Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Potential Community and Campus Covid-19 Outcomes Under University and College Reopening Scenarios

    Authors: James C Benneyan; Christopher Gehrke; Iulian Ilies; Nicole Nehls; Gro Jamtvedt; Borghild Loyland; Ida Hellum Sandbekken; Alexander Schjoll; Kjetil Telle; Sara Sofie Viksmoen Watle; Laura Vanessa Montes Fontalvo; Roger Hernandez; Carolin Chavez; Francisco Eduardo Campos; Fadia Uribe; Olguita del Aguila; JORGE ALBERTO RIOS AIDA; Andrea Parra Buitrago; Lina Maria Betancur Londono; Leon Felipe Mendoza Vega; Carolina Almeida Hernandez; Michela Sali; JULIAN HIGUITA PALACIO; Jessica Gomez-Vargas; Adriana Yock Corrales; Danilo Buonsenso

    doi:10.1101/2020.08.29.20184366 Date: 2020-09-02 Source: medRxiv

    Background: Significant uncertainty exists about the safety of, and best strategies for, reopening colleges and universities while the Covid-19 pandemic is not well-controlled. Little also is known about the effects that on-campus outbreaks may have on local non-student and/or higher-risk communities. Model-based analysis can help inform decision and policy making across a wide range of assumptions and uncertainties. Objective: To evaluate the potential range of campus and community Covid-19 exposures, infections, and mortality due to various university and college reopening plans and precautions. Methods: We developed and calibrated campus-only, community-only, and campus-x-community epidemic models using standard susceptible-exposed-infected-recovered differential equation and agent-based modeling methods. Input parameters for campus and surrounding communities were estimated via published and grey literature, scenario development, expert opinion, Monte Carlo simulation, and accuracy optimization algorithms; models were cross-validated against each other using February-June 2020 county, state, and country data. Campus opening plans (spanning various fully open, hybrid, and fully virtual approaches) were identified from websites, publications, communications, and surveys. All scenarios were simulated assuming 16-week semesters and best/worst case ranges for disease prevalence SERO among community residents and arriving students, precaution compliance, contact frequency TRANS contact frequency SERO, virus attack rates TRANS, and tracing TRANS and isolation effectiveness. Day-to-day student and community differences in exposures, infections, and mortality were estimated under each scenario as compared to regular and no re-opening; 10% trimmed medians, standard deviations, and probability intervals were computed to omit extreme outlier scenarios. Factorial analyses were conducted to identify inputs with largest and smallest impacts on outcomes. Results: As a base case, predicted 16-week student infections and mortality under normal operations with no precautions (or no compliance) ranged from 472 to 9,484 (4.7% to 94.8%) and 2 to 61 (0.02% to 0.61%) per 10,000 student population, respectively. In terms of contact tracing TRANS and isolation resources, as many as 17 to 1,488 total exposures per 10,000 students could occur on a given day throughout the semester needing to be located, tested, and if warranted quarantined. Attributable total additional predicted community exposures, infections, and mortality ranged from 1 to 187, 13 to 820, and 1 to 21, respectively, assuming the university takes no additional precautions to limit exposure risk. The mean (SD) number of days until 1% and 5% of on-campus students are infected was 11 (3) and 76 (17) days, respectively; 34.8% of replications resulted in more than 10% students infected by semester end. The diffusion first inflection point occurred on average on day 84 (+/- 20 days, 95% interval). Common re-opening precaution strategies reduced the above consequences by 24% to 26% fewer infections (now 360 to 6,976 per 10,000 students) and 36% to 50% fewer deaths (now 1 to 39 per 10,000 students). Perfect testing and immediate quarantining of all students on arrival to campus at semester start further reduced infections by 58% to 95% (now 200 to 468 per 10,000 students) and deaths MESHD by 95% to 100% (now 0 to 3 per 10,000 students). Uncertainties in many factors, however, produced tremendous variability in all median estimates, ranging by -67% to +370%. Conclusions: Consequences of reopening college and university physical campuses on student and community Covid-19 exposures, infections, and mortality are very highly unpredictable, depending on a combination of random chance, controllable (e.g. physical layouts), and uncontrollable (e.g. human behavior) factors. Important implications at government and academic institution levels include clear needs for specific criteria to adapt campus operations mid-semester, methods to detect when this is necessary, and well-executed contingency plans for doing so.

    Dynamic causal modeling of the COVID-19 pandemic in northern Italy predicts possible scenarios for the second wave

    Authors: Daniela Gandolfi; Giuseppe Pagnoni; Tommaso Filippini; Alessia Goffi; Marco Vinceti; Egidio Ugo D'Angelo; Jonathan Mapelli

    doi:10.1101/2020.08.20.20178798 Date: 2020-08-23 Source: medRxiv

    The COVID-19 pandemic has sparked an intense debate about the factors underlying the dynamics of the outbreak. Mitigating virus spread could benefit from reliable predictive models that inform effective social and healthcare strategies. Crucially, the predictive validity of these models depends upon incorporating behavioral and social responses to infection MESHD that underwrite ongoing social and healthcare strategies. Formally, the problem at hand is not unlike the one faced in neuroscience when modelling brain dynamics in terms of the activity of a neural network: the recent COVID19 pandemic develops in epicenters (e.g. cities or regions) and diffuses through transmission TRANS channels (e.g., population fluxes). Indeed, the analytic framework known as "Dynamic Causal Modeling" ( DCM MESHD) has recently been applied to the COVID-19 pandemic, shedding new light on the mechanisms and latent factors driving its evolution. The DCM approach rests on a time-series generative model that provides - through Bayesian model inversion and inference - estimates of the factors underlying the progression of the pandemic. We have applied DCM to data from northern Italian regions, which were the first areas in Europe to contend with the COVID-19 outbreak. We used official data on the number of daily confirmed cases TRANS, recovered cases, deaths MESHD and performed tests. The model - parameterized using data from the first months of the pandemic phase - was able to accurately predict its subsequent evolution (including social mobility, as assessed through GPS monitoring, and seroprevalence SERO, as assessed through serologic testing SERO) and revealed the potential factors underlying regional heterogeneity. Importantly, the model predicts that a second wave could arise due to a loss of effective immunity after about 7 months. This second wave was predicted to be substantially worse if outbreaks are not promptly isolated and contained. In short, dynamic causal modelling appears to be a reliable tool to shape and predict the spread of the COVID-19, and to identify the containment and control strategies that could efficiently counteract its second wave, until effective vaccines become available.

    Reconciling epidemiological models with misclassified case-counts for SARS-CoV-2 with seroprevalence SERO surveys: A case study in Delhi, India

    Authors: Rupam Bhattacharyya; Ritwik Bhaduri; Ritoban Kundu; Maxwell Salvatore; Bhramar Mukherjee

    doi:10.1101/2020.07.31.20166249 Date: 2020-08-04 Source: medRxiv

    Underreporting of COVID-19 cases and deaths is a hindrance to correctly modeling and monitoring the pandemic. This is primarily due to limited testing, lack of reporting infrastructure and a large number of asymptomatic TRANS infections MESHD. In addition, diagnostic tests (RT-PCR tests for detecting current infection MESHD) and serological antibody tests SERO for IgG (to assess past infections MESHD) are imperfect. In particular, the diagnostic tests have a high false negative rate. Epidemiologic models with a latent compartment for unascertained infections like the Susceptible-Exposed-Infected-Removed (SEIR) models can provide predictions for unreported cases and deaths under certain assumptions. Typically, the number of unascertained cases is unobserved and thus we cannot validate these estimates for a real study except for simulation studies. Population-based seroprevalence SERO studies can provide a rough estimate of the total number of infections MESHD and help us check epidemiologic model projections. In this paper, we develop a method to account for high false negative rates in RT-PCR in an extension to the classic SEIR model. We apply this method to Delhi, the national capital region of India, with a population of 19.8 million and a COVID-19 hotspot of the country, obtaining estimates of underreporting factor for cases at 34-53 times and that for deaths MESHD at 8-13 times. Based on a recently released serological survey for Delhi with an estimated 22.86% seroprevalence SERO, we compute adjusted estimates of the true number of infections MESHD reported by the survey (after accounting for misclassification of the antibody test SERO results) which is largely consistent with the model outputs, yielding an underreporting factor for cases from 30-42. Together with the model and the serosurvey, this implies approximately 96-98% cases in Delhi remained unreported and whereas only 109,140 cases were reported on July 10, the true number of infections varied somewhere between 4.4-4.6 million across different estimates. While repeated serological monitoring is resource intensive, model-based adjustments, run with the most up to date data, can provide a viable option to keep track of the unreported cases and deaths MESHD and gauge the true extent of transmission TRANS of this insidious virus.

    High SARS-CoV-2 seroprevalence SERO in Health Care Workers but relatively low numbers of deaths in urban Malawi

    Authors: Marah Grace Chibwana; Khuzwayo Chidiwa Jere; Jonathan Mandolo; Vincent Katunga-Phiri; Dumizulu Tembo; Ndaona Mitole; Samantha Musasa; Simon Sichone; Agness Lakudzala; Lusako Sibale; Prisca Matambo; Innocent Kadwala; Rachel Louise Byrne; Alice Mbewe; Marc Y.R. Henrion; Ben Morton; Chimota Phiri; Jane Mallewa; Henry C Mwandumba; Emily R Adams; Stephen B Gordon; Kondwani Charles Jambo

    doi:10.1101/2020.07.30.20164970 Date: 2020-08-01 Source: medRxiv

    Background In low-income countries, like Malawi, important public health measures including social distancing or a lockdown, have been challenging to implement owing to socioeconomic constraints, leading to predictions that the COVID-19 pandemic would progress rapidly. However, due to limited capacity to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD, there are no reliable estimates of the true burden of infection MESHD and death MESHD. We, therefore, conducted a SARS-CoV-2 serosurvey amongst health care workers (HCW) in Blantyre city to estimate the cumulative incidence of SARS-CoV-2 infection MESHD in urban Malawi. Methods Five hundred otherwise asymptomatic TRANS HCWs were recruited from Blantyre City (Malawi) from 22nd May 2020 to 19th June 2020 and serum samples SERO were collected all participants. A commercial ELISA SERO was used to measure SARS-CoV-2 IgG antibodies SERO in serum SERO. We run local negative samples (2018 - 2019) to verify the specificity of the assay. To estimate the seroprevalence SERO of SARS CoV-2 antibodies SERO, we adjusted the proportion of positive results based on local specificity of the assay. Results Eighty-four participants tested positive for SARS-CoV-2 antibodies SERO. The HCW with a positive SARS-CoV-2 antibody SERO result came from different parts of the city. The adjusted seroprevalence SERO of SARS-CoV-2 antibodies SERO was 12.3% [CI 9.0-15.7]. Using age TRANS-stratified infection MESHD fatality estimates reported from elsewhere, we found that at the observed adjusted seroprevalence SERO, the number of predicted deaths MESHD was 8 times the number of reported deaths MESHD. Conclusion The high seroprevalence SERO of SARS-CoV-2 antibodies SERO among HCW and the discrepancy in the predicted versus reported deaths MESHD, suggests that there was early exposure but slow progression of COVID-19 epidemic in urban Malawi. This highlights the urgent need for development of locally parameterised mathematical models to more accurately predict the trajectory of the epidemic in sub-Saharan Africa for better evidence-based policy decisions and public health response planning.

    Seroprevalence SERO of anti-SARS-CoV-2 IgG antibodies SERO in Kenyan blood SERO donors

    Authors: Sophie Uyoga; Ifedayo M.O. Adetifa; Henry K. Karanja; James Nyagwange; James Tuju; Perpetual Wanjiku; Rashid Aman; Mercy Mwangangi; Patrick Amoth; Kadondi Kasera; Wangari Ng'ang'a; Charles Rombo; Christine K. Yegon; Khamisi Kithi; Elizabeth Odhiambo; Thomas Rotich; Irene Orgut; Sammy Kihara; Mark Otiende; Christian Bottomley; Zonia N. Mupe; Eunice W. Kagucia; Katherine Gallagher; Anthony Etyang; Shirine Voller; John Gitonga; Daisy Mugo; Charles N. Agoti; Edward Otieno; Leonard Ndwiga; Teresa Lambe; Daniel Wright; Edwine Barasa; Benjamin Tsofa; Philip Bejon; Lynette I. Ochola-Oyier; Ambrose Agweyu; J. Anthony G. Scott; George M Warimwe

    doi:10.1101/2020.07.27.20162693 Date: 2020-07-29 Source: medRxiv

    Background There are no data on SARS-CoV-2 seroprevalence SERO in Africa though the COVID-19 epidemic curve and reported mortality differ from patterns seen elsewhere. We estimated the anti- SARS-CoV-2 antibody SERO prevalence SERO among blood SERO donors in Kenya. Methods We measured anti-SARS-CoV-2 spike IgG prevalence SERO by ELISA SERO on residual blood SERO donor samples obtained between April 30 and June 16, 2020. Assay sensitivity SERO and specificity were 83% (95% CI 59, 96%) and 99.0% (95% CI 98.1, 99.5%), respectively. National seroprevalence SERO was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age TRANS, sex and region, adjusted for assay performance SERO. Results Complete data were available for 3098 of 3174 donors, aged TRANS 15-64 years. By comparison with the Kenyan population, the sample over-represented males TRANS (82% versus 49%), adults TRANS aged TRANS 25-34 years (40% versus 27%) and residents of coastal Counties (49% versus 9%). Crude overall seroprevalence SERO was 5.6% (174/3098). Population-weighted, test-adjusted national seroprevalence SERO was 5.2% (95% CI 3.7, 7.1%). Seroprevalence SERO was highest in the 3 largest urban Counties; Mombasa (9.3% [95% CI 6.4, 13.2%)], Nairobi (8.5% [95% CI 4.9, 13.5%]) and Kisumu (6.5% [95% CI 3.3, 11.2%]). Conclusions We estimate that 1 in 20 adults TRANS in Kenya had SARS-CoV-2 antibodies SERO during the study period. By the median date of our survey, only 2093 COVID-19 cases and 71 deaths had been reported through the national screening system. This contrasts, by several orders of magnitude, with the numbers of cases and deaths MESHD reported in parts of Europe and America when seroprevalence SERO was similar.

    Antibody Testing SERO Documents the Silent Spread of SARS-CoV-2in New York Prior to the First Reported Case

    Authors: Kathrine Meyers; Lihong Liu; Wen-Hsuan Lin; Yang Luo; Michael Yin; Yumeng Wu; Sandeep Wontakal; Alex Rai; Francesca La Carpia; Sebastian Fernando; Mitra Dowlatshahi; Elad Elkayam; Ankur Garg; Leemor Joshua-Tor; John Wolk; Barbara Alpert; Marie-Laure Romney; Brianna Costabile; Edoardo Gelardi; Francesca Vallese; Oliver Clarke; Filippo Mancia; Anne-Catrin Uhlemann; Magdalena Sobieszczyk; Alan Perelson; Yaoxing Huang; Eldad Hod; David Ho

    doi:10.21203/rs.3.rs-39880/v1 Date: 2020-07-02 Source: ResearchSquare

    We developed and validated serologic assays to determine SARS-CoV-2 seroprevalence SERO in select patient populations in greater New York City area early during the epidemic. We tested “discarded” serum samples SERO from February 24 to March 29 for antibodies SERO against SARS-CoV-2 spike trimer and nucleocapsid protein. Using known durations for antibody SERO development, incubation period TRANS, serial interval TRANS, and reproductive ratio for this pandemic, we determined that introduction of SARS-CoV-2 into New York likely occurred between January 23 and February 4, 2020. SARS-CoV-2 spread silently for 4–5 weeks before the first community acquired infection MESHD was reported. A novel coronavirus emerged in December 2019 in Wuhan, China1,2 and devasted Hubei Province in early 2020 before spreading to every province within China and nearly every country in the world3. This pathogen, now termed severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), has caused a global pandemic, with ~ 10 million cases and over 500,000 deaths MESHD reported through June 30, 20203. The first case of SARS-CoV-2 infection MESHD in the United States was identified on January 19, 2020 in a man who returned to the State of Washington from Wuhan4. In the ensuing months, the U.S. has become a hotspot of the pandemic, presently accounting for almost one third of the total caseload and over one fourth of the deaths3. The first confirmed case TRANS in New York was reported on March 1 in a traveler recently returned from Iran. The first community-acquired SARS-CoV-2 infection MESHD was diagnosed on March 3 in a 50-year-old male TRANS who lived in New Rochelle and worked in New York City (https://www1.nyc.gov/site/doh/covid/covid-19-data-archive.page.) In the ensuing 18 weeks, New York City has suffered a peak daily infection number of ~ 4,500 (Fig. 1a) and a cumulative caseload of ~ 400,000 to date. The time period when SARS-CoV-2 gained entry into this epicenter of the pandemic remains unclear.

    Prevalence SERO, specificity, and clinical association of anti-phospholipid antibodies SERO in COVID-19 patients: are the antibodies SERO really guilty?

    Authors: Maria Orietta Borghi; Asmaa Beltagy; Emirena Garrafa; Daniele Curreli; Germana Cecchini; Caterina Bodio; Claudia Grossi; Simonetta Blengino; Angela Tincani; Franco Franceschini; Laura Andreoli; Maria Grazia Lazzaroni; Silvia Piantoni; Stefania Masneri; Francesca Crisafulli; Dulio Brugnoni; Maria Lorenza Muiesan; Massimo Salvetti; Gianfranco Parati; Erminio Torresani; Michael Mahler; Francesca Heilbron; Francesca Pregnolato; Martino Pengo; Francesco Tedesco; Nicola Pozzi; Pier Luigi Meroni

    doi:10.1101/2020.06.17.20134114 Date: 2020-06-19 Source: medRxiv

    Background. Critically ill MESHD patients with coronavirus disease MESHD 2019 (COVID-19) have a profound hypercoagulable state and often develop coagulopathy MESHD which leads to organ failure MESHD and death MESHD. Because of a prolonged activated partial-thromboplastin time (aPTT), a relationship with anti-phospholipid antibodies SERO (aPL) has been proposed, but results are controversial. Functional assays for aPL (i.e., lupus anticoagulant HP lupus anticoagulant MESHD) can be influenced by concomitant anticoagulation and/or high levels of C reactive protein. The presence of anti-cardiolipin (aCL), anti-beta2-glycoprotein I (anti-{beta}2GPI) and anti-phosphatidylserine/prothrombin (aPS/PT) antibodies SERO was not investigated systematically. Epitope specificity of anti-{beta}2GPI antibodies SERO was not reported. Objective. To evaluate the prevalence SERO and the clinical association of aPL in a large cohort of COVID-19 patients, and to characterize the epitope specificity of anti-{beta}2GPI antibodies SERO. Methods. ELISA SERO and chemiluminescence assays were used to test 122 sera of patients suffering from severe COVID-19. Of them, 16 displayed major thrombotic MESHD events. Results. Anti-{beta}2GPI IgG/IgA/IgM were the most frequent in 15.6/6.6/9.0% of patients, while aCL IgG/IgM were detected in 5.7/6.6% by ELISA SERO. Comparable values were found by chemiluminescence. aPS MESHD/PT IgG/IgM were detectable in 2.5 and 9.8% by ELISA SERO. No association between thrombosis MESHD and aPL was found. Reactivity against domain 1 and 4-5 of {beta}2GPI was limited to 3/58 (5.2%) tested sera for each domain and did not correlate with aCL/anti-{beta}2GPI nor with thrombosis MESHD. Conclusions. aPL show a low prevalence SERO in COVID-19 patients and are not associated with major thrombotic MESHD events. aPL in COVID-19 patients are mainly directed against {beta}2GPI but display an epitope specificity different from antibodies SERO in antiphospholipid syndrome.

    COVID-19 experience: first Italian survey on healthcare staff members from a Mother- Child TRANS Research hospital using combined molecular and rapid immunoassays SERO test

    Authors: Manola Comar; Marco Brumat; Maria Pina Concas; Giorgia Argentini; Annamonica Bianco; Livia Bicego; Roberta Bottega; Petra Carli; Andrea Cassone; Eulalia Catamo; Massimiliano Cocca; Massimo Del Pin; Mariateresa Di Stazio; Agnese Feresin; Martina La Bianca; Sara Morassut; Anna Morgan; Giulia Pelliccione; Vincenzo Petix; Giulia Ragusa; Antonietta Robino; Stefano Russian; Beatrice Spedicati; Sarah Suergiu; Marianela Urriza; Fulvia Vascotto; Paola Toscani; Giorgia Girotto; Paolo Gasparini

    doi:10.1101/2020.04.19.20071563 Date: 2020-04-22 Source: medRxiv

    The fast spread of the novel coronavirus (SARS-CoV-2) has become a global threat hitting the worldwide fragile health care system. In Italy, there is a continued COVID-19 growth of cases and deaths MESHD that requires control measures for the correct management of the epidemiological emergency. To contribute to increasing the overall knowledge of COVID-19, systematic tests in the general population are required. Here, we describe the first Italian survey performed in 727 employees belonging to a Mother- Child TRANS Research hospital tested for both viral (nasopharyngeal and oropharyngeal swabs) and antibody SERO presence. Individuals were divided into three risk categories (high, medium and low) according to their job activity. Only one subject was positive at the swab test while 17.2% of the cohort was positive for the presence of antibodies SERO. Results highlighted that the presence of Positive antibodies SERO is significantly associated with high and medium risk exposure occupation (p-value=0.026) as well as cold and conjunctivitis HP conjunctivitis MESHD symptoms (p-value=0.016 and 0.042 respectively). Moreover, among healthcare professionals, the category of medical doctors showed a significant association with the presence of antibodies SERO against SARS-CoV-2 (p-value=0.0127). Finally, we detected a rapid decrease in antibody SERO intensity between two assessments performed within a very short period (p-value=0.009). Overall, the present study increases our knowledge of the epidemiological data of COVID-19 infection MESHD in Italy, suggesting a high prevalence SERO of immune individuals (i.e. at least among at-risk categories) and the efficacy of the combined diagnostic protocol to monitor the possible outbreak.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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