Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021–2024.

SARS-CoV-2 continues to transmit and evolve in humans and animals. White-tailed deer (Odocoileus virginianus) have been previously identified as a zoonotic reservoir for SARS-CoV-2 with high rates of infection and probable spillback into humans. Here we report sampling 1,127 white-tailed deer (WTD) in Pennsylvania, and a genomic analysis of viral dynamics spanning 1,017 days between April 2021 and January 2024. To assess viral load and genotypes, RNA was isolated from retropharyngeal lymph nodes and analyzed using RT-qPCR and viral whole genome sequencing. Samples showed a 14.64% positivity rate by RT-qPCR. Analysis showed no association of SARS-CoV-2 prevalence with age, sex, or diagnosis with Chronic Wasting Disease. From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. The viral variants identified included 17 Alpha, 11 Delta, and 14 Omicron. Alpha largely stopped circulating in humans around September 2021, but persisted in WTD as recently as March of 2023. Phylodynamic analysis of pooled genomic data from Pennsylvania documents at least 12 SARS-CoV-2 spillovers from humans into WTD, including a recent series of Omicron spillovers. Prevalence was higher in WTD in regions with crop coverage rather than forest, suggesting an association with proximity to humans. Analysis of seasonality showed increased prevalence in winter and spring. Multiple examples of recurrent mutations were identified associated with transmissions, suggesting WTD-specific evolutionary pressures. These data document ongoing infections in white-tailed deer, probable onward transmission in deer, and a remarkable rate of new spillovers from humans. Author summary: SARS-CoV-2 continues to evolve and circulate in humans and animals. Sometimes accumulating genetic changes give rise to new viral variants, the origins of which are incompletely understood and may involve transmissions between humans and animals. White-tailed deer (Odocoileus virginianus) is one of several host species known to harbor SARS-CoV-2 at high prevalence. We thus studied circulation and evolutionary dynamics of SARS-CoV-2 in 1,127 white-tailed deer in Pennsylvania from 2021 to 2024. Prevalence was higher in white-tailed deer in regions with crop coverage rather than forest. Analysis of seasonality showed increased prevalence in winter and spring. Our viral genome sequence analysis identified white-tailed deer as a SARS-CoV-2 reservoir of ancestral and highly divergent lineages consistent with genetic distances similar to new variants that have emerged in the human population. We found multiple examples of recurrent mutations in independent suspected spillover events, consistent with selective pressures in white-tailed deer. Together, these findings provide a unique longitudinal perspective on SARS-CoV-2 circulation, persistence, and evolution in Pennsylvania wild white-tailed deer. [ABSTRACT FROM AUTHOR]