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

Bradley Pickering, Oliver Lung, Finlay Maguire, Peter Kruczkiewicz, Jonathon D Kotwa, Tore Buchanan, Marianne Gagnier, Jennifer L Guthrie, Claire M Jardine, Alex Marchand-Austin, Ariane Massé, Heather McClinchey, Kuganya Nirmalarajah, Patryk Aftanas, Juliette Blais-Savoie, Hsien-Yao Chee, Emily Chien, Winfield Yim, Andra Banete, Bryan D Griffin, Lily Yip, Melissa Goolia, Matthew Suderman, Mathieu Pinette, Greg Smith, Daniel Sullivan, Josip Rudar, Oksana Vernygora, Elizabeth Adey, Michelle Nebroski, Guillaume Goyette, Andrés Finzi, Geneviève Laroche, Ardeshir Ariana, Brett Vahkal, Marceline Côté, Allison J McGeer, Larissa Nituch, Samira Mubareka, Jeff Bowman, Nature microbiology 7, 2011-2024 (2022)
DOI
10.1038/s41564-022-01268-9
Share
tweet


Abstract

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.