OmniVira

Literature detail

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.
PMID 35840592 2022 Sci Rep eng epublish
PubMed DOI Browse context

Article

Publication summary

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.

COVID-19 Deer SARS-CoV-2 Viral Zoonoses Animals Environmental Monitoring Humans Risk Assessment Odocoileus virginianus

Structured evidence records

Evidence records

3 total
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.80
Key finding

Genomic analysis reconstructed SARS-CoV-2 transmission between humans and white-tailed deer, identifying human-to-deer spillovers and widespread deer-to-deer transmission with no observed deer-to-human spillback.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

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.

Genes or proteins
whole genome
Analysis methods
genomic data analysis; phylogenetic reconstruction
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

The study reports multiple human-to-deer SARS-CoV-2 spillover events leading to onward transmission among deer.

Virus
SARS-CoV-2
Location
multiple locations
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
Study design
genomic analysis
Transmission direction
human-to-animal
Geographic raw
multiple locations
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.90
Key finding

White-tailed deer populations showed extensive SARS-CoV-2 infection and transmission, emphasizing the importance of continued zoonotic surveillance using genomic data.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

High prevalence of SARS-CoV-2 infection in white-tailed deer has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission ... highlights the need for active surveillance at the human-animal interface.

Method
genomic data