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Won SY, Kim YC. The first meta-analysis of the G96S single nucleotide polymorphism (SNP) of the prion protein gene ( PRNP) with chronic wasting disease in white-tailed deer. Front Vet Sci 2024; 11:1437189. [PMID: 39679175 PMCID: PMC11638237 DOI: 10.3389/fvets.2024.1437189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 11/18/2024] [Indexed: 12/17/2024] Open
Abstract
Background Prion diseases are irreversible infectious neurodegenerative diseases caused by a contagious form of prion protein (PrPSc). Since chronic wasting disease (CWD)-infected white-tailed deer are strong carriers of the prion seed through corpses via scavenger animals, preemptive control based on genetic information for a culling system is necessary. However, the risk of CWD-related genetic variants has not been fully evaluated. In the present study, we carried out a quantitative estimation of the risk of a G96S single nucleotide polymorphism (SNP) of the PRNP gene to CWD infection in white-tailed deer. Methods We carried out a literature search for genetic data of the G96S (c.286G>A) SNP of the PRNP gene from CWD-infected white-tailed deer and matched controls. We performed a meta-analysis using incorporated eligible studies to evaluate the association of the G96S SNP of the PRNP gene with susceptibility to CWD in white-tailed deer. Results We identified a strong association between the G96S (c.286G>A) SNP of the PRNP gene and susceptibility to CWD infection in white-tailed deer using meta-analysis. We observed the most significant association in the recessive model (odds ratio = 3.0050, 95% confidence interval: 2.0593; 4.3851, p < 0.0001), followed by the additive model (odds ratio = 2.7222, 95% confidence interval: 1.9028; 3.8945, p < 0.0001) and the heterozygote (AA vs. AG) comparison (odds ratio = 2.7405, 95% confidence interval: 1.9215; 3.9085, p < 0.0001). Conclusion To the best of our knowledge, this was the first meta-analysis of the association between the G96S (c.286G>A) SNP of the PRNP gene and susceptibility to CWD infection.
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Affiliation(s)
| | - Yong-Chan Kim
- Department of Biological Sciences, Andong National University, Andong, Republic of Korea
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2
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Ketz AC, Robinson SJ, Johnson CJ, Samuel MD. Pathogen‐mediated selection and management implications for white‐tailed deer exposed to chronic wasting disease. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Alison C. Ketz
- Wisconsin Cooperative Research Unit Department of Forest and Wildlife Ecology University of Wisconsin Madison WI USA
| | - Stacie J. Robinson
- NOAA Hawaiian Monk Seal Research Program Pacific Islands Fisheries Science Center Honolulu HI USA
| | - Chad J. Johnson
- Medical Microbiology and Immunology University of Wisconsin Madison WI USA
| | - Michael D. Samuel
- Department of Forest and Wildlife Ecology University of Wisconsin Madison WI USA
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3
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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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4
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Miller WL, Walter WD. Spatial heterogeneity of prion gene polymorphisms in an area recently infected by chronic wasting disease. Prion 2019; 13:65-76. [PMID: 30777498 PMCID: PMC7000142 DOI: 10.1080/19336896.2019.1583042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genetic variability in the prion protein (Prnp) gene influences host susceptibility to many pathogenic prion diseases. Understanding the distribution of susceptible Prnp variants and determining factors influencing spatial genetic patterns are important components of many chronic wasting disease mitigation strategies. Here, we describe Prnp variability in white-tailed deer (Odocoileus virginianus) from the Mid-Atlantic region of the United States of America, an area with a recent history of infection and low disease incidence. This population is characterized by lower rates of polymorphism and significantly higher frequencies of the more susceptible 96GG genotype compared to previously surveyed populations. The prevalence of the most susceptible genotypes at disease-associated loci did vary among subregions, indicating that populations have innate differences in genotype-dictated susceptibility.
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Affiliation(s)
- William L Miller
- a Pennsylvania Cooperative Fish and Wildlife Research Unit, Department of Ecosystem Science and Management, Intercollege Graduate Degree Program in Ecology , The Pennsylvania State University , University Park , PA , USA
| | - W David Walter
- b U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit , The Pennsylvania State University , University Park , PA , USA
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5
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Brandt AL, Green ML, Ishida Y, Roca AL, Novakofski J, Mateus-Pinilla NE. Influence of the geographic distribution of prion protein gene sequence variation on patterns of chronic wasting disease spread in white-tailed deer (Odocoileus virginianus). Prion 2018; 12:204-215. [PMID: 30041562 PMCID: PMC6277178 DOI: 10.1080/19336896.2018.1474671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Managing and controlling the spread of diseases in wild animal populations is challenging, especially for social and mobile species. Effective management benefits from information about disease susceptibility, allowing limited resources to be focused on areas or populations with a higher risk of infection. Chronic wasting disease (CWD), a transmissible spongiform encephalopathy that affects cervids, was detected in Colorado in the late 1960s. CWD was detected in Illinois and Wisconsin in 2002 and has since spread through many counties. Specific nucleotide variations in the prion protein gene (PRNP) sequence have been associated with reduced susceptibility to CWD in white-tailed deer. Though genetic resistance is incomplete, the frequency of deer possessing these mutations in a population is an important factor in disease spread (i.e. herd immunity). In this study we sequenced 625 bp of the PRNP gene from a sampling of 2433 deer from Illinois and Wisconsin. In north-central Illinois where CWD was first detected, counties had a low frequency of protective haplotypes (frequency <0.20); whereas in northwestern Illinois counties, where CWD cases have only more recently been detected, the frequency of protective haplotypes (frequency >0.30) was much higher (p < 0.05). Protective haplotype frequencies varied significantly among infected and uninfected geographic areas. The frequency of protective PRNP haplotypes may contribute to population level susceptibility and may shape the way CWD has spread through Illinois. Analysis of PRNP haplotype distribution could be a useful tool to assess CWD risk and allocate resources to contain and reduce the spread of infection.
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Affiliation(s)
- Adam L Brandt
- a Illinois Natural History Survey-Prairie Research Institute , University of Illinois at Urbana-Champaign , Urbana , IL , USA.,b Division of Natural Sciences , St. Norbert College , De Pere , Wisconsin , USA
| | - Michelle L Green
- a Illinois Natural History Survey-Prairie Research Institute , University of Illinois at Urbana-Champaign , Urbana , IL , USA.,c Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Yasuko Ishida
- c Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Alfred L Roca
- a Illinois Natural History Survey-Prairie Research Institute , University of Illinois at Urbana-Champaign , Urbana , IL , USA.,c Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Jan Novakofski
- c Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Nohra E Mateus-Pinilla
- a Illinois Natural History Survey-Prairie Research Institute , University of Illinois at Urbana-Champaign , Urbana , IL , USA.,c Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , IL , USA
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6
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Brandt AL, Kelly AC, Green ML, Shelton P, Novakofski J, Mateus-Pinilla NE. Prion protein gene sequence and chronic wasting disease susceptibility in white-tailed deer (Odocoileus virginianus). Prion 2016; 9:449-62. [PMID: 26634768 PMCID: PMC4964855 DOI: 10.1080/19336896.2015.1115179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The sequence of the prion protein gene (PRNP) affects susceptibility to spongiform encephalopathies, or prion diseases in many species. In white-tailed deer, both coding and non-coding single nucleotide polymorphisms have been identified in this gene that correlate to chronic wasting disease (CWD) susceptibility. Previous studies examined individual nucleotide or amino acid mutations; here we examine all nucleotide polymorphisms and their combined effects on CWD. A 626 bp region of PRNP was examined from 703 free-ranging white-tailed deer. Deer were sampled between 2002 and 2010 by hunter harvest or government culling in Illinois and Wisconsin. Fourteen variable nucleotide positions were identified (4 new and 10 previously reported). We identified 68 diplotypes comprised of 24 predicted haplotypes, with the most common diplotype occurring in 123 individuals. Diplotypes that were found exclusively among positive or negative animals were rare, each occurring in less than 1% of the deer studied. Only one haplotype (C, odds ratio 0.240) and 2 diplotypes (AC and BC, odds ratios of 0.161 and 0.108 respectively) has significant associations with CWD resistance. Each contains mutations (one synonymous nucleotide 555C/T and one nonsynonymous nucleotide 286G/A) at positions reported to be significantly associated with reduced CWD susceptibility. Results suggest that deer populations with higher frequencies of haplotype C or diplotypes AC and BC might have a reduced risk for CWD infection – while populations with lower frequencies may have higher risk for infection. Understanding the genetic basis of CWD has improved our ability to assess herd susceptibility and direct management efforts within CWD infected areas.
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Affiliation(s)
- Adam L Brandt
- a Illinois Natural History Survey ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
| | - Amy C Kelly
- a Illinois Natural History Survey ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
| | - Michelle L Green
- a Illinois Natural History Survey ; University of Illinois at Urbana-Champaign ; Urbana , IL USA ;,b Department of Animal Sciences ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
| | - Paul Shelton
- c Illinois Department of Natural Resources ; Division of Wildlife Resources ; Springfield , IL USA
| | - Jan Novakofski
- b Department of Animal Sciences ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
| | - Nohra E Mateus-Pinilla
- a Illinois Natural History Survey ; University of Illinois at Urbana-Champaign ; Urbana , IL USA ;,b Department of Animal Sciences ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
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7
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Blanchong JA, Robinson SJ, Samuel MD, Foster JT. Application of genetics and genomics to wildlife epidemiology. J Wildl Manage 2016. [DOI: 10.1002/jwmg.1064] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Julie A. Blanchong
- Department of Natural Resource Ecology and Management; Iowa State University; 339 Science II Ames IA 50011 USA
| | | | - Michael D. Samuel
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit; University of Wisconsin; 204 Russell Labs, 1630 Linden Dr. Madison WI 53706 USA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular and Biomedical Sciences; University of New Hampshire; 291 Rudman Hall Durham NH 03824 USA
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8
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Wickner RB, Kelly AC. Prions are affected by evolution at two levels. Cell Mol Life Sci 2016; 73:1131-44. [PMID: 26713322 PMCID: PMC4762734 DOI: 10.1007/s00018-015-2109-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/30/2022]
Abstract
Prions, infectious proteins, can transmit diseases or be the basis of heritable traits (or both), mostly based on amyloid forms of the prion protein. A single protein sequence can be the basis for many prion strains/variants, with different biological properties based on different amyloid conformations, each rather stably propagating. Prions are unique in that evolution and selection work at both the level of the chromosomal gene encoding the protein, and on the prion itself selecting prion variants. Here, we summarize what is known about the evolution of prion proteins, both the genes and the prions themselves. We contrast the one known functional prion, [Het-s] of Podospora anserina, with the known disease prions, the yeast prions [PSI+] and [URE3] and the transmissible spongiform encephalopathies of mammals.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 225, 8 Center Drive MSC 0830, Bethesda, MD, 20892-0830, USA.
| | - Amy C Kelly
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 225, 8 Center Drive MSC 0830, Bethesda, MD, 20892-0830, USA.
- NCAUR, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA.
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9
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Murdoch BM, Murdoch GK. Genetics of Prion Disease in Cattle. Bioinform Biol Insights 2015; 9:1-10. [PMID: 26462233 PMCID: PMC4589088 DOI: 10.4137/bbi.s29678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 12/03/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE) is a prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. As a transmissible disease of livestock, it has impacted food safety, production practices, global trade, and profitability. Genetic polymorphisms that alter the prion protein in humans and sheep are associated with transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that nonsynonymous mutations in the bovine prion gene (PRNP) are associated with classical BSE (C-BSE) disease susceptibility, though two bovine PRNP insertion/deletion polymorphisms, in the putative region, are associated with susceptibility to C-BSE. However, these associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. This article provides a review of the current state of genetic knowledge regarding prion diseases in cattle.
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Affiliation(s)
- Brenda M Murdoch
- Animal and Veterinary Science, University of Idaho, Moscow, ID, USA
| | - Gordon K Murdoch
- Animal and Veterinary Science, University of Idaho, Moscow, ID, USA
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10
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Matsumoto T, Samuel MD, Bollinger T, Pybus M, Coltman DW. Association mapping of genetic risk factors for chronic wasting disease in wild deer. Evol Appl 2012; 6:340-52. [PMID: 23467626 PMCID: PMC3586622 DOI: 10.1111/eva.12003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 07/11/2012] [Indexed: 01/06/2023] Open
Abstract
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.
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Affiliation(s)
- Tomomi Matsumoto
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
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11
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Robinson SJ, Samuel MD, Johnson CJ, Adams M, McKenzie DI. Emerging prion disease drives host selection in a wildlife population. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2012; 22:1050-9. [PMID: 22645831 DOI: 10.1890/11-0907.1] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.
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Affiliation(s)
- Stacie J Robinson
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Room 208 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706, USA.
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12
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Robinson SJ, Samuel MD, O'Rourke KI, Johnson CJ. The role of genetics in chronic wasting disease of North American cervids. Prion 2012; 6:153-62. [PMID: 22460693 DOI: 10.4161/pri.19640] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Chronic wasting disease (CWD) is a major concern for the management of North American cervid populations. This fatal prion disease has led to declines in populations which have high CWD prevalence and areas with both high and low infection rates have experienced economic losses in wildlife recreation and fears of potential spill-over into livestock or humans. Research from human and veterinary medicine has established that the prion protein gene (Prnp) encodes the protein responsible for transmissible spongiform encephalopathies (TSEs). Polymorphisms in the Prnp gene can lead to different prion forms that moderate individual susceptibility to and progression of TSE infection. Prnp genes have been sequenced in a number of cervid species including those currently infected by CWD (elk, mule deer, white-tailed deer, moose) and those for which susceptibility is not yet determined (caribou, fallow deer, sika deer). Over thousands of sequences examined, the Prnp gene is remarkably conserved within the family Cervidae; only 16 amino acid polymorphisms have been reported within the 256 amino acid open reading frame in the third exon of the Prnp gene. Some of these polymorphisms have been associated with lower rates of CWD infection and slower progression of clinical CWD. Here we review the body of research on Prnp genetics of North American cervids. Specifically, we focus on known polymorphisms in the Prnp gene, observed genotypic differences in CWD infection rates and clinical progression, mechanisms for genetic TSE resistance related to both the cervid host and the prion agent and potential for natural selection for CWD-resistance. We also identify gaps in our knowledge that require future research.
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Affiliation(s)
- Stacie J Robinson
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, USA.
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13
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Seabury CM, Bhattarai EK, Taylor JF, Viswanathan GG, Cooper SM, Davis DS, Dowd SE, Lockwood ML, Seabury PM. Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PLoS One 2011; 6:e15811. [PMID: 21283515 PMCID: PMC3023705 DOI: 10.1371/journal.pone.0015811] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 11/24/2010] [Indexed: 01/02/2023] Open
Abstract
The white-tailed deer (Odocoileus virginianus) represents one of the most successful and widely distributed large mammal species within North America, yet very little nucleotide sequence information is available. We utilized massively parallel pyrosequencing of a reduced representation library (RRL) and a random shotgun library (RSL) to generate a complete mitochondrial genome sequence and identify a large number of putative single nucleotide polymorphisms (SNPs) distributed throughout the white-tailed deer nuclear and mitochondrial genomes. A SNP validation study designed to test specific classes of putative SNPs provides evidence for as many as 10,476 genome-wide SNPs in the current dataset. Based on cytogenetic evidence for homology between cow (Bos taurus) and white-tailed deer chromosomes, we demonstrate that a divergent genome may be used for estimating the relative distribution and density of de novo sequence contigs as well as putative SNPs for species without draft genome assemblies. Our approach demonstrates that bioinformatic tools developed for model or agriculturally important species may be leveraged to support next-generation research programs for species of biological, ecological and evolutionary importance. We also provide a functional annotation analysis for the de novo sequence contigs assembled from white-tailed deer pyrosequencing reads, a mitochondrial phylogeny involving 13,722 nucleotide positions for 10 unique species of Cervidae, and a median joining haplotype network as a putative representation of mitochondrial evolution in O. virginianus. The results of this study are expected to provide a detailed template enabling genome-wide sequence-based studies of threatened, endangered or conservationally important non-model organisms.
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Affiliation(s)
- Christopher M Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
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14
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Gilch S, Chitoor N, Taguchi Y, Stuart M, Jewell JE, Schätzl HM. Chronic wasting disease. Top Curr Chem (Cham) 2011; 305:51-77. [PMID: 21598099 DOI: 10.1007/128_2011_159] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chronic wasting disease (CWD) is a prion disease of free-ranging and farmed ungulates (deer, elk, and moose) in North America and South Korea. First described by the late E.S. Williams and colleagues in northern Colorado and southern Wyoming in the 1970s, CWD has increased tremendously both in numerical and geographical distribution, reaching prevalence rates as high as 50% in free-ranging and >90% in captive deer herds in certain areas of USA and Canada. CWD is certainly the most contagious prion infection, with significant horizontal transmission of infectious prions by, e.g., urine, feces, and saliva. Dissemination and persistence of infectivity in the environment combined with the appearance in wild-living and migrating animals make CWD presently uncontrollable, and pose extreme challenges to wild-life disease management. Whereas CWD is extremely transmissible among cervids, its trans-species transmission seems to be restricted, although the possible involvement of rodent and carnivore species in environmental transmission has not been fully evaluated. Whether or not CWD has zoonotic potential as had Bovine spongiform encephalopathy (BSE) has yet to be answered. Of note, variant Creutzfeldt-Jakob disease (vCJD) was only detected because clinical presentation and age of patients were significantly different from classical CJD. Along with further understanding of the molecular biology and pathology of CWD, its transmissibility and species restrictions and development of methods for preclinical diagnosis and intervention will be crucial for effective containment of this highly contagious prion disease.
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Affiliation(s)
- Sabine Gilch
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA
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15
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Murdoch BM, Clawson ML, Yue S, Basu U, McKay S, Settles M, Capoferri R, Laegreid WW, Williams JL, Moore SS. PRNP haplotype associated with classical BSE incidence in European Holstein cattle. PLoS One 2010; 5. [PMID: 20862290 PMCID: PMC2940907 DOI: 10.1371/journal.pone.0012786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/23/2010] [Indexed: 01/13/2023] Open
Abstract
Background Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease of cattle. The bovine prion gene (PRNP) contains regions of both high and low linkage disequilibrium (LD) that appear to be conserved across Bos taurus populations. The region of high LD, which spans the promoter and part of intron 2, contains polymorphic loci that have been associated with classical BSE status. However, the complex genetic architecture of PRNP has not been systematically tested for an association with classical BSE. Methodology/Principal Findings In this study, haplotype tagging single nucleotide polymorphisms (htSNPs) within PRNP were used to test for association between PRNP haplotypes and BSE disease. A combination of Illumina goldengate assay, sequencing and PCR amplification was used to genotype 18 htSNPs and 2 indels in 95 BSE case and 134 control animals. A haplotype within the region of high LD was found to be associated with BSE unaffected animals (p-value = 0.000114). Conclusion/Significance A PRNP haplotype association with classical BSE incidence has been identified. This result suggests that a genetic determinant in or near PRNP may influence classical BSE incidence in cattle.
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Affiliation(s)
- Brenda M Murdoch
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Edmonton, Canada.
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