Corpus overview


Overview

MeSH Disease

Human Phenotype

Falls (6)

Fever (3)

Anxiety (2)

Cough (2)

Confusion (1)


Transmission

Seroprevalence
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    Isolation Considered Epidemiological Model for the Prediction of COVID-19 Trend in Tokyo, Japan

    Authors: Motoaki Utamura; Makoto Koizumi; Seiichi Kirikami

    doi:10.1101/2020.07.31.20165829 Date: 2020-07-31 Source: medRxiv

    Background: Coronavirus Disease MESHD 2019 (COVID19) currently poses a global public health threat. Although no exception, Tokyo, Japan was affected at first by only a small epidemic. Medical collapse nevertheless nearly happened because no predictive method existed for counting patients. A standard SIR epidemiological model and its derivatives predict susceptible, infectious, and removed (recovered/ deaths MESHD) cases but ignore isolation of confirmed cases TRANS. Predicting COVID19 trends with hospitalized and infectious people in field separately is important to prepare beds and develop quarantine strategies. Methods: Time-series COVID19 data from February 28 to May 23, 2020 in Tokyo were adopted for this study. A novel epidemiological model based on delay differential equation was proposed. The model can evaluate patients in hospitals and infectious cases in the field. Various data such as daily new cases, cumulative infections MESHD, patients in hospital, and PCR test positivity ratios were used to examine the model. This approach derived an alternative formulation equivalent to the standard SIR model. Its results were compared quantitatively with those of the present isolation model. Results: The basic reproductive number TRANS, inferred as 2.30, is a dimensionless parameter composed of modeling parameters. Effects of intervention to mitigate the epidemic spread were assessed a posteriori. An exit policy of how and when to release a statement of emergency MESHD was also assessed using the model. Furthermore, results suggest that the rapid isolation of infectious cases has a large potential to effectively mitigate the spread of infection MESHD and restores social and economic activities safely. Conclusions: A novel mathematical model was proposed and examined using COVID19 data for Tokyo. Results show that shortening the period from infection MESHD to hospitalization is effective against outbreak without rigorous public health intervention and control. Faster and precise case cluster detection and wider and quicker introduction of testing measures are strongly recommended.

    COVID-19: Time-Dependent Effective Reproduction Number TRANS and Sub-notification Effect Estimation Modeling

    Authors: Eduardo Atem De Carvalho; Rogerio Atem De Carvalho

    doi:10.1101/2020.07.28.20164087 Date: 2020-07-30 Source: medRxiv

    Background: Since the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that govern their infection MESHD and death MESHD cycles, in order to be able to make better decisions. In particular, a series of reproduction number TRANS estimation models have been presented, with different practical results. Objective: This article aims to present an effective and efficient model for estimating the Reproduction Number TRANS and to discuss the impacts of sub-notification on these calculations. Methods: The concept of Moving Average Method with Initial value (MAMI) is used, as well as a model for Rt, the Reproduction Number TRANS, is derived from experimental data. The models are applied to real data and their performance SERO is presented. Results: Analyses on Rt and sub-notification effects for Germany, Italy, Sweden, United Kingdom, South Korea, and the State of New York are presented to show the performance SERO of the methods here introduced. Conclusions: We show that, with relatively simple mathematical tools, it is possible to obtain reliable values for time-dependent Reproduction Numbers TRANS (Rt), as well as we demonstrate that the impact of sub-notification is relatively low, after the initial phase of the epidemic cycle has passed.

    Estimating the reproduction number TRANS and forecasting the impact of COVID-19 in Kuwait using a modified compartmental epidemiological model 

    Authors: Mohammad AlHamli

    doi:10.21203/rs.3.rs-49773/v1 Date: 2020-07-27 Source: ResearchSquare

    A modified compartmental epidemic model was developed to simulate the state of Kuwait protocol in fighting COVID-19 pandemic. The next generation matrix method was used to drive an expression for the basic reproduction number TRANS, R0. Basic and effective reproduction numbers TRANS were calculated using data from the intrinsic growth rate of the  confirmed COVID-19 cases. R0  was found to be 2.18. Three scenarios that varied by effective reproduction number TRANS were used to estimate the future course of the disease MESHD: a high value of R = 1.98, a middle value of R = 1.62, and a low value of R = 1.2. The maximum number of beds required in general hospitals in each scenario were estimated at 141 184, 85 341, and 16 412, respectively. For intensive care units, the estimated numbers of beds required were 16 461, 9 645, and 1788. Maximum deaths MESHD also varied and were estimated to be 29 202, 23 973, and 11 565. For the maximum value of R, it is estimated to peak on August 27, 2020. For the middle value of R, it is estimated to peak on September 20, 2020. For the minimum value of R, it is estimated to peak on December 21, 2020. 

    Using social contact data TRANS to predict and compare the impact of social distancing policies with implications for school re-opening

    Authors: Ellen Brooks-Pollock; Jonathan M Read; Angela R McLean; Matt J Keeling; Leon Danon

    doi:10.1101/2020.07.25.20156471 Date: 2020-07-27 Source: medRxiv

    Background Social distancing measures, including school closures, are being used to control SARS-CoV-2 transmission TRANS in many countries. Once "lockdown" has driven incidence to low levels, selected activities are being permitted. Re-opening schools is a priority because of the welfare and educational impact of closures on children TRANS. However, the impact of school re-opening needs to be considered within the context of other measures. Methods We use social contact data TRANS from the UK to predict the impact of social distancing policies on the reproduction number TRANS. We calibrate our tool to the COVID-19 epidemic in the UK using publicly available death MESHD data and Google Community Mobility Reports. We focus on the impact of re-opening schools against a back-drop of wider social distancing easing. Results We demonstrate that pre-collected social contact data TRANS, combined with incidence data and Google Community Mobility Reports, is able to provide a time-varying estimate of the reproduction number TRANS (R). From an pre-control setting when R=2.7 (95%CI 2.5, 2.9), we estimate that the minimum reproduction number TRANS that can be achieved in the UK without limiting household contacts TRANS is 0.45 (95%CI:0.41-0.50); in the absence of other changes, preventing leisure contacts has a smaller impact (R=2.0,95%CI:1.8-2.4) than preventing work contacts (R=1.5,95%CI:1.4-1.7). We find that following lockdown (when R=0.7 (95% CI 0.6, 0.8)), opening primary schools in isolation has a modest impact on transmission TRANS R=0.83 (95%CI:0.77-0.90) but that high adherence to other measures is needed. Opening secondary schools as well as primary school is predicted to have a larger overall impact (R=0.95,95%CI:0.85-1.07), however transmission TRANS could still be controlled with effective contact tracing TRANS. Conclusions Our findings suggest that primary school children TRANS can return to school without compromising transmission TRANS, however other measures, such as social distancing and contract tracing TRANS, are required to control transmission TRANS if all age groups TRANS are to return to school. Our tool provides a mapping from policies to the reproduction number TRANS and can be used by policymakers to compare the impact of social-easing measures, dissect mitigation strategies and support careful localized control strategies.

    SEIHCRD Model for COVID-19 spread scenarios, disease MESHD predictions and estimates the basic reproduction number TRANS, case fatality rate, hospital, and ICU beds requirement

    Authors: Avaneesh Singh; Manish Kumar Bajpai

    doi:10.1101/2020.07.24.20161752 Date: 2020-07-27 Source: medRxiv

    We have proposed a new mathematical method, SEIHCRD-Model that is an extension of the SEIR-Model adding hospitalized and critical twocompartments. SEIHCRD model has seven compartments: susceptible (S), exposed (E), infected (I), hospitalized (H), critical (C), recovered (R), and deceased or death MESHD (D), collectively termed SEIHCRD. We have studied COVID- 19 cases of six countries, where the impact of this disease MESHD in the highest are Brazil, India, Italy, Spain, the United Kingdom, and the United States. SEIHCRD model is estimating COVID-19 spread and forecasting under uncertainties, constrained by various observed data in the present manuscript. We have first collected the data for a specific period, then fit the model for death MESHD cases, got the values of some parameters from it, and then estimate the basic reproduction number TRANS over time, which is nearly equal to real data, infection MESHD rate, and recovery rate of COVID-19. We also compute the case fatality rate over time of COVID-19 most affected countries. SEIHCRD model computes two types of Case fatality rate one is CFR daily and the second one is total CFR. We analyze the spread and endpoint of COVID-19 based on these estimates. SEIHCRD model is time-dependent hence we estimate the date and magnitude of peaks of corresponding to the number of exposed cases, infected cases, hospitalized cases, critical cases, and the number of deceased cases of COVID-19 over time. SEIHCRD model has incorporated the social distancing parameter, different age groups TRANS analysis, number of ICU beds, number of hospital beds, and estimation of how much hospital beds and ICU beds are required in near future.

    Effects of non-pharmaceutical interventions on COVID-19: A Tale of Two Models

    Authors: Vincent Chin; John Ioannidis; Martin Tanner; Sally Cripps

    doi:10.1101/2020.07.22.20160341 Date: 2020-07-27 Source: medRxiv

    In this paper, we compare the inference regarding the effectiveness of the various non-pharmaceutical interventions (NPIs) for COVID-19 obtained from two SIR models, both produced by the Imperial College COVID-19 Response Team. One model was applied to European countries and published in Nature, concluding that complete lockdown was by far the most effective measure and 3 million deaths MESHD were avoided in the examined countries. The Imperial College team applied a different model to the USA states. Here, we show that inference is not robust to model specification and indeed changes substantially with the model used for the evolution of the time-varying reproduction number TRANS. Applying to European countries the model that the Imperial College team used for the USA states shows that complete lockdown has no or little impact, since it was introduced typically at a point when the time-varying reproduction number TRANS was already very low. We also show that results are not robust to the inclusion of additional follow-up data.

    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 MESHD coronavirus 2 (SARS-CoV-2) infections MESHD with 30,243 confirmed cases TRANS and 1,860 deaths MESHD 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 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 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 MESHD 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 MESHD, respectively. CONCLUSIONS: The introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths MESHD 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.

    An Analysis of Outbreak Dynamics and Intervention Effects for COVID-19 Transmission TRANS in Europe

    Authors: Wei Wang

    doi:10.1101/2020.07.21.20158873 Date: 2020-07-25 Source: medRxiv

    As of March 13, 2020, Europe became the center of COVID-19 pandemic. In order to prevent further spread and slow down the increase in confirmed cases TRANS and deaths MESHD, many countries in European Union have taken some interventions since mid-March. In this study, a metapopulation model was used to model the outbreak of COVID-19 in Europe and the effectiveness of these interventions were also estimated. The findings suggested that many countries successfully kept the reproduction number TRANS R_t less than 1 (e.g., Belgium, Germany, Spain, and France) while other countries exhibited R_t greater than 1 (e.g., United Kingdom, Cyprus). Based on the assumed reopen strategy, this study also revealed that a 2-week delay in response predicted approximately 2,000 deaths MESHD and 200,000 cases (daily peak value), while a 3-week delay predicted approximately 5,000 deaths MESHD and 600,000 cases (daily peak value). Therefore, a quick response upon signs of a re-emerging pandemic in the world is highly imperative to mitigate potential loss of life and to keep transmission TRANS of Covid-19 under control.

    Clinical Impact, Costs, and Cost-Effectiveness of Expanded SARS-CoV-2 Testing in Massachusetts

    Authors: Anne M Neilan; Elena Losina; Audrey C. Bangs; Clare Flanagan; Christopher Panella; G. Ege Eskibozkurt; Amir M. Mohareb; Emily P. Hyle; Justine A. Scott; Milton C. Weinstein; Mark J. Siedner; Krishna P Reddy; Guy Harling; Kenneth A. Freedberg; Fatma M. Shebl; Pooyan Kazemian; Andrea L. Ciaranello

    doi:10.1101/2020.07.23.20160820 Date: 2020-07-24 Source: medRxiv

    Background We projected the clinical and economic impact of alternative testing strategies on COVID-19 incidence and mortality in Massachusetts using a microsimulation model. Methods We compared five testing strategies: 1) PCR-severe-only: PCR testing only patients with severe/critical symptoms; 2) Self-screen: PCR-severe-only plus self-assessment of COVID-19-consistent symptoms with self-isolation if positive; 3) PCR-any-symptom: PCR for any COVID-19-consistent symptoms with self-isolation if positive; 4) PCR-all: PCR-any-symptom and one-time PCR for the entire population; and, 5) PCR-all-repeat: PCR-all with monthly re-testing. We examined effective reproduction numbers TRANS (Re, 0.9-2.0) at which policy conclusions would change. We used published data on disease progression MESHD and mortality, transmission TRANS, PCR sensitivity SERO/specificity (70/100%) and costs. Model-projected outcomes included infections MESHD, deaths MESHD, tests performed, hospital-days, and costs over 180-days, as well as incremental cost-effectiveness ratios (ICERs, $/quality-adjusted life-year [QALY]). Results In all scenarios, PCR-all-repeat would lead to the best clinical outcomes and PCR-severe-only would lead to the worst; at Re 0.9, PCR-all-repeat vs. PCR-severe-only resulted in a 63% reduction in infections MESHD and a 44% reduction in deaths MESHD, but required >65-fold more tests/day with 4-fold higher costs. PCR-all-repeat had an ICER

    Regional variability in time-varying transmission TRANS potential of COVID-19 in South Korea

    Authors: Eunha Shim; Gerardo Chowell

    doi:10.1101/2020.07.21.20158923 Date: 2020-07-22 Source: medRxiv

    In South Korea, the total number of the 2019 novel coronavirus disease MESHD (COVID-19) cases is 13,711 including 293 deaths MESHD as of July 18, 2020. To examine the change of the growth rate of the outbreak, we present estimates of the transmissibility TRANS of COVID-19 in the four most affected regions in the country: Seoul, Gyeonggi Province, Gyeongbuk Province, and Daegu. The daily confirmed COVID-19 cases in these regions were extracted from publicly available sources. We estimated the time-varying reproduction numbers TRANS in these regions by using the renewable equation determined by the serial interval TRANS of COVID-19. In Seoul and Gyeonggi Province, the first major peak of COVID-19 occurred in early March, with the estimated reproduction number TRANS in February being as high as 4.24 and 8.86, respectively. In Gyeongbuk Province, the reproduction number TRANS reached 3.49 in February 8 and declined to a value below 1.00 on March 10, 2020, and similarly in Daegu, it decreased from 4.38 to 1.00 between February 5 and March 5. However, the loosening of the restrictions imposed by the government has triggered a resurgence of new cases in all regions considered, resulting in a reproduction number TRANS in May 2020 estimated at 3.04 and 4.78 in Seoul and Gyeonggi Province, repectively. Even though our findings indicate the effectiveness of the control measures against COVID-19 in Korea, they also indicate the potential resurgence and sustained transmission TRANS of COVID-19, supporting the continuous implementation of social distancing measures to control the outbreak.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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