Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    COVID-19 herd immunity in the Brazilian Amazon

    Authors: Lewis F Buss; Carlos Augusto Prete Jr.; Claudia MM Abrahim; Alfredo Mendrone Jr.; Tassila Salomon; Cesar de Almeida-Neto; Rafael FO França; Maria C Belotti; Maria PSS Carvalho; Allyson G Costa; Myuki AE Crispim; Suzete C Ferreira; Nelson A Fraiji; Susie Gurzenda; Charles Whittaker; Leonardo T Kamaura; Pedro L Takecian; Márcio K Moikawa; Anna S Nishiya; Vanderson Rocha; Nanci A Salles; Andreza A de Souza Santos; Martirene A da Silva; Brian Custer; Manoel Barral-Netto; Moritz Kraemer; Rafael HM Pererira; Oliver G Pybus; Michael P Busch; Márcia C Castro; Christopher Dye; Vitor H Nascimento; Nuno R Faria; Ester C Sabino

    doi:10.1101/2020.09.16.20194787 Date: 2020-09-21 Source: medRxiv

    The herd immunity threshold is the proportion of a population that must be immune to an infectious disease MESHD, either by natural infection MESHD or vaccination such that, in the absence of additional preventative measures, new cases decline and the effective reproduction number TRANS falls HP below unity. This fundamental epidemiological parameter is still unknown for the recently-emerged COVID-19, and mathematical models have predicted very divergent results. Population studies using antibody testing SERO to infer total cumulative infections can provide empirical evidence of the level of population immunity in severely affected areas. Here we show that the transmission TRANS of SARS-CoV-2 in Manaus, located in the Brazilian Amazon, increased quickly during March and April and declined more slowly from May to September. In June, one month following the epidemic peak, 44% of the population was seropositive for SARS-CoV-2, equating to a cumulative incidence of 52%, after correcting for the false-negative rate of the antibody test SERO. The seroprevalence SERO fell HP in July and August due to antibody SERO waning. After correcting for this, we estimate a final epidemic size of 66%. Although non-pharmaceutical interventions, plus a change in population behavior, may have helped to limit SARS-CoV-2 transmission TRANS in Manaus, the unusually high infection rate suggests that herd immunity played a significant role in determining the size of the epidemic.

    In the long shadow of our best intentions: model-based assessment of the consequences of school reopening during the COVID-19 pandemic

    Authors: Kaitlyn E Johnson; Madison Stoddard; Ryan P Nolan; Douglas E White; Natasha S Hochberg; Arijit Chakravarty; Rahul Kumar Anand; Bikash Ranjan Ray; Rajeshwari Subramaniam; Souvik Maitra; Manuel Antonio Franco; Timothy D Flietstra; Amy J Schuh; Panayampalli S Satheshkumar; Jasmine M Chaitram; S Michele Owen; M G Finn; Jason M Goldstein; Joel M Montgomery; Christina F Spiropoulou

    doi:10.1101/2020.09.18.20197400 Date: 2020-09-18 Source: medRxiv

    As the United States grapples with the ongoing COVID-19 pandemic, a particularly thorny set of questions surrounds the reopening of K-12 schools and universities. The benefits of in-person learning are numerous, in terms of education quality, mental health, emotional well-being, equity and access to food and shelter. Early reports suggested that children TRANS might have reduced susceptibility to COVID-19, and children TRANS have been shown to experience fewer complications than older adults TRANS. Over the past few months, our understanding of COVID-19 has been further shaped by emerging data, and it is now understood that children TRANS are as susceptible to infection as adults TRANS and have a similar viral load during infection MESHD. While the higher prevalence SERO of asymptomatic TRANS disease among children TRANS makes symptom-based isolation strategies ineffective, asymptomatic TRANS patients do not in fact carry a reduced viral load. Based on this updated understanding of the disease, we have used epidemiological modeling to explore the feasibility and consequences of school reopening in the face of differing rates of COVID-19 prevalence SERO and transmission TRANS. Our findings indicate that, regardless of the initial prevalence SERO of the disease, and in the absence of systematic surveillance testing, most schools in the United States can expect to remain open for 20-60 days. At this point, one or more large disease clusters can be expected to be detected, forcing schools to close again. These disease clusters, in turn, can be expected to propagate through the community, with potentially hundreds to thousands of additional cases resulting from each individual school cluster. Thus, our findings suggest that the debate between the risks to student safety and benefits of in-person learning frames a false dual choice. Given the current circumstances in the United States, the most likely outcome in the late fall HP is that students will be deprived of the benefits of in-person learning while having incurred a significant risk to themselves and their communities.

    Apparent reductions in COVID-19 Case Fatality Rates reflect changes in average age TRANS of those testing positive.

    Authors: Alastair Grant; Lucia Castaldo; Aparna Pande; Anirban Bhattacharjee; Amrita Bhattacharyya; Dalim Kumar Baidya; Rahul Kumar Anand; Bikash Ranjan Ray; Rajeshwari Subramaniam; Souvik Maitra; Manuel Antonio Franco; Timothy D Flietstra; Amy J Schuh; Panayampalli S Satheshkumar; Jasmine M Chaitram; S Michele Owen; M G Finn; Jason M Goldstein; Joel M Montgomery; Christina F Spiropoulou

    doi:10.1101/2020.09.18.20197160 Date: 2020-09-18 Source: medRxiv

    Numbers of COVID-19 infections MESHD are rising in many countries, while death MESHD and hospitalisation rates remain low. Infection Fatality Rates (IFR) for individual year classes calculated from seroprevalence SERO data and the ages TRANS of those dying in England show a very strong log-linear relationship with age TRANS, and allow us to predict fatality rates for those testing positive on each day based on their ages TRANS. Since the peak of the epidemic, reductions in the ages TRANS of cases account for an eight fold fall HP in fatality rates. Over the same period, increased testing intensity appears to have increased infections detected amongst the most vulnerable by a factor of at least five, and between 15 and 24 fold in the population as a whole. Together these two factors are sufficient to explain the large observed change in the ratio of deaths MESHD to reported cases. We can also use these methods to give a more precise early warning system of future increases in mortality rates than raw case numbers. Although case numbers are currently increasing markedly, a continuing reduction in numbers of older individuals being infected means that the predicted increase in mortality rates is much slower.

    Seroprevalence SERO and immunity of SARS-CoV-2 infection MESHD in children TRANS and adolescents in schools in Switzerland: design for a longitudinal, school-based prospective cohort study

    Authors: Agne Ulyte; Thomas Radtke; Irene Abela; Sarah H Haile; Julia Braun; Ruedi Jung; Christoph Berger; Alexandra Trkola; Jan Fehr; Milo A Puhan; Susi Kriemler; Anel Nurtay; Lucie Abeler-Dörner; David G Bonsall; Michael V McConnell; Shawn O'Banion; Christophe Fraser; Scott Roberts; Jose A. Gonzalez; Marciano Sablad; Rodrigo Yelin; Wendy Taylor; Kiyoshi Tachikawa; Suezanne Parker; Priya Karmali; Jared Davis; Sean M Sullivan; Steve G. Hughes; Pad Chivukula; Eng Eong Ooi

    doi:10.1101/2020.08.30.20184671 Date: 2020-09-02 Source: medRxiv

    Introduction Seroprevalence SERO and transmission TRANS routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD in children TRANS and adolescents, especially in school setting, are not clear. Resulting uncertainty is reflected in very different decisions on school closures and reopenings across countries. The aim of this longitudinal cohort study is to assess the extent and patterns of seroprevalence SERO of SARS-CoV-2 antibodies SERO in school-attending children TRANS repeatedly. It will examine risk factors for infection MESHD, relationship between seropositivity and symptoms, and temporal persistence of antibodies SERO. Additionally, it will include testing of school personnel and parents TRANS. Methods and analysis The study (Ciao Corona) will enroll a regionally representative, random sample of schools in the canton of Zurich, where 18% of the Swiss population live. Children TRANS aged TRANS 5 to 16 years, attending classes in primary and secondary schools are invited. Venous blood MESHD blood SERO and saliva samples are collected for SARS-CoV-2 serological testing SERO after the first wave of infections (June/July 2020), in fall HP (October/November 2020), and after winter (March/April 2021). Venous blood MESHD blood SERO is also collected for serological testing SERO of parents TRANS and school personnel. Bi-monthly questionnaires to children TRANS, parents TRANS and school personnel cover SARS-CoV-2 symptoms MESHD and tests, health, preventive behavior, lifestyle and quality of life information. Total seroprevalence SERO and cumulative incidence will be calculated. Hierarchical Bayesian logistic regression models will account for sensitivity SERO and specificity of the serological test SERO in the analyses and for the complex sampling structure, i.e., clustering within classes and schools. Ethics and dissemination The study was approved by the Ethics Committee of the Canton of Zurich, Switzerland (2020-01336). The results of this study will be published in peer-reviewed journals and will be made available to study participants and participating schools, the Federal Office of Public Health, and the Educational Department of the canton of Zurich. Trial registration number NCT04448717.

    Testing for coronavirus (SARS-CoV-2) infection MESHD in populations with low infection MESHD prevalence SERO: the largely ignored problem of false positives and the value of repeat testing

    Authors: Cathie Sudlow; Peter Diggle; Oliver Warlow; David Seymour; Ben Gordon; Rhos Walker; Charles Warlow

    doi:10.1101/2020.08.19.20178137 Date: 2020-08-22 Source: medRxiv

    Background: Calls are increasing for widespread SARS-CoV-2 infection MESHD testing of people from populations with a very low prevalence SERO of infection MESHD. We quantified the impact of less than perfect diagnostic test accuracy on populations, and on individuals, in low prevalence SERO settings, focusing on false positives and the role of confirmatory testing. Methods: We developed a simple, interactive tool to assess the impact of different combinations of test sensitivity SERO, specificity and infection MESHD prevalence SERO in a notional population of 100,000. We derived numbers of true positives, true negatives, false positives and false negatives, positive predictive value SERO (PPV, the percentage of test positives that are true positives) and overall test accuracy for three testing strategies: (1) single test for all; (2) add repeat testing in test positives; (3) add further repeat testing in those with discrepant results. We also assessed the impact on test results for individuals having one, two or three tests under these three strategies. Results: With sensitivity SERO of 80%, infection prevalence SERO of 1 in 2,000, and specificity 99.9% on all tests, PPV in the tested population of 100,000 will be only 29% with one test, increasing to >99.5% (100% when rounded to the nearest %) with repeat testing in strategies 2 or 3. More realistically, if specificity is 95% for the first and 99.9% for subsequent tests, single test PPV will be only 1%, increasing to 86% with repeat testing in strategy 2, or 79% with strategy 3 (albeit with 6 fewer false negatives than strategy 2). In the whole population, or in particular individuals, PPV increases as infection MESHD becomes more common in the population but falls HP to unacceptably low levels with lower test specificity. Conclusion: To avoid multiple unnecessary restrictions on whole populations, and in particular individuals, from widespread population testing for SARS-CoV-2, the crucial roles of extremely high test specificity and of confirmatory testing must be fully appreciated and incorporated into policy decisions.

    Fighting COVID-19 spread among nursing home residents even in absence of molecular diagnosis: a retrospective cohort study.

    Authors: Alessio Strazzulla; Paul Tarteret; Maria Concetta Postorino; Marie Picque; Astrid de Pontfarcy; Nicolas Vignier; Catherine Chakvetadze; Coralie Noel; Cecile Drouin; Zine Eddine Benguerdi; Sylvain Diamantis

    doi:10.21203/rs.3.rs-51305/v1 Date: 2020-07-30 Source: ResearchSquare

    Background Access to molecular diagnosis was limited out-of-hospital in France during the 2020 coronavirus disease 2019 (COVID-19) epidemic. This study describes the evolution of COVID-19 outbreak in a nursing home in absence of molecular diagnosis. Methods A monocentric prospective study was conducted in a French nursing home from March 17th, 2020 to June 11th, 2020. Because of lack of molecular tests for severe acute respiratory syndrome 2 (SARS-Cov2) infection MESHD, probable COVID-19 cases were early identified considering only respiratory and not-respiratory symptoms and therefore preventing measures and treatments were enforced. Once available, serology tests were performed at the end of the study.A chronologic description of new cases and deaths MESHD was made together with a description of COVID-19 symptoms. Data about personal characteristics and treatments were collected and the following comparisons were performed: i) probable COVID-19 cases vs asymptomatic TRANS residents; ii) SARS-Cov2 seropositive residents vs seronegative residents. Results Overall, 32/66 (48.5%) residents and 19/39 (48.7%) members of health-care personnel were classified as probable COVID-19 cases. A total of 34/61 (55.7%) tested residents resulted seropositive. Death occurred in 4/66 (6%) residents. Diagnosis according to symptoms had 65% of sensitivity SERO, 78% of specificity, 79% of positive predictive value SERO and 64% of negative predictive value SERO.In resident population, the following symptoms were registered: 15/32 (46.8%) lymphopenia HP lymphopenia MESHD, 15/32 (46.8%) fever HP fever MESHD, 8/32 (25%) fatigue HP fatigue MESHD, 8/32 (25%) cough HP, 6/32 (18.8%) diarrhoea MESHD, 4/32 (12.5%) severe respiratory distress HP requiring oxygen therapy, 4/32 (12.5%) fall HP, 3/32 (9.4%) conjunctivitis HP conjunctivitis MESHD, 2/32 (6.3%) abnormal pulmonary noise at chest examination and 2/32 (6,25%) abdominal pain HP abdominal pain MESHD. Probable COVID-19 cases were older (81.3 vs 74.9; p=0.007) and they had higher prevalence SERO of atrial fibrillation HP atrial fibrillation MESHD (8/32, 25% vs 2/34, 12%; p=0.030); insulin treatment (4/34, 12% vs 0, 0%; p=0.033) and positive SARS-Cov2 serology (22/32, 69% vs 12/34, 35%; p=0.001) than asymptomatic TRANS residents. Seropositive residents had lower prevalence SERO of diabetes MESHD (4/34, 12% vs 9/27, 33%; p=0.041) and angiotensin-converting-enzyme inhibitors’ intake (1/34, 1% vs 5/27, 19%; p=0.042). Conclusions During SARS-Cov2 epidemic, early detection of respiratory and not-respiratory symptoms allowed to enforce extraordinary measures. They achieved limiting contagion and deaths among nursing home residents, even in absence of molecular diagnosis.

    Children TRANS with COVID-19 like symptoms in Italian Pediatric Surgeries: the dark side of the coin

    Authors: Gianfranco Trapani; Vassilios Fanos; Enrico Bertino; Giulia Maiocco; Osama Al Jamal; Michele Fiore; VIncenzo Bembo; Domenico Careddu; Lando Barberio; Luisella Zanino; Giuseppe Verlato

    doi:10.1101/2020.07.27.20149757 Date: 2020-07-29 Source: medRxiv

    BACKGROUND: Symptoms of SARS-CoV-2 infection MESHD in children TRANS are nonspecific and shared with other common acute viral illnesses ( fever HP fever MESHD, respiratory or gastrointestinal symptoms MESHD, and cutaneous signs), thus making clinical differential diagnosis tricky. In Italy, first line management of pediatric care is handed over to Primary Care Pediatricians (PCPs), who were not allowed to directly perform diagnostic tests during the recent COVID-19 outbreak. Without a confirmatory diagnosis, PCPs could only collect information on ''COVID-19 like symptoms'' rather than identify typical COVID-19 symptoms. AIM: To evaluate the prevalence SERO of COVID-19 like symptoms in outpatient children TRANS, during Italian lockdown. To provide PCPs a risk score to be used in clinical practice during the differential diagnosis process. METHODS: A survey was submitted to 50 PCPs (assisting 47,500 children TRANS) from 7 different Italian regions between the 4th of March and the 23rd of May 2020 (total and partial lockdown period). COVID-19 like symptoms in the assisted children TRANS were recorded, as well as presence of confirmed/suspected cases in children TRANS's families, which was taken as proxy of COVID-19. Multivariable logistic regression was accomplished to estimate the risk of having suspected/ confirmed cases TRANS in families, considering symptoms as potential determinants. RESULTS: 2,300 children TRANS (4.8% of overall survey population) fell HP ill with COVID-19 like symptoms, 3.1% and 1.7% during total and partial lockdown period respectively. The concurrent presence of fatigue HP fatigue MESHD, cough HP, and diarrhea HP diarrhea MESHD in children TRANS, in absence of sore throat/ earache MESHD and abnormal skin signs, represents the maximum risk level of having a suspected/ confirmed case TRANS of COVID-19 at home. CONCLUSIONS: The percentage of children TRANS presenting COVID-19 like symptoms at home has been remarkable also during the total lockdown period. The present study identified a pattern of symptoms which could help, in a cost-effective perspective, PCPs in daily clinical practice to define priorities in addressing children TRANS to the proper diagnostic procedure.

    Sleepless in Lockdown: unpacking differences in sleep loss MESHD during the coronavirus pandemicin the UK

    Authors: Jane Falkingham; Maria Evandrou; Min Qin; Athina Vlachantoni

    doi:10.1101/2020.07.19.20157255 Date: 2020-07-21 Source: medRxiv

    Background: Covid-19 has been shown to be having a disproportionate impact on the health of individuals from different ethnic groups and those employed in certain occupations, whilst the indirect impacts of Covid-19, including the closure of schools and business and the move to home working, fall HP disproportionately on the young and on women. These factors may in turn impact upon sleep health. Research on sleep deprivation during the pandemic crisis to date has been limited. The present study aimed to explore the levels and social determinants of self-reported sleep loss among the general population during the Covid-19 pandemic in the UK, with a particular focus on ethnic and gender TRANS disparities. Methods: Newly available national representative survey data from Understanding Society COVID19 Study collected during April 2020 were analysed. These data were linked to Wave 9 of Understanding Society conducted in 2018/19, providing information about the respondents prior to the outbreak of the pandemic. Cross-sectional analysis provided prevalence SERO estimates, whilst analysis of the linked longitudinal data provided incidence estimates. The analytical sample included 15,360 respondents aged TRANS 16 and above; among these, 12,206 reported no problem of sleep loss MESHD before the epidemic. Results: Prevalence SERO and incidence rates of perceived sleep loss were 24.7% and 20.2% respectively. Women (at the level of 31.8% and 27.0%) and individuals from Black, Asian, and minority ethnic (BAME) communities (at the level of 32.0% and 24.6%) were more vulnerable to sleep deprivation MESHD due to the pandemic. Multivariate regression analysis shows that being female TRANS, the presence of young children TRANS in the household, perceived financial difficulties and being a Covid-19-related key worker were all predictive of sleep loss MESHD. Once these covariates were controlled for the bivariate relationship between ethnicity and sleep loss MESHD was reversed, reflecting the complex interaction between the coronavirus epidemic and ethnicity. Conclusions: The pandemic has widened the disparity of sleep deprivation MESHD across different groups, with women with young children TRANS, key workers and people of BAME heritage all experiencing difficulty in sleeping, which in turn may negatively affect mental and physical health and well-being.

    Modeling and Preparedness: The Transmission TRANS Dynamics of COVID-19 Outbreak in Provinces of Ecuador

    Authors: Carlos Enrique Bustamante Orellana; Jordy Jose Cevallos Chavez; Cesar Montalvo; Jeff Sullivan; Edwin Michael; Anuj Mubayi

    doi:10.1101/2020.07.09.20150078 Date: 2020-07-11 Source: medRxiv

    Coronavirus disease MESHD 2019 (COVID-19), a novel infectious disease MESHD first identified in December 2019 in the city of Wuhan of China, is caused by severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). The disease has become a pandemic in just a few months and spread globally with more than 2.89 million cases and 203,000 deaths across 185 countries, as of April 26th, 2020. Ecuador has reported one of the highest rates of COVID-19 in Latin America, with more than 10K cases and 500 deaths MESHD in a country of approximately 17 million people. The dynamics of the outbreak is being observed quite different in different provinces of Ecuador with high reported prevalence SERO in some low population density provinces. In this study, we aim to understand variations in outbreaks between provinces and provide assistance in essential preparedness planning in order to respond effectively to ongoing COVID-19 outbreak. The study estimated the critical level of quarantine rate along with corresponding leakage in order to avoid overwhelming the local health care system. The results suggest that provinces with high population density can avoid a large disease burden provided they initiate early and stricter quarantine measures even under low isolation rate. To best of our knowledge, this study is first from the region to determine which provinces will need much preparation for current outbreak in fall HP and which might need more help.

    Reopening universities during the COVID-19 pandemic: A testing strategy to minimize active cases and delay outbreaks

    Authors: Lior Rennert; Corey Andrew Kalbaugh; Lu Shi; Christopher McMahan

    doi:10.1101/2020.07.06.20147272 Date: 2020-07-07 Source: medRxiv

    Background: University campuses present an ideal environment for viral spread and are therefore at extreme risk of serving as a hotbed for a COVID-19 outbreak. While active surveillance throughout the semester such as widespread testing, contact tracing TRANS, and case isolation, may assist in detecting and preventing early outbreaks, these strategies will not be sufficient should a larger outbreak occur. It is therefore necessary to limit the initial number of active cases at the start of the semester. We examine the impact of pre-semester NAT testing on disease spread TRANS in a university setting. Methods: We implement simple dynamic transmission TRANS models of SARS-CoV-2 infection MESHD to explore the effects of pre-semester testing strategies on the number of active infections MESHD and occupied isolation beds throughout the semester. We assume an infectious period TRANS of 3 days and vary R0 TRANS to represent the effectiveness of disease mitigation strategies throughout the semester. We assume the prevalence SERO of active cases at the beginning of the semester is 5%. The sensitivity SERO of the NAT test is set at 90%. Results: If no pre-semester screening is mandated, the peak number of active infections occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections when effective mitigation strategies ( R0 TRANS = 1.25) are implemented to over 15,000 active infections for less effective strategies ( R0 TRANS = 3). When one NAT test is mandated within one week of campus arrival, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak to 40 days and 17 days, respectively, and result in peak size ranging from 1,000 to over 15,000 active infections. When two NAT tests are mandated, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak through the end of fall HP semester and 20 days, respectively, and result in peak size ranging from less than 1,000 to over 15,000 active infections. If maximum occupancy of isolation beds is set to 2% of the student population, then isolation beds would only be available for a range of 1 in 2 confirmed cases TRANS ( R0 TRANS = 1.25) to 1 in 40 confirmed cases TRANS ( R0 TRANS = 3) before maximum occupancy is reached. Conclusion: Even with highly effective mitigation strategies throughout the semester, inadequate pre-semester testing will lead to early and large surges of the disease and result in universities quickly reaching their isolation bed capacity. We therefore recommend NAT testing within one week of campus return. While this strategy is sufficient for delaying the timing of the outbreak, pre-semester testing would need to be implemented in conjunction with effective mitigation strategies to reduce the outbreak size.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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