OmniVira

SARS-CoV-2 infection in free-ranging white-tailed deer.

Vanessa L Hale1 Patricia M Dennis1,2 Dillon S McBride1 Jacqueline M Nolting1 Christopher Madden1 Devra Huey1 Margot Ehrlich3 Jennifer Grieser4 Jenessa Winston5 Dusty Lombardi6 Stormy Gibson6 Linda Saif1,7 Mary L Killian8 Kristina Lantz8 Rachel M Tell8 Mia Torchetti8 Suelee Robbe-Austerman8 Martha I Nelson9,10 Seth A Faith11 Andrew S Bowman12
Affiliations 12 institutions
  1. Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH, USA.
  2. Cleveland Metroparks Zoo, Cleveland, OH, USA.
  3. The Ohio State University College of Veterinary Medicine, Columbus, OH, USA.
  4. Cleveland Metroparks, Cleveland, OH, USA.
  5. Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH, USA.
  6. Ohio Wildlife Center, Powell, OH, USA.
  7. Center for Food Animal Health, The Ohio State University College of Food, Agriculture, and Environmental Sciences, Wooster, OH, USA.
  8. National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA.
  9. Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  10. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  11. Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
  12. Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH, USA. [email protected].
PMID34942632 DOI10.1038/s41586-021-04353-x Year2022 Journal Nature Languageeng Statusppublish

Abstract

Humans have infected a wide range of animals with SARS-CoV-21-5, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans. No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have been transmitted in wildlife in the USA, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive 'One Health' programmes to monitor the environment, deer and other wildlife hosts globally.

Supporting text Virus Host Location
Phylogeny 805 Amino Acid Sequence 128 Amino Acid Substitution 81 Animals 1948 Animals, Wild 187 COVID-19 425 Deer 46 Evolution, Molecular 176 Humans 1440 Male 224 Ohio 5 One Health 14 SARS-CoV-2 453 Spike Glycoprotein, Coronavirus 274 Viral Zoonoses 65 spike protein, SARS-CoV-2 157

Evidence records

4 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Viral Detection
1 records
OVE5468 Viral Detection
Key finding

SARS-CoV-2 RNA was detected in nasal swabs from free-ranging white-tailed deer (Odocoileus virginianus) in northeast Ohio during early 2021.

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

Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021.

Method
real-time PCR with reverse transcription
Sample type
nasal swabs
Geographic raw
northeast Ohio | USA
Country inferred
USA
Evidence type Reservoir Ecology
1 records
OVE5470 Reservoir Ecology
Key finding

Free-ranging white-tailed deer (Odocoileus virginianus) in northeast Ohio, USA, were found infected and capable of sustaining transmission of SARS-CoV-2, indicating a potential wildlife reservoir.

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

Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature.

Method
real-time PCR with reverse transcription
Sample type
nasal swabs
Geographic raw
northeast Ohio | USA
Country inferred
USA
Transmission Evidence
1 records · 1 evidence types
Evidence type Outbreak Investigation
1 records
OVE5469 Outbreak Investigation
Key finding

Probable deer-to-deer transmission of SARS-CoV-2 lineages B.1.2, B.1.582, and B.1.596 was detected among free-ranging white-tailed deer in northeast Ohio, USA.

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

We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021.

Method
real-time PCR with reverse transcription | phylogenetic analysis
Geographic raw
northeast Ohio, USA
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE5471 Phylogenetic Evolution
Key finding

Phylogenetic analysis showed that SARS-CoV-2 lineages B.1.2, B.1.582, and B.1.596 circulating in white-tailed deer accumulated amino acid substitutions in spike and ORF1 genes rarely found in humans, indicating host-associated evolutionary divergence in deer.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host
Location
Not specified
Supporting text

We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans.

Genes or proteins
spike | ORF1
Analysis methods
phylogenetic analysis | amino acid substitution analysis