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Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission

View ORCID ProfileBradley Pickering, View ORCID ProfileOliver Lung, View ORCID ProfileFinlay Maguire, View ORCID ProfilePeter Kruczkiewicz, View ORCID ProfileJonathan D. Kotwa, View ORCID ProfileTore Buchanan, Marianne Gagnier, View ORCID ProfileJennifer L. Guthrie, View ORCID ProfileClaire M. Jardine, View ORCID ProfileAlex Marchand-Austin, Ariane Massé, Heather McClinchey, View ORCID ProfileKuganya Nirmalarajah, View ORCID ProfilePatryk Aftanas, Juliette Blais-Savoie, Hsien-Yao Chee, Emily Chien, Winfield Yim, Melissa Goolia, Matthew Suderman, Mathieu Pinette, Greg Smith, Daniel Sullivan, Jossip Rudar, Elizabeth Adey, Michelle Nebroski, View ORCID ProfileMarceline Côté, View ORCID ProfileGeneviève Laroche, View ORCID ProfileAllison J. McGeer, View ORCID ProfileLarissa Nituch, View ORCID ProfileSamira Mubareka, View ORCID ProfileJeff Bowman
doi: https://doi.org/10.1101/2022.02.22.481551
Bradley Pickering
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
9Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
10Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg
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  • For correspondence: bradley.pickering@canada.ca samira.mubareka@sunnybrook.ca jeff.bowman@ontario.ca
Oliver Lung
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
11Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Finlay Maguire
2Faculty of Computer Science, Dalhousie University, Nova Scotia, Canada
12Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Nova Scotia, Canada
13Shared Hospital Laboratory, Toronto, Ontario, Canada
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Peter Kruczkiewicz
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Jonathan D. Kotwa
3Sunnybrook Research Institute, Toronto, Ontario, Canada
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Tore Buchanan
4Wildlife Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
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Marianne Gagnier
5Ministère des Forêts, de la Faune et des Parcs, Québec City, Québec, Canada
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Jennifer L. Guthrie
6Public Health Ontario, Toronto, Ontario, Canada
16Department of Microbiology & Immunology, Western University, London, Ontario, Canada
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Claire M. Jardine
7Canadian Wildlife Health Cooperative, Ontario-Nunavut, Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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Alex Marchand-Austin
6Public Health Ontario, Toronto, Ontario, Canada
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Ariane Massé
5Ministère des Forêts, de la Faune et des Parcs, Québec City, Québec, Canada
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Heather McClinchey
8Public Health, Health Protection and Surveillance Policy and Programs Branch, Ontario Ministry of Health
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Kuganya Nirmalarajah
3Sunnybrook Research Institute, Toronto, Ontario, Canada
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Patryk Aftanas
13Shared Hospital Laboratory, Toronto, Ontario, Canada
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Juliette Blais-Savoie
3Sunnybrook Research Institute, Toronto, Ontario, Canada
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Hsien-Yao Chee
3Sunnybrook Research Institute, Toronto, Ontario, Canada
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Emily Chien
3Sunnybrook Research Institute, Toronto, Ontario, Canada
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Winfield Yim
3Sunnybrook Research Institute, Toronto, Ontario, Canada
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Melissa Goolia
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Matthew Suderman
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Mathieu Pinette
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Greg Smith
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Daniel Sullivan
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
11Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Jossip Rudar
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Elizabeth Adey
4Wildlife Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
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Michelle Nebroski
1National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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Marceline Côté
17Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
18Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
19Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
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Geneviève Laroche
17Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
18Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
19Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
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Allison J. McGeer
14Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
20Sinai Health System, Toronto, Ontario, Canada
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Larissa Nituch
4Wildlife Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
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Samira Mubareka
3Sunnybrook Research Institute, Toronto, Ontario, Canada
14Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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  • For correspondence: bradley.pickering@canada.ca samira.mubareka@sunnybrook.ca jeff.bowman@ontario.ca
Jeff Bowman
4Wildlife Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
15Environmental and Life Sciences Graduate Program, Trent University, Ontario, Canada
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  • For correspondence: bradley.pickering@canada.ca samira.mubareka@sunnybrook.ca jeff.bowman@ontario.ca
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Summary

Wildlife reservoirs of SARS-CoV-2 can lead to viral adaptation and spillback from wildlife to humans (Oude Munnink et al., 2021). In North America, there is evidence of spillover of SARS-CoV-2 from humans to white-tailed deer (Odocoileus virginianus), but no evidence of transmission from deer to humans (Hale et al., 2021; Kotwa et al., 2022; Kuchipudi et al., 2021). Through a multidisciplinary research collaboration for SARS-CoV-2 surveillance in Canadian wildlife, we identified a new and highly divergent lineage of SARS-CoV-2. This lineage has 76 consensus mutations including 37 previously associated with non-human animal hosts, 23 of which were not previously reported in deer. There were also mutational signatures of host adaptation under neutral selection. Phylogenetic analysis revealed an epidemiologically linked human case from the same geographic region and sampling period. Together, our findings represent the first evidence of a highly divergent lineage of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵+ Authors jointly supervised the work

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 25, 2022.
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Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission
Bradley Pickering, Oliver Lung, Finlay Maguire, Peter Kruczkiewicz, Jonathan 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, Melissa Goolia, Matthew Suderman, Mathieu Pinette, Greg Smith, Daniel Sullivan, Jossip Rudar, Elizabeth Adey, Michelle Nebroski, Marceline Côté, Geneviève Laroche, Allison J. McGeer, Larissa Nituch, Samira Mubareka, Jeff Bowman
bioRxiv 2022.02.22.481551; doi: https://doi.org/10.1101/2022.02.22.481551
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Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission
Bradley Pickering, Oliver Lung, Finlay Maguire, Peter Kruczkiewicz, Jonathan 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, Melissa Goolia, Matthew Suderman, Mathieu Pinette, Greg Smith, Daniel Sullivan, Jossip Rudar, Elizabeth Adey, Michelle Nebroski, Marceline Côté, Geneviève Laroche, Allison J. McGeer, Larissa Nituch, Samira Mubareka, Jeff Bowman
bioRxiv 2022.02.22.481551; doi: https://doi.org/10.1101/2022.02.22.481551

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