PT  - JOURNAL ARTICLE
AU  - Suresh V. Kuchipudi
AU  - Meera Surendran-Nair
AU  - Rachel M. Ruden
AU  - Michelle Yon
AU  - Ruth H. Nissly
AU  - Rahul K. Nelli
AU  - Lingling Li
AU  - Bhushan M. Jayarao
AU  - Kurt J. Vandegrift
AU  - Costas D. Maranas
AU  - Nicole Levine
AU  - Katriina Willgert
AU  - Andrew J. K. Conlan
AU  - Randall J. Olsen
AU  - James J. Davis
AU  - James M. Musser
AU  - Peter J. Hudson
AU  - Vivek Kapur
TI  - Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer
AID  - 10.1101/2021.10.31.466677
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.10.31.466677
4099  - http://biorxiv.org/content/early/2021/11/06/2021.10.31.466677.short
4100  - http://biorxiv.org/content/early/2021/11/06/2021.10.31.466677.full
AB  - Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission of the virus in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), 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 may be circulating in deer, we tested 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between November 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 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 zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive “One Health” approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.One-Sentence Summary SARS-CoV-2 was detected in one-third of sampled white-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover and deer-to-deer transmission events.Competing Interest StatementThe authors have declared no competing interest.