Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)
Date
2023-11
Authors
Kotwa, Jonathon D.
Lobb, Briallen
Massé, Ariane
Gagnier, Marianne
Aftanas, Patryk
Banerjee, Arinjay
Banete, Andra
Blais-Savoie, Juliette
Bowman, Jeff
Buchanan, Tore
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier
ORCID
Type
Article
Degree Level
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.
Description
Keywords
Virology, Wildlife medicine, Wildlife immunology, Genomics, Immunity, Transcriptomics
Citation
Kotwa, J. D., Lobb, B., Massé, A., Gagnier, M., Aftanas, P., Banerjee, A., Banete, A., Blais-Savoie, J., Bowman, J., Buchanan, T., Chee, H.-Y., Kruczkiewicz, P., Nirmalarajah, K., Soos, C., Vernygora, O., Yip, L., Lindsay, L. R., McGeer, A. J., Maguire, F., … Mubareka, S. (2023). Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus). iScience, 26(11), Article 108319. https://doi.org/10.1016/j.isci.2023.108319
Degree
Department
Program
Advisor
Committee
Part Of
item.page.relation.ispartofseries
DOI
https://doi.org/10.1016/j.isci.2023.108319