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 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 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 The Impact of the November 2020 English National Lockdown on COVID-19 case counts

2021 ◽  
Author(s):  
Paul R Hunter ◽  
Julii Brainard ◽  
Alastair Grant
Keyword(s):  
Reproductive Rate ◽  
Tier 2 ◽  
New Variant ◽  
Tier System ◽  
Obvious Benefit ◽  
Beneficial Impact ◽  
R Value ◽  
The Uk ◽  
Tier 3 ◽  
The Impact

In the UK the epidemic of COVID-19 continues to pose a significant threat to public health. On the 14th October the English government introduced a tier system for control of the epidemic but just 3 weeks later a National lockdown across all areas of England was implemented. When English areas emerged from Lockdown many were placed in different tiers (most typically moved up at least one tier). However, the effectiveness of the tier system has been challenged by the emergence of a new variant of SARS-CoV-2 which appears to be much more infectious. In addition, from early November a trial mass testing service was being run in Liverpool. We used publicly available data of daily cases by local authority (local government areas) and estimated the reproductive rate (R value) of the epidemic based on 7-day case numbers compared with the previous 7-day period. There was a clear surge in infections from a few days before to several days after the lockdown was implemented. But this surge was almost exclusively associated with Tier 1 and Tier 2 authorities. In Tier 3 authorities where hospitality venues were only allowed to operate as restaurants there was no such surge. After this initial surge, cases declined in all three tiers with the R value dropping to a mean of about 0.7 independent of tier. London, The South East and East of England Regions saw rising infection rates in the last week or so of lockdown primarily in children of secondary school age. We could find no obvious benefit of the trial mass screening programme in Liverpool city. We conclude that in Tiers 1 and 2 much of the beneficial impact of the national lockdown was lost probably because of the leak of its likely implementation five days early leading to increased socialising in these areas before the start of lockdown. We further conclude that given that the new variant is estimated to have an R value of between 0.39 and 0.93 greater than previous variants, any lockdown as strict as the November one would be insufficient to reverse the increase in infections by itself. The value of city-wide mass testing to control the epidemic remains uncertain.

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 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 Estimated Dissemination Ratio—A Practical Alternative to the Reproduction Number for Infectious Diseases

2021 ◽  
Vol 9 ◽  
Author(s):  
Francisco J. Pérez-Reche ◽  
Nick Taylor ◽  
Chris McGuigan ◽  
Philip Conaglen ◽  
Ken J. Forbes ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Infectious Diseases ◽  
Real Time ◽  
Early Warning ◽  
Reproduction Number ◽  
Transmission Rate ◽  
Control Measures ◽  
Epidemic Curve ◽  
The Uk ◽  
The Impact

Policymakers require consistent and accessible tools to monitor the progress of an epidemic and the impact of control measures in real time. One such measure is the Estimated Dissemination Ratio (EDR), a straightforward, easily replicable, and robust measure of the trajectory of an outbreak that has been used for many years in the control of infectious disease in livestock. It is simple to calculate and explain. Its calculation and use are discussed below together with examples from the current COVID-19 outbreak in the UK. These applications illustrate that EDR can demonstrate changes in transmission rate before they may be clear from the epidemic curve. Thus, EDR can provide an early warning that an epidemic is resuming growth, allowing earlier intervention. A conceptual comparison between EDR and the commonly used reproduction number is also provided.

scholarly journals Real-time tracking and forecasting of the of COVID-19 outbreak in Kuwait: a mathematical modeling study

2020 ◽  
Author(s):  
Abdullah A. Al-Shammari ◽  
Hamad Ali ◽  
Barrak Al-Ahmad ◽  
Faisal H. Al-Refaei ◽  
Salman Al-Sabah ◽  
...  
Keyword(s):  
Public Health ◽  
Mathematical Modeling ◽  
Maximum Likelihood ◽  
Real Time ◽  
Reproduction Number ◽  
Control Measures ◽  
List Type ◽  
Imported Case ◽  
Real Time Tracking ◽  
Death Cases

AbstractKuwait has been experiencing a COVID-19 outbreak since the first imported case on Feb 24, 2020. Analysis of data from the early stage of COVID-19 outbreak in Kuwait can provide important information about the potential epidemic and healthcare burdens as well as assist in evaluating the potential impact of various outbreak control measures. Such control measures are essentially implemented to achieve a sufficient reduction in the effective reproduction number during an outbreak. In this study, we use a mathematical modeling framework to simulate the outbreak dynamics of SARS-CoV-2 transmission in Kuwait and forecast the potential burden on the healthcare system. We calibrate the model against daily numbers of detected infection and death cases using a maximum likelihood framework and estimate both the basic and effective reproduction numbers. Our results indicate that the early control measures implemented in Kuwait had the effect of delaying the intensity of the outbreak but were unsuccessful in reducing Rt below 1. This highlights a need for a systematic investigation of the current public health interventions as well as a scientific surveillance tool that is sufficiently sensitive to outbreak temporal dynamics. Meanwhile, the developed model can serve as a public health tool to control the current outbreak and can be used to anticipate effective measures should a second wave re-emerge in Kuwait.HighlightsKuwait is experiencing a COVID-19 outbreak since the first imported case on Feb 24, 2020.We develop a mathematical model of disease transmission to provide a real-time tracking and forecasting tool for the epidemic outbreak in Kuwait as well as assess the potential epidemic and healthcare burdens and the effectiveness of early control measures.We calibrate the model against daily numbers of detected infection and death cases using a maximum likelihood framework.We find that early control measures had the effect of delaying and lowering the intensity of the outbreak but were unsuccessful in reducing the effective reproduction number below 1.

scholarly journals An analysis of school absences in England during the Covid-19 pandemic

2021 ◽  
Author(s):  
Emma Southall ◽  
Alex Holmes ◽  
Edward M. Hill ◽  
Benjamin D. Atkins ◽  
Trystan Leng ◽  
...  
Keyword(s):  
Secondary School ◽  
Secondary Schools ◽  
Primary Schools ◽  
School Settings ◽  
Weak Evidence ◽  
New Variant ◽  
Tier System ◽  
School Absences ◽  
The Uk ◽  
Tier 3

AbstractThe introduction of SARS-CoV-2, the virus that causes COVID-19 infection, in the UK in early 2020, resulted in the UK government introducing several control policies in order to reduce the spread of disease. As part of these restrictions, schools were closed to all pupils in March (except for vulnerable and key worker children), before re-opening to certain year groups in June. Finally all school children returned to the classroom in September. In this paper, we analyse the data on school absences from September 2020 to December 2020 as a result of COVID-19 infection and how that varied through time as other measures in the community were introduced. We utilise data from the Educational Settings database compiled by the Department for Education and examine how pupil and teacher absences change in both primary and secondary schools.Our results show that absences as a result of COVID-19 infection rose steadily following the re-opening of schools in September. Cases in teachers were seen to decline during the November lockdown, particularly in those regions that had previously been in tier 3, the highest level of control at the time. Cases in secondary school pupils increased for the first two weeks of the November lockdown, before decreasing. Since the introduction of the tier system, the number of absences owing to confirmed infection in primary schools was observed to be significantly lower than in secondary schools across all regions and tiers.In December, we observed a large rise in the number of absences per school in secondary school settings in the South East and Greater London, but such rises were not observed in other regions or in primary school settings. We conjecture that the increased transmissibility of the new variant in these regions may have contributed to this rise in cases in secondary schools. Finally, we observe a positive correlation between cases in the community and cases in schools in most regions, with weak evidence suggesting that cases in schools lag behind cases in the surrounding community. We conclude that there is not significant evidence to suggest that schools are playing a significant role in driving spread in the community and that careful monitoring may be required as schools re-open to determine the effect associated with open schools upon community incidence.

scholarly journals Estimating the effective sample size in association studies of quantitative traits

2021 ◽  
Author(s):  
Andrey Ziyatdinov ◽  
Jihye Kim ◽  
Dmitry Prokopenko ◽  
Florian Privé ◽  
Fabien Laporte ◽  
...  
Keyword(s):  
Statistical Power ◽  
Quantitative Traits ◽  
Mixed Model ◽  
Association Studies ◽  
Effective Sample Size ◽  
Environment Interaction ◽  
Uk Biobank ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
The Uk

Abstract The effective sample size (ESS) is a metric used to summarize in a single term the amount of correlation in a sample. It is of particular interest when predicting the statistical power of genome-wide association studies (GWAS) based on linear mixed models. Here, we introduce an analytical form of the ESS for mixed-model GWAS of quantitative traits and relate it to empirical estimators recently proposed. Using our framework, we derived approximations of the ESS for analyses of related and unrelated samples and for both marginal genetic and gene-environment interaction tests. We conducted simulations to validate our approximations and to provide a quantitative perspective on the statistical power of various scenarios, including power loss due to family relatedness and power gains due to conditioning on the polygenic signal. Our analyses also demonstrate that the power of gene-environment interaction GWAS in related individuals strongly depends on the family structure and exposure distribution. Finally, we performed a series of mixed-model GWAS on data from the UK Biobank and confirmed the simulation results. We notably found that the expected power drop due to family relatedness in the UK Biobank is negligible.

scholarly journals Impact of COVID-19 pandemic social restriction measures on people with rheumatic and musculoskeletal diseases in the UK: a mixed-methods study

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e048772
Author(s):  
Toby O Smith ◽  
Pippa Belderson ◽  
Jack R Dainty ◽  
Linda Birt ◽  
Karen Durrant ◽  
...  
Keyword(s):  
Mixed Methods ◽  
Qualitative Study ◽  
Online Survey ◽  
Musculoskeletal Diseases ◽  
Community Dwelling ◽  
Secondary Outcome ◽  
Healthcare Provision ◽  
Social Restriction ◽  
The Uk ◽  
The Impact

ObjectivesTo determine the impact of COVID-19 pandemic social restriction measures on people with rheumatic and musculoskeletal diseases (RMDs) and to explore how people adapted to these measures over time.DesignMixed-methods investigation comprising a national online longitudinal survey and embedded qualitative study.SettingUK online survey and interviews with community-dwelling individuals in the East of England.ParticipantsPeople in the UK with RMDs were invited to participate in an online survey. A subsection of respondents were invited to participate in the embedded qualitative study.Primary and secondary outcome measuresThe online survey, completed fortnightly over 10 weeks from April 2020 to August 2020, investigated changes in symptoms, social isolation and loneliness, resilience and optimism. Qualitative interviews were undertaken assessing participant’s perspectives on changes in symptoms, exercising, managing instrumental tasks such a shopping, medication and treatment regimens and how they experienced changes in their social networks.Results703 people with RMDs completed the online survey. These people frequently reported a deterioration in symptoms as a result of COVID-19 pandemic social restrictions (52% reported increase vs 6% reported a decrease). This was significantly worse for those aged 18–60 years compared with older participants (p=0.017). The qualitative findings from 26 individuals with RMDs suggest that the greatest change in daily life was experienced by those in employment. Although some retired people reported reduced opportunity for exercise outside their homes, they did not face the many competing demands experienced by employed people and people with children at home.ConclusionsPeople with RMDs reported a deterioration in symptoms when COVID-19 pandemic social restriction measures were enforced. This was worse for working-aged people. Consideration of this at-risk group, specifically for the promotion of physical activity, changing home-working practices and awareness of healthcare provision is important, as social restrictions continue in the UK.

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