{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T16:09:46Z","timestamp":1771258186700,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009807","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,15]],"date-time":"2022-03-15T00:00:00Z","timestamp":1647302400000}}],"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T00:00:00Z","timestamp":1645574400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Estimating the changes of epidemiological parameters, such as instantaneous reproduction number, <jats:italic>R<\/jats:italic><jats:sub><jats:italic>t<\/jats:italic><\/jats:sub>, is important for understanding the transmission dynamics of infectious diseases. Current estimates of time-varying epidemiological parameters often face problems such as lagging observations, averaging inference, and improper quantification of uncertainties. To address these problems, we propose a Bayesian data assimilation framework for time-varying parameter estimation. Specifically, this framework is applied to estimate the instantaneous reproduction number <jats:italic>R<\/jats:italic><jats:sub><jats:italic>t<\/jats:italic><\/jats:sub> during emerging epidemics, resulting in the state-of-the-art \u2018DARt\u2019 system. With DARt, time misalignment caused by lagging observations is tackled by incorporating observation delays into the joint inference of infections and <jats:italic>R<\/jats:italic><jats:sub><jats:italic>t<\/jats:italic><\/jats:sub>; the drawback of averaging is overcome by instantaneously updating upon new observations and developing a model selection mechanism that captures abrupt changes; the uncertainty is quantified and reduced by employing Bayesian smoothing. We validate the performance of DARt and demonstrate its power in describing the transmission dynamics of COVID-19. The proposed approach provides a promising solution for making accurate and timely estimation for transmission dynamics based on reported data.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009807","type":"journal-article","created":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T18:42:24Z","timestamp":1645641744000},"page":"e1009807","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1496-8923","authenticated-orcid":true,"given":"Xian","family":"Yang","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2947-8783","authenticated-orcid":true,"given":"Shuo","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Yuting","family":"Xing","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4026-0216","authenticated-orcid":true,"given":"Ling","family":"Li","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2080-4762","authenticated-orcid":true,"given":"Richard Yi Da","family":"Xu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7984-8909","authenticated-orcid":true,"given":"Karl J.","family":"Friston","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3075-2161","authenticated-orcid":true,"given":"Yike","family":"Guo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,2,23]]},"reference":[{"key":"pcbi.1009807.ref001","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1001\/jama.2020.6130","article-title":"Association of Public Health Interventions With the Epidemiology of the COVID-19 Outbreak in Wuhan, China.","volume":"323","author":"A Pan","year":"2020","journal-title":"JAMA"},{"key":"pcbi.1009807.ref002","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1126\/science.abb3221","article-title":"Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2).","volume":"368","author":"R Li","year":"2020","journal-title":"Science"},{"key":"pcbi.1009807.ref003","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.1009807.ref004","article-title":"Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand.","author":"M F Neil","year":"2020","journal-title":"Imp Coll COVID-19 Response Team"},{"key":"pcbi.1009807.ref005","article-title":"Impact assessment of non-pharmaceutical interventions against coronavirus disease 2019 and influenza in Hong Kong: an observational study","author":"BJ Cowling","year":"2020","journal-title":"Lancet Public Health"},{"key":"pcbi.1009807.ref006","article-title":"Effect of non-pharmaceutical interventions to contain COVID-19 in China.","author":"S Lai","year":"2020","journal-title":"Nature"},{"key":"pcbi.1009807.ref007","article-title":"Modeling COVID-19 scenarios for the United States","author":"RC Reiner","year":"2020","journal-title":"Nat Med"},{"key":"pcbi.1009807.ref008","doi-asserted-by":"crossref","first-page":"5710","DOI":"10.1038\/s41467-020-19393-6","article-title":"Modelling transmission and control of the COVID-19 pandemic in Australia.","volume":"11","author":"SL Chang","year":"2020","journal-title":"Nat Commun"},{"key":"pcbi.1009807.ref009","first-page":"700","article-title":"A contribution to the mathematical theory of epidemics","volume":"115","author":"WO Kermack","year":"1927","journal-title":"Proc R Soc Lond Ser Contain Pap Math Phys Character"},{"key":"pcbi.1009807.ref010","first-page":"2","article-title":"Estimating individual and household reproduction numbers in an emerging epidemic","author":"C. 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