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 J McGeer; Finlay Maguire; Oliver Lung; Andrew C Doxey; Bradley Pickering; Samira Mubareka

doi:10.1016/j.isci.2023.108319

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

iScience. 2023 Oct 24;26(11):108319. doi: 10.1016/j.isci.2023.108319. eCollection 2023 Nov 17.

Authors

Jonathon D Kotwa¹, Briallen Lobb², Ariane Massé³, Marianne Gagnier³, Patryk Aftanas⁴, Arinjay Banerjee^{2

5

6

7

8}, Andra Banete¹, Juliette Blais-Savoie¹, Jeff Bowman⁹, Tore Buchanan⁹, Hsien-Yao Chee^{1

10}, Peter Kruczkiewicz¹¹, Kuganya Nirmalarajah¹, Catherine Soos^{12

13}, Oksana Vernygora¹¹, Lily Yip¹, L Robbin Lindsay¹⁴, Allison J McGeer^{7

15}, Finlay Maguire^{16

17

4}, Oliver Lung^{11

18}, Andrew C Doxey², Bradley Pickering^{11

19

20}, Samira Mubareka^{1

7}

Affiliations

¹ Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada.
² Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
³ Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs, Québec City, QC G1S 4X4, Canada.
⁴ Shared Hospital Laboratory, Toronto, ON M4N 3M5, Canada.
⁵ Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada.
⁶ Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada.
⁷ Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada.
⁸ Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
⁹ Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON K9J 8M5, Canada.
¹⁰ Global Health Research Center and Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu 215316, China.
¹¹ National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada.
¹² Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Saskatoon, SK S7N 3H5, Canada.
¹³ Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada.
¹⁴ National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada.
¹⁵ Sinai Health System, Toronto, ON M5G 1X5, Canada.
¹⁶ Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada.
¹⁷ Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada.
¹⁸ Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
¹⁹ Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
²⁰ Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.

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.

Keywords: Genomics; Immunity; Transcriptomics; Virology; Wildlife immunology; Wildlife medicine.