Corpus overview


MeSH Disease

Human Phenotype


    displaying 1 - 10 records in total 55
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    Transmission TRANS of SARS-CoV-2 following exposure in school settings: experience from two Helsinki area exposure incidents.

    Authors: Timothee Dub; Elina Erra; Lotta Hagberg; Emmi Sarvikivi; Camilla Virta; Asko Jarvinen; Pamela Osterlund; Niina Ikonen; Anu Haveri; Merit Melin; Timo J Lukkarinen; Hanna Nohynek

    doi:10.1101/2020.07.20.20156018 Date: 2020-07-30 Source: medRxiv

    Background: The role of children TRANS in SARS-CoV-2 transmission TRANS is unclear. We investigated two COVID-19 school exposure incidents in the Helsinki area. Methods: We conducted two retrospective cohort studies after schools exposures, with a household transmission TRANS extension. We defined a case as an exposed person with either a positive RT-PCR, or positive microneutralisation testing (MNT) as confirmation of SARS-CoV-2 nucleoprotein IgG antibodies SERO detection via fluorescent microsphere immunoassay SERO (FMIA). We recruited close school contacts and families of school cases, calculated attack rates TRANS (AR) on school level and families, and identified transmission chains TRANS. Findings: In incident A, the index was a pupil. Participation rate was 74% (89/121), and no cases were identified. In incident B, the index was a member of school personnel. Participation rate was 81% (51/63). AR was 16% (8/51): 6 pupils and 1 member of school personnel were MNT and FMIA positive; 1 pupil had a positive RT-PCR, but negative serology samples. We visited all school cases' families (n=8). The AR among close household contacts TRANS was 42% (9/20 in 3/8 families) but other plausible sources were always reported. At three months post-exposure, 6/8 school cases were re-sampled and still MNT positive. Interpretation: When the index was a child TRANS, no school transmission TRANS was identified, while the occurrence of an adult TRANS case led to a 16% AR. Further cases were evidenced in 3 families, but other transmission chains TRANS were plausible. It is likely that transmission TRANS from children TRANS to adults TRANS is limited. Funding: The Finnish Institute for Health and Welfare funded this study.

    Serial population based serosurvey of antibodies to SARS-CoV-2 SERO in a low and high transmission TRANS area of Karachi, Pakistan

    Authors: Muhammad Imran Nisar; Nadia Ansari; Mashal Amin; Farah Khalid; Aneeta Hotwani; Najeeb Rehman; Arjumand Rizvi; Arslan Memon; Zahoor Ahmed; Ashfaque Ahmed; Junaid Iqbal; Ali Faisal Saleem; Uzma Bashir Aamir; Daniel B Larremore; Bailey Fosdick; Fyezah Jehan

    doi:10.1101/2020.07.28.20163451 Date: 2020-07-29 Source: medRxiv

    Background Pakistan is among the first low- and middle-income countries affected by COVID-19 pandemic. Monitoring progress through serial sero-surveys SERO, particularly at household level, in densely populated urban communities can provide insights in areas where testing is non-uniform. Methods Two serial cross-sectional household surveys were performed in April (phase 1) and June (phase 2) 2020 each in a low- (District Malir) and high- transmission TRANS (District East) area of Karachi, Pakistan. Household were selected using simple random sampling (Malir) and systematic random sampling (East). Individual participation rate from consented households was 82.3% (1000/1215 eligible) in phase 1 and 76.5% (1004/1312 eligible) in phase 2. All household members or their legal guardians answered questions related to symptoms of Covid-19 and provided blood SERO for testing with commercial Elecsys Anti-SARS-CoV-2 immunoassay SERO targeting combined IgG and IgM. Seroprevalence SERO estimates were computed for each area and time point independently. Given correlation among household seropositivity values, a Bayesian regression model accounting for household membership, age TRANS and gender TRANS was used to estimate seroprevalence SERO. These estimates by age TRANS and gender TRANS were then post-stratified to adjust for the demographic makeup of the respective district. The household conditional risk of infection TRANS risk of infection TRANS infection MESHD was estimated for each district and its confidence interval were obtained using a non-parametric bootstrap of households. Findings Post-stratified seroprevalence SERO was estimated to be 0.2% (95% CI 0-0.7) in low-and 0.4% (95% CI 0 - 1.3) in high- transmission TRANS areas in phase 1 and 8.7% (95% CI 5.1-13.1) in low- and 15.1% (95% CI 9.4 -21.7) in high- transmission TRANS areas in phase 2, with no consistent patterns between prevalence SERO rates for males TRANS and females TRANS. Conditional risk of infection TRANS risk of infection TRANS infection MESHD estimates (possible only for phase 2) were 0.31 (95% CI 0.16-0.47) in low- and 0.41(95% CI 0.28-0.52) in high- transmission TRANS areas. Of the 166 participants who tested positive, only 9(5.4%) gave a history of any symptoms. Interpretation A large increase in seroprevalence SERO to SARS-CoV-2 infection MESHD is seen, even in areas where transmission TRANS is reported to be low. Mostly the population is still seronegative. A large majority of seropositives do not report any symptoms. The probability that an individual in a household is infected, given that another household member is infected is high in both the areas. These results emphasise the need to enhance surveillance activities of COVID-19 especially in low- transmission TRANS sites and provide insights to risks of household transmission TRANS in tightly knit neighbourhoods in urban LMIC settings.

    SARS-CoV-2 antibody SERO responses determine disease MESHD severity in COVID-19 infected individuals

    Authors: Cecilie Bo Hansen; Ida Jarlhelt; Laura Pérez-Alós; Lone Hummelshøj Landsy; Mette Loftager; Anne Rosbjerg; Charlotte Helgstrand; Jais Rose Bjelke; Thomas Egebjerg; Joseph G. Jardine; Charlotte Sværke Jørgensen; Kasper Iversen; Rafael Bayarri-Olmos; Peter Garred; Mikkel-Ole Skjoedt

    doi:10.1101/2020.07.27.20162321 Date: 2020-07-29 Source: medRxiv

    Globally, the COVID-19 pandemic has had extreme consequences for the healthcare system and calls for diagnostic tools to monitor and understand the transmission TRANS, pathogenesis and epidemiology, as well as to evaluate future vaccination strategies. Here we have developed novel flexible ELISA SERO-based assays for specific detection of SARS-CoV-2 antibodies SERO against the receptor-binding domain (RBD): An antigen sandwich- ELISA SERO relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Their performance SERO was evaluated in a cohort of 350 convalescent participants with previous COVID-19 infection MESHD, ranging from asymptomatic TRANS to critical cases. We mapped the antibody SERO responses to different areas on protein N and S and showed that the IgM, A and G antibody SERO responses against RBD are significantly correlated to the disease MESHD severity. These assays-and the data generated from them-are highly relevant for diagnostics and prognostics and contribute to the understanding of long-term COVID-19 immunity.

    Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints

    Authors: Manjula Gunawardana; Jessica Breslin; John M Cortez; Sofia Rivera; Simon Webster; F Javier Ibarrondo; Otto O Yang; Richard B Pyles; Christina M Ramirez; Amy P Adler; Peter A Anton; Marc M Baum

    doi:10.1101/2020.07.25.20160812 Date: 2020-07-28 Source: medRxiv

    Background The rapid spread of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) and the associated coronavirus disease MESHD 2019 (COVID-19) have precipitated a global pandemic heavily challenging our social behavior, economy, and healthcare infrastructure. Public health practices currently represent the primary interventions for managing the spread of the pandemic. We hypothesized that frequent, longitudinal workplace disease MESHD surveillance would represent an effective approach to controlling SARS-CoV-2 transmission TRANS among employees and their household members, reducing potential economic consequences and loss of productivity of standard isolation methods, while providing new insights into viral-host dynamics. Methodology and Findings On March 23, 2020 a clinical study (OCIS-05) was initiated at a small Southern California organization. Results from the first 3 months of the ongoing study are presented here. Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. Only participants testing negative were allowed to enter the "safe zone" workplace facility. Optional blood SERO samples were collected at baseline and throughout the 3-month study. Serum SERO virus-specific antibody SERO concentrations (IgG, IgM, and IgA) were measured using a selective, sensitive, and quantitative ELISA assay SERO developed in house. A COVID-19 infection MESHD model, based on traditional SEIR compartmental models combined with Bayesian non-linear mixed models and modern machine learning, was used to predict the number of employees and household members who would have become infected in the absence of workplace surveillance. Two study participants were found to be infected by SARS-CoV-2 during the study. One subject, a household member, tested positive clinically by RT-qPCR prior to enrollment and experienced typical COVID-19 symptoms that did not require hospitalization. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody SERO concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples SERO collected at three timepoints. A single, unrelated employee became positive for SARS-CoV-2 RNA over the course of the study, but remained asymptomatic TRANS with low associated viral RNA copy numbers. The participant did not have detectable serum SERO IgM and IgG concentrations, and IgA concentrations decayed rapidly (half-life: 1.3 d). The employee was not allowed entry to the safe zone workplace until testing negative three consecutive times over 7 d. No other employees or household members contracted COVID-19 over the course of the study. Our model predicted that under the current prevalence SERO in Los Angeles County without surveillance intervention, up to 7 employees (95% CI = 3-10) would have become infected with at most 1 of them requiring hospitalizations and 0 deaths MESHD. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic TRANS participants. The surveillance plan outlined here is scalable and transferrable. The study represents a powerful example on how an innovative public health initiative can be dovetailed with scientific discovery.

    Analyzing the dominant SARS-CoV-2 transmission TRANS modes towards an ab-initio SEIR model

    Authors: Swetaprovo Chaudhuri; Saptarshi Basu; Abhishek Saha

    id:2007.13596v1 Date: 2020-07-27 Source: arXiv

    In this work, different transmission TRANS modes of the SARS-CoV-2 virus and their role in determining the evolution of the Covid-19 pandemic are analyzed. Probability of infection MESHD caused by inhaling infectious droplets (initial, ejection diameters between 0.5-750$\mu m$) and probability of infection MESHD by the corresponding desiccated nuclei that mostly encapsulate the virions post droplet evaporation, are calculated. At typical, air-conditioned yet quiescent, large indoor space, for the average viral loading, and at early times, cough MESHD cough HP droplets of initial diameter between $10 \mu m$ and $50 \mu m$ have the highest infection MESHD probability. However, by the time they are to be inhaled, the diameters are most likely $5-6$ times smaller with respect to their initial diameters. While the initially near unity infection MESHD probability due to droplets (airborne/ballistic) rapidly decays within the first $25$s, the small yet persistent infection MESHD probability of airborne desiccated nuclei decays appreciably only by $1000$s. Combined with molecular collision theory adapted to calculate frequency of contact TRANS frequency of contact SERO between the susceptible population and the droplet/nuclei cloud, infection MESHD probabilities are used to define infection MESHD rate constants, ab-initio, leading to a SEIR model. Assuming the virus sustains equally well within the dried droplet nuclei as in the droplets, the floating nuclei leads to a stronger contribution to the corresponding rate constants with respect to the droplets, in the above-mentioned conditions. Combining both pathways, the basic reproduction number TRANS $\mathcal{R}_0$ caused by cough MESHD cough HP droplets and nuclei are calculated. Viral load, minimum infectious dose, sensitivity SERO of the virus half-life to the phase of its vector, extent of dilution of the respiratory jet/puff by the entraining air are the important factors that determine specific physical modes of transmission TRANS and the pandemic evolution.

    Anti-SARS-CoV-2 IgG antibodies SERO in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission TRANS rates

    Authors: Jakob Peter Armann; Manja Unrath; Carolin Kirsten; Christian Lueck; Alexander Dalpke; Reinhard Berner

    doi:10.1101/2020.07.16.20155143 Date: 2020-07-17 Source: medRxiv

    Background: School closures are part of the SARS-CoV-2 pandemic control measures in many countries, based on the assumption that children TRANS play a similar role in transmitting SARS-CoV-2 as they do in transmitting influenza. We therefore performed a SARS-CoV-2 seropraevalence-study in students and teachers to assess their role in the SARS-CoV-2 transmission TRANS. Methods: Students grade 8-11 and their teachers in 13 secondary schools in eastern Saxony, Germany, were invited to participate in the SchoolCoviDD19 study. Blood SERO samples were collected between May 25th and June 30th, 2020. Anti-SARS-CoV-2 IgG were assed using chemiluminescence immunoassay SERO technology and all samples with a positive or equivocal test result were re-tested with two additional serological tests SERO. Findings: 1538 students and 507 teachers participated in this study. The seropraevalence for SARS-CoV-2 was 0.6%. Even in schools with reported Covid-19 cases before the Lockdown of March 13th no clusters could be identified. 23/24 participants with a household history of COVID-91 were seronegative. By using a combination of three different immunoassays SERO we could exclude 16 participants with a positive or equivocal results after initial testing. Interpretation: Students and teachers do not play a crucial role in driving the SARS-CoV-2 pandemic in a low prevalence SERO setting. Transmission TRANS in families occurs very infrequently, and the number of unreported cases is low in this age group TRANS, making school closures not appear appropriate as a strategy in this low prevalence SERO settings. Funding: This study was supported by a grant from the state of Saxony

    Improved COVID-19 Serology Test Performance SERO by Integrating Multiple Lateral Flow Assays using Machine Learning

    Authors: Cody T Mowery; Alexander Marson; Yun S Song; Chun Jimmie Ye

    doi:10.1101/2020.07.15.20154773 Date: 2020-07-16 Source: medRxiv

    Mitigating transmission TRANS of SARS-CoV-2 has been complicated by the inaccessibility and, in some cases, inadequacy of testing options to detect present or past infection MESHD. Immunochromatographic lateral flow assays (LFAs) are a cheap and scalable modality for tracking viral transmission TRANS by testing for serological SERO immunity, though systematic evaluations have revealed the low performance SERO of some SARS-CoV-2 LFAs. Here, we re-analyzed existing data to present a proof-of-principle machine learning framework that may be used to inform the pairing of LFAs to achieve superior classification performance SERO while enabling tunable False Positive Rates optimized for the estimated seroprevalence SERO of the population being tested.

    Community-level SARS-CoV-2 Seroprevalence SERO Survey in urban slum dwellers of Buenos Aires City, Argentina: a participatory research.

    Authors: Silvana Figar; Vanina Pagotto; Lorena Luna; Julieta Salto; Magdalena Wagner Manslau; Alicia Mistchenko; ANDREA GAMARNIK; Ana Maria Gomez Saldano; Fernan Quiros

    doi:10.1101/2020.07.14.20153858 Date: 2020-07-16 Source: medRxiv

    Background By July 1st, the incidence rate of RT-qPCR SARS-CoV-2 infection MESHD was 5.9% in Barrio Padre Mugica, one of the largest slums in Buenos Aires City. This study aimed to establish the seroprevalence SERO of SARS-CoV-2 three months after the first case was reported. Methods Between June 10th and July 1st, a cross-sectional design was carried out on people over 14 years old, selected from a probabilistic sample of households. A finger prick sample was tested by ELISA SERO to detect IgG-class antibodies SERO against SARS-CoV-2. Multilevel model was applied to understand sector, household and individual conditions associated with seroconvert. Results Prevalence SERO based on IgG was 53.4% (95%IC 52.8% to 54.1%). Among the IgG positive cases, 15% reported having compatible symptoms at some point in the past two months. There is evidence of within-household clustering effect (rho=0.52; 95% IC 0.36-0.67); living with a PCR- confirmed case TRANS doubled the chance of being SARS-CoV2 IgG positive (OR 2.13; 95% IC 1.17-3.85). The highest risk of infection TRANS risk of infection TRANS infection MESHD was found in one of the most deprived areas of the slum, the Bajo autopista sector. Discussion High seroprevalence SERO is shown, for each symptomatic RT-qPCR-confirmed diagnosis, 9 people were IgG positive, indicating a high rate of undetected (probable asymptomatic) infections MESHD asymptomatic TRANS. Given that transmission TRANS among family members TRANS is a leading driver of the disease MESHD`s spread, it is unsurprising that crowded housing situations in slums are directly associated with higher risk of infection TRANS risk of infection TRANS infection MESHD and consequently high seroprevalence SERO levels. This study contributes to the understanding of population immunity against SARS-CoV2, its relation to living conditions and viral spread, for future decision making.

    Clinical utility of targeted SARS-CoV-2 serology testing to aid the diagnosis and management of suspected missed, late or post-COVID-19 infection MESHD syndromes MESHD: results from a pilot service

    Authors: Nicola Sweeney; Blair Merrick; Suzanne Pickering; Rui Pedro Galao; Alina Botgros; Harry D. Wilson; Adrian W. Signell; Gilberto Betancor; Mark Kia Ik Tan; John Ramble; Neophytos Kouphou; Sam Acors; Carl Graham; Jeffrey Seow; Eithne MacMahon; Stuart J. D. Neil; Michael H. Malim; Katie Doores; Sam Douthwaite; Rahul Batra; Gaia Nebbia; Jonathan D. Edgeworth

    doi:10.1101/2020.07.10.20150540 Date: 2020-07-11 Source: medRxiv

    Objectives: Determine indications and clinical utility of SARS-CoV-2 serology testing in adults TRANS and children TRANS. Design: Prospective evaluation of initial three weeks of a daily Monday to Friday pilot SARS-CoV-2 serology service for patients. Setting: Early post 'first-wave' SARS-CoV-2 transmission TRANS period at single centre London teaching hospital that provides care to the local community, as well as regional and national referral pathways for specialist services. Participants: 110 (72 adults TRANS, 38 children TRANS, age TRANS range 0-83 years, 52.7% female TRANS (n=58)). Interventions: Patient serum SERO from vetted referrals tested on CE marked and internally validated lateral flow immunoassay SERO (LFIA) (SureScreen Diagnostics) detecting antibodies to SARS-CoV-2 SERO spike proteins, with result and clinical interpretation provided to the direct care team. Main outcome measures: Performance SERO characteristics, source and nature of referrals, feasibility and clinical utility of the service, particularly the benefit for clinical decision-making. Results: The LFIA was deemed suitable for clinical advice and decision making following evaluation with 310 serum samples SERO from SARS-CoV-2 PCR positive patients and 300 pre-pandemic samples, giving a sensitivity SERO and specificity of 96.1% and 99.3% respectively. For the pilot, 115 referrals were received leading to 113 tests performed on 108 participants (sample not available for two participants); paediatrics (n=35), medicine (n=69), surgery (n=2) and general practice (n=2). 43.4% participants (n=49) had detectable antibodies to SARS-CoV-2 SERO. There were three main indications for serology; new acute presentations potentially triggered by recent COVID-19 infection MESHD e.g. PIMS-TS (n=26) and pulmonary embolism MESHD pulmonary embolism HP (n=5), potential missed diagnoses in context of a recent compatible illness (n=40), and making infection MESHD control and immunosuppression treatment decisions in persistently SARS-CoV-2 RNA PCR positive individuals (n=6). Conclusions: This study shows acceptable performance SERO characteristics, feasibility and clinical utility of a SARS-CoV-2 serology service using a rapid, inexpensive and portable assay for adults TRANS and children TRANS presenting with a range of clinical indications. Results correlated closely with a confirmatory in-house ELISA SERO. The study showed the benefit of introducing a serology service where there is a reasonable pre-test probability, and the result can be linked with clinical advice or intervention. Experience thus far is that the volume of requests from hospital referral routes are manageable within existing clinical and laboratory services; however, the demand from community referrals has not yet been assessed. Given recent evidence for a rapid decline in antibodies SERO, particularly following mild infection MESHD, there is likely a limited window of opportunity to realise the benefit of serology testing for individuals infected during the 'first-wave' before they potentially fall HP below a measurable threshold. Rapidly expanding availability of serology services for NHS patients will also help understand the long-term implications of serostatus and prior infection MESHD in different patient groups, particularly before emergence of any 'second-wave' outbreak or introduction of a vaccination programme.

    SARS-CoV-2 Seroprevalence SERO Rates of Children TRANS in Louisiana During the State Stay at Home Order.

    Authors: Monika L Dietrich; Elizabeth B Norton; Debra Elliott; Ashley R Smira; Julie A Rouelle; Nell G Bond; Karen Aime-Marcelin; Alisha Prystowsky; Rebecca Kemnitz; Arunava Sarma; Sarah Talia Himmelfarb; Neha Sharma; Addison E Stone; Randall Craver; Alyssa R Lindrose; Leslie A Smitley; Robert B Uddo; Leann Myers; Stacy S Drury; John S Schieffelin; James E Robinson; Kevin J Zwezdaryk

    doi:10.1101/2020.07.07.20147884 Date: 2020-07-08 Source: medRxiv

    Children TRANS (less than 19 years) account for 20% of the US population but currently represent less than 2% of coronavirus disease MESHD 2019 (COVID-19) cases. Because infected children TRANS often have few or no symptoms and may not be tested, the extent of infection MESHD in children TRANS is poorly understood. METHODS During the March 18th-May 15th 2020 Louisiana Stay At Home Order, 1690 blood SERO samples from 812 individuals from a Childrens Hospital were tested for antibodies SERO to severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) spike protein. Demographics, COVID-19 testing, and clinical presentation abstracted from medical records were compared with local COVID-19 cases. RESULTS In total, 62 subjects (7.6%) were found to be seropositive. The median age TRANS was 11 years with 50.4% female TRANS. The presenting complaint of seropositive patients was chronic illness (43.5%). Only 18.2% had a previous positive COVID-19 PCR or antibody test SERO. Seropositivity was significantly associated with parish (counties), race, and residence in a low-income area. Importantly, seropositivity was linearly correlated with cumulative COVID-19 case number for all ages TRANS by parish. CONCLUSION In a large retrospective study, the seropositivity prevalence SERO for SARS-CoV-2 in children TRANS in Louisiana during the mandated Stay At Home Order was 7.6%. Residence location, race, and lower socioeconomic factors were linked to more frequent seropositivity in children TRANS and correlated to regional COVID-19 case rates. Thus, a significant number of children TRANS in Louisiana had SARS-CoV-2 infections MESHD that went undetected and unreported and may have contributed to virus transmission TRANS.

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MeSH Disease
Human Phenotype

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