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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 137,145 papers from 584,398 authors.

Most downloaded biology preprints, since beginning of last month

133,648 results found. For more information, click each entry to expand.

21: Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England
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Posted 08 Mar 2021

Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England
8,046 downloads medRxiv infectious diseases

Daniel J Grint, Kevin Wing, Elizabeth Williamson, Helen I McDonald, Krishnan Bhaskaran, David Evans, Stephen JW Evans, Alex J Walker, George Hickman, Emily Nightingale, Anna Schultze, Christopher T Rentsch, Christopher Bates, Jonathan Cockburn, Helen J Curtis, Caroline E Morton, Sebastian CJ Bacon, Simon Davy, Angel YS Wong, Amir Mehrkar, Laurie Tomlinson, Ian J Douglas, Rohini Mathur, Paula Blomquist, Brian MacKenna, Peter Ingelsby, Richard Croker, John Parry, Frank Hester, Sam Harper, Nicolas J DeVito, Will Hulme, John Tazare, Ben Goldacre, Liam Smeeth, Rosalind M Eggo

The B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (HR: 1.67 (95% CI: 1.34 - 2.09; P<.0001). Absolute risk of death by 28-days increased with age and comorbidities. VOC has potential to spread faster with higher mortality than the pandemic to date.

22: Early effectiveness of COVID-19 vaccination with BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector vaccine on symptomatic disease, hospitalisations and mortality in older adults in England
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Posted 02 Mar 2021

Early effectiveness of COVID-19 vaccination with BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector vaccine on symptomatic disease, hospitalisations and mortality in older adults in England
7,893 downloads medRxiv infectious diseases

Jamie Lopez Bernal, Nick Andrews, Charlotte Gower, Julia Stowe, Chris Robertson, Elise Tessier, Ruth Simmons, Simon Cottrell, Richard Roberts, Mark O’Doherty, Kevin Brown, Claire Cameron, Diane Stockton, Jim McMenamin, Mary Ramsay

ObjectivesTo estimate the real-world effectiveness of the Pfizer/BioNTech BNT162b2 vaccine and Astrazeneca ChAdOx1 vaccine against Confirmed COVID-19, hospitalisations and deaths. To estimate effectiveness on the UK variant of concern. DesignTest negative case control design SettingCommunity COVID-19 PCR testing in England ParticipantsAll adults in England aged 70 years and older (over 7.5 million). All COVID-19 testing in the community among eligible individuals who reported symptoms between 8th December 2020 and 19th February 2021 was included in the analysis. InterventionsOne and two doses of BNT162b2 vaccine. One dose of ChAdOx1 vaccine. Main outcome measuresSymptomatic PCR confirmed SARS-CoV-2 infection, hospitalisations and deaths with COVID-19. ResultsIndividuals aged >=80 years vaccinated with BNT162b2 prior to 4th January, had a higher odds of testing positive in the first 9 days after vaccination (odds ratio up to 1.48, 95%CI 1.23-1.77), indicating that those initially targeted had a higher underlying risk of infection. Vaccine effectiveness was therefore estimated relative to the baseline post-vaccination period. Vaccine effects were noted from 10-13 days after vaccination, reaching an effectiveness of 70% (95% CI 59-78%) from 28-34 days, then plateauing. From 14 days after the second dose a vaccine effectiveness of 89% (95%CI: 85-93%) was seen. Individuals aged >=70 years vaccinated from 4th January had a similar underlying risk of COVID-19 to unvaccinated individuals. With BNT162b2, vaccine effectiveness reached 61% (95%CI 51-69%) from 28-34 days after vaccination then plateaued. With the ChAdOx1 vaccine, vaccine effects were seen from 14-20 days after vaccination reaching an effectiveness of 60% (95%CI 41-73%) from 28-34 days and further increasing to 73% (95%CI 27-90%) from day 35 onwards. On top of the protection against symptomatic disease, cases who had been vaccinated with one dose of BNT162b2 had an additional 43% (95%CI 33-52%) lower risk of emergency hospitalisation and an additional 51% (95%CI 37-62%) lower risk of death. Cases who had been vaccinated with one dose of ChAdOx1 had an additional 37% (95% CI 3-59%) lower risk of emergency hospitalisation. There was insufficient follow-up to assess the effect of ChAdOx1 on mortality due to the later rollout of this vaccine. Combined with the effect against symptomatic disease, this indicates that a single dose of either vaccine is approximately 80% effective at preventing hospitalisation and a single dose of BNT162b2 is 85% effective at preventing death with COVID-19. ConclusionVaccination with either a single dose of BNT162b2 or ChAdOx1 COVID-19 vaccination was associated with a significant reduction in symptomatic SARS-CoV2 positive cases in older adults with even greater protection against severe disease. Both vaccines show similar effects. Protection was maintained for the duration of follow-up (>6 weeks). A second dose of BNT162b2 provides further protection against symptomatic disease but second doses of ChAdOx1 have not yet been rolled out in England. There is a clear effect of the vaccines against the UK variant of concern.

23: COVID-19 vaccine response in pregnant and lactating women: a cohort study
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Posted 08 Mar 2021

COVID-19 vaccine response in pregnant and lactating women: a cohort study
7,682 downloads medRxiv obstetrics and gynecology

Kathryn J. Gray, Evan A. Bordt, Caroline Atyeo, Elizabeth Deriso, Babatunde Akinwunmi, Nicola Young, Aranxta Medina Baez, Lydia L Shook, Dana Cvrk, Kaitlyn James, Rose De Guzman, Sara Brigida, Khady Diouf, Ilona Goldfarb, Lisa M. Bebell, Lael M Yonker, Alessio Fasano, Sayed A Rabi, Michal A Elovitz, Galit Alter, Andrea G. Edlow

Background: Pregnant and lactating women were excluded from initial COVID-19 vaccine trials; thus, data to guide vaccine decision-making are lacking. We sought to evaluate the immunogenicity and reactogenicity of COVID-19 mRNA vaccination in pregnant and lactating women. Methods: 131 reproductive-age vaccine recipients (84 pregnant, 31 lactating, and 16 non-pregnant) were enrolled in a prospective cohort study at two academic medical centers. Titers of SARS-CoV-2 Spike and RBD IgG, IgA and IgM were quantified in participant sera (N=131), umbilical cord sera (N=10), and breastmilk (N=31) at baseline, 2nd vaccine dose, 2-6 weeks post 2nd vaccine, and delivery by Luminex, and confirmed by ELISA. Titers were compared to pregnant women 4-12 weeks from native infection (N=37). Post-vaccination symptoms were assessed. Kruskal-Wallis tests and a mixed effects model, with correction for multiple comparisons, were used to assess differences between groups. Results: Vaccine-induced immune responses were equivalent in pregnant and lactating vs non-pregnant women. All titers were higher than those induced by SARS-CoV-2 infection during pregnancy. Vaccine-generated antibodies were present in all umbilical cord blood and breastmilk samples. SARS-CoV-2 specific IgG, but not IgA, increased in maternal blood and breastmilk with vaccine boost. No differences were noted in reactogenicity across the groups. Conclusions: COVID-19 mRNA vaccines generated robust humoral immunity in pregnant and lactating women, with immunogenicity and reactogenicity similar to that observed in non-pregnant women. Vaccine-induced immune responses were significantly greater than the response to natural infection. Immune transfer to neonates occurred via placental and breastmilk.

24: Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera
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Posted 27 Jan 2021

Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera
7,452 downloads bioRxiv microbiology

Xuping Xie, Yang Liu, Jianying Liu, Xianwen Zhang, Jing Zou, Camila R. Fontes-Garfias, Hongjie Xia, Kena A. Swanson, Mark Cutler, David Cooper, Vineet D Menachery, Scott Weaver, Philip Dormitzer, Pei-Yong Shi

We engineered three SARS-CoV-2 viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion+N501Y+D614G from UK; and E484K+N501Y+D614G from SA. Neutralization geometric mean titers (GMTs) of twenty BTN162b2 vaccine-elicited human sera against the three mutant viruses were 0.81- to 1.46-fold of the GMTs against parental virus, indicating small effects of these mutations on neutralization by sera elicited by two BNT162b2 doses.

25: On the Generation of Medical Dialogues for COVID-19
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Posted 15 May 2020

On the Generation of Medical Dialogues for COVID-19
7,354 downloads medRxiv health informatics

Wenmian Yang, Guangtao Zeng, Bowen Tan, Zeqian Ju, Subrato Chakravorty, Xuehai He, Shu Chen, Xingyi Yang, Qingyang Wu, Zhou Yu, Eric Xing, Pengtao Xie

Under the pandemic of COVID-19, people experiencing COVID19-related symptoms or exposed to risk factors have a pressing need to consult doctors. Due to hospital closure, a lot of consulting services have been moved online. Because of the shortage of medical professionals, many people cannot receive online consultations timely. To address this problem, we aim to develop a medical dialogue system that can provide COVID19-related consultations. We collected two dialogue datasets - CovidDialog - (in English and Chinese respectively) containing conversations between doctors and patients about COVID-19. On these two datasets, we train several dialogue generation models based on Transformer, GPT, and BERT-GPT. Since the two COVID-19 dialogue datasets are small in size, which bear high risk of overfitting, we leverage transfer learning to mitigate data deficiency. Specifically, we take the pretrained models of Transformer, GPT, and BERT-GPT on dialog datasets and other large-scale texts, then finetune them on our CovidDialog datasets. Experiments demonstrate that these approaches are promising in generating meaningful medical dialogue about COVID-19. But more advanced approaches are needed to build a fully useful dialogue system that can offer accurate COVID-related consultations. The data and code are available at https://github.com/UCSD-AI4H/COVID-Dialogue

26: mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
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Posted 19 Jan 2021

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
7,285 downloads bioRxiv immunology

Zijun Wang, Fabian Schmidt, Yiska Weisblum, Frauke Muecksch, Christopher O Barnes, Shlomo Finkin, Dennis Schaefer-Babajew, Melissa Cipolla, Christian Gaebler, Jenna A Lieberman, Thiago Y. Oliveira, Zhi Yang, Morgan E. Abernathy, Kathryn E. Huey-Tubman, Arlene Hurley, Martina Turroja, Kamille A West, Kristie Gordon, Katrina G Millard, Victor Ramos, Justin Da Silva, Jianliang Xu, Robert A Colbert, Roshni Patel, Juan P. Dizon, Cecille Unson-O'Brien, Irina Shimeliovich, Anna Gazumyan, Marina Caskey, Pamela Bjorkman, Rafael Casellas, Theodora Hatziioannou, Paul D. Bieniasz, Michel C Nussenzweig

To date severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected nearly 100 million individuals resulting in over two million deaths. Many vaccines are being deployed to prevent coronavirus disease-2019 (COVID-19) including two novel mRNA-based vaccines. These vaccines elicit neutralizing antibodies and appear to be safe and effective, but the precise nature of the elicited antibodies is not known. Here we report on the antibody and memory B cell responses in a cohort of 20 volunteers who received either the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines. Consistent with prior reports, 8 weeks after the second vaccine injection volunteers showed high levels of IgM, and IgG anti-SARS-CoV-2 spike protein (S), receptor binding domain (RBD) binding titers. Moreover, the plasma neutralizing activity, and the relative numbers of RBD-specific memory B cells were equivalent to individuals who recovered from natural infection. However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin. Consistent with these findings, vaccine-elicited monoclonal antibodies (mAbs) potently neutralize SARS-CoV-2, targeting a number of different RBD epitopes epitopes in common with mAbs isolated from infected donors. Structural analyses of mAbs complexed with S trimer suggest that vaccine- and virus-encoded S adopts similar conformations to induce equivalent anti-RBD antibodies. However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations. Notably, the same mutations were selected when recombinant vesicular stomatitis virus (rVSV)/SARS-CoV-2 S was cultured in the presence of the vaccine elicited mAbs. Taken together the results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid potential loss of clinical efficacy.

27: Excess mortality associated with the COVID-19 pandemic among Californians 18-65 years of age, by occupational sector and occupation: March through October 2020
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Posted 22 Jan 2021

Excess mortality associated with the COVID-19 pandemic among Californians 18-65 years of age, by occupational sector and occupation: March through October 2020
7,167 downloads medRxiv occupational and environmental health

Yea-Hung Chen, Maria Glymour, Alicia Riley, John Balmes, Kate Duchowny, Robert Harrison, Ellicott Matthay, Kirsten Bibbins-Domingo

Background Though SARS-CoV-2 outbreaks have been documented in occupational settings and though there is speculation that essential workers face heightened risks for COVID-19, occupational differences in excess mortality have, to date, not been examined. Such information could point to opportunities for intervention, such as workplace modifications and prioritization of vaccine distribution. Methods and findings Using death records from the California Department of Public Health, we estimated excess mortality among Californians 18--65 years of age by occupational sector and occupation, with additional stratification of the sector analysis by race/ethnicity. During the COVID-19 pandemic, working age adults experienced a 22% increase in mortality compared to historical periods. Relative excess mortality was highest in food/agriculture workers (39% increase), transportation/logistics workers (28% increase), facilities (27%) and manufacturing workers (23% increase). Latino Californians experienced a 36% increase in mortality, with a 59% increase among Latino food/agriculture workers. Black Californians experienced a 28% increase in mortality, with a 36% increase for Black retail workers. Asian Californians experienced an 18% increase, with a 40% increase among Asian healthcare workers. Excess mortality among White working-age Californians increased by 6%, with a 16% increase among White food/agriculture workers. Conclusions Certain occupational sectors have been associated with high excess mortality during the pandemic, particularly among racial and ethnic groups also disproportionately affected by COVID-19. In-person essential work is a likely venue of transmission of coronavirus infection and must be addressed through strict enforcement of health orders in workplace settings and protection of in-person workers. Vaccine distribution prioritizing in-person essential workers will be important for reducing excess COVID mortality.

28: Cannabidiol Inhibits SARS-CoV-2 Replication and Promotes the Host Innate Immune Response
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Posted 10 Mar 2021

Cannabidiol Inhibits SARS-CoV-2 Replication and Promotes the Host Innate Immune Response
6,839 downloads bioRxiv microbiology

Long Chi Nguyen, Dongbo Yang, Vlad Nicolaescu, Thomas Best, Shaonong Chen, J. Brent Friesen, Nir Drayman, Adil Mohamed, Christopher Dann, Diane Silva, Haley Gula, Krysten A. Jones, J. Michael Millis, Bryan C. Dickinson, Savas Tay, Scott A Oakes, Guido F. Pauli, David O. Meltzer, Glenn Randall, Marsha Rich Rosner

The rapid spread of COVID-19 underscores the need for new treatments. Here we report that cannabidiol (CBD), a compound produced by the cannabis plant, inhibits SARS-CoV-2 infection. CBD and its metabolite, 7-OH-CBD, but not congeneric cannabinoids, potently block SARS-CoV-2 replication in lung epithelial cells. CBD acts after cellular infection, inhibiting viral gene expression and reversing many effects of SARS-CoV-2 on host gene transcription. CBD induces interferon expression and up-regulates its antiviral signaling pathway. A cohort of human patients previously taking CBD had significantly lower SARS-CoV-2 infection incidence of up to an order of magnitude relative to matched pairs or the general population. This study highlights CBD, and its active metabolite, 7-OH-CBD, as potential preventative agents and therapeutic treatments for SARS-CoV-2 at early stages of infection.

29: Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7
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Posted 26 Jan 2021

Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7
6,710 downloads bioRxiv immunology

Pengfei Wang, Manoj S. Nair, Lihong Liu, Sho Iketani, Yang Luo, Yicheng Guo, Maple Wang, Jian Yu, Baoshan Zhang, Peter D. Kwong, Barney S Graham, John R Mascola, Jennifer Y Chang, Michael T. Yin, Magdalena E Sobieszczyk, Christos A Kyratsous, Lawrence Shapiro, Zizhang Sheng, Yaoxing Huang, David D Ho

The COVID-19 pandemic has ravaged the globe, and its causative agent, SARS-CoV-2, continues to rage. Prospects of ending this pandemic rest on the development of effective interventions. Single and combination monoclonal antibody (mAb) therapeutics have received emergency use authorization, with more in the pipeline. Furthermore, multiple vaccine constructs have shown promise, including two with ~95% protective efficacy against COVID-19. However, these interventions were directed toward the initial SARS-CoV-2 that emerged in 2019. The recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK and B.1.351 in South Africa is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a few mAbs to the receptor-binding domain (RBD). It is not more resistant to convalescent plasma or vaccinee sera. Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (9.4 fold) and vaccinee sera (10.3-12.4 fold). B.1.351 and emergent variants with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.

30: Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1
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Posted 10 Mar 2020

Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1
6,704 downloads medRxiv infectious diseases

Neeltje van Doremalen, Trenton Bushmaker, Dylan H. Morris, Myndi G Holbrook, Amandine Gamble, Brandi N. Williamson, Azaibi Tamin, Jennifer L. Harcourt, Natalie J. Thornburg, Susan I. Gerber, James O. Lloyd-Smith, Emmie de Wit, Vincent J. Munster

To the EditorA novel human coronavirus, now named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, referred to as HCoV-19 here) that emerged in Wuhan, China in late 2019 is now causing a pandemic1. Here, we analyze the aerosol and surface stability of HCoV-19 and compare it with SARS-CoV-1, the most closely related human coronavirus.2 We evaluated the stability of HCoV-19 and SARS-CoV-1 in aerosols and on different surfaces and estimated their decay rates using a Bayesian regression model (see Supplementary Appendix). All experimental measurements are reported as mean across 3 replicates.

31: A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
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Posted 25 Feb 2021

A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
6,364 downloads medRxiv epidemiology

Medini K Annavajhala, Hiroshi Mohri, Pengfei Wang, Jason E. Zucker, Zizhang Sheng, Angela Gomez-Simmonds, Trevor Bedford, David D Ho, Anne-Catrin Uhlemann

Recent months have seen surges of SARS-CoV-2 infection across the globe along with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature mutations of concern are E484K, which plays a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here, we report the emergence of a novel variant lineage B.1.526 that contains E484K and its alarming rise to dominance in New York City in recent months. This variant is partially or completely resistant to two therapeutic monoclonal antibodies in clinical use. It is also less susceptible to neutralization by convalescent plasma or vaccinee sera by 4.1-fold or 3.3-3.6-fold, respectively. The B.1.526 lineage has now been reported from at least 32 states in the US and numerous other countries. B.1526 has been outpacing B.1.1.7 in Northern Manhattan, and both variants have been spreading throughout New York with comparable estimated doubling times. Such transmission dynamics, together with its resistance to therapeutic antibodies, would warrant B.1.526 as a SARS-CoV-2 variant of concern.

32: Viral cultures for COVID-19 infectivity assessment. Systematic review
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Posted 04 Aug 2020

Viral cultures for COVID-19 infectivity assessment. Systematic review
6,236 downloads medRxiv epidemiology

Tom Jefferson, Elizabeth Spencer, Jon Brassey, Carl Heneghan

Objective To review the evidence from studies comparing SARS-CoV-2 culture, with the results of reverse transcriptase polymerase chain reaction (RT-PCR). Methods We searched LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database for Covid-19 using the terms viral culture or viral replication and associated synonyms up to 10 September 2020. We carried out citation matching and included studies reporting attempts to culture or observe SARS-CoV-2 matching with cutoffs for RT-PCR positivity. One reviewer extracted data for each study and a second reviewer checked end edited the extraction and summarised the narratively by sample: fecal, respiratory, environment, blood or mixed. Where necessary we wrote to corresponding authors of the included or background papers for additional information. We assessed quality using a modified QUADAS 2 risk of bias tool. This is the fourth version of this review that was first published on the 4th of August and updated on the 21t of August, on the 3rd and 10th of September. Results We included 29 studies reporting culturing or observing tissue invasion by SARS-CoV in sputum, naso or oropharyngeal, urine, stool, blood and environmental samples from patients diagnosed with Covid-19. The data are suggestive of a relation between the time from collection of a specimen to test, cycle threshold and symptom severity. The quality of the studies was moderate with lack of standardised reporting. Twelve studies reported that Ct values were significantly lower and log copies higher in samples producing live virus culture. Five studies reported no growth in samples based on a Ct cut-off value. These values ranged from CT > 24 for no growth to Ct > 34 or more. Two studies report a strong relationship between Ct value and ability to recover infectious virus and that the odds of live virus culture reduced by 33% for every one unit increase in Ct. A cut-off RT-PCR Ct > 30 was associated with non-infectious samples. One study that analysed the NSP, N and E gene fragments of the PCR result reported different cut-off thresholds depending on the gene fragment analysed. The duration of RNA shedding detected by PCR was far longer compared to detection of live culture. Six out of eight studies reported RNA shedding for longer than 14 days. Yet, infectivity declines after day 8 even among cases with ongoing high viral loads. A very small proportion of people re-testing positive after hospital discharge or with high Ct are likely to be infectious. Conclusion Prospective routine testing of reference and culture specimens are necessary for each country involved in the pandemic to establish the usefulness and reliability of PCR for Covid-19 and its relation to patient factors. Infectivity is related to the date of onset of symptoms and cycle threshold level. A binary Yes / No approach to the interpretation RT-PCR unvalidated against viral culture will result in false positives with possible segregation of large numbers of people who are no longer infectious and hence not a threat to public health.

33: Indoor transmission of SARS-CoV-2
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Posted 07 Apr 2020

Indoor transmission of SARS-CoV-2
6,093 downloads medRxiv infectious diseases

Hua Qian, Te Miao, Li Liu, Xiaohong Zheng, Danting Luo, Yuguo Li

BackgroundBy early April 2020, the COVID-19 pandemic had infected nearly one million people and had spread to nearly all countries worldwide. It is essential to understand where and how SARS-CoV-2 is transmitted. MethodsCase reports were extracted from the local Municipal Health Commissions of 320 prefectural cities (municipalities) in China, not including Hubei province, between 4 January and 11 February 2020. We identified all outbreaks involving three or more cases and reviewed the major characteristics of the enclosed spaces in which the outbreaks were reported and associated indoor environmental issues. ResultsThree hundred and eighteen outbreaks with three or more cases were identified, involving 1245 confirmed cases in 120 prefectural cities. We divided the venues in which the outbreaks occurred into six categories: homes, transport, food, entertainment, shopping, and miscellaneous. Among the identified outbreaks, 53{middle dot}8% involved three cases, 26{middle dot}4% involved four cases, and only 1{middle dot}6% involved ten or more cases. Home outbreaks were the dominant category (254 of 318 outbreaks; 79{middle dot}9%), followed by transport (108; 34{middle dot}0%; note that many outbreaks involved more than one venue category). Most home outbreaks involved three to five cases. We identified only a single outbreak in an outdoor environment, which involved two cases. ConclusionsAll identified outbreaks of three or more cases occurred in an indoor environment, which confirms that sharing indoor space is a major SARS-CoV-2 infection risk. FundingThe work was supported by the Research Grants Council of Hong (no 17202719, C7025-16G), and National Natural Science Foundation of China (no 41977370).

34: Changes in Solo and Partnered Sexual Behaviors during the COVID-19 Pandemic: Findings from a U.S. Probability Survey
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Posted 11 Jun 2020

Changes in Solo and Partnered Sexual Behaviors during the COVID-19 Pandemic: Findings from a U.S. Probability Survey
5,960 downloads medRxiv sexual and reproductive health

Devon J. Hensel, Molly Rosenberg, Maya Luetke, Tsung-chieh Fu, Debby Herbenick

Background: Research demonstrates that pandemics adversely impact sexual and reproductive health (SRH), but few have examined their impact on participation in sex. We examined self-reported changes in solo and sexual behaviors in U.S. adults during early stages of the public health response to COVID-19. Methods: We conducted an online, nationally representative, cross-sectional survey of U.S. adults (N=1010; aged 18-94 years; 62% response rate) from April 10-20, 2020. We used weighted multinomial logistic regression to examine past month self-reported changes (decreased, stable or increased) in ten solo and partnered sexual behaviors. Predictor variables included: having children at home, past month depressive symptoms, (ACHA 3-item scale), past month loneliness (UCLA 3-Item Loneliness scale), COVID-19 protection behaviors (adapted 12-item scale), perceived COVID-19 consequences (adapted 10-item scale) and COVID-19 knowledge (adapted 10-item scale). Findings: Nearly half of all adults reported some kind of change, most commonly, a decrease, in their sexual behavior in the past month. Having elementary aged children at home, past month depressive symptoms and loneliness and enacting more COVID-19 protective behaviors were associated with both reduced partnered bonding behaviors, such as hugging, cuddling, holding hands and kissing, as well as reduced partnered sexual behaviors, such as oral sex, partnered genital touching and vaginal sex. Greater COVID19 risk perception and greater COVID19 knowledge were associated with mixed effects in behavior outcomes. Interpretations: Our data illustrate the very personal ways in which different pandemic-associated factors may create or inhibit opportunities for solo and partnered sex. The centrality of sexuality to health and well-being, even during pandemics, means that a critical piece of public health prevention and management responses should is ensuring that services and resource that support positive sexual decision making remain open and available.

35: Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays
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Posted 20 Apr 2020

Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays
5,913 downloads medRxiv infectious diseases

Emily R Adams, Mark Ainsworth, Rekha Anand, Monique I Andersson, Kathryn Auckland, J Kenneth Baillie, Eleanor Barnes, Sally Beer, John Bell, Tamsin Berry, Sagida Bibi, Miles Carroll, Senthil Chinnakannan, Elizabeth Clutterbuck, Richard J Cornall, Derrick Crook, Thushan De Silva, Wanwisa Dejnirattisai, Kate E. Dingle, Christina Dold, Alexis Espinosa, David W Eyre, Helen Farmer, Maria Fernandez Mendoza, Dominique Georgiou, Sarah J Hoosdally, Alistair Hunter, Katie Jeffrey, Paul Klenerman, Julian Knight, Clarice Knowles, Andrew J Kwok, Ullrich Leuschner, Robert Levin, Chang Liu, Cesar Lopez-Camacho, Jose Carlos Martinez Garrido, Philippa C Matthews, Hannah McGivern, Alexander J Mentzer, Jonathan Milton, Juthathip Mongkolsapaya, Shona C. Moore, Marta S Oliveira, Fiona Pereira, Elena Perez Lopez, Timothy Peto, Rutger J Ploeg, Andrew Pollard, Tessa Prince, David J. Roberts, Justine K Rudkin, Veronica Sanchez, Gavin R Screaton, Malcolm G Semple, Donal T. Skelly, Jose Slon-Campos, Elliot Nathan Smith, Alberto Jose Sobrino Diaz, Julie Staves, David Stuart, Piyada Supasa, Tomas Surik, Hannah Thraves, Pat Tsang, Lance Turtle, Ann Sarah Walker, Beibei Wang, Charlotte Washington, Nicholas Watkins, James Whitehouse

ABSTRACT Objectives: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Design: We tested plasma for COVID (SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. Setting: We performed laboratory work at the University of Oxford. Participants: We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Main outcome measures: We recorded optical density results from ELISA experiments and positive/negative/invalid results from LFIA devices. Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested [&ge;]10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.

36: The second COVID-19 emergency status declaration for Japan: effects as of February 7, 2021
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Posted 04 Jan 2021

The second COVID-19 emergency status declaration for Japan: effects as of February 7, 2021
5,888 downloads medRxiv public and global health

Junko Kurita, Tamie Sugawara, Yasushi Ohkusa

Background: On January 7, 2021, a second state of emergency was declared in Japan. Object: We evaluated effects of the second emergency status declaration and those of other countermeasures, climate conditions, and mobility through January 21, 2021, when two weeks had passed since the state was activated, as assessed on February 7, 2021. Method: We regressed the effective reproduction number R(t) on temperature, humidity, mobility, and countermeasures such as the two emergency status declarations and GTTC. Results: Estimation results indicate that the second emergency status declaration after GTTC significantly reduced infectiousness as well as the first declaration, controlling for climate condition and mobility. Temperature was found to exert a significant negative effect, although it was not significant if humidity was added as an explanatory variable. Discussion and Conclusion: Results demonstrate that the second emergency status significantly reduced infectiousness.

37: Facemasks and similar barriers to prevent respiratory illness such asCOVID-19: A rapid systematic review
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Posted 06 Apr 2020

Facemasks and similar barriers to prevent respiratory illness such asCOVID-19: A rapid systematic review
5,868 downloads medRxiv infectious diseases

Julii Suzanne Brainard, Natalia Jones, Iain Lake, Lee Hooper, Paul R Hunter

The current pandemic of COVID-19 has lead to conflicting opinions on whether wearing facemasks outside of health care facilities protects against the infection. To better understand the value of wearing facemasks we undertook a rapid systematic review of existing scientific evidence about development of respiratory illness, linked to use of facemasks in community settings. MethodsWe included all study designs. There were 31 eligible studies (including 12 RCTs). Narrative synthesis and random-effects meta-analysis of attack rates for primary and secondary prevention in 28 studies were performed. Results were reported by design, setting and type of face barrier in primary prevention, and by who wore the facemask (index patient or well contacts) in secondary prevention trials. The preferred outcome was influenza-like illness (ILI) but similar outcomes were pooled with ILI when ILI was unavailable. GRADE quality assessment was based on RCTs with support from observational studies. ResultsWhere specific information was available, most studies reported about use of medical grade (surgical paper masks). In 3 RCTs, wearing a facemask may very slightly reduce the odds of developing ILI/respiratory symptoms, by around 6% (OR 0.94, 95% CI 0.75 to 1.19, I 29%, low-certainty evidence). Greater effectiveness was suggested by observational studies. When both house-mates and an infected household member wore facemasks the odds of further household members becoming ill may be modestly reduced by around 19% (OR 0.81, 95%CI 0.48 to 1.37, I 45%, 5 RCTs, low certainty evidence). The protective effect was very small if only the well person (OR 0.93, 95% CI 0.68 to 1.28, I 11%, 2 RCTs, low uncertainty evidence) or the infected person wore the facemask (very low certainty evidence). DiscussionBased on the RCTs we would conclude that wearing facemasks can be very slightly protective against primary infection from casual community contact, and modestly protective against household infections when both infected and uninfected members wear facemasks. However, the RCTs often suffered from poor compliance and controls using facemasks. Across observational studies the evidence in favour of wearing facemasks was stronger. We expect RCTs to under-estimate the protective effect and observational studies to exaggerate it. The evidence is not sufficiently strong to support widespread use of facemasks as a protective measure against COVID-19. However, there is enough evidence to support the use of facemasks for short periods of time by particularly vulnerable individuals when in transient higher risk situations. Further high quality trials are needed to assess when wearing a facemask in the community is most likely to be protective.

38: Associations of the BNT162b2 COVID-19 vaccine effectiveness with patient age and comorbidities
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Posted 17 Mar 2021

Associations of the BNT162b2 COVID-19 vaccine effectiveness with patient age and comorbidities
5,857 downloads medRxiv infectious diseases

Idan Yelin, Rachel Katz, Esma Herzel, Tamar Berman-Zilberstein, Amir Ben-Tov, Jacob Kuint, Sivan Gazit, Tal Patalon, Gabriel Chodick, Roy Kishony

Vaccinations are considered the major tool to curb the current SARS-CoV-2 pandemic. A randomized placebo-controlled trial of the BNT162b2 vaccine has demonstrated a 95% efficacy in preventing COVID-19 disease. These results are now corroborated with statistical analyses of real-world vaccination rollouts, but resolving vaccine effectiveness across demographic groups is challenging. Here, applying a multivariable logistic regression analysis approach to a large patient-level dataset, including SARS-CoV-2 tests, vaccine inoculations and personalized demographics, we model vaccine effectiveness at daily resolution and its interaction with sex, age and comorbidities. Vaccine effectiveness gradually increased post day 12 of inoculation, then plateaued, around 35 days, reaching 91.2% [CI 88.8%-93.1%] for all infections and 99.3% [CI 95.3%-99.9%] for symptomatic infections. Effectiveness was uniform for men and women yet declined mildly but significantly with age and for patients with specific chronic comorbidities, most notably type 2 diabetes. Quantifying real-world vaccine effectiveness, including both biological and behavioral effects, our analysis provides initial measurement of vaccine effectiveness across demographic groups.

39: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
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Posted 31 Jan 2020

Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
5,833 downloads bioRxiv evolutionary biology

Prashant Pradhan, Ashutosh Kumar Pandey, Akhilesh Mishra, Parul Gupta, Praveen Kumar Tripathi, Manoj Balakrishnan Menon, James Gomes, Perumal Vivekanandan, Bishwajit Kundu

This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.

40: SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: Implications for microclot formation in COVID-19
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Posted 08 Mar 2021

SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: Implications for microclot formation in COVID-19
5,721 downloads medRxiv infectious diseases

Lize M Grobbelaar, Chantelle Venter, Mare Vlok, Malebogo Ngoepe, Gert J Laubscher, Petrus J Lourens, Janami Steenkamp, Douglas B Kell, Etheresia Pretorius

Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) -induced infection, the cause of coronavirus disease 2019 (COVID-19), is characterized by unprecedented clinical pathologies. One of the most important pathologies, is hypercoagulation and microclots in the lungs of patients. Here we study the effect of isolated SARS-CoV-2 spike protein S1 subunit as potential inflammagen sui generis. Using scanning electron and fluorescence microscopy as well as mass spectrometry, we investigate the potential of this inflammagen to interact with platelets and fibrin(ogen) directly to cause blood hypercoagulation. Using platelet poor plasma (PPP), we show that spike protein may interfere with blood flow. Mass spectrometry also showed that when spike protein S1 is added to healthy PPP, it results in structural changes to {beta} and {gamma} fibrin(ogen), complement 3, and prothrombin. These proteins were substantially resistant to trypsinization, in the presence of spike protein S1. Here we suggest that, in part, the presence of spike protein in circulation may contribute to the hypercoagulation in COVID-19 positive patients and may cause substantial impairment of fibrinolysis. Such lytic impairment may result in the persistent large microclots we have noted here and previously in plasma samples of COVID-19 patients. This observation may have important clinical relevance in the treatment of hypercoagulability in COVID-19 patients.

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