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 Québec, 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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Several major changes were made to the manuscript in preparation for resubmission. The serology data was removed for resubmission due to lack of sufficient original material for follow-up confirmatory testing for surrogate virus neutralization test positive samples. Manuscript text (all sections), figures, and tables were revised accordingly. We added a transcriptomics analysis of deer nasal swab samples (SARS-CoV-2 RT-PCR-positive and negative) to investigate white-tailed deer host response to SARS-CoV-2 infection. Figures and tables, including supplementary material, were added accordingly. Authors that conducted the analysis and interpretation were added. The manuscript text (all sections) was updated to incorporate the transcriptomics data and to reflect the current state of knowledge. Title was also changed to reflect the scope of the updated manuscript. Supplemental methods, figures, and tables were included.