White-tailed Deer Research Articles

Phenotypic characteristics of successful parental pairs in white-tailed deer: evidence of non-random mating

Phenotypic characteristics of successful parental pairs in white-tailed deer: evidence of non-random mating

Host-pathogen associations inferred from bloodmeal analyses of Ixodes scapularis ticks in a low biodiversity setting.

Tick-borne diseases, such as Lyme disease, babesiosis, and anaplasmosis, pose significant public health burdens. Tick bloodmeal analysis provides a noninvasive sampling method to evaluate tick-host associations and combined with a zoonotic pathogen assay, can generate crucial insights into the epidemiology and transmission of tick-borne diseases by identifying potential key maintenance hosts. We investigated the bloodmeals of questing Ixodes scapularis nymphs. We found that avian hosts, white-footed mice, and white-tailed deer fed the majority of larval ticks and differentially contributed to the prevalence of multiple tick-borne pathogens and pathogen genotypes in a low biodiversity island setting. Unraveling the intricate network of host-vector-pathogen interactions will contribute to improving wildlife management and conservation efforts, to developing targeted surveillance, and vector and host control efforts, ultimately reducing the incidence of tick-borne diseases and improving public health.

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.

Isotope values reveal “canopy effect” in deer territoriality and maize consumption for dogs from archaeological sites in Kentucky dating to the Middle Woodland through Late Fort Ancient time periods

This research analyzes stable carbon, nitrogen, and oxygen isotope values in tooth collagen and enamel to investigate foraging and territorial behavior in white-tailed deer (Odocoileus virginianus Zimmermann) and maize (Zea mays Linneaus) consumption in dogs (Canis familiaris Linneaus). The study analyzed 22 deer teeth from 13 archaeological sites in Kentucky covering a span of approximately 1,500 years of human occupation. The article presents evidence of foraging and territorial behavior in white-tailed deer, identified through the “canopy effect” observed in deer stable carbon isotope values in remains spanning from the Middle Woodland (200 BCE – CE 500) to Late Fort Ancient (CE 1400 – 1680) time periods in Kentucky. Additionally, teeth samples from nine dog and one wolf (Canis lupus Linneaus) were analyzed and indicate significant consumption of maize in seven of the dog samples. These specimens came from seven archaeological sites in Kentucky dating from the Early through Late Fort Ancient (CE 1400 – 1680) time periods. The study also contributes to the growing database of isotope studies in the Eastern Woodlands by presenting carbon and nitrogen isotope values on deer bone collagen from nine deer bone samples from three of the same archaeological sites dating to the Middle Woodland to Early Late Woodland.

Estimation of Contact Time Among Animals from Telemetry Data

Continuous processes in most applications are measured discretely with error. This complicates the task of detecting intersections and the number of intersections between two continuous processes (i.e., when the processes have the same value). Intersections of continuous processes are scientifically important, but challenging to estimate from data. For example, in the field of animal ecology, intersections of the paths of moving animals tracked with satellite technologies can be used to understand disease transmission. We illustrate how to quantify contact between animals using telemetry data (i.e., the recorded locations of an animal over time). We introduce our method to quantify contact time with accessible concepts from introductory stochastic process literature, such as Brownian motion. Then, we provide two data examples using white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) telemetry data in a region with high prevalence of chronic wasting disease. Our work provides a needed connection between existing model-based literature for animal movement and rule-based literature for animal interaction. Further, our work illustrates a unique statistical problem receiving minimal attention with broad applicability in human and livestock tracking.

214 Immuno-detection and stability of SARS-CoV-2 in milk from white-tailed deer

214 Immuno-detection and stability of SARS-CoV-2 in milk from white-tailed deer

Use of livestock by jaguar (Panthera onca) in an agrolandscape of northeastern Mexico

ABSTRACT Jaguars are endangered in Mexico, with negative interactions with livestock producers being one of the main threats to their populations. We collared three jaguars with search Global Positioning System (GPS) clusters to document prey species eaten by them in the Sierra del Abra-Tanchipa Biosphere Reserve (RBSAT) and surrounding agrolandscape, in northeastern Mexico, to determine the relative use of natural prey and livestock. We detected, through examination of the carcasses (scavenging and predation events), 35 individual prey at feeding sites, primarily collared peccary (40% of sites), cattle (23%), and white-tailed deer (20%). Cattle comprised 64% and wild ungulates provided 34% of the estimated biomass in jaguar diets (biomass was calculated based on the estimated mass consumed and the assumption of an edible portion), with cattle consumed only during the dry season. Seasonal use apparently reflected increased encounters between jaguars and livestock during the dry season, probably due to the presence of limited permanent water sources concentrating livestock (and natural prey) along with jaguars taking advantage of the increased vulnerability of livestock during the dry season (either through predation or scavenging).

Causes of mortality in farmed white-tailed deer in the midwestern United States, 2004-2023.

Farmed cervids are of growing economic importance in the midwestern United States. Although diseases of wild and captive cervids have been examined in more northerly climates, little information exists on the health challenges of deer in the Midwest. We characterized and summarized the causes of mortality in farmed white-tailed deer (Odocoileus virginianus) submitted to the University of Missouri Veterinary Medical Diagnostic Laboratory (Columbia, MO, USA) over a 19-y period (2004-2023). Of 388 cases examined, 253 (65%) were carcasses submitted for autopsy, and 135 (35%) cases were tissue samples harvested by field veterinarians. Infectious disease was the most common cause of mortality (n = 335; 86.3%). Of infectious causes, primary pneumonia was most common (n = 140; 41.7%), followed by septicemia (n = 68; 20.1%), and primary enteritis (n = 64; 19.1%). Viruses were detected in 18% of pneumonia cases. The most common non-infectious diagnoses were emaciation and trauma (both 4 each; 1%). Thirteen animals (3.4%) died of unknown causes. Forty-nine percent of cases were juvenile deer <1-y-old. Most cases were received in the summer (212; 54.6%). Infectious diseases, particularly bacteria and viruses, pose a significant health challenge to farmed deer in the midwestern United States.

Modeling platform to assess the effectiveness of single and integrated Ixodes scapularis tick control methods

BackgroundLyme disease continues to expand in Canada and the USA and no single intervention is likely to curb the epidemic.MethodsWe propose a platform to quantitatively assess the effectiveness of a subset of Ixodes scapularis tick management approaches. The platform allows us to assess the impact of different control treatments, conducted either individually (single interventions) or in combination (combined efforts), with varying timings and durations. Interventions include three low environmental toxicity measures in differing combinations, namely reductions in white-tailed deer (Odocoileus virginianus) populations, broadcast area-application of the entomopathogenic fungus Metarhizium anisopliae, and fipronil-based rodent-targeted bait boxes. To assess the impact of these control efforts, we calibrated a process-based mathematical model to data collected from residential properties in the town of Redding, southwestern Connecticut, where an integrated tick management program to reduce I.xodes scapularis nymphs was conducted from 2013 through 2016. We estimated parameters mechanistically for each of the three treatments, simulated multiple combinations and timings of interventions, and computed the resulting percent reduction of the nymphal peak and of the area under the phenology curve.ResultsSimulation outputs suggest that the three-treatment combination and the bait boxes–deer reduction combination had the overall highest impacts on suppressing I. scapularis nymphs. All (single or combined) interventions were more efficacious when implemented for a higher number of years. When implemented for at least 4 years, most interventions (except the single application of the entomopathogenic fungus) were predicted to strongly reduce the nymphal peak compared with the no intervention scenario. Finally, we determined the optimal period to apply the entomopathogenic fungus in residential yards, depending on the number of applications.ConclusionsComputer simulation is a powerful tool to identify the optimal deployment of individual and combined tick management approaches, which can synergistically contribute to short-to-long-term, costeffective, and sustainable control of tick-borne diseases in integrated tick management (ITM) interventions.Graphical

Biodetection of an odor signature in white-tailed deer associated with infection by chronic wasting disease prions.

Chronic wasting disease (CWD) has become a major concern among those involved in managing wild and captive cervid populations. CWD is a fatal, highly transmissible spongiform encephalopathy caused by an abnormally folded protein, called a prion. Prions are present in a number of tissues, including feces and urine in CWD infected animals, suggesting multiple modes of transmission, including animal-to-animal, environmental, and by fomite. CWD management is complicated by the lack of practical, non-invasive, live-animal screening tests. Recently, there has been a focus on how the volatile odors of feces and urine can be used to discriminate between infected and noninfected animals in several different species. Such a tool may prove useful in identifying potentially infected live animals, carcasses, urine, feces, and contaminated environments. Toward this goal, dogs were trained to detect and discriminate CWD infected individuals from non-infected deer in a laboratory setting. Dogs were tested with novel panels of fecal samples demonstrating the dogs' ability to generalize a learned odor profile to novel odor samples based on infection status. Additionally, dogs were transitioned from alerting to fecal samples to an odor profile that consisted of CWD infection status with a different odor background using different sections of gastrointestinal tracts. These results indicated that canine biodetectors can discriminate the specific odors emitted from the feces of non-infected versus CWD infected white-tailed deer as well as generalizing the learned response to other tissues collected from infected individuals. These findings suggest that the health status of wild and farmed cervids can be evaluated non-invasively for CWD infection via monitoring of volatile metabolites thereby providing an effective tool for rapid CWD surveillance.

Scrapie versus Chronic Wasting Disease in White-Tailed Deer.

White-tailed deer are susceptible to scrapie (WTD scrapie) after oronasal inoculation with the classical scrapie agent from sheep. Deer affected by WTD scrapie are difficult to differentiate from deer infected with chronic wasting disease (CWD). To assess the transmissibility of the WTD scrapie agent and tissue phenotypes when further passaged in white-tailed deer, we oronasally inoculated wild-type white-tailed deer with WTD scrapie agent. We found that WTD scrapie and CWD agents were generally similar, although some differences were noted. The greatest differences were seen in bioassays of cervidized mice that exhibited significantly longer survival periods when inoculated with WTD scrapie agent than those inoculated with CWD agent. Our findings establish that white-tailed deer are susceptible to WTD scrapie and that the presence of WTD scrapie agent in the lymphoreticular system suggests the handling of suspected cases should be consistent with current CWD guidelines because environmental shedding may occur.

Cascading effects of mammal host community composition on tick vector occurrence at the urban human–wildlife interface

AbstractHabitat fragmentation and host community composition are implicated as key drivers of changing tick populations and tick‐borne pathogen dynamics, altering infection risk through coupled socioecological pathways that mediate interactions between tick vectors, vertebrate hosts, and humans. Patterns of host diversity may be particularly idiosyncratic across urbanized landscapes, due to trade‐offs between extreme fragmentation that reduces habitat suitability and access, and human activities that artificially increase resource availability for wildlife. We used camera and hair trap surveys and tick sampling to identify links between landscape composition and configuration, the mammalian host community, and the presence of three tick vector species at a human–wildlife interface in New York City, an emerging area within an endemic region for several tick‐borne diseases. We found that human infrastructures, such as the presence of fences in yards, could affect mammal host community composition by changing the “hardness” of edges between urban greenspaces and residential areas. We identified yard‐ and broader landscape‐level features associated with the presence of urban mammal species, and identified cascading effects of host community composition on tick distribution in yards, suggesting management implications for the mitigation of human exposure to tick‐borne pathogens. In particular, we identified a possible role of ubiquitous mesomammals, such as raccoons (Procyon lotor), in transporting Amblyomma americanum ticks between parks and neighboring residential yards, and confirmed the key role of white‐tailed deer (Odocoileus virginianus) for introducing Ixodes scapularis ticks into yards. Our results challenge assumptions that biodiversity loss in human‐modified areas always increases the risk for tick‐borne diseases. Instead, we found many residential sites had higher mammal species richness and higher detection of low reservoir competent (“dilution”) hosts for Borrelia burgdorferi, such as opossums (Didelphis virginiana), than paired forested greenspaces. Our study highlights the importance of disentangling the mechanisms mediating tick‐borne disease hazard as a critical first step toward reducing urban tick‐borne disease risk.

Range-wide salamander densities reveal a key component of terrestrial vertebrate biomass in eastern North American forests.

Characterizing the population density of species is a central interest in ecology. Eastern North America is the global hotspot for biodiversity of plethodontid salamanders, an inconspicuous component of terrestrial vertebrate communities, and among the most widespread is the eastern red-backed salamander, Plethodon cinereus. Previous work suggests population densities are high with significant geographic variation, but comparisons among locations are challenged by lack of standardization of methods and failure to accommodate imperfect detection. We present results from a large-scale research network that accounts for detection uncertainty using systematic survey protocols and robust statistical models. We analysed mark-recapture data from 18 study areas across much of the species range. Estimated salamander densities ranged from 1950 to 34 300 salamanders ha-1, with a median of 9965 salamanders ha-1. We compared these results to previous estimates for P. cinereus and other abundant terrestrial vertebrates. We demonstrate that overall the biomass of P. cinereus, a secondary consumer, is of similar or greater magnitude to widespread primary consumers such as white-tailed deer (Odocoileus virginianus) and Peromyscus mice, and two to three orders of magnitude greater than common secondary consumer species. Our results add empirical evidence that P. cinereus, and amphibians in general, are an outsized component of terrestrial vertebrate communities in temperate ecosystems.

Fine‐scale phenotypic variation of a large herbivore in a pulsed environment

AbstractThe resource rule hypothesis predicts that geographic differences in body size among populations of organisms are due to the amount, availability, and quality of food resources. For instance, the body size of large herbivores is often correlated with soil characteristics because better soils produce better forage. In semiarid environments, rainfall variation is an important driver of forage availability, especially highly nutritious annual forbs. Thus, in such pulsed‐resource environments, it is unclear whether the body size of large herbivores is influenced by fixed resources correlated with soil characteristics, irregular resource pulses correlated with rainfall, or both. Furthermore, it is not clear whether phenotypic expression is a function of forage quality or quantity. During the early autumns of 2011–2018, we captured 4554 white‐tailed deer (Odocoileus virginianus) on seven rangeland sites in the semiarid climate of South Texas, USA. The sites range from coastal to 140 km inland and represent gradients in both soil texture and annual rainfall. We recorded age‐ and sex‐specific indices of skeletal size, antler size, and body mass. Site‐specific soil characteristics explained most of the variation in skeletal size; percent sand was inversely related to skeletal size. For environmentally sensitive phenotypes (antler size and body mass), both soil characteristics and rainfall were influencers; increases in rainfall reduced the negative effect of sand. Percent sand and rainfall were positively correlated with annual biomass of preferred forbs, yet all phenotypic traits declined with increases in forb quantity. Increases in percent shrub cover increased all phenotype sizes. Our data suggest that the phenotypic expression of large herbivores in semiarid environments is driven by forage quality via edaphic characteristics rather than forage quantity via rainfall. Specifically, less sand in the soil allows for the development of shrub communities, which in turn provide a consistent source of forage in a variable, pulsed‐rainfall environment. Although forbs are of higher quality, they are highly ephemeral. The availability of a consistent source of forage may enable white‐tailed deer to extend time invested in body growth, which results in greater phenotype size. Our findings align with the resource rule hypothesis that identifies resource availability as a fundamental element explaining geographical variation in phenotypic expression.

SARS-CoV-2 Seropositivity in Urban Population of Wild Fallow Deer, Dublin, Ireland, 2020-2022.

SARS-CoV-2 can infect wildlife, and SARS-CoV-2 variants of concern might expand into novel animal reservoirs, potentially by reverse zoonosis. White-tailed deer and mule deer of North America are the only deer species in which SARS-CoV-2 has been documented, raising the question of whether other reservoir species exist. We report cases of SARS-CoV-2 seropositivity in a fallow deer population located in Dublin, Ireland. Sampled deer were seronegative in 2020 when the Alpha variant was circulating in humans, 1 deer was seropositive for the Delta variant in 2021, and 12/21 (57%) sampled deer were seropositive for the Omicron variant in 2022, suggesting host tropism expansion as new variants emerged in humans. Omicron BA.1 was capable of infecting fallow deer lung type-2 pneumocytes and type-1-like pneumocytes or endothelial cells ex vivo. Ongoing surveillance to identify novel SARS-CoV-2 reservoirs is needed to prevent public health risks during human-animal interactions in periurban settings.

Maternal behaviors influence survival of ungulate neonates under heavy predation risk.

Predators impose top-down forces on prey populations, with the strength of those effects often varying over space and time and among demographic groups. In ungulates, predation risk is typically greatest for neonatal offspring, with some suggesting that predators can key in on adult activity to locate hidden neonates. However, few field studies to date have been able to directly assess the influence of maternal care on ungulate neonate survival. Using a population of white-tailed deer under heavy coyote predation pressure, we tested the maternal dispersion hypothesis, which suggests the dispersion of maternal activity temporally and spatially attenuates risk of predation for ungulate neonates during this vulnerable altricial phase. We compared support for this hypothesis with more commonly tested hypotheses regarding the influence of habitat conditions and intrinsic factors on neonatal survival. Fawn survival to 16 weeks was 27.7%, with coyotes accounting for 59% of fawn mortalities. In support of our maternal temporal diffusion hypothesis, we found that neonatal survival decreased as more maternal visits (proportionally) occurred at night. The only other significant (p < .1) predictor of fawn survival was birth timing, with fawn survival decreasing as the season progressed. Given that fawn survival declined as the proportion of nighttime visits increased, and that wild pig presence and human disturbance can push doe and fawn activity toward nocturnal hours, additional research is needed to determine whether managing pig and human disturbance can decrease fawn mortality. More broadly, given the importance of recruitment in ungulate population dynamics, our finding opens a potentially important new line of inquiry on how maternal behaviors influence predation risk in large animal predator-prey ecology.

Effective Field Sampling of Rectoanal Mucosa-Associated Lymphoid Tissue for Antemortem Chronic Wasting Disease Testing in White-tailed Deer.

Chronic wasting disease (CWD) is a fatal prion disease of cervids that has spread across much of North America. Although gold standard CWD diagnostics involve postmortem testing of medial retropharyngeal lymph nodes or obex (brain stem), a key tissue sample for antemortem testing is rectoanal mucosa-associated lymphoid tissue (RAMALT). However, collection of an adequate sample (i.e., enough lymphoid follicles) may be affected by factors such as deer age, repeated sampling, skill of the sampler, and adverse conditions during collection. Here, we document the protocol used to train personnel for RAMALT collection in a large study of free-ranging white-tailed deer (Odocoileus virginianus) in Wisconsin, USA, and determine factors that contributed to the occurrence of inadequate RAMALT samples. Our training protocol included hands-on experience with postmortem tissues, as well as a mentored collection process in the field. Collection of RAMALT under field conditions was highly successful, with 763/806 (94.7%) samples deemed adequate for subsequent testing. Although inadequate samples were rare, they were more likely to occur with older deer and when samples were collected at dusk (i.e., limited ambient lighting). We conclude that RAMALT collection can be highly successful under adverse field conditions, including with technicians with limited prior veterinary experience, and we provide details of our training program to facilitate repeatability in other antemortem CWD testing efforts.

Lack of prion transmission barrier in human PrP transgenic Drosophila

While animal prion diseases are a threat to human health, their zoonotic potential is generally inefficient because of interspecies prion transmission barriers. New animal models are required to provide an understanding of these prion transmission barriers and to assess the zoonotic potential of animal prion diseases. To address this goal, we generated Drosophila transgenic for human or non-human primate PrP and determined their susceptibility to known pathogenic prion diseases, namely vCJD and classical BSE, and that with unknown pathogenic potential, namely CWD. Adult Drosophila transgenic for M129 or V129 human PrP, or non-human primate PrP developed a neurotoxic phenotype and showed an accelerated loss of survival after exposure to vCJD, classical BSE, or CWD prions at the larval stage. vCJD prion strain identity was retained after passage in both M129 and V129 human PrP Drosophila. All of the primate PrP fly lines accumulated prion seeding activity and concomitantly developed a neurotoxic phenotype, generally including accelerated loss of survival, after exposure to CWD prions derived from different cervid species, including North American white-tailed deer and muntjac, and European reindeer and moose. These novel studies show that primate PrP transgenic Drosophila lack known prion transmission barriers since, in mammalian hosts, V129 human PrP is associated with severe resistance to classical BSE prions, while both human and cynomolgus macaque PrP are associated with resistance to CWD prions. Significantly, our data suggest that interspecies differences in the amino acid sequence of PrP may not be a principal determinant of the prion transmission barrier.

Widespread exposure to SARS-CoV-2 in wildlife communities

Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022–September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.

A method for characterizing disease emergence curves from paired pathogen detection and serology data

Abstract Wildlife disease surveillance programs and research studies track infection and identify risk factors for wild populations, humans and agriculture. Often, several types of samples are collected from individuals to provide more complete information about an animal's infection history. Methods that jointly analyse multiple data streams to study disease emergence and drivers of infection via epidemiological process models remain underdeveloped. Joint‐analysis methods can more thoroughly analyse all available data, more precisely quantifying epidemic processes, outbreak status, and risks. We contribute a paired data modelling approach that analyses multiple samples from individuals. We use ‘characterization maps’ to link paired data to epidemiological processes through a hierarchical statistical observation model. Our approach can provide both Bayesian and frequentist estimates of epidemiological parameters and state. Our approach can also incorporate test sensitivity and specificity, and we propose model fit diagnostics. We motivate our approach through the need to use paired pathogen and antibody detection tests to estimate parameters and infection trajectories for the widely applicable susceptible, infectious, recovered (SIR) model. We contribute general formulas to link characterization maps to arbitrary process models and datasets and an extended SIR model that better accommodates paired data. We find via simulation that paired data can more efficiently estimate SIR parameters than unpaired data, requiring samples from 5 to 10 times fewer individuals. We use our method to study SARS‐CoV‐2 in wild white‐tailed deer (Odocoileus virginianus) from three counties in the United States. Estimates for average infectious times corroborate captive animal studies. The estimated average cumulative proportion of infected deer across the three counties is 73%, and the basic reproductive number (R0) is 1.88. Wildlife disease surveillance programs and research studies can use our methods to jointly analyse paired data to estimate epidemiological process parameters and track outbreaks. Paired data analyses can improve precision and accuracy when sampling is limited. Our methods use general statistical theory to let applications extend beyond the SIR model we consider and to more complicated examples of paired data. The methods can also be embedded in larger hierarchical models to provide landscape‐scale risk assessment and identify drivers of infection.