized patients, respectively. While only 5{middle dot}2% of patients were ICU admitted, case fatality rates outside ICU were 17{middle dot}70% and 4{middle dot}65% in test-positive and test-negative non-ICU admitted patients, correspondingly. The independent associates of death were age [≥] 70 years, testing positive with rRT-PCR test, having immunodeficiency disorders and ICU admission.\n\nConclusionsHospitalized COVID-19 patients with mild symptoms despite positive chest CT changes and major comorbidities were more probable to have negative rRT-PCR test result, hence lower case fatality rate and a more favorable outcome.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Saeed Nemati", + "author_inst": "Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Hamid Reza Najari", + "author_inst": "1. Department of Internal Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; 2. Deputy of health, Qazvin University of Medical S" + }, + { + "author_name": "Anita Eftekharzadeh", + "author_inst": "Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti Universiy School of Medicine, Tehran, Iran" + }, + { + "author_name": "Amir Mohammad Kazemifar", + "author_inst": "Department of Internal Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Ali Qandian", + "author_inst": "Office of Communicable Disease, Deputy of health, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Pedram Fattahi", + "author_inst": "Cancer Research Center, Cancer Research Institute, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Maedeh Zokaei Nikoo", + "author_inst": "Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Shiva Leghaei", + "author_inst": "Office of Communicable Disease, Deputy of health, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Mohammad Reza Rouhollahi", + "author_inst": "1. Cancer Research Center, Cancer Research Institute, Tehran University of Medical Sciences, Tehran, Iran; 2. Clinical Cancer Research Center (CCRC), Milad Hosp" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.21.20074757", "rel_title": "Knowledge, attitude, practice and perception regarding COVID-19 among students in Bangladesh: Survey in Rajshahi University", @@ -1538072,73 +1539020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20075440", - "rel_title": "Estimating the number of COVID-19-related infections, deaths and hospitalizations in Iran under different physical distancing and isolation scenarios: A compartmental mathematical modeling", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075440", - "rel_abs": "BackgroundIran is one of the countries that has been overwhelmed with COVID-19. We aimed to estimate the total number of COVID-19 related infections, deaths, and hospitalizations in Iran under different physical distancing and isolation scenarios.\n\nMethodsWe developed a Susceptible-Exposed-Infected-Removed (SEIR) model, parameterized to the COVID-19 pandemic in Iran. We used the model to quantify the magnitude of the outbreak in Iran and assess the effectiveness of isolation and physical distancing under five different scenarios (A: 0% isolation, through E: 40% isolation of all infected cases). We used Monte-Carlo simulation to calculate the 95% uncertainty intervals (UI).\n\nFindingsUnder scenario A, we estimated 5,196,000 (UI 1,753,000 - 10,220,000) infections to happen till mid-June with 966,000 (UI 467,800 - 1,702,000) hospitalizations and 111,000 (UI 53,400 - 200,000) deaths. Successful implantation of scenario E would reduce the number of infections by 90% (i.e. 550,000) and change the epidemic peak from 66,000 on June 9th to 9,400 on March 1st. Scenario E also reduces the hospitalizations by 92% (i.e. 74,500), and deaths by 93% (i.e. 7,800).\n\nInterpretationWith no approved vaccination or therapy, we found physical distancing and isolation that includes public awareness and case-finding/isolation of 40% of infected people can reduce the burden of COVID-19 in Iran by 90% by mid-June.\n\nFundingWe received no funding for this work.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIran has been heavily impacted by the COVID-19 outbreak, and the virus has now spread to all of its provinces. Iran has been implementing different levels of partial physical distancing and isolation policies in the past few months. We searched PubMed and preprint archives for articles published up to April 15, 2020 that included information about control measures against COVID-19 in Iran using the following terms: (\"coronavirus\" OR \"2019-nCoV\" OR \"COVID-19\") AND \"Iran\" AND (\"intervention\" OR \"prevention\" OR \"physical distancing\" OR \"social distancing\"). We found no studies that had quantified the impact of policies in Iran.\n\nAdded value of this studyGiven the scarcity of evidence on the magnitude of the outbreak and the burden of COVID-19 in Iran, we used multiple sources of data to estimate the number of COVID-19 infections, hospitalizations, and deaths under different physical distancing and isolation scenarios until mid-June. We showed that implementing no control measures could lead to over five million infections in Iran; [~]19% of whom would be hospitalized, and [~]2% would die. However, under our most optimistic scenario, these estimates could be reduced by [~]90%.\n\nImplications of all the available evidenceWith no effective vaccination or treatment, advocating and enforcing physical distancing and isolation along with public education on prevention measures could significantly reduce the burden of COVID-19 in Iran. Nonetheless, even under the most optimistic scenario, the burden of COVID-19 would be substantial and well beyond the current capacity of the healthcare system in Iran.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hamid Sharifi", - "author_inst": "HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical S" - }, - { - "author_name": "Yunes Jahani", - "author_inst": "Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran" - }, - { - "author_name": "Ali Mirzazadeh", - "author_inst": "Department of Epidemiology and Biostatistics, Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Milad Ahmadi Gohari", - "author_inst": "Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran" - }, - { - "author_name": "Mehran Nakhaeizadeh", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran" - }, - { - "author_name": "Mostafa Shokoohi", - "author_inst": "University of Toronto, Dalla Lana School of Public Health" - }, - { - "author_name": "Sana Eybpoosh", - "author_inst": "Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran" - }, - { - "author_name": "Hamid Reza Tohidinik", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran" - }, - { - "author_name": "Ehsan Mostafavi", - "author_inst": "Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran" - }, - { - "author_name": "Davood Khalili", - "author_inst": "Prevention of Metabolic Disorders Research Center, Research Institute for education Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Seyed Saeed Hashemi Nazari", - "author_inst": "Prevention of Cardiovascular Disease Research Center, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Scie" - }, - { - "author_name": "Mohammad Karamouzian", - "author_inst": "School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Ali Akbar Haghdoost", - "author_inst": "Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20075572", "rel_title": "Forecast and interpretation of daily affected people during 21 days lockdown due to COVID 19 pandemic in India", @@ -1539102,6 +1539983,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.059576", + "rel_title": "Introductions and early spread of SARS-CoV-2 in France", + "rel_date": "2020-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.059576", + "rel_abs": "Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fabiana Gambaro", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Artem Baidaliuk", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flora Donati", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Melanie Albert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Andreea Alexandru", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maud Vanpeene", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Meline Bizard", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Angela Brisebarre", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marion Barbet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fawzi Derrar", + "author_inst": "Institut Pasteur of Algiers" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Vincent Enouf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.20.20064899", "rel_title": "Epidemiological characteristics of COVID-19 in medical staff members of neurosurgery departments in Hubei province: A multicentre descriptive study", @@ -1539722,109 +1540674,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.21.20073833", - "rel_title": "Collateral damage: the impact on cancer outcomes of the COVID-19pandemic", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073833", - "rel_abs": "BackgroundCancer diagnostics and surgery have been disrupted by the response of healthcare services to the COVID-19 pandemic. Progression of cancers during delay will impact on patient long-term survival.\n\nMethodsWe generated per-day hazard ratios of cancer progression from observational studies and applied these to age-specific, stage-specific cancer survival for England 2013-2017. We modelled per-patient delay of three months and six months and periods of disruption of one year and two years. Using healthcare resource costing, we contextualise attributable lives saved and life years gained from cancer surgery to equivalent volumes of COVID-19 hospitalisations.\n\nFindingsPer year, 94,912 resections for major cancers result in 80,406 long-term survivors and 1,717,051 life years gained. Per-patient delay of six months would cause attributable death of 10,555 of these individuals with loss of 205,024 life years. For cancer surgery, average life years gained (LYGs) per patient are 18{middle dot}1 under standard conditions and 15{middle dot}9 with a delay of six months (a loss of 2{middle dot}3 LYG per patient). Taking into account units of healthcare resource (HCRU), surgery results on average per patient in 2{middle dot}25 resource-adjusted life years gained (RALYGs) under standard conditions and 1{middle dot}98 RALYGs following delay of six months. For 94,912 hospital COVID-19 admissions, there are 474,505 LYGs requiring of 1,097,937 HCRUs. Hospitalisation of community-acquired COVID-19 patients yields on average per patient 5{middle dot}0 LYG and 0{middle dot}43 RALYGs.\n\nInterpretationDelay of six months in surgery for incident cancers would mitigate 43% of life years gained by hospitalisation of an equivalent volume of admissions for community acquired COVID-19. This rises to 62% when considering resource-adjusted life-years gained. To avoid a downstream public health crisis of avoidable cancer deaths, cancer diagnostic and surgical pathways must be maintained at normal throughput, with rapid attention to any backlog already accrued.\n\nFundingBreast Cancer Now, Cancer Research UK, Bobby Moore Fund for Cancer Research, National Institute for Health Research (NIHR)", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Amit Sud", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Michael E. Jones", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "John Broggio", - "author_inst": "National Cancer Registration and Analysis Service, Public Health England" - }, - { - "author_name": "Chey Loveday", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Bethany Torr", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Alice Garrett", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "David L. Nicol", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Shaman Jhanji", - "author_inst": "Royal Marsden NHS Foundation Trust; Institute of Cancer Research" - }, - { - "author_name": "Stephen A. Boyce", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Phillip Ward", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Jonathan M. Handy", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Nadia Yousaf", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "James Larkin", - "author_inst": "Royal Marsden NHS Foundation Trust; Institute of Cancer Research" - }, - { - "author_name": "Yae-Eun Suh", - "author_inst": "Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Stephen Scott", - "author_inst": "RM Partners, West London Cancer Alliance, Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Paul D.P. Pharoah", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Charles Swanton", - "author_inst": "The Francis Crick Institute; University College London Cancer Institute" - }, - { - "author_name": "Christopher Abbosh", - "author_inst": "The Francis Crick Institute; University College London Cancer Institute" - }, - { - "author_name": "Matthew Williams", - "author_inst": "Imperial College Healthcare NHS Trust; Imperial College London" - }, - { - "author_name": "Georgios Lyratzopoulos", - "author_inst": "National Cancer Registration and Analysis Service, Public Health England; University College London" - }, - { - "author_name": "Richard Houlston", - "author_inst": "Institute of Cancer Research" - }, - { - "author_name": "Clare Turnbull", - "author_inst": "Institute of Cancer Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.04.21.20063263", "rel_title": "A web-based Diagnostic Tool for COVID-19 Using Machine Learning on Chest Radiographs (CXR)", @@ -1541020,6 +1541869,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20072157", + "rel_title": "Multiple drivers of the COVID-19 spread: role of climate, international mobility, and region-specific conditions", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072157", + "rel_abs": "The novel Coronavirus Disease 2019 (COVID-19) has spread quickly across the globe. Here, we evaluated the role of climate (temperature and precipitation), region-specific susceptibility (BCG vaccination, malaria infection, and elderly population) and international traveller population (human mobility) in shaping the geographical patterns of COVID-19 cases across 1,055 countries/regions, and examined the sequential shift of multiple drivers of the accumulated cases from December, 2019 to April 12, 2020. The accumulated numbers of COVID-19 cases (per 1 million population) were well explained by a simple regression model. The explanatory power (R2) of the model increased up to > 70% in April 2020 as the COVID-19 spread progressed. Climate, host mobility, and host susceptibility largely explained the variance of the COVID-19 cases (per 1 million population), and their explanatory power improved as the pandemic progressed; the relative importance of host mobility and host susceptibility have been greater than that of climate. The number of days from outbreak onset showed greater explanatory power in the earlier stages of COVID-19 spread but rapidly lost its influence. Our findings demonstrate that the COVID-19 pandemic is deterministically driven by climate suitability, cross-border human mobility, and region-specific susceptibility. The present distribution of COVID-19 cases has not reached an equilibrium and is changing daily, especially in the Southern Hemisphere. Nevertheless, the present results, based on mapping the spread of COVID-19 and identifying multiple drivers of this outbreak trajectory, may contribute to a better understanding of the COVID-19 disease transmission risk and the measures against long-term epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yasuhiro Kubota", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Takayuki Shiono", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Buntarou Kusumoto", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Junichi Fujinuma", + "author_inst": "University of the Ryukyus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.22.20076141", "rel_title": "COVID-19: Public Compliance with and Public Support for Stay-at-Home Mitigation Strategies", @@ -1541508,57 +1542388,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.21.20073114", - "rel_title": "Deaths from Covid-19: Who are the forgotten victims?", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073114", - "rel_abs": "BackgroundWith the global pandemic of coronavirus disease 2019 (Covid-19) there has been disruption to normal clinical activity in response to the increased demand on health services. There are reports of a reduction in non-Covid-19 emergency presentations. Consequentially, there are concerns that deaths from non-Covid-19 causes could increase. We examined recent reported population-based mortality rates, compared with expected rates, and compared any excess in deaths with the number of deaths attributed to Covid-19.\n\nMethodsNational agency and death registration reports were searched for numbers of deaths attributed to Covid-19 and overall mortality that had been publicly reported by 06 May 2020. Data on the number of deaths attributed to Covid-19, the total number of deaths registered in the population and the historical average over at least 3 years were collected. Data were available for 4 European countries (England & Wales, Scotland, Netherlands and Italy) and New York State, United States of America.\n\nResultsThere was an increase in observed, compared with expected, mortality in Scotland (+68%), England and Wales (+74%), the Netherlands (+58%), Italy (+39%) and New York state (+49%). Of these deaths, only 73% in Scotland, 71 % in England and Wales, 53% in the Netherlands, 54% in Italy and 79% in New York state were attributed to Covid-19 leaving a number of excess deaths not attributed to Covid-19. In the 5-week period of study, Scotland, 10% of the excess of deaths were attributed to dementia/Alzheimers disease and 7% to cardiovascular causes.\n\nConclusionA substantial proportion of excess deaths observed during the current COVID-19 pandemic are not attributed to COVID-19 and may represent unrecognised deaths due to Covid-19, an excess of deaths due to other causes, or both. The impact of Covid-19 on mortality and morbidity from other causes needs to be quantified and addressed in public health planning.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kieran Docherty", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Jawad Butt", - "author_inst": "Rigshospitalet Copenhagen University Hospital" - }, - { - "author_name": "Rudolf de Boer", - "author_inst": "University of Groningen" - }, - { - "author_name": "Pooja Dewan", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Lars Koeber", - "author_inst": "Rigshospitalet Copenhagen University Hospital" - }, - { - "author_name": "Aldo Maggioni", - "author_inst": "Associazione Nazionale Medici Cardiologi Ospedalieri Research Center" - }, - { - "author_name": "John McMurray", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Scott Solomon", - "author_inst": "Division of Cardiovascular Medicine, Brigham and Women's Hospital" - }, - { - "author_name": "Pardeep Singh Jhund", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.20.20072918", "rel_title": "Clinical features of coronavirus disease 2019 (COVID-19) in a cohort of patients with disability due to spinal cord injury", @@ -1542322,6 +1543151,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.20.20072892", + "rel_title": "Estimation of Undetected Covid-19 Infections in India", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072892", + "rel_abs": "Background and ObjectivesWhile the number of detected COVID-19 infections are widely available, an understanding of the extent of undetected COVID-19 cases is urgently needed for an effective tackling of the pandemic and as a guide to lifting the lockdown. The aim of this work is to estimate and predict the true number of COVID-19 (detected and undetected) infections in India for short to medium forecast horizons. In particular, using publicly available COVID-19 infection data upto 16th April 2020, we predict the true number of infections in India during and upto the end of the formal lockdown period (21st April 2020).\n\nMethodsThe high death rate observed in most COVID-19 hit countries is suspected to be a function of the undetected infections existing in the population. An estimate of the age weighted infection fatality rate (IFR) of the disease of 0.41%, specifically calculated by taking into account the age structure of Indian population, is already available in the literature. In addition, the recorded case fatality rate (CFR= 0.70%) of Kerala, the only state in India to report single digit new infections over the second week of April, is used as a second estimate of the IFR. These estimates are used to formulate a relationship between deaths recorded and the true number of infections. The estimated undetected and detected cases time series based on these two IFR estimates are then used to fit a discrete time multivariate infection model to predict the total infections at the end of the formal lockdown period.\n\nResultsIn two consecutive fortnights during the lockdown, it was noted that the rise in detected infections has decreased by 2.7 times. For an IFR of 0.41%, the rise in undetected infections decreased by 3.2 times and the predicted number of total infections in India is 3.14 lakhs. While for an IFR of 0.70%, the rise in undetected cases decreased by 3.3 times and the total number of infections predicted on 21st April is 1.75 lakhs.\n\nInterpretation and ConclusionsThe behaviour of the undetected cases over time effectively illustrates the effects of lockdown and increased testing. From our estimates, it is found that the lockdown has brought down the undetected to detected cases ratio, and has consequently dampened the increase in the number of total cases. However, even though the rate of rise in total infections has fallen, the lifting of the lockdown should be done keeping in mind that 1.75 to 3 lakhs undetected cases will already exist in the population on 21st April.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Siuli Mukhopadhyay", + "author_inst": "Department of Mathematics, Indian Institute of Technology Bombay" + }, + { + "author_name": "Debraj Chakraborty", + "author_inst": "Indian Institute of Technology Bombay" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072462", "rel_title": "ESTIMATING R0 OF SARS-COV-2 IN HEALTHCARE SETTINGS", @@ -1543042,37 +1543894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.20.20073080", - "rel_title": "The risk of SARS-CoV-2 transmission in the healthcare setting and potential impact of cohorting strategies", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20073080", - "rel_abs": "BackgroundSince its onset, the COVID-19 pandemic has caused significant morbidity and mortality worldwide, with particularly severe outcomes in healthcare institutions and congregate settings. To mitigate spread, healthcare systems have been cohorting patients to limit contacts between uninfected patients and potentially infected patients or healthcare workers (HCWs). A major challenge in managing the pandemic is the presence of currently asymptomatic individuals capable of transmitting the virus, who could introduce COVID-19 into uninfected cohorts. The optimal combination of personal protective equipment (PPE) and testing approaches to prevent these events is unclear, especially in light of ongoing limitations in access to both.\n\nMethodsUsing stochastic simulations with an SEIR model we quantified and compared the impacts of PPE use, patient and HCWs testing, and cohorting.\n\nFindingsIn the base case without testing or PPE, the healthcare system was rapidly overwhelmed, and became a net contributor to the force of infection. We found that effective use of PPE by both HCWs and patients could prevent this scenario, while random testing of apparently asymptomatic individuals on a weekly basis was less effective. We also found that even imperfect use of PPE could provide substantial protection by decreasing the force of infection, and that creation of smaller patient/HCW subcohorts can provide additional resilience to outbreak development.\n\nInterpretationThese findings reinforce the importance of ensuring adequate PPE supplies even in the absence of testing, and provide support for strict subcohorting regimens to reduce outbreak potential in healthcare institutions.\n\nFundingNational Institute of General Medical Sciences, National Institutes of Health.\n\nResearch in contextO_ST_ABSEvidence beforeC_ST_ABSPreserving healthcare from outbreaks of respiratory viruses is a longstanding concern, brought into sharp relief by the covid-19 pandemic. Early case series and numerous anecdotal reports suggest that health care workers (HCWs) and patients receiving treatment for conditions other than SARS-CoV-2 infection are at elevated risk of becoming infected, and the consequences of infections in long term care facilities are well known. In addition, the early stages of the pandemic have been marked by shortages of personal protective equipment (PPE) and diagnostic testing, but the most effective strategies for their use given the specific characteristics of SARS-CoV-2 transmission are unclear.\n\nValue addedOur research plainly shows the importance of presymptomatic transmission. Given reasonable estimates of this, random testing of currently asymptomatic staff and patients once a week is not able to prevent large outbreaks. We show that PPE is, as expected, the most effective intervention and moreover even suboptimal PPE use is highly beneficial. To further limit transmission, we show the benefit of sub-cohorting into smaller groups of HCWs and patients. When the force of infection in the community is low, this can entirely prevent the establishment of infection in a large fraction of healthcare.\n\nImplicationsPPE should be used throughout healthcare, on the assumption that any patient or HCWs is potentially infected. Further work should determine the most effective means of PPE for the non-COVID cohort. If PPE resources are limited, whether in general or due to a second surge, we recommend subcohorting to limit the impact of introductions from the community.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Joel C Miller", - "author_inst": "School of Engineering at Mathematical Sciences, La Trobe University, Bundoora, VIC" - }, - { - "author_name": "Xueting Qiu", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University" - }, - { - "author_name": "Derek MacFadden", - "author_inst": "Ottawa Hospital Research Institute, Ottawa, Canada" - }, - { - "author_name": "William P Hanage", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.20.20073023", "rel_title": "Estimated surge in hospitalization and intensive care due to the novel coronavirus pandemic in the Greater Toronto Area, Canada: a mathematical modeling study with application at two local area hospitals", @@ -1543892,6 +1544713,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.23.057810", + "rel_title": "TARGETED PROTEOMICS FOR THE DETECTION OF SARS-COV-2 PROTEINS.", + "rel_date": "2020-04-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.23.057810", + "rel_abs": "The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry based (MS) proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Karel Bezstarosti", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Mart M Lamers", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Wouter AS Doff", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Peter C Wever", + "author_inst": "Jeroen Bosch Hospital" + }, + { + "author_name": "Khoa TD Thai", + "author_inst": "Star-shl diagnostic laboratories" + }, + { + "author_name": "Jeroen JA van Kampen", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Bart L Haagmans", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Jeroen AA Demmers", + "author_inst": "Erasmus University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.22.046565", "rel_title": "Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals Broad Potential Host Range of SARS-CoV-2", @@ -1544656,41 +1545524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.18.20071142", - "rel_title": "Is there evidence that BCG vaccination has non-specific protective effects for COVID 19 infections or is it an illusion created by lack of testing?", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20071142", - "rel_abs": "The goal of this paper is to showcase that the COVID-19 disease pattern is evolving and to study the relationship between mandatory BCG policy and caseload/million or death/per million. We analyze seven recent publications on the impact of BCG vaccinations on the development of COVID19 illness and extend presented findings using the latest data from April 10, 2020. We analyze data from 98 countries and we extend existing models by adding the dimension of COVID-19-related testing conducted by the analyzed countries. Similarly to prior studies, we find that COVID-19 attributable case and death incidences across countries share a relationship with a countrys BCG vaccination inclusion in the national immunization program when testing is not taken into consideration. However, this relationship vanishes when we add the dimension of testing. We observe that case and death incidences conditional on testing do not get affected by the countries BCG vaccination inclusion in the national immunization program. Therefore, we show that there is no statistical evidence to support the assertion that inclusion of BCG vaccination in national immunization program (NIP) has any impact of COVID 19 infections (cases) or mortality.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shivendu Shivendu", - "author_inst": "University fo South Florida" - }, - { - "author_name": "Saurav Chakraborty", - "author_inst": "University of Louisville" - }, - { - "author_name": "Agnieszka Onuchowska", - "author_inst": "University of South Florida" - }, - { - "author_name": "Arpit Srivastava", - "author_inst": "University of South Florida" - }, - { - "author_name": "Ankita Patidar", - "author_inst": "University of South Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.18.20071134", "rel_title": "Cluster of COVID-19 in northern France: A retrospective closed cohort study", @@ -1545782,6 +1546615,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071654", + "rel_title": "A study on control of novel corona-virus (2019-nCoV) disease process by using PID controller", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071654", + "rel_abs": "BackgroundIn this paper, the SEIR dynamic model will be used to model the epidemic of coronvirus (2019-nCoV)disease. The SEIR model has been used to model infectious diseases in Malaysia.Then, the spread and control of the disease is simulated applying a PID controller. The results of this study show that the implementation of strict restrictions such as quarantine, social distancing and closure of gathering centers is effective in controlling the disease. Using the results and analyzing them, it was found that early and strict implementation of strict restrictions such as quarantine, social distance and closure of centers with a high percentage of community is very important to control this disease and prevent irreparable economic losses and depreciation of medical staff.\n\nObjectiveModeling the prevalence and control of corona-virus (2019-nCoV)and the impact of government actions using control engineering methods.\n\nMethodIn this study, the SEIR dynamic model was used and the common data on the prevalence of the virus in Wuhan, China and Malaysia were used. As an example, the use of control target schemes is simulated in this paper.\n\nResultsThe findings of this study use control methods and forecasting in control engineering to provide a clear picture of macro-decisions for different governments in the field of infectious diseases.\n\nConclusionManagement and control schemes such as travel restrictions, quarantine, social distance and closure of offices, higher education institutions must be implemented immediately to prevent major economic and social losses. The implementation of these restrictions should not be delayed during the outbreak of corona-virus(2019-nCoV) infectious diseases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "habibollah arasteh rad", + "author_inst": "Institute of applied Inteligent Systems Of University of Tehran" + }, + { + "author_name": "arshia badi", + "author_inst": "Institute of applied Inteligent Systems Of University of Tehran" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.18.20070821", "rel_title": "Estimating the Prevalence of COVID-19 in the United States: Three Complementary Approaches", @@ -1546490,33 +1547346,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.16.20067751", - "rel_title": "Estimates of COVID-19 case-fatality risk from individual-level data", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067751", - "rel_abs": "When calculated from aggregate data on confirmed cases and deaths, the case-fatality risk (CFR) is a simple ratio between the former and the latter, which is prone to numerous biases. With individual-level data, the CFR can be estimated as a true measure of risk as the proportion of incidence for the disease. We present the first estimates of the CFR for COVID-19 by age and sex based on event history modelling of the risk of dying among confirmed positive individuals in the Canadian province of Ontario, which maintains one of the few individual-level datasets on COVID-19 in the world.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Simona Bignami", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Daniela Ghio", - "author_inst": "Joint Research Center European Commission" - }, - { - "author_name": "Ari Van Assche", - "author_inst": "HEC Montreal" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20067587", "rel_title": "Impact of blood analysis and immune function on the prognosis of patients with COVID-19", @@ -1547560,6 +1548389,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.17.20068601", + "rel_title": "The effect of BCG vaccination on COVID-19 examined by a statistical approach: no positive results from the Diamond Princess and cross-national differences previously reported by world-wide comparisons are flawed in several ways", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068601", + "rel_abs": "Recently, the controversial hypothesis that past BCG (Bacillus Calmette-Guerin) vaccination reduces infection or severity of COVID-19 has been proposed. The present study examined this hypothesis using statistical approaches based on the public data. Three approaches were utilized: 1) comparing the infection and mortality ratio of people on the cruise ship Diamond Princess, 2) comparing the number of mortalities among nations, and 3) comparing the maximum daily increase rate of total mortalities among nations. The result of 1) showed that there is no significant difference in infection per person onboard or mortality-infection between Japanese citizens vs. US citizens and BCG obligatory nations vs. non-BCG obligatory nations on the Diamond Princess. The result of 2) showed that the number of mortalities among nations is similar to the previous studies, but this analysis also considered the timing of COVID-19 arrival in each nation. After correcting for arrival time, previously reported effect of BCG vaccination on decreasing total mortality disappeared. This is because nations that lack BCG vaccination are concentrated in Western Europe, which is near an epicenter of COVID-19. Therefore some previous reports are now considered to be affected by this artifact; the result may have been flawed by dispersal from an epicenter. However, some results showed weakly significant differences in the number of deaths at a particular time among BCG obligatory and non-BCG nations (especially the use of Japanese BCG strain Tokyo 172). However, these results are affected by the results of three countries and the effect of BCG vaccination remains inconclusive. The result of 3) showed that the maximum daily increasing rate in death among nations showed no significant difference among BCG vaccination policies. In the present study, although some results showed statistically significant differences among BCG vaccination policies, they may be affected by the impact of various other factors, such as national infection-control policies, social distancing, behavioral changes of people, possible previous local epidemics of closely related viruses, or inter-population differences in ACE2 or other genetic polymorphism. Further research is needed to better understand the underlying cause of the observed differences in infection and mortality of the disease among nations. Nevertheless, our results show that the effect of past BCG vaccination, if any, can be masked by many other factors. Therefore, the possible effect might be relatively small. In fact, in Japan, where almost all citizens have been vaccinated, COVID-19 cases are constantly increasing. Given the importance of peoples behavior in preventing viral propagation, the spread of optimism triggered by this hypothesis would be harmful to BCG vaccination nations.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Masakazu Asahara", + "author_inst": "Aichi Gakuin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069716", "rel_title": "Years of life lost due to the psychosocial consequences of COVID19 mitigation strategies based on Swiss data", @@ -1547964,53 +1548812,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.04.17.20070094", - "rel_title": "COVID-19 Outbreak Prediction with Machine Learning", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070094", - "rel_abs": "Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sina F. Ardabili", - "author_inst": "Thuringian Institute of Sustainability and Climate Protection, 07743 Jena, Germany" - }, - { - "author_name": "Amir MOSAVI", - "author_inst": "Obuda University" - }, - { - "author_name": "Pedram Ghamisi", - "author_inst": "Machine Learning Group, Exploration Division, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden" - }, - { - "author_name": "Filip Ferdinand", - "author_inst": "Department of Mathematics and Informatics, J. Selye University, 94501 Komarno, Slovakia" - }, - { - "author_name": "Annamaria R. Varkonyi-Koczy", - "author_inst": "Department of Mathematics and Informatics, J. Selye University, 94501 Komarno, Slovakia" - }, - { - "author_name": "Uwe Reuter", - "author_inst": "Faculty of Civil Engineering, Technische University Dresden" - }, - { - "author_name": "Timon Rabczuk", - "author_inst": "Institute of Structural Mechanics (ISM), Bauhaus-University Weimar, 99423 Weimar, Germany" - }, - { - "author_name": "Peter M. Atkinson", - "author_inst": "Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.17.20070086", "rel_title": "Estimating the impact of COVID-19 control measures using a Bayesian model of physical distancing", @@ -1548930,6 +1549731,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.052290", + "rel_title": "Dynamical asymmetry exposes 2019-nCoV prefusion spike", + "rel_date": "2020-04-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.052290", + "rel_abs": "The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. The study finds 2019-nCoV to adopt a unique strategy by undertaking a dynamic conformational asymmetry induced by a few unique inter-chain interactions. This results in two prevalent asymmetric structures of spike where one or two spike heads lifted up undergoing a dynamic transition likely to enhance rapid recognition of the host-cell receptor turning on its high-infectivity. The crucial interactions identified in this study are anticipated to potentially affect the efficacy of therapeutic targets.\n\nOne Sentence SummaryInter-chain-interaction driven rapid symmetry breaking strategy adopted by the prefusion trimeric spike protein likely to make 2019-nCoV highly infective.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Susmita Roy", + "author_inst": "Indian Institute of Science Education and Research Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.04.16.20068163", "rel_title": "Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones", @@ -1549694,29 +1550514,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.16.20068312", - "rel_title": "COVID-19 Outbreak Situations in Bangladesh: An Empirical Analysis", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20068312", - "rel_abs": "COVID-19 disease, as popularly known as Coronavirus 2019 disease, has been emerged from Wuhan, China in December 2019 and now is a pandemic for almost every nation in the earth. It affects every country without considering countrys race, nationality and economic status. This paper aims at analysing primarily the current situations of Bangladesh and predicting infections and deaths for moderated term intervals by a proposed projection technique called Infection Trajectory-Pathway Strategy (ITPS) and for short term intervals prediction for total infections, deaths along with total number of severe patients and Intensive Care Unit (ICU) patients by polynomial regression modeling approach. Since April 7, Bangladesh has started to face critical situations as the number of infections has accelerated very fast in the following days. However, the fatality rate decreases considerably from 15.7 on April 1 to 4.9 on April 14, which is still high among the south asian countries. Of the 1012 cases reported on April 14, almost 70% are the male, 42% are from the capital Dhaka. We have found that the potential pathway of infections for Bangldesh would be the similar pathways that are experienced by Austria, Netherlands, Israel, France and United Kingdom. These countries are ahead a number of weeks and days in terms of infection cases since their 100-th confirmed cases. Our proposed projection method ITPS suggests that by May 10, Bangladesh will cross 12000 incidences and 720 deaths which, by May 16 will be 27000 and 1644 respectively. On the other hand, the regression model suggests that by the end of April, total number of infections, deaths, severe patients and ICU patients will be 5780, 347, 775, and 694 respectively. This study will be favorable for the administrative units of Bangladesh to plan for the next few weeks and to consider various aspects related to the control of COVID-19 outspread in Bangladesh.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Md Hasinur Rahaman Khan", - "author_inst": "University of Dhaka, Bangladesh" - }, - { - "author_name": "Ahmed Hossain", - "author_inst": "North South University, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20068213", "rel_title": "Coronavirus Disease (COVID-19) Pandemic: An Overview of Systematic Reviews", @@ -1550380,6 +1551177,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071605", + "rel_title": "Spatial analysis of COVID-19 spread in Iran: Insights into geographical and structural transmission determinants at a province level", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071605", + "rel_abs": "The Islamic Republic of Iran reported its first COVID-19 cases by 19th February 2020, since then it has become one of the most affected countries, with more than 73,000 cases and 4,585 deaths at the date. Spatial modeling could be used to approach an understanding of structural and sociodemographic factors that have impacted COVID-19 spread at a province-level in Iran. In the present paper, we developed a spatial statistical approach to describe how COVID-19 cases are spatially distributed and to identify significant spatial clusters of cases and how the socioeconomic features of Iranian provinces might predict the number of cases. We identified a cluster of provinces with significantly higher rates of COVID-19 cases around Tehran, which indicated that the spread of COVID-19 within Iran was spatially correlated. Urbanized, highly connected provinces with older population structures and higher average temperatures were the most susceptible to present a higher number of COVID-19 cases. Interestingly, literacy is a protective factor that might be directly related to health literacy and compliance with public health measures. These features indicate that policies related to social distancing, protecting older adults, and vulnerable populations, as well as promoting health literacy, might be targeted to reduce SARS-CoV2 spread in Iran. Our approach could be applied to model COVID-19 outbreaks in other countries with similar characteristics or in case of an upturn in COVID-19 within Iran.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ricardo Ram\u00edrez-Aldana", + "author_inst": "Research Division, Instituto Nacional de Geriatr\u00eda (INGER), Anillo Perif. 2767, San Jeronimo Lidice, La Magdalena Contreras, 10200, Mexico City, Mexico." + }, + { + "author_name": "Juan Carlos Gomez-Verjan", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.19.20071712", "rel_title": "Potential magnitude of COVID-19-induced healthcare resource depletion in Ontario, Canada", @@ -1550976,37 +1551800,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.17.20070292", - "rel_title": "COVID-19 Epidemic Dynamics and Population Projections from Early Days of Case Reporting in a 40 million population from Southern India", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070292", - "rel_abs": "India reported its first COVID19 case on 30 January 2020. Since then the epidemic has taken different trajectories across different geographical locations in the country. This study explores the population aggregated trajectories of COVID19 susceptible, infected and recovered or dead cases in the south Indian state of Telangana with a population of approximately 40 million. Information on cases reported from March 2 to April 4 was collated from government records. The susceptible-infected-removed (SIR) model for the spread of an infectious disease was used. Transmission parameters were extracted from existing literature that has emerged over past weeks from other regions with similar population densities as Telangana. Optimisation algorithms were used to get basic reproduction rate for different phases of nonpharmaceutical interventions rolled by the government. Peak accumulation is projected towards end of July with 36% of the population being infected by August 2020 if the population lockdown or social distancing mechanism is not continued. The number of deaths assuming no intervention is projected to be 488000 (95% CI: (329400, 646600)). A draconian enforcement of population lockdown combined with hand and face hygiene adherence would reduce the transmission by at least 99.7% whereas partial social distancing and hygiene would reduce it by 51.2%. Transmission parameters reported should be interpreted with caution as they are population aggregated and do not consider unique characteristics of susceptibility among micro-clusters and vulnerable individuals. More data will need to be collected to optimize transmission parameters and evaluate the full complexity, to simulate real world scenarios in the models.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rashmi Pant", - "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" - }, - { - "author_name": "Lincoln Priyadarshi Choudhry", - "author_inst": "Krashapana consultancy private limited" - }, - { - "author_name": "Jammy Guru Rajesh", - "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" - }, - { - "author_name": "Vijay V Yeldandi", - "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.17.20070318", "rel_title": "Effects of medical resource capacities and intensities of public mitigation measures on outcomes of COVID-19 outbreaks", @@ -1551702,6 +1552495,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20064691", + "rel_title": "Development and validation of an early warning score (EWAS) for predicting clinical deterioration in patients with coronavirus disease 2019", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20064691", + "rel_abs": "BackgroundSince the pandemic outbreak of coronavirus disease 2019 (COVID-19), the health system capacity in highly endemic areas has been overwhelmed. Approaches to efficient management are urgently needed. We aimed to develop and validate a score for early prediction of clinical deterioration of COVID-19 patients.\n\nMethodsIn this retrospective multicenter cohort study, we included 1138 mild to moderate COVID-19 patients admitted to 33 hospitals in Guangdong Province from December 27, 2019 to March 4, 2020 (N =818; training cohort), as well as two hospitals in Hubei Province from January 21 to February 22, 2020 (N =320; validation cohort) in the analysis.\n\nResultsThe 14-day cumulative incidences of clinical deterioration were 7.9% and 12.1% in the training and validation cohorts, respectively. An Early WArning Score (EWAS) (ranging from 0 to 4.5), comprising of age, underlying chronic disease, neutrophil to lymphocyte ratio, C-reactive protein, and D-dimer levels, was developed (AUROC: 0.857). By applying the EWAS, patients were categorized into low-, medium-, and high risk groups (cut-off values: two and three). The 14-day cumulative incidence of clinical deterioration in the low-risk group was 1.8%, which was significantly lower than the incidence rates in the medium-(14.4%) and high-risk (40.9%) groups (P <.001). The predictability of EWAS was similar in the validation cohort (AUROC =0.781), patients in the low-, medium-, and high-risk groups had 14-day cumulative incidences of 2.6%, 10.0%, and 25.7%, respectively (P <.001).\n\nConclusionThe EWAS, which is based on five common parameters, can predict COVID-19-related clinical deterioration and may be a useful tool for a rapid triage and establishing a COVID-19 hierarchical management system that will greatly focus clinical management and medical resources to reduce mortality in highly endemic areas.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Yabing Guo", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Yingxia Liu", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Jiatao Lu", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Rong Fan", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Fuchun Zhang", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Xueru Yin", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Zhihong Liu", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Qinglang Zeng", + "author_inst": "Honghu People's Hospital" + }, + { + "author_name": "Jing Yuan", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Shufang Hu", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Qiongya Wang", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Baolin Liao", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Mingxing Huang", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Sichun Yin", + "author_inst": "The Ninth Dongguan People's Hospital" + }, + { + "author_name": "Xilin Zhang", + "author_inst": "The Fourth Foshan People's Hospital" + }, + { + "author_name": "Rui Xin", + "author_inst": "Guangdong Second Provincial General Hospital" + }, + { + "author_name": "Zhanzhou Lin", + "author_inst": "Huizhou Central People's Hospital" + }, + { + "author_name": "Changzheng Hu", + "author_inst": "Jiangmen Central Hospital" + }, + { + "author_name": "Boliang Zhao", + "author_inst": "The First Zhaoqing People's Hospital" + }, + { + "author_name": "Ridong He", + "author_inst": "Zhanjiang Central People's Hospital" + }, + { + "author_name": "Minfeng Liang", + "author_inst": "The First Foshan People's Hospital" + }, + { + "author_name": "Zheng Zhang", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Li Liu", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Jian Sun", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Lu Tang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Lisi Deng", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Jinyu Xia", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Xiaoping Tang", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Lei Liu", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Jinlin Hou", + "author_inst": "Nanfang Hospital, Southern Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20064931", "rel_title": "Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region", @@ -1552406,65 +1553334,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.17.20058545", - "rel_title": "Histopathology and Ultrastructural Findings of Fatal COVID-19 Infections", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20058545", - "rel_abs": "BackgroundSARS-CoV-2 is the cause of an ongoing pandemic with a projected 100,000 to 240,000 U.S. deaths. To date, documentation of histopathologic features in fatal cases of COVID-19 has been limited due to small sample size and incomplete organ sampling.\n\nMethodsPost-mortem examinations were performed on 12 fatal COVID-19 cases in Washington State during February-March 2020. Clinical and laboratory data were reviewed. Tissue examination of all major organs was performed by light microscopy and electron microscopy. The presence of viral RNA in sampled tissues was tested by RT-PCR.\n\nResultsAll 12 patients were older with significant preexisting comorbidities. The major pulmonary finding was diffuse alveolar damage in the acute and/or organizing phases with virus identified in type I and II pneumocytes by electron microscopy. The kidney demonstrated viral particles in the tubular epithelium, endothelium, and podocytes without significant inflammation. Viral particles were also observed in the trachea and large intestines. SARS-CoV-2 RNA was detected in the cardiac tissue of a patient with lymphocytic myocarditis. RT-PCR also detected viral RNA in the subcarinal lymph nodes, liver, spleen, and large intestines.\n\nConclusionSARS-CoV-2 represents the third novel coronavirus to cause widespread human disease since 2002. Similar to SARS and MERS, the primary pathology was diffuse alveolar damage with virus located in the pneumocytes. However, other major organs including the heart and kidneys may be susceptible to viral replication and damage leading to increased mortality in those with disseminated disease. Understanding the pathology of SARS-CoV-2 will be essential to design effective therapies.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Benjamin T Bradley", - "author_inst": "University of Washington" - }, - { - "author_name": "Heather Maioli", - "author_inst": "University of Washington, Seattle, WA" - }, - { - "author_name": "Robert Johnston", - "author_inst": "King County Medical Examiner's Office, Seattle, WA" - }, - { - "author_name": "Irfan Chaudhry", - "author_inst": "King County Medical Examiner's Office, Seattle, WA" - }, - { - "author_name": "Susan L. Fink", - "author_inst": "University of Washington, Seattle, WA" - }, - { - "author_name": "Haodong Xu", - "author_inst": "University of Washington, Seattle, WA" - }, - { - "author_name": "Behzad Najafian", - "author_inst": "University of Washington, Seattle, WA" - }, - { - "author_name": "Desiree Marshall", - "author_inst": "University of Washington, Seattle, WA" - }, - { - "author_name": "J. Matthew Lacy", - "author_inst": "Snohomish County Medical Examiner's Office, Everett, WA" - }, - { - "author_name": "Timothy Williams", - "author_inst": "King County Medical Examiner's Office" - }, - { - "author_name": "Nicole Yarid", - "author_inst": "King County Medical Examiner's Office" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.04.15.20066266", "rel_title": "A Randomized, Single-blind, Group sequential, Active-controlled Study to evaluate the clinical efficacy and safety of \u03b1-Lipoic acid for critically ill patients with coronavirus disease 2019(COVID-19)", @@ -1553852,6 +1554721,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.20.051219", + "rel_title": "Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays", + "rel_date": "2020-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.051219", + "rel_abs": "SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kate H.D. Crawford", + "author_inst": "University of Washington" + }, + { + "author_name": "Rachel Eguia", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrea N Loes", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Keara D Malone", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Caitlin R Wolf", + "author_inst": "University of Washington" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael Murphy", + "author_inst": "University of Washington" + }, + { + "author_name": "Deleah Pettie", + "author_inst": "University of Washington" + }, + { + "author_name": "Neil P King", + "author_inst": "University of Washington" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.20.051581", "rel_title": "Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease", @@ -1554664,25 +1555604,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.15.20066712", - "rel_title": "COVID-19 outbreak in Greece has passed its rising inflection point and stepping into its peak", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066712", - "rel_abs": "Since the beginning of 2020, COVID-19 is the most urgent and challenging task for the international scientific community, in order to identify its behaviour, track its progress and plan effective mitigation policies. In this study, Greece is the main focus for assessing the national outbreak and estimating the general trends and outlook of it. Multiple data analytics procedures, spectral decomposition and curve-fitting formulations are developed based on the data available at hand. Standard SIEQRDP epidemic modelling is applied for Greece and for the general region around it, providing hints for the outbreak progression in the mid- and long-term, for various infections under-reporting rates. The overall short-term outlook for Greece seems to be towards positive, with a downward trend in infections rate daily increase (i.e., now beyond the exponential growth rate), a possible peak within a few days beyond April 14th, as well as the high availability level of ICU w.r.t. expected demand at peak. On the negative side, the fade-out period seems to be in the order of several months, with high probability of recurrent surges of the outbreak. The mitigation policies for the next day should be focused on close tracking of the epidemic via large-scale tests, strict border checking in international travelling and an adaptive plan for selective activation of mitigation measures when deemed necessary.\n\nSignificance StatementThis study focuses on the COVID-19 outbreak in Greece and provides data-driven epidemic modelling and experimental results regarding the current state. Based on these results, the overall short-term outlook for Greece seems to be towards positive, having recently passed the rising inflection point and approaching the peak of the infections, and most probably capable of covering the projected ICU demand peak by a large margin. On the downside, the fade-out period seems to be in the order of several months, with high probability of recurrent surges of the outbreak. The next day mitigation policies need to be carefully planned, highly adaptive and based on close tracking of the outbreak via large-scale testing in the general population.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Harris V Georgiou", - "author_inst": "University of Piraeus" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.15.20064980", "rel_title": "Crowding and the epidemic intensity of COVID-19 transmission", @@ -1555446,6 +1556367,157 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.17.046375", + "rel_title": "Rapid development of an inactivated vaccine for SARS-CoV-2", + "rel_date": "2020-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.046375", + "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has brought about an unprecedented crisis, taking a heavy toll on human health, lives as well as the global economy. There are no SARS-CoV-2-specific treatments or vaccines available due to the novelty of this virus. Hence, rapid development of effective vaccines against SARS-CoV-2 is urgently needed. Here we developed a pilot-scale production of a purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc), which induced SARS-CoV-2-specific neutralizing antibodies in mice, rats and non-human primates. These antibodies potently neutralized 10 representative SARS-CoV-2 strains, indicative of a possible broader neutralizing ability against SARS-CoV-2 strains circulating worldwide. Immunization with two different doses (3g or 6 g per dose) provided partial or complete protection in macaques against SARS-CoV-2 challenge, respectively, without any antibody-dependent enhancement of infection. Systematic evaluation of PiCoVacc via monitoring clinical signs, hematological and biochemical index, and histophathological analysis in macaques suggests that it is safe. These data support the rapid clinical development of SARS-CoV-2 vaccines for humans.\n\nOne Sentence SummaryA purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc) confers complete protection in non-human primates against SARS-CoV-2 strains circulating worldwide by eliciting potent humoral responses devoid of immunopathology", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Qiang Gao", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Linlin Bao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Haiyan Mao", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lin Wang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Kangwei Xu", + "author_inst": "Division of Respiratory Virus Vaccines, National Institute for Food and Drug Control" + }, + { + "author_name": "minnan Yang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yajing Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Ling Zhu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Nan Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhe Lv", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Hong Gao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Xiaoqin Ge", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Biao Kan", + "author_inst": "National Institute for Communicable Disease Control and Prevention, China CDC" + }, + { + "author_name": "Yaling Hu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Jiangning Liu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Fang Cai", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Deyu Jiang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Yanhui Yin", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Chengfeng Qin", + "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Jing Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Xuejie Gong", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Xiuyu Lou", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wen Shi", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Dongdong Wu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Hengming Zhang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Lang Zhu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Wei Deng", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Yurong Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Jinxing Lu", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Changgui Li", + "author_inst": "Division of Respiratory Virus Vaccines, National Institute for Food and Drug Control" + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Weidong Yin", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Yanjun Zhang", + "author_inst": "Zhejiang Center for Disease Control and Prevention" + }, + { + "author_name": "Chuan Qin", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.20060160", "rel_title": "Patient-derived mutations impact pathogenicity of SARS-CoV-2", @@ -1556130,53 +1557202,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.04.17.045161", - "rel_title": "An in silico map of the SARS-CoV-2 RNA Structurome", - "rel_date": "2020-04-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.045161", - "rel_abs": "SARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ryan J Andrews", - "author_inst": "Iowa State University" - }, - { - "author_name": "Jake M Peterson", - "author_inst": "Iowa State University" - }, - { - "author_name": "Hafeez F Haniff", - "author_inst": "Scripps Florida" - }, - { - "author_name": "Jonathan Chen", - "author_inst": "Scripps Florida" - }, - { - "author_name": "Cristopher Williams", - "author_inst": "Scripps Florida" - }, - { - "author_name": "Maison Greffe", - "author_inst": "Scripps Florida" - }, - { - "author_name": "Matthew D Disney", - "author_inst": "Scripps Florida" - }, - { - "author_name": "Walter N Moss", - "author_inst": "Iowa State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.17.047548", "rel_title": "Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets", @@ -1557420,6 +1558445,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.14.20065466", + "rel_title": "Modelling strategies to predict hospital demand during the COVID-19 outbreak in Bogota, Colombia", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065466", + "rel_abs": "Colombia, like many developing nations, does not have a strong health system able to respond to a pandemic of the magnitude of Covid-19. There is an increasing need to create a model that allows particular clinics and hospitals to estimate the number of patients that require Intensive Care Units-ICU care (critical), and the number of patients that require hospital care (severe), but not ICU care, in order to manage their limited resources.\n\nThis paper presents a prediction of the total number of ICU and regular beds that will be needed during the pandemic COVID-19 for Bogota-Colombia. We use a SEIR model that includes three different compartments of infection: those who can stay at home, those in regular hospital beds and those in need of ICU treatment. The model allows for a time varying transmission rate which we use to incorporate the measures introduced by the government over the period of one semester. The model predicts that by mid October 2020, the city will need 4 524 prevalent ICUs needed and 16 738 regular hospital beds needed. By the third week of July 2020, the number of patients that need ICUs will overpass the capacity set at 1 200 beds for ICU hospital beds in the city. The model predicts that the death toll by the same date will reach 1 752 people and the number of cases will be 30 216 inhabitants by then. We provide a Shiny app available in https://claudia-rivera-rodriguez.shinyapps.io/shinyappcovidclinic/. The original values in the app reproduce the results of this paper, but the parameters and starting values can be changed according to the users needs. COVID-19 has posed too many challenges to health systems around the globe, this model is an useful tool for cities, hospitals and clinics in Colombia that need to prepare for the excess demand of services that a pandemic like this one generates. Unfortunately, the model predicts that by the third week of July the projected capacity of the system in Bogota will not be enough. We expect the lockdown rules strength in the future days, so the death toll is not as bad as predicted by this model.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Claudia Rivera-Rodriguez", + "author_inst": "The University of Auckland" + }, + { + "author_name": "Beatriz Piedad Urdinola", + "author_inst": "National University of Colombia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.14.20065706", "rel_title": "Has mortality due to other causes increased during the Covid-19 pandemic? Early evidence from England and Wales", @@ -1557900,37 +1558948,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.15.20066548", - "rel_title": "Social Isolation as a predictor for mortality: Implications for COVID-19 prognosis", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066548", - "rel_abs": "The health benefits of social support have been widely documented. However, the social distancing practices from the COVID-19 pandemic is causing social disruption on a grand scale, potentially causing poor health outcomes. Through Google Trends analysis, we found a COVID-19-related surge in interest surrounding \"loneliness.\" We assessed if social isolation and loneliness increase the risk for all-cause and cardiovascular disease (CVD) mortality (ICD-10: I00-I99) and used the data to create a conceptual framework. Using the 10-year overall and cardiovascular mortality follow-up data (n = 12,019) from the National Health and Nutrition Examination Survey (1999-2008), we conducted survival analyses and found that individuals who experience social isolation or loneliness have a significantly higher likelihood of overall and CVD mortality than those without support. These effects generally remained strong with further adjustment for NHANES-detected health and demographic differences showing the need to address COVID-19 related loneliness through increasing social nearing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sri Banerjee", - "author_inst": "Walden University School of Health Sciences" - }, - { - "author_name": "Gary Burkholder", - "author_inst": "Walden University School of Psychology" - }, - { - "author_name": "Beyan Sana", - "author_inst": "Johns Hopkins University COVID-19 team" - }, - { - "author_name": "Mihalyi Szirony", - "author_inst": "Walden University School of Counseling" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20066480", "rel_title": "Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus", @@ -1558778,6 +1559795,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.044503", + "rel_title": "SARS-CoV-2 is transmitted via contact and via the air between ferrets.", + "rel_date": "2020-04-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.044503", + "rel_abs": "SARS-CoV-2, a coronavirus that newly emerged in China in late 2019 1,2 and spread rapidly worldwide, caused the first witnessed pandemic sparked by a coronavirus. As the pandemic progresses, information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets. Intranasal inoculation of donor ferrets resulted in a productive upper respiratory tract infection and long-term shedding, up to 11 to 19 days post-inoculation. SARS-CoV-2 transmitted to four out of four direct contact ferrets between 1 and 3 days after exposure and via the air to three out of four independent indirect recipient ferrets between 3 and 7 days after exposure. The pattern of virus shedding in the direct contact and indirect recipient ferrets was similar to that of the inoculated ferrets and infectious virus was isolated from all positive animals, showing that ferrets were productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings 3.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mathilde Richard", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Adinda Kok", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Dennis de Meulder", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Theo M. Bestebroer", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Mart M. Lamers", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Nisreen M.A. Okba", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Martje Fentener van Vlissingen", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Barry Rockx", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Bart L. Haagmans", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Ron A.M. Fouchier", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Sander Herfst", + "author_inst": "ErasmusMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.20064733", "rel_title": "Chest Computed Tomography for the Diagnosis of Patients with Coronavirus Disease 2019 (COVID-19): A Rapid Review and Meta-Analysis", @@ -1559446,89 +1560526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.13.20064360", - "rel_title": "Supportive Care for Patient with Respiratory Diseases: An Umbrella Review", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064360", - "rel_abs": "BackgroundSupportive treatment is an important and effective part of the management for patients with life-threatening diseases. This study aims to identify and evaluate the forms of supportive care for patients with respiratory diseases.\n\nMethodsAn umbrella review of supportive care for patient respiratory diseases was undertaken. We comprehensively searched the following databases: Medline, EMBASE, Web of Science, CNKI (China National Knowledge Infrastructure), Wanfang Data and CBM (SinoMed) from their inception to 31 March 2020, and other sources to identify systematic reviews and meta-analyses related to supportive treatments for patient with respiratory diseases including COVID-19, SARS, MERS and influenza. We assessed the methodological quality using the AMSTAR score and the quality of the evidence for the primary outcomes of each included systematic review and meta-analysis.\n\nResultsWe included 18 systematic reviews and meta-analyses in this study. Most studies focused on the respiratory and circulatory support. Ten studies were of high methodological quality, five studies of medium quality, and three studies of low quality. According to four studies extracorporeal membrane oxygenation did not reduce mortality in adults (OR/RR ranging from 0.71 to 1.28), but two studies reported significantly lower mortality in patients receiving venovenous extracorporeal membrane oxygenation than in the control group (OR/RR ranging from 0.38 to 0.73). Besides, monitoring of vital signs and increasing the number of medical staff may also reduce the mortality in patients with respiratory diseases.\n\nConclusionsOur overview suggests that supportive care may reduce the mortality of patients with respiratory diseases to some extent. However, the quality of evidence for the primary outcomes in the included studies was low to moderate. Further systematic reviews and meta-analyses are needed to address the evidence gap regarding the supportive care for SARS, MERS and COVID-19.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Xufei Luo Sr.", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Meng Lv Jr.", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Xiaoqing Wang Jr.", - "author_inst": "Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Xin Long Jr.", - "author_inst": "Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Mengjuan Ren Jr.", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Xianzhuo Zhang Sr.", - "author_inst": "The First School of Clinical Medicine, Lanzhou University" - }, - { - "author_name": "Yunlan Liu Jr.", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Weiguo Li Sr.", - "author_inst": "Chongqing Key Laboratory of Pediatrics" - }, - { - "author_name": "Qi Zhou Jr.", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - }, - { - "author_name": "Yanfang Ma Jr.", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - }, - { - "author_name": "Toshio Fukuoka Sr.", - "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital" - }, - { - "author_name": "Hyeong Sik Ahn Jr.", - "author_inst": "Department of Preventive Medicine, Korea University College of Medicine" - }, - { - "author_name": "Myeong Soo Lee Sr.", - "author_inst": "Korea Cochrane Centre, Korea" - }, - { - "author_name": "Zhengxiu Luo Sr.", - "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" - }, - { - "author_name": "Enmei Liu Sr.", - "author_inst": "Department of Respiratory Medicine, Childrens Hospital of Chongqing Medical University" - }, - { - "author_name": "Xiaohui Wang Jr.", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Yaolong Chen Sr.", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.14.20065094", "rel_title": "Rapid Open Development and Clinical Validation of Multiple New 3D-Printed Nasopharyngeal Swabs in Response to the COVID-19 Pandemic", @@ -1560420,6 +1561417,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20067348", + "rel_title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20067348", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription polymerase chain reaction (RT-PCR) assay, to detect the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are critical, as increased diagnostic availability and efficiency would benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including benchmarking with 597 clinically diagnosed patient samples against a standardised and sensitive diagnostic system, show that direct RT-PCR is a viable option to extraction-based COVID-19 diagnostics. Furthermore, using controlled amounts of active SARS-CoV-2, we evaluated performance of generic buffers as sample medium for the direct RT-PCR assay, identifying several suitable formulations. We also confirmed the effectiveness of heat inactivation of SARS-CoV-2 by plaque assay. Significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feed directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ioanna Smyrlaki", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Ekman", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Antonio Lentini", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Nuno Rufino de Sousa", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Natali Papanicoloau", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Vondracek", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Johan Aarum", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Hamzah Safari", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Shaman Muradrasoli", + "author_inst": "Public Health Agency of Sweden" + }, + { + "author_name": "Antonio Gigliotti Rothfuchs", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jan Albert", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Bj\u00f6rn H\u00f6gberg", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Bj\u00f6rn Reinius", + "author_inst": "Karolinska Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20064501", "rel_title": "What influences COVID-19 infection rates: A statistical approach to identify promising factors applied to infection data from Germany", @@ -1560716,29 +1561780,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.15.20065532", - "rel_title": "Estimation of Tunisia COVID-19 infected cases based on mortality rate", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065532", - "rel_abs": "Estimating the number of people affected by COVID-19 is crucial in deciding which public health policies to follow. The authorities in different countries carry out mortality counts. We propose that the mortality reported in each country can be used to create an index of the number of actual cases at a given time. The specificity of whether or not deaths are rapid or not by COVID-19 also affects the number of actual cases. The number of days between the declaration of illness and death varies between 12 and 18 days. For a delay of 18 days, and using an estimated mortality rate of 2%, the number of cases in April 2020 in Tunisia would be 5 580 people. The pessimistic scenario predicts 22 320 infected people, and the most optimistic predicts 744 (which is the number of reported cases on April 12, 2020). Modeling the occurrence of COVID-19 cases is critical to assess the impact of policies to prevent the spread of the virus.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ines Abdeljaoued-Tej", - "author_inst": "BIMS Laboratory, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia" - }, - { - "author_name": "Marc Dhenain", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.12.20062679", "rel_title": "Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases", @@ -1561510,6 +1562551,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.20061044", + "rel_title": "EFFECTIVENESS OF BASELINE AND POST-PROCESSED CHEST X-RAY IN NONEARLY COVID-19 PATIENTS", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20061044", + "rel_abs": "BackgroundCT is a very sensitive technique to detect pneumonia in COVID-19 patients. However, it is impaired by high costs, logistic issues and high risk of exposure.\n\nChest x-ray (CXR) is a low-cost, low-risk, not time consuming technique and is emerging as the recommended imaging modality to use in COVID-19 pandemic.\n\nThis technique, although less sensitive than CT-scan, can provide useful information about pulmonary involvement.\n\nPurposeTo describe chest x-ray features of COVID-19 pneumonia and to evaluate the sensitivity of this technique in detecting pneumonia. A further scope is to assess the effectiveness of a post-processing algorithm in improving lung lesions detectability.\n\nMaterials and Methods72 patients with laboratory-confirmed COVID-19 underwent bedside chest X-ray.\n\nTwo radiologists were asked to express their opinion about: (i) presence of pneumonia (negative or positive); (ii) localization (unilateral or bilateral); (iii) topography (according to pulmonary fields); (iv) density (non consolidative ground-glass or inhomogeneous opacities; consolidative nodular-type or triangular; mixed consolidative e non-consolidative); and (v) presence of pleural effusion. The point (i) was evaluated separately, while the other points in consensus.\n\nA quality assessment of post-processed x-ray images was performed by two different readers.\n\nResultsThe agreement about presence of pneumonia was almost perfect with K value of 0.933 and p < 0.001.\n\nSensitivity was 69%.\n\nThe following findings were seen: unilateral lung involvement in 50%; lower lung lesions in 54%; peripheral distribution in 48%; and non-consolidative pattern in 44%.\n\nPost-processed images improved the detection of lesions in 7 out 72 patients ({cong}10%)\n\nConclusionCXR owns a good sensitivity in detecting COVID-19 lung involvement. Use of post-processing algorithm can improve detection of lesions. Our data support recommendations of the Radiological Society of North America (RSNA) to consider chest x-ray as first step imaging examination in Covid-19 patients.\n\nSUMMARYBedside CXR has a good sensitivity in evaluating COVID-19 lung involvement in hospitalized patients and should be considered as the first step imaging technique according to RSNA recommendations.\n\nKEY RESULTSO_LIBedside CXR has a good sensitivity in evaluating COVID-19 lung involvement in non-early clinical cases.\nC_LIO_LIThe most common findings of lung involvement were slight different from the well-described CT-ones, with less common patterns of bilateral and peripheral distribution.\nC_LIO_LIPost-processing algorithm enhances detection of pulmonary lesions.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Michele Gaeta", + "author_inst": "University of Messina" + }, + { + "author_name": "Giuseppe Cicero", + "author_inst": "University of Messina" + }, + { + "author_name": "Maria Adele Marino", + "author_inst": "University of Messina" + }, + { + "author_name": "Tommaso D'Angelo", + "author_inst": "University of Messina" + }, + { + "author_name": "Enrico Maria Mormina", + "author_inst": "University of Messina" + }, + { + "author_name": "Silvio Mazziotti", + "author_inst": "University of Messina" + }, + { + "author_name": "Alfredo Blandino", + "author_inst": "University of Messina" + }, + { + "author_name": "Giulio Siracusano", + "author_inst": "University of Catania" + }, + { + "author_name": "Aurelio La Corte", + "author_inst": "University of Catania" + }, + { + "author_name": "Massimo Chiappini", + "author_inst": "Instituto Nazionale di Geofisica e Vulcanologia" + }, + { + "author_name": "Giovanni Finocchio", + "author_inst": "University of Messina" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.12.20062695", "rel_title": "Shut it down: a cross country panel analysis on the efficacy of lockdown measures", @@ -1561918,25 +1563018,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.12.20062919", - "rel_title": "Analysis of the SARS-Cov-2 epidemic in Lombardy (Italy) in its early phase. Are we going in the right direction?", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062919", - "rel_abs": "BACKGROUNDWe described the epidemiological features of the codiv-19 outbreak, and evaluated the impact of interventions measures on the epidemic in the Lombardy region, Italy.\n\nMETHODSLaboratory-confirmed covid-19 cases reported through the beginning of April were extracted from the Italian Civil Protection database. Based on key events and interventions, we divided the epidemic into three periods: before February 21, from February 22 to early March, after early March. We compared epidemiological characteristics across periods and developed a modified susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions. We explicitly took into account for unascertained cases (positive cases with no symptoms or mild symptoms that have not been accounted for in official statistics).\n\nRESULTSCurrently, the number of positive active cases has increased to around 30,000 in the Lombardy region. Due to restriction measures, the effective reproduction number dropped from 3.33 (95% CI: 2.03-3.69) during the first period, to 2.36 (95% CI: 2.21-2.70) during the second period. In the third period, the effective reproduction number is estimated to have dropped to 1.49 (95% CI: 1.35-1.62). The model estimates a great proportion of unascertained cases, about 90% of infected people has not been accounted for in official statistics.\n\nCONCLUSIONSConsiderable countermeasures have slowed down the covid-19 outbreak in the Lombardy region. However, notwithstanding the long-lasting lockdown period, the epidemic is still not under control. The effective reproduction number, according to the model used in this work, is still greater than 1.0. Estimation of unascertained cases has important implications on continuing surveillance and interventions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Angelo Riccio", - "author_inst": "Universita' Parthenope di Napoli" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.12.20062588", "rel_title": "An SEIR Model for Assessment of Current COVID-19 Pandemic Situation in the UK", @@ -1562740,6 +1563821,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.13.20063644", + "rel_title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063644", + "rel_abs": "BackgroundAs governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. It is likely different countries and populations respond differently to the same NPIs and that these differences are reflected in the epidemic development.\n\nMethodsWe build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R0, due to changes in mobility patterns. We utilize mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R0 is estimated through the model.\n\nFindingsThe changes in mobility have a large overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The grocery and pharmacy sector is estimated to account for 97 % of the reduction in R0 (95% confidence interval [0{middle dot}79,0{middle dot}99]).\n\nInterpretationOur model predicts three-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium.\n\nFundingFinancial support: Swedish Research Council for Natural Science, grant No. VR-2016-06301 and Swedish E-science Research Center. Computational resources: Swedish National Infrastructure for Computing, grant No. SNIC-2019/3-319.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Patrick Bryant", + "author_inst": "Stockholm University/Science for Life Laboratory" + }, + { + "author_name": "Arne Elofsson", + "author_inst": "Stockholm University/Science for Life Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.13.20063610", "rel_title": "The December 2019 New Corona Virus Disease (SARS-CoV-2) Outbreak: A Behavioral Infectious Disease Policy Model", @@ -1563128,37 +1564232,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.14.20063636", - "rel_title": "Automated and semi-automated contact tracing: Protocol for a rapid review of available evidence and current challenges to inform the control of COVID-19", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20063636", - "rel_abs": "IntroductionTraditional approaches to case-finding, case isolation, and contact tracing methods have so far proved insufficient on their own to prevent the development of local epidemics of COVID-19 in many high-income countries despite relatively advanced public health systems. As a result, many governments have resorted to widespread social distancing measures and mass quarantines ( lock-downs) to reduce transmission and to prevent healthcare systems from being overwhelmed. However, such measures impose heavy human and societal costs. Automated or semi-automated digital contact tracing, in conjunction with scaled-up community testing, has been proposed as a key part of exit strategies from lockdowns. However, the effectiveness of these approaches to contact tracing is unclear, and to be effective, trusted, and widely adopted such technology must overcome several challenges.\n\nMethods and analysisWe will perform a rapid systematic review to assess the effectiveness of automated and semi-automated digital tools for contact tracing, and identify key considerations for successful implementation, to inform the control of COVID-19. We will search PubMed, EMBASE, EBSCO Medical COVID information portal, OVID Global Health, Cochrane Library, medRxiv, BioRxiv, and arXiv for peer-reviewed and pre-print papers on automated or semi-automated digital tools for contact tracing of COVID-19, another respiratory disease with pandemic potential (limited to SARS, MERS, or pandemic influenza), or Ebola, in human populations. Studies will be eligible if published in English between 1 January 2000 and 14 April 2020. We will synthesise study findings narratively and will consider meta-analysis if [≥] 3 suitable studies with comparable interventions and outcomes are available.\n\nEthics and disseminationEthical approval is not required for this review. We plan to disseminate findings via pre-print, journal publication, through social media and web-based platforms and through direct stakeholder engagement.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Isobel Braithwaite", - "author_inst": "Institute of Health Informatics, University College London" - }, - { - "author_name": "Tom Callender", - "author_inst": "Department of Applied Health Research, University College London" - }, - { - "author_name": "Miriam Bullock", - "author_inst": "UCL Collaborative Centre for Inclusion Health, University College London" - }, - { - "author_name": "Rob Aldridge", - "author_inst": "Institute of Health Informatics, University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.11.20061713", "rel_title": "The Potential role of Particulate Matter in the Spreading of COVID-19 in Northern Italy: First Evidence-based Research Hypotheses", @@ -1563758,6 +1564831,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.11.20061721", + "rel_title": "COVID-19-related mortality by age groups in Europe: A meta-analysis", + "rel_date": "2020-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061721", + "rel_abs": "Background and ObjectivesTo date, more than 1,000,000 confirmed cases and 65,000 deaths due to coronavirus disease 2019 (COVID-19) have been reported globally. Early data have indicated that older patients are at higher risk of dying from COVID-19 than younger ones, but precise international estimates of the age-breakdown of COVID-19-related deaths are lacking.\n\nMaterials and MethodsWe evaluated the distribution of COVID-19-related fatalities by age groups in Europe. On April 6, 2020, we systematically reviewed COVID-19-related mortality data from 32 European countries (European Union/European Economic Area and the United Kingdom). We collated official reports provided by local Public Health or Ministry of Health websites. We included countries if they provided data regarding more than 10 COVID-19-related deaths stratified by age according to pre-specified groups (i.e., < 40, 40-69, [≥] 70 years). We used random-effects meta-analysis to estimate the proportion of age groups among all COVID-19-related fatalities.\n\nResultsThirteen European countries were included in the review, for a total of 31,864 COVID-19-related deaths (range: 27-14,381 per country). In the main meta-analysis (including data from Germany, Hungary, Italy, Netherlands, Portugal, Spain, Switzerland; 21,522 COVID-19-related fatalities), the summary proportions of persons < 40, 40-69, and [≥] 70 years of age among all COVID-19-related deaths were 0.1% (0.0-0.2%; I2 24%), 12.8% (10.3-15.6%; I2 94%), and 84.8% (81.3-88.1%; I2 96%), respectively.\n\nConclusionsPeople under 40 years of age represent a small fraction of the total number of COVID-19-related deaths in Europe. These results may help health authorities respond to public concerns and guide future physical distancing and mitigation strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "J\u00e9r\u00e9mie F. Cohen", + "author_inst": "Inserm UMR 1153, Universite de Paris" + }, + { + "author_name": "Dani\u00ebl A. Korevaar", + "author_inst": "Department of Respiratory Medicine, Amsterdam University Medical Center, University of Amsterdam, PO Box 22700, 1100 DE, Amsterdam, The Netherlands" + }, + { + "author_name": "Soraya Matczak", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Jos\u00e9phine Brice", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Martin Chalumeau", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Julie Toubiana", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.12.20062869", "rel_title": "Cardiovascular Diseases and COVID-19 Mortality and Intensive Care Unit Admission: A Systematic Review and Meta-analysis", @@ -1564198,57 +1565310,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.11.20059170", - "rel_title": "Delayed-Phase Thrombocytopenia in Patients of Coronavirus Disease 2019 (COVID-19)", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20059170", - "rel_abs": "The pandemic COVID-19 pneumonia has engulfed the entire world. Hematopoietic system can also be affected by COVID-19. Thrombocytopenia at admission was prevalent, while late-phase or delayed-phase thrombocytopenia is obscure. This retrospective single-center case series analyzed patients with COVID-19 at the Union Hospital, Wuhan, China, from January 25th to March 9th, 2020. Analysis began on March 11th, 2020. COVID-19 associated delayed-phase thrombocytopenia was occurred in 11.8% percent of enrolled patients. The delayed-phase thrombocytopenia in COVID-19 is prone to develop in elderly patients or patients with low lymphocyte count on admission. The delayed-phase thrombocytopenia is significantly associated with increased length of hospital stay and higher ICU admission rate. Delayed-phase nadir platelet counts demonstrated a high and significantly negative linear correlation with B cell percentages and serum IL-6 levels. We also presented bone marrow aspiration pathology of three patients with delayed-phase thrombocytopenia, showing impaired maturation of megakaryocytes. We speculated that the delayed-phase platelet destruction might be mediated by antibodies, and suggest immunoregulatory treatment in severe patients to improve outcomes. Besides, clinicians need to pay attention to the delayed-phase thrombocytopenia especially at 3-4 weeks after symptom onset.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hao Zhou", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medial College, Huazhong University of Science and Technology" - }, - { - "author_name": "Wanxin Chen", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Ziping Li", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Bohan Yang", - "author_inst": "Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Qiong Zhou", - "author_inst": "Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Ping Wang", - "author_inst": "Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jianhua Zhu", - "author_inst": "Laboratory of Clinical Immunology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xuexing Chen", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Peng Yang", - "author_inst": "Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.04.11.20062018", "rel_title": "Assessment of N95 respirator decontamination and re-use for SARS-CoV-2", @@ -1565031,6 +1566092,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060905", + "rel_title": "COVID-19: A model correlating BCG vaccination to protection from mortality implicates trained immunity", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060905", + "rel_abs": "O_LIWe use a data quality model to demonstrate that BCG vaccination is correlated with protection from death from COVID19\nC_LIO_LIFrom a mechanistic perspective, BCG is well described to elicit its protective non-specific effects through the process of trained immunity.\nC_LIO_LITherapeutically enhancing trained immunity may therefore be an important mechanism in protection from the lethal effects of COVID19\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Cameron M. Green", + "author_inst": "Fresh Software A.G." + }, + { + "author_name": "Stephanie Fanucchi", + "author_inst": "Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town" + }, + { + "author_name": "Ezio T. Fok", + "author_inst": "Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands" + }, + { + "author_name": "Simone J.C.F.M. Moorlag", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Jorge Dominguez-Andres", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Yutaka Negishi", + "author_inst": "Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands" + }, + { + "author_name": "Leo A.B. Joosten", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Mihai G. Netea", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Musa M. Mhlanga", + "author_inst": "Radboud University, Radboud Institute for Molecular Life Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.11.20062372", "rel_title": "Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection", @@ -1565531,45 +1566643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.10.20060525", - "rel_title": "When Resources Are Scarce - Feasibility of Emergency Ventilation of Two Patients With One Ventilator", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060525", - "rel_abs": "A potential shortage of intensive care ventilators has led to the idea to ventilate more than one patient with a single ventilator. Besides other problems, this is associated with the lack of knowledge concerning distribution of tidal volume and the patients individual respiratory system mechanics.\n\nIn this study we used two simple hand-manufactured adaptors to connect physical models of two adult respiratory systems to one ventilator. The artificial lungs were ventilated in the pressure-controlled mode and we investigated if disconnecting one lung from the ventilation circuit for several breaths would allow to determine reliably the other lungs tidal volume and compliance.\n\nCompliances and volumes were measured both with the ventilator and external sensors corresponded well. However, tidal volumes measured via the ventilator were smaller compared to the tidal volumes measured via the external sensors with an absolute error of 5.3 {+/-} 2.5%. The tidal volumes of the individual artificial lungs were distributed in proportion to the compliances and did not differ relevantly when both artificial lungs were connected to when one was disconnected.\n\nWe conclude that in case of emergency, ventilation of two patients with one ventilator requires two simple hand-crafted tubes as adaptors and available standard breathing circuit components. In such a setting, respiratory system mechanics and tidal volume of each individual patient can be reliably measured during short term clamping of the tracheal tube of the respective other patient.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Peter C. Reinacher", - "author_inst": "Department of Stereotactic and Functional Neurosurgery, Medical Center, University of Freiburg, Germany and Fraunhofer Institute for Laser Technology, Aachen, " - }, - { - "author_name": "Thomas E. Schlaepfer", - "author_inst": "Department of Interventional Biological Psychiatry, University of Freiburg, Germany and The Johns Hopkins University, Baltimore, MD, USA" - }, - { - "author_name": "Martin A. Schick", - "author_inst": "Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Germany" - }, - { - "author_name": "Juergen Beck", - "author_inst": "Department of Neurosurgery, Medical Center, University of Freiburg, Germany" - }, - { - "author_name": "Hartmut Buerkle", - "author_inst": "Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Germany" - }, - { - "author_name": "Stefan Schumann", - "author_inst": "Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.12.20059972", "rel_title": "Challenges in control of Covid-19: short doubling time and long delay to effect of interventions", @@ -1566581,6 +1567654,57 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.04.14.041962", + "rel_title": "De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery", + "rel_date": "2020-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.14.041962", + "rel_abs": "The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosettas FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5 UTR; the reverse complement of the 5 UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3 UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m, and 3 UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ( FARFAR2-SARS-CoV-2, https://github.com/DasLab/FARFAR2-SARS-CoV-2; and FARFAR2-Apo-Riboswitch, at https://github.com/DasLab/FARFAR2-Apo-Riboswitch) include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ramya Rangan", + "author_inst": "Stanford University" + }, + { + "author_name": "Andrew M. Watkins", + "author_inst": "Stanford University" + }, + { + "author_name": "Jose Chacon", + "author_inst": "Stanford University" + }, + { + "author_name": "Wipapat Kladwang", + "author_inst": "Stanford University" + }, + { + "author_name": "Ivan N. Zheludev", + "author_inst": "Stanford University" + }, + { + "author_name": "Jill Townley", + "author_inst": "Eterna Massive Open Laboratory" + }, + { + "author_name": "Mats Rynge", + "author_inst": "University of Southern California" + }, + { + "author_name": "Gregory Thain", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Rhiju Das", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.08.20058180", "rel_title": "Impact of COVID-19 pandemic on severity of illness and resources required during intensive care in the greater New York City area", @@ -1567025,37 +1568149,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20059659", - "rel_title": "How do environmental, economic and health factors influence regional vulnerability to COVID-19?", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059659", - "rel_abs": "We have studied the correlations between twelve environmental, economic and health variables, by carrying out a statistical analysis of the fatality rate of COVID-19 in 14 countries. Our statistical analysis indicates that, among the 12 variables, the diabetes percentage of the total population and the extent of the population ages 65 and older in each country are correlated most strongly with the total number of deaths in them. Although the strength of the correlations between the variables and the total ND may change as the ongoing pandemic evolves, the study highlights the importance of integrating regional-specific variables in the modelling efforts aimed at projecting how the spread of the virus may influence different parts of the world.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Pejman Tahmasebi", - "author_inst": "University of Wyoming" - }, - { - "author_name": "Salome M.S. Shokri-Kuehni", - "author_inst": "Imperial College London" - }, - { - "author_name": "Muhammad Sahimi", - "author_inst": "University of Southern California" - }, - { - "author_name": "Nima Shokri", - "author_inst": "The University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20059683", "rel_title": "Case- fatality rate in COVID- 19 patients: A meta-analysis of publicly accessible database", @@ -1567711,6 +1568804,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060616", + "rel_title": "Chaos, Percolation and the Coronavirus Spread: the Italian case", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060616", + "rel_abs": "A model based on chaotic maps and turbulent flows is applied to the spread of Coronavirus for each Italian region in order to obtain useful information and help to contrast it. We divide the regions into different risk categories and discuss anomalies. The worst cases are confined between the Appenine and the Alps mountain ranges but the situation seem to improve closer to the sea. The Veneto region gave the most efficient response so far and some of their resources could be diverted to other regions, in particular more tests to the Lombardia, Liguria, Piemonte, Marche and V. Aosta regions, which seem to be worst affected. We noticed worrying anomalies in the Lazio, Campania and Sicilia regions to be monitored. We stress that the number of fatalities we predicted on March 12 has been confirmed daily by the bulletins. This suggests a change of strategy in order to reduce such number maybe moving the weaker population (and negative to the virus test) to beach resorts, which should be empty presently. The ratio deceased/positives on April 4, 2020 is 5.4% worldwide, 12.3% in Italy, 1.4% in Germany, 2.7% in the USA, 10.3% in the UK and 4.1% in China. These large fluctuations should be investigated starting from the Italian regions, which show similar large fluctuations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aldo Bonasera", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Giacomo Bonasera", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Suylatu Zhang", + "author_inst": "Inner Mongolia University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.10.20060673", "rel_title": "COVID-19 lockdowns cause global air pollution declines with implications for public health risk", @@ -1568335,29 +1569455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.09.20059881", - "rel_title": "Next weeks of SARS-CoV-2: Projection model to predict time evolution scenarios of accumulated cases in Spain", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059881", - "rel_abs": "Background and objectivesSARS-CoV-2 is a new type of coronavirus that can affect people and causes respiratory disease, COVID-19. It is affecting the entire planet and we focus in Spain, where the first case was detected at the end of January 2020 and in recent weeks it has increased in many cases. We need predictive models in order to be efficient and take actions. The general goal of this work is present a new model of SARS-CoV-2 to predict different scenarios of accumulated cases in Spain.\n\nMaterial and methodsIn this short report is used a model proposed previously, based on a parametric model Weibull and in a the library BDSbiost3 developed in R to infer and predict different scenarios of the evolution of SARS-CoV-2 for the accumulated cases in Spain after the spread that affects Spain detected at the end of January of this year.\n\nResultsIn the analyses presented, projective curves have been generated for the evolution of accumulated cases in which they reach about 4,000 cases or about 15,000 cases, for which the lines of the day in which the value for 90 will be reached can be seen vertically 90, 95 and 99% of the asymptote (maximum number of cases, from that day they will begin to descend or remain the same), that is why the vertical lines would indicate the brake of the disease. For the worst-case scenario, it takes 118, 126 or 142 days to reach the maximum number of cases (n = 15,000) to reach 90, 95 and 99% of the asymptote (maximum number of cases), respectively. This means translated in a time scale that in the worst case the virus will not stop its progress, in Spain, until summer 2020, hopefully before.\n\nComments and conclusionsThis model could be used to plan the resources and see if the policies or means dedicated to the virus are slowing the progress of the virus or it is necessary to implement others that are more effective, and can also validate a method for future outbreaks of diseases such as these.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "TONI MONLEON-GETINO Sr.", - "author_inst": "UNIVERSITY OF BARCELONA" - }, - { - "author_name": "Jaume Canela-Soler", - "author_inst": "University of Barcelona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.08.20058842", "rel_title": "The Epidemiological Implications of Incarceration Dynamics in Jails for Community, Corrections Officer, and Incarcerated Population Risks from COVID-19", @@ -1569125,6 +1570222,25 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.04.11.20061432", + "rel_title": "Application of COVID-19 pneumonia diffusion data to predict epidemic situation", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061432", + "rel_abs": "ObjectiveTo evaluate novel coronavirus pneumonia cases by establishing the mathematical model of the number of confirmed cases daily, and to assess the current situation and development of the epidemic situation, so as to provide a digital basis for decision-making.\n\nMethodsThe number of newly confirmed covid-19 cases per day was taken as the research object, and the seven-day average value (M) and the sequential value (R) of M were calculated to study the occurrence and development of covid-19 epidemic through the analysis of charts and data.\n\nResultsM reflected the current situation of epidemic development; R reflected the current level of infection and the trend of epidemic development.\n\nConclusionThe current data can be used to evaluate the number of people who have been infected, and when R < 1, the peak of epidemic can be predicted.\n\nPrefaceIn December 2019, a number of cases of pneumonia with unknown causes were found in some hospitals in Wuhan, Hubei province, China. On 11 March 2020, the director-general of the world health organization (WHO), Tedros Adhanom Ghebreyesus, announced that based on the assessment, WHO believes that the current outbreak of COVID-19 can be called a global pandemic. By early April 2020, there were more than one million confirmed cases worldwide.\n\nCOVID-19 has developed from sporadic cases to pandemic in a short period of 3 months. The analysis and research of its infectious data will help to prevent and control the next stage of epidemic prevention and other infectious diseases in the future.\n\nIn this paper, COVID-19 rounded average of seven days (M), and Ms ring ratio (R) are used to predict the current potential patients data, and the relative state of epidemic prevention and control is judged through the graphic features and characteristic data, so as to provide evidence for the prevention and control decisions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Zhenguo Wu", + "author_inst": "Xi'an Jioatong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.12.037580", "rel_title": "Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection", @@ -1569773,33 +1570889,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.10.20061176", - "rel_title": "Multi-Stage Group Testing Optimizes COVID-19 Mass Population Testing", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061176", - "rel_abs": "BackgroundSARS-CoV-2 test kits are in critical shortage in many countries. This limits large-scale population testing and hinders the effort to identify and isolate infected individuals.\n\nObjectivesHerein, we developed and evaluated multi-stage group testing schemes that test samples in groups of various pool sizes in multiple stages. Through this approach, groups of negative samples can be eliminated with a single test, avoiding the need for individual testing and achieving considerable savings of resources.\n\nStudy designWe designed and parameterized various multi-stage testing schemes and compared their efficiency at different prevalence rates using computer simulations.\n\nResultsWe found that three-stage testing schemes with pool sizes of maximum 16 samples can test up to three and seven times as many individuals with the same number of test kits for prevalence rates of around 5% and 1%, respectively. We propose an adaptive approach, where the optimal testing scheme is selected based on the expected prevalence rate.\n\nConclusionThese group testing schemes could lead to a major reduction in the number of testing kits required and help improve large-scale population testing in general and in the context of the current COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jens Niklas Eberhardt", - "author_inst": "Max Planck Institute for Mathematics, Bonn" - }, - { - "author_name": "Nikolas Peter Breuckmann", - "author_inst": "University College London" - }, - { - "author_name": "Christiane Sigrid Eberhardt", - "author_inst": "Center for Vaccinology and Department of Pediatrics, University Hospitals of Geneva" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.10.20060293", "rel_title": "A SIMPLE COLORIMETRIC MOLECULAR DETECTION OF NOVEL CORONAVIRUS (COVID-19), AN ESSENTIAL DIAGNOSTIC TOOL FOR PANDEMIC SCREENING", @@ -1570595,6 +1571684,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.10.036533", + "rel_title": "Structural interactions between pandemic SARS-CoV-2 spike glycoprotein and human Furin protease", + "rel_date": "2020-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.036533", + "rel_abs": "The SARS-CoV-2 pandemic is an urgent global public health emergency and warrants investigating molecular and structural studies addressing the dynamics of viral proteins involved in host cell adhesion. The recent comparative genomic studies highlight the insertion of Furin protease site in the SARS-CoV-2 spike glycoprotein alerting possible modification in the viral spike protein and its eventual entry to host cell and presence of Furin site implicated to virulence. Here we structurally show how Furin interacts with the SARS-CoV-2 spike glycoprotein homotrimer at S1/S2 region, which underlined the mechanism and mode of action, which is a key for host cell entry. Unravelling the structural features of biding site opens the arena in rising bonafide antibodies targeting to block the Furin cleavage and have great implications in the development of Furin inhibitors or therapeutics.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Naveen Vankadari", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.10.036020", "rel_title": "Analysis of Ten Microsecond simulation data of SARS-CoV-2 dimeric main protease", @@ -1571267,53 +1572375,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.08.20058248", - "rel_title": "U.S. county-level characteristics to inform equitable COVID-19 response", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058248", - "rel_abs": "BackgroundThe spread of Coronavirus Disease 2019 (COVID-19) across the United States confirms that not all Americans are equally at risk of infection, severe disease, or mortality. A range of intersecting biological, demographic, and socioeconomic factors are likely to determine an individuals susceptibility to COVID-19. These factors vary significantly across counties in the United States, and often reflect the structural inequities in our society. Recognizing this vast inter-county variation in risks will be critical to mounting an adequate response strategy.\n\nMethods and FindingsUsing publicly available county-specific data we identified key biological, demographic, and socioeconomic factors influencing susceptibility to COVID-19, guided by international experiences and consideration of epidemiological parameters of importance. We created bivariate county-level maps to summarize examples of key relationships across these categories, grouping age and poverty; comorbidities and lack of health insurance; proximity, density and bed capacity; and race and ethnicity, and premature death. We have also made available an interactive online tool that allows public health officials to query risk factors most relevant to their local context.\n\nOur data demonstrate significant inter-county variation in key epidemiological risk factors, with a clustering of counties in certain states, which will result in an increased demand on their public health system. While the East and West coast cities are particularly vulnerable owing to their densities (and travel routes), a large number of counties in the Southeastern states have a high proportion of at-risk populations, with high levels of poverty, comorbidities, and premature death at baseline, and low levels of health insurance coverage.\n\nThe list of variables we have examined is by no means comprehensive, and several of them are interrelated and magnify underlying vulnerabilities. The online tool allows readers to explore additional combinations of risk factors, set categorical thresholds for each covariate, and filter counties above different population thresholds.\n\nConclusionCOVID-19 responses and decision making in the United States remain decentralized. Both the federal and state governments will benefit from recognizing high intra-state, inter-county variation in population risks and response capacity. Many of the factors that are likely to exacerbate the burden of COVID-19 and the demand on healthcare systems are the compounded result of long-standing structural inequalities in US society. Strategies to protect those in the most vulnerable counties will require urgent measures to better support communities attempts at social distancing and to accelerate cooperation across jurisdictions to supply personnel and equipment to counties that will experience high demand.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Taylor Chin", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Rebecca Kahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Ruoran Li", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Jarvis T. Chen", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Nancy Krieger", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Caroline O. Buckee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Satchit Balsari", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Mathew V. Kiang", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.06.20054114", "rel_title": "A streamlined approach to rapidly detect SARS-CoV-2 infection, avoiding RNA extraction", @@ -1572001,6 +1573062,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.08.20054023", + "rel_title": "There are asymptomatic and pre-symptomatic patients infected with COVID-19. So what? Pandemic response implications", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20054023", + "rel_abs": "Asymptomatic but infectious people have been reported in many infectious diseases. Asymptomatic and pre-symptomatic carriers would be a hidden reservoir of COVID-19.\n\nAimThis review identifies primary empirical evidence about the ability of asymptomatic carriers to infect others with COVID-19 pandemic and reflects on the implications for control measures.\n\nMethodsA systematic review is followed by a narrative report and commentary inclusion criteria were: studies reporting primary data on asymptomatic or pre-symptomatic patients, who were considered to have passed on COVID-19 infection; and published in indexed journals or in peer review between January 1 and March 31, 2020.\n\nResultsNine articles reported on 83 asymptomatic or pre-symptomatic persons.\n\nConclusionsThe evidence confirms COVID-19 transmission from people who were asymptomatic at the time. A series of implications for health service response are laid out.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nelson Aguirre-Duarte", + "author_inst": "The University of Auckland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.09.20059014", "rel_title": "How much India detecting SARS-CoV-2 Infections? A model-based estimation", @@ -1572441,57 +1573521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.07.20056440", - "rel_title": "Convalescent Plasma to Treat COVID-19: Chinese Strategy and Experiences", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056440", - "rel_abs": "The COVID-19 is currently spreading around the world, which has posed significant threats to global health and economy. Convalescent plasma is confirmed effective against the novel corona virus in preliminary studies. In this paper, we first described the therapeutic schedule, antibody detection method, indications, contraindications of the convalescent plasmas, and reported the operability of the treatment by case study.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Shiyao Pei", - "author_inst": "Department of Dermatology, Hunan Engineering Research Center of Skin Heath and Disease, Xiangya Hospital, Central South University, Changsha, Hunan Province, Ch" - }, - { - "author_name": "Xi Yuan", - "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" - }, - { - "author_name": "Zhimin Zhimin Zhang", - "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" - }, - { - "author_name": "Run Run Yao", - "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" - }, - { - "author_name": "Yubin Xie", - "author_inst": "Department of Blood Transfusion Laboratory of Changsha Blood Center, 509 Wanjiali North Road, Changsha 410001, Hunan Province, China" - }, - { - "author_name": "Minxue Minxue Shen", - "author_inst": "Department of Dermatology, Hunan Engineering Research Center of Skin Heath and Disease, Xiangya Hospital, Central South University, Changsha, Hunan Province, Ch" - }, - { - "author_name": "Bijuan Bijuan Li", - "author_inst": "Department of Blood Transfusion of Xiangya Hospital, Central South University, Changsha, Hunan Province, China" - }, - { - "author_name": "Xiang Chen", - "author_inst": "Department of Dermatology, Hunan Engineering Research Center of Skin Heath and Disease, Xiangya Hospital, Central South University, Changsha, Hunan Province, Ch" - }, - { - "author_name": "Mingzhu Yin", - "author_inst": "Xiangya Hospital, Central South University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.06.20055392", "rel_title": "A study of SARS-CoV-2 evolution in Italy: from early days to secondary effects after social distancing", @@ -1573271,6 +1574300,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20057851", + "rel_title": "Age-stratified Infection Probabilities Combined with Quarantine-Modified SEIR Model in the Needs Assessments for COVID-19", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057851", + "rel_abs": "We use the age-stratified COVID-19 infection and death distributions from China (more than 44,672 infectious as of February 11, 2020) as an estimate for a study areas infection and morbidity probabilities at each age group. We then apply these probabilities into the actual age-stratified population to predict infectious individuals and deaths at peak. Testing with different countries shows the predicted infectious skewing with the countrys median age and age stratification, as expected. We added a Q parameter to the classic SEIR compartmental model to include the effect of quarantine (Q-SEIR). The projections from the age-stratified probabilities give much lower predicted incidences of infection than the Q-SEIR model. As expected, quarantine tends to delay the peaks for both Exposed and Infectious, and to flatten the curve or lower the predicted values for each compartment. These two estimates were used as a range to inform planning and response to the COVID-19 threat.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vena Pearl Bongolan", + "author_inst": "Department of Computer Science, UP Diliman, Philippines" + }, + { + "author_name": "Jose Marie Antonio Minoza", + "author_inst": "Department of Computer Science, UP Diliman, Philippines" + }, + { + "author_name": "Romulo de Castro", + "author_inst": "Center for Informatics, University of San Agustin, Iloilo City, Philippines" + }, + { + "author_name": "Jesus Emmanuel Sevilleja", + "author_inst": "National Center for Mental Health, Mandaluyong City, Philippines" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20058040", "rel_title": "Blood glucose is a representative of the clustered indicators of multi-organ injury for predicting mortality of COVID-19 in Wuhan, China", @@ -1573783,49 +1574843,6 @@ "type": "confirmatory results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.08.20058214", - "rel_title": "Characterizing key attributes of the epidemiology of COVID-19 in China: Model-based estimations", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058214", - "rel_abs": "BackgroundA novel coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China in late 2019. The resulting disease, Coronavirus Disease 2019 (COVID-2019), soon became a pandemic. This study aims to characterize key attributes of the epidemiology of this infection in China.\n\nMethodsAn age-stratified mathematical model was constructed to describe the transmission dynamics and estimate the age-specific differences in the biological susceptibility to the infection, age-assortativeness in transmission mixing, case fatality rate (CFR), and transition in rate of infectious contacts (and reproduction number R0) following introduction of mass interventions.\n\nResultsThe model estimated the infectious contact rate in early epidemic at 0.59 contacts per day (95% uncertainty interval (UI)=0.48-0.71). Relative to those 60-69 years of age, susceptibility to the infection was only 0.06 in those [≤]19 years, 0.34 in 20-29 years, 0.57 in 30-39 years, 0.69 in 40-49 years, 0.79 in 50-59 years, 0.94 in 70-79 years, and 0.88 in [≥]80 years. The assortativeness in transmission mixing by age was very limited at 0.004 (95% UI=0.002-0.008). Final CFR was 5.1% (95% UI=4.8-5.4%). R0 rapidly declined from 2.1 (95% UI=1.8-2.4) to 0.06 (95% UI=0.05-0.07) following onset of interventions.\n\nConclusionAge appears to be a principal factor in explaining the patterns of COVID-19 transmission dynamics in China. The biological susceptibility to the infection seems limited among children, intermediate among young to mid-age adults, but high among those >50 years of age. There was no evidence for differential contact mixing by age, consistent with most transmission occurring in households rather than in schools or workplaces.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Houssein H Ayoub", - "author_inst": "Department of Mathematics, Statistics, and Physics, Qatar University, Doha, Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" - }, - { - "author_name": "Ghina R Mumtaz", - "author_inst": "Department of Epidemiology and population Health, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Shaheen Seedat", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" - }, - { - "author_name": "Susanne F Awad", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" - }, - { - "author_name": "Monia Makhoul", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.09.031252", "rel_title": "In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles", @@ -1574480,6 +1575497,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.04.08.20057679", + "rel_title": "COVID-19 Epidemic Analysis using Machine Learning and Deep Learning Algorithms", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057679", + "rel_abs": "The catastrophic outbreak of Severe Acute Respiratory Syndrome - Coronavirus (SARS-CoV-2) also known as COVID-2019 has brought the worldwide threat to the living society. The whole world is putting incredible efforts to fight against the spread of this deadly disease in terms of infrastructure, finance, data sources, protective gears, life-risk treatments and several other resources. The artificial intelligence researchers are focusing their expertise knowledge to develop mathematical models for analyzing this epidemic situation using nationwide shared data. To contribute towards the well-being of living society, this article proposes to utilize the machine learning and deep learning models with the aim for understanding its everyday exponential behaviour along with the prediction of future reachability of the COVID-2019 across the nations by utilizing the real-time information from the Johns Hopkins dashboard.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Narinder Singh Punn", + "author_inst": "Indian Institute of Information Technology Allahabad" + }, + { + "author_name": "Sanjay Kumar Sonbhadra", + "author_inst": "Indian Institute of Information Technology Allahabad" + }, + { + "author_name": "Sonali Agarwal", + "author_inst": "Indian Institute of Information Technology Allahabad" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.07.20057224", "rel_title": "UV light dosage distribution over irregular respirator surfaces. Methods and implications for safety", @@ -1575044,25 +1576088,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.07.20056937", - "rel_title": "Modeling the COVID-19 pandemic - parameter identification and reliability of predictions", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056937", - "rel_abs": "In this paper, we try to identify the parameters for two elementary epidemic models, the so-called SI- and SIS-models, via non-linear regression using data of the COVID-19 pandemic. This is done based on the data for the number of daily infections. Studying the history of predictions made, we attempt to estimate their reliability concerning the future course of the epidemic. We validate this procedure using data for the case numbers in China and South Korea. Then we apply it in order to find predictions for Germany, Italy and the United States. The results are encouraging, but no final judgment on the validity of the procedure can yet be made.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Klaus Hackl", - "author_inst": "Ruhr-Universitaet Bochum" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.06.20053934", "rel_title": "Estimation of the percentages of asymptomatic patients and undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing", @@ -1575662,6 +1576687,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20056291", + "rel_title": "Risk factors for mortality of adult inpatients with Coronavirus disease 2019 (COVID-19): a systematic review and meta-analysis of retrospective studies", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20056291", + "rel_abs": "PurposeCoronavirus disease 2019 (COVID-19) is an emerging disease that was first reported in Wuhan city, the capital of Hubei province in China, and has subsequently spread worldwide. Risk factors for mortality have not been well summarized. Current meta-analysis of retrospective cohort studies was done to summarize available findings on the association between age, gender, comorbidities and risk of death from COVID-19 infection.\n\nMethodsOnline databases including Web of Science, PubMed, Scopus, Cochrane Library and Google scholar were searched to detect relevant publications up to 1 May 2020, using relevant keywords. To pool data, random-effects model was used. Furthermore, sensitivity analysis and publication bias test were also done.\n\nResultsIn total, 14 studies with 29,909 COVID-19 infected patients and 1,445 cases of death were included in the current meta-analysis. Significant associations were found between older age ([≥]65 vs <65 years old) (pooled ORs=4.59, 95% CIs=2.61-8.04, p<0.001), gender (male vs female) (pooled ORs=1.50, 95% CIs=1.06-2.12, p=0.021) and risk of death from COVID-19 infection. In addition, hypertension (pooled ORs=2.70, 95% CIs= 1.40-5.24, p=0.003), cardiovascular diseases (CVDs) (pooled ORs=3.72, 95% CIs=1.77-7.83, p=0.001), diabetes (pooled ORs=2.41, 95% CIs=1.05-5.51, p=0.037), chronic obstructive pulmonary disease (COPD) (pooled ORs=3.53, 95% CIs=1.79-6.96, p<0.001) and cancer (pooled ORs=3.04, 95% CIs=1.80-5.14, p<0.001), were associated with higher risk of mortality.\n\nConclusionOlder age ([≥]65 years old), male gender, hypertension, CVDs, diabetes, COPD and malignancies were associated with greater risk of death from COVID-19 infection. These findings could help clinicians to identify patients with poor prognosis at an early stage.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mohammad Parohan", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Sajad Yaghoubi", + "author_inst": "Iranshahr University of Medical Sciences" + }, + { + "author_name": "Asal Seraji", + "author_inst": "Islamic Azad University, Damavand Branch" + }, + { + "author_name": "Mohammad Hassan Javanbakht", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Payam Sarraf", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mahmoud Djalali", + "author_inst": "Tehran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.07.20055723", "rel_title": "SARS-CoV-2 infection in Health Care Workers in a large public hospital in Madrid, Spain, during March 2020", @@ -1576166,45 +1577230,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.06.20050575", - "rel_title": "Pulmonary and Cardiac Pathology in Covid-19: The First Autopsy Series from New Orleans", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20050575", - "rel_abs": "SARS-CoV-2 has rapidly spread across the United States, causing extensive morbidity and mortality, though the histopathologic basis of severe disease cases has yet to be studied in detail. Over the past century, autopsy has contributed significantly to our understanding of numerous disease processes, but for several reasons, autopsy reports following deaths related to SARS- CoV-2 have thus far been limited across the globe. We report on the relevant cardiopulmonary findings in the first series of autopsies in the United States, with the cause of death being due to SARS-CoV-2 infection. These cases identify key pathologic states potentially contributing to severe disease and decompensation in these patients.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sharon E. Fox", - "author_inst": "LSU Health Sciences Center - New Orleans/ Southeast Louisiana Veterans Healthcare System" - }, - { - "author_name": "Aibek Akmatbekov", - "author_inst": "LSU Health Sciences Center - New Orleans" - }, - { - "author_name": "Jack L. Harbert", - "author_inst": "LSU Health Sciences Center - New Orleans" - }, - { - "author_name": "Guang Li", - "author_inst": "Tulane University" - }, - { - "author_name": "J. Quincy Brown", - "author_inst": "Tulane University" - }, - { - "author_name": "Richard S. Vander Heide", - "author_inst": "LSU Health Sciences Center - New Orleans" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.04.07.20045617", "rel_title": "Textile Masks and Surface Covers - A 'Universal Droplet Reduction Model'Against Respiratory Pandemics", @@ -1576956,6 +1577981,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.033522", + "rel_title": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif", + "rel_date": "2020-04-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.033522", + "rel_abs": "Disclaimer textThe authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vincent Navratil", + "author_inst": "PRABI, Rhone Alpes Bioinformatics Center, UCBL, Lyon1, Universite de Lyon, Lyon, France" + }, + { + "author_name": "Sonia Longhi", + "author_inst": "AFMB lab, CNRS & Aix-Marseille University" + }, + { + "author_name": "Marie Hardwick", + "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, U" + }, + { + "author_name": "Christophe Combet", + "author_inst": "Centre de Recherche en Cancerologie de Lyon, UMR Inserm U1052, CNRS 5286, Universite Claude Bernard Lyon 1, Centre Leon Berard, Lyon, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.07.20057315", "rel_title": "Clinical analysis and early differential diagnosis of suspected pediatric patients with 2019 novel coronavirus infection", @@ -1577320,25 +1578376,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.08.20057489", - "rel_title": "Signature of State measures on the COVID-19 Pandemic in China, Italy, and USA", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057489", - "rel_abs": "We show the dynamics of COVID-19 outbreak in Italy and USA, in comparison with China, and the early response of the countries. Our mathematical techniques makes it possible to calculate the rate of growth of the cases efficiently, and provides a good understanding of future trends in Italy and USA. The evolution of the real time data makes it possible to analyse the suitability of steps taken to eradicate the pandemic by the countries. We compare the day to day development of the coronavirus cases in Italy and USA, that keeping in view the population pyramid and the population density, leads us to understand possible difference in the number of effected population.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Farhan Saif", - "author_inst": "Quaid-i-Azam University, Islamabad" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.06.028522", "rel_title": "Systemic analysis of tissue cells potentially vulnerable to SARS-CoV-2 infection by the protein-proofed single-cell RNA profiling of ACE2, TMPRSS2 and Furin proteases", @@ -1578586,6 +1579623,121 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.07.023903", + "rel_title": "Structural and functional analysis of a potent sarbecovirus neutralizing antibody", + "rel_date": "2020-04-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.023903", + "rel_abs": "SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths1,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of a SARS survivor infected in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Dora Pinto", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "University of Washington" + }, + { + "author_name": "Martina Beltramello", + "author_inst": "Humabs BioMed SA" + }, + { + "author_name": "Alexandra C. Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "Siro Bianchi", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Stefano Jaconi", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Katja Culap", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Fabrizia Zatta", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Alessia Peter", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Barbara Guarino", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Roberto Spreafico", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Elisabetta Cameroni", + "author_inst": "Humabs Biomed" + }, + { + "author_name": "James Brett Case", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Rita E. Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Colin Havenar-Daughton", + "author_inst": "Vir Biotehcnology" + }, + { + "author_name": "Gyorgy Snell", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Herbert W. Virgin", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Antonio Lanzavecchia", + "author_inst": "Institute for Research in Biomedicine" + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Katja Fink", + "author_inst": "Humabs Biomed" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.04.07.028589", "rel_title": "The IMPDH inhibitor merimepodib suppresses SARS-CoV-2 replication in vitro.", @@ -1579306,105 +1580458,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.09.033233", - "rel_title": "Structural basis for the inhibition of COVID-19 virus main protease by carmofur, an antineoplastic drug", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.033233", - "rel_abs": "The antineoplastic drug Carmofur was shown to inhibit SARS-CoV-2 main protease (Mpro). Here the X-ray crystal structure of Mpro in complex with Carmofur reveals that the carbonyl reactive group of Carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30 M) and it is a promising lead compound to develop new antiviral treatment for COVID-19.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Zhenming Jin", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Yao Zhao", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Yuan Sun", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China." - }, - { - "author_name": "Bing Zhang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Haofeng Wang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Yan Wu", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China." - }, - { - "author_name": "Yan Zhu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Chen Zhu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Tianyu Hu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiaoyu Du", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Yinkai Duan", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Jing Yu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiaobao Yang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiuna Yang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Kailin Yang", - "author_inst": "Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA" - }, - { - "author_name": "Xiang Liu", - "author_inst": "State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University" - }, - { - "author_name": "Luke W. Guddat", - "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Gengfu Xiao", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Leike Zhang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Haitao Yang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Zihe Rao", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.04.08.033001", "rel_title": "Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract", @@ -1580179,6 +1581232,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.04.20052308", + "rel_title": "The basic reproduction number and prediction of the epidemic size of the novel coronavirus (COVID-19) in Shahroud, Iran", + "rel_date": "2020-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20052308", + "rel_abs": "ObjectivesTo estimate the basic reproduction number (R0) of COVID-19 in the early stage of the epidemic and predict the expected number of new cases in Shahroud, Northeast of Iran.\n\nMethodsThe R0 of COVID-19 was estimated using the serial interval distribution and the number of incidence cases. The serial interval was fit with a gamma distribution. The probable incidence and cumulative incidence in the next 30 days were predicted using the assumption that daily incidence follows a Poisson distribution determined by daily infectiousness. Data analysis was done using \"earlyR\" and \"projections\" packages in R software.\n\nResultsThe maximum-likelihood value of R0 was 2.7 (95% confidence interval (CI): 2.1 to 3.4) for the COVID-19 epidemic in the early 14 days and decreased to 1.13 (95% CI: 1.03 to 1.25) by the end of the day 41. The expected average number of new cases in Shahroud is 9.0{+/-}3.8 case/day, which means an estimated total of 271 (95% CI: 178-383) new cases in the next 30 days.\n\nConclusionsIt is essential to reduce the R0 to values below one. Therefore, we strongly recommend enforcing and continuing the current preventive measures, restricting travel, and providing screening tests for a larger proportion of the population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ahmad Khosravi", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Reza Chaman", + "author_inst": "Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Marzieh Rohani-Rasaf", + "author_inst": "Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Fariba Zare", + "author_inst": "Center for Health Related Social and Behavioral Sciences Research, Shahroud University of Medical Sciences, Shahroud, Iran." + }, + { + "author_name": "Shiva Mehravaran", + "author_inst": "ASCEND Center for Biomedical Research, Morgan State University, Baltimore, USA" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052845", "rel_title": "Use Crow-AMSAA Method to predict the cases of the Coronavirus 19 in Michigan and U.S.A", @@ -1580655,45 +1581747,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.05.026450", - "rel_title": "Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses", - "rel_date": "2020-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.05.026450", - "rel_abs": "SARS-CoV-2 poses an immediate, major threat to public health across the globe. Here we report an in-depth molecular analysis to reconstruct the evolutionary origins of the enhanced pathogenicity of SARS-CoV-2 and other coronaviruses that are severe human pathogens. Using integrated comparative genomics and machine learning techniques, we identify key genomic features that differentiate SARS-CoV-2 and the viruses behind the two previous deadly coronavirus outbreaks, SARS-CoV and MERS-CoV, from less pathogenic coronaviruses. These features include enhancement of the nuclear localization signals in the nucleocapsid protein and distinct inserts in the spike glycoprotein that appear to be associated with high case fatality rate of these coronaviruses as well as the host switch from animals to humans. The identified features could be crucial elements of coronavirus pathogenicity and possible targets for diagnostics, prognostication and interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Noam Auslander", - "author_inst": "NCBI/NIH" - }, - { - "author_name": "Ayal B Gussow", - "author_inst": "NCBI/NIH" - }, - { - "author_name": "Guilhem Faure", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Yuri I. Wolf", - "author_inst": "NCBI/NLM/NIH" - }, - { - "author_name": "Feng Zhang", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Eugene V. Koonin", - "author_inst": "NCBI/NIH" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.03.20052498", "rel_title": "Data-Driven Study of the the COVID-19 Pandemic via Age-Structured Modelling and Prediction of the Health System Failure in Brazil amid Diverse Intervention Strategies", @@ -1581529,6 +1582582,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.04.20052696", + "rel_title": "Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20052696", + "rel_abs": "The ongoing novel coronavirus disease (COVID-19) pandemic has rapidly spread in early 2020, causing tens of thousands of deaths, over a million cases and widespread socioeconomic disruption. With no vaccine available and numerous national healthcare systems reaching or exceeding capacity, interventions to limit transmission are urgently needed. While there is broad agreement that travel restrictions and closure of non-essential businesses and schools are beneficial in limiting local and regional spread, recommendations around the use of face masks for the general population are less consistent internationally. In this study, we examined the role of face masks in mitigating the spread of COVID-19 in the general population, using epidemic models to estimate the total reduction of infections and deaths under various scenarios. In particular, we examined the optimal deployment of face masks when resources are limited, and explored a range of supply and demand dynamics. We found that face masks, even with a limited protective effect, can reduce infections and deaths, and can delay the peak time of the epidemic. We consistently found that a random distribution of masks in the population was a suboptimal strategy when resources were limited. Prioritizing coverage among the elderly was more beneficial, while allocating a proportion of available resources for diagnosed infected cases provided further mitigation under a range of scenarios. In summary, face mask use, particularly for a pathogen with relatively common asymptomatic carriage, can effectively provide some mitigation of transmission, while balancing provision between vulnerable healthy persons and symptomatic persons can optimize mitigation efforts when resources are limited.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Colin J Worby", + "author_inst": "Broad Institute" + }, + { + "author_name": "Hsiao-Han Chang", + "author_inst": "National Tsing Hua University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052720", "rel_title": "Mitigating COVID-19 outbreak via high testing capacity and strong transmission-intervention in the United States", @@ -1581989,37 +1583065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.06.20052159", - "rel_title": "Efficient and Practical Sample Pooling High-Throughput PCR Diagnosis of COVID-19", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20052159", - "rel_abs": "In the global effort to combat the COVID-19 pandemic, governments and public health agencies are striving to rapidly increase the volume and rate of diagnostic testing. The most common form of testing today employs Polymerase Chain Reaction in order to identify the presence of viral RNA in individual patient samples one by one. This process has become one of the most significant bottlenecks to increased testing, especially due to reported shortages in the chemical reagents needed in the PCR reaction.\n\nRecent technical advances have enabled High-Throughput PCR, in which multiple samples are pooled into one tube. Such methods can be highly efficient, saving large amounts of time and reagents. However, their efficiency is highly dependent on the frequency of positive samples, which varies significantly across regions and even within regions as testing criterion and conditions change.\n\nHere, we present two possible optimized pooling strategies for diagnostic SARS-CoV-2 testing on large scales, both addressing dynamic conditions. In the first, we employ a simple information-theoretic heuristic to derive a highly efficient re-pooling protocol: an estimate of the target frequency determines the initial pool size, and any subsequent pools found positive are re-pooled at half-size and tested again. In the range of very rare target (<0.05), this approach can reduce the number of necessary tests dramatically, for example, achieving a reduction by a factor of 50 for a target frequency of 0.001. The second method is a simpler approach of optimized one-time pooling followed by individual tests on positive pools. We show that this approach is just as efficient for moderate target-product frequencies (0.05<0.2), for example, achieving a two-fold in the number of when the frequency of positive samples is 0.07.\n\nThese strategies require little investment, and they offer a significant reduction in the amount of materials, equipment and time needed to test large numbers of samples. We show that both these pooling strategies are roughly comparable to the absolute upper-bound efficiency given by Shannons source coding theorem. We compare our strategies to the naive way of testing and to alternative matrix-pooling methods. Most importantly, we offer straightforward, practical pooling instructions for laboratories that perform large scale PCR assays to diagnose SARS-CoV-2 viral particles. These two pooling strategies may offer ways to alleviate the bottleneck currently preventing massive expansion of SARS-CoV-2 testing around the world.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Haran Shani-Narkiss", - "author_inst": "Center for Brain Sciences, Hebrew University of Jerusalem" - }, - { - "author_name": "Omri David Gilday", - "author_inst": "Center for Brain Sciences, Hebrew University of Jerusalem" - }, - { - "author_name": "Nadav Yayon", - "author_inst": "Center for Brain Sciences, Hebrew University of Jerusalem" - }, - { - "author_name": "Itamar Daniel Landau", - "author_inst": "Center for Brain Sciences, Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.04.20052241", "rel_title": "A Systematic Meta-Analysis of CT Features of COVID-19: Lessons from Radiology", @@ -1582695,6 +1583740,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.06.20053918", + "rel_title": "Thoughts on Higher Medical Education Under Major Public Health Emergencies: Thinking Ahead After COVID-19 Outbreak", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20053918", + "rel_abs": "ImportanceThe spread of coronavirus disease 2019 (COVID-19) has posed great threat to peoples health and several medical schools in the world suspended classes as a precaution against the virus. China has also adopted precautionary measures to keep medical schools running without suspending classes. Thinking ahead after COVID-19 Outbreak is important.\n\nObjectiveTo explore the most suitable teaching and learning pattern in medical school during COVID-19 Outbreak.\n\nDesignThis study is a case-control study. We had tried to apply a new blended teaching model based on 5G network that combined team-based learning (TBL) and online interaction to the students before the outbreak and then universities responded to the COVID-19 outbreak by closing campuses and shifting to other forms of distance learning. In other word, the courses started using blended teaching model before COVID-19 outbreak and might last using other forms of distance learning throughout the pandemic. Five Point Likert Scale Questionnaires which contains 20 items were used, and the effect of the two kinds of teaching patterns was compared by evaluating the indicators of core competencies of students including professionalism, attitude towards learning, knowledge and learning skills, teamwork skills, motivation in learning, adaptability and acceptance of the courses and network environment.\n\nSettingOur study based on a single center.\n\nParticipantsFifty fourth-year medical students receiving the \"5+3\" pattern courses regarding internal medicine were enrolled in the study.\n\nExposure(s) (for observational studies)The teaching and learning patter started using blended teaching model before COVID-19 outbreak and might last using other forms of distance learning throughout the pandemic.\n\nMain Outcome(s)According to the descriptive statistical analysis of the first part of the questionnaire (question 1-16), the average score of adaptability and acceptance of the courses is 2.60 lower than 3, indicating that students are more adapted to other forms of distance learning during COVID-19 outbreak; the average score of the rest of the questions is higher than 3, indicating that blended teaching model based on 5G network is superior to other forms of distance learning. The number of male students who are inclined to the blended teaching model based on 5G network is 0.13 times as much as that of female students (95%CI:0.028[~]0.602, p=0.009).\n\nResultsOnline forms of distance learning were accepted by the students. Female students had higher expectations on the course and were more likely to adapt well to the change during the COVID-19 outbreak. However, all students preferred the blended teaching model based on 5G network that combined team-based learning (TBL) and online interaction before the pandemic.\n\nConclusionIt indicates that medical education based on 5G network that combined team-based learning (TBL) and online interaction is a more suitable option to teach medical students online. Chinas experience in online higher medical education may serve as a reference to other countries during the pandemic.\n\nKey pointO_ST_ABSQuestionsC_ST_ABSWhat are the reflections on approaches to teaching and learning during COVID-19 Outbreak?\n\nFindingsFifty fourth-year medical students receiving the \"5+3\" pattern courses regarding internal medicine were enrolled. Five Point Likert Scale Questionnaires which contains 20 items were used. This study indicates that medical education based on 5G network that combined team-based learning (TBL) and online interaction is a more suitable option to teach medical students online during COVID-19 outbreak.\n\nMeaningChinas experience in online higher medical education may serve as a reference to other countries during the pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wei Lin", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Yan Chen", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Songchang Shi", + "author_inst": "Fujian Provincial Hospital South Branch" + }, + { + "author_name": "Jixing Liang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Huibin Huang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liantao Li", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liangchun Cai", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liyao Zong", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Nengying Wang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Junping Wen", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Gang Chen", + "author_inst": "Fujian Provincial Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2020.04.03.20052936", "rel_title": "An \"Infodemic\": Leveraging High-Volume Twitter Data to Understand Public Sentiment for the COVID-19 Outbreak", @@ -1583175,69 +1584279,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.04.20053579", - "rel_title": "Adaptive cyclic exit strategies from lockdown to suppress COVID-19 and allow economic activity", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053579", - "rel_abs": "Many countries have applied lockdown that helped suppress COVID-19, but with devastating economic consequences. Here we propose exit strategies from lockdown that provide sustainable, albeit reduced, economic activity. We use mathematical models to show that a cyclic schedule of 4-day work and 10-day lockdown, or similar variants, can prevent resurgence of the epidemic while providing part-time employment. The cycle pushes the reproduction number R below one by reduced exposure time and by exploiting the virus latent period: those infected during work days reach peak infectiousness during lockdown days. The number of work days can be adapted in response to observations. Throughout, full epidemiological measures need to continue including hygiene, physical distancing, compartmentalization, testing and contact tracing. This conceptual framework, when combined with other interventions to control the epidemic, can offer the beginnings of predictability to many economic sectors.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Omer Karin", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yinon M. Bar-On", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Tomer Milo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Itay Katzir", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Avi Mayo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yael Korem", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Boaz Dudovich", - "author_inst": "Applied Materials" - }, - { - "author_name": "Eran Yashiv", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Amos J. Zehavi", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Nadav Davidovich", - "author_inst": "Ben-Gurion University" - }, - { - "author_name": "Ron Milo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Uri Alon", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.05.20054528", "rel_title": "Estimating number of cases and spread of Coronavirus disease 2019 (COVID-19) in the United Kingdom using critical care admissions, February to March 2020", @@ -1584049,6 +1585090,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.31.20048652", + "rel_title": "Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048652", + "rel_abs": "BackgroundThe reasons for the large differences between countries in the sizes of their SARS CoV-2 epidemics is unknown. Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV-1. We hypothesized that population level usage of face masks may be negatively associated SARS CoV-2 spread.\n\nMethodsAt a country level, linear regression was used to assess the association between COVID-19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID-19 epidemic and testing intensity.\n\nResultsEight of the 49 countries with available data advocated wearing face masks in public - China, Czechia, Hong Kong, Japan, Singapore, South Korea, Thailand and Malaysia. In multivariate analysis face mask use was negatively associated with number of COVID-19 cases/inhabitant (coef. -326, 95% CI -601- -51, P=0.021). Testing intensity was positively associated with COVID-19 cases (coef. 0.07, 95% CI 0.05-0.08, P<0.001).\n\nConclusionWhilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Chris Kenyon", + "author_inst": "Institute of Tropical Medicine, Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20048165", "rel_title": "Association of BCG vaccination policy with prevalence and mortality of COVID-19", @@ -1584613,29 +1585673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.03.20052084", - "rel_title": "Quantifying the effect of quarantine control in Covid-19 infectious spread using machine learning", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052084", - "rel_abs": "Since the first recording of what we now call Covid-19 infection in Wuhan, Hubei province, China on Dec 31, 2019 (CHP 2020), the disease has spread worldwide and met with a wide variety of social distancing and quarantine policies. The effectiveness of these responses is notoriously difficult to quantify as individuals travel, violate policies deliberately or inadvertently, and infect others without themselves being detected (Li et al. 2020a; Wu & Leung 2020; Wang et al. 2020; Chinazzi et al. 2020; Ferguson et al. 2020; Kraemer et al. 2020). Moreover, the publicly available data on infection rates are themselves unreliable due to limited testing and even possibly under-reporting (Li et al. 2020b). In this paper, we attempt to interpret and extrapolate from publicly available data using a mixed first-principles epidemiological equations and data-driven neural network model. Leveraging our neural network augmented model, we focus our analysis on four locales: Wuhan, Italy, South Korea and the United States of America, and compare the role played by the quarantine and isolation measures in each of these countries in controlling the effective reproduction number Rt of the virus. Our results unequivocally indicate that the countries in which rapid government interventions and strict public health measures for quarantine and isolation were implemented were successful in halting the spread of infection and prevent it from exploding exponentially. In the case of Wuhan especially, where the available data were earliest available, we have been able to test the predicting ability of our model by training it from data in the January 24th till March 3rd window, and then matching the predictions up to April 1st. Even for Italy and South Korea, we have a buffer window of one week (25 March - 1 April) to validate the predictions of our model. In the case of the US, our model captures well the current infected curve growth and predicts a halting of infection spread by 20 April 2020. We further demonstrate that relaxing or reversing quarantine measures right now will lead to an exponential explosion in the infected case count, thus nullifying the role played by all measures implemented in the US since mid March 2020.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Raj Dandekar", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "George Barbastathis", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20048892", "rel_title": "Impact of viral epidemic outbreaks on mental health of healthcare workers: a rapid systematic review", @@ -1585419,6 +1586456,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.31.20049387", + "rel_title": "The impacts of diagnostic capability and prevention measures on transmission dynamics of COVID-19 in Wuhan", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049387", + "rel_abs": "BackgroundAlthough by late February 2020 the COVID-19 epidemic was effectively controlled in Wuhan, China, the virus has since spread around the world and been declared a pandemic on March 11. Estimating the effects of interventions, such as transportation restrictions and quarantine measures, on the early COVID-19 transmission dynamics in Wuhan is critical for guiding future virus containment strategies. Since the exact number of COVID-19 infected cases is unknown, the number of documented cases was used by many disease transmission models to infer epidemiological parameters. However, this means that it would not be possible to adequately estimate epidemiological parameters and the effects of intervention measures, because the percentage of all infected cases that were documented changed during the first 2 months of the epidemic as a consequence of a gradually increasing diagnostic capability.\n\nMethodsTo overcome the limitations, we constructed a stochastic susceptible-exposed-infected-quarantined-recovered (SEIQR) model, accounting for intervention measures and temporal changes in the proportion of new documented infections out of total new infections, to characterize the transmission dynamics of COVID-19 in Wuhan across different stages of the outbreak. Pre-symptomatic transmission was taken into account in our model, and all epidemiological parameters were estimated using Particle Markov-chain Monte Carlo (PMCMC) method.\n\nResultsOur model captured the local Wuhan epidemic pattern as a two-peak transmission dynamics, with one peak on February 4 and the other on February 12, 2020. The impact of intervention measures determined the timing of the first peak, leading to an 86% drop in the Re from 3.23 (95% CI, 2.22 to 4.20) to 0.45 (95% CI, 0.20 to 0.69). An improved diagnostic capability led to the second peak and a higher proportion of documented infections. Our estimated proportion of new documented infections out of the total new infections increased from 11% (95% CI 1% - 43%) to 28% (95% CI 4% - 62%) after January 26 when more detection kits were released. After the introduction of a new diagnostic criterion (case definition) on February 12, a higher proportion of daily infected cases were documented (49% (95% CI 7% - 79%)).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jingbo LIANG", + "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Hsiang-Yu Yuan", + "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Lindsey Wu", + "author_inst": "Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, United Kingdom" + }, + { + "author_name": "Dirk Udo Pfeiffer", + "author_inst": "Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Hong Kong, China" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.31.20049452", "rel_title": "A Covid-19 case mortality rate without time delay systematics", @@ -1585835,45 +1586903,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.01.20049908", - "rel_title": "The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049908", - "rel_abs": "BackgroundNon-pharmaceutical interventions have been implemented to reduce transmission of SARS-CoV-2 in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been critical to support evidence-based policymaking during the early stages of the epidemic.\n\nMethodsWe used a stochastic age-structured transmission model to explore a range of intervention scenarios, including the introduction of school closures, social distancing, shielding of elderly groups, self-isolation of symptomatic cases, and extreme \"lockdown\"-type restrictions. We simulated different durations of interventions and triggers for introduction, as well as combinations of interventions. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (intensive care unit, ICU) treatment, and deaths.\n\nFindingsWe found that mitigation measures aimed at reducing transmission would likely have decreased the reproduction number, but not sufficiently to prevent ICU demand from exceeding NHS availability. To keep ICU bed demand below capacity in the model, more extreme restrictions were necessary. In a scenario where \"lockdown\"-type interventions were put in place to reduce transmission, these interventions would need to be in place for a large proportion of the coming year in order to prevent healthcare demand exceeding availability.\n\nInterpretationThe characteristics of SARS-CoV-2 mean that extreme measures are likely required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSAs countries have moved from early containment efforts to planning for the introduction of large-scale non-pharmaceutical interventions to control COVID-19 outbreaks, epidemic modelling studies have explored the potential for extensive social distancing measures to curb transmission. However, it remains unclear how different combinations of interventions, timings, and triggers for the introduction and lifting of control measures may affect the impact of the epidemic on health services, and what the range of uncertainty associated with these estimates would be.\n\nAdded value of this studyUsing a stochastic, age-structured epidemic model, we explored how eight different intervention scenarios could influence the number of new cases and deaths, as well as intensive care beds required over the projected course of the epidemic. We also assessed the potential impact of local versus national targeting of interventions, reduction in leisure events, impact of increased childcare by grandparents, and timing of triggers for different control measures. We simulated multiple realisations for each scenario to reflect uncertainty in possible epidemic trajectories.\n\nImplications of all the available evidenceOur results support early modelling findings, and subsequent empirical observations, that in the absence of control measures, a COVID-19 epidemic could quickly overwhelm a healthcare system. We found that even a combination of moderate interventions - such as school closures, shielding of older groups and self-isolation - would be unlikely to prevent an epidemic that would far exceed available ICU capacity in the UK. Intermittent periods of more intensive lockdown-type measures are predicted to be effective for preventing the healthcare system from being overwhelmed.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nicholas G Davies", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Amy Gimma", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "-" - }, - { - "author_name": "W. John Edmunds", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.01.20050401", "rel_title": "Inflow restrictions can prevent epidemics when contact tracing efforts are effective but have limited capacity", @@ -1586513,6 +1587542,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.02.20050773", + "rel_title": "Exponential phase of covid19 expansion is not driven by climate at global scale", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050773", + "rel_abs": "The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport, on the rate of daily increase of COVID-19. We found that global connections, represented by countries importance in the global air transportation network, is the main explanation for the growth rate of COVID-19 in different countries. Climate, geographic distance and socioeconomics had a milder effect in this big picture analysis. Geographic distance and climate were significant barriers in the past but were surpassed by the human engine that allowed us to colonize most of our planet land surface. Our results indicate that the current claims that the growth rate of COVID-19 may be lower in warmer and humid tropical countries should be taken very carefully, at risk to disturb well-established and effective policy of social isolation that may help to avoid higher mortality rates due to the collapse of national health systems.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Marco Tulio Pacheco Coelho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Joao Fabricio Mota Rodrigues", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Anderson Matos Medina", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Paulo Scalco", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Levi Carina Terribile", + "author_inst": "Universidade Federal de Jatai" + }, + { + "author_name": "Bruno Vilela", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Jose Alexandre Felizola Diniz-Filho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Ricardo Dobrovolski", + "author_inst": "Universidade Federal da Bahia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.02.20050922", "rel_title": "Inferring COVID-19 spreading rates and potential change points for case number forecasts", @@ -1587053,37 +1588129,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.04.02.20051177", - "rel_title": "Could SARS-CoV-2 be transmitted via speech droplets?", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051177", - "rel_abs": "Speaking may be a primary mode of transmission of SARS-CoV-2. Considering that reports of asymptomatic transmission account for 50-80% of COVID-19 cases and that saliva has peak viral loads at time of patient presentation, droplet emission while speaking could be a significant factor driving transmission and warrants further study. We used a planar beam of laser light passing through a dust-free enclosure to detect saliva droplets emitted while speaking. We found that saying the words Stay Healthy generates thousands of droplets that are otherwise invisible to the naked eye. A damp homemade cloth face mask dramatically reduced droplet excretion, with none of the spoken words causing a droplet rise above the background. Our preliminary findings have important implications for pandemic mitigation efforts.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Philip Anfinrud", - "author_inst": "Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA" - }, - { - "author_name": "Christina E Bax", - "author_inst": "Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA" - }, - { - "author_name": "Valentyn Stadnytskyi", - "author_inst": "Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA" - }, - { - "author_name": "Adriaan Bax", - "author_inst": "Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20051136", "rel_title": "Rapid and accurate identification of COVID-19 infection through machine learning based on clinical available blood test results", @@ -1587779,6 +1588824,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.02.022384", + "rel_title": "One-step RNA extraction for RT-qPCR detection of 2019-nCoV", + "rel_date": "2020-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.02.022384", + "rel_abs": "The global outbreak of coronavirus disease 2019 (COVID-19) has placed an unprecedented burden on healthcare systems as the virus spread from the initial 27 reported cases in the city of Wuhan, China to a global pandemic in under three month[1]. Resources essential to monitoring virus transmission have been challenged with a demand for expanded surveillance. The CDC 2019-nCoV Real-Time Diagnostic Panel uses a real-time reverse transcription polymerase chain reaction (RT-PCR) consisting of two TaqMan probe and primer sets specific for the 2019-nCoV N gene, which codes for the nucleocapsid structural protein that encapsulates viral RNA, for the qualitative detection of 2019-nCoV viral RNA in respiratory samples. To isolate RNA from respiratory samples, the CDC lists RNA extraction kits from four manufacturers. In anticipation of a limited supply chain of RNA extraction kits and the need for test scalability, we sought to identify alternative RNA extraction methods. Here we show that direct lysis of respiratory samples can be used in place of RNA extraction kits to run the CDC 2019-nCoV Real-Time Diagnostic assay with the additional benefits of higher throughput, lower cost, faster turnaround and possibly higher sensitivity and improved safety.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Monica Sentmanat", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Evguenia Kouranova", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Xiaoxia Cui", + "author_inst": "Washington University in St. Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.02.019075", "rel_title": "Rapid community-driven development of a SARS-CoV-2 tissue simulator", @@ -1588411,65 +1589483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.01.20047357", - "rel_title": "Detecting SARS-CoV-2 at point of care: Preliminary data comparing Loop-mediated isothermal amplification (LAMP) to PCR", - "rel_date": "2020-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20047357", - "rel_abs": "BackgroundThe need for a fast and reliable test for COVID-19 is paramount in managing the current pandemic. A cost effective and efficient diagnostic tool as near to the point of care (PoC) as possible would be a game changer in current testing. We tested reverse transcription loop mediated isothermal amplification (RT-LAMP), a method which can produce results in under 30 minutes, alongside standard methods in a real-life clinical setting.\n\nMethodsThis service improvement project piloted a research RT-LAMP method on nasal and pharyngeal swabs on 21 residents in a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We calculated the sensitivity, specificity, positive and negative predictive values of a single RT-LAMP swab compared to RT-PCR, as per STARD guidelines. We also recorded vital signs of patients to correlate clinical and laboratory information.\n\nFindingsThe novel method accurately detected 8/10 PCR positive cases and identified a further 3 positive cases. Eight further cases were negative using both methods. Using repeated RT-PCR as a \"gold standard\", the sensitivity and specificity of the novel test were 80% and 73% respectively. Positive predictive value (PPV) was 73% and negative predictive value (NPV) was 83%. We also observed hypothermia to be a significant early clinical sign in a number of COVID-19 patients in this setting.\n\nInterpretationRT-LAMP testing for SARS-CoV-2 was found to be promising, fast, easy to use and to work equivalently to RT-PCR methods. Definitive studies to evaluate this method in larger cohorts are underway. RT-LAMP has the potential to transform COVID-19 detection, bringing rapid and accurate testing to the point of care. This method could be deployed in mobile testing units in the community, care homes and hospitals to detect disease early and prevent spread.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Marc F Osterdahl", - "author_inst": "Department of Ageing & Health, Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Karla A Lee", - "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" - }, - { - "author_name": "Mary Ni Lochlainn", - "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" - }, - { - "author_name": "Stuart Wilson", - "author_inst": "MicrosensDx Ltd, 2 Royal College Street, London, UK" - }, - { - "author_name": "Sam Douthwaite", - "author_inst": "Department of Infection, Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Rachel Horsfall", - "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" - }, - { - "author_name": "Alyce Sheedy", - "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" - }, - { - "author_name": "Simon D Goldenberg", - "author_inst": "Department of Infection, Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Christoper J Stanley", - "author_inst": "MicrosensDx Ltd, 2 Royal College Street, London, UK" - }, - { - "author_name": "Tim D Spector", - "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" - }, - { - "author_name": "Claire Steves", - "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20042614", "rel_title": "Computed Tomography Findings and Short-term follow-up with Novel Coronavirus Pneumonia", @@ -1589265,6 +1590278,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.01.20049668", + "rel_title": "Spatial variability in the risk of death from COVID-19 in Italy, 2020", + "rel_date": "2020-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049668", + "rel_abs": "ObjectivesItaly has been disproportionately affected by the COVID-19 pandemic, becoming the nation with the third highest death toll in the world as of May 10th, 2020. We analyzed the severity of COVID-19 pandemic across 20 Italian regions.\n\nMethodWe manually retrieved the daily cumulative numbers of laboratory-confirmed cases and deaths attributed to COVID-19 across 20 Italian regions. For each region, we estimated the crude case fatality ratio and time-delay adjusted case fatality ratio (aCFR). We then assessed the association between aCFR and sociodemographic, health care and transmission factors using multivariate regression analysis.\n\nResultsThe overall aCFR in Italy was estimated at 17.4%. Lombardia exhibited the highest aCFR (24.7%) followed by Marche (19.3%), Emilia Romagna (17.7%) and Liguria (17.6%). Our aCFR estimate was greater than 10% for 12 regions. Our aCFR estimates were statistically associated with population density and cumulative morbidity rate in a multivariate analysis.\n\nConclusionOur aCFR estimates for overall Italy and for 7 out of 20 regions exceeded those reported for the most affected region in China. Our findings highlight the importance of social distancing to suppress incidence and reduce the death risk by preventing saturating the health care system.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Sushma Dahal", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.31.20049007", "rel_title": "Harmonizing heterogeneous endpoints in COVID-19 trials without loss of information - an essential step to facilitate decision making", @@ -1589721,25 +1590761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.31.20049155", - "rel_title": "Parametric analysis of early data on COVID-19 expansion in selected European countries", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049155", - "rel_abs": "We analyze the early data on COVID-19 expansion in selected European countries using an analytical parametric model. A description of the time dependence of the disease expansion and a method to evaluate trends of the expansion are proposed. Several features are observed in the data, namely a high predictability of the expansion of disease in Italy and a convergence of the \"pushback\" parameter towards a limiting value in all the countries where restrictive measures have been adopted. Basic predictions for the evolution of the disease expansion are made for selected countries with a stable evolution in the parametric space of the model. The findings presented here should contribute to the understanding of the behavior of the disease expansion and the role of the restrictive measures on the evolution of the expansion.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Martin Spousta", - "author_inst": "Charles University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.31.20049486", "rel_title": "Simple model for Covid-19 epidemics - back-casting in China and forecasting in the US", @@ -1590355,6 +1591376,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.03.31.20048439", + "rel_title": "Research on the Influence of Information Diffusion on the Transmission of the Novel Coronavirus (COVID-19)", + "rel_date": "2020-04-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048439", + "rel_abs": "With the rapid development of mobile Internet in China, the information of the epidemic is full-time and holographic, and the role of information diffusion in epidemic control is increasingly prominent. At the same time, the publicity of all kinds of big data also provides the possibility to explore the impact of media information diffusion on disease transmission. This paper explores the mechanism of the influence of information diffusion on the spread of the novel coronavirus, develops a model of the interaction between information diffusion and disease transmission based on the SIR model, and empirically tests the role and mechanism of information diffusion in the spread of COCID-19 by using econometric method. The result shows that there was a significant negative correlation between the information diffusion and the spread of the novel coronavirus; The result of robust test shows that the spread of both epidemic information and protection information hindered the further spread of the epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lin Shanlang", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Ma Chao", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Lin Ruofei", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Huang Junpei", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Xu Ruohan", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Yuan Aini", + "author_inst": "School of Economics and Management, Tongji University, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.03.31.20047142", "rel_title": "Clinical features and outcomes of 2019 novel coronavirus-infected patients with high plasma BNP levels", @@ -1590943,29 +1592003,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.01.019463", - "rel_title": "Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations", - "rel_date": "2020-04-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.01.019463", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens. Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Saif M. Khodary", - "author_inst": "Cairo University" - }, - { - "author_name": "Ali Mostafa Anwar", - "author_inst": "Cairo University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.03.31.018978", "rel_title": "A SARS-CoV-2 Vaccination Strategy Focused on Population-Scale Immunity", @@ -1591661,6 +1592698,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.30.20047589", + "rel_title": "The Institutional and Cultural Context of Cross-National Variation in COVID-19 Outbreaks", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047589", + "rel_abs": "BackgroundThe COVID-19 pandemic poses an unprecedented and cascading threat to the health and economic prosperity of the worlds population.\n\nObjectivesTo understand whether the institutional and cultural context influences the COVID-19 outbreak.\n\nMethodsAt the ecological level, regression coefficients are examined to figure out contextual variables influencing the pandemics exponential growth rate across 96 countries.\n\nResultsWhile a strong institutional context is negatively associated with the outbreak (B = -0.55 ... -0.64, p < 0.001), the pandemics growth rate is steeper in countries with a quality education system (B = 0.33, p < 0.001). Countries with an older population are more affected (B = 0.46, p < 0.001). Societies with individualistic (rather than collectivistic) values experience a flatter rate of pathogen proliferation (B = -0.31, p < 0.001), similarly for higher levels of power distance (B = -0.32, p < 0.001). Hedonistic values, that is seeking indulgence and not enduring restraints, are positively related to the outbreak (B = 0.23, p = 0.001).\n\nConclusionsThe results emphasize the need for public policy makers to pay close attention to the institutional and cultural context in their respective countries when instigating measures aimed at constricting the pandemics growth.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Wolfgang Messner", + "author_inst": "University of South Carolina" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20047894", "rel_title": "Forecasting the CoViD19 Diffusion in Italy and the Related Occupancy of Intensive Care Units", @@ -1592025,73 +1593081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.29.20047159", - "rel_title": "SARS-CoV-2 infection in health care workers: a retrospective analysis and a model study", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20047159", - "rel_abs": "BackgroundThere had been a preliminary occurrence of human-to-human transmissions between healthcare workers (HCWs), but risk factors in the susceptibility for COVID-19, and infection patterns among HCWs have largely remained unknown.\n\nMethodsRetrospective data collection on demographics, lifestyles, contact status with infected subjects for 118 HCWs (include 12 COVID-19 HCWs) from a single-center. Sleep quality and working pressure were evaluated by Pittsburgh Sleep Quality Index (PSQI) and The Nurse Stress Index (NSI), respectively. Follow-up duration was from Dec 25, 2019, to Feb 15, 2020. Risk factors and transmission models of COVID-19 among HCWs were analyzed and constructed.\n\nFindingsA high proportion of COVID-19 HCWs had engaged in night shift-work (75.0% vs. 40.6%) and felt they were working under pressure (66.7% vs. 32.1%) than uninfected HCWs. COVID-19 HCWs had higher total scores of PSQI and NSI than uninfected HCWs. Furthermore, these scores were both positively associated with COVID-19 risk. An individual-based model (IBM) estimated the outbreak duration among HCWs in a non-typical COVID-19 ward at 62-80 days and the basic reproduction number R0 =1.27 [1.06, 1.61]. By reducing the average contact rate per HCW by a 1.35 factor and susceptibility by a 1.40 factor, we can avoid an outbreak of the basic case among HCWs.\n\nInterpretationPoor sleep quality and high working pressure were positively associated with high risks of COVID-19. A novel IBM of COVID-19 transmission is suitable for simulating different outbreak patterns in a hospital setting.\n\nFundingFundamental Research Funds for the Central Universities", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yansen Bai Sr.", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xuan Wang Sr.", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Qimin Huang Sr.", - "author_inst": "Applied Mathematics and Statistics, Case Western Reserve University" - }, - { - "author_name": "Han Wang Sr.", - "author_inst": "Department of Biochemistry, Case Western Reserve University" - }, - { - "author_name": "David Gurarie", - "author_inst": "Center for Global Health and Diseases, School of Medicine, Case Western Reserve University" - }, - { - "author_name": "Martial Ndeffo-Mbah", - "author_inst": "School of Public Health, Texas A&M University, College Station" - }, - { - "author_name": "Fei Fan", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Peng Fu", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Mary Ann Horn", - "author_inst": "Applied Mathematics and Statistics, Case Western Reserve University" - }, - { - "author_name": "Shuai Xu", - "author_inst": "Computer and Data Science Department, Case Western Reserve University" - }, - { - "author_name": "Anirban Mondal", - "author_inst": "Applied Mathematics and Statistics, Case Western Reserve University" - }, - { - "author_name": "Xiaobing Jiang Sr.", - "author_inst": "Union Hospitaol, Huazhong University of Science and Technology" - }, - { - "author_name": "Hongyang Zhao", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.30.20047415", "rel_title": "Risk factors for severe corona virus disease 2019 (COVID-19) patients : a systematic review and meta analysis", @@ -1592731,6 +1593720,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.29.20043547", + "rel_title": "Health Communication Through News Media During the Early Stage of the COVID-19 Outbreak in China: A Digital Topic Modeling Approach", + "rel_date": "2020-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20043547", + "rel_abs": "BackgroundIn December 2019, some COVID-19 cases were first reported and soon the disease broke out. As this dreadful disease spreads rapidly, the mass media has been active in community education on COVID-19 by delivering health information about this novel coronavirus.\n\nMethodsWe adopted the Huike database to extract news articles about coronavirus from major press media, between January 1st, 2020, to February 20th, 2020. The data were sorted and analyzed by Python software and Python package Jieba. We sought a suitable topic number using the coherence number. We operated Latent Dirichlet Allocation (LDA) topic modeling with the suitable topic number and generated corresponding keywords and topic names. We divided these topics into different themes by plotting them into two-dimensional plane via multidimensional scaling.\n\nFindingsAfter removing duplicates, 7791 relevant news reports were identified. We listed the number of articles published per day. According to the coherence value, we chose 20 as our number of topics and obtained their names and keywords. These topics were categorized into nine primary themes based on the topic visualization figure. The top three popular themes were prevention and control procedures, medical treatment and research, global/local social/economic influences, accounting for 32{middle dot}6%, 16{middle dot}6%, 11{middle dot}8% of the collected reports respectively.\n\nInterpretationThe Chinese mass media news reports lag behind the COVID-19 outbreak development. The major themes accounted for around half the content and tended to focus on the larger society than on individuals. The COVID-19 crisis has become a global issue, and society has also become concerned about donation and support as well as mental health. We recommend that future work should address the mass medias actual impact on readers during the COVID-19 crisis through sentiment analysis of news data.\n\nFundingNational Social Science Foundation of China (18CXW021)\n\nEvidence before this studyThe novel coronavirus related news reports have engaged public attention in China during the COVID-19 crisis. Topic modeling of these news articles can produce useful information about the significance of mass media for early health communication. We searched the Huike database, the most professional Chinese media content database, using the search term \"coronavirus\" for related news articles published from January 1st, 2020, to February 20th, 2020. We found that these articles can be classified into different themes according to their emphasis, however, we found no other studies apply topic modeling method to study them.\n\nAdded value of this studyTo our knowledge, this study is the first to investigate the patterns of health communications through media and the role the media have played and are still playing in the light of the current COVID-19 crisis in China with topic modeling method. We compared the number of articles each day with the outbreak development and identified theres a delay in reporting COVID-19 outbreak progression for Chinese mass media. We identify nine main themes for 7791 collected news reports and detail their emphasis respectively.\n\nImplications of all the available evidenceOur results show that the mass media news reports play a significant role in health communication during the COVID-19 crisis, government can strengthen the report dynamics and enlarge the news coverage next time another disease strikes. Sentiment analysis of news data are needed to assess the actual effect of the news reports.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Qian Liu", + "author_inst": "School of Journalism and Communication, National Media Experimental Teaching Demonstration Center, Jinan University, Guangzhou, China; Department of Communicati" + }, + { + "author_name": "Zequan Zheng", + "author_inst": "International School, Jinan University, China; Faculty of Medicine, Jinan University, China" + }, + { + "author_name": "Jiabin Zheng", + "author_inst": "International School, Jinan University, China; Faculty of Medicine, Jinan University, China" + }, + { + "author_name": "Qiuyi Chen", + "author_inst": "School of Journalism and Communication, National Media Experimental Teaching Demonstration Center, Jinan University, Guangzhou, China" + }, + { + "author_name": "Guan Liu", + "author_inst": "Faculty of Computer Centre, Jinan University, China" + }, + { + "author_name": "Sihan Chen", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Bojia Chu", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Hongyu Zhu", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Babatunde Akinwunmi", + "author_inst": "Pulmonary and Critical Care Medicine Unit, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard University, Boston, Massachuset" + }, + { + "author_name": "Jian Huang", + "author_inst": "MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk" + }, + { + "author_name": "Casper J. P. Zhang", + "author_inst": "School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Wai-kit Ming", + "author_inst": "Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.29.20046565", "rel_title": "Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020", @@ -1593246,29 +1594298,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.03.29.008631", - "rel_title": "Azithromycin and ciprofloxacin have a chloroquine-like effect on respiratory epithelial cells", - "rel_date": "2020-03-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.29.008631", - "rel_abs": "There is interest in the use of chloroquine/hydroxychloroquine (CQ/HCQ) and azithromycin (AZT) in COVID-19 therapy. Employing cystic fibrosis respiratory epithelial cells, here we show that drugs AZT and ciprofloxacin (CPX) act as acidotropic lipophilic weak bases and confer in vitro effects on intracellular organelles similar to the effects of CQ. These seemingly disparate FDA-approved antimicrobials display a common property of modulating pH of endosomes and trans-Golgi network. We believe this may in part help understand the potentially beneficial effects of CQ/HCQ and AZT in COVID-19, and that the present considerations of HCQ and AZT for clinical trials should be extended to CPX.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Vojo Deretic", - "author_inst": "University of New Mexico School of Medicine" - }, - { - "author_name": "Graham S Timmins", - "author_inst": "UNiversity of New Mexico HSC" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.29.014290", "rel_title": "Sequence variation among SARS-CoV-2 isolates in Taiwan", @@ -1594252,6 +1595281,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.27.20043299", + "rel_title": "Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20043299", + "rel_abs": "Over 10 percent of recovered and discharged patients retested positive for SARS-CoV-2, raising a public health concern whether they could be potential origins of infection. In this study, we found that detectable viral genome in discharged patients might only mean the presence of viral fragments, and could hardly form an infection origin for its extremely low concentration.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fengyu Hu", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Fengjuan Chen", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Yaping Wang", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Teng Xu", + "author_inst": "Vision Medicals" + }, + { + "author_name": "Xiaoping Tang", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Feng Li", + "author_inst": "Guangzhou Eighth People Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.25.20043505", "rel_title": "Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release", @@ -1594912,69 +1595980,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.27.20045153", - "rel_title": "Evaluations of serological test in the diagnosis of 2019 novel coronavirus (SARS-CoV-2) infections during the COVID-19 outbreak", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045153", - "rel_abs": "The ongoing SARS-CoV-2 outbreak has killed over twenty-one thousand and sickened over four hundred thousand people worldwide, posing a great challenge to global public health. A sensitive and accurate diagnosis method will substantially help to control disease expansion. Here, we developed a chemiluminescence-immunoassay method based on the recombinant nucleocapsid antigen and the magnetic beads for diagnosis of SARS-CoV-2 infections and surveillance of antibody changing pattern.\n\nSerums from 29 healthy individuals, 51 tuberculosis patients, and 79 SARS-CoV-2 confirmed patients were employed to evaluate the performance of this approach. Compared to the IgM testing, the IgG testing was more reliable in which it identified 65 SARS-CoV-2 infections from the 79 confirmed patients and only two false-positive cases from the 80 control group with a sensitivity and specificity reaching 82.28% and 97.5%, respectively. However, only a slight difference (not statistically significant) in the detected cases of SARS-CoV-2 infections was observed between the IgM and IgG testing manner in patients at a different time of onset of disease. A performance comparison between an ELISA kit using the same nucleocapsid antigen and our chemiluminescence method was undertaken. The same false-positive cases were seen in both methods from the paired control group, while ELISA kit can only detect half of the SARS-CoV-2 infections from paired SARS-CoV-2 confirmed patients group than that of the chemiluminescence method, indicating a higher performance for the chemiluminescence-immunoassay approach. Together, our studies provide a useful and valuable serological testing tool for the diagnosis of SARS-CoV-2 infections in the community.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Dachuan Lin", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Lei Liu", - "author_inst": "Shenzhen Third People's Hospital" - }, - { - "author_name": "Mingxia Zhang", - "author_inst": "Shenzhen Third People's Hospital" - }, - { - "author_name": "Yunlong Hu", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Qianting Yang", - "author_inst": "Shenzhen Third People's Hospital" - }, - { - "author_name": "Jiubiao Guo", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Youchao Dai", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Yuzhong Xu", - "author_inst": "Shenzhen Baoan people's hospital" - }, - { - "author_name": "Yi Cai", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Xinchun Chen", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Kaisong Huang", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Zheng Zhang", - "author_inst": "Shenzhen Third Peoples Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20045336", "rel_title": "A COVID-19 Infection Risk Model for Frontline Health Care Workers", @@ -1595578,6 +1596583,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.27.20045252", + "rel_title": "Estimation of protection for COVID-19 in children from epidemiological information and estimate effect of policy in Japan", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045252", + "rel_abs": "BackgroundIncidence in children was much less than in adults during the COVID-19 outbreak. Sports and entertainment events were canceled (VEC) in Japan for two weeks during 26 February - 13 March. Most schools were closed (SC).\n\nObjectWe construct a susceptible-infected-recovered model using three age classes and estimate the basic reproduction number (R0) and protection level among children simultaneously. Then we simulate SC and VEC effects.\n\nMethodWe used data of patients with symptoms in Japan during 14 January to assess SC and VEC introduction. Effects of SC and VEC were incorporated into the model through change in the contact pattern or frequencies among age classes.\n\nResultsResults suggest R0 as 2.86 [95%CI of 2.73, 2.97]. The protection level was estimated as 0.4 [0.2, 0.7]. SC and VEC can reduce the total number of patients significantly, by 6-7%.\n\nDiscussion and ConclusionThe estimated R0 was similar to that found from other studies in China and Japan. We found a significant protection level among children, and by effects of SC and VEC. Introduction", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Center for Medical Sciences, Ibaraki Prefectural University of Health Sciences, Ibaraki, Japan" + }, + { + "author_name": "Yoshiyuki Sugishita", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.27.20044958", "rel_title": "Research on the Influence of Effective Distance Between Cities on the Cross-regional Transmission of COVID-19", @@ -1596038,29 +1597074,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.27.20044891", - "rel_title": "Evaluating the effectiveness of social distancing interventions against COVID-19", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20044891", - "rel_abs": "SARS-CoV-2 has infected over 140,000 people as of March 14, 2020. We use a mathematical model to investigate the effectiveness of social distancing interventions lasting six weeks in a middle-sized city in the US. We explore four social distancing strategies by reducing the contacts of adults over 60 years old, adults over 60 years old and children, all adults (25, 75 or 95% compliance), and everyone in the population. Our results suggest that social distancing interventions can avert cases by 20% and hospitalizations and deaths by 90% even with modest compliance within adults as long as the intervention is kept in place, but the epidemic is set to rebound once the intervention is lifted. Our models suggest that social distancing interventions will buy crucial time but need to occur in conjunction with testing and contact tracing of all suspected cases to mitigate transmission of SARS-CoV-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Laura Matrajt", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Tiffany Leung", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.26.20044826", "rel_title": "Children are unlikely to have been the primary source of household SARS-CoV-2 infections", @@ -1596996,6 +1598009,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.03.26.20044388", + "rel_title": "The more I fear about COVID-19, the more I wear medical masks: A survey on risk perception and medical masks uses", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044388", + "rel_abs": "The legal behaviors in using medical masks in public have been finally promulgated by the Vietnamese Government after 47 days since the WHO declared the Public Health Emergency of International Concern (PHEIC) due to the COVID-19 pandemic. From a sample of 345 Vietnamese respondents aged from 15 to 47 years, this brief note found that the risk perception of COVID-19 danger significantly increases the likelihood of wearing the medical masks. In addition, there is a weak evidence about the differences in age under the COVID-19 outbreaks. More noticeably, those who use masks before COVID-19 pandemic tend to maintain their behaviors. Our results offer the insightful into Vietnamese citizens responses in terms of using medical masks; even the uses of this method are still controversial. Our results are robust by performing Exploratory Factor Analysis for five features and further regressions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Toan D Huynh", + "author_inst": "University of Economics HCMC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.03.28.20046110", "rel_title": "Which Measures are Effective in Containing COVID-19?Empirical Research Based on Prevention and Control Cases in China", @@ -1597488,37 +1598520,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.28.013920", - "rel_title": "Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9", - "rel_date": "2020-03-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.28.013920", - "rel_abs": "Many of the proteins produced by SARS-CoV-2 have related counterparts across the Severe Acute Respiratory Syndrome (SARS-CoV) family. One such protein is non-structural protein 9 (Nsp9), which is thought to mediate both viral replication and virulence. Current understanding suggests that Nsp9 is involved in viral genomic RNA reproduction. Nsp9 is thought to bind RNA via a fold that is unique to this class of betacoronoaviruses although the molecular basis for this remains ill-defined. We sought to better characterise the SARS-CoV-2 Nsp9 protein and subsequently solved its X-ray crystal structure, in an apo-form and, unexpectedly, in a peptide-bound form with a sequence originating from a rhinoviral 3C protease sequence (LEVL). The structure of the SARS-CoV-2 Nsp9 revealed the high level of structural conservation within the Nsp9 family. The exogenous peptide binding site is close to the dimer interface and impacted on the relative juxtaposition of the monomers within the homodimer. Together we have established a protocol for the production of SARS-CoV-2 Nsp9, determined its structure and identified a peptide-binding site that may warrant further study from the perspective of understanding Nsp9 function.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Dene Littler", - "author_inst": "Monash University" - }, - { - "author_name": "Benjamin Gully", - "author_inst": "Monash University" - }, - { - "author_name": "Rhys N Colson", - "author_inst": "Biomedicine Discovery Institute, Monash University" - }, - { - "author_name": "Jamie Rossjohn", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.03.28.20045997", "rel_title": "Development and external validation of a prognostic multivariable model on admission for hospitalized patients with COVID-19", @@ -1598322,6 +1599323,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044651", + "rel_title": "A deductive approach to modeling the spread of COVID-19", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044651", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), previously known as 2019-nCoV, is responsible for the atypical pneumonia pandemic designated as Coronavirus Disease 2019 (COVID-19). The number of cases continues to grow exponentially reaching 492,000 people in 175 countries as of March 25, 2020. 22,169 people ([~]4.5%) infected with SARS-COV-2 virus have died. We have developed an exponential regression model using the COVID-19 case data (Jan 22 - Mar 22, 2020). Our primary model uses designated Phase 1 countries, who exceed 2500 cases on Mar 22. The model is then applied to Phase 2 countries: those that escaped the initial Phase 1 global expansion of COVID-19. With the exception of stabilizing countries (South Korea, Japan, and Iran) all Phase 1 countries are growing exponentially, as per I2500(t) = 120.4 x e0.238t, with a rate, r = 0.238 {+/-} 0.068. Excluding China, the BRICS developing nations and Australia are in Phase 2. Case data from Phase 2 countries are following the model derived from Phase 1 countries. In the absence of measures employed to flatten the curve including social distancing, quarantine, and healthcare expansion, our model projects over 274,000 cases and 12,300 deaths in the US by Mar 31. India can expect 123,000 cases by April 16. By flattening the curve to the growth rate of stabilizing countries (r = 0.044 {+/-} 0.062), the US would prevent 8,500 deaths by Mar 31, and India would prevent 5,500 deaths by April 16.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Pranav Kumar Mishra", + "author_inst": "Kasturba Medical College, Manipal; Manipal Academy of Higher Education" + }, + { + "author_name": "Shekhar Mishra", + "author_inst": "Discovery Science and Innovation Management" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.25.20043927", "rel_title": "Dangers of ACE inhibitor and ARB usage in COVID-19: evaluating the evidence", @@ -1598754,61 +1599778,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.30.20044099", - "rel_title": "COVID-19 transmission in Mainland China is associated with temperature and humidity: a time-series analysis", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20044099", - "rel_abs": "COVID-19 has become a pandemic. The influence of meteorological factors on the transmission and spread of COVID-19 if of interest. This study sought to examine the associations of daily average temperature (AT) and relative humidity (ARH) with the daily count of COVID-19 cases in 30 Chinese provinces (in Hubei from December 1, 2019 to February 11, 2020 and in other provinces from January 20, 2020 to Februarys 11, 2020). A Generalized Additive Model (GAM) was fitted to quantify the province-specific associations between meteorological variables and the daily cases of COVID-19 during the study periods. In the model, the 14-day exponential moving averages (EMAs) of AT and ARH, and their interaction were included with time trend and health-seeking behavior adjusted. Their spatial distributions were visualized. AT and ARH showed significantly negative associations with COVID-19 with a significant interaction between them (0.04, 95% confidence interval: 0.004-0.07) in Hubei. Every 1{degrees}C increase in the AT led to a decrease in the daily confirmed cases by 36% to 57% when ARH was in the range from 67% to 85.5%. Every 1% increase in ARH led to a decrease in the daily confirmed cases by 11% to 22% when AT was in the range from 5.04{degrees}C to 8.2{degrees}C. However, these associations were not consistent throughout Mainland China.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Hongchao Qi", - "author_inst": "Department of Epidemiology and Health Statistics, Fudan University, China. Department of Biostatistics, Erasmus University Medical Center, The Netherlands." - }, - { - "author_name": "Shuang Xiao", - "author_inst": "Department of Epidemiology and Health Statistics, Fudan University, China." - }, - { - "author_name": "Runye Shi", - "author_inst": "Department of Epidemiology and Health Statistics, Fudan University, China." - }, - { - "author_name": "Michael P. Ward", - "author_inst": "Sydney School of Veterinary Science, The University of Sydney, Camden NSW, Australia" - }, - { - "author_name": "Yue Chen", - "author_inst": "Department of Epidemiology and Community Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario, Canada" - }, - { - "author_name": "Wei Tu", - "author_inst": "Department of Geology and Geography, Georgia Southern University, Statesboro, GA 30460, USA" - }, - { - "author_name": "Qing Su", - "author_inst": "Department of Epidemiology and Health Statistics, Fudan University, China." - }, - { - "author_name": "Wenge Wang", - "author_inst": "Department of Epidemiology and Health Statistics, Fudan University, China." - }, - { - "author_name": "Xinyi Wang", - "author_inst": "Department of Epidemiology and Health Statistics, Fudan University, China." - }, - { - "author_name": "Zhijie Zhang", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.26.20044081", "rel_title": "Extrapolation of Infection Data for the CoVid-19 Virus and Estimate of the Pandemic Time Scale.", @@ -1599660,6 +1600629,29 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.03.26.009605", + "rel_title": "Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response.", + "rel_date": "2020-03-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.26.009605", + "rel_abs": "The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need to understand the biology of the virus inside cells, but this kind of studies are still scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. In the present study, we use the publicly available proteomics data from this study to re-analyze the mechanisms altered by the virus infection by impact pathways analysis and network analysis. Proteins linked to inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be regulated. The up-regulation of the inflammatory-related proteins observed could be linked to the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignacio Ortea", + "author_inst": "Instituto de Investigacion e Innovacion Biomedica de Cadiz (INiBICA)" + }, + { + "author_name": "Jens-Ole Bock", + "author_inst": "Cobo Technologies Aps" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.03.27.012906", "rel_title": "RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses", @@ -1600148,57 +1601140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.22.20041285", - "rel_title": "Elevated serum IgM levels indicate poor outcome in patients with coronavirus disease 2019 pneumonia: A retrospective case-control study", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20041285", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pneumonia outbreak began in Wuhan and pandemics tend to occur. Although SARS-CoV-2-specific immunoglobulins have been detected in serum of COVID-19 patients, their dynamics and association with outcomes have not been characterized.\n\nMethodsA total of 116 hospitalized patients with confirmed COVID-19 pneumonia and SARS-CoV-2-specific immunoglobulins tested in Tongji hospital were retrospectively investigated. Clinical, laboratory, radiological characteristics and outcomes data were compared between mild-moderate group and died group. Further, a paired case-control study was conducted where each deceased case was matched to three mild-moderate patients of similar age.\n\nFindingsAmong 116 subjects included, 101 mild-moderate patients survived and 15 cases died. SARS-CoV-2-specific IgM levels peaked in forth week after onset of COVID-19 pneumonia, while serum IgG levels increased over 8 weeks. Serum IgM levels were higher in deceased patients than mild-moderate patients (P = 0.024), but not IgG. Serum IgM levels were negatively correlated with clinical outcome, eosinophil count and albumin levels (r = -0.269, P = 0.003; r = -0.188, P = 0.043; and r = -0.198, P = 0.033, resp.). The area under the ROC curve (AUC) for IgM antibody was 0.681 (95% CI: 0.517-0.845, P = 0.024). In case-control study paired by age, serum IgM was higher in deceased patients than mild-moderate patients (P = 0.019), positively correlated with leucocyte count (r = 0.260, P = 0.045), while negatively correlated with clinical outcome and albumin levels (r = -0.337, P = 0.008; r = -0.265, P = 0.041). AUC for IgM levels was 0.704 (95% CI: 0.534-0.873, P = 0.019).\n\nInterpretationThese results indicate that dynamics of SARS-CoV-2 specific IgM and IgG antibodies was similar with that of SARS-CoV, while elevated serum IgM levels indicate poor outcome in patients with COVID-19 pneumonia.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Zhihua Wang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Huijun Li", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Jingjing Li", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Chunguang Yang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Xiaolin Guo", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Zhiquan Hu", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Zhiqiang Chen", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Shaogang Wang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Jihong Liu", - "author_inst": "Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.22.20041244", "rel_title": "Delaying the COVID-19 epidemic in Australia: Evaluating the effectiveness of international travel bans", @@ -1601154,6 +1602095,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042234", + "rel_title": "Mechanical Ventilator Milano (MVM):A Novel Mechanical Ventilator Designed for Mass Scale Production in response to the COVID-19 Pandemics", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042234", + "rel_abs": "We present here the design of the Mechanical Ventilator Milano (MVM), a novel mechanical ventilator designed for mass scale production in response to the COVID-19 pandemics, to compensate for the dramatic shortage of such ventilators in many countries. This ventilator is an electro-mechanical equivalent of the old, reliable Manley Ventilator. Our design is optimized to permit large sale production in short time and at a limited cost, relying on off-the-shelf components, readily available worldwide from hardware suppliers. Operation of the MVM requires only a source of compressed oxygen (or compressed medical air) and electrical power. The MVM control and monitoring unit can be connected and networked via WiFi so that no additional electrical connections are necessary other than the connection to the electrical power.\n\nAt this stage the MVM is not a certified medical device. Construction of the first prototypes is starting with a team of engineers, scientists and computing experts. The purpose of this paper is to disseminate the conceptual design of the MVM broadly and to solicit feed-back from the scientific and medical community to speed the process of review, improvement and possible implementation.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Galbiati Cristiano", + "author_inst": "Physics Department, Princeton University, Princeton, NJ 08544, USA" + }, + { + "author_name": "Walter Bonivento", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Mauro Caravati", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Marco Razeti", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Sandro DeCecco", + "author_inst": "Physics Department, Sapienza Universit`a di Roma, Roma 00185, Italy and INFN Sezione di Roma, Roma 00185, Italy" + }, + { + "author_name": "Giuliana Fiorillo", + "author_inst": "Physics Department, Universita degli Studi Federico II di Napoli, Napoli 80126, Italy and INFN Napoli, Napoli 80126, Italy" + }, + { + "author_name": "Federico Gabriele", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Roberto Tartaglia", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Alessandro Razeto", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Davide Sablone", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Eugenio Scapparone", + "author_inst": "INFN Bologna, Bologna 40126, Italy" + }, + { + "author_name": "Gemma Testera", + "author_inst": "INFN Genova, Genova 16146, Italy" + }, + { + "author_name": "Marco Rescigno", + "author_inst": "INFN Sezione di Roma, Roma 00185, Italy" + }, + { + "author_name": "Davide Franco", + "author_inst": "APC, Universite Paris Diderot, CNRS/IN2P3, CEA/Irfu, Obs de Paris, USPC, Paris 75205, France" + }, + { + "author_name": "Iza Kochanek", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Cary Kendziora", + "author_inst": "Fermi National Accelerator Laboratory, Batavia, IL 60510, USA" + }, + { + "author_name": "Stephen H. Pordes", + "author_inst": "Fermi National Accelerator Laboratory, Batavia, IL 60510, USA" + }, + { + "author_name": "Hanguo Wang", + "author_inst": "Physics and Astronomy Department, University of California, Los Angeles, CA 90095, USA" + }, + { + "author_name": "Andrea Ianni", + "author_inst": "Physics Department, Princeton University, Princeton, NJ 08544, USA" + }, + { + "author_name": "Art McDonald", + "author_inst": "Department of Physics, Engineering Physics and Astronomy, Queen s University, Kingston, ON K7L 3N6, Canada" + }, + { + "author_name": "L. Molinari Tosatti", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "T. Dinon", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "M. Malosio", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "D. Minuzzo", + "author_inst": "AZ Pneumatica S.r.l., Misinto (MB) 20826, Italy" + }, + { + "author_name": "A. Zardoni", + "author_inst": "AZ Pneumatica S.r.l., Misinto (MB) 20826, Italy" + }, + { + "author_name": "A. Prini", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.03.23.004176", "rel_title": "Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens", @@ -1601722,61 +1602782,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.26.20044370", - "rel_title": "Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044370", - "rel_abs": "BackgroundWe investigated a likely scenario of COVID-19 spreading in Brazil through the complex airport network of the country, for the 90 days after the first national occurrence of the disease. After the confirmation of the first imported cases, the lack of a proper airport entrance control resulted in the infection spreading in a manner directly proportional to the amount of flights reaching each city, following first occurrence of the virus coming from abroad.\n\nMethodologyWe developed a SIR (Susceptible-Infected-Recovered) model divided in a metapopulation structure, where cities with airports were demes connected by the number of flights. Subsequently, we further explored the role of Manaus airport for a rapid entrance of the pandemic into indigenous territories situated in remote places of the Amazon region.\n\nResultsThe expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to the airport closeness centrality within the Brazilian air transportation network. There was a clear pattern in the expansion of the pandemic, with a stiff exponential expansion of cases for all cities. The more an airport showed closeness centrality, the greater was its vulnerability to SARS-CoV-2.\n\nConclusionsWe discussed the weak pandemic control performance of Brazil in comparison with other tropical, developing countries, namely India and Nigeria. Finally, we proposed measures for containing virus spreading taking into consideration the scenario of high poverty.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Servio Pontes Ribeiro", - "author_inst": "UFOP, Brazil" - }, - { - "author_name": "Wesley Dattilo", - "author_inst": "Inecol, Mexico" - }, - { - "author_name": "Alcides Castro e Silva", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "Alexandre Barbosa Reis", - "author_inst": "UFOP, Brazil" - }, - { - "author_name": "Aristoteles Goes-Neto", - "author_inst": "UFMG, Brazil" - }, - { - "author_name": "Luiz Alcantara", - "author_inst": "Fiocruz, Brazil" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Fiocruz, Brazil" - }, - { - "author_name": "Wendel Coura-vital", - "author_inst": "UFOP, Brazil" - }, - { - "author_name": "Geraldo Wilson Fernandes", - "author_inst": "UFMG, Brazil" - }, - { - "author_name": "Vasco Ariston Azevedo", - "author_inst": "UFMG, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.23.20039842", "rel_title": "Air Pollution Reduction and Mortality Benefit during the COVID-19 Outbreak in China", @@ -1602504,6 +1603509,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.03.23.20041889", + "rel_title": "Coincidence of COVID-19 epidemic and olfactory dysfunction outbreak", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041889", + "rel_abs": "BackgroundRecent surge of olfactory dysfunction in patients who were referred to ENT clinics and concurrent COVID-19epidemic in Iran motivated us to evaluate anosmic/hyposmic patients to find any relation between these two events.\n\nMethodsThis is a cross-sectional study with an online checklist on voluntary cases in all provinces of Iran between the 12th and 17th March, 2020. Cases was defined as self-reported anosmia/hyposmia in responders fewer than 4 weeks later (from start the of COVID-19 epidemic in Iran). Variables consist of clinical presentations, related past medical history, family history of recent respiratory tract infection and hospitalization.\n\nResultsIn this study 10069 participants aged 32.5{+/-}8.6 (7-78) years, 71.13% female and 81.68% non-smoker completed online checklist. They reported 10.55% a history of a trip out of home town and 1.1% hospitalization due to respiratory problems recently. From family members 12.17% had a history of severe respiratory disease in recent days and 48.23% had anosmia/hyposmia.\n\nCorrelation between the number of olfactory disorder and reported COVID-19 patients in all 31 provinces till 16th March 2020 was highly significant (Spearman correlation coefficient=0.87, p-Value<0.001). The onset of anosmia was sudden in 76.24% and till the time of filling the questionnaire in 60.90% of patients decreased sense of smell was constant. Also 83.38 of this patients had decreased taste sensation in association with anosmia.\n\nConclusionsIt seems that we have a surge in outbreak of olfactory dysfunction happened in Iran during the COVID-19 epidemic. The exact mechanism of anosmia/hyposmia in COVID-19 patients needs further investigations.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Seyed Hamid Reza Bagheri", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Ali Mohammad Asghari", + "author_inst": "Skull base research center, The five senses institute, Iran University of Medical Sciences" + }, + { + "author_name": "Mohammad Farhadi", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Ahmad Reza Shamshiri", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences" + }, + { + "author_name": "Ali Kabir", + "author_inst": "Minimally Invasive Surgery Research Center, Iran University of Medical Sciences" + }, + { + "author_name": "Seyed Kamran Kamrava", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Maryam Jalessi", + "author_inst": "Skull base research center, The five senses institute, Iran University of Medical Sciences" + }, + { + "author_name": "Alireza Mohebbi", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Rafieh Alizadeh", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences, Tehran" + }, + { + "author_name": "Ali Asghar Honarmand", + "author_inst": "Electronic learning Committee, Iran Medical Council" + }, + { + "author_name": "Babak Ghalehbaghi", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Alireza Salimi", + "author_inst": "Department of anesthesiology, Shahid Beheshti University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2020.03.24.20042796", "rel_title": "Reproducibility and reporting practices in COVID-19 preprint manuscripts", @@ -1603204,29 +1604272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.23.20040501", - "rel_title": "Climate affects global patterns of COVID-19 early outbreak dynamics", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20040501", - "rel_abs": "Environmental factors are well known to affect spatio-temporal patterns of infectious disease outbreaks, but whether the recent rapid spread of COVID-19 across the globe is related to local environmental conditions is highly debated. We assessed the impact of environmental factors (temperature, humidity and air pollution) on the global patterns of COVID-19 early outbreak dynamics during January-May 2020, controlling for several key socio-economic factors and airport connections. We showed that during the earliest phase of the global outbreak (January-March), COVID-19 growth rates were non-linearly related to climate, with fastest spread in regions with a mean temperature of ca. 5{degrees}C, and in the most polluted regions. However, environmental effects faded almost completely when considering later outbreaks, in keeping with the progressive enforcement of containment actions. Accordingly, COVID-19 growth rates consistently decreased with stringent containment actions during both early and late outbreaks. Our findings indicate that environmental drivers may have played a role in explaining the early variation among regions in disease spread. With limited policy interventions, seasonal patterns of disease spread might emerge, with temperate regions of both hemispheres being most at risk of severe outbreaks during colder months. Nevertheless, containment measures play a much stronger role and overwhelm impacts of environmental variation, highlighting the key role for policy interventions in curbing COVID-19 diffusion within a given region. If the disease will become seasonal in the next years, information on environmental drivers of COVID-19 can be integrated with epidemiological models to inform forecasting of future outbreak risks and improve management plans.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Gentile Francesco Ficetola", - "author_inst": "University of Milan" - }, - { - "author_name": "Diego Rubolini", - "author_inst": "University of Milan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.23.20040394", "rel_title": "Anaesthesia and infection control in cesarean section of pregnant women with coronavirus disease 2019 (COVID-19)", @@ -1604078,6 +1605123,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042291", + "rel_title": "Fundamental principles of epidemic spread highlight the immediate need forlarge-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042291", + "rel_abs": "The spread of a novel pathogenic infectious agent eliciting protective immunity is typically characterised by three distinct phases: (I) an initial phase of slow accumulation of new infections (often undetectable), (II) a second phase of rapid growth in cases of infection, disease and death, and (III) an eventual slow down of transmission due to the depletion of susceptible individuals, typically leading to the termination of the (first) epidemic wave. Before the implementation of control measures (e.g. social distancing, travel bans, etc) and under the assumption that infection elicits protective immunity, epidemiological theory indicates that the ongoing epidemic of SARS-CoV-2 will conform to this pattern.\n\nHere, we calibrate a susceptible-infected-recovered (SIR) model to data on cumulative reported SARS-CoV-2 associated deaths from the United Kingdom (UK) and Italy under the assumption that such deaths are well reported events that occur only in a vulnerable fraction of the population. We focus on model solutions which take into consideration previous estimates of critical epidemiological parameters such as the basic reproduction number (R0), probability of death in the vulnerable fraction of the population, infectious period and time from infection to death, with the intention of exploring the sensitivity of the system to the actual fraction of the population vulnerable to severe disease and death.\n\nOur simulations are in agreement with other studies that the current epidemic wave in the UK and Italy in the absence of interventions should have an approximate duration of 2-3 months, with numbers of deaths lagging behind in time relative to overall infections. Importantly, the results we present here suggest the ongoing epidemics in the UK and Italy started at least a month before the first reported death and have already led to the accumulation of significant levels of herd immunity in both countries. There is an inverse relationship between the proportion currently immune and the fraction of the population vulnerable to severe disease.\n\nThis relationship can be used to determine how many people will require hospitalisation (and possibly die) in the coming weeks if we are able to accurately determine current levels of herd immunity. There is thus an urgent need for investment in technologies such as virus (or viral pseudotype) neutralization assays and other robust assays which provide reliable read-outs of protective immunity, and for the provision of open access to valuable data sources such as blood banks and paired samples of acute and convalescent sera from confirmed cases of SARS-CoV-2 to validate these. Urgent development and assessment of such tests should be followed by rapid implementation at scale to provide real-time data. These data will be critical to the proper assessment of the effects of social distancing and other measures currently being adopted to slow down the case incidence and for informing future policy direction.\n\nDisclaimer(a) This material is not final and is subject to be updated any time. (b) Code used will be made available as soon as possible. (c) Contact for press enquiries: Cairbre Sugrue, cairbre@sugruecomms.com, +44 (0)7502 203 769.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + }, + { + "author_name": "Robert Paton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Craig Thompson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sunetra Gupta", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.24.20042705", "rel_title": "Mathematical modeling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada", @@ -1604930,33 +1606010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.24.20042218", - "rel_title": "Estimating the ascertainment rate of SARS-CoV-2 infection in Wuhan, China: implications for management of the global outbreak", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042218", - "rel_abs": "We sought to estimate the ascertainment ratio of SARS-CoV-2 infection in Wuhan, China, using a modified Bayesian SEIR model with publicly reported case data. We estimated it at 0.465% (95%CI: 0.464-0.466%), implying that the outbreak in Wuhan was abated by depletion of susceptibles, rather than public health action alone. This suggests a high-transmissibility/low-severity profile for the current pandemic and raises doubt about whether suppression, rather than mitigation, is a feasible goal.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Theodore Lytras", - "author_inst": "National Public Health Organization, Athens, Greece" - }, - { - "author_name": "Georgios Panagiotakopoulos", - "author_inst": "National Public Health Organization, Athens, Greece" - }, - { - "author_name": "Sotirios Tsiodras", - "author_inst": "National Public Health Organization, Athens, Greece" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.21.990770", "rel_title": "Potent human neutralizing antibodies elicited by SARS-CoV-2 infection", @@ -1605760,6 +1606813,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.21.20040139", + "rel_title": "Tracking and forecasting milepost moments of the epidemic in the early-outbreak: framework and applications to the COVID-19", + "rel_date": "2020-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040139", + "rel_abs": "BackgroundThe outbreak of the 2019 novel coronavirus (COVID-19) has attracted global attention. In the early stage of the outbreak, the most important question concerns some meaningful milepost moments, including (1) the time when the number of daily confirmed cases decreases, (2) the time when the number of daily confirmed cases becomes smaller than that of the daily removed (recovered and death), (3) the time when the number of daily confirmed cases becomes zero, and (4) the time when the number of patients treated in hospital is zero, which indicates the end of the epidemic. Intuitively, the former two can be regarded as two important turning points which indicate the alleviation of epidemic to some extent, while the latter two as two \"zero\" points, respectively. Unfortunately, it is extremely difficult to make right and precise prediction due to the limited amount of available data at a early stage of the outbreak.\n\nMethodTo address it, in this paper, we propose a flexible framework incorporating the effectiveness of the government control to forecast the whole process of a new unknown infectious disease in its early-outbreak. Specially, we first establish the iconic indicators to characterize the extent of epidemic spread, yielding four periods of the whole process corresponding to the four meaningful milepost moments: two turning points and two \"zero\" points. Then we develop the tracking and forecasting procedure with mild and reasonable assumption. Finally we apply it to analyze and evaluate the COVID-19 using the public available data for mainland China beyond Hubei Province from the China Centers for Disease Control (CDC) during the period of Jan 29th, 2020, to Feb 29th, 2020, which shows the effectiveness of the proposed procedure.\n\nResultsResults show that our model can clearly outline the development of the epidemic at a very early stage. The first prediction results on Jan 29th reveal that the first and second milepost moments for mainland China beyond Hubei Province would appear on Jan 31st and Feb 14th respectively, which are only one day and three days behind the real world situations. Forecasting results indicate that the number of newly confirmed cases will become zero in the mid-late March, and the number of patients treated in the hospital will become zero between mid-March and mid-April in mainland China beyond Hubei Province. The framework proposed in this paper can help people get a general understanding of the epidemic trends in counties where COVID-19 are raging as well as any other outbreaks of new and unknown infectious diseases in the future.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Huiwen Wang", + "author_inst": "School of Economics and Management, Beihang University, Beijing, China" + }, + { + "author_name": "Yanwen Zhang", + "author_inst": "School of Economics and Management, Beihang University, Beijing, China" + }, + { + "author_name": "Shan Lu", + "author_inst": "School of Statistics and Mathematics, Central University of Finance and Economics, Beijing, China" + }, + { + "author_name": "Shanshan Wang", + "author_inst": "School of Economics and Management, Beihang University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.22.20034504", "rel_title": "High risk of infection caused posttraumatic stress symptoms in individuals with poor sleep quality: A study on influence of coronavirus disease (COVID-19) in China", @@ -1606512,105 +1607596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.03.19.20038984", - "rel_title": "An exploratory randomized, controlled study on the efficacy and safety of lopinavir/ritonavir or arbidol treating adult patients hospitalized with mild/moderate COVID-19 (ELACOI)", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20038984", - "rel_abs": "BackgroundAntiviral therapies against the novel coronavirus SARS-CoV-2, which has caused a global pandemic of respiratory illness called COVID-19, are still lacking.\n\nMethodsOur study (NCT04252885, named ELACOI), was an exploratory randomized (2:2:1) controlled trial assessing the efficacy and safety of lopinavir/ritonavir (LPV/r) or arbidol monotherapy for treating patients with mild/moderate COVID-19.\n\nFindingsThis study successfully enrolled 86 patients with mild/moderate COVID-19 with 34 randomly assigned to receive LPV/r, 35 to arbidol and 17 with no antiviral medication as control. Baseline characteristics of the three groups were comparable. The primary endpoints, the average time of positive-to-negative conversion of SARS-CoV-2 nucleic acid and conversion rates at days 7 and 14, were similar between groups (all P>0.05). There were no differences between groups in the secondary endpoints, the rates of antipyresis, cough alleviation, or improvement of chest CT at days 7 or 14 (all P>0.05). At day 7, eight (23.5%) patients in the LPV/r group, 3 (8.6%) in the arbidol group and 2(11.8%) in the control group showed a deterioration in clinical status from moderate to severe/critical(P =0.206). Overall, 12 (35.3%) patients in the LPV/r group and 5 (14.3%) in the arbidol group experienced adverse events during the follow-up period. No apparent adverse event occurred in the control group.\n\nConclusionsLPV/r or arbidol monotherapy present little benefit for improving the clinical outcome of patients hospitalized with mild/moderate COVID-19 over supportive care.\n\nFundingThis study was supported by project 2018ZX10302103-002, 2017ZX10202102-003-004 and Infectious Disease Specialty of Guangzhou High-level Clinical Key Specialty (2019-2021).", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Yueping Li", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Zhiwei Xie", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Weiyin Lin", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Weiping Cai", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Chunyan Wen", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Yujuan Guan", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Xiaoneng Mo", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Jian Wang", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Yaping Wang", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Ping Peng", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Xudan Chen", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Wenxin Hong", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Guangming Xiao", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Jinxin Liu", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Lieguang Zhang", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Fengyu Hu", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Feng Li", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Feng Li", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Fuchun Zhang", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Xilong Deng", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Linghua Li", - "author_inst": "Guangzhou Eighth People's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.19.20039198", "rel_title": "The local stability of a modified multi-strain SIR model for emerging viral strains", @@ -1607418,6 +1608403,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.19.20032532", + "rel_title": "Geo temporal distribution of 1,688 Chinese healthcare workers infected with COVID-19 in severe conditions, a secondary data analysis", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20032532", + "rel_abs": "IntroductionThe COVID-19 outbreak is posing an unprecedented challenge to healthcare workers. This study analyzes the geo-temporal effects on disease severity for the 1,688 Chinese healthcare workers infected with COVID-19.\n\nMethodUsing the descriptive results recently reported by the Chinese CDC, we compare the percentage of infected healthcare workers in severe conditions over time and across three areas in China, and the fatality rate of infected healthcare workers with all the infected individuals in China aged 22-59 years.\n\nResultsAmong the infected Chinese healthcare workers whose symptoms onset appeared during the same ten-day period, the percentage of those in severe conditions decreased statistical significantly from 19.7% (Jan 11 - 20) to 14.4% (Jan 21 - 31) to 8.7% (Feb 1 - 11). Across the country, there was also a significant difference in the disease severity among patients symptoms onset during the same period, with Wuhan being the most severe (17%), followed by Hubei Province (10.4%), and the rest of China (7.0%). The case fatality rate for the 1,688 infected Chinese healthcare workers was significantly lower than that for the 29,798 infected patients aged 20-59 years--0.3% (5/1,688) vs. 0.65% (193/29,798), respectively.\n\nConclusionThe disease severity improved considerably over a short period of time in China. The more severe conditions in Wuhan compared to the rest of the country may be attributable to the draconian lockdown. The clinical outcomes of infected Chinese healthcare workers may represent a more accurate estimation of the severity of COVID-19 for those who have access to quality healthcare.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wayne Gao", + "author_inst": "Taipei Medical University" + }, + { + "author_name": "Mattia Sanna", + "author_inst": "Taipei Medical University" + }, + { + "author_name": "Chi Pang Wen", + "author_inst": "National Health Research Institute; China Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.19.20039404", "rel_title": "Healthcare worker absenteeism, child care costs, and COVID-19 school closures: a simulation analysis", @@ -1607978,33 +1608990,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.18.20037473", - "rel_title": "Now-casting the COVID-19 epidemic: The use case of Japan, March 2020", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20037473", - "rel_abs": "BackgroundReporting delays in disease surveillance impair the ability to assess the current dynamic of an epidemic. In continuously updated epidemic curves, case numbers for the most recent epidemic week or day usually appear to be lower than the previous, suggesting a decline of the epidemic. In reality, the epidemic curve may still be on the rise, because reporting delay prevents the most recent cases to appear in the case count. In context of the COVID-19 epidemic and for countries planning large international gatherings, such as the Summer Olympic Games in Japan 2020, the ability to assess the actual stage of an epidemic is of outmost importance.\n\nMethodsWe applied now-casting onto COVID-19 data provided by the nCoV-2019 Data Working Group to evaluate the true count of cases, by taking into account reporting delays occurring between date of symptom onset and date of confirmation.\n\nFindingsWe calculated a decrease of reporting delay, from a median delay of ten days in calendar week four 2020 to six days in calendar week eight, resulting in an overall mean of 4.3 days. The confidence intervals of the now-casting indicated an increase of cases in the last reporting days, while case country in that same time period suggested a decline.\n\nInterpretationAs a specific use case this tool may be of particular value for the challenging risk assessment and risk communication in the context of the Summer Olympic Games in Japan 2020 and similar situations elsewhere.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Stephan Gloeckner", - "author_inst": "Department of Epidemiology, Helmholtz Center for Infection Research" - }, - { - "author_name": "Gerard Krause", - "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research" - }, - { - "author_name": "Michael Hoehle", - "author_inst": "Department of Mathematics, Stockholm University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.19.20038950", "rel_title": "A model for COVID-19 prediction in Iran based on China parameters", @@ -1608840,6 +1609825,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.20.20039818", + "rel_title": "Potential Factors for Prediction of Disease Severity of COVID-19 Patients", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039818", + "rel_abs": "ObjectiveCoronavirus disease 2019 (COVID-19) is an escalating global epidemic caused by SARS-CoV-2, with a high mortality in critical patients. Effective indicators for predicting disease severity in SARS-CoV-2 infected patients are urgently needed.\n\nMethodsIn this study, 43 COVID-19 patients admitted in Chongqing Public Health Medical Center were involved. Demographic data, clinical features, and laboratory examinations were obtained through electronic medical records. Peripheral blood specimens were collected from COVID-19 patients and examined for lymphocyte subsets and cytokine profiles by flow cytometry. Potential contributing factors for prediction of disease severity were further analyzed.\n\nResultsA total of 43 COVID-19 patients were included in this study, including 29 mild patients and 14 sever patients. Severe patients were significantly older (61.9{+/-}9.4 vs 44.4{+/-}15.9) and had higher incidence in co-infection with bacteria compared to mild group (85.7%vs27.6%). Significantly more severe patients had the clinical symptoms of anhelation (78.6%) and asthma (71.4%). For laboratory examination, 57.1% severe cases showed significant reduction in lymphocyte count. The levels of Interluekin-6 (IL6), IL10, erythrocyte sedimentation rate (ESR) and D-Dimer (D-D) were significantly higher in severe patients than mild patients, while the level of albumin (ALB) was remarkably lower in severe patients. Further analysis demonstrated that ESR, D-D, age, ALB and IL6 were the major contributing factors for distinguishing severe patients from mild patients. Moreover, ESR was identified as the most powerful factor to predict disease progression of COVID-19 patients.\n\nConclusionAge and the levels of ESR, D-D, ALB and IL6 are closely related to the disease severity of COVID-19 patients. ESR can be used as a valuable indicator for distinguishing severe COVID-19 patients in early stage, so as to increase the survival of severe patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "huizheng zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "xiaoying wang", + "author_inst": "Chongqing Medical and Pharmaceutical College" + }, + { + "author_name": "zongqiang fu", + "author_inst": "Henan Province hospital of traditional chinese" + }, + { + "author_name": "ming luo", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "zhen zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "ke zhang", + "author_inst": "Chongqing emergency center" + }, + { + "author_name": "ying he", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "dongyong wan", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "liwen zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "jing wang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "xiaofeng yan", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "mei han", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "yaokai chen", + "author_inst": "Chongqing Public Health Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.21.001933", "rel_title": "SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability", @@ -1609816,73 +1610868,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.03.18.20035816", - "rel_title": "Development and utilization of an intelligent application for aiding COVID-19 diagnosis", - "rel_date": "2020-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20035816", - "rel_abs": "BackgroundCOVID-19 has been spreading globally since emergence, but the diagnostic resources are relatively insufficient.\n\nResultsIn order to effectively relieve the resource deficiency of diagnosing COVID-19, we developed a machine learning-based diagnosis model on basis of laboratory examinations indicators from a total of 620 samples, and subsequently implemented it as a COVID-19 diagnosis aid APP to facilitate promotion.\n\nConclusionsExternal validation showed satisfiable model prediction performance (i.e., the positive predictive value and negative predictive value was 86.35% and 84.62%, respectively), which guarantees the promising use of this tool for extensive screening.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Zirui Meng", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Minjin Wang", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Huan Song", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Shuo Guo", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Yanbing Zhou", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Weimin Li", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Yongzhao Zhou", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Mengjiao Li", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Xingbo Song", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Yi Zhou", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Qingfeng Li", - "author_inst": "Public Health Clinical Center of Chengdu" - }, - { - "author_name": "Xiaojun Lu", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Binwu Ying", - "author_inst": "West China Hospital of Sichuan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.19.999318", "rel_title": "The first-in-class peptide binder to the SARS-CoV-2 spike protein", @@ -1610758,6 +1611743,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.16.20036939", + "rel_title": "COVID-19: Forecasting short term hospital needs in France", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20036939", + "rel_abs": "1Europe is now considered as the epicenter of the SARS-CoV-2 pandemic, France being among the most impacted country. In France, there is an increasing concern regarding the capacity of the healthcare system to sustain the outbreak, especially regarding intensive care units (ICU). The aim of this study was to estimate the dynamics of the epidemic in France, and to assess its impact on healthcare resources for each French metropolitan Region. We developed a deterministic, age-structured, Susceptible-Exposed-Infectious-Removed (SEIR) model based on catchment areas of each COVID-19 referral hospitals. We performed one month ahead predictions (up to April 14, 2020) for three different scenarios (R0 = 1.5, R0 = 2.25, R0 = 3), where we estimated the daily number of COVID-19 cases, hospitalizations and deaths, the needs in ICU beds per Region and the reaching date of ICU capacity limits. At the national level, the total number of infected cases is expected to range from 22,872 in the best case (R0 = 1.5) to 161,832 in the worst case (R0 = 3), while the total number of deaths would vary from 1,021 to 11,032, respectively. At the regional level, all ICU capacities may be overrun in the worst scenario. Only seven Regions may lack ICU beds in the mild scenario (R0 = 2.25) and only one in the best case. In the three scenarios, Corse may be the first Region to see its ICU capacities overrun. The two other Regions, whose capacity will be overrun shortly after are Grand-Est and Bourgogne-Franche-Comte. Our analysis shows that, even in the best case scenario, the French healthcare system will very soon be overwhelmed. While drastic social distancing measures may temper our results, a massive reorganization leading to an expansion of French ICU capacities seems to be necessary to manage the coming wave of critically affected COVID-19 patients.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cl\u00e9ment Massonnaud", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449; Rouen University Hospital, Department of Biostatistics" + }, + { + "author_name": "Jonathan Roux", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" + }, + { + "author_name": "Pascal Cr\u00e9pey", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.14.20035659", "rel_title": "Maximum entropy method for estimating the reproduction number: An investigation for COVID-19 in China", @@ -1611234,45 +1612246,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.19.20038182", - "rel_title": "A prospect on the use of antiviral drugs to control local outbreaks of COVID-19", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20038182", - "rel_abs": "ObjectiveInvestigate the impact of using antiviral drugs to control local outbreaks of COVID-19.\n\nMethodsUsing a simulation-based model of viral transmission we tested the impact of different intervention measures for the control of COVID-19.\n\nResultsThe use of an antiviral drug, in combination with contact tracing, quarantine and isolation, results in a significant decrease of the mean final size and the peak incidence of local outbreaks of COVID-19, provided delays in contact tracing are small.\n\nConclusionsIntegrating antiviral drugs together with contact tracing and quarantine is predicted through this model to be an effective tool for the control of local outbreaks of COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Andrea Torneri", - "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Pieter Jules Karel Libin", - "author_inst": "Artificial intelligence lab, Department of computer science, Vrije Universiteit Brussel" - }, - { - "author_name": "Joris Vanderlocht", - "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute,Hasselt University, Hasselt, Belgium" - }, - { - "author_name": "Anne-Mieke Vandamme", - "author_inst": "KU Leuven - University of Leuven, Department of Microbiology and ImmunologyRega Institute for Medical Research, Clinical and epidemiological virology, Leuven, B" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven - University of Leuven, Department of Microbiology and ImmunologyRega Institute for Medical Research, Clinical and epidemiological virology, Leuven, B" - }, - { - "author_name": "Niel Hens", - "author_inst": "Hasselt University and University of Antwerp" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.18.20038513", "rel_title": "Dynamic profile of severe or critical COVID-19 cases", @@ -1612020,6 +1612993,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.16.20037135", + "rel_title": "Hydroxychloroquine and Azithromycin as a treatment of COVID-19: preliminary results of an open-label non-randomized clinical trial", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037135", + "rel_abs": "BackgroundChloroquine and hydroxychloroquine have been found to be efficient on SARS-CoV-2, and reported to be efficient in Chinese COV-19 patients. We evaluate the role of hydroxychloroquine on respiratory viral loads.\n\nPatients and methodsPatients were included in a single arm protocol to receive 600mg of hydroxychloroquine daily and their viral load in nasal swabs was tested daily. Depending on their clinical presentation, azithromycin was added to the treatment. Untreated patients from another center and cases refusing the protocol were included as negative controls. Presence and absence of virus at Day6-post inclusion was considered the end point.\n\nResultsTwenty cases were treated in this study and showed a significant reduction of the viral carriage at D6-post inclusion compared to controls, and much lower average carrying duration than reported of untreated patients in the literature. Azithromycin added to hydroxychloroquine was significantly more efficient for virus elimination.\n\nConclusionHydroxychloroquine is significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect is reinforced by azithromycin.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Philippe GAUTRET", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Jean Christophe LAGIER", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Philippe PAROLA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Van Thuan HOANG", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Line MEDDED", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Morgan MAILHE", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Barbara DOUDIER", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Johan COURJON", + "author_inst": "Centre Hospitalier Universitaire de Nice" + }, + { + "author_name": "Valerie GIORDANENGO", + "author_inst": "Centre Hospitalier Universitaire de Nice" + }, + { + "author_name": "Vera ESTEVES VIEIRA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Herve TISSOT DUPONT", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Stephane HONORE", + "author_inst": "Aix Marseille University" + }, + { + "author_name": "Philippe COLSON", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Eric CHABRIERE", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Bernard LA SCOLA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Jean Marc ROLAIN", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Philippe BROUQUI", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Didier RAOULT Sr.", + "author_inst": "IHU Mediterrane Infection, Aix Marseille University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.19.20038844", "rel_title": "A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys", @@ -1612480,209 +1613540,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.18.20038018", - "rel_title": "Antibody responses to SARS-CoV-2 in COVID-19 patients: the perspective application of serological tests in clinical practice", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038018", - "rel_abs": "BackgroundWe aim to investigate the profile of acute antibody response in COVID-19 patients, and provide proposals for the usage of antibody test in clinical practice.\n\nMethodsA multi-center cross-section study (285 patients) and a single-center follow-up study (63 patients) were performed to investigate the feature of acute antibody response to SARS-CoV-2. A cohort of 52 COVID-19 suspects and 64 close contacts were enrolled to evaluate the potentiality of the antibody test.\n\nResultsThe positive rate for IgG reached 100% around 20 days after symptoms onset. The median day of seroconversion for both lgG and IgM was 13 days after symptoms onset. Seroconversion of IgM occurred at the same time, or earlier, or later than that of IgG. IgG levels in 100% patients (19/19) entered a platform within 6 days after seroconversion. The criteria of IgG seroconversion and > 4-fold increase in the IgG titers in sequential samples together diagnosed 82.9% (34/41) of the patients. Antibody test aided to confirm 4 patients with COVID-19 from 52 suspects who failed to be confirmed by RT-PCR and 7 patients from 148 close contacts with negative RT-PCR.\n\nConclusionIgM and IgG should be detected simultaneously at the early phase of infection. The serological diagnosis criterion of seroconversion or the >; 4-fold increase in the IgG titer is suitable for a majority of COVID-19 patients. Serologic test is helpful for the diagnosis of SARS-CoV-2 infection in suspects and close contacts.", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Quan-xin Long", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Hai-jun Deng", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Juan Chen", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Jieli Hu", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Bei-zhong Liu", - "author_inst": "Department of Clinical Laboratory, Yongchuan Hospital Affiliated to Chongqing Medical University" - }, - { - "author_name": "Pu Liao", - "author_inst": "Department of Clinical Laboratory, Chongqing People Hospital, Chongqing, China." - }, - { - "author_name": "Yong Lin", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Li-hua Yu", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Zhan Mo", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Yin-yin Xu", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Fang Gong", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Gui-cheng Wu", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Xian-xiang Zhang", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Yao-kai Chen", - "author_inst": "The Public Health Center, Chongqing, China;" - }, - { - "author_name": "Zhi-jie Li", - "author_inst": "Laboratory department, Chongqing People Hospital, Chongqing, China;" - }, - { - "author_name": "Kun Wang", - "author_inst": "Laboratory department, Chongqing People Hospital, Chongqing, China;" - }, - { - "author_name": "Xiao-li Zhang", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Wen-guang Tian", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China;" - }, - { - "author_name": "Chang-chun Niu", - "author_inst": "Laboratory department, Chongqing People Hospital, Chongqing, China;" - }, - { - "author_name": "Qing-jun Yang", - "author_inst": "Laboratory department, Chongqing People Hospital, Chongqing, China;" - }, - { - "author_name": "Jiang-lin Xiang", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Hong-xin Du", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Hua-wen Liu", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Chunhui Lang", - "author_inst": "Chongqing Three Gorges Central Hospital." - }, - { - "author_name": "Xiao-he Luo", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Shao-bo Wu", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Xiao-ping Cui", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Zheng Zhou", - "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing, China;" - }, - { - "author_name": "Jing Wang", - "author_inst": "The Public Health Center, Chongqing, China;" - }, - { - "author_name": "Cheng-jun Xue", - "author_inst": "The Public Health Center, Chongqing, China;" - }, - { - "author_name": "Xiao-feng Li", - "author_inst": "The Public Health Center, Chongqing, China;" - }, - { - "author_name": "Li Wang", - "author_inst": "The Public Health Center, Chongqing, China;" - }, - { - "author_name": "Xiao-jun Tang", - "author_inst": "School of Public Health and Management, Chongqing Medical University" - }, - { - "author_name": "Yong Zhang", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Jing-fu Qiu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Xia-mao Liu", - "author_inst": "The Second Hospital Affiliated to Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Jin-jing Li", - "author_inst": "The Second Hospital Affiliated to Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "De-chun Zhang", - "author_inst": "Wanzhou People Hosptital, Chongqing, China" - }, - { - "author_name": "Fan Zhang", - "author_inst": "Wanzhou People Hosptital, Chongqing, China" - }, - { - "author_name": "Xue-fei Cai", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Deqiang Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yuan Hu", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Ji-hua Ren", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Ni Tang", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Ping Liu", - "author_inst": "BioScience Co. LTD, Chongqing, China." - }, - { - "author_name": "Qin Li", - "author_inst": "Chongqing Center for Disease Control and Prevention, Chongqing, China" - }, - { - "author_name": "Ai-long Huang", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.17.20037697", "rel_title": "Estimating Spot Prevalence of COVID-19 from Daily Death Data in Italy", @@ -1613658,6 +1614515,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.15.20036368", + "rel_title": "Coronavirus disease-19: The First 7,755 Cases in the Republic of Korea", + "rel_date": "2020-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036368", + "rel_abs": "We report the first 7,755 patients with confirmed COVID-19 in Korea as of March 13, 2020. A total of 66 deaths were identified, resulting case fatality proportion of 0.9%. Older people, and those with coexisting medical conditions were at risk for fatal outcomes. The highest number of cases were from Daegu, followed by Gyeongbuk, with elevated age-stratified case fatality. This summary may help to understand the disease dynamics in the early phase of COVID-19 outbreak, therefore, to guide future public health measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- COVID-19 National Emergency Response Center Korea Centers for Disease Control and Prevention", + "author_inst": "-" + }, + { + "author_name": "Young June Choe", + "author_inst": "Hallym University College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.15.20036350", "rel_title": "Coronavirus disease-19: Summary of 2,370 Contact Investigations of the First 30 Cases in the Republic of Korea", @@ -1614230,33 +1615110,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.13.20035485", - "rel_title": "Impact of the contact and exclusion rates on the spread of COVID-19 pandemic", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035485", - "rel_abs": "We constructed a simple Susceptible-Infected-Infectious-Excluded model of the spread of COVID-19. The model is parametrised only by the average incubation period,{tau} , and two rate parameters: contact rate, rC, and exclusion rate, rE. The rates can be manipulated by non-therapeutic interventions and determine the basic reproduction number, R = rC/rE, and, together with{tau} , the daily multiplication coefficient at the early exponential phase, {beta}. Initial {beta} determines the reduction of rC required to contain epidemic spread. In the long-term, we consider a scenario based on typical social behaviours, in which rC first decreases in response to a surge of daily new cases, forcing people to self-isolate, and then slowly increases when people gradually accept higher risk. Consequently, initial abrupt epidemic spread is followed by a plateau and slow regression. This scenario, although economically and socially devastating, will grant time to develop, produce, and distribute a vaccine, or at least limit daily cases to a manageable number.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marek Kochanczyk", - "author_inst": "Institute of Fundamental Technological Research" - }, - { - "author_name": "Frederic Grabowski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Tomasz Lipniacki", - "author_inst": "Institute of Fundamental Technological Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.15.992818", "rel_title": "An emergent clade of SARS-CoV-2 linked to returned travellers from Iran", @@ -1615232,6 +1616085,57 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.03.15.20035204", + "rel_title": "International expansion of a novel SARS-CoV-2 mutant", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20035204", + "rel_abs": "Letter to the editor. There is no abstract. The summary was showed: SARS-CoV-2 has inevitably mutated during its pandemic spread to cause unpredictable effects on COVID-19 and complicate epidemic control efforts. Here we report that a novel SARS-CoV-2 mutation (ORF3a) appears to be spreading worldwide, which deserves close attention.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Minjin Wang", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Mengjiao Li", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Ruotong Ren", + "author_inst": "1. Genskey Biotechnology Co., Ltd. 2. Department of Hematology, The First Hospital of Lanzhou University" + }, + { + "author_name": "Andreas Brave", + "author_inst": "Department of microbiology,Public Health Agency of Sweden" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Department of Virology,Molecular Genetics of RNA Viruses unit,CNRS UMR-3569, University of Paris, National Reference Center for Respiratory Viruses Institut Pas" + }, + { + "author_name": "En-Qiang Chen", + "author_inst": "Center of Infectious Diseases, West China Hospital of Sichuan University" + }, + { + "author_name": "Zhiyong Zong", + "author_inst": "Department of Infection Control and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Weimin Li", + "author_inst": "Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Binwu Ying", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.10.986711", "rel_title": "Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols", @@ -1615796,49 +1616700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.12.20034686", - "rel_title": "Clinical Characteristics of 34 Children with Coronavirus Disease-2019 in the West of China: a Multiple-center Case Series", - "rel_date": "2020-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.12.20034686", - "rel_abs": "BackgroundUp to 9 March, 2020, 109577 patients were diagnosed with coronavirus disease-2019 (COVID-19) globally. The clinical and epidemiological characteristics of adult patients have been revealed recently. However, the information of paediatric patients remains unclear. We describe the clinical and epidemiological characteristics of paediatric patients to provide valuable insight into early diagnosis of COVID-19 in children, as well as epidemic control policy making.\n\nMethods and FindingsThis retrospective, observational study was a case series performed at 4 hospitals in the west of China. Thirty-four paediatric patients with COVID-19 were included from January 1 to February 25, 2020. And the final follow-up visit was completed by February 28, 2020. Clinical and epidemiological characteristics were analyzed on the basis of demographic data, medical history, laboratory tests, radiological findings, and treatment information. Data analysis was performed on 34 paediatrics patients with COVID-19 aged from 1 to 144 months (median 33.00, IQR 10.00 - 94.25), among whom 14 males (41.18%) were included. 47.60% of patients were noticed without any exposure history. The median incubation period was 10.50 (7.75 - 25.25) days. Infections of other respiratory pathogens were reported in 16 patients (47.06%). The most common initial symptoms were fever (76.47%), cough (58.82%), and expectoration (20.59%). Vomiting (11.76%) and diarrhea (11.76%) were also reported in a considerable portion of cases. A remarkable increase was detected in serum amyloid A for 17 patients (85.00%) and high-sensitivity C-reactive protein for 17 patients (58.62%), while a decrease of prealbumin was noticed in 25 patients (78.13%). In addition, the levels of lactate dehydrogenase was increased significantly in 28 patients (82.35%), as well as -hydroxybutyrate dehydrogenase in 25 patients (73.53%). Patchy lesions in lobules were detected by chest computed tomographic scans in 28 patients (82.36%). The typical feature of ground-glass opacity for adults was rare in paediatric patients (2.94%). A late-onset pattern of lesions in lobules were also noticed. Stratified analysis of the clinical features were not performed due to relatively limited samples.\n\nConclusionsOur data presented the clinical and epidemiological features of paediatric patients systemically. The findings offer new insight into the early identification and intervention of paediatric patients with COVID-19.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LIThe 2019-novel coronavirus (2019-nCoV) infection has spread worldwide rapidly.\nC_LIO_LIEarly identification and intervention are necessary for effective epidemic control in both adults and children, however the clinical and epidemiological characteristics of paediatric patients remains unclear.\nC_LI\n\nWhat did the researchers do and find?O_LIWe collected and analyzed clinical data of 34 paediatric patients with coronavirus disease-2019 (COVID-19) in 4 hospitals of China from January 1 to February 25, 2020.\nC_LIO_LIWe described the clinical and epidemiological features of the patients, and focused on the differences in initial symptoms and radiological findings between paediatric patients and adult patients.\nC_LIO_LIDistinguished from adult patients, higher incidences of fever, vomiting, and diarrhea were noticed on admission in paediatric cases.\nC_LIO_LIPatchy shadows of high density were common in lobules lesions, while the typical features of ground-glass opacity in adults were rare in paediatric cases.\nC_LIO_LIA late-onset pattern of lobules lesions was revealed on the basis of chest computed tomographic scans.\nC_LI\n\nWhat do these findings mean?O_LIThe specific clinical features in paediatric patients should be paid more attention to, when the physicians are dealing with suspected cases.\nC_LIO_LIThe epidemiological model in children was characterized with dominant family cluster transmission and extended incubation period, which should be taken into consideration in policy making for epidemic control.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Che Zhang", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Jiaowei Gu", - "author_inst": "Affiliated Taihe Hospital of Hubei University of Medicine" - }, - { - "author_name": "Quanjing Chen", - "author_inst": "Dongfeng Hospital of Hubei University of Medicine" - }, - { - "author_name": "Na Deng", - "author_inst": "Shiyan People Hospital" - }, - { - "author_name": "Jingfeng Li", - "author_inst": "Affiliated Taihe Hospital of Hubei University of Medicine" - }, - { - "author_name": "Li Huang", - "author_inst": "Affiliated Taihe Hospital of Hubei University of Medicine" - }, - { - "author_name": "Xihui Zhou", - "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.12.20035048", "rel_title": "Immune phenotyping based on neutrophil-to-lymphocyte ratio and IgG predicts disease severity and outcome for patients with COVID-19", @@ -1616682,6 +1617543,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.11.20034512", + "rel_title": "A Method to Model Outbreaks of New Infectious Diseases with Pandemic Potential such as COVID-19", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20034512", + "rel_abs": "The emergence of the novel coronavirus (a.k.a. COVID-19, SARS-CoV-2) out of Wuhan, Hubei Province, China caught the world by surprise. As the outbreak began to spread outside of China, too little was known about the virus to model its transmission with any acceptable accuracy. World governments responded to rampant misinformation about the virus leading to collateral disasters, such as plunging financial markets, that could have been avoided if better models of the outbreak had been available. This is an engineering approach to model the spread of a new infectious disease from sparse data when little is known about the infectious agent itself. The paper is not so much about the model itself - because there are many good scientific approaches to model an epidemic - as it is about crunching numbers when there are barely any numbers to crunch. The coronavirus outbreak in USA is used to illustrate the implementation of this modeling approach. A Monte Carlo approach is implemented by using incubation period and testing efficiency as variables. Among others it is demonstrated that imposing early travel restrictions from infected countries slowed down the outbreak in the USA by about 26 days.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Willem G Odendaal", + "author_inst": "Virginia Tech" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.11.20031096", "rel_title": "Relationship between the ABO Blood Group and the COVID-19 Susceptibility", @@ -1617425,53 +1618305,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.03.13.991570", - "rel_title": "A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV", - "rel_date": "2020-03-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.13.991570", - "rel_abs": "The outbreak of COVID-19, which is caused by SARS-CoV-2 virus, continues to spread globally, but there is currently very little understanding of the epitopes on the virus. In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. CR3022 targets a highly conserved epitope that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV. Structural modeling further demonstrates that the binding site can only be accessed when at least two RBDs on the trimeric S protein are in the \"up\" conformation. Overall, this study provides structural and molecular insight into the antigenicity of SARS-CoV-2.\n\nONE SENTENCE SUMMARYStructural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Nicholas C. Wu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Chang-Chun D. Lee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Ray T. Y. So", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Huibin Lv", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris K. P. Mok", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.13.990242", "rel_title": "Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning", @@ -1618565,6 +1619398,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.09.20033126", + "rel_title": "Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area", + "rel_date": "2020-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033126", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. We aimed to investigate the epidemiological, clinical, laboratory and radiological characteristics of these patients. We included 67 Tibetan patients with confirmed SARS-CoV-2 infection. The patients were divided into two groups based on the presence of clinical symptoms at admission, with 31 and 36 patients in the symptomatic and asymptomatic groups, respectively. The epidemiological, clinical, laboratory and radiological characteristics were extracted and analysed. No patient had a history of exposure to COVID-19 patients from Wuhan or had travelled to Wuhan. The mean age of Tibetan patients was 39.3 years and 59% of the patients were male. Seven patients presented with fever on admission and lymphocytopenia was present in 20 patients. 47 patients had abnormal chest CTs at admission instead of stating that 20 were unchanged. Lactate dehydrogenase levels were increased in 31 patients. Seven patients progressed to severe COVID-19; however, after treatment, their condition was stable. No patients died. Of the 36 asymptomatic patients, the mean age was younger than the symptomatic group (34.4{+/-}17.3vs 44.9{+/-}18.1 years, P=0.02). Lymphocyte count and prealbumin levels were higher in the asymptomatic group than the group with clinical symptoms (1.6{+/-}0.5 vs 1.3{+/-}0.6 and 241.8{+/-}68.2 vs 191.9{+/-}60.3, respectively; P<0.05). Imported cases of COVID-19 in Tibetan patients were generally mild in this high-altitude area. Absence of fever or radiologic abnormalities on initial presentation were common.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yu Lei", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "yunping lan", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "jianli lu", + "author_inst": "363 hospital of chengdu" + }, + { + "author_name": "xiaobo huang", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "bamu silang", + "author_inst": "daofu people's hospital" + }, + { + "author_name": "fan zeng", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.11.20033159", "rel_title": "Prolonged presence of SARS-CoV-2 in feces of pediatric patients during the convalescent phase", @@ -1619125,85 +1619997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.03.09.983247", - "rel_title": "Inhibition of SARS-CoV-2 infection (previously 2019-nCoV) by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion", - "rel_date": "2020-03-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.09.983247", - "rel_abs": "The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be confirmed. Therefore, we herein used a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed plasma membrane fusion capacity superior to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. We then generated a series of lipopeptides and found that the EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than that of EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, potently inhibiting replication of 4 live human coronaviruses, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by currently circulating SARS-CoV-2 and emerging SARSr-CoVs.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Shuai Xia", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan-Jinbo Joint Research Center, Fudan University," - }, - { - "author_name": "Meiqin Liu", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences," - }, - { - "author_name": "Chao Wang", - "author_inst": "State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology" - }, - { - "author_name": "Wei Xu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan-Jinbo Joint Research Center, Fudan University" - }, - { - "author_name": "Qiaoshuai Lan", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan-Jinbo Joint Research Center, Fudan University," - }, - { - "author_name": "Siliang Feng", - "author_inst": "State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology" - }, - { - "author_name": "Feifei Qi", - "author_inst": "Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Re-emerging Infectiou" - }, - { - "author_name": "Linlin Bao", - "author_inst": "Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Re-emerging Infectiou" - }, - { - "author_name": "Lanying Du", - "author_inst": "Lindsley F. Kimball Research Institute, New York Blood Center, New York" - }, - { - "author_name": "Shuwen Liu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Chuan Qin", - "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Fei Sun", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Zhengli Shi", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Yun Zhu", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Shibo Jiang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan-Jinbo Joint Research Center, Fudan University," - }, - { - "author_name": "Lu Lu", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.09.983064", "rel_title": "Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assays Targeting SARS-CoV-2", @@ -1620798,6 +1621591,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.08.980383", + "rel_title": "In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19", + "rel_date": "2020-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.08.980383", + "rel_abs": "We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity and false positives we remove peptides from consideration that have sequence homology or similar chemical characteristics using a progressively larger database of background peptides. Using this pipeline, we can remove 47 peptides from consideration as diagnostic due to the presence of peptides derived from the human proteome. To address the complexity of the human microbiome, we describe a method to create a database of all proteins of relevant abundance in the saliva microbiome. By utilizing a protein-based approach to the microbiome we can more accurately identify peptides that will be problematic in COVID-19 studies which removes 12 peptides from consideration. To identify diagnostic peptides, another 7 peptides are flagged for removal following comparison to the proteome backgrounds of viral and bacterial pathogens of similar clinical presentation. By aligning the protein sequences of SARS-CoV-2 field isolates deposited to date we can identify peptides for removal due to their presence in highly variable regions that may lead to false negatives as the pathogen evolves. We provide maps of these regions and highlight 3 peptides that should be avoided as potential diagnostic or vaccine targets. Finally, we leverage publicly deposited proteomics data from human cells infected with SARS-CoV-2, as well as a second study with the closely related MERS-CoV to identify the two proteins of highest abundance in human infections. The resulting final list contains the 24 peptides most unique and diagnostic of SARS-CoV-2 infections. These peptides represent the best targets for the development of antibodies are clinical diagnostics. To demonstrate one application of this we model peptide fragmentation using a deep learning tool to rapidly generate targeted LCMS assays and data processing method for detecting CoVID-19 infected patient samples.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC=\"FIGDIR/small/980383v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@1d7fd4borg.highwire.dtl.DTLVardef@136563borg.highwire.dtl.DTLVardef@57641dorg.highwire.dtl.DTLVardef@16de9a4_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ben Orsburn", + "author_inst": "UVA School of Medicine" + }, + { + "author_name": "Conor Jenkins", + "author_inst": "Hood College Biology Department" + }, + { + "author_name": "Sierra D Miller", + "author_inst": "Millersville University" + }, + { + "author_name": "Benjamin A Neely", + "author_inst": "Proteomic und Genomic Sciences" + }, + { + "author_name": "Namandje M Bumpus", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.03.10.985150", "rel_title": "A proposal of an alternative primer for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing", @@ -1621422,41 +1622250,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.08.20032847", - "rel_title": "Prediction of COVID-19 Spreading Profiles in South Korea, Italy and Iran by Data-Driven Coding", - "rel_date": "2020-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.08.20032847", - "rel_abs": "This work applies a data-driven coding method for prediction of the COVID-19 spreading profile in any given population that shows an initial phase of epidemic progression. Based on the historical data collected for COVID-19 spreading in 367 cities in China and the set of parameters of the augmented Susceptible-Exposed-Infected-Removed (SEIR) model obtained for each city, a set of profile codes representing a variety of transmission mechanisms and contact topologies is formed. By comparing the data of an early outbreak of a given population with the complete set of historical profiles, the best fit profiles are selected and the corresponding sets of profile codes are used for prediction of the future progression of the epidemic in that population. Application of the method to the data collected for South Korea, Italy and Iran shows that peaks of infection cases are expected to occur before the end of March 2020, and that the percentage of population infected in each city will be less than 0.01%, 0.05% and 0.02%, for South Korea, Italy and Iran, respectively.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Choujun Zhan", - "author_inst": "South China Normal University" - }, - { - "author_name": "Chi K. Tse", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Zhikang Lai", - "author_inst": "Sun Yat-Sen University" - }, - { - "author_name": "Tianyong Hao", - "author_inst": "South China Normal University" - }, - { - "author_name": "Jingjing Su", - "author_inst": "The Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.08.20031658", "rel_title": "Clinical Characteristics of SARS-CoV-2 Pneumonia Compared to Controls in Chinese Han Population", @@ -1622288,6 +1623081,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.05.20031906", + "rel_title": "COVID-19 early warning score: a multi-parameter screening tool to identify highly suspected patients", + "rel_date": "2020-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031906", + "rel_abs": "BACKGROUNDCorona Virus Disease 2019 (COVID-19) is spreading worldwide. Effective screening for patients is important to limit the epidemic. However, some defects make the currently applied diagnosis methods are still not very ideal for early warning of patients. We aimed to develop a diagnostic model that allows for the quick screening of highly suspected patients using easy-to-get variables.\n\nMETHODSA total of 1,311 patients receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleicacid detection were included, whom with a positive result were classified into COVID-19 group. Multivariate logistic regression analyses were performed to construct the diagnostic model. Receiver operating characteristic (ROC) curve analysis were used for model validation.\n\nRESULTSAfter analysis, signs of pneumonia on CT, history of close contact, fever, neutrophil-to-lymphocyte ratio (NLR), Tmax and sex were included in the diagnostic model. Age and meaningful respiratory symptoms were enrolled into COVID-19 early warning score (COVID-19 EWS). The areas under the ROC curve (AUROC) indicated that both of the diagnostic model (training dataset 0.956 [95%CI 0.935-0.977, P < 0.001]; validation dataset 0.960 [95%CI 0.919-1.0, P < 0.001]) and COVID-19 EWS (training dataset 0.956 [95%CI 0.934-0.978, P < 0.001]; validate dataset 0.966 [95%CI 0.929-1, P < 0.001]) had good discrimination capacity. In addition, we also obtained the cut-off values of disease severity predictors, such as CT score, CD8+ T cell count, CD4+ T cell count, and so on.\n\nCONCLUSIONSThe new developed COVID-19 EWS was a considerable tool for early and relatively accurately warning of SARS-CoV-2 infected patients.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Cong-Ying Song", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Jia Xu", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Jian-Qin He", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Yuan-Qiang Lu", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.06.20031955", "rel_title": "Transmission of corona virus disease 2019 during the incubation period may lead to a quarantine loophole", @@ -1622980,61 +1623804,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.05.20031518", - "rel_title": "Clinical characterization and chest CT findings in laboratory-confirmed COVID-19: a systematic review and meta-analysis", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031518", - "rel_abs": "BackgroundImagery techniques have been used as essential parts of diagnostic workup for patients suspected for 2019-nCoV infection, Multiple studies have reported the features of chest computed tomography (CT) scans among a number of 2019-nCoV patients.\n\nMethodStudy Identification was carried out in databases (PubMed, Embase and Cochrane Library) to identify published studies examining the diagnosis, the 2019 novel coronavirus (2019-nCoV). Heterogeneity among reported prevalence was assessed by computing p-values of Cochrane Q-test and I2 -statics. The pooled prevalence of treatment failure was carried out with a fixed effects meta-analysis model, generating the pooled 95% confidence interval. A random-effect model was used to pool the results since this model could incorporate the heterogeneity of the studies and therefore proved a more generalized result.\n\nResultsAccording to the combined results of meta-analysis, the total 55% of corona patients were males. The mean age of the patients was 41.31 (34.14, 48.47). Two prevalent clinical symptoms between patients were fever, cough with prevalence of 85%, and 62%, respectively. Either Ground Glass Opacity GGO or consolidation was seen in 86% but 14% had NO GGO or consolidation.\n\nThe other rare CT symptoms were pericardial effusion, and pleural effusion with 4, 5, 7% prevalence, respectively. The most prevalent event was Either GGO or consolidation in 85% of patients.\n\nConclusionThe most CT-scan abnormality is Either Ground Glass Opacity GGO or consolidation however in few patients none of them might be observed, so trusting in just CT findings will lead to miss some patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Golnaz Vaseghi", - "author_inst": "Isfahan Cardiovascular research center, cardiovascular research institute, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Marjan Mansourian", - "author_inst": "Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Raheleh Karimi", - "author_inst": "Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Kiyan Heshmat-Ghahdarijani", - "author_inst": "Department of Cardiology, Isfahan Cardiovascular Research Center, Isfahan University of Medical Sciences, Iran" - }, - { - "author_name": "Sadegh Baradaran Mahdavi", - "author_inst": "Department of Physical Medicine, Isfahan University of Medical Sciences, Iran" - }, - { - "author_name": "Amirhossein Pezeshki", - "author_inst": "Department of Pathology, Isfahan University of Medical Sciences, Iran" - }, - { - "author_name": "Behrooz Ataei", - "author_inst": "Infectious disease and tropical medicine research center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Alireza Zandifar", - "author_inst": "Applied physiology research center, cardiovascular research institute, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Omid Shafaat", - "author_inst": "Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Shaghayegh Haghjoo Javanmard", - "author_inst": "Applied physiology research center, cardiovascular research institute, Isfahan University of Medical Sciences, Isfahan, Iran" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.03.06.20031278", "rel_title": "The Evaluation of Sleep Disturbances for Chinese Frontline Medical Workers Under the Outbreak of COVID-19", @@ -1623893,6 +1624662,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.02.20030148", + "rel_title": "Validity of Wrist and Forehead Temperature in Temperature Screening in the General Population During the Outbreak of 2019 Novel Coronavirus: a prospective real-world study", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030148", + "rel_abs": "AimsTemperature screening is important in the population during the outbreak of 2019 Novel Coronavirus (COVID-19). This study aimed to compare the accuracy and precision of wrist and forehead temperature with tympanic temperature under different circumstances.\n\nMethodsWe performed a prospective observational study in a real-life population. We consecutively collected wrist and forehead temperatures in Celsius ({degrees}C) using a non-contact infrared thermometer (NCIT). We also measured the tympanic temperature using a tympanic thermometers (IRTT) and defined fever as a tympanic temperature [≥]37.3{degrees}C.\n\nResultsWe enrolled a total of 528 participants including 261 indoor and 267 outdoor participants. We divided outdoor participants into four types according to their means of transportation to the hospital as walk, bicycle, electric vehicle, car, and inside the car. Under different circumstance, the mean difference ranged from -1.72 to -0.56{degrees}C in different groups for the forehead measurements, and -0.96 to -0.61{degrees}C for the wrist measurements. Both measurements had high fever screening abilities in inpatients (wrist: AUC 0.790; 95% CI: 0.725-0.854, P <0.001; forehead: AUC 0.816; 95% CI: 0.757-0.876, P <0.001). The cut-off value of wrist measurement for detecting tympanic temperature [≥]37.3{degrees}C was 36.2{degrees}C with a 86.4% sensitivity and a 67.0% specificity, and the best threshold of forehead measurement was also 36.2{degrees}C with a 93.2% sensitivity and a 60.0% specificity.\n\nConclusionsWrist measurement is more stable than forehead measurement under different circumstance. Both measurements have great fever screening abilities for indoor patients. The cut-off value of both measurements was 36.2{degrees}C. (ClinicalTrials.gov number: NCT04274621)", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ge Chen", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Jiarong Xie", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Guangli Dai", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Peijun Zheng", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xiaqing Hu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Hongpeng Lu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Lei Xu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xueqin Chen", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xiaomin Chen", + "author_inst": "Ningbo First Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.04.20031005", "rel_title": "Case fatality risk of novel coronavirus diseases 2019 in China", @@ -1624497,57 +1625317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.02.20030312", - "rel_title": "Preliminary estimating the reproduction number of the coronavirus disease (COVID-19) outbreak in Republic of Korea from 31 January to 1 March 2020", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030312", - "rel_abs": "The novel coronavirus disease 2019 (COVID-19) outbreak in Republic of Korea has caused 3736 cases and 18 deaths by 1 March 2020. We modeled the transmission process in Republic of Korea with a stochastic model and estimated the basic reproduction number R0 as 2.6 (95%CI: 2.3-2.9) and 3.2 (95%CI: 2.9-3.5), under the assumption that the exponential growth starting 31 January and 5 February, 2020, respectively. Estimates of dispersion term (k) were larger than 10 significantly, which implies few super-spreading events..", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Zian Zhuang", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Shi Zhao", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Qianying Lin", - "author_inst": "University of Michigan" - }, - { - "author_name": "Peihua Cao", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Yijun Lou", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Lin Yang", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Shu Yang", - "author_inst": "Chengdu University of Traditional Chinese Medicine, Chengdu, China" - }, - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Li Xiao", - "author_inst": "College of Medical Information Engineering, Chengdu University of Traditional Chinese Medicine, Chengdu, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.03.20030650", "rel_title": "Immunodepletion with Hypoxemia: A Potential High Risk Subtype of Coronavirus Disease 2019", @@ -1625507,6 +1626276,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.03.20030627", + "rel_title": "SOCRATES: An online tool leveraging a social contact data sharing initiative to assess mitigation strategies for COVID-19", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030627", + "rel_abs": "ObjectiveEstablishing a social contact data sharing initiative and an interactive tool to assess mitigation strategies for COVID-19.\n\nResultsWe organized data sharing of published social contact surveys via online repositories and formatting guidelines. We analyzed this social contact data in terms of weighted social contact matrices, next generation matrices, relative incidence and R0. We incorporated location-specific isolation measures (e.g. school closure or telework) and capture their effect on transmission dynamics. All methods have been implemented in an online application based on R Shiny and applied to COVID-19 with age-specific susceptibility and infectiousness. Using our online tool with the available social contact data, we illustrate that social distancing could have a considerable impact on reducing transmission for COVID-19. The effect itself depends on assumptions made about disease-specific characteristics and the choice of intervention(s).", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lander Willem", + "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Thang Van Hoang", + "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "Centre for the Mathematical Modelling of Infectious Diseases,London School of Hygiene & Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Pietro Coletti", + "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute,Hasselt University, Hasselt, Belgium" + }, + { + "author_name": "Philippe Beutels", + "author_inst": "(1) Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium; (2) School of Public health and Community Med" + }, + { + "author_name": "Niel Hens", + "author_inst": "(1) Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium; (2) Interuniversity Institute of Biostatistic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.03.20030593", "rel_title": "Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China", @@ -1626263,69 +1627071,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.03.02.20028704", - "rel_title": "Monitoring Disease Transmissibility of 2019 Novel Coronavirus Disease in Zhejiang, China", - "rel_date": "2020-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20028704", - "rel_abs": "We monitored the transmissibility of 2019 novel coronavirus disease in Zhejiang accounting the transmissions from imported cases. Even though Zhejiang is one of the worst-affected provinces, an interruption of disease transmission (i.e. instantaneous reproduction numbers <1) was observed in early/mid-February after an early social-distancing response to the outbreak.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ka Chun Chong", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Wei Cheng", - "author_inst": "Zhejiang Province Centre for Disease Control and Prevention" - }, - { - "author_name": "Shi Zhao", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Feng Ling", - "author_inst": "Zhejiang Province Centre for Disease Control and Prevention" - }, - { - "author_name": "Kirran N Mohammad", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Maggie Haitian Wang", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Benny Chung-ying Zee", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Lesley Wei", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Xi Xiong", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Hengyan Liu", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Jingxuan Wang", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Enfu Chen", - "author_inst": "Zhejiang Province Centre for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.02.972927", "rel_title": "Viral Architecture of SARS-CoV-2 with Post-Fusion Spike Revealed by Cryo-EM", @@ -1627204,6 +1627949,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.973255", + "rel_title": "Evidence for RNA editing in the transcriptome of 2019 Novel Coronavirus", + "rel_date": "2020-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.02.973255", + "rel_abs": "The COVID-19 outbreak has become a global health risk and understanding the response of the host to the SARS-CoV-2 virus will help to contrast the disease. Editing by host deaminases is an innate restriction process to counter viruses, and it is not yet known whether it operates against Coronaviruses. Here we analyze RNA sequences from bronchoalveolar lavage fluids derived from infected patients. We identify nucleotide changes that may be signatures of RNA editing: Adenosine-to-Inosine changes from ADAR deaminases and Cytosine-to-Uracil changes from APOBEC ones. A mutational analysis of genomes from different strains of human-hosted Coronaviridae reveals mutational patterns compatible to those observed in the transcriptomic data. Our results thus suggest that both APOBECs and ADARs are involved in Coronavirus genome editing, a process that may shape the fate of both virus and patient.\n\nFor the casual ReaderJust to make a few things clear: - RNA editing and DNA editing are PHYSIOLOGICAL processes. Organisms uses them to (a) try to fight viruses, (b) increase heterogeneity inside cells (on many levels), (c) recognise their own RNA.\n- our work suggests that: (a) cells use RNA editing in trying to deal with Coronaviruses. We don't know to what extent they succeed (and it would be nice if we could help them). (b) Whatever happens, mutations inserted by RNA editing fuel viral evolution. We don't know whether viruses actively exploit this.\n- If you (scientist or not) think our work suggests ANYTHING ELSE, contact us. It can be a first step to help fight these !@#$ coronavirus, or towards a Nobel prize - but we need to discuss it thoroughly.\n- If you think these cellular processes are fascinating, join the club and contact us. We can have a nice cup of tea while chatting how wondrous nature is at coming up with extraordinary solutions...", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Salvatore Di Giorgio", + "author_inst": "Core Research Laboratory, ISPRO, Firenze, 50139, Italy; Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy" + }, + { + "author_name": "Filippo Martignano", + "author_inst": "Core Research Laboratory, ISPRO, Firenze, 50139, Italy; Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy" + }, + { + "author_name": "Maria Gabriella Torcia", + "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy" + }, + { + "author_name": "Giorgio Mattiuz", + "author_inst": "Core Research L 5 aboratory, ISPRO, Firenze, 50139, Italy; Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy" + }, + { + "author_name": "Silvestro G Conticello", + "author_inst": "Institute for Cancer Research, Prevention and Clinical Network (ISPRO); Institute of Clinical Physiology, National Research Council, 56124, Pisa, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.02.28.20029025", "rel_title": "Clinical significance of IgM and IgG test for diagnosis of highly suspected COVID-19 infection", @@ -1628212,25 +1628992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.02.26.20027797", - "rel_title": "Relations of parameters for describing the epidemic of COVID-19 by the Kermack-McKendrick model", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20027797", - "rel_abs": "In order to quantitatively characterize the epidemic of COVID-19, useful relations among parameters describing an epidemic in general are derived based on the Kermack-McKendrick model. The first relation is 1/{tau}grow =1/{tau}trans-1/{tau}inf, where{tau} grow is the time constant of the exponential growth of an epidemic,{tau} trans is the time for a pathogen to be transmitted from one patient to uninfected person, and the infectious time{tau} inf is the time during which the pathogen keeps its power of transmission. The second relation p({infty}) {approx} 1-exp(-(R0-1)/0.60) is the relation between p({infty}), the final size of the disaster defined by the ratio of the total infected people to the population of the society, and the basic reproduction number, R0, which is the number of persons infected by the transmission of the pathogen from one infected person during the infectious time. The third relation 1/{tau}end = 1/{tau}inf-(1-p({infty}))/{tau}trans gives the decay time constant{tau} end at the ending stage of the epidemic. Derived relations are applied to influenza in Japan in 2019 for characterizing the epidemic.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Toshihisa Tomie", - "author_inst": "Changchun University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.29.20029348", "rel_title": "Association of Cardiovascular Manifestations with In-hospital Outcomes in Patients with COVID-19: A Hospital Staff Data", @@ -1629102,6 +1629863,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.20030080", + "rel_title": "Estimation of local novel coronavirus (COVID-19) cases in Wuhan, China from off-site reported cases and population flow data from different sources", + "rel_date": "2020-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030080", + "rel_abs": "BackgroundsIn December 2019, a novel coronavirus (COVID-19) pneumonia hit Wuhan, Hubei Province, China and spread to the rest of China and overseas. The emergence of this virus coincided with the Spring Festival Travel Rush in China. It is possible to estimate total number of cases of COVID-19 in Wuhan, by 23 January 2020, given the cases reported in other cities and population flow data between cities.\n\nMethodsWe built a model to estimate the total number of cases in Wuhan by 23 January 2020, based on the number of cases detected outside Wuhan city in China, with the assumption that if the same screening effort used in other cities applied in Wuhan. We employed population flow data from different sources between Wuhan and other cities/regions by 23 January 2020. The number of total cases was determined by the maximum log likelihood estimation.\n\nFindingsFrom overall cities/regions data, we predicted 1326 (95% CI: 1177, 1484), 1151 (95% CI: 1018, 1292) and 5277 (95% CI: 4732, 5859) as total cases in Wuhan by 23 January 2020, based on different source of data from Changjiang Daily newspaper, Tencent, and Baidu. From separate cities/regions data, we estimated 1059 (95% CI: 918, 1209), 5214 (95% CI: 4659, 5808) as total cases in Wuhan in Wuhan by 23 January 2020, based on different sources of population flow data from Tencent and Baidu.\n\nConclusionSources of population follow data and methods impact the estimates of local cases in Wuhan before city lock down.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zian Zhuang", + "author_inst": "Hong Kong Polytechnic University" + }, + { + "author_name": "Peihua Cao", + "author_inst": "Southern Medical University" + }, + { + "author_name": "Shi Zhao", + "author_inst": "Chinese University of Hong Kong" + }, + { + "author_name": "Yijun Lou", + "author_inst": "Hong Kong Polytechnic University" + }, + { + "author_name": "Weiming Wang", + "author_inst": "Huaiyin Normal University" + }, + { + "author_name": "Shu Yang", + "author_inst": "Chengdu University of Traditional Chinese Medicine, Chengdu, China" + }, + { + "author_name": "Lin Yang", + "author_inst": "The Hong Kong Polytechnic University" + }, + { + "author_name": "Daihai He", + "author_inst": "Hong Kong Polytechnic University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.28.20029173", "rel_title": "Analysis on the Clinical Characteristics of 36 Cases of Novel Coronavirus Pneumonia in Kunming", @@ -1629637,65 +1630445,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.25.20027615", - "rel_title": "Stochastic discrete epidemic modeling of COVID-19 transmission in the Province of Shaanxi incorporating public health intervention and case importation", - "rel_date": "2020-02-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.25.20027615", - "rel_abs": "Before the lock-down of Wuhan/Hubei/China, on January 23rd 2020, a large number of individuals infected by COVID-19 moved from the epicenter Wuhan and the Hubei province due to the Spring Festival, resulting in an epidemic in the other provinces including the Shaanxi province. The epidemic scale in Shaanxi was comparatively small and with half of cases being imported from the epicenter. Based on the complete epidemic data including the symptom onset time and transmission chains, we calculate the control reproduction number (1.48-1.69) in Xian. We could also compute the time transition, for each imported or local case, from the latent, to infected, to hospitalized compartment, as well as the effective reproduction number. This calculation enables us to revise our early deterministic transmission model to a stochastic discrete epidemic model with case importation and parameterize it. Our model-based analyses reveal that the newly generated infections decay to zero quickly; the cumulative number of case-driven quarantined individuals via contact tracing stabilize at a manageable level, indicating that the intervention strategies implemented in the Shaanxi province have been effective. Risk analyses, important for the consideration of \"resumption of work\", show that a large second outbreak is expected if the level of case importation remains at the same level as between January 10th and February 4th 2020. However, if the case importation decreases by 30%, 60% and 90%, the second outbreak if happening will be of small-scale assuming contact tracing and quarantine/isolation remain as effective as before. Finally, we consider the effects of intermittent inflow with a Poisson distribution on the likelihood of multiple outbreaks. We believe the developed methodology and stochastic model provide an important model framework for the evaluation of revising travel restriction rules in the consideration of resuming social-economic activities while managing the disease control with potential case importation.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sanyi Tang", - "author_inst": "Shaanxi Normal Univerity" - }, - { - "author_name": "Biao Tang", - "author_inst": "York University, Canada" - }, - { - "author_name": "Nicola Luigi Bragazzi", - "author_inst": "York Unversity, Canada" - }, - { - "author_name": "Fan Xia", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Tangjuan Li", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Sha He", - "author_inst": "Shaanxi Normal Univerity" - }, - { - "author_name": "Pengyu Ren", - "author_inst": "The Second Affiliated Hospital of Xi'an Jiaotong University" - }, - { - "author_name": "Xia Wang", - "author_inst": "Shaanxi Normal Univerity" - }, - { - "author_name": "Zhihang Peng", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Yanni Xiao", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jianhong Wu", - "author_inst": "York University, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.26.20028472", "rel_title": "The Effects of \"Fangcang, Huoshenshan, and Leishenshan\" Makeshift Hospitals and Temperature on the Mortality of COVID-19", @@ -1630715,6 +1631464,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.02.24.20027649", + "rel_title": "Transmission potential of the New Corona (COVID-19) onboard the Princess Cruises Ship, 2020", + "rel_date": "2020-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027649", + "rel_abs": "An outbreak of COVID-19 developed aboard the Princess Cruises Ship during January-February 2020. Using mathematical modeling and time-series incidence data describing the trajectory of the outbreak among passengers and crew members, we characterize how the transmission potential varied over the course of the outbreak. Our estimate of the mean reproduction number in the confined setting reached values as high as [~]11, which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore (approximate range: 1.1-7). Our findings suggest that Rt decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control. Most recent estimates of Rt reached values largely below the epidemic threshold, indicating that a secondary outbreak of the novel coronavirus was unlikely to occur aboard the Diamond Princess Ship.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.25.20025643", "rel_title": "Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 Pneumonia", @@ -1631339,145 +1632111,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.02.26.964882", - "rel_title": "Structure-based drug design, virtual screening and high-throughput screening rapidly identify antiviral leads targeting COVID-19", - "rel_date": "2020-02-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.26.964882", - "rel_abs": "A new coronavirus (CoV) identified as COVID-19 virus is the etiological agent responsible for the 2019-2020 viral pneumonia outbreak that commenced in Wuhan1-4. Currently there is no targeted therapeutics and effective treatment options remain very limited. In order to rapidly discover lead compounds for clinical use, we initiated a program of combined structure-assisted drug design, virtual drug screening and high-throughput screening to identify new drug leads that target the COVID-19 virus main protease (Mpro). Mpro is a key CoV enzyme, which plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for this virus5,6. Here, we identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of COVID-19 virus Mpro in complex with this compound. Next, through a combination of structure-based virtual and high-throughput screening, we assayed over 10,000 compounds including approved drugs, drug candidates in clinical trials, and other pharmacologically active compounds as inhibitors of Mpro. Six of these inhibit Mpro with IC50 values ranging from 0.67 to 21.4 M. Ebselen also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of this screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases where no specific drugs or vaccines are available.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Zhenming Jin", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiaoyu Du", - "author_inst": "School of Life Sciences, Tsinghua University, Beijing, China" - }, - { - "author_name": "Yechun Xu", - "author_inst": "Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China" - }, - { - "author_name": "Yongqiang Deng", - "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Scienc" - }, - { - "author_name": "Meiqin Liu", - "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Yao Zhao", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Bing Zhang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiaofeng Li", - "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Scienc" - }, - { - "author_name": "Leike Zhang", - "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Chao Peng", - "author_inst": "National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China." - }, - { - "author_name": "Yinkai Duan", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Jing Yu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Lin Wang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Kailin Yang", - "author_inst": "Taussig Cancer Center, Cleveland Clinic, Cleveland, USA" - }, - { - "author_name": "Fengjiang Liu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Rendi Jiang", - "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China." - }, - { - "author_name": "Xinglou Yang", - "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China." - }, - { - "author_name": "Tian You", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiaoce Liu", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Xiuna Yang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Fang Bai", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Hong Liu", - "author_inst": "Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China" - }, - { - "author_name": "Xiang Liu", - "author_inst": "State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University" - }, - { - "author_name": "Luke W. Guddat", - "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Wenqing Xu", - "author_inst": "School of Life Science and Technology, ShanghaiTech University, Shanghai, China." - }, - { - "author_name": "Gengfu Xiao", - "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Chengfeng Qin", - "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Scienc" - }, - { - "author_name": "Zhengli Shi", - "author_inst": "CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Hualiang Jiang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Zihe Rao", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - }, - { - "author_name": "Haitao Yang", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.02.25.965434", "rel_title": "Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2", @@ -1632341,6 +1632974,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025999", + "rel_title": "Generation of antibodies against COVID-19 virus for development of diagnostic tools", + "rel_date": "2020-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025999", + "rel_abs": "The COVID-19 China coronavirus started in Dec 2019 was challenged by the lack of accurate serological diagnostic tool for this deadly disease to quickly identify and isolate the infected patients. The generation of COVID-19-specific antibodies is essential for such tasks. Here we report that polyclonal and monoclonal antibodies were generated by immunizing animals with synthetic peptides corresponding to different areas of Nucleoprotein (N) of COVID-19. The specificities of the COVID-19 antibodies were assessed by Western Blot analysis against NPs from COVID-19, MERS and SARS. Antibodies were used for immunohistochemistry staining of the tissue sections from COVID-19 infected patient, as a potential diagnostic tool. A Sandwich ELISA kit was quickly assembled for quantitation of the virus/NP of COVID-19 concentrations in the vaccine preparations. Development of POCT is also aggressively undergoing.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Maohua Li", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing You'an Hospital, Capital Medical University" + }, + { + "author_name": "Ya Peng", + "author_inst": "Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University" + }, + { + "author_name": "Cuiyan Wang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Wenlin Ren", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Fudong Lv", + "author_inst": "Beijing You'an Hospital, Capital Medical University" + }, + { + "author_name": "Sitao Gong", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Feng Fang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Qianyun Wang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Jianli Li", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Tong Shen", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Hunter Sun", + "author_inst": "AnyGo Technology Co., Ltd" + }, + { + "author_name": "Lei Zhou", + "author_inst": "State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences" + }, + { + "author_name": "Yali Cui", + "author_inst": "College of Life Sciences, Northwest University" + }, + { + "author_name": "Hao Song", + "author_inst": "Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences" + }, + { + "author_name": "Le Sun", + "author_inst": "AbMax Biotechnology Co., LTD" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.23.20026864", "rel_title": "Higher severity and mortality in male patients with COVID-19 independent of age and susceptibility", @@ -1632961,33 +1633673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.24.20027268", - "rel_title": "Estimation of risk factors for COVID-19 mortality - preliminary results", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027268", - "rel_abs": "Since late December 2019 a new epidemic outbreak has emerged from Whuhan, China. Rapidly the new coronavirus has spread worldwide. China CDC has reported results of a descriptive exploratory analysis of all cases diagnosed until the 11th February 2020, presenting the epidemiologic curves and geo-temporal spread of COVID-19 along with case fatality rate according to some baseline characteristics, such as age, gender and several well-established high prevalence comorbidities. Despite this, we intend to increase even further the predictive value of that manuscript by presenting the odds ratio for mortality due to COVID-19 adjusted for the presence of those comorbidities and baseline characteristics such as age and gender. Besides, we present a way to determine the risk of each particular patient, given his characteristics.\n\nWe found that age is the variable that presents higher risk of COVID-19 mortality, where 60 or older patients have an OR = 18.8161 (CI95%[7.1997; 41.5517]). Regarding comorbidities, cardiovascular disease appears to be the riskiest (OR= 12.8328 CI95%[10.2736; 15.8643], along with chronic respiratory disease (OR=7.7925 CI95%[5.5446; 10.4319]). Males are more likely to die from COVID-19 (OR=1.8518 (CI95%[1.5996; 2.1270]). Some limitations such as the lack of information about the correct prevalence of gender per age or about comorbidities per age and gender or the assumption of independence between risk factors are expected to have a small impact on results. A final point of paramount importance is that the equation presented here can be used to determine the probability of dying from COVID-19 for a particular patient, given its age interval, gender and comorbidities associated.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Francisco Caramelo", - "author_inst": "Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra, Portugal; iCBR - Coimbra Institute for Clinical and Biomedical " - }, - { - "author_name": "Nuno Ferreira", - "author_inst": "iCBR - Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Im" - }, - { - "author_name": "Barbara Oliveiros", - "author_inst": "Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra, Portugal; iCBR - Coimbra Institute for Clinical and Biomedical " - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.24.20027375", "rel_title": "Estimation of COVID-2019 burden and potential for international dissemination of infection from Iran", @@ -1634059,6 +1634744,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025866", + "rel_title": "Estimating the Asymptomatic Ratio of 2019 Novel Coronavirus onboard the Princess Cruises Ship, 2020", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025866", + "rel_abs": "The potential infectiousness of asymptomatic COVID-19 cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies. We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 infections onboard the Princess Cruises ship along with the timeline of infections. We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%-20.2%), with most of the infections occurring before the start of the 2-week quarantine.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Katsushi Kagaya", + "author_inst": "Kyoto University" + }, + { + "author_name": "Alexander Zarebski", + "author_inst": "Oxford University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.22.20025460", "rel_title": "Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus", @@ -1634743,41 +1635459,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.18.20024539", - "rel_title": "Clinical characteristics of 50404 patients with 2019-nCoV infection", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.18.20024539", - "rel_abs": "ObjectiveWe aim to summarize reliable evidences of evidence-based medicine for the treatment and prevention of the 2019 novel coronavirus (2019-nCoV) by analyzing all the published studies on the clinical characteristics of patients with 2019-nCoV.\n\nMethodsPubMed, Cochrane Library, Embase, and other databases were searched. Several studies on the clinical characteristics of 2019-nCoV infection were collected for Meta-analysis.\n\nResultsTen studies were included in Meta-analysis, including a total number of 50466 patients with 2019-nCoV infection. Meta-analysis shows that, among these patients, the incidence of fever was 89.1%, the incidence of cough was 72.2%, and the incidence of muscle soreness or fatigue was 42.5%. The incidence of acute respiratory distress syndrome (ARDS) was 14.8%, the incidence of abnormal chest computer tomography (CT) was 96.6%, the percentage of severe cases in all infected cases was 18.1%, and the case fatality rate of patients with 2019-nCoV infection was 4.3%.\n\nConclusionFever and cough are the most common symptoms in patients with 2019-nCoV infection, and most of these patients have abnormal chest CT examination. Several people have muscle soreness or fatigue as well as ARDS. Diarrhea, hemoptysis, headache, sore throat, shock, and other symptoms only occur in a small number of patients. The case fatality rate of patients with 2019-nCoV infection is lower than that of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS).", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Pengfei Sun", - "author_inst": "Zibo Central Hospital" - }, - { - "author_name": "Shuyan Qie", - "author_inst": "Beijing Rehabilitation Hospital of Capital Medical University" - }, - { - "author_name": "Zongjan Liu", - "author_inst": "Beijing Rehabilitation Hospital of Capital Medical University" - }, - { - "author_name": "Jizhen Ren", - "author_inst": "Affiliated Hospital of Qingdao University" - }, - { - "author_name": "Jianing Jianing Xi", - "author_inst": "Beijing Rehabilitation Hospital of Capital Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.19.20024851", "rel_title": "Early Phylogenetic Estimate Of The Effective Reproduction Number Of 2019-nCoV", @@ -1635604,6 +1636285,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.17.952895", + "rel_title": "Functional pangenome analysis provides insights into the origin, function and pathways to therapy of SARS-CoV-2 coronavirus", + "rel_date": "2020-02-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.17.952895", + "rel_abs": "The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells1. The S proteins from SARS-CoV-1 and SARS-CoV-2 are similar2, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-CoV-1-specific neutralizing antibodies to inhibit SARS-CoV-23. Here we used comparative pangenomic analysis of all sequenced Betacoronaviruses to reveal that, among all core gene clusters present in these viruses, the envelope protein E shows a variant shared by SARS and SARS-Cov2 with two completely-conserved key functional features, an ion-channel and a PDZ-binding Motif (PBM). These features trigger a cytokine storm that activates the inflammasome, leading to increased edema in lungs causing the acute respiratory distress syndrome (ARDS)4-6, the leading cause of death in SARS-CoV-1 and SARS-CoV-2 infection7,8. However, three drugs approved for human use may inhibit SARS-CoV-1 and SARS-CoV-2 Protein E, either acting upon the ion channel (Amantadine and Hexamethylene amiloride9,10) or the PBM (SB2035805), thereby potentially increasing the survival of the host, as already demonstrated for SARS-CoV-1in animal models. Hence, blocking the SARS protein E inhibits development of ARDS in vivo. Given that our results demonstrate that the protein E subcluster for the SARS clade is quasi-identical for the key functional regions of SARS-CoV-1 and SARS-CoV-2, we conclude that use of approved drugs shown to act as SARS E protein inhibitors can help prevent further casualties from COVID-2019 while vaccines and other preventive measures are being developed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Intikhab Alam", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Allan K Kamau", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Maxat Kulmanov", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Stefan T Arold", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Arnab T Pain", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Takashi Gojobori", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Carlos M. Duarte", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.02.21.959817", "rel_title": "Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform", @@ -1636280,41 +1637004,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.02.19.956946", - "rel_title": "Structural basis for the recognition of the 2019-nCoV by human ACE2", - "rel_date": "2020-02-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.19.956946", - "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) has been suggested to be the cellular receptor for the new coronavirus (2019-nCoV) that is causing the coronavirus disease 2019 (COVID-19). Like other coronaviruses such as the SARS-CoV, the 2019-nCoV uses the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) to engage ACE2. We most recently determined the structure of the full-length human ACE2 in complex with a neutral amino acid transporter B0AT1. Here we report the cryo-EM structure of the full-length human ACE2 bound to the RBD of the 2019-nCoV at an overall resolution of 2.9 [A] in the presence of B0AT1. The local resolution at the ACE2-RBD interface is 3.5 [A], allowing analysis of the detailed interactions between the RBD and the receptor. Similar to that for the SARS-CoV, the RBD of the 2019-nCoV is recognized by the extracellular peptidase domain (PD) of ACE2 mainly through polar residues. Pairwise comparison reveals a number of variations that may determine the different affinities between ACE2 and the RBDs from these two related viruses.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Renhong Yan", - "author_inst": "Westlake University" - }, - { - "author_name": "Yuanyuan Zhang", - "author_inst": "Westlake University" - }, - { - "author_name": "Yingying Guo", - "author_inst": "Westlake University" - }, - { - "author_name": "Lu Xia", - "author_inst": "Westlake University" - }, - { - "author_name": "Qiang Zhou", - "author_inst": "Westlake University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.02.19.956235", "rel_title": "Crystal structure of the 2019-nCoV spike receptor-binding domain bound with the ACE2 receptor", @@ -1637134,6 +1637823,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.18.955195", + "rel_title": "Structure and immune recognition of the porcine epidemic diarrhea virus spike protein", + "rel_date": "2020-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.18.955195", + "rel_abs": "Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides new insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Robert Kirchdoerfer", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Mahesh Bhandari", + "author_inst": "Iowa State University" + }, + { + "author_name": "Olnita Martini", + "author_inst": "The Scripps Research Intitute" + }, + { + "author_name": "Leigh M Sewell", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Sandhya Bangaru", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Kyoung-Jin Yoon", + "author_inst": "Iowa State University" + }, + { + "author_name": "Andrew Ward", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.02.18.20021881", "rel_title": "Association between 2019-nCoV transmission and N95 respirator use", @@ -1637718,25 +1638450,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.13.20022822", - "rel_title": "Estimating the distribution of the incubation period of 2019 novel coronavirus (COVID-19) infection between travelers to Hubei, China and non-travelers", - "rel_date": "2020-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.13.20022822", - "rel_abs": "ObjectivesAmid the continuing spread of the novel coronavirus (COVID-19), the incubation period of COVID-19 should be regularly re-assessed as more information is available upon the increase in reported cases. The present work estimated the distribution of incubation periods of patients infected in and outside Hubei province of China.\n\nMethodsClinical data were collected from the individual cases reported by the media as they were not fully available on the official pages of the Chinese health authorities. MLE was used to estimate the distributions of the incubation period.\n\nResultsIt was found that the incubation period of patients with no travel history to Hubei was longer and more volatile.\n\nConclusionIt is recommended that the duration of quarantine should be extended to at least 3 weeks.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Char Leung", - "author_inst": "Deakin University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.14.20023168", "rel_title": "A model simulation study on effects of intervention measures in Wuhan COVID-19 epidemic", @@ -1638528,6 +1639241,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.14.20022913", + "rel_title": "Estimating the Efficacy of Traffic Blockage and Quarantine for the Epidemic Caused by 2019-nCoV (COVID-19)", + "rel_date": "2020-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20022913", + "rel_abs": "BackgroundSince the 2019-nCoV (COVID-19) outbreaks in Wuhan, China, the cumulative number of confirmed cases is increasing every day, and a large number of populations all over the world are at risk. The quarantine and traffic blockage can alleviate the risk of the epidemic and the infections, henceforth evaluating the efficacy of such actions is essential to inform policy makers and raise the public awareness of the importance of self-isolation and quarantine.\n\nMethodWe collected confirmed case data and the migration data, and introduced the quarantine factor and traffic blockage factor to the Flow-SEIR model. By varying the quarantine factor and traffic blockage factor, we simulated the change of the peak number and arrival time of infections, then the efficacy of these two intervation measures can be analyzed in our simulation. In our study, the self-protection at home is also included in quarantine.\n\nResultsIn the simulated results, the quarantine and traffic blockage are effective for epidemic control. For Hubei province, the current quarantine factor is estimaed to be 0.405, which means around 40.5% of suceptibles who are close contacting with are in quarantine, and the current traffic blockage factor is estimaed to be 0.66, which indicates around 34% of suceptibles who had flowed out from Hubei. For the other provinces outside Hubei, the current quarantine factor is estimated to be 0.285, and the current traffic blockage factor is estimated to be 0.26. With the quarantine and traffic blockage factor increasing, the number of infections decrease dramatically. We also simulated the start dates of quarantine and traffic blockage at four time points, the simulated results show that the early of warning is also effective for epidemic containing. However, provincial level traffic blockage can only alleviate 21.06% - 22.38% of the peak number of infections. In general, the quarantine is much more effective than the traffic blockage control.\n\nConclusionBoth of quarantine and traffic blockage are effective ways to control the spread of COVID-19. However, the eff icacy of quarantine is found to be much stronger than that of traffic blockage. Considering traffic blockage may also cause huge losses of economy, we propose to gradually deregulate the traffic blockage, and improve quarantine instead. Also, there might be a large number of asymptomatic carriers of COVID-19, the quarantine should be continued for a long time until the epidemic is totally under control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Deqiang Li", + "author_inst": "Southeast University" + }, + { + "author_name": "Zhicheng Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Qinghe Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Zefei Gao", + "author_inst": "Southeast University" + }, + { + "author_name": "Junkai Zhu", + "author_inst": "Southeast University" + }, + { + "author_name": "Junyan Yang", + "author_inst": "Southeast University" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Southeast University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.14.20021535", "rel_title": "Clinical Characteristics of 2019 Novel Infected Coronavirus Pneumonia\uff1aA Systemic Review and Meta-analysis", @@ -1639000,37 +1639756,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.02.07.939207", - "rel_title": "Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019", - "rel_date": "2020-02-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.07.939207", - "rel_abs": "A novel coronavirus (nCoV-2019) was the cause of an outbreak of respiratory illness detected in Wuhan, Hubei Province, China in December of 2019. Genomic analyses of nCoV-2019 determined a 96% resemblance with a coronavirus isolated from a bat in 2013 (RaTG13); however, the receptor binding motif (RBM) of these two genomes share low sequence similarity. This divergence suggests a possible alternative source for the RBM coding sequence in nCoV-2019. We identified high sequence similarity in the RBM between nCoV-2019 and a coronavirus genome reconstructed from a viral metagenomic dataset from pangolins possibly indicating a more complex origin for nCoV-2019.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Matthew C Wong", - "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030 USA" - }, - { - "author_name": "Sara J Javornik Cregeen", - "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030 USA" - }, - { - "author_name": "Nadim J Ajami", - "author_inst": "Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas " - }, - { - "author_name": "Joseph F Petrosino", - "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030 USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.02.05.935387", "rel_title": "Teicoplanin potently blocks the cell entry of 2019-nCoV", @@ -1639866,6 +1640591,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.10.20021725", + "rel_title": "Beyond R0: the importance of contact tracing when predicting epidemics", + "rel_date": "2020-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.10.20021725", + "rel_abs": "The basic reproductive number -- R0 -- is one of the most common and most commonly misapplied numbers in public health. Although often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that two different pathogens can exhibit, even when they have the same R0 [1-3]. Here, we show how to predict outbreak size using estimates of the distribution of secondary infections, leveraging both its average R0 and the underlying heterogeneity. To do so, we reformulate and extend a classic result from random network theory [4] that relies on contact tracing data to simultaneously determine the first moment (R0) and the higher moments (representing the heterogeneity) in the distribution of secondary infections. Further, we show the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19, the uncertainty in outbreak size ranges dramatically. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond R0 when predicting epidemic size.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laurent H\u00e9bert-Dufresne", + "author_inst": "University of Vermont" + }, + { + "author_name": "Benjamin M. Althouse", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Samuel V. Scarpino", + "author_inst": "Northeastern University" + }, + { + "author_name": "Antoine Allard", + "author_inst": "Universit\u00e9 Laval" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.11.20022095", "rel_title": "Primary Care Practitioners' Response to 2019 Novel Coronavirus Outbreak in China", @@ -1640390,65 +1641146,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.03.20020248", - "rel_title": "Estimation of the asymptomatic ratio of novel coronavirus (2019-nCoV) infections among passengers on evacuation flights", - "rel_date": "2020-02-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.03.20020248", - "rel_abs": "A total of 565 Japanese citizens were evacuated from Wuhan, China to Japan. All passengers were screened for symptoms and also undertook reverse transcription polymerase chain reaction testing, identifying 5 asymptomatic and 7 symptomatic passengers testing positive for 2019-nCoV. We show that the screening result is suggestive of the asymptomatic ratio at 41.6%.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hiroshi Nishiura", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Tetsuro Kobayashi", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Takeshi Miyama", - "author_inst": "Osaka Institute of Public Health" - }, - { - "author_name": "Ayako Suzuki", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Sungmok Jung", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Katsuma Hayashi", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Ryo Kinoshita", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Yichi Yang", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Baoyin Yuan", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Andrei R. Akhmetzhanov", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Natalie M Linton", - "author_inst": "Hokkaido University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.03.20020289", "rel_title": "Diarrhea may be underestimated: a missing link in 2019 novel coronavirus", @@ -1641440,6 +1642137,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.02.07.20021071", + "rel_title": "Incorporating Human Movement Data to Improve Epidemiological Estimates for 2019-nCoV", + "rel_date": "2020-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.07.20021071", + "rel_abs": "Estimating the key epidemiological features of the novel coronavirus (2019-nCoV) epidemic proves to be challenging, given incompleteness and delays in early data reporting, in particular, the severe under-reporting bias in the epicenter, Wuhan, Hubei Province, China. As a result, the current literature reports widely varying estimates. We developed an alternative geo-stratified debiasing estimation framework by incorporating human mobility with case reporting data in three stratified zones, i.e., Wuhan, Hubei Province excluding Wuhan, and mainland China excluding Hubei. We estimated the latent infection ratio to be around 0.12% (18,556 people) and the basic reproduction number to be 3.24 in Wuhan before the citys lockdown on January 23, 2020. The findings based on this debiasing framework have important implications to prioritization of control and prevention efforts.\n\nOne Sentence SummaryA geo-stratified debiasing approach incorporating human movement data was developed to improve modeling of the 2019-nCoV epidemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Zhidong Cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Xin Lu", + "author_inst": "National University of Defense Technology" + }, + { + "author_name": "Dirk Pfeiffer", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Lei Wang", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Hongbing Song", + "author_inst": "Chinese PLA Center for Disease Control and Prevention" + }, + { + "author_name": "Tao Pei", + "author_inst": "Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences" + }, + { + "author_name": "Zhongwei Jia", + "author_inst": "Peking University" + }, + { + "author_name": "Daniel Dajun Zeng", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.06.20020941", "rel_title": "Analysis of the epidemic growth of the early 2019-nCoV outbreak using internationally confirmed cases", @@ -1642104,57 +1642852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.04.20020479", - "rel_title": "Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study", - "rel_date": "2020-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.04.20020479", - "rel_abs": "BackgroundA novel coronavirus (2019-nCoV) emerged in Wuhan City, China, at the end of 2019 and has caused an outbreak of human-to-human transmission with a Public Health Emergency of International Concern declared by the World Health Organization on January 30, 2020.\n\nAimWe aimed to estimate the potential risk and geographic range of Wuhan novel coronavirus (2019-nCoV) spread within and beyond China from January through to April, 2020.\n\nMethodsA series of domestic and international travel network-based connectivity and risk analyses were performed, by using de-identified and aggregated mobile phone data, air passenger itinerary data, and case reports.\n\nResultsThe cordon sanitaire of Wuhan is likely to have occurred during the latter stages of peak population numbers leaving the city before Lunar New Year (LNY), with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% UI: 478 - 1349) had 2019-nCoV infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to Wuhans lockdown. The majority of these cities were in Asia, but major hubs in Europe, the US and Australia were also prominent, with strong correlation seen between predicted importation risks and reported cases. Because significant spread has already occurred, a large number of airline travellers (3.3 million under the scenario of 75% travel reduction from normal volumes) may be required to be screened at origin high-risk cities in China and destinations across the globe for the following three months of February to April, 2020 to effectively limit spread beyond its current extent.\n\nConclusionFurther spread of 2019-nCoV within China and international exportation is likely to occur. All countries, especially vulnerable regions, should be prepared for efforts to contain the 2019-nCoV infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Shengjie Lai", - "author_inst": "WorldPop, University of Southampton" - }, - { - "author_name": "Isaac Bogoch", - "author_inst": "Bluedot" - }, - { - "author_name": "Nick Ruktanonchai", - "author_inst": "WorldPop, University of Southampton" - }, - { - "author_name": "Alexander Watts", - "author_inst": "Bluedot" - }, - { - "author_name": "Xin Lu", - "author_inst": "National University of Defense Technology, Changsha" - }, - { - "author_name": "Weizhong Yang", - "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "Fudan University" - }, - { - "author_name": "Kamran Khan", - "author_inst": "Bluedot" - }, - { - "author_name": "Andrew J Tatem", - "author_inst": "WorldPop, University of Southampton" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.04.20020461", "rel_title": "Forecasting the Wuhan coronavirus (2019-nCoV) epidemics using a simple (simplistic) model", @@ -1642862,6 +1643559,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.01.31.20019901", + "rel_title": "Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study", + "rel_date": "2020-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019901", + "rel_abs": "BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.\n\nMethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.\n\nFindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.\n\nInterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.\n\nFundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Adam J Kucharski", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Timothy W Russell", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Charlie Diamond", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "CMMID nCoV working group", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "John Edmunds", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.01.30.20019844", "rel_title": "Early evaluation of the Wuhan City travel restrictions in response to the 2019 novel coronavirus outbreak", @@ -1643422,41 +1644166,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.01.30.927574", - "rel_title": "Nucleotide Analogues as Inhibitors of Viral Polymerases", - "rel_date": "2020-01-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.30.927574", - "rel_abs": "Coronaviruses such as the newly discovered virus from Wuhan, China, 2019-nCoV, and the viruses that cause SARS and MERS, have resulted in regional and global public health emergencies. Based on our molecular insight that the hepatitis C virus and the coronavirus use a similar viral genome replication mechanism, we reasoned that the FDA-approved drug EPCLUSA (Sofosbuvir/Velpatasvir) for the treatment of hepatitis C will also inhibit the above coronaviruses, including 2019-nCoV. To develop broad spectrum anti-viral agents, we further describe a novel strategy to design and synthesize viral polymerase inhibitors, by combining the ProTide Prodrug approach used in the development of Sofosbuvir with the use of 3-blocking groups that we have previously built into nucleotide analogues that function as polymerase terminators.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jingyue Ju", - "author_inst": "Columbia University" - }, - { - "author_name": "Shiv Kumar", - "author_inst": "Columbia University" - }, - { - "author_name": "Xiaoxu Li", - "author_inst": "Columbia University" - }, - { - "author_name": "Steffen Jockusch", - "author_inst": "Columbia University" - }, - { - "author_name": "James J Russo", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.01.28.20019299", "rel_title": "Risk of 2019 novel coronavirus importations throughout China prior to the Wuhan quarantine", @@ -1644075,6 +1644784,121 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.01.25.919787", + "rel_title": "Transmission dynamics of 2019 novel coronavirus (2019-nCoV)", + "rel_date": "2020-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.25.919787", + "rel_abs": "RationaleSeveral studies have estimated basic production number of novel coronavirus pneumonia (NCP). However, the time-varying transmission dynamics of NCP during the outbreak remain unclear.\n\nObjectivesWe aimed to estimate the basic and time-varying transmission dynamics of NCP across China, and compared them with SARS.\n\nMethodsData on NCP cases by February 7, 2020 were collected from epidemiological investigations or official websites. Data on severe acute respiratory syndrome (SARS) cases in Guangdong Province, Beijing and Hong Kong during 2002-2003 were also obtained. We estimated the doubling time, basic reproduction number (R0) and time-varying reproduction number (Rt) of NCP and SARS.\n\nMeasurements and main resultsAs of February 7, 2020, 34,598 NCP cases were identified in China, and daily confirmed cases decreased after February 4. The doubling time of NCP nationwide was 2.4 days which was shorter than that of SARS in Guangdong (14.3 days), Hong Kong (5.7 days) and Beijing (12.4 days). The R0 of NCP cases nationwide and in Wuhan were 4.5 and 4.4 respectively, which were higher than R0 of SARS in Guangdong (R0=2.3), Hongkong (R0=2.3), and Beijing (R0=2.6). The Rt for NCP continuously decreased especially after January 16 nationwide and in Wuhan. The R0 for secondary NCP cases in Guangdong was 0.6, and the Rt values were less than 1 during the epidemic.\n\nConclusionsNCP may have a higher transmissibility than SARS, and the efforts of containing the outbreak are effective. However, the efforts are needed to persist in for reducing time-varying reproduction number below one.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSSince December 29, 2019, pneumonia infection with 2019-nCoV, now named as Novel Coronavirus Pneumonia (NCP), occurred in Wuhan, Hubei Province, China. The disease has rapidly spread from Wuhan to other areas. As a novel virus, the time-varying transmission dynamics of NCP remain unclear, and it is also important to compare it with SARS.\n\nWhat This Study Adds to the FieldWe compared the transmission dynamics of NCP with SARS, and found that NCP has a higher transmissibility than SARS. Time-varying production number indicates that rigorous control measures taken by governments are effective across China, and persistent efforts are needed to be taken for reducing instantaneous reproduction number below one.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Tao Liu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianxiong Hu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianpeng Xiao", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Guanhao He", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Min Kang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zuhua Rong", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lifeng Lin", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Haojie Zhong", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Qiong Huang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Aiping Deng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Weilin Zeng", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaohua Tan", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Siqing Zeng", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zhihua Zhu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jiansen Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Dexin Gong", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Donghua Wan", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Shaowei Chen", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lingchuan Guo", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Yan Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Limei Sun", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wenjia Liang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Tie Song", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianfeng He", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wenjun Ma", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.01.25.919688", "rel_title": "Origin time and epidemic dynamics of the 2019 novel coronavirus", @@ -1644659,29 +1645483,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.01.22.915660", - "rel_title": "Functional assessment of cell entry and receptor usage for lineage B \u03b2-coronaviruses, including 2019-nCoV", - "rel_date": "2020-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.22.915660", - "rel_abs": "Over the past 20 years, several coronaviruses have crossed the species barrier into humans, causing outbreaks of severe, and often fatal, respiratory illness. Since SARS- CoV was first identified in animal markets, global viromics projects have discovered thousands of coronavirus sequences in diverse animals and geographic regions. Unfortunately, there are few tools available to functionally test these novel viruses for their ability to infect humans, which has severely hampered efforts to predict the next zoonotic viral outbreak. Here we developed an approach to rapidly screen lineage B betacoronaviruses, such as SARS-CoV and the recent 2019-nCoV, for receptor usage and their ability to infect cell types from different species. We show that host protease processing during viral entry is a significant barrier for several lineage B viruses and that bypassing this barrier allows several lineage B viruses to enter human cells through an unknown receptor. We also demonstrate how different lineage B viruses can recombine to gain entry into human cells and confirm that human ACE2 is the receptor for the recently emerging 2019-nCoV.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Michael C Letko", - "author_inst": "NIH/NIAID" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIH/NIAID" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.01.20.913368", "rel_title": "Genomic and protein structure modelling analysis depicts the origin and infectivity of 2019-nCoV, a new coronavirus which caused a pneumonia outbreak in Wuhan, China",