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Map of Illinois (orange) and Wisconsin (pink), showing the study area for samples collected between 2002 and 2010. Samples were collected from all counties in gray by hunter harvest or government culling. Counties within the CWD infection area (at least 5 confirmed cases of CWD during the sample period) are darkly shaded; statistical analyses of CWD susceptibility were restricted to individuals originating from these locations thus increasing the probability of disease exposure. Number of samples from each county is indicated below the county name. 

Map of Illinois (orange) and Wisconsin (pink), showing the study area for samples collected between 2002 and 2010. Samples were collected from all counties in gray by hunter harvest or government culling. Counties within the CWD infection area (at least 5 confirmed cases of CWD during the sample period) are darkly shaded; statistical analyses of CWD susceptibility were restricted to individuals originating from these locations thus increasing the probability of disease exposure. Number of samples from each county is indicated below the county name. 

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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 individua...

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... sequences were determined for 703 deer by PCR and Sanger sequencing: 579 tested for CWD (105 testing positive, 474 for which CWD was not detected) and 124 that were not tested. Analyses of disease risk were performed using a reduced dataset (N D 240) consisting of deer originating in counties with more than 5 cases of CWD confirmed by government moni- toring between 2002-2010 (henceforth referred to as the "CWD infection area;" Fig. 1). Addi- tional tested and untested samples were obtained from areas with low risk of CWD (counties with fewer than 5 or no confirmed cases at the time of sampling) to better detect sequence variations, haplotypes, and diplo- types. Statistical significance was determined by logistic regression using the most frequent haplotype, diplotype, genotype, or nucleotide as the reference level. Within the analyzed 626 bp region of the PRNP gene 14 variable positions were identified, 10 previously reported 10,28 and 4 novel sites (299G/A, 308A/ T, 367G/A, and 372G/A). Of the 14 variable sites 6 are non-synonymous (3 novel and 3 pre- viously reported) and result in a change to the amino acid sequence ( Table 1). It is important to note that mutations at nt299, nt308, and nt367 (aa100S/N, aa103N/I and aa123A/T respectively) are of interest as the human equivalents (aa97, aa100, and aa120 respec- tively) are in close proximity to polymorphisms associated with prion disease susceptibility in humans. [31][32][33] Haplotypes were generated from unphased sequences using PHASE v2.1. 34,35 Twenty-four haplotypes were predicted from 703 deer (N=1406 possible haplotype copies), with hap- lotype A occurring most frequently ( Table 1). Nine haplotypes are found exclusively among negative (haplotypes L, Q, S, T, and W), posi- tive (haplotype R) or untested deer (haplotypes U, V, and X); however, each of these haplo- types is rare with a frequency of occurrence less than 1% ( Table 1). Seventeen haplotypes occurred within the CWD infection area and only haplotype C is significantly less likely to be found among deer infected with CWD (P < 0.001, OR D 0.240 and 95% CI D 0.104- 0.503) ( Table ...

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... Even a single amino acid difference can impose a significant energy barrier on the misfolding process, thus slowing or even blocking the molecular event that drives prion disease pathogenesis and transmission dynamics [44]. This explains, for a large part, the sometimes-potent genetic modulation of prion disease susceptibility observed in scrapie [45][46][47][48] and CWD [49][50][51][52], which is governed by alteration of the PRNP gene causing amino acid substitutions in the PrP C structure. ...
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... Nonsynonymous polymorphisms in PRNP gene sequences have different frequencies between CWD positive and CWD negative white-tailed deer, suggesting a protective effect for some protein-altering mutations [14,15]. A general overview of these variants across the family Cervidae is discussed by [16][17][18], [17] identified PRNP haplotype variants, and [18] inferred PrP proteoforms (protein variations encoded by a specific gene [19]) in white-tailed deer. Proteoform (PrP variant) A is overrepresented in CWD-positive individuals, while proteoforms C and F are underrepresented in CWD-positive individuals. ...
... Nonsynonymous polymorphisms in PRNP gene sequences have different frequencies between CWD positive and CWD negative white-tailed deer, suggesting a protective effect for some protein-altering mutations [14,15]. A general overview of these variants across the family Cervidae is discussed by [16][17][18], [17] identified PRNP haplotype variants, and [18] inferred PrP proteoforms (protein variations encoded by a specific gene [19]) in white-tailed deer. Proteoform (PrP variant) A is overrepresented in CWD-positive individuals, while proteoforms C and F are underrepresented in CWD-positive individuals. ...
... Both inferred haplotypes and protein translation was completed using DNA Sequence Polymorphism v6.12.03 (DnaSP6, [36]). Prion protein haplotype and PrP proteoform designations followed those of [17] and [18] respectively. Haplotype and PrP proteoform frequencies were calculated by taking the total number of haplotype or proteoform in each location/time and dividing it by the total number in the sample. ...
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... We inferred haplotypes based on combinations of genotypes at different polymorphic sites using the program PHASE v. 2.1 [55,56]. We performed five independent runs to evaluate consistency in the results, setting the parameters as follows: 100,000 iterations, burn-in of 10,000 and drawing samples every 100 iterations [27,57] and default phase thresholds (90%). In a previous study of a white-tailed deer population in Arkansas, Chafin et al. [47] found 19 PRNP haplotypes based on 14 polymorphic sites. ...
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... Sequences were translated using MEGA X v. 10 (Table 2). In Elad2, SNP c.413A>G encodes serine (S) at codon 138, which is also present in many deer taxa (Table 2); whereas in Elad2, asparagine (N) is encoded at codon 138 (as reported in fallow deer and some caribou; Amino acid sequences of PrP were aligned for some cervid taxa with PRNP haplotype sequence available in GenBank, along with Elad1 and Elad2 (Table 2). ...
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... Susceptibility and clinical progression are associated with non-synonymous and synonymous genetic variation in the functional prion protein gene (PRNP; Chafin et al., 2020;Güere et al., 2020). Single-nucleotide polymorphisms (SNPs) at nucleotide (nt) 60, nt153, nt285, nt286, nt555, and nt676 in deer PRNP have been associated with altered CWD susceptibility or pathogenic processes (Brandt et al., 2015(Brandt et al., , 2018Johnson, Johnson et al., 2006;Wilson et al., 2009). The presence of CWD appears to affect population PRNP allele frequencies over space and time due to selection (Robinson et al., 2012); however, altered CWD susceptibility and pathogenic processes are clearly polygenic traits (Seabury et al., 2020) and disease spread is different in structured populations, which might require different wildlife management practices (Chafin et al., 2020). ...
... The presence of asparagine (N) at aa138 (nt413A) indicates amplification of the pseudogene (Brandt et al., 2015); we therefore filtered out all sequences with this site. SNPs with a total frequency of occurrence of 1% or less were excluded from the analysis. ...
... Haplotype 1 (f = 0.12) did not include any non-synonymous substitutions. Haplotype A (f = 0.30) and Haplotype B (f = 0.25) reported by Brandt et al. (2015Brandt et al. ( , 2018 from northern Illinois were also detected as Haplotype 16 (f = 0.09) and Haplotype 7 (f = 0.05), respectively. ...
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... Full associated sequences have been deposited in GenBank under accession numbers MZ913400 -MZ913401. Thirteen haplotypes were predicted from the 12 SNPs, 11 of which have previously been described [22,40,41]. Of the 13 haplotypes, B was most common (n = 368) and was used as the reference in logistic regression. ...
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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.