Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

Pickering, Bradley; Lung, Oliver; Maguire, Finlay; Kruczkiewicz, Peter; Kotwa, Jonathon D.; Buchanan, Tore; Gagnier, Marianne; Guthrie, Jennifer L.; Jardine, Claire M.; Marchand-Austin, Alex; Massé, Ariane; McClinchey, Heather; Nirmalarajah, Kuganya; Aftanas, Patryk; Blais-Savoie, Juliette; Chee, Hsien-Yao; Chien, Emily; Yim, Winfield; Banete, Andra; Griffin, Bryan D.; Yip, Lily; Goolia, Melissa; Suderman, Matthew; Pinette, Mathieu; Smith, Greg; Sullivan, Daniel; Rudar, Josip; Vernygora, Oksana; Adey, Elizabeth; Nebroski, Michelle; Goyette, Guillaume; Finzi, André; Laroche, Geneviève; Ariana, Ardeshir; Vahkal, Brett; Côté, Marceline; McGeer, Allison J.; Nituch, Larissa; Mubareka, Samira; Bowman, Jeff

doi:https://open-science.canada.ca/handle/123456789/3466

Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

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creativework.keywords - en: Zoonotic and emerging pathogens; Zoonosis; SARS-CoV-2; Viruses--Variation; White-tailed deer --Diseases
creativework.keywords - fr: Pathogènes zoonotiques et émergents; Zoonoses; SRAS-CoV-2; Virus--Variation; Cerf de Virginie--Maladies
dc.contributor.author: Pickering, Bradley; Lung, Oliver; Maguire, Finlay; Kruczkiewicz, Peter; Kotwa, Jonathon D.; Buchanan, Tore; Gagnier, Marianne; Guthrie, Jennifer L.; Jardine, Claire M.; Marchand-Austin, Alex; Massé, Ariane; McClinchey, Heather; Nirmalarajah, Kuganya; Aftanas, Patryk; Blais-Savoie, Juliette; Chee, Hsien-Yao; Chien, Emily; Yim, Winfield; Banete, Andra; Griffin, Bryan D.; Yip, Lily; Goolia, Melissa; Suderman, Matthew; Pinette, Mathieu; Smith, Greg; Sullivan, Daniel; Rudar, Josip; Vernygora, Oksana; Adey, Elizabeth; Nebroski, Michelle; Goyette, Guillaume; Finzi, André; Laroche, Geneviève; Ariana, Ardeshir; Vahkal, Brett; Côté, Marceline; McGeer, Allison J.; Nituch, Larissa; Mubareka, Samira; Bowman, Jeff
dc.date.accepted: 2022-10-13
dc.date.accessioned: 2025-02-24T20:01:22Z
dc.date.available: 2025-02-24T20:01:22Z
dc.date.issued: 2022-11-10
dc.date.submitted: 2022-04-14
dc.description.abstract - en: Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution of viral variants that can emerge to infect humans. In North America, there is phylogenomic evidence of continual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (Odocoileus virginianus) through unknown means, but no evidence of transmission from deer to humans. We carried out an observational surveillance study in Ontario, Canada during November and December 2021 (n = 300 deer) and identified a highly divergent lineage of SARS-CoV-2 in white-tailed deer (B.1.641). This lineage is one of the most divergent SARS-CoV-2 lineages identified so far, with 76 mutations (including 37 previously associated with non-human mammalian hosts). From a set of five complete and two partial deer-derived viral genomes we applied phylogenomic, recombination, selection and mutation spectrum analyses, which provided evidence for evolution and transmission in deer and a shared ancestry with mink-derived virus. Our analysis also revealed an epidemiologically linked human infection. Taken together, our findings provide evidence for sustained evolution of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.
dc.identifier.citation: Pickering, B., Lung, O., Maguire, F., Kruczkiewicz, P., Kotwa, J. D., Buchanan, T., Gagnier, M., Guthrie, J. L., Jardine, C. M., Marchand-Austin, A., Massé, A., McClinchey, H., Nirmalarajah, K., Aftanas, P., Blais-Savoie, J., Chee, H.-Y., Chien, E., Yim, W., Banete, A., Griffin, B. D., Yip, L., Goolia, M., Suderman, M., Pinette, M., Smith, G., Sullivan, D., Rudar, J., Vernygora, O., Adey, E., Nebroski, M., Goyette, G., Finzi, A., Laroche, G., Ariana, A., Vahkal, B., Côté, M., McGeer, A. J., Nituch, L., Mubareka, A., & Bowman, J. (2022). Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Nature Microbiology, 7, 2011–2024. https://doi.org/10.1038/s41564-022-01268-9
dc.identifier.doi: https://doi.org/10.1038/s41564-022-01268-9
dc.identifier.issn: 2058-5276
dc.identifier.uri: https://open-science.canada.ca/handle/123456789/3466
dc.language.iso: en
dc.publisher - en: Springer Nature
dc.rights - en: Creative Commons Attribution 4.0 International (CC BY 4.0)
dc.rights - fr: Creative Commons Attribution 4.0 International (CC BY 4.0)
dc.rights.uri - en: https://creativecommons.org/licenses/by/4.0/
dc.rights.uri - fr: https://creativecommons.org/licenses/by/4.0/deed.fr
dc.subject - en: Viruses; Infectious diseases
dc.subject - fr: Virus; Maladie infectieuse
dc.subject.en - en: Viruses; Infectious diseases
dc.subject.fr - fr: Virus; Maladie infectieuse
dc.title - en: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission
dc.type - en: Article
dc.type - fr: Article
local.article.journaltitle - en: Nature Microbiology
local.article.journalvolume: 7
local.pagination: 2011-2024
local.peerreview - en: Yes
local.peerreview - fr: Oui
local.requestdoi: No

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