scholarly journals Analyzing the Effectiveness of COVID-19 Lockdown Policies Using the Time-Dependent Reproduction Number and the Regression Discontinuity Framework: Comparison between Countries

2021 ◽  
Vol 5 (1) ◽  
pp. 8
Author(s):  
Shangjun Liu ◽  
Tatiana Ermolieva ◽  
Guiying Cao ◽  
Gong Chen ◽  
Xiaoying Zheng
Keyword(s):  
Risk Perception ◽  
Real Time ◽  
Regression Discontinuity ◽  
Reproduction Number ◽  
Epidemic Models ◽  
Time Dependent ◽  
Time Reproduction ◽  
Long Period ◽  
Infection Dynamics ◽  
The Usa

This study compares the effectiveness of COVID-19 control policies on the virus’s spread and on the change of the infection dynamics in China, Germany, Austria, and the USA relying on a regression discontinuity in time and ‘earlyR’ epidemic models. The effectiveness of policies is measured by real-time reproduction number and cases counts. Comparison between the two lockdowns within each country showed the importance of people's risk perception for the effectiveness of the measures. Results suggest that restrictions applied for a long period or reintroduced later may cause at-tenuated effect on the circulation of the virus and the number of casualties.

scholarly journals PIN50 Leveraging Publicly Available Data to Estimate a Real-Time Reproduction Number (Rt) for Covid-19: A Comparison of Two Methods

2021 ◽  
Vol 24 ◽  
pp. S114
Author(s):  
S. Emerson ◽  
K. Johnston ◽  
A. Howarth ◽  
J. Schneider ◽  
M. Friesen ◽  
...  
Keyword(s):  
Real Time ◽  
Reproduction Number ◽  
Time Reproduction

scholarly journals Modelling the impact of the tier system on SARS-CoV-2 transmission in the UK between the first and second national lockdowns

BMJ Open ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. e050346
Author(s):  
Daniel J Laydon ◽  
Swapnil Mishra ◽  
Wes R Hinsley ◽  
Pantelis Samartsidis ◽  
Seth Flaxman ◽  
...  
Keyword(s):  
Real Time ◽  
Reproduction Number ◽  
Secondary Outcome ◽  
Bayesian Hierarchical ◽  
Time Reproduction ◽  
Tier System ◽  
The Uk ◽  
National Trends ◽  
Tier 3 ◽  
The Impact

ObjectiveTo measure the effects of the tier system on the COVID-19 pandemic in the UK between the first and second national lockdowns, before the emergence of the B.1.1.7 variant of concern.DesignThis is a modelling study combining estimates of real-time reproduction number Rt (derived from UK case, death and serological survey data) with publicly available data on regional non-pharmaceutical interventions. We fit a Bayesian hierarchical model with latent factors using these quantities to account for broader national trends in addition to subnational effects from tiers.SettingThe UK at lower tier local authority (LTLA) level. 310 LTLAs were included in the analysis.Primary and secondary outcome measuresReduction in real-time reproduction number Rt.ResultsNationally, transmission increased between July and late September, regional differences notwithstanding. Immediately prior to the introduction of the tier system, Rt averaged 1.3 (0.9–1.6) across LTLAs, but declined to an average of 1.1 (0.86–1.42) 2 weeks later. Decline in transmission was not solely attributable to tiers. Tier 1 had negligible effects. Tiers 2 and 3, respectively, reduced transmission by 6% (5%–7%) and 23% (21%–25%). 288 LTLAs (93%) would have begun to suppress their epidemics if every LTLA had gone into tier 3 by the second national lockdown, whereas only 90 (29%) did so in reality.ConclusionsThe relatively small effect sizes found in this analysis demonstrate that interventions at least as stringent as tier 3 are required to suppress transmission, especially considering more transmissible variants, at least until effective vaccination is widespread or much greater population immunity has amassed.

scholarly journals Short-Term Projection of COVID 19 Cases in Kenya using an Exponential Model

2020 ◽  
Author(s):  
Samuel Kiruri Kirichu
Keyword(s):  
Growth Rate ◽  
Real Time ◽  
Case Fatality Rate ◽  
Reproduction Number ◽  
Case Fatality ◽  
Daily Growth Rate ◽  
Daily Growth ◽  
The Real ◽  
Time Reproduction ◽  
First Case

Abstract Introduction: The COVID-19 disease has spread to over 200 countries and territories since the first case was recorded in Wuhan, China in December 2019. In Kenya, the first case of COVID-19 was recorded on 13th March 2020 and since then over five thousand cases have been confirmed as of 26th June 2020. In the same period, one hundred and forty four mortality cases had been recorded in the country. With the rapid changing situation, timely and reliable data is required for monitoring, planning and rapid decision making with an aim of reversing the already deteriorating situation (economic, health, learning among others) in the country. Methods: The study used the exponential growth model to estimate the daily growth rate and the real-time-effective reproduction number. The study also estimated the naïve and the adjusted Case Fatality Rates. Results: The naïve-Case Fatality Rate of 26th June 2020 which was the 106 day after the first case was confirmed in Kenya was estimated as 2.5% while the adjusted Case Fatality Rate with a lag of 2 days was estimated as 2.6%. The daily exponential growth rate was estimated as 0.22 while the real-time reproduction number as of 26th June 2020 was estimated as 1.28 [95% CI: 1.27 – 1.29]. Conclusion: The daily growth rate and the real-time reproduction number indicated that the outbreak was still growing as of the time of analysis.

scholarly journals Estimation of Time-Dependent Reproduction Number for Global COVID-19 Outbreak

2020 ◽  
Author(s):  
Tatiana Petrova ◽  
Dmitry Soshnikov ◽  
Andrey Grunin
Keyword(s):  
Real Time ◽  
Disease Transmission ◽  
Reproduction Number ◽  
Time Window ◽  
Time Estimation ◽  
Time Dependent ◽  
Single Infection ◽  
Observation Data ◽  
Sir Epidemic Model ◽  
Time Dynamics

Real-time estimation of the parameters characterising infectious disease transmission is important for optimization quarantine interventions during outbreaks. One of the most significant parameters is the effective reproduction number - number of secondary cases produced by a single infection. The current study presents an approach for estimating the effective reproduction number and its application to COVID-19 outbreak. The method is based on fitting SIR epidemic model to observation data in a sliding time window and allows to show real-time dynamics of reproduction number at any phase of epidemic for countries globally. Online data on COVID-19 daily cases of infections, recoveries, deaths are used.Finally, time-dependent reproduction number is explored in connection with dynamics of peoples mobility. The method allows to assess the disease transmission potential and understand the effect of interventions on epidemics spread. It also can be easily adapted to future outbreaks of different pathogens. The tool is available online as Python code from the Github repository.

scholarly journals Impact of the Tier system on SARS-CoV-2 transmission in the UK between the first and second national lockdowns

2021 ◽  
Author(s):  
Daniel J Laydon ◽  
Swapnil Mishra ◽  
Wes R Hinsley ◽  
Pantelis Samartsidis ◽  
Seth Flaxman ◽  
...  
Keyword(s):  
Real Time ◽  
Statistical Power ◽  
Reproduction Number ◽  
Secondary Outcome ◽  
List Type ◽  
Time Reproduction ◽  
Population Immunity ◽  
Tier System ◽  
The Uk ◽  
Tier 3

AbstractObjectiveMeasure the effects of the Tier system on the COVID-19 pandemic in the UK between the first and second national lockdowns, before the emergence of the B.1.1.7 variant of concern.DesignModelling study combining estimates of the real-time reproduction number Rt (derived from UK case, death and serological survey data) with publicly available data on regional non-pharmaceutical interventions. We fit a Bayesian hierarchical model with latent factors using these quantities, to account for broader national trends in addition to subnational effects from Tiers.SettingThe UK at Lower Tier Local Authority (LTLA) level.Primary and secondary outcome measuresReduction in real-time reproduction number Rt.ResultsNationally, transmission increased between July and late September, regional differences notwithstanding. Immediately prior to the introduction of the tier system, Rt averaged 1.3 (0.9 – 1.6) across LTLAs, but declined to an average of 1.1 (0.86 – 1.42) two weeks later. Decline in transmission was not solely attributable to Tiers. Tier 1 had negligible effects. Tiers 2 and 3 respectively reduced transmission by 6% (5%-7%) and 23% (21%-25%). 93% of LTLAs would have begun to suppress their epidemics if every LTLA had gone into Tier 3 by the second national lockdown, whereas only 29% did so in reality.ConclusionsThe relatively small effect sizes found in this analysis demonstrate that interventions at least as stringent as Tier 3 are required to suppress transmission, especially considering more transmissible variants, at least until effective vaccination is widespread or much greater population immunity has amassed.Strengths and limitations of this studyFirst study to measure effects of UK Tier system for SARS-CoV-2 control at national and regional level.Model makes minimal assumptions and is primarily data driven.Insufficient statistical power to estimate effects of individual interventions that comprise Tiers, or their interaction.Estimates show that Tiers 1 and 2 are insufficient to suppress transmission, at least until widespread population immunity has amassed. Emergence of more transmissible variants of concern unfortunately supports this conclusion.

scholarly journals Quantitative modeling and analysis show country-specific optimization of quarantine measures can potentially circumvent COVID19 infection spread post lockdown

2020 ◽  
Author(s):  
Uddipan Sarma ◽  
Bhaswar Ghosh
Keyword(s):  
Reproduction Number ◽  
Transmission Rate ◽  
Fold Increase ◽  
Modeling And Analysis ◽  
Infection Dynamics ◽  
The Usa ◽  
Data Driven Modeling ◽  
Second Wave ◽  
Country Specific ◽  
Infection Spread

AbstractThe COVID19 outbreak, which started in Wuhan, is now spread across 200+ countries with over 6 million reported infections and a death toll over 350 thousand. In response, and primarily in the absence of a vaccine, many countries have implemented lockdown to ensure social distancing and started rigorously quarantining the infected subjects. In this study, we attempt to identify the most potent component(s) in the system that can be manipulated via human intervention. Firstly, analysis of the metadata for 93 countries showed a reduction in the estimated reproduction number (a month post-infection) is correlated to the testing rate in a country. To systematically study the dynamics of infection we next built epidemic models for 23 different countries and calibrated the confirmed, recovered, and dead population trajectories in the model to the respective data from WHO. The countries chosen either had the infection peak long crossed; peak recently reached but still with significant daily infection, or, infection peak is yet to arrive. Our model successfully fits data from all 23 countries and provides us with incubation time, transmission rate, quarantine, recovery, and death rates for each country. With further analysis, we found infection spread towards a much larger second wave can be controlled via a rigorous increase in the quarantine rates that, we show, can be tailored in a country-specific manner; for instance, we found the USA or Spain might require a 10 fold increase in testing/ quarantine rates compared to India to control the second wave post lockdown. Our data-driven modeling and analysis thus pave a way to understand and manipulate the infection dynamics during and post lockdown phases in various countries. The findings can also be used to strategize the testing and quarantine processes to manipulate the spread of the disease in the future.

COVID-19: Time-Dependent Effective Reproduction Number and Sub-notification Effect Estimation Modeling (Preprint)

2020 ◽  
Author(s):  
Eduardo Atem De Carvalho ◽  
Rogerio Atem De Carvalho
Keyword(s):  
New York ◽  
Reproduction Number ◽  
Moving Average ◽  
Real Data ◽  
Time Dependent ◽  
Initial Value ◽  
Health Authorities ◽  
Reproduction Numbers ◽  
Effect Estimation ◽  
The Impact

BACKGROUND Since the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that govern their infection and death cycles, in order to be able to make better decisions. In particular, a series of reproduction number 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 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, is derived from experimental data. The models are applied to real data and their performance 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 of the methods here introduced. CONCLUSIONS We show that, with relatively simple mathematical tools, it is possible to obtain reliable values for time-dependent, incubation period-independent Reproduction Numbers (Rt). We also demonstrate that the impact of sub-notification is relatively low, after the initial phase of the epidemic cycle has passed.

scholarly journals Fractional SIR-Model for Estimating Transmission Dynamics of COVID-19 in India

J ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 86-100
Author(s):  
Nita H. Shah ◽  
Ankush H. Suthar ◽  
Ekta N. Jayswal ◽  
Ankit Sikarwar
Keyword(s):  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Transmission Rate ◽  
Sir Model ◽  
Time Dependent ◽  
Contact Rate ◽  
Distribution Maps ◽  
Fundamental Parameters ◽  
Different Order ◽  
The Basic Reproduction Number

In this article, a time-dependent susceptible-infected-recovered (SIR) model is constructed to investigate the transmission rate of COVID-19 in various regions of India. The model included the fundamental parameters on which the transmission rate of the infection is dependent, like the population density, contact rate, recovery rate, and intensity of the infection in the respective region. Looking at the great diversity in different geographic locations in India, we determined to calculate the basic reproduction number for all Indian districts based on the COVID-19 data till 7 July 2020. By preparing district-wise spatial distribution maps with the help of ArcGIS 10.2, the model was employed to show the effect of complete lockdown on the transmission rate of the COVID-19 infection in Indian districts. Moreover, with the model's transformation to the fractional ordered dynamical system, we found that the nature of the proposed SIR model is different for the different order of the systems. The sensitivity analysis of the basic reproduction number is done graphically which forecasts the change in the transmission rate of COVID-19 infection with change in different parameters. In the numerical simulation section, oscillations and variations in the model compartments are shown for two different situations, with and without lockdown.

scholarly journals Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
François Stüder ◽  
Jean-Louis Petit ◽  
Stefan Engelen ◽  
Marco Antonio Mendoza-Parra
Keyword(s):  
Real Time ◽  
Optimal Solution ◽  
Proof Of Concept ◽  
Gene Encoding ◽  
Spike Gene ◽  
Long Period ◽  
The World ◽  
Receptor Recognition ◽  
Nanopore Dna Sequencing ◽  
Novel Coronavirus

AbstractSince December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants’ occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants’ tracking, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants’ emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant’s tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant’s tracking monitoring thanks to our software RETIVAD. This strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.

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