{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T02:51:19Z","timestamp":1776999079817,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010406","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:00:00Z","timestamp":1663286400000}}],"reference-count":36,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2022,9,6]],"date-time":"2022-09-06T00:00:00Z","timestamp":1662422400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emergency Preparedness and Response"},{"name":"Wellcome Trust and the Royal Society","award":["202562\/Z\/16\/Z"],"award-info":[{"award-number":["202562\/Z\/16\/Z"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["219992\/Z\/19\/Z"],"award-info":[{"award-number":["219992\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/V038613\/1"],"award-info":[{"award-number":["MR\/V038613\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/W011840\/1"],"award-info":[{"award-number":["EP\/W011840\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/R018561\/1"],"award-info":[{"award-number":["EP\/R018561\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["UNS73114"],"award-info":[{"award-number":["UNS73114"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"crossref","award":["INF\\R2\\180067"],"award-info":[{"award-number":["INF\\R2\\180067"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014013","name":"UKRI","doi-asserted-by":"crossref","award":["MR\/V038613\/1"],"award-info":[{"award-number":["MR\/V038613\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Wellcome Trust and the Royal Society","award":["107652\/Z\/15\/Z"],"award-info":[{"award-number":["107652\/Z\/15\/Z"]}]},{"DOI":"10.13039\/100007421","name":"Li Ka Shing Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007421","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute for Health Research Policy Research Programme in Operational Research"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The first year of the COVID-19 pandemic put considerable strain on healthcare systems worldwide. In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and parameterisation of a hospital progression model, EpiBeds, which was coupled to a model of the generalised epidemic. In this model, individuals progress through different pathways (e.g. may recover, die, or progress to intensive care and recover or die) and data from a partially complete patient-pathway line-list was used to provide initial estimates of the mean duration that individuals spend in the different hospital compartments. We then fitted EpiBeds using complete data on hospital occupancy and hospital deaths, enabling estimation of the proportion of individuals that follow the different clinical pathways, the reproduction number of the generalised epidemic, and to make short-term predictions of hospital bed demand. The construction of EpiBeds makes it straightforward to adapt to different patient pathways and settings beyond England. As part of the UK response to the pandemic, EpiBeds provided weekly forecasts to the NHS for hospital bed occupancy and admissions in England, Wales, Scotland, and Northern Ireland at national and regional scales.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010406","type":"journal-article","created":{"date-parts":[[2022,9,6]],"date-time":"2022-09-06T17:51:46Z","timestamp":1662486706000},"page":"e1010406","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":22,"title":["EpiBeds: Data informed modelling of the COVID-19 hospital burden in England"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8433-4010","authenticated-orcid":true,"given":"Christopher E.","family":"Overton","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenzo","family":"Pellis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9938-8452","authenticated-orcid":true,"given":"Helena B.","family":"Stage","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0250-4555","authenticated-orcid":true,"given":"Francesca","family":"Scarabel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8530-0464","authenticated-orcid":true,"given":"Joshua","family":"Burton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Fraser","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Hall","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas A.","family":"House","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Jewell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7107-1656","authenticated-orcid":true,"given":"Anel","family":"Nurtay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filippo","family":"Pagani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrina A.","family":"Lythgoe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,9,6]]},"reference":[{"issue":"1","key":"pcbi.1010406.ref001","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s10729-006-9000-9","article-title":"Short term hospital occupancy prediction","volume":"10","author":"SJ Littig","year":"2007","journal-title":"Health Care Manage Sci"},{"key":"pcbi.1010406.ref002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.orhc.2019.01.002","article-title":"Forecasting arrivals and occupancy levels in an emergency department","volume":"21","author":"W Whitt","year":"2019","journal-title":"Operations Research for Health Care"},{"issue":"1","key":"pcbi.1010406.ref003","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1186\/s12913-021-06509-x","article-title":"Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England","volume":"21","author":"QJ Leclerc","year":"2021","journal-title":"BMC Health Serv Res"},{"key":"pcbi.1010406.ref004","article-title":"Reproduction number (R) and growth rate (r) of the COVID-19 epidemic in the UK: methods of estimation, data sources, causes of heterogeneity, and use as a guide in policy formulation","volume":"2020","author":"R Anderson","year":"2020","journal-title":"The Royal Society"},{"key":"pcbi.1010406.ref005","article-title":"Short-term forecasts to inform the response to the Covid-19 epidemic in the UK","author":"S Funk","year":"2020","journal-title":"medRxiv preprint\u2014BMJ Yale"},{"key":"pcbi.1010406.ref006","unstructured":"Pellis L, Birrell PJ, Blake J, Overton CE, Scarabel F, Stage HB, et al. Estimation of reproduction numbers in real time: conceptual and statistical challenges. Journal of the Royal Statistical Society Series A. (to appear)."},{"key":"pcbi.1010406.ref007","author":"ECDC","year":"2020","journal-title":"COVID-19 surveillance report Week 25, 2020"},{"key":"pcbi.1010406.ref008","author":"ISARIC","year":"2020","journal-title":"ISARIC COVID-19 Report: 08 June 2020"},{"key":"pcbi.1010406.ref009","unstructured":"Coronavirus modelling [Internet]. Norwegian Institute of Public Health. [cited 2021 Sep 10]. Available from: https:\/\/www.fhi.no\/en\/id\/infectious-diseases\/coronavirus\/coronavirus-modelling-at-the-niph-fhi\/."},{"issue":"21","key":"pcbi.1010406.ref010","doi-asserted-by":"crossref","first-page":"2012","DOI":"10.1056\/NEJMoa2004500","article-title":"Covid-19 in Critically Ill Patients in the Seattle Region\u2014Case Series","volume":"382","author":"PK Bhatraju","year":"2020","journal-title":"New England Journal of Medicine"},{"key":"pcbi.1010406.ref011","author":"ICNARC","year":"2020","journal-title":"ICNARC report on COVID-19 in critical care 17 July 2020"},{"key":"pcbi.1010406.ref012","doi-asserted-by":"crossref","first-page":"m1966","DOI":"10.1136\/bmj.m1966","article-title":"Factors associated with hospital admission and critical illness among 5279 people with coronavirus disease 2019 in New York City: prospective cohort study","volume":"369","author":"CM Petrilli","year":"2020","journal-title":"BMJ"},{"issue":"16","key":"pcbi.1010406.ref013","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1001\/jama.2020.5394","article-title":"Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region, Italy","volume":"323","author":"G Grasselli","year":"2020","journal-title":"Jama"},{"key":"pcbi.1010406.ref014","doi-asserted-by":"crossref","first-page":"m1923","DOI":"10.1136\/bmj.m1923","article-title":"Incidence, clinical outcomes, and transmission dynamics of severe coronavirus disease 2019 in California and Washington: prospective cohort study","volume":"369","author":"JA Lewnard","year":"2020","journal-title":"BMJ"},{"issue":"4","key":"pcbi.1010406.ref015","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.jinf.2020.10.033","article-title":"First and second COVID-19 waves in Japan: A comparison of disease severity and characteristics","volume":"82","author":"S Saito","year":"2021","journal-title":"Journal of Infection"},{"issue":"3","key":"pcbi.1010406.ref016","doi-asserted-by":"crossref","first-page":"e0248029","DOI":"10.1371\/journal.pone.0248029","article-title":"First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain","volume":"16","author":"S Iftimie","year":"2021","journal-title":"PloS one"},{"key":"pcbi.1010406.ref017","article-title":"Th\u00e9orie des syst\u00e8mes \u00e9volutifs","volume":"22","author":"T. Vogel","year":"1965","journal-title":"Gauthier-Villars"},{"issue":"1829","key":"pcbi.1010406.ref018","doi-asserted-by":"crossref","first-page":"20200264","DOI":"10.1098\/rstb.2020.0264","article-title":"Challenges in control of COVID-19: short doubling time and long delay to effect of interventions","volume":"376","author":"L Pellis","year":"2021","journal-title":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"key":"pcbi.1010406.ref019","article-title":"COVID-19 infectivity profile correction","author":"P Ashcroft","year":"2020","journal-title":"arXiv preprint arXiv:200706602"},{"issue":"6491","key":"pcbi.1010406.ref020","doi-asserted-by":"crossref","first-page":"eabb6936","DOI":"10.1126\/science.abb6936","article-title":"Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing","volume":"368","author":"L Ferretti","year":"2020","journal-title":"Science"},{"key":"pcbi.1010406.ref021","volume-title":"Retrieved June 12, 2020","author":"FHI COVID-19 modelling team","year":"2020"},{"issue":"6500","key":"pcbi.1010406.ref022","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1126\/science.abc3517","article-title":"Estimating the burden of SARS-CoV-2 in France","volume":"369","author":"H Salje","year":"2020","journal-title":"Science"},{"issue":"1","key":"pcbi.1010406.ref023","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1186\/s12879-021-06371-6","article-title":"Hospital length of stay for COVID-19 patients: Data-driven methods for forward planning","volume":"21","author":"B Vekaria","year":"2021","journal-title":"BMC Infectious Diseases"},{"issue":"8","key":"pcbi.1010406.ref024","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1038\/s41591-020-0962-9","article-title":"Age-dependent effects in the transmission and control of COVID-19 epidemics","volume":"26","author":"NG Davies","year":"2020","journal-title":"Nat Med"},{"key":"pcbi.1010406.ref025","article-title":"Epidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China","author":"Y Dong","year":"2020","journal-title":"Pediatrics"},{"issue":"7821","key":"pcbi.1010406.ref026","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/s41586-020-2488-1","article-title":"Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo\u2019","volume":"584","author":"E Lavezzo","year":"2020","journal-title":"Nature"},{"issue":"10","key":"pcbi.1010406.ref027","doi-asserted-by":"crossref","first-page":"2000180","DOI":"10.2807\/1560-7917.ES.2020.25.10.2000180","article-title":"Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020","volume":"25","author":"K Mizumoto","year":"2020","journal-title":"Eurosurveillance"},{"key":"pcbi.1010406.ref028","author":"H Streeck","year":"2020","journal-title":"Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event"},{"issue":"49","key":"pcbi.1010406.ref029","doi-asserted-by":"crossref","first-page":"2000790","DOI":"10.2807\/1560-7917.ES.2020.25.49.2000790","article-title":"Epidemiological characteristics of COVID-19 cases and estimates of the reproductive numbers 1 month into the epidemic, Italy, 28 January to 31 March 2020","volume":"25","author":"F Riccardo","year":"2020","journal-title":"Eurosurveillance"},{"key":"pcbi.1010406.ref030","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.ijid.2020.04.034","article-title":"The relative transmissibility of asymptomatic COVID-19 infections among close contacts","volume":"94","author":"D He","year":"2020","journal-title":"International Journal of Infectious Diseases"},{"key":"pcbi.1010406.ref031","volume-title":"Modes of Contact and Risk of Transmission in COVID-19: A Prospective Cohort Study 4950 Close Contact Persons in Guangzhou of China [Internet]","author":"L Luo","year":"2020"},{"key":"pcbi.1010406.ref032","doi-asserted-by":"crossref","first-page":"e67308","DOI":"10.7554\/eLife.67308","article-title":"Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections","volume":"10","author":"CJ Illingworth","year":"2021","journal-title":"eLife"},{"key":"pcbi.1010406.ref033","unstructured":"Overton CE. EpiBeds [Internet]. Available from: https:\/\/github.com\/OvertonC\/EpiBeds."},{"issue":"6538","key":"pcbi.1010406.ref034","doi-asserted-by":"crossref","first-page":"eabg3055","DOI":"10.1126\/science.abg3055","article-title":"Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England","volume":"372","author":"NG Davies","year":"2021","journal-title":"Science"},{"issue":"6500","key":"pcbi.1010406.ref035","doi-asserted-by":"crossref","first-page":"eabb9789","DOI":"10.1126\/science.abb9789","article-title":"Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions","volume":"369","author":"J Dehning","year":"2020","journal-title":"Science"},{"issue":"7821","key":"pcbi.1010406.ref036","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41586-020-2521-4","article-title":"Factors associated with COVID-19-related death using OpenSAFELY","volume":"584","author":"EJ Williamson","year":"2020","journal-title":"Nature"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010406","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:00:00Z","timestamp":1663286400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010406","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T18:06:18Z","timestamp":1663351578000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010406"}},"subtitle":[],"editor":[{"given":"Claudio Jos\u00e9","family":"Struchiner","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,9,6]]},"references-count":36,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,9,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010406","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1010406","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,6]]}}}