{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T18:48:24Z","timestamp":1773168504205,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011021","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,4,12]],"date-time":"2023-04-12T00:00:00Z","timestamp":1681257600000}}],"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2023,3,31]],"date-time":"2023-03-31T00:00:00Z","timestamp":1680220800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12171396"],"award-info":[{"award-number":["12171396"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chongqing Science and Technology Program","award":["cstc2020jscx-cylhX0003"],"award-info":[{"award-number":["cstc2020jscx-cylhX0003"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Although some methods for estimating the instantaneous reproductive number during epidemics have been developed, the existing frameworks usually require information on the distribution of the serial interval and\/or additional contact tracing data. However, in the case of outbreaks of emerging infectious diseases with an unknown natural history or undetermined characteristics, the serial interval and\/or contact tracing data are often not available, resulting in inaccurate estimates for this quantity. In the present study, a new framework was specifically designed for joint estimates of the instantaneous reproductive number and serial interval. Concretely, a likelihood function for the two quantities was first introduced. Then, the instantaneous reproductive number and the serial interval were modeled parametrically as a function of time using the interpolation method and a known traditional distribution, respectively. Using the Bayesian information criterion and the Markov Chain Monte Carlo method, we ultimately obtained their estimates and distribution. The simulation study revealed that our estimates of the two quantities were consistent with the ground truth. Seven data sets of historical epidemics were considered and further verified the robust performance of our method. Therefore, to some extent, even if we know only the daily incidence, our method can accurately estimate the instantaneous reproductive number and serial interval to provide crucial information for policymakers to design appropriate prevention and control interventions during epidemics.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011021","type":"journal-article","created":{"date-parts":[[2023,3,31]],"date-time":"2023-03-31T18:15:46Z","timestamp":1680286546000},"page":"e1011021","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["A new method for the joint estimation of instantaneous reproductive number and serial interval during epidemics"],"prefix":"10.1371","volume":"19","author":[{"given":"Chenxi","family":"Dai","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongsheng","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6787-5018","authenticated-orcid":true,"given":"Kaifa","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2023,3,31]]},"reference":[{"key":"pcbi.1011021.ref001","first-page":"3","article-title":"Transmissibility of the influenza virus in the 1918 pandemic.","author":"LF White","year":"2008","journal-title":"PLoS One."},{"key":"pcbi.1011021.ref002","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1001\/jama.1988.03410040131049","article-title":"Smallpox and Its Eradication","volume":"260","author":"SS Hennein","year":"1988","journal-title":"JAMA J Am Med Assoc"},{"key":"pcbi.1011021.ref003","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000471","article-title":"Temporal variability and social heterogeneity in disease transmission: The case of SARS in Hong Kong.","volume":"5","author":"A Cori","year":"2009","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1011021.ref004","doi-asserted-by":"crossref","first-page":"113","DOI":"10.46234\/ccdcw2020.032","article-title":"The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19)\u2014China, 2020.","volume":"2","author":"CDC China","year":"2020","journal-title":"China CDC Wkly."},{"key":"pcbi.1011021.ref005","doi-asserted-by":"crossref","DOI":"10.3390\/v13020202","article-title":"Covid-19: A review on the novel coronavirus disease evolution, transmission, detection, control and prevention.","volume":"13","author":"A Sharma","year":"2021","journal-title":"Viruses."},{"key":"pcbi.1011021.ref006","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/aje\/kwt133","article-title":"A new framework and software to estimate time-varying reproduction numbers during epidemics","volume":"178","author":"A Cori","year":"2013","journal-title":"Am J Epidemiol"},{"key":"pcbi.1011021.ref007","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1002\/sim.3136","article-title":"A likelihood-based method for real-time estimation of the serial interval and reproductive number of an epidemic.","volume":"27","author":"LF White","year":"2008","journal-title":"Stat Med"},{"key":"pcbi.1011021.ref008","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/aje\/kwh255","article-title":"Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal","volume":"160","author":"J Wallinga","year":"2004","journal-title":"Am J Epidemiol"},{"key":"pcbi.1011021.ref009","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1093\/aje\/kwg251","article-title":"The Interval between Successive Cases of an Infectious Disease","volume":"158","author":"PEM Fine","year":"2003","journal-title":"Am J Epidemiol"},{"key":"pcbi.1011021.ref010","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.mbs.2006.10.010","article-title":"A note on generation times in epidemic models","volume":"208","author":"\u00c5. 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