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

Kotwa, J. D.; Masse, A.; Gagnier, M.; Aftanas, P.; Blais-Savoie, J.; Bowman, J.; Buchanan, T.; Chee, H.-Y.; Dibernardo, A.; Kruczkiewicz, P.; Nirmalarajah, K.; Soos, C.; Yip, L.; Lindsay, L. R.; Lung, O.; Pickering, B.; Mubareka, S.

doi:10.1101/2022.01.20.476458

bioRxiv · 10.1101/2022.01.20.476458

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

Kotwa, J. D.·Masse, A.·Gagnier, M.·Aftanas, P.·Blais-Savoie, J.·Bowman, J.·Buchanan, T.·Chee, H.-Y.·Dibernardo, A.·Kruczkiewicz, P.·Nirmalarajah, K.·Soos, C.·Yip, L.·Lindsay, L. R.·Lung, O.·Pickering, B.·Mubareka, S.

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Abstract

White-tailed deer are susceptible to SARS-CoV-2 and represent a highly important species for surveillance. Nasal swabs and retropharyngeal lymph nodes from white-tailed deer (n=258) collected in November 2021 from Quebec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and transcriptomics to further characterize infection and investigate host response to infection. We detected Delta SARS-CoV-2 (AY.44) in deer from the Estrie region; sequences clustered with human sequences from GISAID collected in October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 encoding a truncated protein were detected. Host expression patterns in SARS-CoV-2 infected deer were associated with the innate immune response, including signalling pathways related to anti-viral, pro- and anti-inflammatory signalling, and host damage. Our findings provide preliminary insights of host response to SARS-CoV-2 infection in deer and underscores the importance of ongoing surveillance of key wildlife species for SARS-CoV-2.

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Kotwa, J. D., Masse, A., Gagnier, M., Aftanas, P., Blais-Savoie, J., Bowman, J., Buchanan, T., Chee, H.-Y., Dibernardo, A., Kruczkiewicz, P., Nirmalarajah, K., Soos, C., Yip, L., Lindsay, L. R., Lung, O., Pickering, B., Mubareka, S.. 2022-01-21. First detection of SARS-CoV-2 infection in Canadian wildlife identified in free-ranging white-tailed deer (Odocoileus virginianus) from southern Quebec, Canada. https://doi.org/10.1101/2022.01.20.476458

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