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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.

81: Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
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Posted 22 Dec 2020

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
3,665 downloads medRxiv epidemiology

Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, Jose Lourenco, Luiz Carlos Junior Alcantara, Sergei L. Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N Bhiman, Carolyn Williamson, Tulio de Oliveira

Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.

82: Correlation between Chest CT Severity Scores and the Clinical Parameters of Adult Patients with COVID-19 pneumonia
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Posted 20 Oct 2020

Correlation between Chest CT Severity Scores and the Clinical Parameters of Adult Patients with COVID-19 pneumonia
3,659 downloads medRxiv radiology and imaging

Ghufran Aref Saeed, Waqar Gaba, Asad Shah, Abeer Ahmed Al Helali, Emadullah Raidullah, Ameirah Bader Al Ali, Mohammed Elghazali, Deena Yousef Ahmed, Shaikha Ghanam Al Kaabi, Safaa Almazrouei

PurposeOur aim is to correlate the clinical condition of patients with COVID-19 infection with the 25 Point CT severity score by Chang et al (devised for assessment of ARDS in patients with SARS in 2005). Material and MethodsData of consecutive symptomatic patients who were suspected to have COVID-19 infection and presented to our hospital, was collected from March to April 2020. All patients underwent two consecutive RT-PCR tests and had a non-contrast HRCT scan done at presentation. From the original cohort of 1062 patients, 160 patients were excluded leaving a total number of 902 patients. ResultsThe mean age was 44.2 {+/-}11.9 years [85.3%males, 14.7%females]. CT severity score found to be positively correlated with lymphopenia, increased serum CRP, d-dimer and ferritin levels (p < 0.0001). The oxygen requirements as well as length of hospital stay were increasing with the increase of scan severity. ConclusionThe 25-point CT severity score correlates well with the COVID-19 clinical severity. Our data suggest that chest CT scoring system can aid in predicting COVID-19 disease outcome and significantly correlates with lab tests and oxygen requirements.

83: Examining Unit Costs for COVID-19 Case Management in Kenya
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Posted 13 Oct 2020

Examining Unit Costs for COVID-19 Case Management in Kenya
3,584 downloads medRxiv health economics

Edwine Barasa, Angela Kairu, Wangari Nganga, Marybeth Maritim, Vincent Were, Samuel Akech, Mercy Mwangangi

IntroductionCase management for COVID-19 patients is one of key interventions in country responses to the pandemic. Countries need information on the costs of case management to inform resource mobilization, planning and budgeting, purchasing arrangements, and assessments of the cost-effectiveness of interventions. We estimated unit costs for COVID-19 case management for patients with asymptomatic, mild to moderate, severe, and critical COVID-19 disease in Kenya. MethodsWe estimated per patient per day unit costs of COVID-19 case management for patients that are asymptomatic and those that have mild to moderate, severe, and critical symptoms. For asymptomatic and mild to moderate patients, we estimated unit costs for home-based care and institutional (hospitals and isolation centers). We used an ingredients approach, adopted a health system perspective and patient episode of care as our time horizon. We obtained data on inputs and their quantities from COVID-19 case management guidelines, home based care guidelines, and human resource guidelines, and augmented this with data provided by three public covid-19 treatment hospitals in Kenya. We obtained input prices for services from a recent costing survey of 20 hospitals in Kenya and for pharmaceuticals, non-pharmaceuticals, devices and equipment from market price databases for Kenya. ResultsPer day per patient unit cost for asymptomatic patients and patients with mild to moderate COVID-19 disease under home based care are KES 1,993.01 (USD 18.89) and 1995.17 (USD 18.991) respectively. When these patients are managed in an isolation center of hospital, the same unit costs for asymptomatic patients and patients with mild to moderate disease are 7,415.28 (USD 70.29) and 7,417.44 (USD 70.31) respectively. Per day unit costs for patients with severe COVID-19 disease managed in general hospital wards and those with critical COVID-19 disease admitted in intensive care units are 12,570.75 (USD 119.16) and 59,369.42 (USD 562.79). ConclusionCOVID-19 case management costs are substantial. Unit costs for asymptomatic and mild to moderate COVID-19 patients in home-based care is 4-fold lower compared institutional care of the same patients. Kenya will not only need to mobilize substantial resources to finance COVID-19 case management but also explore additional service delivery adaptations that will reduce unit costs.

84: Interferon Resistance of Emerging SARS-CoV-2 Variants
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Posted 21 Mar 2021

Interferon Resistance of Emerging SARS-CoV-2 Variants
3,425 downloads bioRxiv microbiology

Kejun Guo, Bradley S Barrett, Kaylee L Mickens, Kim J. Hasenkrug, Mario L Santiago

The emergence of SARS-CoV-2 variants with enhanced transmissibility, pathogenesis and resistance to vaccines presents urgent challenges for curbing the COVID-19 pandemic. While Spike mutations that enhance virus infectivity may drive the emergence of these novel variants, studies documenting a critical a role for interferon responses in the early control of SARS-CoV-2 infection, combined with the presence of viral genes that limit these responses, suggest that interferons may also influence SARS-CoV-2 evolution. Here, we compared the potency of 17 different human interferons against 5 viral lineages sampled during the course of the global outbreak that included ancestral and emerging variants. Our data revealed increased interferon resistance in emerging SARS-CoV-2 variants, indicating that evasion of innate immunity is a significant driving force for SARS-CoV-2 evolution. These findings have implications for the increased lethality of emerging variants and highlight the interferon subtypes that may be most successful in the treatment of early infections.

85: The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia
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Posted 04 Dec 2020

The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia
3,412 downloads medRxiv epidemiology

Martin Pavelka, Kevin van Zandvoort, Sam Abbott, Katharine Sherratt, Marek Majdan, CMMID COVID-19 working group, Inštitút Zdravotných Analýz, Pavol Jarčuška, Marek Krajčí, Stefan Flasche, Sebastian Funk

Slovakia conducted multiple rounds of population-wide rapid antigen testing for SARS-CoV-2 in late 2020, combined with a period of additional contact restrictions. Observed prevalence decreased by 58% (95% CI: 57-58%) within one week in the 45 counties that were subject to two rounds of mass testing, an estimate that remained robust when adjusting for multiple potential confounders. Adjusting for epidemic growth of 4.4% (1.1-6.9%) per day preceding the mass testing campaign, the estimated decrease in prevalence compared to a scenario of unmitigated growth was 70% (67-73%). Modelling suggests that this decrease cannot be explained solely by infection control measures, but requires the additional impact of isolation as well as quarantine of household members of those testing positive.

86: Neutralization of SARS-CoV-2 VOC 501Y.V2 by human antisera elicited by both inactivated BBIBP-CorV and recombinant dimeric RBD ZF2001 vaccines
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Posted 02 Feb 2021

Neutralization of SARS-CoV-2 VOC 501Y.V2 by human antisera elicited by both inactivated BBIBP-CorV and recombinant dimeric RBD ZF2001 vaccines
3,406 downloads bioRxiv microbiology

Baoying Huang, Lianpan Dai, Hui Wang, Zhongyu Hu, Wenjie Tan, George F. Gao, Xiaoming Yang

Recently, the emerged and rapidly spreading SARS-CoV-2 variant of concern (VOC) 501Y.V2 with 10 amino acids in spike protein were found to escape host immunity induced by infection or vaccination. Global concerns have been raised for its potential to affect vaccine efficacy. Here, we evaluated the neutralization activities of two vaccines developed in China against 501Y.V2. One is licensed inactivated vaccine BBIBP-CorV and the other one is recombinant dimeric receptor-binding domain (RBD) vaccine ZF2001. Encouragingly, both vaccines largely preserved neutralizing titres, with slightly reduction, against 501Y.V2 authentic virus compare to their titres against both original SARS-CoV-2 and the currently circulating D614G virus. These data indicated that 501Y.V2 variant will not escape the immunity induced by vaccines targeting whole virus or RBD.

87: False positives in reverse transcription PCR testing for SARS-CoV-2
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Posted 01 May 2020

False positives in reverse transcription PCR testing for SARS-CoV-2
3,349 downloads medRxiv epidemiology

Andrew N Cohen, Bruce Kessel, Michael G Milgroom

Contrary to the practice during previous epidemics, with COVID-19 health authorities have treated a single positive result from a PCR-based test as confirmation of infection, irrespective of signs, symptoms and exposure. This is based on a widespread belief that positive results in these tests are highly reliable. However, evidence from external quality assessments and real-world data indicate enough a high enough false positive rate to make positive results highly unreliable over a broad range of scenarios. This has clinical and case management implications, and affects an array of epidemiological statistics, including the asymptomatic ratio, prevalence, and hospitalization and death rates, as well as epidemiologic models. Steps should be taken to raise awareness of false positives and reduce their frequency. The most important immediate action is to check positive results with additional tests, at least when prevalence is low.

88: Predicting the Trajectory of Any COVID19 Epidemic From the Best Straight Line
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Posted 28 Jun 2020

Predicting the Trajectory of Any COVID19 Epidemic From the Best Straight Line
3,277 downloads medRxiv epidemiology

Michael Levitt, Andrea Scaiewicz, Francesco Zonta

A pipeline involving data acquisition, curation, carefully chosen graphs and mathematical models, allows analysis of COVID-19 outbreaks at 3,546 locations world-wide (all countries plus smaller administrative divisions with data available). Comparison of locations with over 50 deaths shows all outbreaks have a common feature: H(t) defined as loge(X(t)/X(t 1)) decreases linearly on a log scale, where X(t) is the total number of Cases or Deaths on day, t (we use ln for loge). The downward slopes vary by about a factor of three with time constants (1/slope) of between 1 and 3 weeks; this suggests it may be possible to predict when an outbreak will end. Is it possible to go beyond this and perform early prediction of the outcome in terms of the eventual plateau number of total confirmed cases or deaths? We test this hypothesis by showing that the trajectory of cases or deaths in any outbreak can be converted into a straight line. Specifically , is a straight line for the correct plateau value N, which is determined by a new method, Best-Line Fitting (BLF). BLF involves a straight-line facilitation extrapolation needed for prediction; it is blindingly fast and amenable to optimization. We find that in some locations that entire trajectory can be predicted early, whereas others take longer to follow this simple functional form. Fortunately, BLF distinguishes predictions that are likely to be correct in that they show a stable plateau of total cases or death (N value). We apply BLF to locations that seem close to a stable predicted N value and then forecast the outcome at some locations that are still growing wildly. Our accompanying web-site will be updated frequently and provide all graphs and data described here.

89: Interim results of the safety and immune-efficacy of 1 versus 2 doses of COVID-19 vaccine BNT162b2 for cancer patients in the context of the UK vaccine priority guidelines
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Posted 17 Mar 2021

Interim results of the safety and immune-efficacy of 1 versus 2 doses of COVID-19 vaccine BNT162b2 for cancer patients in the context of the UK vaccine priority guidelines
3,277 downloads medRxiv oncology

Leticia Monin-Aldama, Adam G. Laing, Miguel Munoz-Ruiz, Duncan R. McKenzie, Irene del Molino del Barrio, Thanussuyah Alaguthurai, Clara Domingo Vila, Thomas S. Hayday, Carl Graham, Jeffrey Seow, Sultan Abdul-Jawad, Shraddha Kamdar, Elizabeth Harvey-Jones, Rosalind Graham, Jack Cooper, Muhammad Khan, Jennifer Vidler, Helen Kakkassery, Shubhankar Sinha, Richard Davis, Liane Dupont, Isaac Francos Quijorna, Puay Lee, Josephine Eum, Maria Conde Poole, Magdalene Joseph, Daniel Davies, Yin Wu, Ana Montes, Mark Harries, Anne Rigg, James Spicer, Michael H Malim, Paul Fields, Piers Patten, Francesca Di Rosa, Sophie Papa, Tim Tree, Katie Doores, Adrian C. Hayday, Sheeba Irshad

Background: The efficacy and safety profile of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been definitively established in immunocompromised patient populations. Patients with a known cancer diagnosis were hitherto excluded from trials of the vaccines currently in clinical use. Methods: This study presents data on the safety and immune efficacy of the BNT162b.2 (Pfizer-BioNTech) vaccine in 54 healthy controls and 151 mostly elderly patients with solid and haematological malignancies, respectively, and compares results for patients who were boosted with BNT162b.2 at 3 weeks versus those who were not. Immune efficacy was measured as antibody seroconversion, T cell responses, and neutralisation of SARS-CoV-2 Wuhan strain and of a variant of concern (VOC) (B1.1.7). We also collected safety data for the BNT162b2 vaccine up to 5 weeks following first dose. Findings: The vaccine was largely well tolerated. However, in contrast to its very high performance in healthy controls (>90% efficacious), immune efficacy of a single inoculum in solid cancer patients was strikingly low (below 40%) and very low in haematological cancer patients (below 15%). Of note, efficacy in solid cancer patients was greatly and rapidly increased by boosting at 21-days (95% within 2 weeks of boost). Too few haematological cancer patients were boosted for clear conclusions to be drawn. Conclusions: Delayed boosting potentially leaves most solid and haematological cancer patients wholly or partially unprotected, with implications for their own health; their environment and the evolution of VOC strains. Prompt boosting of solid cancer patients quickly overcomes the poor efficacy of the primary inoculum in solid cancer patients.

90: Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states
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Posted 19 Mar 2021

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states
3,161 downloads bioRxiv immunology

Sergio H Triana, Dominik Vonficht, Lea Jopp-Saile, Simon Raffel, Raphael Lutz, Daniel R Leonce, Diana Ordonez-Rueda, Beata Ramasz, Tobias Boch, Johann-Christoph Jann, Daniel Nowak, Wolf-Karsten Hofmann, Carsten Muller-Tidow, Daniel Huebschmann, Theodore Alexandrov, Vladimir Benes, Andreas Trumpp, Malte Paulsen, Lars Velten, Simon Haas

Single-cell genomics has transformed our understanding of complex cellular systems. However, excessive costs and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems, and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables the interpretation of functional capacities of such precisely mapped cell states at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.

91: Altered Smell and Taste: anosmia, parosmia and the long impact of Covid-19
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Posted 30 Nov 2020

Altered Smell and Taste: anosmia, parosmia and the long impact of Covid-19
3,158 downloads medRxiv infectious diseases

Duika L Burges Watson, Miglena Campbell, Claire Hopkins, Barry Smith, Chris Kelly, Vincent Deary

Abstract Background: Qualitative olfactory (smell) dysfunctions are a common side effect of post-viral illness and known to impact on quality of life and health status. Evidence is emerging that taste and smell loss are common symptoms of Covid-19 that may emerge and persist long after initial infection. The aim of the present study was to document the impact of post Covid-19 alterations to taste and smell. Methods: We conducted passive and active thematic analysis of user-generated text from 9000 users of the AbScent Covid-19 Smell and Taste Loss moderated Facebook support group from March 24 to 30th September 2020. Results: Participants reported difficulty understanding, explaining and managing altered taste and smell; a lack of interpersonal and professional explanation or support; altered eating; appetite loss, weight change; loss of pleasure in food, eating and social engagement; altered intimacy and an altered relationship to self and others. Conclusions: Our findings suggest altered taste and smell with Covid-19 lead to a severe disruption to daily living that impacts on psychological well-being and health. Moreover, this impact is broad, spanning flavour perception; desire and ability to eat and prepare food; weight gain, loss and nutritional sufficiency; emotional wellbeing; professional practice; intimacy; social bonding and erosion of peoples very sense of reality. Our findings should inform the training, assessment and treatment practices of health care professionals working with long Covid.

92: Integrated analysis of multimodal single-cell data
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Posted 12 Oct 2020

Integrated analysis of multimodal single-cell data
3,158 downloads bioRxiv genomics

Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Maddie J. Lee, Aaron J. Wilk, Charlotte Darby, Michael Zagar, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar B. Fleming, Bertrand Yeung, Angela J. Rogers, M. Juliana McElrath, Catherine A. Blish, Raphael Gottardo, Peter Smibert, Rahul Satija

The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on multiple data types. Here, we introduce "weighted-nearest neighbor analysis", an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of hundreds of thousands of human white blood cells alongside a panel of 228 antibodies to construct a multimodal reference atlas of the circulating immune system. We demonstrate that integrative analysis substantially improves our ability to resolve cell states and validate the presence of previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets, and to interpret immune responses to vaccination and COVID-19. Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets, including paired measurements of RNA and chromatin state, and to look beyond the transcriptome towards a unified and multimodal definition of cellular identity. Availability: Installation instructions, documentation, tutorials, and CITE-seq datasets are available at http://www.satijalab.org/seurat ### Competing Interest Statement In the past three years, RS has worked as a consultant for Bristol-Myers Squibb, Regeneron, and Kallyope, and served as an SAB member for ImmunAI, Apollo Life Sciences GmbH, Nanostring and the NYC Pandemic Response Lab. R.G. has received consulting income from Juno Therapeutics, Takeda, Infotech Soft, Celgene, Merck and has received research support from Janssen Pharmaceuticals and Juno Therapeutics, and declares ownership in CellSpace Biosciences. PS is a co-inventor of a patent related to this work. BZY is an employee at BioLegend Inc., which is the exclusive licensee of the New York Genome Center patent application related to this work.

93: Anti-Spike protein assays to determine post-vaccination antibody levels: a head-to-head comparison of five quantitative assays
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Posted 08 Mar 2021

Anti-Spike protein assays to determine post-vaccination antibody levels: a head-to-head comparison of five quantitative assays
3,090 downloads medRxiv infectious diseases

Thomas Perkmann, Nicole Perkmann-Nagele, Thomas Koller, Patrick Mucher, Astrid Radakovics, Rodrig Marculescu, Michael Wolzt, Oswald F Wagner, Christoph J Binder, Helmuth Haslacher

Background Reliable quantification of the antibody response to SARS-CoV-2 vaccination is highly relevant for identifying possible vaccine failure and estimating the time of protection. Therefore, we aimed to evaluate the performance of five different Anti-SARS-CoV-2 antibody assays regarding the quantification of anti-spike (S) antibodies induced after a single dose of BNT162b2. Methods Sera of n=69 SARS-CoV-2 naive individuals 21+/-1 days after vaccination with BNT162b2 (Pfizer/BioNTech) were tested using the following quantitative SARS-CoV-2 antibody assays: Roche S total antibody, DiaSorin trimeric spike IgG, DiaSorin S1/S2 IgG, Abbott II IgG, and Serion/Virion IgG. Test agreement was assessed by Passing-Bablok regression. Results were further compared to the percent inhibition calculated from a surrogate virus neutralization test (sVNT) by correlation and ROC (receiver-operating-characteristics) analysis. Results Individual values were distributed over several orders of magnitude for all assays evaluated. Although the assays were in good overall agreement (rho=0.80-0.94), Passing-Bablok regression revealed systematic and proportional differences, which could not be eliminated by converting the results to BAU/mL as suggested by the manufacturers. 7 (10%) individuals had a negative sVNT results (i.e. <30% inhibition). These samples were reliably identified by most assays and yielded low binding antibody levels (ROC-AUCs 0.84-0.93). Conclusions Although all assays evaluated showed good correlation, readings from different assays were not interchangeable, even when converted to BAU/mL using the WHO international standard for SARS-CoV-2 immunoglobulin. This highlights the need for further standardization of SARS-CoV-2 serology.

94: Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App
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Posted 21 Oct 2020

Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App
3,071 downloads medRxiv infectious diseases

Carole H Sudre, Benjamin Murray, Thomas Varsavsky, Mark S Graham, Rose S. Penfold, Ruth C. Bowyer, Joan Capdevila Pujol, Kerstin Klaser, Michela Antonelli, Liane S. Canas, Erika Molteni, Marc Modat, M. Jorge Cardoso, Anna May, Sajaysurya Ganesh, Richard Davies, Long Alden Nguyen, David A. Drew, Christina M. Astley, Amit D. Joshi, Jordi Merino, Neli Tsereteli, Tove Fall, Maria F Gomez, Emma L Duncan, Cristina Menni, Frances MK Williams, Paul W Franks, Andrew T. Chan, Jonathan Wolf, Sebastien Ourselin, Tim Spector, Claire J Steves

Reports of "Long-COVID", are rising but little is known about prevalence, risk factors, or whether it is possible to predict a protracted course early in the disease. We analysed data from 4182 incident cases of COVID-19 who logged their symptoms prospectively in the COVID Symptom Study app. 558 (13.3%) had symptoms lasting >=28 days, 189 (4.5%) for >=8 weeks and 95 (2.3%) for >=12 weeks. Long-COVID was characterised by symptoms of fatigue, headache, dyspnoea and anosmia and was more likely with increasing age, BMI and female sex. Experiencing more than five symptoms during the first week of illness was associated with Long-COVID, OR=3.53 [2.76;4.50]. A simple model to distinguish between short and long-COVID at 7 days, which gained a ROC-AUC of 76%, was replicated in an independent sample of 2472 antibody positive individuals. This model could be used to identify individuals for clinical trials to reduce long-term symptoms and target education and rehabilitation services.

95: Emergence of a SARS-CoV-2 E484K variant of interest in Arizona
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Posted 28 Mar 2021

Emergence of a SARS-CoV-2 E484K variant of interest in Arizona
3,038 downloads medRxiv infectious diseases

Peter T Skidmore, Emily A Kaelin, LaRinda A Holland, Rabia Maqsood, Lily I Wu, Nicholas J Mellor, Joy M Blain, Valerie Harris, Joshua LaBaer, Vel Murugan, Efrem S Lim

SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunity and escape mutations. The E484K mutation in the spike protein reduces neutralization by post-vaccination sera and monoclonal antibody therapeutics. We detected the emergence of an E484K harboring variant B.1.243.1 from a common circulating variant (B.1.243) in the United States. In contrast to other instances when the E484K mutation was acquired independently in the parental lineage, genomic surveillance indicates that the B.1.243.1 variant of interest is in the process of being established in Arizona and beginning to cross state borders to New Mexico and Texas. Genomic, epidemiologic and phylogenetic evidence indicates that the B.1.243.1 variant of interest is poised to emerge. These findings demonstrate the critical need to continue tracking SARS-CoV-2 in real-time to inform public health strategies, diagnostics, medical countermeasures and vaccines. Main

96: High Resolution CHEST CT(HRCT) Evaluation in Patients Hospitalized with COVID-19 Infection
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Posted 28 May 2020

High Resolution CHEST CT(HRCT) Evaluation in Patients Hospitalized with COVID-19 Infection
3,027 downloads medRxiv respiratory medicine

Maulin Patel, Junad Chowdhury, Matthew Zheng, Osheen Abramian, Steven Verga, Huaqing Zhao, Nicole Patlakh, David Fleece, Nicholas Montecalvo, Gary Cohen, Maruti Kumaran, Chandra Dass, Gerard Criner

Abstract Introduction: Currently the main diagnostic modality for COVID-19 (Coronavirus disease-2019) is reverse transcriptase polymerase chain reaction (RT-PCR) via nasopharyngeal swab which has high false negative rates. We evaluated the performance of high-resolution computed tomography (HRCT) imaging in the diagnosis of suspected COVID-19 infection compared to RT-PCR nasopharyngeal swab alone in patients hospitalized for suspected COVID-19 infection. Methods: This was a retrospective analysis of 324 consecutive patients admitted to Temple University Hospital. All hospitalized patients who had RT-PCR testing and HRCT were included in the study. HRCTs were classified as Category 1, 2 or 3. Patients were then divided into four groups based on HRCT category and RT-PCR swab results for analysis. Results: The average age of patients was 59.4 (+15.2) years and 123 (38.9%) were female. Predominant ethnicity was African American 148 (46.11%). 161 patients tested positive by RT-PCR, while 41 tested positive by HRCT. 167 (52.02%) had category 1 scan, 63 (19.63%) had category 2 scan and 91 (28.35%) had category 3 HRCT scans. There was substantial agreement between our radiologists for HRCT classification ({kappa} = 0.64). Sensitivity and specificity of HRCT classification system was 77.6 and 73.7 respectively. Ferritin, LDH, AST and ALT were higher in Group 1 and D-dimers levels was higher in Group 3; differences however were not statistically significant. Conclusion: Due to its high infectivity and asymptomatic transmission, until a highly sensitive and specific COVID-19 test is developed, HRCT should be incorporated into the assessment of patients who are hospitalized with suspected COVID-19.

97: The Geometry of Concept Learning
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Posted 21 Mar 2021

The Geometry of Concept Learning
3,003 downloads bioRxiv neuroscience

Ben Sorscher, Surya Ganguli, Haim Sompolinsky

Understanding the neural basis of our remarkable cognitive capacity to accurately learn novel high-dimensional naturalistic concepts from just one or a few sensory experiences constitutes a fundamental problem. We propose a simple, biologically plausible, mathematically tractable, and computationally powerful neural mechanism for few-shot learning of naturalistic concepts. We posit that the concepts we can learn given few examples are defined by tightly circumscribed manifolds in the neural firing rate space of higher order sensory areas. We further posit that a single plastic downstream neuron can learn such concepts from few examples using a simple plasticity rule. We demonstrate the computational power of our simple proposal by showing it can achieve high few-shot learning accuracy on natural visual concepts using both macaque inferotemporal cortex representations and deep neural network models of these representations, and can even learn novel visual concepts specified only through language descriptions. Moreover, we develop a mathematical theory of few-shot learning that links neurophysiology to behavior by delineating several fundamental and measurable geometric properties of high-dimensional neural representations that can accurately predict the few-shot learning performance of naturalistic concepts across all our experiments. We discuss several implications of our theory for past and future studies in neuroscience, psychology and machine learning.

98: The effectiveness of the first dose of BNT162 b 2 vaccine in reducing SARS-CoV-2 infection 13-24 days after immunization: real-world evidence
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Posted 29 Jan 2021

The effectiveness of the first dose of BNT162 b 2 vaccine in reducing SARS-CoV-2 infection 13-24 days after immunization: real-world evidence
2,986 downloads medRxiv infectious diseases

Gabriel Chodcik, Lilac Tene, Tal Patalon, Sivan Gazit, Amir Ben-Tov, Dani Cohen, Khitam Muhsen

Background BNT162b2 vaccines showed high efficacy against COVID-19 in a randomized controlled phase-III trial. A vaccine effectiveness evaluation in real life settings is urgently needed, especially given the global disease surge. Hence, we assessed the short-term effectiveness of the first dose of BNT162b2-vaccine against SARS-CoV-2 infection. Given the BNT162b2 Phase-III results, we hypothesized that the cumulative incidence of SARS-CoV-2 infection among vaccinees will decline after 12 days following immunization compared to the incidence during the preceding days. Methods We conducted a retrospective cohort study using data from 2.6 million-member state-mandated health provider in Israel. Study population consisted of all members aged 16 or above years who were vaccinated with BNT162b2-vaccine between December/19/2020 and January/15/2021. We collected information regarding medical history and positive SARS-CoV-2 polymerase chain reaction test from days after first dose to January/17/2021. Daily and cumulative infection rates in days 13-24 were compared to days 1-12 after first dose using Kaplan-Meier survival analysis and generalized linear models. Findings Data of 503,875 individuals (mean age 59.7 years SD=14.7, 47.8% males) were analyzed, of whom 351,897 had 13-24 days of follow-up. The cumulative incidence of SARS-CoV-2 infection was 0.57% (n=2484) during days 1-12 and 0.27% (n=614) in days 13-24. A 51.4% relative risk reduction (RRR) was calculated in weighted-average daily incidence of SARS-CoV-2 infection from 43.41-per-100,000(SE=12.07) in days 1-12 to 21.08-per-100,000(SE=6.16) in days 13-24 following immunization. The decrement in incidence was evident from day 18 after first dose. Similar RRRs were calculated in individuals aged 60 or above (44.5%), younger individuals (50.2%), females (50.0%) and males (52.1%). Findings were similar in sub-populations and patients with various comorbidities. Conclusions We demonstrated an effectiveness of 51% of BNT162b2 vaccine against SARS-CoV-2 infection 13-24 days after immunization with the first dose. Immunization with the second dose should be continued to attain the anticipated protection.

99: COVID-19 Antibody Seroprevalence in Santa Clara County, California
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Posted 17 Apr 2020

COVID-19 Antibody Seroprevalence in Santa Clara County, California
2,983 downloads medRxiv epidemiology

Eran Bendavid, Bianca Mulaney, Neeraj Sood, Soleil Shah, Emilia Ling, Rebecca Bromley-Dulfano, Cara Lai, Zoe Weissberg, Rodrigo Saavedra-Walker, James Tedrow, Dona Tversky, Andrew Bogan, Thomas Kupiec, Daniel Eichner, Ribhav Gupta, John Ioannidis, Jay Bhattacharya

Background Addressing COVID-19 is a pressing health and social concern. To date, many epidemic projections and policies addressing COVID-19 have been designed without seroprevalence data to inform epidemic parameters. We measured the seroprevalence of antibodies to SARS-CoV-2 in a community sample drawn from Santa Clara County. Methods On April 3-4, 2020, we tested county residents for antibodies to SARS-CoV-2 using a lateral flow immunoassay. Participants were recruited using Facebook ads targeting a sample of individuals living within the county by demographic and geographic characteristics. We estimate weights to adjust our sample to match the zip code, sex, and race/ethnicity distribution within the county. We report both the weighted and unweighted prevalence of antibodies to SARS-CoV-2. We also adjust for test performance characteristics by combining data from 16 independent samples obtained from manufacturer's data, regulatory submissions, and independent evaluations: 13 samples for specificity (3,324 specimens) and 3 samples for sensitivity (157 specimens). Results The raw prevalence of antibodies to SARS-CoV-2 in our sample was 1.5% (exact binomial 95CI 1.1-2.0%). Test performance specificity in our data was 99.5% (95CI 99.2-99.7%) and sensitivity was 82.8% (95CI 76.0-88.4%). The unweighted prevalence adjusted for test performance characteristics was 1.2% (95CI 0.7-1.8%). After weighting for population demographics of Santa Clara County, the prevalence was 2.8% (95CI 1.3-4.7%), using bootstrap to estimate confidence bounds. These prevalence point estimates imply that 54,000 (95CI 25,000 to 91,000 using weighted prevalence; 23,000 with 95CI 14,000-35,000 using unweighted prevalence) people were infected in Santa Clara County by early April, many more than the approximately 1,000 confirmed cases at the time of the survey. Conclusions The estimated population prevalence of SARS-CoV-2 antibodies in Santa Clara County implies that the infection may be much more widespread than indicated by the number of confirmed cases. More studies are needed to improve precision of prevalence estimates. Locally-derived population prevalence estimates should be used to calibrate epidemic and mortality projections.

100: Assessment of Fabric Masks as Alternatives to Standard Surgical Masks in Terms of Particle Filtration Efficiency
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Posted 22 Apr 2020

Assessment of Fabric Masks as Alternatives to Standard Surgical Masks in Terms of Particle Filtration Efficiency
2,928 downloads medRxiv occupational and environmental health

Amy V Mueller, Matthew J. Eden, Jessica J. Oakes, Chiara Bellini, Loretta A Fernandez

In response to the COVID-19 pandemic, cloth masks are being used to control the spread of virus, but the efficacy of these loose-fitting masks is not well known. Here, tools and methods typically used to assess tight-fitting respirators were modified to quantify the efficacy of community- and commercially-produced fabric masks as PPE. Two particle counters concurrently sample ambient air and air inside the masks; mask performance is evaluated by mean particle removal efficiency and statistical variability when worn as designed and with a nylon overlayer, to independently assess fit and material. Worn as designed both commercial surgical masks and cloth masks had widely varying effectiveness (53-75% and 28-90% filtration efficiency, respectively). Most surgical-style masks improved with the nylon overlayer, indicating poor fit. This rapid testing method uses widely available hardware, requires only a few calculations from collected data, and provides both a holistic and aspect-wise evaluation of mask performance.

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