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. 2024 Dec 6;16(12):1886.
doi: 10.3390/v16121886.

Low Prevalence of SARS-CoV-2 in Farmed and Free-Ranging White-Tailed Deer in Florida

Savannah G Grace  1 , Kristen N Wilson  1 , Rayann Dorleans  1 , Zoe S White  1 , Ruiyu Pu  2 , Natasha N Gaudreault  3 , Konner Cool  3 , Juan M Campos Krauer  4 , Laura E Franklin  1 , Bambi C Clemons  5 , Kuttichantran Subramaniam  2   6 , Juergen A Richt  3 , John A Lednicky  2   7 , Maureen T Long  2 , Samantha M Wisely  1   2
Affiliations

Low Prevalence of SARS-CoV-2 in Farmed and Free-Ranging White-Tailed Deer in Florida

Savannah G Grace et al. Viruses. .

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in multiple animal species, including white-tailed deer (WTD), raising concerns about zoonotic transmission, particularly in environments with frequent human interactions. To understand how human exposure influences SARS-CoV-2 infection in WTD, we compared infection and exposure prevalence between farmed and free-ranging deer populations in Florida. We also examined the timing and viral variants in WTD relative to those in Florida's human population. Between 2020 and 2022, we collected respiratory swabs (N = 366), lung tissue (N = 245), retropharyngeal lymph nodes (N = 491), and serum specimens (N = 381) from 410 farmed and 524 free-ranging WTD. Specimens were analyzed using RT-qPCR for infection and serological assays for exposure. SARS-CoV-2 infection was detected in less than 1% of both northern Florida farmed (0.85%) and free-ranging (0.76%) WTD. No farmed deer possessed virus-neutralizing antibodies, while one free-ranging WTD tested positive for SARS-CoV-2 antibodies (3.45%). Viral sequences in infected WTD matched peaks in human cases and circulating variants, indicating human-to-deer spillover but at a lower frequency than reported elsewhere. Our findings suggest a reduced risk of SARS-CoV-2 spillover to WTD in northern Florida compared to other regions, highlighting the need for further research on transmission dynamics across North America.

Keywords: Florida; SARS-CoV-2; white-tailed deer; zoonotic transmission.

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Conflict of interest statement

The JAR laboratory received support from Tonix Pharmaceuticals, Xing Technologies, and Genus plc outside of the reported work. J.A.R. is an inventor on patents and patent applications on the use of antivirals and vaccines for the treatment and prevention of virus infections, owned by Kansas State University, KS. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
Geographic distribution of WTD sampling efforts from 2020 to 2022 and SARS-CoV-2-positive cases. (A) Total number of farmed WTD specimens by county. (B) Total number of free-ranging WTD specimens by county. (C) Counties with SARS-CoV-2 RNA positive cases as determined by RT-PCR. (D) Counties with SARS-CoV-2 neutralizing antibodies positive WTD.
Figure 2
Figure 2
Temporal distribution of all specimens from farmed and free-ranging WTD and the timing of SARS-CoV-2 positives for infection or virus-neutralizing antibodies. WTD status is color-coded, with sex distinctions. An asterisk denotes the virus-neutralizing antibody-positive deer, while all others were positive for viral infection by RT-qPCR.
Figure 3
Figure 3
The temporal distribution of SARS-CoV-2 lineages in Florida humans and WTD from 2020 to 2022. The black line depicts the cumulative human cases in counties with confirmed positive WTD. Positioned above the graph, designated time points mark instances of positive WTD alongside the discerned SARS-CoV-2 lineages determined through whole genome sequencing. An asterisk denotes the virus-neutralizing antibody-positive WTD, while all others were positive for SARS-CoV-2 infection by RT-qPCR.
Figure 4
Figure 4
Maximum likelihood cladogram of the relationships of the whole genome SARS-CoV-2 nucleotide sequences isolated from Florida humans and farmed WTD. The SARS-CoV-2 isolates include their accession references from either NCBI or GISAID, location, WHO variant name, Pangolin lineage, and collection date. Nodes with black circles are supported by bootstrap values of >90%. The tree was rooted with the Wuhan-Hu-1 reference strain. The farmed WTD isolates are in red, and the Delta clad is highlighted in yellow.
See this image and copyright information in PMC

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