OmniVira

Literature detail

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

Bradley Pickering1,2,3 Oliver Lung4,5 Finlay Maguire6,7,8,9 Peter Kruczkiewicz4 Jonathon D Kotwa9 Tore Buchanan10 Marianne Gagnier11 Jennifer L Guthrie12,13 Claire M Jardine14 Alex Marchand-Austin12 Ariane Massé11 Heather McClinchey15 Kuganya Nirmalarajah9 Patryk Aftanas8 Juliette Blais-Savoie9 Hsien-Yao Chee9 Emily Chien9 Winfield Yim9 Andra Banete9 Bryan D Griffin9 Lily Yip9 Melissa Goolia4 Matthew Suderman4 Mathieu Pinette4 Greg Smith4 Daniel Sullivan4,5 Josip Rudar4 Oksana Vernygora4 Elizabeth Adey10 Michelle Nebroski4 Guillaume Goyette16 Andrés Finzi16,17 Geneviève Laroche18,19,20 Ardeshir Ariana18,19,20 Brett Vahkal18,19,20 Marceline Côté18,19,20 Allison J McGeer21,22 Larissa Nituch10 Samira Mubareka23,24 Jeff Bowman25,26
Affiliations 26 institutions
  1. National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada. [email protected].
  2. Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA. [email protected].
  3. Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada. [email protected].
  4. National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada.
  5. Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
  6. Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
  7. Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada.
  8. Shared Hospital Laboratory, Toronto, Ontario, Canada.
  9. Sunnybrook Research Institute, Toronto, Ontario, Canada.
  10. Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada.
  11. Ministère des Forêts, de la Faune et des Parcs, Quebec City, Quebec, Canada.
  12. Public Health Ontario, Toronto, Ontario, Canada.
  13. Department of Microbiology & Immunology, Western University, London, Toronto, Ontario, Canada.
  14. Canadian Wildlife Health Cooperative, Ontario-Nunavut, Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada.
  15. Public Health, Health Protection and Surveillance Policy and Programs Branch, Ontario Ministry of Health, Toronto, Ontario, Canada.
  16. Centre de Recherche du CHUM, Montréal, Quebec, Canada.
  17. Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Quebec, Canada.
  18. Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.
  19. Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada.
  20. Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada.
  21. Sinai Health System, Toronto, Ontario, Canada.
  22. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
  23. Sunnybrook Research Institute, Toronto, Ontario, Canada. [email protected].
  24. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. [email protected].
  25. Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada. [email protected].
  26. Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada. [email protected].
PMID 36357713 2022 Nat Microbiol eng ppublish
PubMed DOI Browse context

Article

Publication summary

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.

COVID-19 Deer Animals Humans SARS-CoV-2 Odocoileus virginianus SARS-CoV-2 variants

Structured evidence records

Evidence records

5 total
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.90
Key finding

SARS-CoV-2 lineage B.1.641 detected in white-tailed deer showed shared ancestry with mink-derived viruses, indicating cross-species transmission between mink and deer.

Virus
SARS-CoV-2
Location
Canada Canada
Supporting text

Phylogenomic, recombination, selection and mutation spectrum analyses provided evidence for evolution and transmission in deer and a shared ancestry with mink-derived virus.

Method
phylogenomic analysis; recombination analysis; selection analysis; mutation spectrum analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
Ontario, Canada
Country inferred
Canada
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenomic and comparative analyses of deer-derived SARS-CoV-2 genomes revealed a highly divergent lineage B.1.641 with numerous mutations and evolutionary connectivity to mink-derived viruses, indicating sustained genomic evolution in white-tailed deer.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

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). 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.

Genes or proteins
whole genome
Analysis methods
phylogenomic analysis; recombination analysis; selection analysis; mutation spectrum analysis
Recombination Or Reassortment 1 records
Recombination Or Reassortment Extraction confidence 0.80
Key finding

Analyses identified recombination signals in the SARS-CoV-2 B.1.641 lineage from white-tailed deer, showing shared ancestry with mink-derived virus, indicating recombination may have contributed to its emergence.

Host
Not specified
Location
Not specified
Supporting text

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.

Event type
recombination
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

Phylogenomic and epidemiologic analyses showed deer-to-human transmission of a divergent SARS-CoV-2 lineage (B.1.641) in Ontario, Canada.

Virus
SARS-CoV-2
Location
Canada Canada
Supporting text

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.

Method
phylogenomic analysis; recombination analysis; selection analysis; mutation spectrum analysis
Study design
observational surveillance study
Transmission direction
animal-to-human
Geographic raw
Ontario, Canada
Country inferred
Canada
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Surveillance of 300 white-tailed deer in Ontario, Canada detected a highly divergent SARS-CoV-2 lineage (B.1.641).

Virus
SARS-CoV-2
Location
Canada Canada
Supporting text

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).

Method
observational surveillance study; phylogenomic analysis
Geographic raw
Ontario, Canada
Country inferred
Canada