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Raudabaugh DB, Ishida Y, Haley NJ, Brown WM, Novakofski J, Roca AL, Mateus-Pinilla NE. County-wide assessments of Illinois white-tailed deer (Odocoileus virginianus) prion protein gene variation using improved primers and potential implications for management. PLoS One 2022; 17:e0274640. [PMID: 36449540 PMCID: PMC9710747 DOI: 10.1371/journal.pone.0274640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 12/05/2022] Open
Abstract
Chronic wasting disease (CWD) is a fatal, highly infectious prion disease that affects captive and wild cervids. Chronic wasting disease is the only known transmissible spongiform encephalopathy affecting free-ranging wildlife. In CWD-positive deer, some haplotypes of the prion protein gene PRNP are detected at lower frequencies as compared to CWD-negative deer, as are some variants of the prion protein PrP. Here, we examined wild, hunter-harvested CWD-negative white-tailed deer (Odocoileus virginianus) to determine whether there were geographical or temporal differences in the PRNP haplotypes, PRNP diplotypes, PrP proteoforms, and in the proportion of deer with at least one protective haplotype. We sampled 96-100 hunter-harvested deer per county at two time points in the Illinois counties of Jo Daviess, LaSalle, and Winnebago, chosen based on their geographic locations and known occurrence of CWD. The entire coding region of PRNP was sequenced, with haplotypes, diplotypes, and PrP proteoforms inferred. Across time, in Winnebago there was a significant increase in PrP proteoform F (p = 0.034), which is associated with a lower vulnerability to CWD. In every county, there was an increase over time in the frequency of deer carrying at least one protective haplotype to CWD, with a significant increase (p = 0.02) in the Jo Daviess County CWD infected region. We also found that primer combination was important as there was an 18.7% difference in the number of the deer identified as homozygous depending on primer usage. Current Illinois state management practices continue to remove CWD infected deer from locally infected areas helping to keep CWD prevalence low. Nonetheless, continued research on spatial and temporal changes in PRNP haplotypes, PrP proteoforms, and levels of deer vulnerability among Illinois deer will be important for the management of CWD within the state of Illinois and beyond.
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Affiliation(s)
- Daniel B. Raudabaugh
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
- * E-mail: (NEMP); (DBR)
| | - Yasuko Ishida
- Department of Animal Science, University of Illinois, Urbana, Illinois, United States of America
| | - Nicholas J. Haley
- Department of Microbiology and Immunology, Midwestern University, Glendale, AZ, United States of America
| | - William M. Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, United States of America
| | - Jan Novakofski
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
- Department of Animal Science, University of Illinois, Urbana, Illinois, United States of America
| | - Alfred L. Roca
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
- Department of Animal Science, University of Illinois, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Nohra E. Mateus-Pinilla
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
- Department of Animal Science, University of Illinois, Urbana, Illinois, United States of America
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, United States of America
- * E-mail: (NEMP); (DBR)
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Impact of landcover composition and density of localized deer culling sites on chronic wasting disease prevalence. Prev Vet Med 2022; 208:105774. [DOI: 10.1016/j.prevetmed.2022.105774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 09/20/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022]
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Perrin-Stowe TI, Ishida Y, Reed DM, Terrill EE, Ryder OA, Novakofski JE, Mateus-Pinilla NE, Pukazhenthi BS, Roca AL. Extrapolating the susceptibility of Eld’s deer (Rucervus eldii thamin) to chronic wasting disease from prion protein gene (PRNP) polymorphisms. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.1007100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
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.
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Varga C, McDonald P, Brown WM, Shelton P, Roca AL, Novakofski JE, Mateus‐Pinilla NE. Evaluating the ability of a locally focused culling program in removing chronic wasting disease infected free-ranging white-tailed deer in Illinois, USA, 2003-2020. Transbound Emerg Dis 2022; 69:2867-2878. [PMID: 34953169 PMCID: PMC9786818 DOI: 10.1111/tbed.14441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/13/2021] [Accepted: 12/22/2021] [Indexed: 12/30/2022]
Abstract
In northern Illinois, chronic wasting disease (CWD) was first identified in free-ranging white-tailed deer (Odocoileus virginianus; hereafter referred to as "deer") in 2002. To reduce CWD transmission rates in Illinois, wildlife biologists have conducted locally focussed culling of deer since 2003 in areas where CWD has been detected. We used retrospective spatial, temporal and space-time scan statistical models to identify areas and periods where culling removed higher than expected numbers of CWD-positive deer. We included 490 Public Land Survey "sections" (∼2.59 km2 ) from 15 northern Illinois counties in which at least one deer tested positive for CWD between 2003 and 2020. A negative binomial regression model compared the proportion of CWD positive cases removed from sections with at least one CWD case detected in the previous years, "local area 1 (L1)," to the proportion of CWD cases in adjacent sections-L2, L3, and L4-designated by their increasing distance from L1. Of the 14,661 deer removed and tested via culling, 325 (2.22 %) were CWD-positive. A single temporal CWD cluster occurred in 2020. Three spatial clusters were identified, with a primary cluster located at the border of Boone and Winnebago counties. Four space-time clusters were identified with a primary cluster in the northern portion of the study area from 2003 to 2005 that overlapped with the spatial cluster. The proportion of CWD cases removed from L1 (3.92, 95% CI, 2.56-6.01) and L2 (2.32, 95% CI, 1.50-3.59) were significantly higher compared to L3. Focussing culling efforts on accessible properties closest to L1 areas results in more CWD-infected deer being removed, which highlights the value of collaborations among landowners, hunters, and wildlife management agencies to control CWD. Continuous evaluation and updating of the culling and surveillance programs are essential to mitigate the health burden of CWD on deer populations in Illinois.
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Affiliation(s)
- Csaba Varga
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA,Carl R. Woese Institute for Genomic BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Patrick McDonald
- Illinois Department of Natural ResourcesDivision of Wildlife ResourcesSpringfieldIllinoisUSA
| | - William M. Brown
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Paul Shelton
- Illinois Department of Natural ResourcesDivision of Wildlife ResourcesSpringfieldIllinoisUSA
| | - Alfred L. Roca
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA,Illinois Natural History Survey‐Prairie Research InstituteUniversity of Illinois Urbana‐ChampaignChampaignIllinoisUSA,Department of Animal SciencesUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Jan E. Novakofski
- Illinois Natural History Survey‐Prairie Research InstituteUniversity of Illinois Urbana‐ChampaignChampaignIllinoisUSA,Department of Animal SciencesUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Nohra E. Mateus‐Pinilla
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA,Illinois Natural History Survey‐Prairie Research InstituteUniversity of Illinois Urbana‐ChampaignChampaignIllinoisUSA,Department of Animal SciencesUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
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London EW, Roca AL, Novakofski JE, Mateus-Pinilla NE. A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus. J Hered 2022; 113:479-489. [PMID: 35511871 PMCID: PMC9308042 DOI: 10.1093/jhered/esac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recreational, commercial, and food source value for many households. We present a genome generated using DNA from a single Illinois white-tailed sequenced on the PacBio Sequel II platform and assembled using Wtdbg2. Omni-C chromatin conformation capture sequencing was used to scaffold the genome contigs. The final assembly was 2.42 Gb, consisting of 508 scaffolds with a contig N50 of 21.7 Mb, a scaffold N50 of 52.4 Mb, and a BUSCO complete score of 93.1%. Thirty-six chromosome pseudomolecules comprised 93% of the entire sequenced genome length. A total of 20 651 predicted genes using the BRAKER pipeline were validated using InterProScan. Chromosome length assembly sequences were aligned to the genomes of related species to reveal corresponding chromosomes.
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Affiliation(s)
- Evan W London
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alfred L Roca
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jan E Novakofski
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nohra E Mateus-Pinilla
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Ott-Conn CN, Blanchong JA, Larson WA. Prion protein polymorphisms in Michigan white-tailed deer ( Odocoileus virginianus). Prion 2021; 15:183-190. [PMID: 34751633 PMCID: PMC8583003 DOI: 10.1080/19336896.2021.1990628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Chronic Wasting Disease (CWD), a well-described transmissible spongiform encephalopathy of the Cervidae family, is associated with the aggregation of an abnormal isoform (PrPCWD) of the naturally occurring host prion protein (PrPC). Variations in the PrP gene (PRNP) have been associated with CWD rate of infection and disease progression. We analysed 568 free-ranging white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties for PRNP polymorphisms. Sampling included 185 CWD-positive, 332 CWD non-detected, and an additional 51 CWD non-detected paired to CWD-positives by sex, age, and harvest location. We found 12 polymorphic sites of which 5 were non-synonymous and resulted in a change in amino acid composition. Thirteen haplotypes were predicted, of which 11 have previously been described. Using logistic regression, consistent with other studies, we found haplotypes C (OR = 0.488, 95% CI = 0.321–0.730, P < 0.001) and F (OR = 0.122, 95% CI = 0.007–0.612, P < 0.05) and diplotype BC (OR = 0.340, 95% CI = 0.154–0.709, P < 0.01) were less likely to be found in deer infected with CWD. As has also been documented in other studies, the presence of a serine at amino acid 96 was less likely to be found in deer infected with CWD (P < 0.001, OR = 0.360 and 95% CI = 0.227–0.556). Identification of PRNP polymorphisms associated with reduced vulnerability to CWD in Michigan deer and their spatial distribution can help managers design surveillance programmesand identify and prioritize areas for CWD management.
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Affiliation(s)
- Caitlin N Ott-Conn
- Michigan Department of Natural Resources, Wildlife Disease Laboratory, Lansing, USA
| | - Julie A Blanchong
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, USA
| | - Wes A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Juneau, AK, USA
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Roh IS, Kim YC, Kim HJ, Won SY, Jeong MJ, Hwang JY, Kang HE, Sohn HJ, Jeong BH. Polymorphisms of the prion-related protein gene are strongly associated with cervids' susceptibility to chronic wasting disease. Vet Rec 2021; 190:e940. [PMID: 34562285 DOI: 10.1002/vetr.940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 07/28/2021] [Accepted: 08/28/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Chronic wasting disease (CWD) is a cervid prion disease that is caused by abnormal prion protein (PrPSc ). Recent studies have reported that prion family genes showed a strong association with the susceptibility of several types of prion diseases. To date, an association study of the prion-related protein gene (PRNT) has not been performed in any type of cervid prion disease. METHODS In the present study, we investigated PRNT polymorphisms in large deer, including 235 elk, 257 red deer and 150 sika deer. We compared genotype, allele and haplotype frequencies of PRNT polymorphisms between CWD-negative animals and CWD-positive animals to find an association of PRNT polymorphisms with the susceptibility of CWD. RESULTS We found a total of five novel single nucleotide polymorphisms (SNPs) in the cervid PRNT gene. Interestingly, we observed significantly different distributions of genotypes and allele frequencies of three PRNT SNPs, including c.108C>T, c.159+30C>T and c.159+32A>C, between CWD-negative and CWD-positive red deer. In addition, significant differences of two haplotype frequencies in red deer were found between the CWD-negative and CWD-positive groups. However, the association identified in the red deer was not found in elk and sika deer. CONCLUSION To the best of our knowledge, this report is the first to describe the strong association of PRNT SNPs with the susceptibility of CWD.
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Affiliation(s)
- In-Soon Roh
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hyo-Jin Kim
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Sae-Young Won
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
| | - Min-Ju Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ji-Yong Hwang
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hae-Eun Kang
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hyun-Joo Sohn
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
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