Genetic susceptibility to chronic wasting disease in free-ranging white-tailed deer: Complement component C1q and Prnp polymorphisms

The genetic basis of susceptibility to chronic wasting disease (CWD) in free-ranging cervids is of great interest. Association studies of disease susceptibility in free-ranging populations, however, face considerable challenges including: the need for large sample sizes when disease is rare, animals of unknown pedigree create a risk of spurious results due to population admixture, and the inability to control disease exposure or dose. We used an innovative matched case–control design and conditional logistic regression to evaluate associations between polymorphisms of complement C1q and prion protein (Prnp) genes and CWD infection in white-tailed deer from the CWD endemic area in southcentral Wisconsin. To reduce problems due to admixture or disease-risk confounding, we used neutral genetic (microsatellite) data to identify closely related CWD-positive (n = 68) and CWD-negative (n = 91) female deer to serve as matched cases and controls. Cases and controls were also matched on factors (sex, location, age) previously demonstrated to affect CWD infection risk. For Prnp, deer with at least one Serine (S) at amino acid 96 were significantly less likely to be CWD-positive relative to deer homozygous for Glycine (G). This is the first characterization of genes associated with the complement system in white-tailed deer. No tests for association between any C1q polymorphism and CWD infection were significant at p \u3c 0.05. After controlling for Prnp, we found weak support for an elevated risk of CWD infection in deer with at least one Glycine (G) at amino acid 56 of the C1qC gene. While we documented numerous amino acid polymorphisms in C1q genes none appear to be strongly associated with CWD susceptibility

Precision of cementum annuli method for aging male white-tailed deer.

The most common method used to estimate ages of harvested white-tailed deer (Odocoileus virginianus) and other cervids is a criterion based on tooth replacement-and-wear (TRW). Previous studies have shown this method is prone to considerable error because TRW is partially subjective. A presumably more accurate, but more labor intensive and expensive, method to estimate age involves the counting of cementum annuli (CA) of cross-sectioned incisors. Quantifying rate of error of the CA aging method is not possible without known-aged specimens, but precision of duplicate CA age estimates for two teeth may be related to accuracy if identical factors influence both CA accuracy and precision. The objective of this research was to identify and assess factors affecting precision of paired CA ages as well as evaluate congruence between TRW and CA age estimates. We obtained paired CA age estimates from a laboratory specializing in CA aging for 473 adult (≥ 1 year old), male white-tailed deer harvested in Iowa (USA; 2014-2018). Not all CA age estimates of paired incisors agreed with one another and probability of agreement between the paired CA ages decreased as the certainty level of the CA ages provided by the laboratory decreased and was dependent upon the batches in which they were aged by the laboratory. We also estimated the age of 1,292 adult, male deer using both TRW and CA methods and compared the congruence between the TRW and CA age estimates. Congruence rates of CA and TRW ages differed among age classes (80% congruence in yearling TRW age classification, 65% with 2-year-olds, 78% with ≥3-year-olds). Our results showed that CA aging is imperfect and that the certainty level is an important factor to consider with CA ages, as shown in previous research, as is the batch in which the teeth were aged. We also confirmed previous studies' findings that CA and TRW ages for adult deer are not always congruent, particularly in age classes other than the yearling age class. Our results suggest managers are best served by using TRW to age adult deer as yearlings or ≥2-years-old. If additional age classes are required, CA aging is likely to be a better tool than TRW

Detection of lymphoproliferative disease virus in Iowa Wild Turkeys (Meleagris gallopavo): Comparison of two sections of the proviral genome.

An accurate diagnostic test is an essential aspect of successfully monitoring and managing wildlife diseases. Lymphoproliferative Disease Virus (LPDV) is an avian retrovirus that was first identified in domestic turkeys in Europe and was first reported in a Wild Turkey (Meleagris gallopavo) in the United States in 2009. It has since been found to be widely distributed throughout North America. The majority of studies have utilized bone marrow and PCR primers targeting a 413-nucleotide sequence of the gag gene of the provirus to detect infection. While prior studies have evaluated the viability of other tissues for LPDV detection (whole blood, spleen, liver, cloacal swabs) none to date have studied differences in detection rates when utilizing different genomic regions of the provirus. This study examined the effectiveness of another section of the provirus, a 335-nucleotide sequence starting in the U3 region of the LTR (Long Terminal Repeat) and extending into the Matrix of the gag region (henceforth LTR), for detecting LPDV. Bone marrow samples from hunter-harvested Wild Turkeys (n = 925) were tested for LPDV with the gag gene and a subset (n = 417) including both those testing positive and those where LPDV was not detected was re-tested with LTR. The positive percent agreement (PPA) was 97.1% (68 of 70 gag positive samples tested positive with LTR) while the negative percent agreement (NPA) was only 68.0% (236 of 347 gag negative samples tested negative with LTR). Cohen's Kappa (κ = 0.402, Z = 10.26, p<0.0001) and the McNemar test (OR = 55.5, p<0.0001) indicated weak agreement between the two gene regions. We found that in Iowa Wild Turkeys use of the LTR region identified LPDV in many samples in which we failed to detect LPDV using the gag region and that LTR may be more appropriate for LPDV surveillance and monitoring. However, neither region of the provirus resulted in perfect detection and additional work is necessary to determine if LTR is more reliable in other geographic regions where LPDV occurs

Pairwise comparison of LPDV detected (+) and undetected (-) samples using the <i>gag</i> and LTR sections of the provirus.

Pairwise comparison of LPDV detected (+) and undetected (-) samples using the gag and LTR sections of the provirus.</p

CSV file containing the Wild Turkey LPDV infection status dataset.

CSV file containing the Wild Turkey LPDV infection status dataset.</p

S1 File -

An accurate diagnostic test is an essential aspect of successfully monitoring and managing wildlife diseases. Lymphoproliferative Disease Virus (LPDV) is an avian retrovirus that was first identified in domestic turkeys in Europe and was first reported in a Wild Turkey (Meleagris gallopavo) in the United States in 2009. It has since been found to be widely distributed throughout North America. The majority of studies have utilized bone marrow and PCR primers targeting a 413-nucleotide sequence of the gag gene of the provirus to detect infection. While prior studies have evaluated the viability of other tissues for LPDV detection (whole blood, spleen, liver, cloacal swabs) none to date have studied differences in detection rates when utilizing different genomic regions of the provirus. This study examined the effectiveness of another section of the provirus, a 335-nucleotide sequence starting in the U3 region of the LTR (Long Terminal Repeat) and extending into the Matrix of the gag region (henceforth LTR), for detecting LPDV. Bone marrow samples from hunter-harvested Wild Turkeys (n = 925) were tested for LPDV with the gag gene and a subset (n = 417) including both those testing positive and those where LPDV was not detected was re-tested with LTR. The positive percent agreement (PPA) was 97.1% (68 of 70 gag positive samples tested positive with LTR) while the negative percent agreement (NPA) was only 68.0% (236 of 347 gag negative samples tested negative with LTR). Cohen’s Kappa (κ = 0.402, Z = 10.26, pLTR region identified LPDV in many samples in which we failed to detect LPDV using the gag region and that LTR may be more appropriate for LPDV surveillance and monitoring. However, neither region of the provirus resulted in perfect detection and additional work is necessary to determine if LTR is more reliable in other geographic regions where LPDV occurs.</div

Evaluation of LTR as a diagnostic test for LPDV infection against the standard (<i>gag</i>) using positive percent agreement (PPA), negative percent agreement (NPA), Cohen’s kappa, and McNemar’s odds ratio (OR).

Evaluation of LTR as a diagnostic test for LPDV infection against the standard (gag) using positive percent agreement (PPA), negative percent agreement (NPA), Cohen’s kappa, and McNemar’s odds ratio (OR).</p