Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

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.