Corpus overview


Overview

MeSH Disease

Human Phenotype

Falls (25)

Pneumonia (1)

Growth delay (1)

Shock (1)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 25
    records per page




    Estimation of Effective Reproduction Number TRANS for COVID-19 in Bangladesh and its districts

    Authors: Al-Ekram Elahee Hridoy; Mohammad Naim; Edris Alam; Nazim Uddin Emon; Imrul Hasan Tipo; Shekh Md. Shajid Hasan Tusher; Safaet Alam; Mohammad Safiqul Islam

    doi:10.1101/2020.08.04.20168351 Date: 2020-08-06 Source: medRxiv

    Background Bangladesh is going through an unprecedented crisis since the onset of the COVID-19 pandemic. Throughout the COVID-19 pandemic, the reproduction number TRANS of COVID-19 swarmed in the scientific community and public media due to its simplicity in explaining an infectious disease MESHD dynamic. This paper aims to estimate the effective reproduction number TRANS (Rt) for COVID-19 over time in Bangladesh and its districts using reported cases. Methods Adapted methods derived from Bettencourt and Ribeiro (2008), which is a sequential Bayesian approach using the compartmental Susceptible-Infectious-Recovered (SIR) model, have been used to estimate Rt. Findings As of July 21, the mean Rt is 1.32(0.98-1.70, 90% HDI), with a median of 1.16(0.99-1.34 90% HDI). The initial Rt of Bangladesh was 3, whereas the Rt on the day of imposing nation-wide lockdown was 1.47, at the end of lockdown phase 1 was 1.06, at the end of lockdown phase 2 was 1.33. Each phase of nation-wide lockdown has contributed to the decline of effective reproduction number TRANS (Rt) for Bangladesh by 28.44%, and 26.70%, respectively, implying moderate effectiveness of the epidemic response strategies. Interpretation and Conclusion The mean Rt fell HP by 13.55% from May 31 to July 21, 2020, despite easing of lockdown in Bangladesh. The Rt continued to fall HP below the threshold value one steadily from the beginning of July and sustained around 1. The mean Rt fell HP by 13.55% from May 31 to July 21, 2020, despite easing of lockdown in Bangladesh. As of July 21, the current estimate of Rt is 1.07(0.92-1.15: 90% HDI), meaning that an infected individual is spreading the virus to an average of one other, with 0.07 added chance of infecting a second individual. This whole research recommends two things- broader testing and careful calibration of measures to keep Rt a long way below the crucial threshold one.

    The basic reproduction number TRANS of SARS-CoV-2: a scoping review of available evidence

    Authors: Ann Barber; John M Griffin; Miriam Casey; Aine Collins; Elizabeth A Lane; Quirine Ten Bosch; Mart De Jong; David Mc Evoy; Andrew W Byrne; Conor G McAloon; Francis Butler; Kevin Hunt; Simon J More

    doi:10.1101/2020.07.28.20163535 Date: 2020-07-30 Source: medRxiv

    Background: The transmissibility TRANS of SARS-CoV-2 determines both the ability of the virus to invade a population and the strength of intervention that would be required to contain or eliminate the spread of infection MESHD. The basic reproduction number TRANS, R0 TRANS, provides a quantitative measure of the transmission TRANS potential of a pathogen. Objective: Conduct a scoping review of the available literature providing estimates of R0 TRANS for SARS-CoV-2, provide an overview of the drivers of variation in R0 TRANS estimates and the considerations taken in the calculation of the parameter. Design: Scoping review of available literature between the 01 December 2019 and 07 May 2020. Data sources: Both peer-reviewed and pre-print articles were searched for on PubMed, Google Scholar, MedRxiv and BioRxiv. Selection criteria: Studies were selected for review if (i) the estimation of R0 TRANS represented either the initial stages of the outbreak or the initial stages of the outbreak prior to the onset of widespread population restriction (lockdown), (ii) the exact dates of the study period were provided and (iii) the study provided primary estimates of R0 TRANS. Results: A total of 20 R0 TRANS estimates were extracted from 15 studies. There was substantial variation in the estimates reported. Estimates derived from mathematical models fell HP within a wider range of 1.94-6.94 than statistical models which fell HP between the range of 2.2 to 4.4. Several studies made assumptions about the length of the infectious period TRANS which ranged from 5.8-20 days and the serial interval TRANS which ranged from 4.41-14 days. For a given set of parameters a longer duration of infectiousness or a longer serial interval TRANS equates to a higher R0 TRANS. Several studies took measures to minimise bias in early case reporting, to account for the potential occurrence of super-spreading events, and to account for early sub-exponential epidemic growth. Conclusions: The variation in reported estimates of R0 TRANS reflects the complex nature of the parameter itself, including the context (i.e. social/spatial structure), the methodology used to estimate the parameter, and model assumptions. R0 TRANS is a fundamental parameter in the study of infectious disease MESHD dynamics however it provides limited practical applicability outside of the context in which it was estimated, and should be calculated and interpreted with this in mind.

    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 MESHD 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 MESHD 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 MESHD 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 MESHD 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 MESHD disease spread TRANS spread 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 MESHD 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 MESHD occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections MESHD when effective mitigation strategies ( R0 TRANS = 1.25) are implemented to over 15,000 active infections MESHD 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 MESHD. 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 MESHD. 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 MESHD 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.

    COVID-19 screening strategies that permit the safe re-opening of college campuses

    Authors: A David Paltiel; Amy Zheng; Rochelle P Walensky

    doi:10.1101/2020.07.06.20147702 Date: 2020-07-07 Source: medRxiv

    Importance: The COVID-19 pandemic poses an existential threat to many US residential colleges: either they open their doors to students in September or they risk serious financial consequences. Objective: To define SARS-CoV-2 screening performance SERO standards that would permit the safe return of students to campus for the Fall HP 2020 semester. Design: Decision and cost-effectiveness analysis linked to a compartmental epidemic model to evaluate campus screening using tests of varying frequency (daily-weekly), sensitivity SERO (70%-99%), specificity (98%-99.7%), and cost ($10-$50/test). Reproductive numbers TRANS Rt = {1.5, 2.5, 3.5} defined three epidemic scenarios, with additional infections MESHD imported via exogenous shocks MESHD shocks HP. We generally adhered to US government guidance for parameterization data. Participants: A hypothetical cohort of 5000 college- age TRANS, uninfected students. Main Outcome(s) and Measure(s): Cumulative tests, infections MESHD, and costs; daily isolation dormitory census; incremental cost-effectiveness; and budget impact. All measured over an 80-day, abbreviated semester. Results: With Rt = 2.5, daily screening with a 70% sensitive, 98% specific test produces 85 cumulative student infections MESHD and isolation dormitory daily census averaging 108 (88% false positives). Screening every 2 (7) days nets 135 (3662) cumulative infections MESHD and daily isolation census 66 (252) with 73% (4%) false positives. Across all scenarios, test frequency exerts more influence on outcomes than test sensitivity SERO. Cost-effectiveness analysis selects screening every {2, 1, 7} days with a 70% sensitive test as the preferred strategy for Rt = {2.5, 3.5, 1.5}, implying a screening cost of {$470, $920, $120} per student per semester. Conclusions & Relevance: Rapid, inexpensive and frequently conducted screening (even if only 70% sensitive) would be cost-effective and produce a modest number of COVID-19 infections MESHD. While the optimal screening frequency hinges on the success of behavioral interventions to reduce the base severity of transmission TRANS (Rt), this could permit the safe return of student to campus.

    Behavioral changes before lockdown, and decreased retail and recreation mobility during lockdown, contributed most to the successful control of the COVID-19 epidemic in 35 Western countries

    Authors: Koen Deforche; Jurgen Vercauteren; Viktor Müller; Anne-Mieke Vandamme

    doi:10.1101/2020.06.20.20136382 Date: 2020-06-23 Source: medRxiv

    The COVID-19 pandemic has prompted a lockdown in many countries to control the exponential spread of the SARS-CoV-2 virus. This resulted in curbing the epidemic by reducing the time-varying basic reproduction number TRANS (Rt) to below one. Governments are looking for evidence to balance the demand of their citizens to ease some of the restriction, against the fear of a second peak in infections MESHD. More details on the specific circumstances that promote exponential spread (i.e. Rt>1) and the measures that contributed most to a reduction in Rt are needed. Here we show that in 33 of 35 Western countries (32 European, plus Israel, USA and Canada), Rt fell HP to around or below one during lockdown (March - May 2020). One third of the effect happened already on average 6 days before the lockdown, with lockdown itself causing another major drop in transmission TRANS. Country-wide compulsory usage of masks was implemented only in Slovakia 10 days into lockdown, and on its own reduced transmission TRANS by half. During lockdown, decreased mobility in retail and recreation was an independent predictor of lower Rt during lockdown, while changes in other types of mobility were not. These results are consistent with anecdotal evidence that large recreational gatherings are super-spreading events, and may even suggest that infections MESHD during day-to-day contact at work are not sufficient to spark exponential growth. Our data suggest measures that will contribute to avoiding a second peak include a tight control on circumstances that facilitate massive spread such as large gatherings especially indoors, physical distancing, and mask use.

    Can medication mitigate the need for a strict lock down?: A mathematical study of control strategies for COVID-19 infection MESHD

    Authors: Mohsin Ali; Mudassar Imran; Adnan Khan

    doi:10.21203/rs.3.rs-35440/v1 Date: 2020-06-14 Source: ResearchSquare

    BackgroundCOVID-19 is a pandemic that has swept across the world in 2020. To date the only effective control mechanisms were non-pharmaceutical interventions, however there have been encouraging reports regarding possible medication in the literature, with emergency MESHD approval given to some drugs in various countries.MethodsWe formulate a deterministic epidemic model to study the effects of medication on the transmission TRANS dynamics of Corona Virus Disease MESHD (COVID-19). We are especially interested in how the availability of medication could change the necessary quarantine measures for effective control of the disease MESHD. We model the transmission TRANS by extending the SEIR model to include asymptomatic TRANS, quarantined, isolated and medicated population compartments.ResultsWe calculate the basic reproduction number TRANS R0 TRANS and show that for R0 TRANS<1 the disease MESHD dies out and for R0 TRANS>1 the disease MESHD is endemic. Using sensitivity SERO analysis we establish that R0 TRANS is most sensitive to the rates of quarantine and medication. We also study how the effectiveness and the rate of medication along with the quarantine rate affect R0 TRANS. We devise optimal quarantine, medication and isolation strategies, noting that availability of medication reduces the duration and severity of the lock-down needed for effective disease MESHD control.ConclusionOur study also reinforces the idea that with the availability of medication, while the severity of the lock downs can be eased over time some social distancing protocols need to be observed, at least till a vaccine is found. We also analyze the COVID-19 outbreak data for four different countries, in two of these, India and Pakistan the curve is still rising, and in he other two, Italy and Spain, the epidemic curve is now falling HP due to effective quarantine measures. We provide estimates of R0 and the proportion of asymptomatic TRANS individuals in the population for these countries.

    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 MESHD 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 MESHD 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.

    Can medication mitigate the need for a strict lock down?: A mathematical study of control strategies for COVID-19 infection MESHD

    Authors: Mohsin Ali; Mudassar Imran; Adnan Khan

    doi:10.1101/2020.05.29.20116749 Date: 2020-05-29 Source: medRxiv

    We formulate a deterministic epidemic model to study the effects of medication on the transmission TRANS dynamics of Corona Virus Disease MESHD (COVID-19). We are especially interested in how the availability of medication could change the necessary quarantine measures for effective control of the disease MESHD. We model the transmission TRANS by extending the SEIR model to include asymptomatic TRANS, quarantined, isolated and medicated population compartments. We calculate the basic reproduction number TRANS R_0 TRANS and show that for R_0 TRANS<1 the disease MESHD dies out and for R_0 TRANS>1 the disease MESHD is endemic. Using sensitivity SERO analysis we establish that R_0 TRANS is most sensitive to the rates of quarantine and medication. We also study how the effectiveness and the rate of medication along with the quarantine rate affect R_0 TRANS. We devise optimal quarantine, medication and isolation strategies, noting that availability of medication reduces the duration and severity of the lock-down needed for effective disease MESHD control. Our study also reinforces the idea that with the availability of medication, while the severity of the lock downs can be eased over time some social distancing protocols need to be observed, at least till a vaccine is found. We also analyze the COVID-109 outbreak data for four different countries, in two of these, India and Pakistan the curve is still rising, and in he other two, Italy and Spain, the epidemic curve is now falling HP due to effective quarantine measures. We provide estimates of R_0 TRANS and the proportion of asymptomatic TRANS individuals in the population for these countries.

    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.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).

Sources


Annotations

All
None
MeSH Disease
Human Phenotype
Transmission
Seroprevalence


Export subcorpus as Endnote

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.