Corpus overview


MeSH Disease

Infections (197)

Disease (146)

Coronavirus Infections (86)

Death (55)

Fever (53)

Human Phenotype

Fever (53)

Cough (44)

Pneumonia (38)

Fatigue (17)

Lymphopenia (15)


symptom onset (356)

age categories (109)

Transmission (100)

gender (58)

fomite (51)

    displaying 1 - 10 records in total 358
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    COVID-19 Test & Trace TRANS Success Determinants: Modeling On A Network

    Authors: Ofir Reich

    doi:10.1101/2020.08.05.20168799 Date: 2020-08-06 Source: medRxiv

    What determines the success of a COVID-19 Test & Trace TRANS policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing TRANS, we find that important determinants of successful containment are: (i) the time from symptom onset TRANS until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced TRANS. Comparatively less important is (iii) the time of test analysis and contact tracing TRANS. When the share of contacts successfully traced TRANS is higher, the Test & Trace TRANS Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic TRANS patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace TRANS systems and policies could affect all three parameters, Symptom Onset TRANS to Test Time should be considered, alongside test turnaround time and contact tracing TRANS coverage, as a key determinant of Test & Trace TRANS success.

    Serology assessment of antibody SERO response to SARS-CoV-2 in patients with COVID-19 by rapid IgM/IgG antibody test SERO

    Authors: Yang De Marinis; Torgny Sunnerhagen; Pradeep Bompada; Anna Blackberg; Runtao Yang; Joel Svensson; Ola Ekstrom; Karl-Fredrik Eriksson; Ola Hansson; Leif Groop; Isabel Goncalves; Magnus Rasmussen

    doi:10.1101/2020.08.05.20168815 Date: 2020-08-06 Source: medRxiv

    The coronavirus disease MESHD 2019 (COVID-19) pandemic has created a global health- and economic crisis. Lifting confinement restriction and resuming to normality depends greatly on COVID-19 immunity screening. Detection of antibodies SERO to severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) which causes COVID-19 by serological methods is important to diagnose a current or resolved infection MESHD. In this study, we applied a rapid COVID-19 IgM/IgG antibody test SERO and performed serology assessment of antibody SERO response to SARS-CoV-2. In PCR-confirmed COVID-19 patients (n=45), the total antibody SERO detection rate is 92% in hospitalized patients and 79% in non-hospitalized patients. We also studied antibody SERO response in relation to time after symptom onset TRANS and disease MESHD severity, and observed an increase in antibody SERO reactivity and distinct distribution patterns of IgM and IgG following disease progression MESHD. The total IgM and IgG detection is 63% in patients with < 2 weeks from disease MESHD onset; 85% in non-hospitalized patients with > 2 weeks disease MESHD duration; and 91% in hospitalized patients with > 2 weeks disease MESHD duration. We also compared different blood SERO sample types and suggest a potentially higher sensitivity SERO by serum SERO/ plasma SERO comparing with whole blood SERO measurement. To study the specificity of the test, we used 69 sera/ plasma SERO samples collected between 2016-2018 prior to the COVID-19 pandemic, and obtained a test specificity of 97%. In summary, our study provides a comprehensive validation of the rapid COVID-19 IgM/IgG serology test, and mapped antibody SERO detection patterns in association with disease MESHD progress and hospitalization. Our study supports that the rapid COVID-19 IgM/IgG test may be applied to assess the COVID-19 status both at the individual and at a population level.

    Two SARS-CoV-2 IgG Immunoassays SERO Comparison and Time-Course Profile of Antibodies SERO Response

    Authors: Ruggero Dittadi; Haleh Afshar; Paolo Carraro

    id:202008.0114/v1 Date: 2020-08-05 Source:

    The role of the immune response to SARS-CoV-2 infection MESHD is not yet well known, in particular about the persistence of circulating antibodies SERO. The aim of the study is to compare the results of two automated systems for the determination of IgG antibodies SERO against SARS CoV-2 and to assess the time course of the IgG response after the onset of symptoms TRANS for a period longer than that evaluated to date. IgG were measured in 98 specimens of 55 subjects with COVID-19 (time from the onset of symptoms TRANS from 3 to 109 days) using the automated tests "Abbott SARS-COV-2 IgG" and the "MAGLUMI 2019-nCoV IgG". The two methods had a concordance of 91.8%, but the quantitative correlation showed very dispersed results. All the specimens resulted positive after 17 days from the onset of the synptoms. However, the median concentrations of IgG, after a rapid increase up to about 20 days, quickly decrease to about 15% of the maximum for Maglumi. The same samples measured by Architect showed a quite constant trend up to 80 day, and then an only moderate decline. The titer of IgG against SARS-CoV-2 in patients exposed to COVID-19 may significantly and rapidly decrease, with a different time-course depending on the method used for the determination.

    Evaluation of Serological SARS-CoV-2 Lateral Flow Assays for Rapid Point of Care Testing

    Authors: Steven E Conklin; Kathryn Martin; Yukari C Manabe; Haley A Schmidt; Morgan Keruly; Ethan Klock; Charles S Kirby; Owen R Baker; Reinaldo E Fernandez; Yolanda J Eby; Justin Hardick; Kathryn Shaw-Saliba; Richard E Rothman; Patrizio P Caturegli; Andrew R Redd; Aaron AR Tobian; Evan M Bloch; H Benjamin Larman; Thomas C Quinn; William Clarke; Oliver Laeyendecker

    doi:10.1101/2020.07.31.20166041 Date: 2020-08-04 Source: medRxiv

    Background. Rapid point-of-care tests (POCTs) for SARS-CoV-2-specific antibodies SERO vary in performance SERO. A critical need exists to perform head-to-head comparison of these assays. Methods. Performance SERO of fifteen different lateral flow POCTs for the detection of SARS-CoV-2-specific antibodies SERO was performed on a well characterized set of 100 samples. Of these, 40 samples from known SARS-CoV-2-infected, convalescent individuals (average of 45 days post symptom onset TRANS) were used to assess sensitivity SERO. Sixty samples from the pre-pandemic era (negative control), that were known to have been infected with other respiratory viruses (rhinoviruses A, B, C and/or coronavirus 229E, HKU1, NL63 OC43) were used to assess specificity. The timing of seroconversion was assessed on five POCTs on a panel of 272 longitudinal samples from 47 patients of known time since symptom onset TRANS. Results. For the assays that were evaluated, the sensitivity SERO and specificity for any reactive band ranged from 55%-97% and 78%-100%, respectively. When assessing the performance SERO of the IgM and the IgG bands alone, sensitivity SERO and specificity ranged from 0%-88% and 80%-100% for IgM and 25%-95% and 90%-100% for IgG. Longitudinal testing revealed that median time post symptom onset TRANS to a positive result was 7 days (IQR 5.4, 9.8) for IgM and 8.2 days (IQR 6.3 to 11.3). Conclusion. The testing performance SERO varied widely among POCTs with most variation related to the sensitivity SERO of the assays. The IgM band was most likely to misclassify pre-pandemic samples. The appearance of IgM and IgG bands occurred almost simultaneously.

    A distinct innate immune signature marks progression from mild to severe COVID-19

    Authors: Stéphane Chevrier; Yves Zurbuchen; Carlo Cervia; Sarah Adamo; Miro E Raeber; Natalie de Souza; Sujana Sivapatham; Andrea Jacobs; Esther Bächli; Alain Rudiger; Melina Stüssi-Helbling; Lars C Huber; Dominik J Schaer; Jakob Nilsson; Onur Boyman; Bernd Bodenmiller

    doi:10.1101/2020.08.04.236315 Date: 2020-08-04 Source: bioRxiv

    Coronavirus disease MESHD 2019 (COVID-19) manifests with a range of severities, but immune signatures of mild and severe disease MESHD are still not fully understood. Excessive inflammation MESHD has been postulated to be a major factor in the pathogenesis of severe COVID-19 and innate immune mechanisms are likely to be central in the inflammatory response. We used 40-plex mass cytometry and targeted serum SERO proteomics to profile innate immune cell populations from peripheral blood SERO of patients with mild or severe COVID-19 and healthy controls. Sampling at different stages of COVID-19 allowed us to reconstruct a pseudo-temporal trajectory of the innate immune response. Despite the expected patient heterogeneity, we identified consistent changes during the course of the infection MESHD. A rapid and early surge of CD169+ monocytes associated with an IFN{gamma}+MCP-2+ signature quickly followed symptom onset TRANS; at symptom onset TRANS, patients with mild and severe COVID-19 had a similar signature, but over the course of the disease MESHD, the differences between patients with mild and severe disease MESHD increased. Later in the disease MESHD course, we observed a more pronounced re-appearance of intermediate/non-classical monocytes and mounting systemic CCL3 and CCL4 levels in patients with severe disease MESHD. Our data provide new insights into the dynamic nature of the early inflammatory response to severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD and identifies sustained pathological innate immune responses as a likely key mechanism in severe COVID-19, further supporting investigation of targeted anti-inflammatory interventions in severe COVID-19.

    Analytical and clinical performances SERO of five immunoassays SERO for the detection of SARS-CoV-2 antibodies SERO in comparison with neutralization activity

    Authors: Mario Plebani; Andrea Padoan; Laura Sciacovelli; Francesco Bonfante; Matteo Pagliari; Dania Bozzato; Chiara Cosma; Alessio Bortolami; Davide Negrini; Silvia Zuin

    doi:10.1101/2020.08.01.20166546 Date: 2020-08-04 Source: medRxiv

    Background. Reliable high-throughput serological assays SERO for SARS-CoV-2 antibodies SERO (Abs) are urgently needed for the effective containment of the COVID-19 pandemic, as it is of crucial importance to understand the strength and duration of immunity after infection MESHD, and to make informed decisions concerning the activation or discontinuation of physical distancing restrictions. Methods. In 184 serum samples SERO from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances SERO of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay SERO (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT). Findings. Precision results ranged from 0.9% to 11.8% for all assays. Elecsys anti-SARS-CoV-2 demonstrated linearity of results at concentrations within the cut-off value. Overall, sensitivity SERO ranged from 78.5 to 87.8%, and specificity, from 97.6 to 100%. On limiting the analysis to samples collected 12 days after onset of symptoms TRANS, the sensitivity SERO of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. The strongest PRNT50 correlation with antibody SERO levels was obtained with ENZY-Well SARS-CoV-2 IgG (rho = 0.541, p < 0.001). Interpretation. The results confirmed that all immunoassays SERO had an excellent specificity, whereas sensitivity SERO varied across immunoassays SERO, depending strongly on the time interval between symptoms onset TRANS and sample collection. Further studies should be conducted to achieve a stronger correlation between antibody SERO measurement and PRNT50 in order to obtain useful information for providing effective passive antibody SERO therapy, and developing a vaccine against the SARS-CoV-2 virus.

    Evidence for sustained mucosal and systemic antibody SERO responses to SARS-CoV-2 antigens in COVID-19 patients

    Authors: Baweleta Isho; Kento T Abe; Michelle Zuo; Alainna J Jamal; Bhavisha Rathod; Jenny H Wang; Zhijie Li; Gary Chao; Olga L Rojas; Yeo Myong Bang; Annie Pu; Natasha Christie-Holmes; Christian Gervais; Derek Ceccarelli; Payman Samavarchi-Tehrani; Furkan Guvenc; Patrick Budylowski; Angel Li; Aimee Paterson; Yue Feng Yun; Lina G Marin; Lauren Caldwell; Jeffrey L Wrana; Karen Colwill; Frank Sicheri; Samira Mubareka; Scott D Gray-Owen; Steven J Drews; Walter L Siqueira; Miriam Barrios-Rodiles; Mario Ostrowski; James M Rini; Yves Durocher; Allison J McGeer; Jennifer L Gommerman; Anne-Claude Gingras

    doi:10.1101/2020.08.01.20166553 Date: 2020-08-04 Source: medRxiv

    While the antibody SERO response to SARS-CoV-2 has been extensively studied in blood SERO, relatively little is known about the mucosal immune response and its relationship to systemic antibody SERO levels. Since SARS-CoV-2 initially replicates in the upper airway, the antibody SERO response in the oral cavity is likely an important parameter that influences the course of infection MESHD. We developed enzyme linked immunosorbent assays SERO to detect IgA and IgG antibodies SERO to the SARS-CoV-2 spike protein (full length trimer) and its receptor binding domain (RBD) in serum SERO (n=496) and saliva (n=90) of acute and convalescent patients with laboratory-diagnosed COVID-19 ranging from 3-115 days post- symptom onset TRANS (PSO), compared to negative controls. Anti-CoV-2 antibody SERO responses were readily detected in serum SERO and saliva, with peak IgG levels attained by 16-30 days PSO. Whereas anti-CoV-2 IgA antibodies SERO rapidly decayed, IgG antibodies SERO remained relatively stable up to 115 days PSO in both biofluids. Importantly, IgG responses in saliva and serum SERO were correlated, suggesting that antibodies SERO in the saliva may serve as a surrogate measure of systemic immunity.

    Correlation between daily infections MESHD and fatality rate due to Covid-19 in Germany

    Authors: Dieter Mergel

    doi:10.1101/2020.08.03.20167304 Date: 2020-08-04 Source: medRxiv

    The daily Covid-19 fatality rate is modelled with a trend line based on nominal day-to-day reproduction rates and a cosine to take account of weekly fluctuations. The fatality trajectory represented by this trend line can be projected from the number of daily infections MESHD by assuming a time lapse between symptom onset TRANS and death MESHD between 17 and 19 days and a nominal time-dependent fatality rate. The time trajectory of this fatality rate suggests a change of the infection MESHD dynamics at April 3, with an increase from 2.5% to 6% within 20 days perhaps indicating spread of infection MESHD to more vulnerable people. Later in summer, the nominal fatality rate decreases down to 1% in mid-July raising the question whether Covid-19 is intrinsically less lethal in summer. Although the time trajectories of infections MESHD and fatality are pronouncedly different, the reproduction rates obtained therefrom are similar indicating that the infection MESHD dynamics may reasonably well be deduced from the potentially biased reported infection MESHD rate if it is biased consistently, i.e. the same way, over an extended period of time. The administrative measures to contain the pandemic seem not to have an immediate effect on the infection MESHD dynamics but well the ease of restrictions. An effect of mask wearing on decreasing lethality cannot be excluded.

    Viral cultures for COVID-19 infectivity assessment. Systematic review

    Authors: Tom Jefferson; Elizabeth Spencer; Jon Brassey; Carl Heneghan

    doi:10.1101/2020.08.04.20167932 Date: 2020-08-04 Source: medRxiv

    We report the results of a review of the evidence from studies comparing SARS-CoV-2 culture with reverse transcriptase polymerase chain reaction (rt-PCR), as viral culture represents the best indicator of current infection MESHD and infectiousness of the isolate. We identified fourteen studies succeeding in culturing or observing tissue invasion by SARS-CoV in sputum, naso or oropharyngeal, urine, stool and environmental samples from patients diagnosed with Covid-19. The data are suggestive of a relation between the time from collection of a specimen to test, copy threshold, and symptom severity, but the quality of the studies was moderate with lack of standardised reporting and lack of testing of PCR against viral culture or infectivity in animals. This limits our current ability to quantify the relationship between viral load, cycle threshold and viable virus detection and ultimately the usefulness of PCR use for assessing infectiousness of patients. Prospective routine testing of reference and culture specimens are necessary for each country involved in the pandemic to establish the usefulness and reliability of PCR for Covid-19 and its relation to patients factors such as date of onset of symptoms TRANS and copy threshold, in order to help predict infectivity.

    Early transmission TRANS dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama.

    Authors: Danilo Franco; Claudia Gonzalez; Leyda E Abrego; Jean P Carrera; Yamilka Diaz; Yaset Caisedo; Ambar Moreno; Oris Chavarria; Jessica Gondola; Marlene Castillo; Elimelec Valdespino; Melissa Gaitan; Jose Martinez-Mandiche; Lizbeth Hayer; Pablo Gonzalez; Carmen Lange; Yadira Molto; Dalis Mojica; Ruben Ramos; Maria Mastelari; Lizbeth Cerezo; Lourdes Moreno; Christl A Donnelly; Nuno R. Faria; Juan M Pascale; Sandra Lopez-Verges; Alexander A Martinez

    doi:10.1101/2020.07.31.20160929 Date: 2020-08-04 Source: medRxiv

    Background With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease MESHD control strategies. We investigated the early transmission TRANS patterns of the virus and the outcomes of mitigation measures in the country. Methods We collected information from epidemiological surveillance, including contact tracing TRANS, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number TRANS (Rt) using date of symptom onset TRANS in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission TRANS of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission TRANS dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission TRANS clusters is crucial to interrupt local transmission TRANS of SARS-CoV-2 in a region.

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MeSH Disease
Human Phenotype

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