OmniVira

Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States.

Aijing Feng1,2,3 Sarah Bevins4 Jeff Chandler5 Thomas J DeLiberto6 Ria Ghai7 Kristina Lantz8 Julianna Lenoch4 Adam Retchless9 Susan Shriner5 Cynthia Y Tang1,3,10 Suxiang Sue Tong9 Mia Torchetti8 Anna Uehara9 Xiu-Feng Wan11,12,13,14,15
Affiliations 15 institutions
  1. Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA.
  2. Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
  3. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
  4. USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA.
  5. National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA.
  6. USDA APHIS Wildlife Services, Fort Collins, CO, USA. [email protected].
  7. One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
  8. National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA.
  9. National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
  10. MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
  11. Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA. [email protected].
  12. Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA. [email protected].
  13. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. [email protected].
  14. MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA. [email protected].
  15. Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA. [email protected].
PMID37429851 DOI10.1038/s41467-023-39782-x Year2023 Journal Nature communications Nat Commun Languageeng Statusepublish

Abstract

SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.

Supporting text Virus Host Location
COVID-19 425 Deer 46 Animals 1948 Humans 1440 SARS-CoV-2 453 Washington 3 Odocoileus virginianus 11 SARS-CoV-2 variants 86

Evidence records

4 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Viral Detection
1 records
OVE7159 Viral Detection
Key finding

SARS-CoV-2, including Alpha, Gamma, Delta, and Omicron variants, was detected and sequenced from respiratory samples collected from free-ranging white-tailed deer in Washington, D.C. and 26 states of the United States.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host
Location
United States
Supporting text

We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants.

Method
viral sequencing | molecular detection
Sample type
respiratory samples
Geographic raw
Washington, D.C. | United States
Country inferred
USA
Evidence type Reservoir Ecology
1 records
OVE7163 Reservoir Ecology
Key finding

Multiple SARS-CoV-2 lineages became enzootic and co-circulated within free-ranging white-tailed deer populations across states in the United States, indicating persistent circulation in this host species.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host
Location
United States
Supporting text

We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.

Method
genomic sequencing | evolutionary analyses | surveillance sampling of free-ranging deer
Sample type
respiratory samples
Geographic raw
United States
Country inferred
USA
Transmission Evidence
1 records · 1 evidence types
Evidence type Cross-species Transmission
1 records
OVE7160 Cross-species Transmission
Key finding

Genomic analyses identified at least 109 independent SARS-CoV-2 spillover events from humans to free-ranging white-tailed deer.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host human Homo sapiens Natural host
Location
United States
Supporting text

Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans.

Method
evolutionary analysis | genomic sequencing
Study design
evolutionary genomic analysis of deer SARS-CoV-2 sequences
Transmission direction
human-to-animal
Geographic raw
United States
Functional Mechanism
1 records · 1 evidence types
Evidence type Molecular Adaptation
1 records
OVE7162 Molecular Adaptation
Key finding

SARS-CoV-2 exhibited recurring amino acid substitutions in spike and other proteins indicative of molecular adaptation to white-tailed deer.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
Not specified
Location
Not specified
Supporting text

Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.

Genes or proteins
spike protein
Mechanism types
host-range expansion