Free-ranging White-tailed Deer Research Articles

Persistence of viral RNA in North American elk experimentally infected with an ancestral strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

White-tailed deer (Odocoileus virginianus) have emerged as a reservoir host for SARS-CoV-2 given their susceptibility to infection and demonstrated high rates of seroprevalence and infection across the United States. As SARS-CoV-2 circulates within free-ranging white-tailed deer populations, there is the risk of transmission to other wildlife species and even back to the human population. The goal of this study was to determine the susceptibility, shedding, and immune response of North American elk (Cervus elaphus canadensis) to experimental infection with SARS-CoV-2, to determine if another wide-ranging cervid species could potentially serve as a reservoir host for the virus. Here we demonstrate that while North American elk do not develop clinical signs of disease, they do develop a neutralizing antibody response to infection, suggesting the virus is capable of replicating in this mammalian host. Additionally, we demonstrate SARS-CoV-2 RNA presence in the medial retropharyngeal lymph nodes of infected elk three weeks after experimental infection. Consistent with previous observations in humans, these data may highlight a mechanism of viral persistence for SARS-CoV-2 in elk.

Predicting the odds of chronic wasting disease with Habitat Risk software

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) across the US and Canada as well as to Scandinavia and South Korea. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies have employed epidemiological models to understand long-term environmental risk. However, continued rapid spread of CWD into new regions of the continent has underscored the need for extension of these models into broader tools applicable for wide use by wildlife agencies. Additionally, efforts to semi-automate models will facilitate access of technical scientific methods to broader users. We introduce software (Habitat Risk) designed to link a previously published epidemiological model with spatially referenced environmental and disease testing data to enable agency personnel to make up-to-date, localized, data-driven predictions regarding the odds of CWD detection in surrounding areas after an outbreak is discovered. Habitat Risk requires pre-processing publicly available environmental datasets and standardization of disease testing (surveillance) data, after which an autonomous computational workflow terminates in a user interface that displays an interactive map of disease risk. We demonstrated the use of the Habitat Risk software with surveillance data of white-tailed deer from Tennessee, USA.

An individual-based model for direct and indirect transmission of chronic wasting disease in free-ranging white-tailed deer

Chronic wasting disease (CWD) is an infectious prion disease that infects members of the Cervidae family (i.e., deer) resulting in widespread ecological, economic, and recreational ramifications. We introduce a spatially explicit individual-based model (IBM) that integrates individual deer movement and behavior with population and disease dynamics to forecast CWD in populations of free-ranging white-tailed deer (Odocoileus virginianus). We use a Susceptible-Exposed-Infectious-Dead (S-E-I-D) epidemiological framework to explore spatiotemporal dynamics of CWD within an agriculturally dominated area in Michigan, USA. The IBM results closely mimicked documented short- and long-term dynamics of white-tailed deer populations and CWD in the Midwestern, USA. We applied pattern-oriented modeling using annual apparent CWD prevalence rates reported by Midwestern state wildlife agencies to validate the disease model. The introduction of a single infected deer to the modeled landscape (93 km2) led to an outbreak of CWD in 100 out of 350 model simulations (29 %); prevalence never exceeded 1.47 % for repetitions where the outbreak ended. For the 100 simulations where disease persisted, the deer population declined by 87 % by year 50 following initial introduction of CWD. Mean (±SD) prevalence after 5, 10, 25, and 50 years was 1.1 % (±1.0 %), 3.4 % (±3.3 %), 46.5 % (±18.8 %), and 51.8 % (±18.1 %), respectively, which highly correlated (r = 0.99) with annual CWD prevalence reported in Wisconsin white-tailed deer populations for years 1–21 post initial detection. Combined with a global sensitivity analysis, the IBM indicated that prevalence of CWD at year 20 was most sensitive to harvest rate of yearling and adult female deer and least sensitive to prion shedding rate, prion half-life, and deer group numbers, indicating that deer population parameters were more influential than disease parameters on CWD dynamics. Our IBM serves as a tool to explore and better understand indirect and direct transmission of CWD within free-ranging cervid populations. Users of this model can adjust parameter values to explore how interactions among individual deer and between deer and their environment affect CWD dynamics. This IBM also serves as a framework for applying and assessing spatially and temporally explicit management scenarios.

PREGNANCY RATE AND NUMBER OF FETUSES OF WHITE-TAILED DEER RELATED TO BODY MEASUREMENTS AND SERUM METABOLITES

This study aimed to assess the association between fertility and the number of fetuses of free-ranging concentrate-supplemented white-tailed deer (Odocoileus virginianus, texanus, Mearns 1898) from northern Mexico (27 °N) with body measurements and serum metabolites indicative of nutritional status. We studied 119 female deer (31 yearlings and 88 adults) captured in January 2021 using a net gun fired from a helicopter. Ultrasound scanning showed 100 and 97.8 % pregnancy rate and 1.52 ± 0.51 and 1.50 ± 0.59 fetuses/pregnant doe for yearlings and adult does, respectively, with no difference (p > 0.05) between age classes Thoracic circumference (cm) was higher (85.9 ± 4.9 vs. 84.1 ± 4.2; p = 0.039) for does carrying twins vs. singles. None of the serum metabolites indicative of nutritional status affected the fetal number of pregnant does. It was concluded that free-ranging white-tailed deer receiving concentrate supplementation in winter on a semi-arid rangeland has a high reproductive potential. Also, these results indicate that variation in maternal age within this population was not a significant driver of reproductive metrics of white-tailed deer. The plane of nutrition used in the present study was reflected in adequate serum metabolites indicative of nutritional status. Also, thoracic circumference may have prognostic value as a physical marker of multiple fetuses in female white-tailed deer.

Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

White-tailed deer (WTD) are susceptible to SARS-CoV-2 and represent an important species for surveillance. Samples from WTD (n= 258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and host transcriptomics to further characterize infection and investigate host response. We detected Delta SARS-CoV-2 (B.1.617.2) in WTD from the Estrie region; sequences clustered with human sequences from October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 were detected. Host expression patterns in SARS-CoV-2 infected WTD were associated with the innate immune response, including signaling pathways related to anti-viral, pro- and anti-inflammatory signaling, and host damage. We found limited correlation between genes associated with innate immune response from human and WTD nasal samples, suggesting differences in responses to SARS-CoV-2 infection. Our findings provide preliminary insights into host response to SARS-CoV-2 infection in naturally infected WTD.

Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

The zoonotic origin of the COVID-19 pandemic virus highlights the need to fill the vast gaps in our knowledge of SARS-CoV-2 ecology and evolution in non-human hosts. Here, we detected that SARS-CoV-2 was introduced from humans into white-tailed deer more than 30 times in Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2–8 months, disseminating across hundreds of kilometers. Newly developed Bayesian phylogenetic methods quantified how SARS-CoV-2 evolution is not only three-times faster in white-tailed deer compared to the rate observed in humans but also driven by different mutational biases and selection pressures. The long-term effect of this accelerated evolutionary rate remains to be seen as no critical phenotypic changes were observed in our animal models using white-tailed deer origin viruses. Still, SARS-CoV-2 has transmitted in white-tailed deer populations for a relatively short duration, and the risk of future changes may have serious consequences for humans and livestock.

SARS-CoV-2 Neutralizing Antibodies in Free-Ranging Fallow Deer (Dama dama) and Red Deer (Cervus elaphus) in Suburban and Rural Areas in Spain

Effective control of zoonotic infectious diseases requires identifying the animal species involved in the infectious cycle as transmitters or reservoirs where the pathogen could persist and evolve, increasing the risk of reintroduction of new variants in humans and animals. Multiple surveillance studies have detected the presence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) or specific antibodies in free-ranging white-tailed deer (Odocoileus virginianus) in North America, being the wild mammal species with the most reported cases of SARS-CoV-2 infection. However, so far, all attempts to detect the infection in European cervids have been unsuccessful. In this study, we demonstrated the presence of specific antibodies against SARS-CoV-2 in European fallow deer (Dama dama) and red deer (Cervus elaphus) in Spain. However, all samples of European roe deer (Capreolus capreolus), taxonomically related to the American white-tailed deer, were seronegative for the virus. We tested 215 serum samples from roe deer (n = 116), red deer (n = 63), and fallow deer (n = 36) collected in eight provinces of central-southern Spain between 2017 and 2022. We first screened sera by a surrogate virus neutralization test (sVNT) ELISA based on the binding of the receptor-binding domain of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor and then confirmed positive samples by a conventional virus neutralization test (cVNT) against the Alpha, Delta, and Omicron variants. Four fallow deer and two red deer samples were seropositive in both neutralization assays. Four samples of fallow deer and one of red deer, collected in a suburban park near Madrid in February 2022, had antibodies against the Alpha, Delta, and Omicron variants, while a seropositive sample of red deer, collected in a rural area in February 2021, was specific for the Delta variant. All samples collected before the start of the pandemic in Spain were seronegative for sVNT, which also indicates that there are not cross-reactive antibodies potentially elicited by other viruses antigenically related to SARS-CoV-2. The results indicate probable human-to-deer transmission of SARS-CoV-2, but do not clarify whether there was subsequent spread within herds.

Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States

SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.

Experimental oral delivery of the systemic acaricide moxidectin to free-ranging white-tailed deer (Artiodactyla: Cervidae) parasitized by Amblyomma americanum (Ixodida: Ixodidae).

Orally delivered, host-targeted, systemic acaricide treatment has potential to be an effective areawide tick abatement strategy. Past efforts using ivermectin for livestock were reported effective at controlling both Amblyomma americanum (L.) and Ixodes scapularis Say on Odocoileus virginianus (Zimmermann). However, the labeled 48-day withdrawal period for human consumption largely prevented utilization of this strategy targeting I. scapularis in autumn, when peak adult host-seeking activity coincides with regulated white-tailed deer hunting seasons. The modern-day compound moxidectin is the active ingredient in the pour-on formulation Cydectin (5 mg moxidectin/ml; Bayer Healthcare LLC), with a labeled 0-day withdrawal period for human consumption of treated cattle. We sought to re-examine the systemic acaricide approach for tick management by determining if we could successfully deliver Cydectin to free-ranging white-tailed deer. Over 2 yr in late spring/early summer, coinciding with adult and nymphal A. americanum activity, we fed Cydectin-coated corn to free-ranging white-tailed deer in coastal Connecticut. Through serum analysis, we documented moxidectin levels at or above those previously reported effective for control of ectoparasites (5-8 ppb for moxidectin and ivermectin) in 24 of 29 white-tailed deer captured (83%) while exposed to treated corn. While we did not document differences in burdens of parasitizing A. americanum based on moxidectin sera levels, we did document fewer engorged specimens on deer with increased sera levels. The systemic use of moxidectin for tick management in critical reproductive hosts has the potential to be effective in an areawide capacity while also permitting human consumption of treated venison.

Ticks harbor and excrete chronic wasting disease prions

Chronic wasting disease (CWD) is a fatal neurodegenerative disease caused by infectious prions (PrPCWD) affecting cervids. Circulating PrPCWD in blood may pose a risk for indirect transmission by way of hematophagous ectoparasites acting as mechanical vectors. Cervids can carry high tick infestations and exhibit allogrooming, a common tick defense strategy between conspecifics. Ingestion of ticks during allogrooming may expose naïve animals to CWD, if ticks harbor PrPCWD. This study investigates whether ticks can harbor transmission-relevant quantities of PrPCWD by combining experimental tick feeding trials and evaluation of ticks from free-ranging white-tailed deer (Odocoileus virginianus). Using the real-time quaking-induced conversion (RT-QuIC) assay, we show that black-legged ticks (Ixodes scapularis) fed PrPCWD-spiked blood using artificial membranes ingest and excrete PrPCWD. Combining results of RT-QuIC and protein misfolding cyclic amplification, we detected seeding activity from 6 of 15 (40%) pooled tick samples collected from wild CWD-infected white-tailed deer. Seeding activities in ticks were analogous to 10–1000 ng of CWD-positive retropharyngeal lymph node collected from deer upon which they were feeding. Estimates revealed a median infectious dose range of 0.3–42.4 per tick, suggesting that ticks can take up transmission-relevant amounts of PrPCWD and may pose a CWD risk to cervids.

Tissue distribution of angiotensin-converting enzyme 2 (ACE2) receptor in wild animals with a focus on artiodactyls, mustelids and phocids

Natural cases of zooanthroponotic transmission of SARS-CoV-2 to animals have been reported during the COVID-19 pandemic, including to free-ranging white-tailed deer (Odocoileus virginianus) in North America and farmed American mink (Neovison vison) on multiple continents. To understand the potential for angiotensin-converting enzyme 2 (ACE2)-mediated viral tropism we characterised the distribution of ACE2 receptors in the respiratory and intestinal tissues of a selection of wild and semi-domesticated mammals including artiodactyls (cervids, bovids, camelids, suids and hippopotamus), mustelid and phocid species using immunohistochemistry. Expression of the ACE2 receptor was detected in the bronchial or bronchiolar epithelium of several European and Asiatic deer species, Bactrian camel (Camelus bactrianus), European badger (Meles meles), stoat (Mustela erminea), hippopotamus (Hippopotamus amphibious), harbor seal (Phoca vitulina), and hooded seal (Cystophora cristata). Further receptor mapping in the nasal turbinates and trachea revealed sparse ACE2 receptor expression in the mucosal epithelial cells and occasional occurrence in the submucosal glandular epithelium of Western roe deer (Capreolus capreolus), moose (Alces alces alces), and alpaca (Vicunga pacos). Only the European badger and stoat expressed high levels of ACE2 receptor in the nasal mucosal epithelium, which could suggest high susceptibility to ACE2-mediated respiratory infection. Expression of ACE2 receptor in the intestinal cells was ubiquitous across multiple taxa examined. Our results demonstrate the potential for ACE2-mediated viral infection in a selection of wild mammals and highlight the intra-taxon variability of ACE2 receptor expression, which might influence host susceptibility and infection.

Regional Copper Deficiency in White-Tailed Deer

Minerals are critical in maintaining health and physiological function in wildlife. Geographic variation in soil and forage mineral concentration may predispose wildlife to mineral imbalances, where a common symptom is restricted somatic growth. We investigated if mineral imbalances could explain localized differences in morphology of white-tailed deer (Odocoileus virginianus) occurring in geographically proximate sites with similar management, climate, and habitat. We collected serum samples and morphological measurements from free-ranging white-tailed deer captured during 2011-2019 from coastal and inland rangeland sites in South Texas, USA. We measured mineral concentrations in serum from captured deer at each location. Asymptotic deer body mass and antler size averaged 8% - 20% smaller for deer at the coastal compared to the inland site. The proportion of deer with deficient levels of serum copper was greater at the coastal site (66% versus 14%). Our results suggest regional mineral deficiencies in deer may limit antler and body development. Wildlife managers should be aware of all aspects of wildlife nutrition and the importance of considering nutrients beyond energy and protein.

Distinctive Gross Presentation in Free-Ranging White-Tailed Deer (Odocoileus virginianus) with Rabies.

The white-tailed deer (Odocoileus virginianus) is a popular game species in North America and often lives in close proximity to humans and domestic animals. Deer with neurologic signs are of high interest to the general public and wildlife managers because of disease and safety concerns. Our aim was to describe diagnostic findings from free-ranging white-tailed deer diagnosed with rabies from across the eastern US from 2000 to 2021, with emphasis on gross lesions in the skin and soft tissue overlying the skull. We reviewed diagnostic reports of white-tailed deer cases submitted to the Southeastern Cooperative Wildlife Disease Study for those diagnosed with rabies from 2000 to 2021. Rabies virus infection was confirmed by immunohistochemistry or fluorescent antibody test of brain, or both. Nine adult deer from five states were diagnosed with rabies, including seven (78%) females and two (22%) males. Three (33%) deer were found dead, and six (67%) were humanely dispatched for abnormal behavior. Six deer heads were examined grossly and had lesions, including forehead or periorbital alopecia, cutaneous erythema, abrasions and ulcers, and subcutaneous edema. Histologic examination was performed for eight of nine cases, all of which had intraneuronal eosinophilic inclusion (Negri) bodies in cerebrum, cerebellum, or both. Most (6/8; 75%) had perivascular lymphoplasmacytic encephalitis. Rabies should be considered a differential diagnosis in deer with this pattern of head lesions, suggestive of head rubbing or head pressing.

Informing Surveillance through the Characterization of Outbreak Potential of Chronic Wasting Disease in White-Tailed Deer

Understanding the role that an environmental prion reservoir plays in the outbreak dynamics of chronic wasting disease (CWD) in free ranging white-tailed deer (Odocoileus virginianus) is critical for the allocation of disease surveillance resources by state and provincial wildlife agencies. We hypothesized that demographic, ecological, and epidemiological configurations naturally attenuate epidemic risk despite the introduction of infectious prions into a susceptible population of deer, but the magnitude of infectious prions in the environmental prion reservoir complicate outbreak expectations. We developed a Susceptible-Latent-Exposed-Infective (SLEI) compartment model to represent the dynamics of CWD epidemics in free-ranging white-tailed deer, then used the basic reproductive ratio (R0) to pinpoint counties under which pathogenic introduction (transport of infectious bodily fluids, tissues, and carcasses through natural or anthropogenic means) naturally produced (or failed to produce) an epidemic. We found that the outlook for an epidemic hinged on transmission rates, the magnitude of environmental contamination, and system type (density-, frequency-, or density/frequency-dependent). CWD can persistently infect individuals living in a contaminated environment even if direct transmission is insufficient to sustain circulation. Theoretical results show that transmission of CWD cannot be exclusively density dependent, and must behave as either a mix between frequency and density dependent, or strictly frequency dependent. While the compartment model is a simplistic representation of reality and did not contain many complicating biological considerations, it was immediately useful in hypothesis generation, motivating the collection of additional data for use in more biologically detailed models, and in the allocation of finite surveillance resources to place emphasis on data collection in areas where an introduction of infectious prions is comparatively more likely to result in an epidemic.

Tissue-specific biochemical differences between chronic wasting disease prions isolated from free-ranging white-tailed deer (Odocoileus virginianus)

Chronic wasting disease (CWD) is an invariably fatal prion disease affecting cervid species worldwide. Prions can manifest as distinct strains that can influence disease pathology and transmission. CWD is profoundly lymphotropic, and most infected cervids likely shed peripheral prions replicated in lymphoid organs. However, CWD is a neurodegenerative disease, and most research on prion strains has focused on neurogenic prions. Thus, a knowledge gap exists comparing neurogenic prions to lymphogenic prions. In this study, we compared prions from the obex and lymph nodes of naturally exposed white-tailed deer to identify potential biochemical strain differences. Here, we report biochemical evidence of strain differences between the brain and lymph node from these animals. Conformational stability assays, glycoform ratio analyses, and immunoreactivity scanning across the structured domain of the prion protein that refolds into the amyloid aggregate of the infectious prion reveal significantly more structural and glycoform variation in lymphogenic prions than neurogenic prions. Surprisingly, we observed greater biochemical differences among neurogenic prions than lymphogenic prions across individuals. We propose that the lymphoreticular system propagates a diverse array of prions from which the brain selects a more restricted pool of prions that may be quite different than those from another individual of the same species. Future work should examine the biological and zoonotic impact of these biochemical differences and examine more cervids from multiple locations to determine if these differences are conserved across species and locations.

Spreading of SARS-CoV-2 from hamsters to humans

Spreading of SARS-CoV-2 from hamsters to humans

Genomic architecture of phenotypic extremes in a wild cervid

Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

Evaluating the ability of a locally focused culling program in removing chronic wasting disease infected free-ranging white-tailed deer in Illinois, USA, 2003-2020.

In northern Illinois, chronic wasting disease (CWD) was first identified in free-ranging white-tailed deer (Odocoileus virginianus; hereafter referred to as "deer") in 2002. To reduce CWD transmission rates in Illinois, wildlife biologists have conducted locally focussed culling of deer since 2003 in areas where CWD has been detected. We used retrospective spatial, temporal and space-time scan statistical models to identify areas and periods where culling removed higher than expected numbers of CWD-positive deer. We included 490 Public Land Survey "sections" (∼2.59 km2 ) from 15 northern Illinois counties in which at least one deer tested positive for CWD between 2003 and 2020. A negative binomial regression model compared the proportion of CWD positive cases removed from sections with at least one CWD case detected in the previous years, "local area 1 (L1)," to the proportion of CWD cases in adjacent sections-L2, L3, and L4-designated by their increasing distance from L1. Of the 14,661 deer removed and tested via culling, 325 (2.22 %) were CWD-positive. A single temporal CWD cluster occurred in 2020. Three spatial clusters were identified, with a primary cluster located at the border of Boone and Winnebago counties. Four space-time clusters were identified with a primary cluster in the northern portion of the study area from 2003 to 2005 that overlapped with the spatial cluster. The proportion of CWD cases removed from L1 (3.92, 95% CI, 2.56-6.01) and L2 (2.32, 95% CI, 1.50-3.59) were significantly higher compared to L3. Focussing culling efforts on accessible properties closest to L1 areas results in more CWD-infected deer being removed, which highlights the value of collaborations among landowners, hunters, and wildlife management agencies to control CWD. Continuous evaluation and updating of the culling and surveillance programs are essential to mitigate the health burden of CWD on deer populations in Illinois.

SARS-CoV-2 infection in free-ranging white-tailed deer.

Humans have infected a wide range of animals with SARS-CoV-21-5, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans. No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have been transmitted in wildlife in the USA, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive 'One Health' programmes to monitor the environment, deer and other wildlife hosts globally.

Population genomics of free-ranging Great Plains white-tailed and mule deer reflects a long history of interspecific hybridization.

Hybridization is a natural process at species‐range boundaries that may variably promote the speciation process or break down species barriers but minimally will influence management outcomes of distinct populations. White‐tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) have broad and overlapping distributions in North America and a recognized capacity for interspecific hybridization. In response to contemporary environmental change to any of one or multiple still‐unknown factors, mule deer range is contracting westward accompanied by a westward expansion of white‐tailed deer, leading to increasing interactions, opportunities for gene flow, and associated conservation implications. To quantify genetic diversity, phylogenomic structure, and dynamics of hybridization in sympatric populations of white‐tailed and mule deer, we used mitochondrial cytochrome b data coupled with SNP loci discovered with double‐digest restriction site‐associated DNA sequencing. We recovered 25,018 SNPs across 92 deer samples from both species, collected from two regions of western Kansas. Eight individuals with unambiguous external morphology representing both species were of hybrid origin (8.7%), and represented the product of multi‐generational backcrossing. Mitochondrial data showed both ancient and recent directional discordance with morphological species assignments, reflecting a legacy of mule deer males mating with white‐tailed deer females. Mule deer had lower genetic diversity than white‐tailed deer, and both mitochondrial and nuclear data suggest contemporary mule deer effective population decline. Landscape genetic analyses show relative isolation between the two study regions for white‐tailed deer, but greater connectivity among mule deer, with predominant movement from north to south. Collectively, our results suggest a long history of gene flow between these species in the Great Plains and hint at evolutionary processes that purge incompatible functional genomic elements as a result of hybridization. Surviving hybrids evidently may be reproductive, but with unknown consequences for the future integrity of these species, population trajectories, or relative susceptibility to emerging pathogens.