Corpus overview


MeSH Disease

Human Phenotype

Cough (1)


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

    Authors: Swetaprovo Chaudhuri; Saptarshi Basu; Abhishek Saha

    id:2007.13596v2 Date: 2020-07-27 Source: arXiv

    Identifying the relative importance of the different transmission TRANS routes of the SARS-CoV-2 virus is an urgent research priority. To that end, the different transmission TRANS routes, and their role in determining the evolution of the Covid-19 pandemic are analyzed in this work. Probability of infection MESHD caused by inhaling virus-laden droplets (initial, ejection diameters between $0.5-750\mu m$) and the corresponding desiccated nuclei that mostly encapsulate the virions post droplet evaporation, are individually calculated. At typical, air-conditioned yet quiescent indoor space, for average viral loading, cough MESHD cough HP droplets of initial diameter between $10-50 \mu m$ have the highest infection MESHD probability. However, by the time they are inhaled, the diameters reduce to about $1/6^{th}$ of their initial diameters. While the initially near unity infection MESHD probability due to droplets rapidly decays within the first $25s$, the small yet persistent infection MESHD probability of desiccated nuclei decays appreciably only by $\mathcal{O} (1000s)$, assuming the virus sustains equally well within the dried droplet nuclei as in the droplets. 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 rate constants are derived ab-initio, leading to a SEIR model applicable for any respiratory event - vector combination. Viral load, minimum infectious dose, sensitivity SERO of the virus half-life to the phase of its vector and dilution of the respiratory jet/puff by the entraining air are shown to mechanistically determine specific physical modes of transmission TRANS and variation in the basic reproduction number TRANS $\mathcal{R}_0$, from first principle calculations.

    Characterizing the Qatar advanced-phase SARS-CoV-2 epidemic

    Authors: Laith J Abu-Raddad; Hiam Chemaitelly; Houssein H Ayoub; Zaina Al Kanaani; Abdullatif Al Khal; Einas Al Kuwari; Adeel A Butt; Peter Coyle; Andrew Jeremijenko; Anvar Hassan Kaleeckal; Ali Nizar Latif; Robert C Owen; Hanan F Abdul Rahim; Samya A Al Abdulla; Mohamed G Al Kuwari; Mujeeb C Kandy; Hatoun Saeb; Shazia Nadeem N. Ahmed; Hamad Eid Al Romaihi; Devendra Bansal; Louise Dalton; Sheikh Mohammad Al Thani; Roberto Bertollini

    doi:10.1101/2020.07.16.20155317 Date: 2020-07-19 Source: medRxiv

    ABSTRACT Background: Qatar has a population of 2.8 million, over half of whom are expatriate craft and manual workers (CMW). We aimed to characterize the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) epidemic in Qatar. Methods: A series of epidemiologic studies were conducted including analysis of the national SARS-CoV-2 PCR testing and hospitalization database, community surveys assessing current infection MESHD, ad-hoc PCR testing campaigns in workplaces and residential areas, serological testing SERO for antibody SERO on blood SERO specimens collected for routine clinical screening/management, national Coronavirus Diseases MESHD 2019 (COVID-19) death MESHD registry, and a mathematical model. Results: By July 10, 397,577 individuals had been PCR tested for SARS-CoV-2, of whom 110,986 were positive, a positivity cumulative rate of 27.9% (95% CI: 27.8-28.1%). PCR positivity of nasopharyngeal swabs in a national community survey (May 6-7) including 1,307 participants was 14.9% (95% CI: 11.5-19.0%); 58.5% of those testing positive were asymptomatic TRANS. Across 448 ad-hoc PCR testing campaigns in workplaces and residential areas including 26,715 individuals, pooled mean PCR positivity was 15.6% (95% CI: 13.7-17.7%). SARS-CoV-2 antibody SERO prevalence SERO was 24.0% (95% CI: 23.3-24.6%) in 32,970 residual clinical blood SERO specimens. Antibody SERO prevalence SERO was only 47.3% (95% CI: 46.2-48.5%) in those who had at least one PCR positive result, but it was 91.3% (95% CI: 89.5-92.9%) among those who were PCR positive >3 weeks before serology testing. There were substantial differences in exposure to infection MESHD by nationality and sex, reflecting risk differentials between the craft/manual workers and urban populations. As of July 5, case severity rate, based on the WHO severity classification, was 3.4% and case fatality rate was 1.4 per 1,000 persons. Model-estimated daily number of infections MESHD and active- infection MESHD prevalence SERO peaked at 22,630 and 5.7%, respectively, on May 21 and May 23. Attack rate TRANS (ever infection MESHD) was estimated at 53.5% on July 12. R0 TRANS ranged between 1.45-1.68 throughout the epidemic. Rt was estimated at 0.70 on June 15, which was hence set as onset date for easing of restrictions. Age TRANS was by far the strongest predictor of severe, critical, or fatal infection MESHD. Conclusions: Qatar has experienced a large SARS-CoV-2 epidemic that is rapidly declining, apparently due to exhaustion of susceptibles. The epidemic demonstrated a classic susceptible-infected-recovered 'SIR' dynamics with a rather stable R0 TRANS of about 1.6. The young demographic structure of the population, in addition to a resourced public health response, yielded a milder disease MESHD burden and lower mortality than elsewhere.

    Diagnostics and spread of SARS-CoV-2 in Western Africa: An observational laboratory-based study from Benin

    Authors: Anges Yadouleton; Anna-Lena Sander; Andres Moreira-Soto; Carine Tchibozo; Gildas Hounkanrin; Yvette Badou; Carlo Fischer; Nina Krause; Petas Akogbeto; Edmilson F. de Oliveira Filho; Anges Dossou; Sebastian Bruenink; Melchior AIssi; Mamoudou Harouna Djingarey; Benjamin Hounkpatin; Michael Nagel; Jan felix Drexler

    doi:10.1101/2020.06.29.20140749 Date: 2020-07-08 Source: medRxiv

    Information on severe acute respiratory syndrome MESHD coronavirus-2 (SARS-CoV-2) spread in Africa is limited by fragile 2 surveillance systems and insufficient diagnostic capacity. 3 We assessed the coronavirus disease MESHD-19 (COVID-19)-related diagnostic workload in Benin, Western Africa, 4 characterized SARS-CoV-2 genomes from 12 acute cases of COVID-19, used those together with public data to 5 estimate SARS-CoV-2 transmission TRANS dynamics in a Bayesian framework, validated a widely used diagnostic dual target 6 RT-PCR kit donated to African countries, and conducted serological analyses in 68 sera from confirmed COVID-19 7 cases and from febrile patients sampled before the predicted SARS-CoV-2 introduction. 8 We found a 15-fold increase in the monthly laboratory workload due to COVID-19. Genomic surveillance showed 9 introductions of three distinct SARS-CoV-2 lineages. SARS-CoV-2 genome-based analyses yielded an R0 TRANS estimate of 10 4.4 (95% confidence interval: 2.0-7.7), suggesting intense spread of SARS-CoV-2 in Africa. RT-PCR-based tests 11 were highly sensitive but showed variation of internal controls and between diagnostic targets. Commercially available 12 SARS-CoV-2 ELISAs SERO showed up to 25% false-positive results depending on antigen and antibody SERO types, likely due 13 to unspecific antibody SERO responses elicited by acute malaria MESHD according to lack of SARS-CoV-2-specific neutralizing 14 antibody SERO responses and relatively higher parasitemia MESHD in those sera. 15 We confirm an overload of the diagnostic capacity in Benin and provide baseline information on the usability of 16 genome-based surveillance in resource-limited settings. Sero-epidemiological studies SERO Sero-epidemiological studies SERO needed to assess SARS-CoV-2 17 spread may be put at stake by low specificity of tests in tropical settings globally. The increasing diagnostic challenges 18 demand continuous support of national and supranational African stakeholders.

    Modeling the Impact of School Reopening on SARS-CoV-2 Transmission TRANS

    Authors: Benjamin Lee; John P Hanley; Sarah Nowak; Jason HT Bates; Laurent Hébert-Dufresne

    doi:10.21203/ Date: 2020-06-28 Source: ResearchSquare

    Background Mathematical modeling studies have suggested that pre-emptive school closures alone have little overall impact on SARS-CoV-2 transmission TRANS, but reopening schools in the background of community contact reduction presents a unique scenario that has not been fully assessed.Methods Therefore, we adapted a previously published SIR (susceptible-infectious-recovered) model using contact information from Shanghai to model school reopening under various conditions.Results We find that reopening schools for all children TRANS would maintain effective R0 < 1 up to a baseline R0 TRANS of 3.3 provided that daily contacts among children TRANS 10–19 years are reduced to 33% of baseline. This finding was robust to various estimates of susceptibility to infection MESHD in children TRANS relative to adults TRANS (up to 50%) and to estimates of various levels of concomitant reopening in the rest of the community, with minimal change in transmission TRANS when contact frequency TRANS contact frequency SERO in the rest of the community was returned up to 40% of baseline.Conclusions These results suggest that schools can reopen safely with proper precautions during conditions of extreme contact reduction and during conditions of reasonable levels of reopening in the rest of the community.

    Evaluating COVID-19 screening strategies based on serological tests SERO

    Authors: Michela Baccini; Alessandra Mattei; Emilia Rocco; Giulia Vannucci; Fabrizia Mealli

    doi:10.1101/2020.06.12.20129403 Date: 2020-06-14 Source: medRxiv

    Background. Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. Although RT-PCR is the most reliable technique to detect ongoing infections MESHD, serological tests SERO are frequently proposed as tools in heterogeneous screening strategies. We analyze the performance SERO of a screening strategy proposed in Tuscany (Italy), which first uses qualitative rapid tests SERO for antibody SERO detection, and then RT-PCR tests on the positive subjects. Methods. We simulate the number of RT-PCR tests required by the screening strategy and the undetected ongoing infections MESHD in a pseudo-population of 500000 subjects, under different prevalence SERO scenarios and assuming a sensitivity SERO of the serological test SERO ranging from 0.50 to 0.80 (specificity=0.98). A compartmental model is used to predict the number of new infections MESHD generated by the false negatives two months after the screening, under different values of the infection MESHD reproduction number TRANS. Results. Assuming a sensitivity SERO equal to 0.80 and a prevalence SERO of 0.3%, the screening procedure would require on average 11167.6 RT-PCR tests and would produce 300 false negatives, responsible after two months of a number of contagions ranging from 526 to 1132, under the optimistic scenario of a reproduction number TRANS between 0.5 to 1. Costs and false negatives increase with the prevalence SERO. Conclusions. The analyzed screening procedure should be avoided unless the prevalence SERO and the rate of contagion are very low. The cost and effectiveness of the screening strategies should be evaluated in the actual context of the epidemic, accounting for the fact that it may change over time.

    COVID-19 Exposure Risk of Healthcare Personnel in Digestive Endoscopy: A Prospective Study

    Authors: Lorenzo Dioscoridi; Chiara Carrisi

    doi:10.21203/ Date: 2020-05-26 Source: ResearchSquare

    Background: Of many descriptive papers about healthcare workers’ (HW) COVID-19 infection, asymptomatic MESHD asymptomatic TRANS cases have not yet considered. Aims: The present study calculated the numbers of COVID-19 patients afferent to GI endoscopy and the number of positive HW using nasopharyngeal swabs (NS), serological rapid IgM/IgG tests SERO (SRT) and serological quantitative IgG test (SQT).Methods: The study was conducted from 2ndto 30thApril 2020. All the recommended national and international indications on infection MESHD control measures were followed. Out of 1227 patients accepted, 1009 were included in the study. 38 HW were tested by NS, SRT and SQT. Descriptive statistical analyses were used to summarize the data.Results: 17 patients were diagnosed COVID-19 positive at NS. 9 patients were known positive at the time of the endoscopy and 8 were diagnosed COVID-19 positive after the procedure. Of the 38 HW, 2 were positive both to NS and SRT with IgM/IgG lines; 7 showed IgG line only at SRT, confirmed by SQT with negative NS. Other 7 HW showed not well-defined line of IgG at SRT, confirmed negative by SQT. The two cases positive to NS and IgM/IgG SRT were asymptomatic TRANS. The crude contagion’s rate ( R0 TRANS)was 0.41 and 1.7% of COVID-19 patients caused 19% of positive cases in HW.Conclusions: Not previously diagnosed COVID-19 patients expose HW to additional and incalculable risk of contamination. Association between different tests reduced the variability related to possible confounding factors and increases the accuracy. Since most cases in HW seem to go asymptomatic TRANS, large-scale tests using both NS and SRT for both HW and patients should be recommended to minimize the risk of in-hospital infection’s relapses.

    Population-scale testing can suppress the spread of COVID-19

    Authors: Jussi Taipale; Paul Romer; Sten Linnarsson

    doi:10.1101/2020.04.27.20078329 Date: 2020-05-01 Source: medRxiv

    We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) isolation of infected individuals. We show here that at a sufficient rate of testing and isolation, the R0 TRANS of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. The approach does not rely on strong and/or unrealistic assumptions about test accuracy, compliance to isolation, population structure or epidemiological parameters, and its success can be monitored in real time by measuring the change of the test positivity rate over time. In addition to the rate of compliance and false negatives, the required rate of testing is dependent on the design of the testing regime, with concurrent testing outperforming random sampling of individuals. Provided that results are reported rapidly, the test SERO frequency required to suppress an epidemic is linear with respect to R0 TRANS, to the infectious period TRANS, and to the fraction of susceptible individuals. Importantly, the testing regime would be effective at any level of prevalence SERO, and additive to other interventions such as contact tracing TRANS and social distancing. It would also be robust to failure, as even in the case where the testing rate would be insufficient to collapse the epidemic, it would still reduce the number of infected individuals in the population, improving both public health and economic conditions. A mass-produced, disposable antigen or RNA test that could be used at home would be ideal, due to the optimal performance SERO of concurrent tests that return immediate results.

    Inferring epidemic parameters for COVID-19 from fatality counts in Mumbai

    Authors: Sourendu Gupta

    id:2004.11677v1 Date: 2020-04-23 Source: arXiv

    Epidemic parameters are estimated through Bayesian inference using the daily fatality counts in Mumbai during the period from March 31 to April 14. A doubling time of 5.5 days (median with 95% CrI of 4.6-6.9 days) is observed. In the SEIR model this gives the basic reproduction rate R_0 TRANS of 3.4 (median with 95% CrI of 2.4-4.8). Using as input the infection MESHD fatality rate and the interval between infection MESHD and death MESHD, the number of infections MESHD in Mumbai is inferred. It is found that the ratio of the number of test positives to the total infections MESHD is 0.13\% (median), implying that tests are currently finding 1 out of 750 cases of infection MESHD. After correcting for different testing rates, this result is compatible with a measurement of the ratio made recently via serological testing SERO in the USA. From the estimates of the number of infections MESHD we infer that the first COVID-19 cases were seeded in Mumbai between late December 2019 and early February 2020. provided the doubling times remained unchanged since then. We remark on some public health implications if the rate of growth cannot be controlled in about a week.

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MeSH Disease
Human Phenotype

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