Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020

    Authors: Mohamed Elhakim; Saleh Banoita Tourab; Ahmed Zouiten

    doi:10.1101/2020.08.03.20167692 Date: 2020-08-04 Source: medRxiv

    Background: First cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease MESHD as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing TRANS. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts TRANS of each positive case, which allowed for a rapid control of the epidemic. Methods: COVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020. Results: A total of 1,401 confirmed cases TRANS of COVID-19 were included in the study with 4 related deaths MESHD (CFR: 0.3%) and an attack rate TRANS of 0.15%. Males TRANS represented (68.4%) of the cases, with the age group TRANS 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced TRANS, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic TRANS cases. Recoveries reached 69% of the infected cases with R0 TRANS (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%). Conclusion: Djibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.

    Epidemic Dynamics of COVID-19 Based on SEAIUHR Model Considering Asymptomatic TRANS Cases in Henan Province, China

    Authors: Chunyu Li; Yuchen Zhu; Chang Qi; Lili Liu; Dandan Zhang; Xu Wang; Kaili She; Yan Jia; Tingxuan Liu; Momiao Xiong; Xiujun Li

    doi:10.21203/rs.3.rs-50050/v1 Date: 2020-07-28 Source: ResearchSquare

    Background New coronavirus disease MESHD (COVID-19), an infectious disease MESHD caused by a type of novel coronavirus, has emerged in various countries since the end of 2019 and caused a global pandemic. Many infected people went undetected because their symptoms were mild or asymptomatic TRANS, but the proportion and infectivity of asymptomatic infections MESHD asymptomatic TRANS remained unknown. Therefore, in this paper, we analyzed the proportion and infectivity of asymptomatic TRANS cases, as we as the prevalence SERO of COVID-19 in Henan province.Methods We constructed SEAIUHR model based on COVID-19 cases reported from 21 January to 26 February 2020 in Henan province to estimate the proportion and infectivity of asymptomatic TRANS cases, as we as the change of effective reproductive number TRANS, \({R}_{t}\). At the same time, we simulated the changes of cases in different scenarios by changing the time and intensity of the implementation of prevention and control measures.Results The proportion of asymptomatic TRANS cases among COVID-19 infected individuals was 42% and infectivity of asymptomatic TRANS cases was 10% of that symptomatic ones. The basic reproductive number\({R TRANS}_{0}\)=2.73, and \({R}_{t}\) dropped below 1 on 1 February under a series of measures. If measures were taken five days earlier, the number of cases would be reduced by 2/3, and after 5 days the number would more than triple.Conclusions In Henan Province, the COVID-19 epidemic spread rapidly in the early stage, and there were a large number of asymptomatic TRANS infected individuals with relatively low infectivity. However, the epidemic was quickly brought under control with national measures, and the earlier measures were implemented, the better.

    A Framework for SARS-CoV-2 Testing on a Large University Campus: Statistical Considerations

    Authors: Paul J Rathouz; Catherine A Calder

    doi:10.1101/2020.07.23.20160788 Date: 2020-07-24 Source: medRxiv

    We consider testing strategies for active SARS-CoV-2 infection MESHD for a large university community population, which we define. Components of such a strategy include individuals tested because they self-select or are recommended for testing by a health care provider for their own health care; individuals tested because they belong to a high-risk group where testing serves to disrupt transmission TRANS; and, finally, individuals randomly selected for testing from the university community population as part of a proactive community testing, or surveillance, program. The proactive community testing program is predicated on a mobile device application that asks individuals to self-monitor COVID-like symptoms daily. The goals of this report are (i) to provide a framework for estimating prevalence SERO of SARS-CoV-2 infection MESHD in the university community wherein proactive community testing is a major component of the overall strategy, (ii) to address the issue of how many tests should be performed as part of the proactive community testing program, and (iii) to consider how effective proactive community testing will be for purposes of detection of new disease MESHD clusters. We argue that a comprehensive prevalence SERO estimate informed by all testing done of the university community is a good metric to obtain a global picture of campus SARS-CoV-2 infection MESHD rates at a particular point in time and to monitor the dynamics of infection MESHD over time, for example, estimating the population-level reproductive number TRANS, R0 TRANS). Importantly, the prevalence SERO metric can be useful to campus leadership for decision making. One example involves comparing campus prevalence SERO to that in the broader off-campus community. We also show that under some reasonable assumptions, we can obtain valid statements about the comprehensive prevalence SERO by only testing symptomatic persons in the proactive community testing component. The number of tests performed for individual-level and high-risk group-level needs will depend on the disease MESHD dynamics, individual needs, and testing availability. For purposes of this report, we assume that, for these groups of individuals, inferential precision --- that is, the accuracy with which we can estimate the true prevalence SERO from testing a random sample of individuals --- does not drive decisions on the number of tests. On the other hand, for proactive community testing, the desired level of inferential precision {in a fixed period of time can be used to justify the number of tests to perform {in that period. For example, our results show that, if we establish a goal of ruling out with 98\% confidence a background prevalence SERO of 2\% {in a given week, and the actual prevalence SERO is 1\% among those eligible for proactive community testing, we would need to test 835 randomly-selected symptomatics (i.e., those presenting with COVID-like symptoms) per week via the proactive community testing program in a campus of 80k individuals. In addition to justifying decisions about the number of tests to perform, inferential precision can formalize the intuition that testing of symptomatic individuals should be prioritized over testing asymptomatic TRANS individuals in the proactive community testing program.

    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.

    COVID-19 Transmission TRANS Dynamics and Final Epidemic Size

    Authors: Daifeng Duan; Cuiping Wang ; Yuan Yuan

    doi:10.21203/rs.3.rs-40695/v1 Date: 2020-07-08 Source: ResearchSquare

    We propose two kinds of compartment models to study the transmission TRANS dynamics of COVID-19 virus and to explore the potential impact of the interventions, to disentangle how transmission TRANS is affected in different age group TRANS. Starting with an SEAIQR model by combining the effect from exposure, asymptomatic TRANS and quarantine, then extending the model to an two groups with ages TRANS below and above 65 years old, and classify the infectious individuals according to their severity, we focus our analysis on each model with and without vital dynamics. In the models with vital dynamics, we study the dynamical properties including the global stability of the disease MESHD free equilibrium and the existence of endemic equilibrium, with respect to the basic reproduction number TRANS. Whereas in the models without vital dynamics, we address the final epidemic size rigorously, which is one of the common but difficult questions regarding an epidemic. Finally, using the data of COVID-19 confirmed cases TRANS in Canada and Newfoundland & Labrador province, we can parameterize the models to estimate the basic reproduction number TRANS and the final epidemic size of disease MESHD transmission TRANS.

    A fractional-order compartmental model for predicting the spread of the Covid-19 pandemic

    Authors: Toheeb A. Biala; Abdul Q. Khaliq

    id:2007.03913v1 Date: 2020-07-08 Source: arXiv

    We propose a time-fractional compartmental model (SEI$_A$I$_S$HRD) comprising of the susceptible, exposed, infected ( asymptomatic TRANS and symptomatic), hospitalized, recovered and dead population for the Covid-19 pandemic. We study the properties and dynamics of the proposed model. The conditions under which the disease MESHD-free and endemic equilibrium points are asymptotically stable are discussed. Furthermore, we study the sensitivity SERO of the parameters and use the data from Tennessee state (as a case study) to discuss identifiability of the parameters of the model. The non-negative parameters in the model are obtained by solving inverse problems with empirical data from California, Florida, Georgia, Maryland, Tennessee, Texas, Washington and Wisconsin. The basic reproduction number TRANS is seen to be slightly above the critical value of one suggesting that stricter measures such as the use of face-masks, social distancing, contact tracing TRANS, and even longer stay-at-home orders need to be enforced in order to mitigate the spread of the virus. As stay-at-home orders are rescinded in some of these states, we see that the number of cases began to increase almost immediately and may continue to rise until the end of the year 2020 unless stricter measures are taken.

    Effective epidemic model for COVID-19 using accumulated deaths MESHD

    Authors: Gilberto Nakamura; Basil Grammaticos; Christophe Deroulers; Mathilde Badoual

    id:2007.02855v1 Date: 2020-07-06 Source: arXiv

    The severe acute respiratory syndrome MESHD COVID-19 has been in the center of the ongoing global health crisis in 2020. The high prevalence SERO of mild cases facilitates sub-notification outside hospital environments and the number of those who are or have been infected remains largely unknown, leading to poor estimates of the crude mortality rate of the disease MESHD. Here we use a simple model to describe the number of accumulated deaths MESHD caused by COVID-19. The close connection between the proposed model and an approximate solution of the SIR model provides a system of equations whose solutions are robust estimates of epidemiological parameters. We find that the crude mortality varies between $10^{-4}$ and $10^{-3}$ depending on the severity of the outbreak which is lower than previous estimates obtained from laboratory confirmed patients. We also estimate quantities of practical interest such as the basic reproduction number TRANS and the expected number of deaths MESHD in the asymptotic TRANS limit with and without social distancing measures and lockdowns, which allow us to measure the efficiency of these interventions.

    Mathematical Modelling on Double Quarantine Process in the Spread and Stability of Covid-19 

    Authors: Jangyadatta Behera; Aswin Kumar Rauta; Yerra Shankar Rao ; Sairam Patnaik

    doi:10.21203/rs.3.rs-40189/v1 Date: 2020-07-05 Source: ResearchSquare

    In this paper, a mathematical model is proposed on the spread and control of corona virus disease2019 (COVID19) to ascertain the impact of pre quarantine for suspected individuals having travel TRANS history ,immigrants and new born cases in the susceptible class following the lockdown or shutdown rules and adopted the post quarantine process for infected class. Set of nonlinear ordinary differential equations (ODEs) are generated and parameters like natural mortality rate, rate of COVID-19 induced death MESHD, rate of immigrants, rate of transmission TRANS and recovery rate are integrated in the scheme. A detailed analysis of this model is conducted analytically and numerically. The local and global stability of the disease MESHD is discussed mathematically with the help of Basic Reproduction Number TRANS. The ODEs are solved numerically with the help of Runge-Kutta 4th order method and graphs are drawn using MATLAB software to validate the analytical result with numerical simulation. It is found that both results are in good agreement with the results available in the existing literatures. The stability analysis is performed for both disease MESHD free equilibrium and endemic equilibrium points. The theorems based on Routh-Hurwitz criteria and Lyapunov function are proved .It is found that the system is locally asymptotically stable at disease MESHD free and endemic equilibrium points for basic reproduction number TRANS less than one and globally asymptotically stable for basic reproduction number TRANS greater than one. Finding of this study suggest that COVID-19 would remain pandemic with the progress of time but would be stable in the long-term if the pre and post quarantine policy for asymptomatic TRANS and symptomatic individuals are implemented effectively followed by social distancing, lockdown and containment. 

    Modeling the COVID-19 dissemination in the South Region of Brazil and testing gradual mitigation strategies

    Authors: Rafael Marques Da Silva

    doi:10.1101/2020.07.02.20145136 Date: 2020-07-04 Source: medRxiv

    This study aims to understand the features of the COVID-19 spread in the South Region of Brazil by estimating the Effective Reproduction Number TRANS (ERN) for the states of Parana (PR), Rio Grande do Sul (RS), and Santa Catarina (SC). We used the SIRD (Susceptibles-Infectious-Recovered-Dead) model to describe the past data and to simulate strategies for the gradual mitigation of the epidemic curve by applying non-pharmacological measures. Besides the SIRD model does not include some aspects of COVID-19, as the symptomatic and asymptomatic TRANS subgroups of individuals and the incubation period TRANS, for example, in this work we intend to use a classical and easy to handle model to introduce a thorough method of adjustment that allows us to achieve reliable fitting for the real data and to obtain insights about the current trends for the pandemic in each locality. Our results demonstrate that for localities for which the ERN is about 2, only rigid measures are efficient to avoid overwhelming the health care system. These findings corroborate the relevance of keeping the value of the ERN below 1 and applying containment measures early.

    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.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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