{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:46:53Z","timestamp":1792788413138,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1014784","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000}}],"reference-count":93,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"Princeton Catalysis Initiative"},{"name":"Princeton Precision Health"},{"DOI":"10.13039\/100020601","name":"High Meadows Environmental Institute, Princeton University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002551","name":"Seoul National University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002551","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Research Foundation of Korea (NRF), Korea government","award":["RS-2026-25474574"],"award-info":[{"award-number":["RS-2026-25474574"]}],"id":[{"id":"https:\/\/ror.org\/013aysd81","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Research Foundation of Korea (NRF), Global-LAMP Program, Ministry of Education","award":["RS-2023-00301976"],"award-info":[{"award-number":["RS-2023-00301976"]}],"id":[{"id":"https:\/\/ror.org\/013aysd81","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Cancer Institute, National Institutes of Health","award":["Prime Contract No. 75N91019D00024, Task Order No. 75N91023F00016"],"award-info":[{"award-number":["Prime Contract No. 75N91019D00024, Task Order No. 75N91023F00016"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Many respiratory pathogens co-circulate within human populations. Yet, how pathogen community structure shapes the dynamics of infectious diseases remains poorly understood. At the population level, investigating polymicrobial dynamics, with potential underlying competitive or cooperative interactions, is challenging, because of confounding factors such as differing seasonality. This is particularly true for endemic pathogens which typically exhibit stable periodic dynamics. Their disruption due to the implementation of non-pharmaceutical interventions during the COVID-19 pandemic thus represents a unique large-scale natural experiment that can be leveraged to provide valuable insights into the complex interplay between respiratory pathogens. Here, we focus on the population dynamics of human rhinovirus (common cold) and on the potential viral interference of influenza A virus (flu A), which is hypothesized to account for their asynchronous circulation. Using a Bayesian framework, we first show based on simulations that exogenous perturbations can be a powerful tool to disentangle the contribution of pathogen interaction from other epidemiological factors. We then apply our framework to surveillance time series from the US and Canada spanning the COVID-19 pandemic. We estimate key parameters of rhinovirus but find no conclusive support for an influence of influenza A virus at the population level.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1014784","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T17:56:19Z","timestamp":1789149379000},"page":"e1014784","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Leveraging perturbations to infer the population dynamics of human rhinovirus and interaction of influenza A virus"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5761-1361","authenticated-orcid":true,"given":"Wakinyan","family":"Benhamou","sequence":"first","affiliation":[{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["Department of Ecology and Evolutionary Biology"]},{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["High Meadows Environmental Institute"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Howerton","sequence":"additional","affiliation":[{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["Department of Ecology and Evolutionary Biology"]},{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["High Meadows Environmental Institute"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sang Woo","family":"Park","sequence":"additional","affiliation":[{"name":"Seoul National University","place":["Seoul, Korea"],"department":["School of Biological Sciences"]},{"name":"Seoul National University","place":["Seoul, Korea"],"department":["Institute for Data Innovation in Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9cile","family":"Viboud","sequence":"additional","affiliation":[{"name":"National Institutes of Health","place":["Bethesda, Maryland, United States of America"],"department":["Fogarty International Center"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. Jessica E.","family":"Metcalf","sequence":"additional","affiliation":[{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["Department of Ecology and Evolutionary Biology"]},{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["High Meadows Environmental Institute"]},{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["Princeton School of Public and International Affairs"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan T.","family":"Grenfell","sequence":"additional","affiliation":[{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["Department of Ecology and Evolutionary Biology"]},{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["High Meadows Environmental Institute"]},{"name":"Princeton University","place":["Princeton, New Jersey, United States of America"],"department":["Princeton School of Public and International Affairs"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"issue":"1","key":"pcbi.1014784.ref001","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1128\/CMR.00077-12","article-title":"Human rhinoviruses","volume":"26","author":"SE Jacobs","year":"2013","journal-title":"Clin Microbiol Rev"},{"issue":"1","key":"pcbi.1014784.ref002","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s40348-016-0049-3","article-title":"Mechanism of human rhinovirus infections","volume":"3","author":"D Blaas","year":"2016","journal-title":"Mol Cell Pediatr"},{"key":"pcbi.1014784.ref003","doi-asserted-by":"crossref","first-page":"2412","DOI":"10.3389\/fmicb.2017.02412","article-title":"Rhinovirus Biology, Antigenic Diversity, and Advancements in the Design of a Human Rhinovirus Vaccine","volume":"8","author":"CC Stobart","year":"2017","journal-title":"Front Microbiol"},{"key":"pcbi.1014784.ref004","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.15337.1","article-title":"Recent advances in understanding rhinovirus immunity","volume":"7","author":"S Makris","year":"2018","journal-title":"F1000Res"},{"key":"pcbi.1014784.ref005","article-title":"Epidemiology of viral respiratory infections","author":"AS Monto","year":"2002","journal-title":"Am J Med"},{"issue":"1","key":"pcbi.1014784.ref006","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s44298-023-00008-y","article-title":"Rhinovirus dynamics across different social structures","volume":"1","author":"MM Luka","year":"2023","journal-title":"Npj Viruses"},{"key":"pcbi.1014784.ref007","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/oxfordjournals.epirev.a036024","article-title":"Mechanisms of transmission of rhinovirus infections","volume":"10","author":"JO Hendley","year":"1988","journal-title":"Epidemiologic Reviews"},{"issue":"4","key":"pcbi.1014784.ref008","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1007\/BF00145641","article-title":"Transmission and control of rhinovirus colds","volume":"3","author":"LC Jennings","year":"1987","journal-title":"Eur J Epidemiol"},{"issue":"10","key":"pcbi.1014784.ref009","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1002\/jmv.20956","article-title":"Environmental contamination with rhinovirus and transfer to fingers of healthy individuals by daily life activity","volume":"79","author":"B Winther","year":"2007","journal-title":"J Med Virol"},{"key":"pcbi.1014784.ref010","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1093\/infdis\/156.3.442","article-title":"Aerosol transmission of rhinovirus colds","volume":"156","author":"EC Dick","year":"1987","journal-title":"Journal of Infectious Diseases"},{"issue":"8","key":"pcbi.1014784.ref011","first-page":"733","article-title":"COVID-19 Shuts Doors to Flu but Keeps Them Open to Rhinoviruses","volume":"10","author":"I Kiseleva","year":"2021","journal-title":"Biology (Basel)"},{"key":"pcbi.1014784.ref012","doi-asserted-by":"crossref","unstructured":"Shaw SM, Pyle CJ, Patel ND, Edwards MR, Wang Z, Tregoning JS, et al. 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