OmniVira

Literature detail

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].
PMID 37429851 2023 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

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.

COVID-19 Deer Animals Humans SARS-CoV-2 Washington Odocoileus virginianus SARS-CoV-2 variants

Structured evidence records

Evidence records

6 total
Spillover Event 2 records
Spillover Event Extraction confidence 1.00
Key finding

Genomic analyses revealed at least 109 independent human-to-deer spillback events of SARS-CoV-2 involving free-ranging white-tailed deer.

Virus
SARS-CoV-2
Location
United States United States
Supporting text

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

Method
sequencing; evolutionary analysis
Study design
genomic surveillance
Transmission direction
human-to-animal
Geographic raw
United States
Country inferred
United States
Spillover Event Extraction confidence 1.00
Key finding

Three potential deer-to-human SARS-CoV-2 spillover events were identified from genetic evidence.

Virus
SARS-CoV-2
Location
United States United States
Supporting text

Evolutionary analyses showed ... three cases of potential spillover from white-tailed deer back to humans.

Method
sequencing; evolutionary analysis
Study design
genomic surveillance
Transmission direction
animal-to-human
Geographic raw
United States
Country inferred
United States
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.95
Key finding

SARS-CoV-2 was transmitted between white-tailed deer, confirming deer-to-deer cross-species transmission within cervid populations.

Virus
SARS-CoV-2
Location
United States United States
Supporting text

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.

Method
sequencing; evolutionary analyses
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
United States
Country inferred
United States
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.90
Key finding

Evolutionary analyses of SARS-CoV-2 sequences from white-tailed deer revealed repeated human-to-deer spillovers, local transmission, and adaptive amino acid changes in spike and other proteins.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

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 local deer-to-deer transmission and recurring amino acid substitutions across spike and other proteins.

Genes or proteins
spike; other proteins
Analysis methods
sequence analysis; evolutionary analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.90
Key finding

SARS-CoV-2 exhibited recurrent amino acid substitutions in spike and other proteins consistent with adaptation to white-tailed deer following human-to-deer spillover.

Virus
SARS-CoV-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.

Genes or proteins
spike
Mechanism types
molecular_adaptation; host_adaptation
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Large-scale surveillance detected multiple SARS-CoV-2 variants in respiratory samples from free-ranging white-tailed deer across the United States.

Virus
SARS-CoV-2
Location
United States 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
sequencing
Sample type
respiratory samples
Geographic raw
Washington, D.C. and 26 states in the United States
Country inferred
United States