{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T02:26:11Z","timestamp":1775096771234,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T00:00:00Z","timestamp":1735516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes for Health Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Coronavirus Variants Rapid Response Network","award":["ARR-175622"],"award-info":[{"award-number":["ARR-175622"]}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes for Health Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Coronavirus Variants Rapid Response Network","award":["ARR-175622"],"award-info":[{"award-number":["ARR-175622"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Infectious disease transmission to different host species makes eradication very challenging and expands the diversity of evolutionary trajectories taken by the pathogen. Since the beginning of the ongoing COVID-19 pandemic, SARS-CoV-2 has been transmitted from humans to many different animal species, in which viral variants of concern could potentially evolve. Previously, using available whole genome consensus sequences of SARS-CoV-2 from four commonly sampled animals (mink, deer, cat, and dog), we inferred similar numbers of transmission events from humans to each animal species. Using a genome-wide association study, we identified 26 single nucleotide variants (SNVs) that tend to occur in deer\u2014more than any other animal\u2014suggesting a high rate of viral adaptation to deer. The reasons for this rapid adaptive evolution remain unclear, but within-host evolution\u2014the ultimate source of the viral diversity that transmits globally\u2014could provide clues. Here, we quantify intra-host SARS-CoV-2 genetic diversity across animal species and show that deer harbor more intra-host SNVs (iSNVs) than other animals, providing a larger pool of genetic diversity for natural selection to act upon. Mixed infections involving more than one viral lineage are unlikely to explain the higher diversity within deer. Rather, a combination of higher mutation rates, longer infections, and species-specific selective pressures are likely explanations. Combined with extensive deer-to-deer transmission, the high levels of within-deer viral diversity help explain the apparent rapid adaptation of SARS-CoV-2 to deer.<\/jats:p>","DOI":"10.1093\/ve\/veae117","type":"journal-article","created":{"date-parts":[[2024,12,29]],"date-time":"2024-12-29T23:21:49Z","timestamp":1735514509000},"source":"Crossref","is-referenced-by-count":2,"title":["Within-host genetic diversity of SARS-CoV-2 across animal species"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-8310-3657","authenticated-orcid":false,"given":"Sana","family":"Naderi","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, McGill University , 3775 University Street Montreal, QC H3A 2B4,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Selena M","family":"Sagan","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, McGill University , 3775 University Street Montreal, QC H3A 2B4,","place":["Canada"]},{"name":"Department of Microbiology and Immunology, The University of British Columbia , 2350 Health Sciences Mall #1365 Vancouver, BC V6T 1Z3,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B. Jesse","family":"Shapiro","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, McGill University , 3775 University Street Montreal, QC H3A 2B4,","place":["Canada"]},{"name":"McGill Genome Centre , 740 avenue Dr Penfield Montreal, QC H3A 0G1,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,12,30]]},"reference":[{"key":"2025071112113861200_R1","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1016\/j.cell.2015.07.020","article-title":"Clinical sequencing uncovers origins and evolution of Lassa virus","volume":"162","author":"Andersen","year":"2015","journal-title":"Cell"},{"key":"2025071112113861200_R2","doi-asserted-by":"publisher","first-page":"1901","DOI":"10.1016\/j.cell.2020.10.049","article-title":"Case study: prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with 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