Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)
Jonathon D. Kotwa, Briallen Lobb, Ariane Massé, Marianne Gagnier, Patryk Aftanas, Arinjay Banerjee, Andra Banete, Juliette Blais-Savoie, Jeff Bowman, Tore Buchanan, Hsien-Yao Chee, Peter Kruczkiewicz, Kuganya Nirmalarajah, Catherine Soos, Oksana Vernygora, Lily Yip, L. Robbin Lindsay, Allison McGeer, Finlay Maguire, Oliver Lung, Andrew C. Doxey, Bradley Pickering, Samira Mubareka
Abstract
White-tailed deer (WTD) are susceptible to SARS-CoV-2 and represent an important species for surveillance. Samples from WTD (n = 258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and host transcriptomics to further characterize infection and investigate host response. We detected Delta SARS-CoV-2 (B.1.617.2) in WTD from the Estrie region; sequences clustered with human sequences from October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 were detected. Host expression patterns in SARS-CoV-2 infected WTD were associated with the innate immune response, including signaling pathways related to anti-viral, pro- and anti-inflammatory signaling, and host damage. We found limited correlation between genes associated with innate immune response from human and WTD nasal samples, suggesting differences in responses to SARS-CoV-2 infection. Our findings provide preliminary insights into host response to SARS-CoV-2 infection in naturally infected WTD.