Recent research has identified widespread SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus; WTD) in the United States, where the novel virus spilled over from humans into wildlife. To better understand the degree to which white-tailed deer are infected in New York, we conducted a comprehensive evaluation of deer infection and variant type using the retropharyngeal lymph nodes of 5,426 hunter-harvested WTD over the past two hunting seasons (2020-21, 2021-22). Our objective was to identify “hotspots” of infection (areas with higher than expected infection prevalence) in WTD and to explore why those hotspots occurred.

We used the SaTScan spatial analysis software to identify statistically significant clusters of infection. While infections were found in deer across NYS, hotspots were seen in Allegany, Livingston, Chemung, Tioga, Tompkins, Orange, Sullivan, and Lewis counties. Although it was presumed that infections in deer resulted from contact with humans, these hotspots are far away from urban centers with high human densities. Our analysis is a critical first step to understanding the risks of virus spillover and spillback between humans and wild WTD.