Corpus overview


MeSH Disease

Human Phenotype

There are no HP terms in the subcorpus


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    A logistic model of CoV-2 propagation

    Authors: Robert F Weiss

    doi:10.1101/2020.07.20.20157826 Date: 2020-07-26 Source: medRxiv

    We describe an elemental logistic model for the propagation of CoV-2 in a community and illustrate the sensitivity SERO of the model to key parameters such as R0 TRANS, the initial rate of infections MESHD per infected person, and A0 , the fraction of infected people developing neutralizing antibodies SERO. We demonstrate the importance of the duration of immunity in the population, the development of waves of new cases of infection MESHD, and the effect of premature opening of local economies.

    Dynamics of SARS-CoV-2 with Waning Immunity in the UK Population

    Authors: Thomas Crellen; Li Pi; Emma Davis; Timothy M Pollington; Tim C D Lucas; Diepreye Ayabina; Anna Borlase; Jaspreet Toor; Kiesha Prem; Graham F Medley; Petra Klepac; T Deirdre Hollingsworth

    doi:10.1101/2020.07.24.20157982 Date: 2020-07-25 Source: medRxiv

    The dynamics of immunity are crucial to understanding the long-term patterns of the SARS-CoV-2 pandemic. While the duration and strength of immunity to SARS-CoV-2 is currently unknown, specific antibody SERO titres to related coronaviruses SARS-CoV and MERS-CoV have been shown to wane in recovered individuals, and immunity to seasonal circulating coronaviruses is estimated to be shorter than one year. Using an age TRANS-structured, deterministic model, we explore different potential immunity dynamics using contact data TRANS from the UK population. In the scenario where immunity to SARS-CoV-2 lasts an average of three months for non-hospitalised individuals, a year for hospitalised individuals, and the effective reproduction number TRANS (Rt) after lockdown is 1.2 (our worst case scenario), we find that the secondary peak occurs in winter 2020 with a daily maximum of 409,000 infectious individuals; almost three-fold greater than in a scenario with permanent immunity. Our models suggests that longitudinal serological surveys to determine if immunity in the population is waning will be most informative when sampling takes place from the end of the lockdown until autumn 2020. After this period, the proportion of the population with antibodies to SARS-CoV-2 SERO is expected to increase due to the secondary peak. Overall, our analysis presents considerations for policy makers on the longer term dynamics of SARS-CoV-2 in the UK and suggests that strategies designed to achieve herd immunity may lead to repeated waves of infection MESHD if immunity to re- infection MESHD is not permanent.

    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.

    Social-distancing effectiveness tracking of the COVID-19 hotspot Stockholm

    Authors: Joachim Oberhammer

    doi:10.1101/2020.06.30.20143487 Date: 2020-07-02 Source: medRxiv

    Background: The COVID-19 outbreak in Stockholm, Sweden, is characterized by a near-absence of governmental interventions and high fatalities in the care home population. This study analyses the outbreak and the social-distancing effectiveness timeline in the general population and the care homes. Methods: A novel distributed-compartmental, time-variant epidemiological model was designed specifically for COVID-19 transmission TRANS characteristics, featuring a/pre/symptomatic transmission TRANS, a non-linear hospital model, a weakly-coupled sub-model for the care-home population, and parametrized continuous social-distancing functions. The model parameters and the social-distancing timelines are determined by randomization and Monte-Carlo simulations analysing real-world data. Findings: Despite a high initial reproduction number TRANS (3.29) and the near-absence of governmental interventions, the model quantitated that the transmission TRANS rate in the general population was suppressed by 73%, and in the care homes by 79%. The measures in the care homes took effect 4.8 days delayed; and if applied 4 or 8 days earlier, the fatalities could have been reduced by 63.2% or 89.9%. The infected population is estimated to 16.2% (June 10). An expected underestimation of population immunity by antibody SERO studies is confirmed. The infection MESHD fatality ratio extrapolates to 0.61% (peak: 1.34%). The model indicates a seasonal effect which effectively suppressed a new rise. An analysed large-scale public event had no large influence. The asymptomatic TRANS ratio was determined to 35%. Interpretation: The proposed model and methods have proven to analyse a COVID-19 outbreak and to re-construct the social-distancing behaviour with unprecedented accuracy, confirming even minor details indicated by mobility-data analysis, and are applicable to other regions and other emerging infectious diseases MESHD of similar transmission TRANS characteristics. The self-regulation of the population in Stockholm, influenced by advices by the authorities, was able to suppress a COVID-19 outbreak to a level far beyond that the stringency index of governmental interventions suggests. Proper timing of effective measures in the care homes is important to reduce fatalities.

    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.

    Visualizing the invisible: The effect of asymptomatic TRANS transmission TRANS on the outbreak dynamics of COVID-19

    Authors: Mathias Peirlinck; Kevin Linka; Francisco Sahli Costabal; Eran Bendavid; Jayanta Bhattacharya; John Ioannidis; Ellen Kuhl

    doi:10.1101/2020.05.23.20111419 Date: 2020-05-26 Source: medRxiv

    Understanding the outbreak dynamics of the COVID-19 pandemic has important implications for successful containment and mitigation strategies. Recent studies suggest that the population prevalence SERO of SARS-CoV-2 antibodies SERO, a proxy for the number of asymptomatic TRANS cases, could be an order of magnitude larger than expected from the number of reported symptomatic cases. Knowing the precise prevalence SERO and contagiousness of asymptomatic TRANS transmission TRANS is critical to estimate the overall dimension and pandemic potential of COVID-19. However, at this stage, the effect of the asymptomatic TRANS population, its size, and its outbreak dynamics remain largely unknown. Here we use reported symptomatic case data in conjunction with antibody SERO seroprevalence SERO studies, a mathematical epidemiology model, and a Bayesian framework to infer the epidemiological characteristics of COVID-19. Our model computes, in real time, the time-varying contact rate of the outbreak, and projects the temporal evolution and credible intervals of the effective reproduction number TRANS and the symptomatic, asymptomatic TRANS, and recovered populations. Our study quantifies the sensitivity SERO of the outbreak dynamics of COVID-19 to three parameters: the effective reproduction number TRANS, the ratio between the symptomatic and asymptomatic TRANS populations, and the infectious periods TRANS of both groups For nine distinct locations, our model estimates the fraction of the population that has been infected and recovered by Jun 15, 2020 to 24.15% (95% CI: 20.48%-28.14%) for Heinsberg (NRW, Germany), 2.40% (95% CI: 2.09%-2.76%) for Ada County (ID, USA), 46.19% (95% CI: 45.81%-46.60%) for New York City (NY, USA), 11.26% (95% CI: 7.21%-16.03%) for Santa Clara County (CA, USA), 3.09% (95% CI: 2.27%-4.03%) for Denmark, 12.35% (95% CI: 10.03%-15.18%) for Geneva Canton (Switzerland), 5.24% (95% CI: 4.84%-5.70%) for the Netherlands, 1.53% (95% CI: 0.76%-2.62%) for Rio Grande do Sul (Brazil), and 5.32% (95% CI: 4.77%-5.93%) for Belgium. Our method traces TRANS the initial outbreak date in Santa Clara County back to January 20, 2020 (95% CI: December 29, 2019 - February 13, 2020). Our results could significantly change our understanding and management of the COVID-19 pandemic: A large asymptomatic TRANS population will make isolation, containment, and tracing TRANS of individual cases challenging. Instead, managing community transmission TRANS through increasing population awareness, promoting physical distancing, and encouraging behavioral changes could become more relevant.

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MeSH Disease
Human Phenotype

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