Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission
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Published:2022-11-10
Issue:12
Volume:7
Page:2011-2024
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ISSN:2058-5276
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Container-title:Nature Microbiology
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language:en
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Short-container-title:Nat Microbiol
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 Andrés, Laroche Geneviève, Ariana Ardeshir, Vahkal Brett, Côté Marceline, McGeer Allison J., Nituch Larissa, Mubareka Samira, Bowman JeffORCID
Abstract
AbstractWildlife 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.
Funder
Canadian Food Inspection Agency Dalhousie University Public Health Agency of Canada Fonds de Recherche du Québec - Santé
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Microbiology (medical),Genetics,Applied Microbiology and Biotechnology,Immunology,Microbiology
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