Identification and initial characterization of novel prion protein gene (PRNP) variants in wild Montana mule deer

 ORIGINAL RESEARCH article Front. Vet. Sci., 13 July 2026 Sec. Veterinary Epidemiology and Economics Volume 13 - 2026 | https://doi.org/10.3389/fvets.2026.1861004

Identification and initial characterization of novel prion protein gene (PRNP) variants in wild Montana mule deer

Alyssa L. Seerley .jpeg Alyssa L. Seerley 1 M Michael T. Rothfuss 2 B Bridget M. Gray 1 M Mylene A. Sebogo 1 B Bethelhem A. Manakelew 1 J June I. Pounder 1 B Bruce E. Bowler 2 M Moses J. Leavens 1 Andrea L. Grindeland Panter .jpeg Andrea L. Grindeland Panter 1* 1. Weissman Hood Institute at Touro University, McLaughlin Research Institute for Biomedical Sciences, Great Falls, MT, United States 2. Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, United States

Abstract

Chronic Wasting Disease (CWD) is a transmissible spongiform encephalopathy (TSE) of cervids (elk, deer, moose, and reindeer) that is increasing in prevalence and expanding to new geographical areas. TSEs, commonly referred to as prion diseases, are fatal neurodegenerative diseases that occur in a variety of mammals, including humans, and typically exhibit species-specific characteristics. This study reports the sequencing of the prion protein gene (PRNP) in retropharyngeal lymph node samples from 358 Montana mule deer (Odocoileus hemionus) and the identification of 36 PRNP genetic variants, many of which have not been reported previously. Further investigations tracked spatiotemporal characteristics of variants to hunting districts, year of harvest, and CWD status. PRNP polymorphisms V12F, D20G, R40Q, and S225F were examined with EmCAST computational predictions to determine the relationship between sequence and structural variations providing further insights into mechanisms affecting CWD outcomes. EmCAST predictions suggest the novel variant V12F phenotype is attributable to functional changes such as altered protein–protein interactions that might be linked to the CWD positive status of the samples. Notably, the analysis of S225F by EmCAST predicted that S225F is a neutral variation for folded PrP and incompatible with fibril PrP, suggesting a potential structural mechanism for reduced fibril PrP formation, which is consistent with the previously proposed protective role of this variant. The CWD-positive samples harboring PRNP variants were examined with the prion RT-QuIC assay, including the novel variant V12F, which resulted in prion seeding activity.

snip…

Future studies such as this may determine protective genetic variants from CWD driven genetic selection in Montana. Interestingly, rather than identifying beneficial variants, our data revealed a number of novel PRNP variants that were CWD positive, modeled for protein stability, and were confirmed to have PrP seeding activity. It is well established in the prion field that certain strains show differential molecular compatibility with amplification substrates, as demonstrated for CJD subtypes defined by PRNP codon 129 polymorphisms (51, 52). Likewise, in CWD studies, RT-QuIC is commonly used as one of many methods to determine prion strains via differences in prion seeding activity (53–55). Without further information on the wild cervid samples, analysis on this data set was limited to binary confirmation of CWD status. However, studies such as ours underline the potential use of the RT-QuIC assay in CWD diagnostic and surveillance programs. With complete epidemiological and demographic information, RT-QuIC could provide insight into disease staging including early stages of disease that otherwise go undetected giving crucial knowledge to how cervid populations are managed and surveyed.

snip…

5 Conclusion The value of studying PRNP diversity in a newly endemic population is three-fold. First, the opportunity to establish a baseline database of PRNP variant emergence prior to strong CWD-driven selection at newly endemic timepoints is a unique opportunity. This baseline window will narrow as CWD becomes more widely established and disease-driven selection increasingly shapes PRNP allele frequencies. Second, the chance to observe variant emergence over time, as CWD epidemiologic factors are still not completely understood among wild cervid populations. Third, the opportunity to identify emerging PRNP polymorphisms which can be studied further in the laboratory to better determine if these substitutions might change disease phenotypes or harbor new prion strains.

While research is underway for innovative approaches to reduce the spread of CWD through practical applications of improving diagnostics and treatments, disease management tools are currently limited (30, 72). Development of genetic databases such as ours provide wildlife managers with information which may be utilized in CWD management decisions, potentially making a bigger impact in newly endemic regions with lower prevalences than in regions with higher disease prevalence numbers. Identifying novel and previously described PRNP variants may support more targeted CWD management decisions. Incorporating PRNP sequencing as an additional tool could help prioritize areas for CWD surveillance sampling. Because PRNP polymorphisms have been shown to alter disease susceptibility and modify phenotypes in cervid populations (72), knowledge of location and prevalence of these variants alongside other epidemiologic factors may also improve predictions of CWD trajectories and be incorporated into wildlife management strategies. Our study contributes valuable information on PRNP variants identified in wild mule deer, the timing and geographical location of the variants, and the effects on prion protein folding and seeding activity. In addition to the identification of 36 polymorphisms, this study highlights the need for further investigations into RT-QuIC detection of early stages of disease. Both of these findings have the potential to greatly influence and expand the current understand of CWD nationwide as well as provides relevant and valuable context for management decisions in Montana.

https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2026.1861004/full

All Years Chronic Wasting Disease (CWD) Sample Data (2017 - Present)

2,159 Positive CWD Samples

Species    Positive Samples    Total Samples

Mule Deer    670    25,216

White-tailed Deer    1,473    28,644

Elk    13    7,160

Moose    3    366

Total    2,159    61,386

https://www.arcgis.com/apps/dashboards/ccd4d1ee5d7e47bbb16e431102468173#

Current Season Chronic Wasting Disease (CWD) Sample Data (July 2026 - Present)

4 WTD and 1 Mule Deer Positive

https://www.arcgis.com/apps/dashboards/ccd4d1ee5d7e47bbb16e431102468173#

Montana Current Season Chronic Wasting Disease (CWD) Sample Data (July 2025 - Present) 447 Positive Samples

Current Season Chronic Wasting Disease (CWD) Sample Data (July 2025 - Present)

Samples by Species

Species    Positive Samples    Total Samples

Mule Deer    179    3,092

White-tailed Deer    264    4,693

Elk    4    1,031

Moose    0    47

Total    447    8,863

https://www.arcgis.com/apps/dashboards/ccd4d1ee5d7e47bbb16e431102468173

SUNDAY, JANUARY 25, 2026

Montana Current Season Chronic Wasting Disease (CWD) Sample Data (July 2025 - Present) 440 Positive Samples

https://mtfwp.maps.arcgis.com/apps/dashboards/ccd4d1ee5d7e47bbb16e431102468173

https://prpsc.proboards.com/thread/199/montana-detects-positive-cases-july

https://chronic-wasting-disease.blogspot.com/2026/01/montana-current-season-chronic-wasting.html

PROBLEM STATEMENT 6B: REVEAL GENETICS OF PRION DISEASE SUSCEPTIBILITY.

Greater frequency of chronic wasting disease in free-ranging elk genetically tolerant to disease progression raises concerns related to prion transmission and strain evolution.

Animal Disease Research Unit, Pullman, Washington

Genetic variations in the prion protein gene of Rocky Mountain elk do not confer complete resistance to fatal infection by chronic wasting disease. However, elk carrying one or two copies of the amino acid leucine (L) variant at position 132 of the prion protein (132L*, where * is either M for methionine or L) survive much longer than 132MM elk. An ARS researcher in Pullman, Washington, in collaboration with researchers at the University of Wyoming, the University of California at Davis, the National Park Service, and the Animal and Plant Health Inspection Service, found a higher frequency of 132L* elk in areas of Wyoming with high infection rates, consistent with the expected positive effect of prolonged survival on reproduction. However, the frequency of chronic wasting disease infection in 132L* elk was also higher than previous estimates. To improve the long-term management of native elk populations, these findings underscore the importance of determining the effects of prolonged infection on disease transmission from 132L* elk and the potential for driving prion strain diversification.

https://www.ars.usda.gov/ARSUserFiles/np103/AnnualReports/Final%20NP103%20FY2024%20Annual%20Report.updated%205.30.25.pdf

Research Project: Elucidating the Pathobiology and Transmission of Transmissible Spongiform Encephalopathies

Location: Virus and Prion Research

Title: Update: CWD genetic resistance project at NADC

Author item Cassmann, Eric item Greenlee, Justin Submitted to: North American Deer Farmer Publication Type: Trade Journal Publication Acceptance Date: 11/5/2023 Publication Date: 11/15/2023 Citation: Cassmann, E.D., Greenlee, J.J. 2023.

Update: CWD genetic resistance project at NADC. North American Deer Farmer. P. 83. Interpretive Summary: Technical Abstract: In March of 2020, we began a study to examine the susceptibility of whitetail deer with rare prion protein genotypes to chronic wasting disease (CWD). In the sequence of amino acids that make up the deer prion protein, there are several locations that are variable. These variations are sometimes called polymorphisms. In the data collected from depopulations, whitetail deer with certain prion gene polymorphisms were not positive for CWD. In 2019, Dr. Nick Haley published a paper that showed H95/S96, HH95, and S96/K226 deer from depopulated herds in the US were not CWD positive. Based on the overall low number of deer with these genotypes () we’re unable to determine if they were resistant to CWD or if there were too few deer with these genotypes to be statistically represented in the positive cases. It’s also possible that they could be partially susceptible with longer incubation times than deer with generic (wild type) prion genotypes. Samples gathered at depopulation represent a snapshot of the herd. It is possible these rare genotypes were exposed, but had not yet accumulated abnormal prion protein to a level detectable by the detection methods used. The NADC susceptibility study was initiated to help answer these questions.

We studied deer with polymorphisms at 3 amino acid locations (codons): 95, 96, and 226. Wild type deer are QQ95GG96QQ226. Whitetail deer with wild type prion genotypes were inoculated with CWD and co-housed with other whitetail deer (contact deer) that had rare prion protein genotypes. The genotypes of contact deer included QH95GS96QQ226, QH95GG96QK226, QQ95GS96QQ226, QQ95SS96QQ226, Q95GS96QK226, and QQ95GG96KK226 (bolded text indicates a prion gene polymorphism).

During the first year, we collected feces, saliva, nasal swabs, skin, blood, and rectal biopsies from the inoculated and contact deer to determine if deer are CWD positive and the period of CWD shedding. After the first year, we started collecting rectal biopsies annually on the contact deer, but all other samples are still collected every three months.

Eight out of ten (8/10) inoculated deer developed clinical signs for CWD and tested positive after necropsy (Figure 1). The average time from inoculation to euthanasia of these eight inoculated deer was 23 months.

Two inoculated deer are still on-study; one of these deer has tested positive for CWD on rectal biopsy IHC.

To date, two deer from the contact group have developed CWD clinical signs and tested positive (Figure 2). The positive deer from the contact group had the GS96QK226 and KK226 genotypes.

We have detected CWD prions in rectal biopsies with IHC in three other contact deer as of October 2023. Their prion genotypes are GS96, QH95GS96, and GS96QK226.

As the experiment continues, we hope to answer 2 main questions. (1) Are there any prion protein polymorphisms that make deer resistant to CWD, and (2) what are the CWD shedding dynamics in deer with detectable CWD. One potential outcome of the study would be identifying genotypes with very long incubation periods that, while susceptible to CWD, still could be used to manage CWD.

https://www.ars.usda.gov/research/publications/publication/?seqNo115=410188

Update: CWD genetic resistance project at NADC 1) Are there any prion protein polymorphisms that make deer resistant to CWD, and (2) what are the CWD shedding dynamics in deer with detectable CWD. One potential outcome of the study would be identifying genotypes with very long incubation periods that, while susceptible to CWD, still could be used to manage CWD.

https://www.ars.usda.gov/research/publications/publication/?seqNo115=410188

Another potential and likely outcome of this study, imo, is that genotypes developed with very long incubation, could therefore, if released into the wild, could help spread cwd even further, exposing even more wild species, and surrounding environments, for even longer periods of time, due to the longer incubation, a terrible potential outcome, one that must be avoided at all cost, imo…terry

SATURDAY, APRIL 11, 2026

Chronic Wasting Disease CWD TSE PrP, Cervid, Genetic Manipulation, Unforeseen Circumstances

https://chronic-wasting-disease.blogspot.com/2026/04/chronic-wasting-disease-cwd-tse-prp.html

FRIDAY, MAY 01, 2026

Oklahoma House Bill 3270 FAILED, Great News for Hunters and Wildlife

https://chronic-wasting-disease.blogspot.com/2026/05/oklahoma-house-bill-3270-failed-great.html

SUNDAY, MAY 04, 2025

Texas Senate Bill 2651 establishment of a pilot program to breed deer resistant to CWD TSE Prion, what could go wrong?

https://chronic-wasting-disease.blogspot.com/2025/05/texas-senate-bill-2651-establishment-of_4.html

FRIDAY, FEBRUARY 21, 2025

LEGISLATING CWD TSE Prion, Bills to release Genetically Modified Cervid into the wild, what could go wrong?

https://chronic-wasting-disease.blogspot.com/2025/02/legislating-cwd-tse-prion-bills-to.html

MONDAY, JUNE 09, 2025

Genetic Approaches and Tools to Prevent, Control, and Eradicate Transmissible Spongiform Encephalopathies 2024 Annual Report ARS Research

https://chronic-wasting-disease.blogspot.com/2025/06/genetic-approaches-and-tools-to-prevent.html

Department for Environment, Food and Rural Affairs

Preliminary Outbreak Assessment

Chronic wasting disease prions in cervids and wild pigs in North America

26 January 2026

Disease report

Chronic wasting disease (CWD) is a fatal neurodegenerative disease of cervids, such as deer, elk, moose and reindeer. It is caused by prions – infectious proteins that cause normal cellular prion proteins to misfold (CIDRAP, 2025). The disease is widespread in captive and free-ranging cervids in North America (Figure 1). For the first time, CWD prions have also been detected in the tissues of wild pigs (Sus scrofa) caught in CWD-affected areas of the USA (Soto et al. 2025). This discovery emerged from a study designed to investigate potential interactions between wild pigs and CWD prions, as wild pigs often coexist with cervids, which can shed prions into the environment. The following assessment discusses the epidemiology of CWD in North America and the detection of CWD prions in wild pigs. It also considers the potential implications for Great Britain.

Conclusion

CWD has continued to spread among captive and free-ranging cervids in North America since it was first detected in the 1960s. The finding of CWD prions in wild pigs in the USA suggests they could contribute towards transmission of the disease, influencing its epidemiology, geographic distribution and interspecies spread. However, further research is needed to confirm this. CWD has never been reported in Great Britain and the current risk of CWD prions being introduced into Great Britain’s wild pig or cervid population ranges from very low to negligible.

Readers are reminded to be vigilant for signs of CWD. Information on how to spot the disease can be found here. Suspected cases must be reported immediately to the Defra Rural Services Helpline on 03000 200 301. In Wales, call 0300 303 8268. In Scotland, contact your local Field Services Office. Failure to do so is an offence. We will continue to monitor the situation.

Authors • Lawrence Finn • Dr. Lauren Perrin • John Spiropoulos • Dr. Helen RobertsDepartment for Environment, Food and Rural Affairs

References

snip…see full report;

https://assets.publishing.service.gov.uk/media/697a3b013c71d838df6bd413/CWD_Prions_in_Cervids_and_Wild_Pigs_in_North_America.pdf

WEDNESDAY, JANUARY 28, 2026

Chronic wasting disease prions in cervids and wild pigs in North America Preliminary Outbreak

https://journals.asm.org/doi/10.1128/mbio.01800-25

https://media.ark.org/agri/Moore_2017_Swine_CWD.pdf

https://transmissiblespongiformencephalopathy.blogspot.com/2026/01/chronic-wasting-disease-prions-in.html

cwd to sheep

Chronic Wasting Disease CWD vs Scrapie TSE Prion

https://www.ars.usda.gov/research/publications/publication/?seqNo115=410511

Detection of infectivity in orally inoculated pigs using mouse bioassay raises the possibility that naturally exposed pigs could act as a reservoir of CWD infectivity. Currently, swine rations in the U.S. could contain animal derived components including materials from deer or elk. In addition, feral swine could be exposed to infected carcasses in areas where CWD is present in wildlife populations. The current feed ban in the U.S. is based exclusively on keeping tissues from TSE infected cattle from entering animal feeds. These results indicating the susceptibility of pigs to CWD, coupled with the limitations of the current feed ban, indicates that a revision of the feed ban may be necessary to protect swine production and potentially human health.

https://www.ars.usda.gov/research/publications/publication/?seqNo115=353091

https://www.ars.usda.gov/research/project/?accnNo=432011&fy=2017

https://www.ars.usda.gov/research/publications/publication/?seqNo115=337105

https://www.ars.usda.gov/research/publications/publication/?seqNo115=326166

Research Project: Elucidating the Pathobiology and Transmission of Transmissible Spongiform Encephalopathies

Location: Virus and Prion Research

Title: Differentiation of scrapie from chronic wasting disease in white-tailed deer

Accomplishments

1. 01 Determined that white-tailed deer (WTD) infected with scrapie from sheep can transmit the disease to other deer under conditions mimicking natural exposure. It has long been suggested that prion disease in deer (chronic wasting disease (CWD)) was caused by the prion agent from sheep. The prion disease that affects sheep, scrapie, has been recognized for hundreds of years. However, chronic wasting disease, a similar disease found in WTD, has only been recognized since the 1960s. ARS researchers in Ames, Iowa, showed that white-tailed deer sick with scrapie from sheep can infect other deer under conditions mimicking natural exposure. Furthermore, this work shows that CWD is difficult to differentiate from WTD infected with scrapie. WTD scrapie prions accumulate in the lymphoreticular system in a manner similar to CWD, meaning that environmental contamination may occur through feces, saliva, and other body fluids of scrapie affected WTD as has been shown for CWD. The presence of WTD infected with scrapie could confound mitigation efforts for chronic wasting disease. This information informs regulatory officials, the farmed cervid industry, and officials tasked with protecting animal health such as state Departments of Agriculture, Natural Resources, or Parks and Wildlife with regard to a disease similar to CWD but arising from sheep scrapie that could be present in WTD that have contact with scrapie affected sheep and/or goats.

https://www.ars.usda.gov/research/project/?accnNo=440677&fy=202

CWD TSE Prion 2026

THURSDAY, SEPTEMBER 24, 2026

***> Looming Crisis U. S. Transmissible Spongiform Encephalopathy TSE Prion, in Cattle, Cervid, Sheep, Pigs, and Humans, oh my <***

https://transmissiblespongiformencephalopathy.blogspot.com/2026/09/looming-crisis-u-s-transmissible.html

https://prpsc.proboards.com/thread/246/looming-crisis-prion-cattle-cervid

Tuesday, June 9, 2026

***> Hazard identification for the risks to terrestrial animal health from the import of hay and straw, BSE, CWD, Scrapie, TSE, Prion

https://www.gov.uk/government/publications/hazard-identification-for-the-risks-to-terrestrial-animal-health-from-the-import-of-hay-and-straw/hazard-identification-for-the-risks-to-terrestrial-animal-health-from-the-import-of-hay-and-straw

https://defrauktseprp.blogspot.com/2026/06/hazard-identification-for-risks-to.html

***> 1. 01 Determined that white-tailed deer (WTD) infected with scrapie from sheep can transmit the disease to other deer under conditions mimicking natural exposure.

https://www.ars.usda.gov/research/project/?accnNo=440677&fy=202

https://www.ars.usda.gov/research/publications/publication/?seqNo115=336834

https://wwwnc.cdc.gov/eid/article/30/8/24-0007_article

see;

https://nor-98.blogspot.com/2016/09/goat-k222-prpc-polymorphic-variant-does.html

https://transmissiblespongiformencephalopathy.blogspot.com/2026/04/us-report-scrapie-cwd-cattle-sheep-pigs.html

***> Scrapie TSE Prion, Singeltary review, October 2026

https://scrapie-usa.blogspot.com/2026/10/scrapie-tse-prion-singeltary-review.html

https://prpsc.proboards.com/thread/250/scrapie-prion-singeltary-review-2026

Chronic Wasting Disease CWD TSE Prion, Economical, Environmental, Zoonotic, Risk Factors 2026

https://transmissiblespongiformencephalopathy.blogspot.com/2026/02/chronic-wasting-disease-cwd-tse-prion.html

***> USA Report, Scrapie, CWD, BSE, TSE, Cattle, Sheep, Pigs, Cervid, Humans, Zoonotic, 2026

April 2026

https://fdabse589.blogspot.com/2026/04/usa-report-scrapie-cwd-bse-tse-cattle.html

https://www.researchgate.net/publication/403956772_USA_Report_Scrapie_CWD_BSE_TSE_Cattle_Sheep_Pigs_Cervid_Humans_Zoonotic_2026

APHIS USDA Captive CWD Herds Update by State March 2026 Update

https://prpsc.proboards.com/thread/243/aphis-captive-herd-status-september

https://chronic-wasting-disease.blogspot.com/2026/09/aphis-captive-herd-cwd-status-september.html

SATURDAY, SEPTEMBER 19, 2026

Texas 5th Captive Herd Depopulated This Year Due To Positive CWD TSE Prion

https://chronic-wasting-disease.blogspot.com/2026/09/texas-5th-captive-herd-depopulated-this.html

https://prpsc.proboards.com/thread/242/texas-captive-deer-herd-depopulated

***> Cervid CWD TSE PrP Transmission to Humans, has it already happened and being masked as sporadic CJD, What if? July 2026 Review

https://chronic-wasting-disease.blogspot.com/2026/07/cervid-cwd-tse-prp-transmission-to.html

https://prpsc.proboards.com/thread/224/cervid-transmission-humans-july-review

WEDNESDAY, SEPTEMBER 2, 2026

A new chapter for CWRU’s Prion Center

https://prionunitusaupdate.blogspot.com/2026/09/a-new-chapter-for-cwrus-prion-center.html

https://prpsc.proboards.com/thread/239/new-chapter-cwru-prion-center

Terry S. Singeltary Sr.