White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns transmit the virus to other captive deer. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we evaluated 283 samples collected from 151 free-living and 132 captive deer in Iowa from April through December 2020 for the presence of SARS-CoV-2 RNA. 33.2% were positive. Notably, between Nov 23, 2020, and January 10, 2021, 82.5% had detectable SARS-CoV-2 RNA.
Whole genome sequencing of the positive samples identified 12 SARS-CoV-2 lineages, with B.1.2, and B.1.311 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.