{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:19:09Z","timestamp":1772173149884,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010724","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T00:00:00Z","timestamp":1670371200000}}],"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,23]],"date-time":"2022-11-23T00:00:00Z","timestamp":1669161600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000276","name":"Department of Health and Social Care","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000276","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Medical Research Council (MRC) Centre for Global Infectious Disease Analysis"},{"name":"National Institute for Health Research (NIHR) Health Protection Research Unit"},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["200861\/Z\/16\/Z, 200187\/Z\/15\/Z"],"award-info":[{"award-number":["200861\/Z\/16\/Z, 200187\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["US, U01CK0005-01-02"],"award-info":[{"award-number":["US, U01CK0005-01-02"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"NIHR","doi-asserted-by":"crossref","award":["Professorship"],"award-info":[{"award-number":["Professorship"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000272","name":"NIHR","doi-asserted-by":"crossref","award":["Senior Investigator Award"],"award-info":[{"award-number":["Senior Investigator Award"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["205456\/Z\/16\/Z"],"award-info":[{"award-number":["205456\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018814","name":"MRC-PHE Centre for Environment and Health","doi-asserted-by":"publisher","award":["MR\/L01341X\/1, MR\/S019669\/1"],"award-info":[{"award-number":["MR\/L01341X\/1, MR\/S019669\/1"]}],"id":[{"id":"10.13039\/501100018814","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Health Data Research UK"},{"DOI":"10.13039\/501100013342","name":"NIHR Imperial Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013342","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NIHR HPRUs in Chemical and Radiation Threats and Hazards, and Environmental Exposures and Health"},{"name":"British Heart Foundation Centre for Research Excellence at Imperial College London","award":["RE\/18\/4\/34215"],"award-info":[{"award-number":["RE\/18\/4\/34215"]}]},{"name":"UK Dementia Research Institute at Imperial","award":["MC_PC_17114"],"award-info":[{"award-number":["MC_PC_17114"]}]},{"DOI":"10.13039\/501100022111","name":"Huo Family Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100022111","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>t<\/jats:italic>\n                      <\/jats:sub>\n                      ) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>t<\/jats:italic>\n                      <\/jats:sub>\n                      of each relaxation of restrictions.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>t<\/jats:italic>\n                      <\/jats:sub>\n                      increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>t<\/jats:italic>\n                      <\/jats:sub>\n                      increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec005\">\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays\/closures playing a significant part.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pcbi.1010724","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T11:19:13Z","timestamp":1669288753000},"page":"e1010724","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Trends in SARS-CoV-2 infection prevalence during England\u2019s roadmap out of lockdown, January to July 2021"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8086-4495","authenticated-orcid":true,"given":"Oliver","family":"Eales","sequence":"first","affiliation":[]},{"given":"Haowei","family":"Wang","sequence":"additional","affiliation":[]},{"given":"David","family":"Haw","sequence":"additional","affiliation":[]},{"given":"Kylie E. C.","family":"Ainslie","sequence":"additional","affiliation":[]},{"given":"Caroline E.","family":"Walters","sequence":"additional","affiliation":[]},{"given":"Christina","family":"Atchison","sequence":"additional","affiliation":[]},{"given":"Graham","family":"Cooke","sequence":"additional","affiliation":[]},{"given":"Wendy","family":"Barclay","sequence":"additional","affiliation":[]},{"given":"Helen","family":"Ward","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7815-7989","authenticated-orcid":true,"given":"Ara","family":"Darzi","sequence":"additional","affiliation":[]},{"given":"Deborah","family":"Ashby","sequence":"additional","affiliation":[]},{"given":"Christl A.","family":"Donnelly","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Elliott","sequence":"additional","affiliation":[]},{"given":"Steven","family":"Riley","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,11,23]]},"reference":[{"key":"pcbi.1010724.ref001","first-page":"27","article-title":"Impact of a Nationwide Lockdown on SARS-CoV-2 Transmissibility, Italy","author":"G Guzzetta","year":"2021","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1010724.ref002","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1001\/jama.2020.7878","article-title":"Public Health Measures and the Reproduction Number of SARS-CoV-2","volume":"323","author":"TV Inglesby","year":"2020","journal-title":"JAMA"},{"key":"pcbi.1010724.ref003","first-page":"13","article-title":"Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England","author":"ES Knock","year":"2021","journal-title":"Sci Transl Med"},{"key":"pcbi.1010724.ref004","first-page":"118","article-title":"The effects of school closures on SARS-CoV-2 among parents and teachers","author":"J Vlachos","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010724.ref005","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0140-6736(20)32661-1","article-title":"Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK","volume":"397","author":"M Voysey","year":"2021","journal-title":"Lancet"},{"key":"pcbi.1010724.ref006","doi-asserted-by":"crossref","first-page":"2603","DOI":"10.1056\/NEJMoa2034577","article-title":"Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine","volume":"383","author":"FP Polack","year":"2020","journal-title":"N Engl J Med"},{"key":"pcbi.1010724.ref007","article-title":"10 Downing. Prime Minister announces national lockdown.","author":"Street Prime Minister\u2019s Office","year":"2021","journal-title":"In: GOV.UK [Internet]."},{"key":"pcbi.1010724.ref008","unstructured":"COVID-19 Response\u2014Spring 2021 (Summary). In: GOV.UK [Internet]. [cited 11 Jan 2022]. Available from: https:\/\/www.gov.uk\/government\/publications\/covid-19-response-spring-2021\/covid-19-response-spring-2021-summary."},{"key":"pcbi.1010724.ref009","unstructured":"Prime Minister\u2019s Office,. Vaccination programme accelerated as Step 4 is paused. In: GOV.UK [Internet]. 14 Jun 2021 [cited 12 Jan 2022]. Available from: https:\/\/www.gov.uk\/government\/news\/vaccination-programme-accelerated-as-step-4-is-paused."},{"key":"pcbi.1010724.ref010","doi-asserted-by":"crossref","first-page":"eabn8347","DOI":"10.1126\/science.abn8347","article-title":"Rapid increase in Omicron infections in England during December 2021: REACT-1 study","volume":"375","author":"P Elliott","year":"2022","journal-title":"Science"},{"key":"pcbi.1010724.ref011","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1159\/000507587","article-title":"Epidemic Surveillance of Covid-19: Considering Uncertainty and Under-Ascertainment.","volume":"38","author":"V Ricoca Peixoto","year":"2020","journal-title":"Portuguese Journal of Public Health"},{"key":"pcbi.1010724.ref012","doi-asserted-by":"crossref","first-page":"200","DOI":"10.12688\/wellcomeopenres.16228.1","article-title":"REal-time Assessment of Community Transmission (REACT) of SARS-CoV-2 virus: Study protocol.","volume":"5","author":"S Riley","year":"2020","journal-title":"Wellcome Open Research"},{"key":"pcbi.1010724.ref013","first-page":"269","article-title":"Weighting survey results","volume":"28","author":"T. Sharot","year":"1986","journal-title":"J Mark Res Soc"},{"key":"pcbi.1010724.ref014","doi-asserted-by":"crossref","first-page":"100604","DOI":"10.1016\/j.epidem.2022.100604","article-title":"Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number","volume":"40","author":"O Eales","year":"2022","journal-title":"Epidemics"},{"key":"pcbi.1010724.ref015","article-title":"The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo","author":"MD Hoffman","year":"2011","journal-title":"arXiv [stat.CO]."},{"key":"pcbi.1010724.ref016","unstructured":"Stan Development Team. RStan: the R interface to Stan. 2020. Available from: http:\/\/mc-stan.org\/."},{"key":"pcbi.1010724.ref017","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/S1473-3099(20)30287-5","article-title":"Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study","volume":"20","author":"Q Bi","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1010724.ref018","article-title":"Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England","author":"S Abbott","year":"2022","journal-title":"bioRxiv"},{"key":"pcbi.1010724.ref019","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1177\/0962280216673676","article-title":"Estimating age-specific reproductive numbers-A comparison of methods","volume":"27","author":"CB Moser","year":"2018","journal-title":"Stat Methods Med Res"},{"key":"pcbi.1010724.ref020","unstructured":"Official UK Coronavirus Dashboard. [cited 20 Mar 2022]. Available from: https:\/\/coronavirus.data.gov.uk\/."},{"key":"pcbi.1010724.ref021","unstructured":"COVID-19 Genomic Surveillance\u2013Wellcome Sanger Institute. [cited 21 Feb 2022]. Available from: https:\/\/covid19.sanger.ac.uk\/lineages\/raw."},{"key":"pcbi.1010724.ref022","first-page":"599","article-title":"How generation intervals shape the relationship between growth rates and reproductive numbers","volume":"274","author":"J Wallinga","year":"2007","journal-title":"Proc Biol Sci"},{"key":"pcbi.1010724.ref023","article-title":"Social contacts in the UK from the CoMix social contact survey Report for survey week 69","author":"C Jarvis","year":"2021","journal-title":"London School of Hygiene and Tropical Medicine"},{"key":"pcbi.1010724.ref024","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1016\/S0140-6736(21)02276-5","article-title":"Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study","volume":"398","author":"R Sonabend","year":"2021","journal-title":"Lancet"},{"key":"pcbi.1010724.ref025","article-title":"Context-specific emergence and growth of the SARS-CoV-2 Delta variant.","author":"M Kraemer","year":"2021","journal-title":"Res Sq."},{"key":"pcbi.1010724.ref026","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S1473-3099(20)30785-4","article-title":"The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 131 countries","volume":"21","author":"Y Li","year":"2021","journal-title":"Lancet Infect Dis"},{"key":"pcbi.1010724.ref027","doi-asserted-by":"crossref","first-page":"3560","DOI":"10.1038\/s41467-021-23865-8","article-title":"Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States","volume":"12","author":"B Yang","year":"2021","journal-title":"Nat Commun"},{"key":"pcbi.1010724.ref028","doi-asserted-by":"crossref","first-page":"e053371","DOI":"10.1136\/bmjopen-2021-053371","article-title":"Do school closures and school reopenings affect community transmission of COVID-19? A systematic review of observational studies","volume":"11","author":"S Walsh","year":"2021","journal-title":"BMJ Open"},{"key":"pcbi.1010724.ref029","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1186\/s12916-021-02107-0","article-title":"CMMID COVID-19 Working Group, et al. Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data","volume":"19","author":"JD Munday","year":"2021","journal-title":"BMC Med"},{"key":"pcbi.1010724.ref030","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1038\/s41467-021-20991-1","article-title":"Assessing the influence of climate on wintertime SARS-CoV-2 outbreaks","volume":"12","author":"RE Baker","year":"2021","journal-title":"Nat Commun."},{"key":"pcbi.1010724.ref031","doi-asserted-by":"crossref","first-page":"102","DOI":"10.12688\/wellcomeopenres.17723.1","article-title":"Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2.","volume":"7","author":"O Eales","year":"2022","journal-title":"Wellcome Open Res"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010724","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T00:00:00Z","timestamp":1670371200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010724","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T13:48:36Z","timestamp":1670420916000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010724"}},"subtitle":[],"editor":[{"given":"Benjamin","family":"Althouse","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,11,23]]},"references-count":31,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010724","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.06.02.22275900","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,23]]}}}