PSIV-7 Zoonotic transmission and analysis of SARS-CoV-2 in White-tailed Deer

Abstract White-tailed deer (WTD) frequently interact with humans through hunting, butchering, deer farms, game ranches, and their ability to live in close proximity. Due to the ongoing COVID pandemic, we chose a One Health approach to assess potential SARS-CoV-2 transmission between WTD, wildlife, and humans during the 2022 and 2023 Virginia hunting seasons in a residential neighborhood compared with surrounding rural timber and cattle farms. The study involved analyzing SARS-CoV-2 in legally harvested WTD and other wildlife, conducting surveys with residents and hunters at the study sites, and retrospectively reviewing SARS-CoV-2 databases. Serologic SARS-CoV-2 studies used lateral flow assays (LFA) and a confirmatory enzyme-linked immunosorbent assay. Viral nasopharyngeal analysis included a commercially available screening antigen LFA, transcription-mediated amplification (TMA), and confirmatory reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Over a 2-yr period, SARS-CoV-2 antibody serology screening in WTD showed 47% seropositivity (7/15) in the neighborhood and 32% seropositivity (7/22) on the farms. In 2022, 27 WTD and 54 other wildlife tested negative for SARS-CoV-2 using both TMA and RT-qPCR, contrasting with the 16.3% infection rate among human residents and participating hunters. In 2023, 17% (3/18) of WTD and 9.5% (2/21) of eastern grey squirrels (EGS) tested positive for at least one viral target (N, E, S genes) by RT-qPCR. Rapid antigen LFA was positive in one RT-qPCR positive WTD with a high titer (Cq< 30). The two low titer (Cq >30) RT-qPCR positive WTD and 14 RT-qPCR negative WTD tested negative by antigen LFA. This comparative evaluation of WTD RT-qPCR and LFA correlates with the reported sensitivity and clinical utility of antigen LFA in humans. SARS-CoV-2 whole genome sequence data for the high titer neighborhood WTD was generated using GridIONx5 sequencer (Oxford Nanopore Technologies), identifying it as variant XBB.1.16.6 with no unusual mutations. This variant constituted approximately 5% of SARS-CoV-2 within humans in Central Virginia at the time of collection. Sanger sequencing using ARTIC amplicons provided partial spike gene sequences from one farm WTD and one neighborhood EGS. Common omicron mutations were identified, alongside two novel mutations within the N-terminus and receptor binding domains: S:Q14R and S:V511I. All 8 hunters who came into contact with RT-qPCR positive wildlife showed no development of SARS-CoV-2-related symptoms within 1 wk of exposure. In conclusion, these results indicate increased SARS-CoV-2 exposure in WTD with a greater human population gradient, expressing similar temporal SARS-CoV-2 variants and gene sequences, supporting zoonotic transmission. Furthermore, the rapid LFA used in this study demonstrates its potential as a cost-effective screening tool for on-site evaluation of SARS-CoV-2 in WTD carcasses, herd health monitoring, and biosecurity purposes for hunters, wildlife biologists, and the captive deer industry.