Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Journal Article · 24 January 2022 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.2121644119 · OSTI ID:1890125

Kuchipudi, Suresh V. ^[1]; Surendran-Nair, Meera  ^[1]; Ruden, Rachel M.  ^[2]; Yon, Michele ^[1]; Nissly, Ruth H.  ^[1]; Vandegrift, Kurt J. ^[1]; Nelli, Rahul K.  ^[3]; Li, Lingling ^[1]; Jayarao, Bhushan M. ^[1]; Maranas, Costas D. ^[1]; Levine, Nicole ^[1]; Willgert, Katriina  ^[4]; Conlan, Andrew K.  ^[4]; Olsen, Randall J. ^[5]; Davis, James J. ^[6]; Musser, James M.  ^[5]; Hudson, Peter J.  ^[1]; Kapur, Vivek  ^[1]

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1. Pennsylvania State Univ., University Park, PA (United States)
2. Iowa Department of Natural Resources, Des Moines, IA (United States); Iowa State Univ., Ames, IA (United States)
3. Iowa State Univ., Ames, IA (United States)
4. Univ. of Cambridge (United Kingdom)
5. Houston Methodist Hospital, Houston, TX (United States); Weill Cornell Medical College, New York, NY (United States)
6. Argonne National Lab. (ANL), Lemont, IL (United States)

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States)
• Sponsoring Organization: Houston Methodist Research Institute; National Institutes of Health (NIH); National Science Foundation (NSF); US Fish and Wildlife Service; USDA; USDOE
• Grant/Contract Number: AC02-06CH11357
• OSTI ID: 1890125
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 6 Vol. 119; ISSN 0027-8424
• Publisher: National Academy of SciencesCopyright Statement
• Country of Publication: United States
• Language: English