Predicting the spread-risk potential of chronic wasting disease to sympatric ungulate species

A foundational description of Antilocapra americana pronghorn core osteohistology

Cranial bony projections ("headgear") have diverse forms and functions, such as defense, species recognition, mate selection, and thermoregulation. Most commonly, they are associated with the artiodactyl infraorder, Pecora. All pecoran headgear-antlers, horns, ossicones, and pronghorns-are osseous protrusions of the frontal or parietal bone with an integumentary covering, although there is taxonomic, developmental, and compositional variation. However, compared with other pecorans, there is a dearth of literature addressing extant antilocaprids-Antilocapra americana. This study provides a foundational osteohistological description of A. americana pronghorn cores in order to start building a framework to better understand the complex interplay among microanatomy, development, behavior, environment, and phylogenetic history of pronghorn headgear. Osteohistological analysis of adult A. americana pronghorn cores reveal the inner medullary region is composed of trabecular bone. Based on similar studies in bovids, we propose that these trabeculae may function to reduce the effects of repeated loading incurred by intraspecific combat. The deep aspect of the outer region was found to be composed of compacted coarse cancellous bone and primary bone remodeled to dense Haversian bone, in both male and female specimens, respectively, and superficially composed of highly vascularized fibrolamellar bone. The presence of fibrolamellar bone may indicate that the bone is fast-growing, and its presence at the periosteal surface suggests protracted growth of the pronghorn core beyond sexual maturity.

Predicting chronic wasting disease in white-tailed deer at the county scale using machine learning

Continued spread of chronic wasting disease (CWD) through wild cervid herds negatively impacts populations, erodes wildlife conservation, drains resource dollars, and challenges wildlife management agencies. Risk factors for CWD have been investigated at state scales, but a regional model to predict locations of new infections can guide increasingly efficient surveillance efforts. We predicted CWD incidence by county using CWD surveillance data depicting white-tailed deer (Odocoileus virginianus) in 16 eastern and midwestern US states. We predicted the binary outcome of CWD-status using four machine learning models, utilized five-fold cross-validation and grid search to pinpoint the best model, then compared model predictions against the subsequent year of surveillance data. Cross validation revealed that the Light Boosting Gradient model was the most reliable predictor given the regional data. The predictive model could be helpful for surveillance planning. Predictions of false positives emphasize areas that warrant targeted CWD surveillance because of similar conditions with counties known to harbor CWD. However, disagreements in positives and negatives between the CWD Prediction Web App predictions and the on-the-ground surveillance data one year later underscore the need for state wildlife agency professionals to use a layered modeling approach to ensure robust surveillance planning. The CWD Prediction Web App is at https://cwd-predict.streamlit.app/ .

Inter- and intra-species conversion efficacies of Norwegian prion isolates estimated by serial protein misfolding cyclic amplification

Prion diseases, including chronic wasting disease (CWD) in cervids, are fatal neurodegenerative disorders caused by the misfolding of cellular prion proteins. CWD is known to spread among captive and free-ranging deer in North America. In 2016, an outbreak of contagious CWD was detected among wild reindeer in Norway, marking the first occurrence of the disease in Europe. Additionally, new sporadic forms of CWD have been discovered in red deer in Norway and moose in Fennoscandia. We used serial protein misfolding cyclic amplification to study the ability of Norwegian prion isolates from reindeer, red deer, and moose (two isolates), as well as experimental classical scrapie from sheep, to convert a panel of 16 brain homogenates (substrates) from six different species with various prion protein genotypes. The reindeer CWD isolate successfully converted substrates from all species except goats. The red deer isolate failed to convert sheep and goat substrates but exhibited amplification in all cervid substrates. The two moose isolates demonstrated lower conversion efficacies. The wild type isolate propagated in all moose substrates and in the wild type red deer substrate, while the other isolate only converted two of the moose substrates. The experimental classical scrapie isolate was successfully propagated in substrates from all species tested. Thus, reindeer CWD and classical sheep scrapie isolates were similarly propagated in substrates from different species, suggesting the potential for spillover of these contagious diseases. Furthermore, the roe deer substrate supported conversion of three isolates suggesting that this species may be vulnerable to prion disease.

Effect of legal regulation of supplemental feeding on space use of red deer in an area with chronic wasting disease

Supplemental feeding of cervids during winter is a widespread management practice, but feeding may increase the risk of disease transmission. Therefore, legal regulations to limit supplemental feeding are often implemented when dealing with severe infectious diseases, such as chronic wasting disease (CWD) in cervids. However, it is currently unclear whether these regulations result in decreased spatial clustering and aggregation as intended. Supplemental feeding is expected to restrict the movement of cervids. Therefore, a ban on feeding may also result in wider space use and a risk of geographic spread of disease. The space use of 63 GPS-marked red deer (Cervus elaphus) was investigated before (n = 34) and after (n = 29) the implementation of a legal regulation aimed at limiting the supplemental feeding of cervids during winter in a CWD-affected region of Nordfjella, Norway. Snow depth was the main determinant of the space use for red deer. A moderate reduction in the number of GPS positions in spatial clusters was evident during periods of deep snow once the ban was in place. Sizes of core areas (Kernel 50%), home ranges (Kernel 95%), and dispersion (MCP 100%, number of 1 km2 pixels visited per deer) declined from January to March and with increasing snow depth. Dispersion (number of 1 km2 pixels visited per deer) did not depend on snow depth after the ban, and red deer used larger areas when snow depth was high after the ban compared to before. The ban on supplementary feeding had no effect on size of core areas or home ranges. Several potential factors can explain the overall weak effect of the ban on space use, including the use of agricultural fields by red deer, other anthropogenic feeding, and landscape topography. This study highlights that snow depth is the main factor determining space use during winter, and it remains to be determined whether the moderate reduction in spatial clustering during deep snow after the ban was sufficient to lower the risk of disease transmission.

Extrapolating the susceptibility of Eld’s deer (Rucervus eldii thamin) to chronic wasting disease from prion protein gene (PRNP) polymorphisms

Chronic wasting disease (CWD) is a prion disease of North American cervids. The transmission of CWD to endangered cervid species is of concern for captive breeding programs. Trans-species transmission could occur via direct contact with infected wild deer, or via prion contaminated fomites. Variation in the prion protein gene, PRNP, is associated with differences in CWD susceptibility among cervids. We therefore sequenced PRNP in 36 endangered Eld’s deer (Rucervus eldii thamin), detecting five synonymous and two non-synonymous SNPs. Three haplotypes were inferred, suggesting that genetic management in captive breeding programs has been effective at maintaining PRNP diversity. The haplotypes encoded two PrP protein variants. The more common Eld’s deer PrP variant encodes methionine at codon 208 and glutamine at codon 226. Because this protein variant is identical to a common PrP variant in white-tailed deer and mule deer and is especially common in white-tailed deer positive for CWD, we recommend reducing the frequency of this variant in the breeding stock, while implementing strict management practices to avoid exposure to wild North American cervids. The frequency of the other PrP variant, which differs from variants present in these North American cervids, was low. It has the potential to reduce susceptibility to CWD and thus could be increased in frequency. While PRNP haplotype frequencies should be shifted, genetic diversity should be maintained. Ultimately protein diversity may be protective should CWD infect the species, and trans-species polymorphisms are suggestive of past balancing selection and a potential fitness advantage for PRNP diversity.

Selection and demography drive range-wide patterns of MHC-DRB variation in mule deer

BACKGROUND

Standing genetic variation is important especially in immune response-related genes because of threats to wild populations like the emergence of novel pathogens. Genetic variation at the major histocompatibility complex (MHC), which is crucial in activating the adaptive immune response, is influenced by both natural selection and historical population demography, and their relative roles can be difficult to disentangle. To provide insight into the influences of natural selection and demography on MHC evolution in large populations, we analyzed geographic patterns of variation at the MHC class II DRB exon 2 locus in mule deer (Odocoileus hemionus) using sequence data collected across their entire broad range.

RESULTS

We identified 31 new MHC-DRB alleles which were phylogenetically similar to other cervid MHC alleles, and one allele that was shared with white-tailed deer (Odocoileus virginianus). We found evidence for selection on the MHC including high dN/dS ratios, positive neutrality tests, deviations from Hardy-Weinberg Equilibrium (HWE) and a stronger pattern of isolation-by-distance (IBD) than expected under neutrality. Historical demography also shaped variation at the MHC, as indicated by similar spatial patterns of variation between MHC and microsatellite loci and a lack of association between genetic variation at either locus type and environmental variables.

CONCLUSIONS

Our results show that both natural selection and historical demography are important drivers in the evolution of the MHC in mule deer and work together to shape functional variation and the evolution of the adaptive immune response in large, well-connected populations.

Review on PRNP genetics and susceptibility to chronic wasting disease of Cervidae

To date, chronic wasting disease (CWD) is the most infectious form of prion disease affecting several captive, free ranging and wild cervid species. Responsible for marked population declines in North America, its geographical spread is now becoming a major concern in Europe. Polymorphisms in the prion protein gene (PRNP) are an important factor influencing the susceptibility to prions and their rate of propagation. All reported cervid PRNP genotypes are affected by CWD. However, in each species, some polymorphisms are associated with lower attack rates and slower progression of the disease. This has potential consequences in terms of genetic selection, CWD diffusion and strain evolution. CWD also presents a zoonotic risk due to prions capacity to cross species barriers. This review summarizes our current understanding of CWD control, focusing on PRNP genetic, strain diversity and capacity to infect other animal species, including humans.

Chronic wasting disease: a cervid prion infection looming to spillover

The spread of chronic wasting disease (CWD) during the last six decades has resulted in cervid populations of North America where CWD has become enzootic. This insidious disease has also been reported in wild and captive cervids from other continents, threatening ecosystems, livestock and public health. These CWD "hot zones" are particularly complex given the interplay between cervid PRNP genetics, the infection biology, the strain diversity of infectious prions and the long-term environmental persistence of infectivity, which hinder eradication efforts. Here, we review different aspects of CWD including transmission mechanisms, pathogenesis, epidemiology and assessment of interspecies infection. Further understanding of these aspects could help identify "control points" that could help reduce exposure for humans and livestock and decrease CWD spread between cervids.

OPPORTUNISTIC SURVEILLANCE OF CAPTIVE AND FREE-RANGING BIGHORN SHEEP (OVIS CANADENSIS) IN COLORADO, USA, FOR TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHIES

Bighorn sheep (Ovis canadensis) are predicted to have a degree of susceptibility to the transmissible spongiform encephalopathies (TSE) chronic wasting disease and scrapie. We opportunistically screened 127 captive bighorn sheep and 152 free-ranging bighorn sheep in Colorado, US for the presence of TSE over a period of 35 yr. None of the animals demonstrated clinical signs, gross pathology, histopathology, or immunohistochemical staining patterns suggestive of TSE.

Characterization of the prion protein gene in axis deer (Axis axis) and implications for susceptibility to chronic wasting disease

Axis deer (Axis axis) occur both in captivity and free-ranging populations in portions of North America, but to-date, no data exist pertaining to the species’ susceptibility to CWD. We sequenced the prion protein gene (PRNP) from axis deer. We then compared axis deer PrP^C sequences and amino acid polymorphisms to those of CWD susceptible species. A single PRNP allele with no evidence of intraspecies variation was identified in axis deer that indicates axis deer PRNP is most similar to North American elk (Cervus canadensis) PRNP. Therefore, axis deer may be susceptible to CWD. We recommend proactively increasing CWD surveillance for axis deer, particularly where CWD has been detected and axis deer are sympatric with native North American CWD susceptible species.

Considering the use of the terms strain and adaptation in prion research

Evolutionary biologists and disease biologists use the terms strain and adaptation in Chronic Wasting Disease (CWD) research in different ways. In evolutionary biology, a strain is a nascent genetic lineage that can be described by a genealogy, and a phylogenetic nomenclature constructed to reflect that genealogy. Prion strains are described as showing distinct host range, clinical presentation, disease progression, and neuropathological and PrP biochemical profiles, and lack information that would permit phylogenetic reconstruction of their history. Prion strains are alternative protein conformations, sometimes derived from the same genotype. I suggest referring to prion strains as ecotypes, because the variant phenotypic conformations ("strains") are a function of the interaction between PRNP amino acid genotype and the host environment. In the case of CWD, a prion ecotype in white-tailed deer would be described by its genotype and the host in which it occurs, such as the H95 + ecotype. However, an evolutionary nomenclature is difficult because not all individuals with the same PRNP genotype show signs of CWD, therefore creating a nomenclature reflecting and one-to-one relationship between PRNP genealogy and CWD presence is difficult. Furthermore, very little information exists on the phylogenetic distribution of CWD ecotypes in wild deer populations. Adaptation has a clear meaning in evolutionary biology, the differential survival and reproduction of individual genotypes. If a new prion ecotype arises in a particular host and kills more hosts or kills at an earlier age, it is the antithesis of the evolutionary definition of adaptation. However, prion strains might be transmitted across generations epigenetically, but whether this represents adaptation depends on the fitness consequences of the strain. Protein phenotypes of PRNP that cause transmissible spongiform encephalopathies (TSEs), and CWD, are maladaptive and would not be propagated genetically or epigenetically via a process consistent with an evolutionary view of adaptation. I suggest terming the process of prion strain origination "phenotypic transformation", and only adaptation if evidence shows they are not maladaptive and persist over evolutionary time periods (e.g., thousands of generations) and across distinct species boundaries (via inheritance). Thus, prion biologists use strain and adaptation, historically evolutionary terms, in quite different ways.

Cervid Prion Protein Polymorphisms: Role in Chronic Wasting Disease Pathogenesis

Chronic wasting disease (CWD) is a prion disease found in both free-ranging and farmed cervids. Susceptibility of these animals to CWD is governed by various exogenous and endogenous factors. Past studies have demonstrated that polymorphisms within the prion protein (PrP) sequence itself affect an animal's susceptibility to CWD. PrP polymorphisms can modulate CWD pathogenesis in two ways: the ability of the endogenous prion protein (PrP^C) to convert into infectious prions (PrP^Sc) or it can give rise to novel prion strains. In vivo studies in susceptible cervids, complemented by studies in transgenic mice expressing the corresponding cervid PrP sequence, show that each polymorphism has distinct effects on both PrP^C and PrP^Sc. It is not entirely clear how these polymorphisms are responsible for these effects, but in vitro studies suggest they play a role in modifying PrP epitopes crucial for PrP^C to PrP^Sc conversion and determining PrP^C stability. PrP polymorphisms are unique to one or two cervid species and most confer a certain degree of reduced susceptibility to CWD. However, to date, there are no reports of polymorphic cervid PrP alleles providing absolute resistance to CWD. Studies on polymorphisms have focused on those found in CWD-endemic areas, with the hope that understanding the role of an animal's genetics in CWD can help to predict, contain, or prevent transmission of CWD.

Genetic and evolutionary considerations of the Chronic Wasting Disease - Human species barrier

Transmissible spongiform encephalopathies can jump species barriers. In relatively few cases is the possible route of transmission thought to be known, mostly involving humans, cattle and sheep. It is thought that sheep might be the cause of Bovine Spongiform Encephalopathy (BSE) and Chronic Wasting Disease (CWD) in cervids, and that humans might have gotten prion disease (e.g., vCJD) from eating meat from BSE⁺ cows. A looming societal question is whether humans will acquire a prion disease from ingesting prions from CWD⁺ deer. On an evolutionary tree of the PRNP gene in mammals, deer, sheep and cow are relatively closely related, whereas these three species are relatively distant from humans. If a prion disease jumped the species barrier from cow to humans, the phylogenetic gap from deer to humans is no greater, and sheer evolutionary distance alone cannot explain a CWD species barrier in humans. Aspects of the PRNP gene were compared among these species to search for genetic differences that might influence the permeability of the species barrier. Human prion disease has been associated with having more than four copies of the octarepeat unit (PHGGGWG), whereas deer, sheep and cow all have three copies. Two amino acid positions in the metal-binding region (96 and 97) have been implicated in species barriers (Breydo and Uversky, 2011), whereas no variation was detected in white-tailed deer and mule deer with and without CWD, or in black-tailed deer, Key deer or Coues deer. Four out of 10 differences between deer and human in the β2-α2 loop might preclude CWD prions from converting human PrP^C to PrP^Sc because of disruption of a steric zipper. The reasons for a CWD species barrier between deer and humans, if there is one, is still unresolved.