First detection of SARS-CoV-2 infection in Canadian wildlife identified in free-ranging white-tailed deer (Odocoileus virginianus) from southern Québec, Canada

• Published in: bioRxiv
• Main Authors: Kotwa, Jonathon D, Massé, Ariane, Gagnier, Marianne, Aftanas, Patryk, Blais-Savoie, Juliette, Bowman, Jeff, Buchanan, Tore, Hsien-Yao Chee, Dibernardo, Antonia, Kruczkiewicz, Peter, Nirmalarajah, Kuganya, Soos, Catherine, Yip, Lily, L Robbin Lindsay, Lung, Oliver, Pickering, Bradley, Mubareka, Samira
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 21.01.2022
• Subjects: Deer; Gene deletion; Genomes; Lymph nodes; Odocoileus virginianus; Severe acute respiratory syndrome coronavirus 2; Surveillance; Thorax; Whole genome sequencing; Wildlife; Canada
• DOI: 10.1101/2022.01.20.476458

White-tailed deer are susceptible to SARS-CoV-2 and represent a relevant species for surveillance. We investigated SARS-CoV-2 infection in white-tailed deer in Québec, Canada. In November 2021, 251 nasal swabs and 104 retropharyngeal lymph nodes from 258 deer were analyzed for SARS-CoV-2 RNA, whole genome sequencing and virus isolation and 251 thoracic cavity fluid samples were tested for neutralizing antibodies. We detected SARS-CoV-2 RNA in three nasal swabs from the Estrie region and virus was isolated from two samples; evidence of past exposure was detected among deer from the same region. Viral sequences were assigned to lineage AY.44, a sublineage of B.1.617.2. All deer sequences clustered with human GISAID sequences collected in October 2021 from Vermont USA, which borders the Estrie region. Mutations in the S-gene and a deletion in ORF8 encoding a truncated protein were detected. These findings underscore the importance of ongoing surveillance of key wildlife species for SARS-CoV-2. Competing Interest Statement The authors have declared no competing interest.