Cervid Species Research Articles

Transmission, Strain Diversity, and Zoonotic Potential of Chronic Wasting Disease.

Chronic wasting disease (CWD) is a prion disease affecting several species of captive and free-ranging cervids. In the past few decades, CWD has been spreading uncontrollably, mostly in North America, resulting in a high increase of CWD incidence but also a substantially higher number of geographical regions affected. The massive increase in CWD poses risks at several levels, including contamination of the environment, transmission to animals cohabiting with cervids, and more importantly, a putative transmission to humans. In this review, I will describe the mechanisms and routes responsible for the efficient transmission of CWD, the strain diversity of natural CWD, its spillover and zoonotic potential and strategies to minimize the CWD threat.

Antler tine homologies and cervid systematics: A review of past and present controversies with special emphasis on Elaphurus davidianus.

Antlers are the most conspicuous trait of cervids and have been used in the past to establish a classification of their fossil and living representatives. Since the availability of molecular data, morphological characters have generally become less important for phylogenetic reconstructions. In recent years, however, the appreciation of morphological characters has increased, and they are now more frequently used in addition to molecular data to reconstruct the evolutionary history of cervids. A persistent challenge when using antler traits in deer systematics is finding a consensus on the homology of structures. Here, we review early and recent attempts to homologize antler structures and objections to this approach, compare and evaluate recent advances on antler homologies, and critically discuss these different views in order to offer a basis for further scientific exchange on the topic. We further present some developmental aspects of antler branching patterns and discuss their potential for reconstructing cervid systematics. The use of heterogeneous data for reconstructing phylogenies has resulted in partly conflicting hypotheses on the systematic position of certain cervid species, on which we also elaborate here. We address current discussions on the use of different molecular markers in cervid systematics and the question whether antler morphology and molecular data can provide a consistent picture on the evolutionary history of cervids. In this context, special attention is given to the antler morphology and the systematic position of the enigmatic Pere David's deer (Elaphurus davidianus).

Non-native Nematode Ashworthius sidemi Currently Dominates the Abomasal Parasite Community of Cervid Hosts in the Czech Republic

Ashworthius sidemi is an abomasal nematode typical for Asiatic cervids such as sambar (Rusa unicolor) or sika deer (Cervus nippon). This non-native parasite was introduced into Europe via sika deer in the late 19th and early 20th centuries. The current dynamic spread of this parasite amongst autochthonous wild cervids occurs independently of human activities, and A. sidemi has a negative impact on the health of wild ruminants and may pose a threat to the conservation of endangered wild ungulates and to livestock. This invasive parasite has been previously detected in the Czech Republic, but more accurate information on A. sidemi is required. Only limited information is generally available on the factors influencing the spread of abomasal nematodes in wild ruminants, so more information is necessary for planning effective strategies of parasite control. We therefore conducted a survey on the abomasal nematodes in cervids in both game reserves and hunting grounds across the Czech Republic, taking into account the hosts (species, age, sex) and environmental factors (monthly average temperature). The abomasa of 104 animals belonging to five cervid species originating from various locations of the country were collected. Data on host (species, sex, and age group) and the monthly average temperature in the region were obtained for each animal. The parasitological analyses indicated that 92% of the abomasa were infected by nematodes. Ashworthius sidemi was the most prevalent (72%) and abundant (80% of the total recovered individuals) nematode species and was detected in all cervid species except white-tailed deer. The intensity of A. sidemi was highest in roe deer (Capreolus capreolus) and fallow deer (Dama dama), but A. sidemi abundance did not depend substantially on the host or environmental factors. In contrast, the abundance of nematodes from the subfamily Ostertagiinae was influenced by the host species and temperature. Parasitic load was significantly higher in roe deer and during the warmer periods of the survey. We also detected another non-native nematode species, Spiculopteragia houdemeri. The results of our study suggest that the non-native nematode A. sidemi is now widespread amongst cervid hosts in the Czech Republic, probably due to the high sensitivity of autochthonous cervids to A. sidemi infections as well as adaptation of this parasite to the current climatic conditions of this country.

Spreading speed of chronic wasting disease across deer groups with overlapping home ranges

Chronic wasting disease (CWD) is a fatal disease of cervid species that continues to spread across North America and now in Europe. It poses a threat to cervid populations and the local ecological and economic communities that depend on them. Although empirical studies have shown that host home range overlap and male dispersal are important in the spread of disease, there are few mechanistic models explicitly considering those factors. We built a spatio-temporal, differential equation model for CWD spreading with restricted movement of hosts within home ranges. The model incorporates both direct and environmental transmission within and between groups as well as male dispersal. We compared the relative influence of host density, sex ratio, home range size, and male dispersal distance on the spreading speed using sensitivity analysis. We also assessed the effect of landscape heterogeneity, quantified as edge density, on the spreading speed of CWD because it jointly alters the host density and home range size. Our model binds the theoretical study of CWD spreading speed together with empirical studies on deer home ranges and sets a base for models in 2D space to evaluate management and control strategies.

Forage availability, supplementary feed and ungulate density: Associations with ungulate damage in pine production forests

Populations of large herbivores, including members of the deer family Cervidae, are expanding across and within many regions of the northern hemisphere. Because their browsing on trees can result in economic losses to forestry and strongly affect ecosystems, it is becoming increasingly important to understand how best to mitigate resultant damage. Previous research has highlighted the importance of regulating deer density and the availability of alternative forage to reduce browsing damage levels in conifer production stands. However, often only one or two proxies of forage availability have been used instead of applying a broad foodscape approach and more knowledge is needed to understand which types of alternative forage best mitigate damage. We conducted field inventories of damage that occurred during the previous fall/winter in 112 production stands in southern Sweden, while also measuring forage availability and cervid faecal pellets in the surrounding landscape (16 ha). Local landowners provided data on supplementary feeding. We found that variation in cervid (Alces alces, Capreolus capreolus, Cervus elaphus and Dama dama) browsing damage to top shoots or stems of young Scots pine trees (Pinus sylvestris, hereon pine), was better explained by the availability of alternative natural forage (using several indices and species of trees and shrubs) than by supplementary feeding. The proportion of damaged pine trees was higher in stands with a lower density of pine stems; in landscapes with a lower density of key broadleaf tree species (genera Sorbus, Salix, Populus and Quercus); and in landscapes with more open land (agricultural fields and paddocks). Damage was also higher in stands where relatively large amounts of moose faeces was found, while not related to the amount of faeces from other cervid species. The amount of supplementary feed (silage or other types such as root vegetables) did not explain variation in pine damage, but the result was possibly affected by relatively few study areas supplying sufficient data on supplementary feeding. The results from our inventory illustrate the efficacy of using naturally growing forage to mitigate browsing damage to young pine trees in managed landscapes. Creation of such forage is also recommended over supplementary feeding because of co-benefits to forest biodiversity and ecosystem services.

Survey of Culicoides-borne bluetongue and Schmallenberg viruses at the wildlife-livestock interface in Doñana National Park (Spain).

A cross-sectional study was carried out to assess the circulation of bluetongue virus (BTV) and Schmallenberg virus (SBV) within the wild and domestic ungulate host community in Doñana National Park (southwestern Spain). A total of 440 animals, including 138 cattle, 102 red deer (Cervus elaphus), 101 fallow deer (Dama dama) and 99 wild boar (Sus scrofa), were sampled in 2015 during the seasonal peak of Culicoides spp. (summer-autumn). Serum and spleen samples were analysed to detect exposure (using commercial blocking ELISAs) and infection (by RT-PCR), respectively, to BTV and SBV. Cattle were not tested by BTV-bELISA because all were previously vaccinated against BTV serotypes 1 and 4. High BTV seroprevalences were found in red deer (97.0%) and fallow deer (64.7%). Antibodies against SBV were detected in 37.0% of cattle, 16.8% of red deer, 23.5% of fallow deer and 2.0% of wild boar. Thirty-eight of the 203 deer (18.7%; 17 red deer and 21 fallow deer) were co-exposed to both viral agents. BTV-4 RNA was confirmed in four red deer and two fallow deer. SBV RNA was found in two fallow deer. Co-infections were not detected. Our results indicate high exposure, widespread distribution and active circulation of BTV and SBV in the ruminant community in the study area. We provide additional evidence for the potential role of wild cervids as reservoirs of these Culicoides-borne viruses in two different epidemiological scenarios: with vaccination (BTV) and without vaccination (SBV) of sympatric livestock. This study highlights the importance of wildlife surveillance, particularly of cervid species, for the proper execution of control programmes of Culicoides-borne diseases in extensively reared livestock.

Extended application of the rapid post-mortem test kit for bovine spongiform encephalopathy to chronic wasting disease.

Chronic wasting disease (CWD) is a prion disease affecting cervid species primarily in the United States of America and Canada; however, it is now emerging in Scandinavian countries. Although CWD cases have not been reported in Japan, in case of a CWD outbreak occuring, it is critical to prepare for testing a large number of specimens. The present study showed that a rapid post-mortem test kit, which is used for bovine spongiform encephalopathy surveillance in Japan, is valid for the detection of CWD prion.

From Deer-to-Deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in humans, has a broad host range, and is able to infect domestic and wild animal species. Notably, white-tailed deer (WTD, Odocoileus virginianus), the most widely distributed cervid species in the Americas, were shown to be highly susceptible to SARS-CoV-2 in challenge studies and reported natural infection/exposure rates approaching 30–40% in free-ranging WTD in the U.S. Thus, understanding the infection and transmission dynamics of SARS-CoV-2 in WTD is critical to prevent future zoonotic transmission to humans, at the human-WTD interface during hunting or venison farming, and for implementation of effective disease control measures. Here, we demonstrated that following intranasal inoculation with SARS-CoV-2 B.1 lineage, WTD fawns (~8-month-old) shed infectious virus up to day 5 post-inoculation (pi), with high viral loads shed in nasal and oral secretions. This resulted in efficient deer-to-deer transmission on day 3 pi. Consistent a with lack of infectious SARS-CoV-2 shedding after day 5 pi, no transmission was observed to contact animals added on days 6 and 9 pi. We have also investigated the tropism and sites of SARS-CoV-2 replication in adult WTD (3–4 years of age). Infectious virus was detected up to day 6 pi in nasal secretions, and from various respiratory-, lymphoid-, and central nervous system tissues, indicating broad tissue tropism and multiple sites of virus replication. The study provides important insights on the infection and transmission dynamics of SARS-CoV-2 in WTD, a wild animal species that is highly susceptible to infection and with the potential to become a reservoir for the virus in the field.

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.

Large animal models for chronic wasting disease.

Chronic wasting disease (CWD) is a fatal neurodegenerative prion disease of cervid species including deer, elk, moose and reindeer. The disease has shown both geographic and species expansion since its discovery in the late 1960’s and is now recognized in captive and free-ranging cervid populations in North America, Asia and Europe. The facile transmission of CWD is unique among prion diseases and has resulted in growing concern for cervid populations and human public health. The development of native cervid host models with longitudinal monitoring has revealed new insights about CWD pathogenesis and transmission dynamics. More than 20 years of experimental studies conducted in these models, using biologically relevant routes of infection, have led to better understanding of many aspect of CWD infections. This review addresses some of these insights, including: (i) the temporal intra-host trafficking of CWD prions in tissues and bodily fluids, (ii) the presence of infectivity shed in bodily excretions that may help explain the facile transmission of CWD, (iii) mother-to-offspring CWD transmission, (iv) the influence of some Prnp polymorphisms on CWD susceptibility, and (vi) continued development of vaccine strategies to mitigate CWD.

Reduction of Chronic Wasting Disease Prion Seeding Activity following Digestion by Mountain Lions.

ABSTRACTChronic wasting disease (CWD) is a transmissible prion disease first observed in the 1960s in North America. This invariably fatal disease affects multiple cervid species in the wild and in captivity. In addition to the several known transmission pathways involving cervid host species, prions have been detected in the feces of crows and coyotes after consumption of experimentally spiked tissues. This raises questions about the role of cervid consumers in the perpetuation of CWD. Mountain lions have been shown to preferentially select CWD-infected prey and are also apparently resistant to infection. In this study, two captive mountain lions were fed ground mule deer muscle tissue spiked with brain-derived CWD prions, and lion feces were collected for 1 week afterward. The input brain and resulting fecal materials were analyzed using the highly sensitive real-time quaking-induced conversion (RT-QuIC) assay to quantify prion seeding activity. We recovered only 2.8 to 3.9% of input CWD prions after passage through the mountain lions’ gastrointestinal tracts. Interestingly, CWD prions were shed only in the first defecation following consumption. Our data support the possibility that mountain lions feeding upon infected carcasses could excrete CWD prions in their feces over a short period of time but also suggest that most of the ingested prions are eliminated or sequestered by this large predator.IMPORTANCE CWD prions appear to spread naturally among susceptible cervid species in captivity and in the wild. A better understanding of all the ways these prions move, persist, and subsequently infect target species through the environment is critical to developing comprehensive disease control strategies. In our study, we show limited, transient pass-through of CWD prions in an apex predator, the mountain lion, using the highly sensitive RT-QuIC assay on feces collected after lions were fed prion-spiked muscle tissue. Prions were detected in feces only in the first defecation after exposure. Moreover, the amount of CWD prions recovered in feces was reduced by >96% after passing through the lion digestive system. This indicates that mountain lions may have some potential to distribute CWD prions within their home ranges but that they also effectively eliminate most of the CWD prions they consume.

Variation in the PRNP gene of Pere David’s deer (Elaphurus davidianus) may impact genetic vulnerability to chronic wasting disease

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy caused by prions that has spread across cervid species in North America since the 1960s and has recently been detected in Eurasian cervids. The Association of Zoos and Aquariums (AZA) considers CWD to be of major concern for cervids in AZA-accredited facilities because of the indirect transmission risk of the disease and the impact of CWD regulatory protocols on captive breeding programs. Vulnerability to CWD is affected by variation in the PRNP gene that encodes the prion protein. We therefore sequenced PRNP in Pere David’s deer (Elaphurus davidianus), a species that was extinct in the wild for more than a century and descends from ca. 11 founders. In 27 individuals, we detected two PRNP haplotypes, designated Elad1 (51 of 54 sequences) and Elad2 (3 of 54 sequences). The two haplotypes are separated by four single nucleotide polymorphisms (SNPs), three of which are non-synonymous. Both Elad1 and Elad2 have polymorphisms that in other cervid taxa are associated with reduced vulnerability to CWD. The two haplotypes are more similar in sequence to PRNP in other cervids than to each other. This suggests that PRNP in cervids may have been under long-term balancing selection, as has been shown for PRNP in non-cervid taxa, and which could account for the presence of multiple haplotypes among founders. There may be a fitness benefit in maintaining both PRNP haplotypes in the species because variation in the prion protein amino acid sequence can limit transmission of CWD.

Detection of Anaplasma phagocytophilum in Wild and Farmed Cervids in Poland.

Background: The role of cervids in the circulation of A. phagocytophilum has not yet been clearly determined; however, several species of wild and farm cervids may be a natural reservoir of this bacteria. Methods: Spleen and liver tissue samples were taken from 207 wild (red deer, roe deer, fallow deer and moose) and farmed cervids (red deer and fallow deer) from five geographical areas. These were tested for the A. phagocytophilum 16S rDNA partial gene by nested PCR. Results: Anaplasma spp. were detected in 91 of 207 examined cervids (prevalence 43.9%). Three different variants of 16S rDNA partial gene were reported, one for the first time. Anaplasma phagocytophilum was more often detected in young specimens than in adults and more often in the spleen than in the liver. Conclusions: Cervids from the four sites across Poland were found to be major natural reservoirs of various strains of A. phagocytophilum. This is the first study to use spleen and liver as biological material to detect A. phagocytophilum in moose in Poland.

Anchoring the CerEla1.0 Genome Assembly to Red Deer (Cervus elaphus) and Cattle (Bos taurus) Chromosomes and Specification of Evolutionary Chromosome Rearrangements in Cervidae.

Simple SummaryThe red deer (Cervus elaphus) de novo genome assembly (CerEla1.0) has provided a great resource for genetic studies in various deer species. In this study, we used gene order comparisons between C. elaphus CerEla1.0 and B. taurus ARS-UCD1.2 genome assemblies and fluorescence in situ hybridization (FISH) with bovine BAC probes to verify the red deer-bovine chromosome relationships and anchor the CerEla1.0 C-scaffolds to karyotypes of both species. We showed the homology between bovine and deer chromosomes and determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds. Using a set of BAC probes, we were able to narrow the positions of evolutionary chromosome breakpoints defining the family Cervidae. In addition, we revealed several errors in the current CerEla1.0 genome assembly. Finally, we expanded our analysis to other Cervidae and confirmed the locations of the cervid evolutionary fissions and orientation of the fused chromosomes in eight cervid species. Our results can serve as a basis for necessary improvements of the red deer genome assembly and provide support to other genetic studies in Cervidae.The family Cervidae groups a range of species with an increasing economic significance. Their karyotypes share 35 evolutionary conserved chromosomal segments with cattle (Bos taurus). Recent publication of the annotated red deer (Cervus elaphus) whole genome assembly (CerEla1.0) has provided a basis for advanced genetic studies. In this study, we compared the red deer CerEla1.0 and bovine ARS-UCD1.2 genome assembly and used fluorescence in situ hybridization with bovine BAC probes to verify the homology between bovine and deer chromosomes, determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds and specified positions of the cervid evolutionary chromosome breakpoints. In addition, we revealed several incongruences between the current deer and bovine genome assemblies that were shown to be caused by errors in the CerEla1.0 assembly. Finally, we verified the centromere-to-centromere orientation of evolutionarily fused chromosomes in seven additional deer species, giving a support to previous studies on their chromosome evolution.

Seroepidemiology of Aino Virus in Farmed and Free-Ranging Cervids in the Republic of Korea.

Aino virus is an infectious, non-contagious, vector-borne agent that has been implicated in arthrogryposis-hydranencephaly syndrome in newborn cattle, sheep, and goats. Information about reservoirs and host animal species susceptible to Aino virus remains unclear. To further explore the role of cervids in Aino virus infection transmission, we investigated cervid sera to determine the prevalence of Aino virus-neutralizing antibodies and to identify factors correlated with antibody positivity. We screened cervid serum samples collected in the Republic of Korea to better understand infection patterns in this animal species. Overall, Aino virus infection was widespread; 75 of 716 (10.5%, 95% [95% CI] = 8.4–13.4) farmed-cervid serum samples collected from 292 herds contained antibodies to Aino virus. Serological evidence of Aino virus infection was demonstrated in 5 of 43 free-ranging cervids, accounting for a prevalence rate of ~11.6% (95% CI = 4.6–26.4). Our results revealed that age class and geographic location affected seroprevalence. The main risk factors associated with Aino virus seroprevalence were older age (> 2 years old, OR = 2.221, 95% CI = 1.209–4.079, P = 0.009 in adults), southern provinces (OR = 2.432, 95% CI = 1.445–4.093, P = 0.001), and western provinces (OR = 1.905, 95% CI = 1.041–3.488, P = 0.034). The results in this study suggest that cervid species might serve as important hosts for the transmission of Aino virus, highlighting the need for careful monitoring of Aino virus infections in cervids.

Chronic wasting disease in Norway-A survey of prion protein gene variation among cervids.

Susceptibility of cervids to Chronic Wasting Disease (CWD), a prion disease, can be modulated by variations in the prion protein gene (PRNP), encoding the cellular prion protein (PrPC ). In prion diseases, PrPC is conformationally converted to pathogenic conformers (PrPSc ), aggregates of which comprise infectious prions. CWD has recently been observed in its contagious form in Norwegian reindeer (Rangifer tarandus) and in novel, potentially sporadic forms, here called 'atypical CWD', in moose (Alces alces) and red deer (Cervus elaphus). To estimate relative susceptibility of different Norwegian cervid species to CWD, their non-synonymous PRNP variants were analyzed. In reindeer, seven PRNP alleles were observed and in red deer and moose two alleles were present, whereas roe deer (Capreolus capreolus) PRNP was monomorphic. One 'archetypal' PRNP allele associated with susceptibility was common to all four cervid species. The distribution of PRNP alleles differed between wild and semi-domesticated reindeer, with alleles associated with a high susceptibility occurring, on average, above 55% in wild reindeer and below 20% in semi-domesticated reindeer. This difference may reflect the diverse origins of the populations and/or selection processes during domestication and breeding. Overall, PRNP genetic data indicate considerable susceptibility to CWD among Norwegian cervids and suggest that PRNP homozygosity may be a risk factor for the atypical CWD observed in moose. The CWD isolates found in the Norwegian cervid species differ from those previously found in Canada and USA. Our study provides an overview of the PRNP genetics in populations exposed to these emerging strains that will provide a basis for understanding these strains' dynamics in relation to PRNP variability.

Genetic diversity of cervid Trypanosoma theileri in Honshu sika deer (Cervus nippon) in Japan.

The taxonomy of ruminant Trypanosoma theileri and its relatives (Kinetoplastida: Trypanosomatidae) is controversial, with recent phylogenetic studies segregating T. theileri in cattle and other ruminants worldwide into two major genetic lineages (the TthI and TthII clades) based on genetic markers. In the present study, T. theileri-like trypanosomes isolated from Honshu sika deer (Cervus nippon) in the western Japan (YMG isolate) were genetically characterized using a number of genetic markers. Sika deer trypanosomes of the YMG isolate were genetically different from the Trypanosoma sp. TSD1 isolate previously recorded from Hokkaido sika deer in northern Japan, with the former trypanosome isolate being genetically closer to European cervid trypanosomes and the bovine T. theileri TthII lineage. In contrast, the latter isolate exhibited greater relatedness to North American cervid trypanosomes and the bovine T. theileri TthI lineage, although a clear genetic distinction between these was apparent. Furthermore, trypanosomes in Honshu sika deer from the central part of Japan harboured additional genetic diversity and were closer to either TSD1 or YMG isolates, while distinct from known T. theileri-related genotypes. Importantly, cervids and wild ruminants worldwide might harbour divergent descendants of a T. theileri ancestor, which exhibit rigid host specificity to either bovines or cervid species.

North American and Norwegian Chronic Wasting Disease Prions Exhibit Different Potential for Interspecies Transmission and Zoonotic Risk.

Chronic wasting disease (CWD) is a rapidly spreading prion disorder affecting various species of wild and captive cervids. The risk that CWD poses to cohabiting animals or more importantly to humans is largely unknown. In this study, we investigated differences in the capacity of CWD isolates obtained from 6 different cervid species to induce prion conversion in vitro by protein misfolding cyclic amplification. We define and quantify spillover and zoonotic potential indices as the efficiency by which CWD prions sustain prion generation in vitro at expenses of normal prion proteins from various mammals and human, respectively. Our data suggest that reindeer and red deer from Norway could be the most transmissible CWD prions to other mammals, whereas North American CWD prions were more prone to generate human prions in vitro. Our results suggest that Norway and North American CWD prions correspond to different strains with distinct spillover and zoonotic potentials.

Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus)

Chronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest, USA. Farmed deer originated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances of Akkermansia, Lachnospireacea UCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.

Pathogen-mediated selection favours the maintenance of innate immunity gene polymorphism in a widespread wild ungulate.

Toll-like receptors (TLR) play a central role in recognition and host frontline defence against a wide range of pathogens. A number of recent studies have shown that TLR genes (Tlrs) often exhibit large polymorphism in natural populations. Yet, there is little knowledge on how this polymorphism is maintained and how it influences disease susceptibility in the wild. In previous work, we showed that some Tlrs exhibit similarly high levels of genetic diversity as genes of the Major Histocompatibility Complex (MHC), and signatures of contemporary balancing selection in roe deer (Capreolus capreolus), the most abundant cervid species in Europe. Here, we investigated the evolutionary mechanisms by which pathogen-mediated selection could shape this innate immunity genetic diversity by examining the relationships between Tlr (Tlr2, Tlr4 and Tlr5) genotypes (heterozygosity status and presence of specific alleles) and infections with Toxoplasma and Chlamydia, two widespread intracellular pathogens known to cause reproductive failure in ungulates. We showed that Toxoplasma and Chlamydia exposures vary significantly across years and landscape features with few co-infection events detected and that the two pathogens exert antagonistic selection on Tlr2 polymorphism. By contrast, we found limited support for Tlr heterozygote advantage. Our study confirmed the importance of looking beyond Mhc genes in wildlife immunogenetic studies. It also emphasized the necessity to consider multiple pathogen challenges and their spatiotemporal variation to improve our understanding of vertebrate defence evolution against pathogens.