OmniVira

Literature detail

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].
PMID 34942632 2022 Nature eng ppublish
PubMed DOI Browse context

Article

Publication summary

Humans have infected a wide range of animals with SARS-CoV-2<sup>1-5</sup>, 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.

Phylogeny Amino Acid Sequence Amino Acid Substitution Animals Animals, Wild COVID-19 Deer Evolution, Molecular Humans Male Ohio One Health SARS-CoV-2 Spike Glycoprotein, Coronavirus Viral Zoonoses spike protein, SARS-CoV-2

Structured evidence records

Evidence records

5 total
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.90
Key finding

Probable deer-to-deer transmission of SARS-CoV-2 lineages was observed among free-ranging white-tailed deer.

Virus
SARS-CoV-2
Location
United States northeast Ohio in the USA, United States
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 and ORF1 that are observed infrequently in humans.

Method
real-time PCR with reverse transcription
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
northeast Ohio in the USA
Country inferred
United States
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.85
Key finding

SARS-CoV-2 lineages B.1.2, B.1.582, and B.1.596 acquired amino acid substitutions in the spike and ORF1 proteins after transmission among white-tailed deer.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596)... 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; genetic analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.80
Key finding

During deer-to-deer transmission, SARS-CoV-2 acquired amino acid substitutions in the spike protein, particularly within the receptor-binding domain, and in ORF1 that were rare in humans, suggesting host-associated molecular adaptation.

Virus
SARS-CoV-2
Host
Not specified
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 protein; ORF1
Mechanism types
molecular_evolution; receptor_binding
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

Free-ranging white-tailed deer in northeast Ohio were infected by SARS-CoV-2 variants originating from humans, demonstrating human-to-deer spillback.

Virus
SARS-CoV-2
Location
United States northeast Ohio in the USA, United States
Supporting text

Humans have infected a wide range of animals with SARS-CoV-2, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer 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
Study design
field surveillance
Transmission direction
human-to-animal
Geographic raw
northeast Ohio in the USA
Country inferred
United States
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

SARS-CoV-2 RNA was detected by RT-PCR in nasal swabs from free-ranging white-tailed deer sampled in northeast Ohio, USA, indicating infection among local deer populations.

Virus
SARS-CoV-2
Location
United States northeast Ohio, 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
Country inferred
United States