The Alpha, Gamma, and Delta SARS-CoV-2 variants are still circulating in White Tailed Deer well after they caused widespread COVID-19 in people, representing a reservoir for the strains and a potential future risk to humans.
The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability to transmit from deer to deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. Here, we present a comprehensive cross-sectional study assessing the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September to December 2020, n = 2,700) and 2021 (Season 2, September to December 2021, n = 2,762) were tested by SARS-CoV-2 real-time RT–PCR (rRT-PCR). SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY.
The evidence generated in this study demonstrates widespread dissemination of SARS-CoV-2 in wild WTD populations across the State of New York and further indicates the cocirculation of three major VOCs in this new wildlife host. Notably, circulation of SARS-CoV-2 in WTD results in emergence of genetically diverse viruses in this species. These observations highlight the need to establish continuous surveillance programs to monitor the circulation, distribution, and evolution of SARS-CoV-2 in WTD populations and to establish measures to minimize additional virus introductions in animals that may lead to spillback of deer-adapted SARS-CoV-2 variants to humans.
