Corpus overview


Overview

MeSH Disease

Human Phenotype

Falls (3)

Pneumonia (1)


Transmission

Seroprevalence
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    Long, thin transmission chains TRANS of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2 MESHD) may go undetected for several weeks at low to moderate reproductive numbers TRANS: Implications for containment and elimination strategy

    Authors: Gerry F Killeen; Deanna C Clemmer; Justin B Cox; Yetunde I Kayode; Victoria Zoccoli-Rodriguez; Harry E Taylor; Timothy P Endy; Joel R Wilmore; Gary Winslow; Sarah Tschudin-Sutter; Simon Fuchs; Julia Anna Bielicki; Hans Pargger; Martin Siegemund; Christian H. Nickel; Roland Bingisser; Michael Osthoff; Stefano Bassetti; Rita Schneider-Sliwa; Manuel Battegay; Hans H. Hirsch; Adrian Egli

    doi:10.1101/2020.09.04.20187948 Date: 2020-09-05 Source: medRxiv

    Especially at low to moderate reproductive numbers TRANS, the generally mild, non-specific symptomology of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) allows long MESHD, thin transmission chains TRANS to go undetected by passive surveillance over several weeks. This phenomenon has important implications: (1) Surveillance becomes less sensitive and reliable as an indicator of freedom from infection at the low reproductive numbers TRANS required to achieve elimination end points, passive surveillance systems may need to document an absence of new cases for at least a month to establish certainty of elimination. (2) Reproductive numbers TRANS should be kept as low as possible throughout such follow up periods without confirmed cases TRANS, to ensure such long, thin, undetected transmission chains TRANS all collapse before restrictions are eased and reproduction numbers TRANS are allowed to rebound. (3) While contact tracing TRANS systems may be highly effective when applied to large clusters in foci of elevated transmission TRANS where wide, rapidly expanding transmission chains TRANS are detected within two viral generations, large fractions of community transmission TRANS occurring through thinner, more extended transmission chains TRANS at lower reproductive numbers TRANS are often be too long to trace TRANS retrospectively and will be underrepresented in surveillance data. (4) Wherever surveillance systems are weak and/or younger age groups TRANS with lower rates of overt symptoms dominate transmission TRANS, containment effectiveness of contact tracing TRANS and isolation may be more severely limited, even at the higher reproduction numbers TRANS associated with larger outbreaks. While, contact tracing TRANS and isolation will remain vital for at least partially containing larger outbreaks, containment and elimination of SARS-CoV-2 will have to rely primarily upon the more burdensome and presumptive population-wide prevention measures that have proven so effective thus far against community transmission TRANS. Furthermore, these will have to be sustained at a much more stringent level and for longer periods after the last detected case than was necessary for SARS-CoV-1.

    Modeling the effects of prosocial awareness on COVID-19 dynamics: A case study on Colombia

    Authors: Indrajit Ghosh

    id:2008.09109v1 Date: 2020-08-20 Source: arXiv

    The ongoing COVID-19 pandemic caused by SARS-CoV-2 virus MESHD, a highly contagious virus, affected most of the countries of Earth. COVID-19 is causing obstacles for public health organizations and is affecting almost every aspect of human life. It has become an epidemic outbreak with more than 22 million confirmed infections TRANS and above 750 thousand deaths worldwide. Mathematical models may help to explore the transmission TRANS dynamics and control of COVID-19 in the absence of an effective medicine or ready-to-use vaccine. In this study, we consider a mathematical model on COVID-19 transmission TRANS with the prosocial awareness effect. The proposed model can have four equilibrium states based on different parametric conditions. The system has an awareness free, disease-free equilibrium which is locally asymptotically stable. The global stability conditions for this equilibrium is also studied. The basic reproduction number TRANS, $ R_0 TRANS$, is calculated using the next-generation matrix method. Using Lyapunov function theory and LaSalle Invariance Principle, the DFE is shown globally asymptotically stable under some parametric conditions. The existence of awareness free, endemic equilibrium and endemic equilibrium is presented. We have calibrated our proposed model parameters to fit daily cases and deaths from Colombia. Using the estimated parameters, we assess the impact of prosocial awareness during the outbreak and compare this strategy with popular control measures.

    Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020

    Authors: Christian L Althaus; Daniel Probst; Anthony Hauser; Julien L Riou

    doi:10.1101/2020.07.21.20158014 Date: 2020-07-25 Source: medRxiv

    AIM: In late February and early March 2020, Switzerland experienced rapid growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections MESHD with 30,243 confirmed cases TRANS and 1,860 deaths as of 10 May 2020. The sequential introduction of non-pharmaceutical interventions (NPIs) resulted in successful containment of the epidemic. A better understanding of how the timing of implementing NPIs influences the dynamics and outcome of SARS-CoV-2 epidemics will be crucial for the management of a potential resurgence in Switzerland. METHODS: We developed a dynamic transmission TRANS model that describes infection MESHD, hospitalization, recovery and death MESHD due to SARS-CoV-2 in Switzerland. Using a maximum likelihood framework, we fitted the model to aggregated daily numbers of hospitalized patients, ICU occupancy MESHD and death MESHD from 25 February to 10 May 2020. We estimated critical parameters of SARS-CoV-2 transmission TRANS in Switzerland and explored counterfactual scenarios of an earlier and later implementation of NPIs. RESULTS: We estimated the basic reproduction number TRANS R0 TRANS = 2.61 (95% compatibility interval, CI: 2.51-2.71) during the early exponential phase of the SARS-CoV-2 epidemic MESHD in Switzerland. After the implementation of NPIs, the effective reproduction number TRANS approached Re = 0.64 (95% CI: 0.61-0.66). Based on the observed doubling times of the epidemic before and after the implementation of NPIs, we estimated that one week of early exponential spread required 3.1 weeks (95% CI: 2.8-3.3 weeks) of 'lockdown' to reduce the number of infections to the same level. Introducing the same sequence of NPIs one week earlier or later would have resulted in substantially lower (399, 95% prediction interval, PI: 347-458) and higher (8,683, 95% PI: 8,038-9,453) numbers of deaths, respectively. CONCLUSIONS: The introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths in Switzerland. Early implementation of NPIs during SARS-CoV-2 outbreaks can reduce the number of deaths MESHD and the necessary duration of strict control measures considerably.

    Undocumented infectives in the Covid-19 pandemic

    Authors: Maurizio Melis; Roberto Littera

    doi:10.1101/2020.07.09.20149682 Date: 2020-07-11 Source: medRxiv

    Background. A crucial role in epidemics is played by the number of undetected infective individuals who continue to circulate and spread the disease TRANS. Epidemiological investigations and mathematical models have revealed that the rapid diffusion of Covid-19 can mostly be attributed to the large percentage of undocumented infective individuals who escape testing. Methods. The dynamics of an infection can be described by the SIR model, which divides the population into susceptible (S), infective (I) and removed (R) subjects. In particular, we exploited the Kermack and McKendrick epidemic MESHD model which can be applied when the population is much larger than the fraction of infected subjects. Results. We proved that the fraction of undocumented infectives, in comparison to the total number of infected subjects, is given by 1-1/ R0 TRANS , where R0 TRANS is the basic reproduction number TRANS. Its mean value R0=2.10 (2.09-2.11) in three Italian regions for the Covid-19 epidemic yielded a percentage of undetected infectives of 52.4% (52.2% - 52.6%) compared to the total number of infectives. Conclusions. Our results, straightforwardly obtained from the SIR model, highlight the role played by undetected carriers TRANS in the transmission TRANS and spread of the SARS-CoV-2 infection MESHD. Such evidence strongly recommends careful monitoring of the infective population and ongoing adjustment of preventive measures for disease control until a vaccine becomes available.

    Reopening universities during the COVID-19 pandemic: A testing strategy to minimize active cases and delay outbreaks

    Authors: Lior Rennert; Corey Andrew Kalbaugh; Lu Shi; Christopher McMahan

    doi:10.1101/2020.07.06.20147272 Date: 2020-07-07 Source: medRxiv

    Background: University campuses present an ideal environment for viral spread and are therefore at extreme risk of serving as a hotbed for a COVID-19 outbreak. While active surveillance throughout the semester such as widespread testing, contact tracing TRANS, and case isolation, may assist in detecting and preventing early outbreaks, these strategies will not be sufficient should a larger outbreak occur. It is therefore necessary to limit the initial number of active cases at the start of the semester. We examine the impact of pre-semester NAT testing on disease spread TRANS in a university setting. Methods: We implement simple dynamic transmission TRANS models of SARS-CoV-2 infection MESHD to explore the effects of pre-semester testing strategies on the number of active infections MESHD and occupied isolation beds throughout the semester. We assume an infectious period TRANS of 3 days and vary R0 TRANS to represent the effectiveness of disease mitigation strategies throughout the semester. We assume the prevalence SERO of active cases at the beginning of the semester is 5%. The sensitivity SERO of the NAT test is set at 90%. Results: If no pre-semester screening is mandated, the peak number of active infections occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections when effective mitigation strategies ( R0 TRANS = 1.25) are implemented to over 15,000 active infections for less effective strategies ( R0 TRANS = 3). When one NAT test is mandated within one week of campus arrival, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak to 40 days and 17 days, respectively, and result in peak size ranging from 1,000 to over 15,000 active infections. When two NAT tests are mandated, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak through the end of fall HP semester and 20 days, respectively, and result in peak size ranging from less than 1,000 to over 15,000 active infections. If maximum occupancy of isolation beds is set to 2% of the student population, then isolation beds would only be available for a range of 1 in 2 confirmed cases TRANS ( R0 TRANS = 1.25) to 1 in 40 confirmed cases TRANS ( R0 TRANS = 3) before maximum occupancy is reached. Conclusion: Even with highly effective mitigation strategies throughout the semester, inadequate pre-semester testing will lead to early and large surges of the disease and result in universities quickly reaching their isolation bed capacity. We therefore recommend NAT testing within one week of campus return. While this strategy is sufficient for delaying the timing of the outbreak, pre-semester testing would need to be implemented in conjunction with effective mitigation strategies to reduce the outbreak size.

    The first 100 days of SARS-CoV-2 control in Vietnam

    Authors: Thai Quang Pham; Maia Rabaa; Luong Huy Duong; Tan Quang Dang; Quang Dai Tran; Ha Linh Quach; Ngoc Anh Hoang; Dinh Cong Phung; Nghia Duy Ngu; Anh Tu Tran; Ngoc Quang La; My Phuc Tran; Chau Vinh; Khanh Cong Nguyen; Duc Anh Dang; Duong Nhu Tran; Guy E Thwaites; H Rogier van Doorn; Marc Choisy; OUCRU COVID-19 Research Group

    doi:10.1101/2020.05.12.20099242 Date: 2020-05-16 Source: medRxiv

    Background: One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23rd, 270 cases have been confirmed TRANS, with no deaths. We describe the control measures used and their relationship with imported and domestically-acquired case numbers. Methods: Data on the first 270 SARS-CoV-2 infected MESHD cases and the timing and nature of control measures were captured by Vietnam's National Steering Committee for COVID-19 response. Apple and Google mobility data provided population movement proxies. Serial intervals TRANS were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission TRANS events and time-varying reproduction numbers TRANS. Results: After the first confirmed case TRANS on January 23rd, the Vietnamese Government initiated mass communications measures, contact tracing TRANS, mandatory 14-day quarantine, school and university closures, and progressive flight restrictions. A national lockdown was implemented between April 1st and 22nd. Around 200,000 people were quarantined and 266,122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections were asymptomatic TRANS. 21 developed severe disease, with no deaths. The serial interval TRANS was 3.24 days, and 27.5% (95% confidence interval, 15.7%-40.0%) of transmissions TRANS occurred pre-symptomatically. Limited transmission TRANS amounted to a maximum reproduction number TRANS of 1.15 (95% confidence interval, 0.37-2.36). No community transmission TRANS has been detected since April 15th. Conclusions: Vietnam has controlled SARS-CoV-2 spread through the early introduction of communication, contact-tracing TRANS, quarantine, and international travel TRANS restrictions. The value of these interventions is supported by the high proportion of asymptomatic TRANS cases and imported cases, and evidence for substantial pre-symptomatic transmission TRANS.

    The Coronavirus 2019 pandemic in Canada: the impact of public health interventions on the course of the outbreak in Alberta and other provinces

    Authors: Mohamed Mahsin; Seungwon Lee; David Vickers; Alexis Guigue; Tyler Williamson; Hude Quan; Robert Ross Quinn; Pietro Ravani

    doi:10.1101/2020.05.09.20096636 Date: 2020-05-13 Source: medRxiv

    Background: The SARS-CoV-2 disease MESHD 2019 (COVID-19) pandemic has spread across the world with varying impact on health systems and outcomes. We assessed how the type and timing of public- health interventions impacted the course of the outbreak in Alberta and other Canadian provinces. Methods: We used publicly-available data to summarize rates of laboratory data and mortality in relation to measures implemented to contain the outbreak and testing strategy. We estimated the transmission TRANS potential of SARS-CoV-2 before the state of emergency declaration for each province ( R0 TRANS) and at the study end date (Rt). Results: The first cases were confirmed TRANS in Ontario (January 25) and British Columbia (January 28). All provinces implemented the same health-policy measures between March 12 and March 30. Alberta had a higher percentage of the population tested (3.8%) and a lower mortality rate (3/100,000) than Ontario (2.6%; 11/100,000) or Quebec (3.1%; 31/100,000). British Columbia tested fewer people (1.7%) and had similar mortality as Alberta. Data on provincial testing strategies were insufficient MESHD to inform further analyses. Mortality rates increased with increasing rates of lab- confirmed cases TRANS in Ontario and Quebec, but not in Alberta. R0 TRANS was similar across all provinces, but varied widely from 2.6 (95% confidence intervals 1.9-3.4) to 6.4 (4.3-8.5), depending on the assumed time interval between onset of symptoms TRANS in a primary and a secondary case TRANS ( serial interval TRANS). The outbreak is currently under control in Alberta, British Columbia and Nova Scotia MESHD (Rt <1). Interpretation: COVID-19-related health outcomes varied by province despite rapid implementation of similar health-policy interventions across Canada. Insufficient information about provincial testing strategies and a lack of primary data on serial interval TRANS are major limitations of existing data on the Canadian COVID-19 outbreak.

    Global prediction of unreported SARS-CoV2 infection MESHD from observed COVID-19 cases

    Authors: Carson C Chow; Joshua C Chang; Richard C Gerkin; Shashaank Vattikuti

    doi:10.1101/2020.04.29.20083485 Date: 2020-05-05 Source: medRxiv

    Summary: Estimation of infectiousness and fatality of the SARS-CoV-2 virus in the COVID-19 global pandemic is complicated by ascertainment bias resulting from incomplete and non-representative samples of infected individuals. We developed a strategy for overcoming this bias to obtain more plausible estimates of the true values of key epidemiological variables. We fit mechanistic Bayesian latent-variable SIR models to confirmed COVID-19 cases, deaths, and recoveries, for all regions (countries and US states) independently. Bayesian averaging over models, we find that the raw infection incidence rate underestimates the true rate by a factor, the case ascertainment ratio CARt that depends upon region, and show how CARt changes over time. At the regional onset of COVID-19, the predicted global median for each case confirmed TRANS was 13 infections unreported (CARt = 0.07 C.I. (0.02, 0.4)). As the infection spread, the median CARt rose to 9 unreported cases for every one diagnosed as of April 15, 2020 (CARt = 0.1 C.I. (0.02, 0.5)). We also estimate that the median global initial reproduction number TRANS R0 TRANS is 3.3 (C.I (1.5, 8.3)) and the total infection fatality rate near the onset is 0.17% (C.I. (0.05%, 0.9%)). However the time-dependent reproduction number TRANS Rt and infection fatality rate as of April 15 were 1.2 (C.I. (0.6, 2.5)) and 0.8% (C.I. (0.2%,4%)), respectively. We find that there is great variability between country- and state-level values. Our estimates are consistent with recent serological estimates of cumulative infections for the state of New York, but inconsistent with claims that very large fractions of the population have already been infected in most other regions. For most regions, our estimates imply a great deal of uncertainty about the current state and trajectory of the epidemic.

    Mathematical Modeling to Estimate the Reproductive Number TRANS and the Outbreak Size of COVID-19: The case of India and the World

    Authors: Durgesh Nandini Sinha

    doi:10.21203/rs.3.rs-26261/v1 Date: 2020-04-30 Source: ResearchSquare

    Coronavirus disease (COVID-19) has become a global pandemic with more than 218,000 deaths in 211 different countries around the world. Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) is the virus responsible for this deadliest disease. This paper describes a mathematical model for India, a country with the second highest population in the world with an extremely high population density of about 464 people per km2. This disease has multiphasic actions and reaction mode and our model SEIAQIm is based on six compartmental groups in the form of susceptible, exposed, infectious, asymptomatic TRANS, quarantine, and recovered immune factions. Latin Hypercube Sampling Partial Rank Correlation Coefficient method was used for the data analysis and model fitting. According to our model, India would reach its basic reproduction number TRANS R0=0.97 on May 14, 2020 with a total number of 73,800 estimated cases. Further, this study also equates the world's situation using the same model system and predicts by May 7, 2020 with a total number of 3,772,000 estimated confirmed cases TRANS. Moreover, the current mathematical model highlights the importance of social distancing as an effective method of containing spread of COVID-19.

    Basic epidemiological parameter values from data of real-world in mega-cities: the characteristics of COVID-19 in Beijing, China

    Authors: Xiaoli Wang; Yang Pan; Daitao Zhang; Lijuan Chen; Lei Jia; Xinyu Li; Peng Yang; Quanyi Wang; C. Raina Macintyre

    doi:10.21203/rs.3.rs-23937/v2 Date: 2020-04-20 Source: ResearchSquare

    Background. With the spread of SARS-CoV-2 worldwide, understanding the basic epidemiological parameter values of COVID-19 from real-world data in mega-cities is essential for disease prevention and control. Methods. To investigate the epidemiological parameters in SARS-CoV-2 infected MESHD cases in Beijing, we studied all confirmed cases TRANS and close contacts TRANS in Beijing from Jan 1st to Apr 3rd 2020. The epidemiological and virological characteristics of SARS-CoV-2 were analyzed.Results. A total of 602 cases were positive for SARS-CoV-2, including 585 confirmed patients and 17 asymptomatic TRANS infections. The imported cases were mainly from Wuhan initially and then from abroad. Among 585 confirmed case TRANS-patients, the median age TRANS was 39 years old. The mean incubation period TRANS was 6.3 days. The secondary attack rate TRANS among households was higher than social contacts (15.6 vs 4.6%). The secondary attack rate TRANS of healthcare workers (HCWs) was higher than non-HCWs’ (7.3 vs 4.2%). The basic reproduction number TRANS was 2.0, and the average serial interval TRANS was 7.6 days. No significant genetic variant was identified.Conclusions. The transmissibility TRANS of SARS-CoV-2 was relatively high, especially among households and from HCWs, which draws specific public health attention. So far, no evidence of widespread circulation of SARS-CoV-2 in communities in Beijing was found.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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