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

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.

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

10.1101/2021.02.23.21252277 ◽

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.

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

10.1101/2021.01.03.21249169 ◽

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.

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

Frontiers in Public Health ◽

10.3389/fpubh.2021.675065 ◽

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.

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

BMJ Open ◽

10.1136/bmjopen-2021-048772 ◽

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

Value in Health ◽

10.1016/j.jval.2021.04.1238 ◽

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

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Cardiovascular-related deaths at the beginning of the COVID-19 outbreak: a prospective analysis based on the UK Biobank

BMJ Open ◽

10.1136/bmjopen-2020-046931 ◽

2021 ◽

Vol 11 (6) ◽

pp. e046931

Author(s):

Junren Wang ◽

Jianwei Zhu ◽

Huazhen Yang ◽

Yao Hu ◽

Yajing Sun ◽

...

Keyword(s):

Primary Diagnosis ◽

Secondary Outcome ◽

Hospital Inpatient ◽

Reference Period ◽

Stress Reactions ◽

Uk Biobank ◽

The Uk ◽

The Impact ◽

Distinct Increase ◽

Related Mortality

ObjectiveTo assess the impact of the COVID-19 outbreak on cardiovascular disease (CVD) related mortality and hospitalisation.DesignCommunity-based prospective cohort study.SettingThe UK Biobank.Participants421 372 UK Biobank participants who were registered in England and alive as of 1 January 2020.Primary and secondary outcome measuresThe primary outcome of interest was CVD-related death, which was defined as death with CVD as a cause in the death register. We retrieved information on hospitalisations with CVD as the primary diagnosis from the UK Biobank hospital inpatient data. The study period was 1 January 2020 to June 30 2020, and we used the same calendar period of the three preceding years as the reference period. In order to control for seasonal variations and ageing of the study population, standardised mortality/incidence ratios (SMRs/SIRs) with 95% CIs were used to estimate the relative risk of CVD outcomes during the study period, compared with the reference period.ResultsWe observed a distinct increase in CVD-related deaths in March and April 2020, compared with the corresponding months of the three preceding years. The observed number of CVD-related deaths (n=218) was almost double in April, compared with the expected number (n=120) (SMR=1.82, 95% CI 1.58 to 2.07). In addition, we observed a significant decline in CVD-related hospitalisations from March onwards, with the lowest SIR observed in April (0.45, 95% CI 0.41 to 0.49).ConclusionsThere was a distinct increase in the number of CVD-related deaths in the UK Biobank population at the beginning of the COVID-19 outbreak. The shortage of medical resources for hospital care and stress reactions to the pandemic might have partially contributed to the excess CVD-related mortality, underscoring the need of sufficient healthcare resources and improved instructions to the public about seeking healthcare in a timely way.

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Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data

BMC Medicine ◽

10.1186/s12916-021-02107-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

James D. Munday ◽

Christopher I. Jarvis ◽

Amy Gimma ◽

Kerry L. M. Wong ◽

Kevin van Zandvoort ◽

...

Keyword(s):

Reproduction Number ◽

Transmission Rate ◽

Transmission Risk ◽

Individual Level ◽

Face To Face ◽

School Settings ◽

Contact Rates ◽

Contact Survey ◽

The Uk ◽

The Impact

Abstract Background Schools were closed in England on 4 January 2021 as part of increased national restrictions to curb transmission of SARS-CoV-2. The UK government reopened schools on 8 March. Although there was evidence of lower individual-level transmission risk amongst children compared to adults, the combined effects of this with increased contact rates in school settings and the resulting impact on the overall transmission rate in the population were not clear. Methods We measured social contacts of > 5000 participants weekly from March 2020, including periods when schools were both open and closed, amongst other restrictions. We combined these data with estimates of the susceptibility and infectiousness of children compared with adults to estimate the impact of reopening schools on the reproduction number. Results Our analysis indicates that reopening all schools under the same measures as previous periods that combined lockdown with face-to-face schooling would be likely to increase the reproduction number substantially. Assuming a baseline of 0.8, we estimated a likely increase to between 1.0 and 1.5 with the reopening of all schools or to between 0.9 and 1.2 reopening primary or secondary schools alone. Conclusion Our results suggest that reopening schools would likely halt the fall in cases observed between January and March 2021 and would risk a return to rising infections, but these estimates relied heavily on the latest estimates or reproduction number and the validity of the susceptibility and infectiousness profiles we used at the time of reopening.

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The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study

10.1101/2020.06.05.20123448 ◽

2020 ◽

Cited By ~ 1

Author(s):

Trystan Leng ◽

Connor White ◽

Joe Hilton ◽

Adam Kucharski ◽

Lorenzo Pellis ◽

...

Keyword(s):

Reproduction Number ◽

Base Case ◽

Exit Strategy ◽

Epidemic Threshold ◽

Case Scenario ◽

Base Case Scenario ◽

The Social ◽

The Uk ◽

The Impact ◽

Epidemic Risk

AbstractBackgroundDuring the Covid-19 lockdown, contact clustering in social bubbles may allow extending contacts beyond the household at minimal additional risk and hence has been considered as part of modified lockdown policy or a gradual lockdown exit strategy. We estimated the impact of such strategies on epidemic and mortality risk using the UK as a case study.MethodsWe used an individual based model for a synthetic population similar to the UK, that is stratified into transmission risks from the community, within the household and from other households in the same social bubble. The base case considers a situation where non-essential shops and schools are closed, the secondary household attack rate is 20% and the initial reproduction number is 0.8. We simulate a number of strategies including variations of social bubbles, i.e. the forming of exclusive pairs of households, for particular subsets of households (households including children and single occupancy households), as well as for all households. We test the sensitivity of the results to a range of alternative model assumptions and parameters.ResultsClustering contacts outside the household into exclusive social bubbles is an effective strategy of increasing contacts while limiting some of the associated increase in epidemic risk. In the base case scenario social bubbles reduced cases and fatalities by 17% compared to an unclustered increase of contacts. We find that if all households were to form social bubbles the reproduction number would likely increase to 1.1 and therefore beyond the epidemic threshold of one. However, strategies that allow households with young children or single occupancy households to form social bubbles only increased the reproduction number by less than 10%. The corresponding increase in morbidity and mortality is proportional to the increase in the epidemic risk but is largely focussed in older adults independently of whether these are included in the social bubbles.ConclusionsSocial bubbles can be an effective way of extending contacts beyond the household limiting the increase in epidemic risk, if managed appropriately.

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Study protocol for COvid-19 Vascular sERvice (COVER) study: The impact of the COVID-19 pandemic on the provision, practice and outcomes of vascular surgery

10.1101/2020.05.27.20114322 ◽

2020 ◽

Author(s):

Ruth A Benson

Keyword(s):

Vascular Surgery ◽

Service Provision ◽

British Society ◽

Tier 2 ◽

Patient Level ◽

Tier 1 ◽

Ethical Approval ◽

The Uk ◽

Tier 3 ◽

The Impact

ABSTRACTBackgroundThe novel Coronavirus Disease 2019 (COVID-19) pandemic is having a profound impact on global healthcare. Shortages in staff, operating theatre space and intensive care beds has led to a significant reduction in the provision of surgical care. Even vascular surgery, often insulated from resource scarcity due to its status as an urgent specialty, has limited capacity due to the pandemic. Furthermore, many vascular surgical patients are elderly with multiple comorbidities putting them at increased risk of COVID-19 and its complications. There is an urgent need to investigate the impact on patients presenting to vascular surgeons during the COVID-19 pandemic.Methods and AnalysisThe COvid-19 Vascular sERvice (COVER) study has been designed to investigate the worldwide impact of the COVID-19 pandemic on vascular surgery, at both service provision and individual patient level. COVER is running as a collaborative study through the Vascular and Endovascular Research Network (VERN) with the support of numerous national (Vascular Society of Great Britain and Ireland, British Society of Endovascular Therapy, British Society of Interventional Radiology, Rouleaux Club) and an evolving number of international organisations (Vascupedia, SingVasc, Audible Bleeding (USA), Australian and New Zealand Vascular Trials Network (ANZVTN)). The study has 3 ‘Tiers’: Tier 1 is a survey of vascular surgeons to capture longitudinal changes to the provision of vascular services within their hospital; Tier 2 captures data on vascular and endovascular procedures performed during the pandemic; and Tier 3 will capture any deviations to patient management strategies from prepandemic best practice. Data submission and collection will be electronic using online survey tools (Tier 1: SurveyMonkey® for service provision data) and encrypted data capture forms (Tiers 2 and 3: REDCap® for patient level data). Tier 1 data will undergo real-time serial analysis to determine longitudinal changes in practice, with country-specific analyses also performed. The analysis of Tier 2 and Tier 3 data will occur on completion of the study as per the prespecified statistical analysis plan.Ethical ApprovalEthical approval from the UK Health Research Authority has been obtained for Tiers 2 and 3 (20/NW/0196 Liverpool Central). Participating centres in the UK will be required to seek local research and development approval. Non-UK centres will need to obtain a research ethics committee or institutional review board approvals in accordance with national and/or local requirements.ISRCTN: 80453162 (https://doi.org/10.1186/ISRCTN80453162)Ethical Approval: 20/NW/0196 Liverpool Central, IRAS: 282224

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

10.21203/rs.3.rs-21900/v2 ◽

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.

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