{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:52:13Z","timestamp":1790776333039,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013723","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T00:00:00Z","timestamp":1763942400000}}],"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T00:00:00Z","timestamp":1763510400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100025287","name":"Center for Forecasting and Outbreak Analytics","doi-asserted-by":"publisher","award":["CDC-RFA-FT-23-0069"],"award-info":[{"award-number":["CDC-RFA-FT-23-0069"]}],"id":[{"id":"10.13039\/100025287","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Mathematical and computational models are often used to forecast respiratory infectious disease burden, including to inform healthcare capacity. We aimed to characterize pathways of clinical progression associated with SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) infections using data from patients aged 0 to &gt;90 years in an integrated healthcare system, whose encounters were monitored across all levels of acuity spanning virtual, ambulatory, and inpatient care settings. Using parametric survival models, we estimated probabilities of progression and distributions of time to progression from each setting to all higher-acuity settings on a cascade encompassing the following classes of events or encounters: symptoms onset; diagnostic testing; telehealth or other virtual care appointment; outpatient physician office visit; urgent care presentation; emergency department presentation; hospital admission; mechanical ventilation; and death. Our analyses included data from 59,668, 22,705, and 1,668 episodes associated with positive SARS-CoV-2, influenza, and RSV tests, respectively, between 1 April 2023 and 31 March 2024. First clinical encounters occurred in inpatient settings for only 4.7%, 3.4%, and 18.7% of SARS-CoV-2, influenza, and RSV episodes, respectively, with median times (interquartile range) of 6.8 (3.6-13.2), 6.6 (3.5-12.1), and 6.4 (3.8-10.6) days from symptoms onset to admission. Overall, 7.9% of SARS-CoV-2 episodes, 5.8% of influenza episodes, and 33.8% of RSV episodes resulted in inpatient admission, ventilation, or death. Between 40.4-62.1%, 71.6-87.3%, and 47.9-58.7% of SARS-CoV-2, influenza, and RSV infections, respectively, had encounters in lower-acuity virtual care, outpatient, or urgent care settings. For all three viruses, the proportions of cases receiving care at each level of acuity increased with older age and greater numbers of comorbid conditions. Median durations of hospital stay were 4.2 (2.6, 7.3), 4.0 (2.3, 6.8), and 4.3 (2.5, 7.4) days for SARS-CoV-2, influenza, and RSV episodes resulting in admission. These estimates provide a basis for modeling real-world clinical care requirements and the progression of respiratory viral infections.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013723","type":"journal-article","created":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T18:42:25Z","timestamp":1763577745000},"page":"e1013723","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population"],"prefix":"10.1371","volume":"21","author":[{"given":"Noah T.","family":"Parker","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vennis","family":"Hong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregg S.","family":"Davis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena","family":"Pomichowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iris A.","family":"Reyes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fagen","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola F.","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Rodriguez-Barraquer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2336-8476","authenticated-orcid":true,"given":"Sara Y.","family":"Tartof","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5417-8475","authenticated-orcid":true,"given":"Joseph A.","family":"Lewnard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,11,19]]},"reference":[{"key":"pcbi.1013723.ref001","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s40121-024-01080-4","article-title":"Burden of Acute Respiratory Infections Caused by Influenza Virus, Respiratory Syncytial Virus, and SARS-CoV-2 with Consideration of Older Adults: A Narrative Review","volume":"14","author":"WP Hanage","year":"2025","journal-title":"Infect Dis Ther"},{"issue":"27","key":"pcbi.1013723.ref002","doi-asserted-by":"crossref","first-page":"3960","DOI":"10.1016\/j.vaccine.2018.05.057","article-title":"Economic burden of seasonal influenza in the United States","volume":"36","author":"WCWS Putri","year":"2018","journal-title":"Vaccine"},{"issue":"2","key":"pcbi.1013723.ref003","doi-asserted-by":"crossref","DOI":"10.1093\/infdis\/jiad559","article-title":"The Annual Economic Burden of Respiratory Syncytial Virus in Adults in the United States","volume":"230","author":"J Carrico","year":"2024","journal-title":"J Infect Dis"},{"key":"pcbi.1013723.ref004","doi-asserted-by":"crossref","first-page":"100738","DOI":"10.1016\/j.epidem.2023.100738","article-title":"The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy","volume":"46","author":"SL Loo","year":"2024","journal-title":"Epidemics"},{"key":"pcbi.1013723.ref005","unstructured":"Ferguson N, Laydon D, Nedjati G i l a n i G, Imai N, Ainslie K, Baguelin M, et al. 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