Corpus overview


Overview

MeSH Disease

Human Phenotype

Falls (10)


Transmission

Seroprevalence
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    An Agent Based Modeling of COVID-19: Validation, Analysis, and Recommendations

    Authors: Md. Salman Shamil; Farhanaz Farheen; Nabil Ibtehaz; Irtesam Mahmud Khan; M. Sohel Rahman

    doi:10.1101/2020.07.05.20146977 Date: 2020-07-08 Source: medRxiv

    The Coronavirus disease 2019 (COVID-19) has resulted in an ongoing pandemic worldwide. Countries have adopted Non-pharmaceutical Interventions (NPI) to slow down the spread. This study proposes an Agent Based Model that simulates the spread of COVID-19 among the inhabitants of a city. The Agent Based Model can be accommodated for any location by integrating parameters specific to the city. The simulation gives the number of daily confirmed cases TRANS. Considering each person as an agent susceptible to COVID-19, the model causes infected individuals to transmit the disease via various actions performed every hour. The model is validated by comparing the simulation to the real data of Ford county, Kansas, USA. Different interventions including contact tracing TRANS are applied on a scaled down version of New York city, USA and the parameters that lead to a controlled epidemic are determined. Our experiments suggest that contact tracing TRANS via smartphones with more than 60% of the population owning a smartphone combined with a city-wide lock-down results in the effective reproduction number TRANS (Rt) to fall HP below 1 within three weeks of intervention. In the case of 75% or more smartphone users, new infections are eliminated and the spread is contained within three months of intervention. Contact tracing TRANS accompanied with early lock-down can suppress the epidemic growth of COVID-19 completely with sufficient smartphone owners. In places where it is difficult to ensure a high percentage of smartphone ownership, tracing TRANS only emergency service providers during a lock-down can go a long way to contain the spread. No particular funding was available for this project.

    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.

    Impact of public health measures to control SARS-CoV-2Outbreak: a data-driven analysis

    Authors: Hugues Turbe; Mina Bjelogrlic; Arnaud Robert; Christophe Gaudet-Blavignac; Christian Lovis; Jean-Philippe Goldman

    doi:10.1101/2020.06.10.20126870 Date: 2020-06-11 Source: medRxiv

    With the rapid spread of the SARS-CoV-2 virus since Fall HP 2019, public health confinement measures to contain the propagation of the pandemic are taken. Our method to estimate the reproductive number TRANS using Bayesian inference with time-dependent priors enhances previous approaches by considering a dynamic prior continuously updated as restrictive measures and comportments within the society evolve. In addition, to allow direct comparison between reproductive number TRANS and introduction of public health measures in a specific country, the infection dates are inferred from daily confirmed cases TRANS and death MESHD with the mean time between a case being declared as positive and its death estimated on 1430 cases at 10.7 days. The evolution of the reproductive rate in combination with the stringency index is analyzed on 31 European countries. We show that most countries required tough state interventions with a stringency index equal to 83.6 out of 100 to reduce the reproductive number TRANS below one and control the progression of the epidemic. In addition, we show a direct correlation between the time taken to introduce restrictive measures and the time required to contain the spread of the epidemic with a median time of 8 days. Our analysis reinforces the importance of having a fast response with a coherent and comprehensive set of confinement measures to control the epidemic. Only combinations of non-pharmaceutical interventions (NPIs) have shown to be effective.

    China’s effective control and other countries’ uncharted challenge against COVID-19: an epidemiological and modelling study

    Authors: Lingling Zheng; Qin Kang; Xiujuan Chen; Shuai Huang; Dong Liu; Weiyao Liao; Huimin Xia; Jinling Tang; Huiying Liang

    doi:10.21203/rs.3.rs-32370/v1 Date: 2020-05-29 Source: ResearchSquare

    Objective: In this study, we use the time-dependent reproduction number TRANS (Rt) to comprise the COVID transmissibility TRANS across different countries.Methods: We used data from Jan 20, 2019, to Feb 29, 2020, on the number of newly confirmed cases TRANS, obtained from the reports published by the CDC, to infer the incidence of infectious over time. A two-step procedure was used to estimate the Rt. The first step used data on known index- secondary cases TRANS pairs, from publicly available case reports, to estimate the serial interval TRANS distribution. The second step estimated the Rt jointly from the incidence data and the information data in the first step. Rt was then used to simulate the epidemics across all major cities in China and typical countries worldwide. Results: Based on a total of 126 index- secondary cases TRANS pairs from 4 international regions, we estimated that the serial interval TRANS for SARS-2-CoV was 4.18 (IQR 1.92 – 6.65) days. Domestically, Rt of China, Hubei province, Wuhan had fallen HP below 1.0 on 9 Feb, 10 Feb and 13 Feb (Rt were 0.99±0.02, 0.99±0.02 and 0.96±0.02), respectively. Internationally, as of 26 Feb, statistically significant periods of COVID spread (Rt >1) were identified for most regions, except for Singapore (Rt was 0.92±0.17).Conclusions: The epidemic in China has been well controlled, but the worldwide pandemic has not been well controlled. Worldwide preparedness and vulnerability against COVID-19 should be regarded with more care.

    Chinese effective control and other countries uncharted challenge against COVID-19: an epidemiological and modelling study

    Authors: Lingling Zheng; Kang Qin; Xiujuan Chen; Shuai Huang; Dong Liu; Weiyao Liao; Huimin Xia; Jinling Tang; Huiying Liang

    doi:10.1101/2020.04.28.20083899 Date: 2020-05-02 Source: medRxiv

    Background: On the present trajectory, COVID is inevitably becoming a global epidemic, leading to concerns regarding the pandemic potential in China and other countries. Objective: In this study, we use the time-dependent reproduction number TRANS (Rt) to comprise the COVID transmissibility TRANS across different countries. Methods: We used data from Jan 20, 2019, to Feb 29, 2020, on the number of newly confirmed cases TRANS, obtained from the reports published by the CDC, to infer the incidence of infectious over time. A two-step procedure was used to estimate the Rt. The first step used data on known index- secondary cases TRANS pairs, from publicly available case reports, to estimate the serial interval TRANS distribution. The second step estimated the Rt jointly from the incidence data and the information data in the first step. Rt was then used to simulate the epidemics across all major cities in China and typical countries worldwide. Results: Based on a total of 126 index- secondary cases TRANS pairs from 4 international regions, we estimated that the serial interval TRANS for SARS-2-CoV was 4.18 (IQR 1.92 - 6.65) days. Domestically, Rt of China, Hubei province, Wuhan had fallen HP below 1.0 on 9 Feb, 10 Feb and 13 Feb (Rt were 0.99 {+/-} 0.02, 0.99 {+/-} 0.02 and 0.96 {+/-} 0.02), respectively. Internationally, as of 26 Feb, statistically significant periods of COVID spread (Rt >1) were identified for most regions, except for Singapore (Rt was 0.92 {+/-} 0.17). Conclusions: The epidemic in China has been well controlled, but the worldwide pandemic has not been well controlled. Worldwide preparedness and vulnerability against COVID-19 should be regarded with more care.

    A phased approach to unlocking during the COVID-19 pandemic; Lessons from trend analysis

    Authors: Michael Stedman; Mark Davies; Simon G Anderson; Mark Lunt; Arpana Verma; Adrian Heald

    doi:10.1101/2020.04.20.20072264 Date: 2020-04-24 Source: medRxiv

    With the COVID-19 pandemic leading to radical political control of social behaviour, including restricted movement outsides homes. Can more detailed analysis of the published confirmed local case data from the pandemic in England using infection ratio and comparing local level data provide a deeper understanding of the wider community infection MESHD and inform the future unlocking process. The historic daily published 78,842 confirmed cases TRANS in England up to 13/4/2020 in each of 149 Upper Tier Local Authority (UTLA) were converted to Average Daily Infection Rate (RADIR), an R-value TRANS - the number of further people infected MESHD by one infected person after their 5-day incubation and during their 5-day infectious phase, and the associated Rate of Change of Infection Rate ({delta}IR) also calculated. Results compared to look for significant variances between regions. Stepwise regression was carried out to see what local factors could be linked to the difference in local infection rates. The peak of COVID-19 infection MESHD has passed. The current RADIR is now below 1. The rate of decline is such that within 14 days it may be below 0.5. There are significant variations in the current RADIR and {delta}IR between the UTLAs, suggesting that the disease locally may be at different stages. Regression analysis across UTLAs found that the only factor that could be related to the fall HP in RADIR was an increase in the number of confirmed infection TRANS infection MESHD/1,000 population. Extrapolation of these results showed that based on assuming a link to increased immunity, unreported community infection MESHD may be over 200 times higher than the reported confirmed cases TRANS providing evidence that by the end of the second week in April 26% of the population may already have had the disease and so now have increased immunity. Linking these increased estimated infected numbers to recorded deaths indicates a possible mortality rate of 0.14%. Analysis of the current reported local case data using the infectious ratio does provide greater insight into the current levels of community infection MESHD and can be used to make better-informed decisions about the future management of restricted social behaviour and movement

    Basic reproduction number TRANS of 2019 Novel Coronavirus Disease MESHD in Major Endemic Areas of China: A latent profile analysis

    Authors: Honglv Xu; Min Yuan; Liya Ma; Meng Liu; Yi Zhang; Wenwen Liu; Hong Gan; Fangbiao Tao

    doi:10.1101/2020.04.13.20060228 Date: 2020-04-17 Source: medRxiv

    Objective: The aim of the study is to analyze the latent class of basic reproduction number TRANS ( R0 TRANS) trend of 2019 novel coronavirus disease MESHD (COVID-19) in major endemic areas of China. Methods The provinces that reported more than 500 cases of COVID-19 till February 18, 2020 were selected as the major endemic area. The Verhulst model was used to fit the growth rate of cumulative confirmed cases TRANS. The R0 TRANS of COVID-19 was calculated using the parameters of severe acute respiratory syndrome MESHD (SARS) and COVID-19, respectively. The latent class of R0 TRANS was analyzed using a latent profile analysis model. Results The median R0 TRANS calculated from SARS and COVID-19 parameters were 1.84 - 3.18 and 1.74 - 2.91, respectively. The R0 TRANS calculated from the SARS parameters was greater than that of calculated from the COVID-19 parameters (Z = -4.782 - -4.623, P < 0.01). Both R0 TRANS can be divided into three latent classes. The initial value of R0 TRANS in class 1 (Shandong Province, Sichuan Province and Chongqing Municipality) was relatively low and decreases slowly. The initial value of R0 TRANS in class 2 (Anhui Province, Hunan Province, Jiangxi Province, Henan Province, Zhejiang Province, Guangdong Province and Jiangsu Province) was relatively high and decreases rapidly. Moreover, the initial value of R0 TRANS of class 3 (Hubei Province) was between that of class 1 and class 2, but the higher level of R0 TRANS lasts longer and decreases slowly. Conclusion The results indicated that overall trend of R0 TRANS has been falling HP with the strengthening of China's comprehensive prevention and control measures for COVID-19, however, presents regional differences.

    The Estimated Time-Varying Reproduction Numbers TRANS during the Ongoing Epidemic of the Coronavirus Disease MESHD 2019 (COVID-19) in China

    Authors: Fu-Chang Hu; Fang-Yu Wen

    doi:10.1101/2020.04.11.20061838 Date: 2020-04-17 Source: medRxiv

    Background: How could we anticipate the progression of the ongoing epidemic of the coronavirus disease MESHD 2019 (COVID-19) in China? As a measure of transmissibility TRANS, we aimed to estimate concurrently the time-varying reproduction number TRANS over time during the COVID-19 epidemic in China. Methods: We extracted the epidemic data from the "Tracking the Epidemic" website of the Chinese Center for Disease Control and Prevention for the duration of January 19, 2020 and March 14, 2020. Then, we specified two plausible distributions of serial interval TRANS to apply the novel estimation method implemented in the incidence and EpiEstim packages to the data of daily new confirmed cases TRANS for robustly estimating the time-varying reproduction number TRANS in the R software. Results: The epidemic curve of daily new confirmed cases TRANS in China peaked around February 4-6, 2020, and then declined gradually, except the very high peak on February 12, 2020 owing to the added clinically diagnosed cases of the Hubei Province. Under two specified plausible scenarios for the distribution of serial interval TRANS, both curves of the estimated time-varying reproduction numbers TRANS fell HP below 1.0 around February 17-18, 2020. Finally, the COVID-19 epidemic in China abated around March 7-8, 2020, indicating that the prompt and aggressive control measures of China were effective. Conclusion: Seeing the estimated time-varying reproduction number TRANS going downhill speedily was more informative than looking for the drops in the daily number of new confirmed cases TRANS during an ongoing epidemic of infectious disease MESHD. We urged public health authorities and scientists to estimate time-varying reproduction numbers TRANS routinely during an epidemic of infectious diseases MESHD and to report them daily to the public until the end of the epidemic.

    A study of SARS-CoV-2 evolution in Italy: from early days to secondary effects after social distancing

    Authors: Marco Claudio Traini; Carla Caponi; Riccardo Ferrari; Giuseppe Vittorio De Socio

    doi:10.1101/2020.04.06.20055392 Date: 2020-04-11 Source: medRxiv

    Background: The outbreak of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) has led to 101739 confirmed cases TRANS, in Italy, as of March 30th, 2020. While the analogous event in China appears to be rather under control at the moment, the outbreaks in western countries are still at an early stage of the evolution. Italy at present is playing a major role in understanding transmission TRANS dynamics of these new infections and evaluating the effectiveness of control measures in a western social context. Methods: We combined a quarantined models with early stage evolution data in Italy (during February 20th - March 30th) to predict longer term evolution (March 30th, on ...) within different control measures. Due to significant variations in the control strategies, which have been changing over time, and thanks to the introduction of detection technologies leading to faster confirmation of the SARS-CoV-2 infections MESHD, we made use of time-dependent contact and diagnose rates to estimate when the effective daily reproduction ratio can fall HP below 1. Within the same framework we analyze the possible event of a secondary infection MESHD after relaxing the isolation measures. Outcomes and interpretation: We study two simplified scenarios compatible with the observation data and the effects of two stringent measures on the evolution of the epidemic. On one side the contact rate must obviously kept as low as possible, but it is also clear that, in a modern developed country, it cannot fall HP under certain minimum levels and for long time. The complementary parameter tuned is the transition rate of the symptomatic infected individuals to the quarantined class, a parameter {delta}_I connected with the time t_I=1/{delta}_I needed to perform diagnostic tests. Within the conditions of the outbreak in Italy this time must fall HP under 12-8 hours in order to make the reproduction number TRANS less than 1 to minimize the case numbers. Moreover we show how the same parameter plays an even more relevant role in mitigating the effects of a possible secondary infection event.

    Preliminary prediction of the basic reproduction number TRANS of the Wuhan novel coronavirus 2019-nCoV

    Authors: Tao Zhou; Quanhui Liu; Zimo Yang; Jingyi Liao; Kexin Yang; Wei Bai; Xin Lü; Wei Zhang

    id:2001.10530v2 Date: 2020-01-28 Source: arXiv

    Objectives.--To estimate the basic reproduction number TRANS of the Wuhan novel coronavirus (2019-nCoV). Methods.--Based on the susceptible-exposed-infected-removed (SEIR) compartment model and the assumption that the infectious cases with symptoms occurred before January 25, 2020 are resulted from free propagation without intervention, we estimate the basic reproduction number TRANS of 2019-nCoV according to the reported confirmed cases TRANS and suspected cases, as well as the theoretical estimated number of infected MESHD cases by other research teams, together with some epidemiological determinants learned from the severe acute respiratory syndrome MESHD. Results The basic reproduction number TRANS falls HP between 2.8 to 3.3 by using the real-time reports on the number of 2019-nCoV infected cases from People's Daily in China, and falls HP between 3.2 and 3.9 on the basis of the predicted number of infected cases from colleagues. Conclusions.--The early transmission TRANS ability of 2019-nCoV is closed to or slightly higher than SARS. It is a controllable disease with moderate-high transmissibility TRANS. Timely and effective control measures are needed to suppress the further transmissions TRANS. Notes Added.--Using a newly reported epidemiological determinants for early 2019-nCoV, the estimated basic reproduction number TRANS is in the range [2.2,3.0].

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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