Nature Communications (Aug 2023)
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
- Dillon S. McBride,
- Sofya K. Garushyants,
- John Franks,
- Andrew F. Magee,
- Steven H. Overend,
- Devra Huey,
- Amanda M. Williams,
- Seth A. Faith,
- Ahmed Kandeil,
- Sanja Trifkovic,
- Lance Miller,
- Trushar Jeevan,
- Anami Patel,
- Jacqueline M. Nolting,
- Michael J. Tonkovich,
- J. Tyler Genders,
- Andrew J. Montoney,
- Kevin Kasnyik,
- Timothy J. Linder,
- Sarah N. Bevins,
- Julianna B. Lenoch,
- Jeffrey C. Chandler,
- Thomas J. DeLiberto,
- Eugene V. Koonin,
- Marc A. Suchard,
- Philippe Lemey,
- Richard J. Webby,
- Martha I. Nelson,
- Andrew S. Bowman
Affiliations
- Dillon S. McBride
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine
- Sofya K. Garushyants
- Division of Intramural Research, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- John Franks
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Andrew F. Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
- Steven H. Overend
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine
- Devra Huey
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine
- Amanda M. Williams
- Infectious Diseases Institute, The Ohio State University
- Seth A. Faith
- Infectious Diseases Institute, The Ohio State University
- Ahmed Kandeil
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Sanja Trifkovic
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Lance Miller
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Trushar Jeevan
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Anami Patel
- PathAI Diagnostics
- Jacqueline M. Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine
- Michael J. Tonkovich
- Ohio Department of Natural Resources, Division of Wildlife
- J. Tyler Genders
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services
- Andrew J. Montoney
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services
- Kevin Kasnyik
- Columbus and Franklin County Metro Parks
- Timothy J. Linder
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Disease Program
- Sarah N. Bevins
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Disease Program
- Julianna B. Lenoch
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Disease Program
- Jeffrey C. Chandler
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Wildlife Disease Diagnostic Laboratory
- Thomas J. DeLiberto
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services
- Eugene V. Koonin
- Division of Intramural Research, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Marc A. Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
- Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Richard J. Webby
- Department of Infectious Diseases, St Jude Children’s Research Hospital
- Martha I. Nelson
- Division of Intramural Research, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine
- DOI
- https://doi.org/10.1038/s41467-023-40706-y
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 15
Abstract
Abstract The zoonotic origin of the COVID-19 pandemic virus highlights the need to fill the vast gaps in our knowledge of SARS-CoV-2 ecology and evolution in non-human hosts. Here, we detected that SARS-CoV-2 was introduced from humans into white-tailed deer more than 30 times in Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2–8 months, disseminating across hundreds of kilometers. Newly developed Bayesian phylogenetic methods quantified how SARS-CoV-2 evolution is not only three-times faster in white-tailed deer compared to the rate observed in humans but also driven by different mutational biases and selection pressures. The long-term effect of this accelerated evolutionary rate remains to be seen as no critical phenotypic changes were observed in our animal models using white-tailed deer origin viruses. Still, SARS-CoV-2 has transmitted in white-tailed deer populations for a relatively short duration, and the risk of future changes may have serious consequences for humans and livestock.
