{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T17:42:13Z","timestamp":1790790133759,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1012883","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,1,30]],"date-time":"2025-01-30T00:00:00Z","timestamp":1738195200000}}],"reference-count":87,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2025,1,24]],"date-time":"2025-01-24T00:00:00Z","timestamp":1737676800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Penn University Research Foundation"},{"name":"Penn Center for Global Genomics and Health Equity Keystone Pilot Grant","award":["GGHE-KP-2021-001"],"award-info":[{"award-number":["GGHE-KP-2021-001"]}]},{"name":"Penn Center for Research on Coronaviruses and Other Emerging Pathogens"},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["R61\/33-HL137063"],"award-info":[{"award-number":["R61\/33-HL137063"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Penn Center for AIDS Research","award":["P30-AI045008"],"award-info":[{"award-number":["P30-AI045008"]}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    SARS-CoV-2 continues to transmit and evolve in humans and animals. White-tailed deer (\n                    <jats:italic>Odocoileus virginianus<\/jats:italic>\n                    ) have been previously identified as a zoonotic reservoir for SARS-CoV-2 with high rates of infection and probable spillback into humans. Here we report sampling 1,127 white-tailed deer (WTD) in Pennsylvania, and a genomic analysis of viral dynamics spanning 1,017 days between April 2021 and January 2024. To assess viral load and genotypes, RNA was isolated from retropharyngeal lymph nodes and analyzed using RT-qPCR and viral whole genome sequencing. Samples showed a 14.64% positivity rate by RT-qPCR. Analysis showed no association of SARS-CoV-2 prevalence with age, sex, or diagnosis with Chronic Wasting Disease. From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. The viral variants identified included 17 Alpha, 11 Delta, and 14 Omicron. Alpha largely stopped circulating in humans around September 2021, but persisted in WTD as recently as March of 2023. Phylodynamic analysis of pooled genomic data from Pennsylvania documents at least 12 SARS-CoV-2 spillovers from humans into WTD, including a recent series of Omicron spillovers. Prevalence was higher in WTD in regions with crop coverage rather than forest, suggesting an association with proximity to humans. Analysis of seasonality showed increased prevalence in winter and spring. Multiple examples of recurrent mutations were identified associated with transmissions, suggesting WTD-specific evolutionary pressures. These data document ongoing infections in white-tailed deer, probable onward transmission in deer, and a remarkable rate of new spillovers from humans.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1012883","type":"journal-article","created":{"date-parts":[[2025,1,24]],"date-time":"2025-01-24T14:20:44Z","timestamp":1737728444000},"page":"e1012883","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021\u20132024"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8887-7242","authenticated-orcid":true,"given":"Andrew D.","family":"Marques","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Hogenauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Bauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Gibison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beatrice","family":"DeMarco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Sherrill-Mix","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carter","family":"Merenstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald G.","family":"Collman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roderick B.","family":"Gagne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4740-4056","authenticated-orcid":true,"given":"Frederic D.","family":"Bushman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,1,24]]},"reference":[{"key":"ppat.1012883.ref001","unstructured":"Organization WH. 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Pereira","year":"2022","journal-title":"Ecohealth"},{"issue":"2","key":"ppat.1012883.ref005","article-title":"SARS-CoV-2 infection in captive hippos (Hippopotamus amphibius), Belgium","volume":"13","author":"F Vercammen","year":"2023","journal-title":"Animals (Basel)"},{"issue":"5","key":"ppat.1012883.ref006","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s10344-022-01608-4","article-title":"Detection of SARS-CoV-2 in a free ranging leopard (Panthera pardus fusca) in India","volume":"68","author":"S Mahajan","year":"2022","journal-title":"Eur J Wildl Res"},{"issue":"5","key":"ppat.1012883.ref007","doi-asserted-by":"crossref","first-page":"e3346","DOI":"10.1111\/tbed.14625","article-title":"Detection of SARS-CoV-2 clade B.1.2 in three snow leopards","volume":"69","author":"L Wang","year":"2022","journal-title":"Transbound Emerg Dis"},{"key":"ppat.1012883.ref008","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.jcpa.2022.03.005","article-title":"Natural 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Kemp","year":"2021","journal-title":"Nature"},{"issue":"2","key":"ppat.1012883.ref040","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.jiph.2018.09.008","article-title":"Epidemiology and predictors of survival of MERS-CoV infections in Riyadh region, 2014\u20132015","volume":"12","author":"FS Al-Jasser","year":"2019","journal-title":"J Infect Public Health"},{"issue":"12","key":"ppat.1012883.ref041","doi-asserted-by":"crossref","first-page":"1834","DOI":"10.3201\/eid1212.060401","article-title":"Review of bats and SARS","volume":"12","author":"L Wang","year":"2006","journal-title":"Emerg Infect Dis"},{"key":"ppat.1012883.ref042","volume-title":"An annual report on the status of white-tailed deer - the foundation of the hunting industry in North America","author":"National Deer Association S","year":"2022"},{"key":"ppat.1012883.ref043","volume-title":"Monitoring deer populations in Pennsylvania","author":"CR 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