OmniVira

Transmission history of SARS-CoV-2 in humans and white-tailed deer.

Katriina Willgert1 Xavier Didelot2 Meera Surendran-Nair3,4 Suresh V Kuchipudi3,4 Rachel M Ruden5,6 Michele Yon3 Ruth H Nissly3,4 Kurt J Vandegrift7 Rahul K Nelli6 Lingling Li3 Bhushan M Jayarao3 Nicole Levine4,8 Randall J Olsen9,10,11 James J Davis12,13 James M Musser9,10,11 Peter J Hudson7 Vivek Kapur4,8 Andrew J K Conlan14
Affiliations 14 institutions
  1. Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. [email protected].
  2. School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK.
  3. Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
  4. Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
  5. Wildlife Bureau, Iowa Department of Natural Resources, Des Moines, IA, USA.
  6. Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
  7. The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
  8. Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA.
  9. Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.
  10. Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.
  11. Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA.
  12. University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, USA.
  13. Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, 60439, USA.
  14. Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
PMID35840592 DOI10.1038/s41598-022-16071-z Year2022 Journal Scientific reports Sci Rep Languageeng Statusepublish

Abstract

The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human-animal interface.

Supporting text Virus Host Location
COVID-19 425 Deer 46 SARS-CoV-2 453 Viral Zoonoses 65 Animals 1948 Environmental Monitoring 5 Humans 1440 Risk Assessment 13 Odocoileus virginianus 11

Evidence records

2 total
Transmission Evidence
2 records · 2 evidence types
Evidence type Outbreak Investigation
1 records
OVE6161 Outbreak Investigation
Key finding

High prevalence of SARS-CoV-2 infection in white-tailed deer indicates deer-to-deer transmission following multiple human-to-deer spillovers.

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

High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission.

Method
genomic data analysis | phylogenetic reconstruction
Evidence type Cross-species Transmission
1 records
OVE6159 Cross-species Transmission
Key finding

Several human-to-deer spillover events of SARS-CoV-2 have resulted in infection of white-tailed deer populations.

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

High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission.

Method
genomic data analysis | epidemiological inference
Study design
genomic and epidemiological reconstruction of interspecies transmission
Transmission direction
human-to-animal