A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies.

BACKGROUND: Studies on haemosporidian diversity, including origin of human malaria parasites, malaria's zoonotic dynamic, and regional biodiversity patterns, have used target gene approaches. However, current methods have a trade-off between scalability and data quality. Here, a long-read Next-Generation Sequencing protocol using PacBio HiFi is presented. The data processing is supported by a pipeline that uses machine-learning for analysing the reads. METHODS: A set of primers was designed to target approximately 6 kb, almost the entire length of the haemosporidian mitochondrial genome. Amplicons from different samples were multiplexed in an SMRTbell® library preparation. A pipeline (HmtG-PacBio Pipeline) to process the reads is also provided; it integrates multiple sequence alignments, a machine-learning algorithm that uses modified variational autoencoders, and a clustering method to identify the mitochondrial haplotypes/species in a sample. Although 192 specimens could be studied simultaneously, a pilot experiment with 15 specimens is presented, including in silico experiments where multiple data combinations were tested. RESULTS: The primers amplified various haemosporidian parasite genomes and yielded high-quality mt genome sequences. This new protocol allowed the detection and characterization of mixed infections and co-infections in the samples. The machine-learning approach converged into reproducible haplotypes with a low error rate, averaging 0.2% per read (minimum of 0.03% and maximum of 0.46%). The minimum recommended coverage per haplotype is 30X based on the detected error rates. The pipeline facilitates inspecting the data, including a local blast against a file of provided mitochondrial sequences that the researcher can customize. CONCLUSIONS: This is not a diagnostic approach but a high-throughput method to study haemosporidian sequence assemblages and perform genotyping by targeting the mitochondrial genome. Accordingly, the methodology allowed for examining specimens with multiple infections and co-infections of different haemosporidian parasites. The pipeline enables data quality assessment and comparison of the haplotypes obtained to those from previous studies. Although a single locus approach, whole mitochondrial data provide high-quality information to characterize species pools of haemosporidian parasites.

A review of chronic wasting disease (CWD) spread, surveillance, and control in the United States captive cervid industry.

Chronic wasting disease (CWD) is a fatal prion disease of the family Cervidae that circulates in both wild and captive cervid populations. This disease threatens the health and economic viability of the captive cervid industry, which raises cervids in contained spaces for purposes such as hunting and breeding. Given the high transmissibility and long incubation period of CWD, the introduction and propagation of the infectious prion protein within and between captive cervid farms could be devastating to individual facilities and to the industry as a whole. Despite this risk, there does not yet exist a literature review that summarizes the scientific knowledge, to date, about CWD spread, surveillance, or control measures. Our review, which focused on peer reviewed, primary research conducted in the United States, sought to address this need by searching Google Scholar, Scopus, and Web of Science with a five-term keyword string containing terms related to the (1) location, (2) species affected, (3) disease, (4) captive cervid industry, and (5) topic of focus. Between the three databases, there were 190 articles that were selected for further examination. Those articles were then read to determine if they were about CWD spread, surveillance, and/or control in captive cervid facilities. The 22 articles that met these inclusion criteria were evaluated in detail and discussed, with recommendations for future collaborative work between captive cervid owners, government agencies, and researchers. This work will help to address, inform, and mitigate the rising problem of CWD spread and establishment.

Farmers' Knowledge and Practices About Ticks and Tickborne Diseases in Illinois.

OBJECTIVE: Tickborne diseases (TBDs) in Illinois have increased in recent years. A growing body of literature indicates that the risk of exposure to ticks and tickborne diseases is higher among outdoor workers, including farmers. However, information is lacking on awareness of ticks and tickborne diseases among this demographic. This study aimed to determine the knowledge and awareness among Illinois farmers regarding ticks and tickborne diseases. METHODS: A Knowledge, Attitudes & Prevention practices (KAP) survey was developed and administered to capture information regarding farmers' knowledge and attitudes about ticks and TBDs. Tick drags were conducted on a subset of properties as an incentive to complete the survey and to compare farmers' knowledge or expectations of ticks on their land with ticks collected. RESULTS: Fifty farmers participated in the survey, and 17 allowed tick drags. Only 60% of respondents had at least moderate knowledge about ticks gained through family and friends (56%), medical and healthcare personnel (48%), and the internet (44%). Responses varied by the type of commodity produced by the farmer. Fifty percent of participants reported knowledge about the blacklegged tick, 34% for the American dog tick, and 42% for the lone star tick; this knowledge also varied by farm type. Most farmers (54%) agreed that preventative behaviors could protect against tickborne diseases. Self-reported knowledge was significantly and directly associated with knowledge scores (p < .001). CONCLUSION: Knowledge of ticks and TBDs was lower among crop farmers than beef or mixed commodity farmers, but farmers generally have moderate knowledge of tick species in Illinois. Many participants expressed low concern over contracting a TBD, but many were also dissatisfied with the level of tick prevention measures that they follow. These results can be utilized to fill in knowledge gaps and develop informational materials to help farmers protect themselves against ticks and TBDs.

Current and Future Habitat Suitability Models for Four Ticks of Medical Concern in Illinois, USA.

The greater U.S. Midwest is on the leading edge of tick and tick-borne disease (TBD) expansion, with tick and TBD encroachment into Illinois occurring from both the northern and the southern regions. To assess the historical and future habitat suitability of four ticks of medical concern within the state, we fit individual and mean-weighted ensemble species distribution models for Ixodes scapularis, Amblyomma americanum, Dermacentor variabilis, and a newly invading species, Amblyomma maculatum using a variety of landscape and mean climate variables for the periods of 1970-2000, 2041-2060, and 2061-2080. Ensemble model projections for the historical climate were consistent with known distributions of each species but predicted the habitat suitability of A. maculatum to be much greater throughout Illinois than what known distributions demonstrate. The presence of forests and wetlands were the most important landcover classes predicting the occurrence of all tick species. As the climate warmed, the expected distribution of all species became strongly responsive to precipitation and temperature variables, particularly precipitation of the warmest quarter and mean diurnal range, as well as proximity to forest cover and water sources. The suitable habitat for I. scapularis, A. americanum, and A. maculatum was predicted to significantly narrow in the 2050 climate scenario and then increase more broadly statewide in the 2070 scenario but at reduced likelihoods. Predicting where ticks may invade and concentrate as the climate changes will be important to anticipate, prevent, and treat TBD in Illinois.

The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus).

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks.

County-wide assessments of Illinois white-tailed deer (Odocoileus virginianus) prion protein gene variation using improved primers and potential implications for management.

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.

Impact of landcover composition and density of localized deer culling sites on chronic wasting disease prevalence.

Chronic Wasting Disease (CWD), the prion disease of the Cervidae family, has been managed in Illinois deer since it was first detected in the Fall of 2002. Management uses a state-sponsored localized focus culling (LFC) program, implemented as close as possible to previously identified CWD-infected locations (TRSs (township/range/section)). We used hunter-harvest and LFC deer from 4621 and 435 unique TRSs, respectively, over 16 years of surveillance and management (2003-2017). We divided the study area into groups of TRSs with similar landcover types (SPLT) to assess CWD hunter-harvest prevalence at LFC and non-LFC sites by landcover composition. We also evaluate the importance of the month when LFC was implemented and determine whether the density of LFC sites or the total number of deer removed by LFC predicts hunter-harvest CWD prevalence. The percentage of CWD positive samples from hunters was lower than for LFC samples (for the study area and SPLTs). The probability of CWD increased by 5.24% for all the SPLT groups combined in the study area, by 4.6% from areas without an LFC nearby, and by 1.21% for areas with a prior LFC nearby. For all the TRS in the study area, low CWD odds (<1) in hunter-harvest deer were found in three SPLTs, in two SPLTs within TRSs with non-LFC, and five in five SPLTs within TRSs with LFC. The results suggest the importance of accounting for landcover composition to implement and sustain management in habitats with a higher risk of CWD. Our findings support that hunter-harvest alone cannot control CWD and the critical need for continued LFC intervention. For the whole study area-regardless of landcover composition-LFC in January was more important in decreasing hunter-harvest CWD prevalence than when LFC was conducted in March. However, the LFC conducted in January, February, and March were equally important when evaluating the month per habitat. Furthermore, the density of LFC sites in proximity to known infected areas is a better predictor of CWD than the number of deer removed by LFC, suggesting that increasing the density of LFC sites has a greater impact on CWD. The proximity of LFC to infected areas helps control CWD. Ultimately, landowners' and hunters' collaborations with the CWD surveillance and management programs are critical to protecting the Illinois wild deer herd; this study demonstrates their ongoing and valuable contributions to protecting this natural and public resource.

Knowledge, attitudes, and practices of Illinois medical professionals related to ticks and tick-borne disease.

Background: The rising incidence of tick-borne disease (TBD) underscores the importance of proficiency in TBD diagnosis. Clinicians' knowledge about vector ticks and TBDs in their area may influence whether patients are questioned about potential tick exposure and the consideration of diagnostic testing for TBDs. Objective: Our objective was to assess the knowledge, attitudes, and practices of Illinois clinicians towards ticks and TBDs. The study aimed to 1) identify predictors associated with knowledge, 2) identify knowledge gaps, and 3) evaluate attitudes and practices related to TBDs. Methods: A web-based knowledge, attitudes, and practices survey about Illinois ticks and TBDs was disseminated to physicians, mid-level practitioners, and nurses between August 2020 and February 2022. Poisson regression analysis was conducted to identify predictors of higher scores. Results: Of 346 respondents, 80% correctly identified Lyme disease as endemic to Illinois, and 95% were familiar with diagnostic testing for Lyme. Knowledge of other TBDs present in the state was highest among physicians, yet only 26% of physicians believed Rocky Mountain spotted fever (RMSF) to be present in Illinois, and only 17% believed ehrlichiosis to be endemic. Only 32% of physicians knew the cause of Alpha-gal syndrome and fewer than 18% were aware of available diagnostic testing. Tick or TBD-related education within the past two years was the most significant predictor of higher scores, increasing overall knowledge scores by 26% (RR 1.26, 95% CI 1.13-1.41) and increasing scores specific to TBDs by 42% (RR 1.42, 95% CI 1.19-1.69). Conclusion: Illinois clinicians were informed about Lyme disease but lacked knowledge of other TBDs endemic to the state, including RMSF, ehrlichiosis, and Alpha-gal syndrome. The strongest predictor of knowledge was tick/TBD training in the previous two years, highlighting the importance of frequent region-specific training on ticks and TBDs.

Knowledge, attitudes, and practices of veterinary professionals towards ticks and tick-borne diseases in Illinois.

Objective: A lack of standardized surveillance or reporting of tick-borne diseases (TBDs) in Illinois creates uncertainty for veterinarians regarding TBDs occurring within their practice geography or which TBDs may be encroaching on their area from neighboring territories. Therefore, the objective of this study was to gauge the knowledge, attitudes, and practices of veterinary professionals in Southern and Central Illinois to establish a foundation for targeting educational and outreach programs that address knowledge gaps. Sample: 72 veterinary professionals in Central and Southern Illinois. Procedures: An online knowledge, attitudes, and practices survey was distributed to veterinary professionals in Southern and Central Illinois. Poisson regression analyses were conducted to determine factors associated with knowledge scores and the estimated number of TBD cases diagnosed. Results: Knowledge scores were significantly higher among veterinary practitioners with recent (within the last 5 years) training on TBD. The number of cases of TBD diagnosed was higher among those reporting concern about TBD, and among those who routinely test for TBDs. The types of diseases diagnosed were heavily influenced by the diagnostic method used. Clinical relevance: This study paints a cohesive picture of human factors associated with diagnosing veterinary diseases and TBD prevalence in Southern and Central Illinois. Our results highlight the importance and practical value of veterinary continuing education on ticks and TBDs for both companion animals and public health. Building capacity for training veterinarians in parasitology using partnerships between academia and industry may strengthen the knowledge and understanding of ticks and tick-borne pathogens in the veterinary community.

A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus.

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.

Spatial epidemiology of hemorrhagic disease in Illinois wild white-tailed deer.

Epizootic hemorrhagic disease (EHD) and bluetongue (BT) are vector-borne viral diseases that affect wild and domestic ruminants. Clinical signs of EHD and BT are similar; thus, the syndrome is referred to as hemorrhagic disease (HD). Syndromic surveillance and virus detection in North America reveal a northern expansion of HD. High mortalities at northern latitudes suggest recent incursions of HD viruses into northern geographic areas. We evaluated the occurrence of HD in wild Illinois white-tailed deer from 1982 to 2019. Our retrospective space-time analysis identified high-rate clusters of HD cases from 2006 to 2019. The pattern of northward expansion indicates changes in virus-host-vector interactions. Serological evidence from harvested deer revealed prior infection with BTV. However, BTV was not detected from virus isolation in dead deer sampled during outbreaks. Our findings suggest the value of capturing the precise geographic location of outbreaks, the importance of virus isolation to confirm the cause of an outbreak, and the importance of expanding HD surveillance to hunter-harvested wild white-tailed deer. Similarly, it assists in predicting future outbreaks, allowing for targeted disease and vector surveillance, helping wildlife agencies communicate with the public the cause of mortality events and viral hemorrhagic disease outcomes at local and regional scales.

Effects of tick surveillance education on knowledge, attitudes, and practices of local health department employees.

BACKGROUND: The number of cases of tick-borne diseases in humans is increasing rapidly within Illinois. The responsibility for increased surveillance of tick-borne disease cases and tick vectors is being placed on local health departments throughout the United States, but they often lack the funding, time, and/or training needed to perform said surveillance. The aims of this study were to develop, deliver, and determine the effectiveness of tick surveillance training workshops for local health department employees within Illinois. METHODS: We developed and delivered in-person training at local health department offices in each of six Illinois Department of Public Health Environmental Health Regions between April-May of 2019. Pre-, post-, and six-month follow-up questionnaires on knowledge, attitudes, and practices with regards to tick surveillance were administered to training participants. Paired student's t-test or Wilcoxon signed-rank test were used to compare knowledge, attitudes, and practices scores between questionnaires with Cohen's d being used to calculate effect sizes associated with t-tests. McNemar's and McNemar-Bowker tests were used to evaluate individual questions. Spearman's rank correlation was used to evaluate the relationship between knowledge, attitudes, and practices at pre-, post-, and six-month follow-up. RESULTS: Seventy-six employees from 40 local health departments that represent 44% (45/102) of Illinois counties attended at least one training workshop. Of these attendees, 81.5% (62/76) participated in at least one survey, 79% (60/76) in the in-person pre-training survey, 74% (56/76) in the in-person post-training survey, and 22% (17/76) in the online six-month follow-up survey. The average knowledge score was significantly increased by 8.21 (95% CI:7.28-9.14) points from pre-training to post-training. The average overall attitude score significantly increased by 5.29 (95% CI: 3.91-6.66) points from pre- to post-training. There were no significant differences in practice scores. CONCLUSIONS: Our study found the training was effective in increasing the knowledge of ticks, tick-borne diseases, and surveillance as well as promoting positive attitudes related to surveillance. While the training, by itself, was not associated with increases in surveillance practices, we were able to empower local public health officials with the knowledge and positive attitudes needed to enact change.

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.

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.

Bluetongue and Epizootic Hemorrhagic Disease in the United States of America at the Wildlife-Livestock Interface.

Bluetongue (BT) and epizootic hemorrhagic disease (EHD) cases have increased worldwide, causing significant economic loss to ruminant livestock production and detrimental effects to susceptible wildlife populations. In recent decades, hemorrhagic disease cases have been reported over expanding geographic areas in the United States. Effective BT and EHD prevention and control strategies for livestock and monitoring of these diseases in wildlife populations depend on an accurate understanding of the distribution of BT and EHD viruses in domestic and wild ruminants and their vectors, the Culicoides biting midges that transmit them. However, national maps showing the distribution of BT and EHD viruses and the presence of Culicoides vectors are incomplete or not available at all. Thus, efforts to accurately describe the potential risk of these viruses on ruminant populations are obstructed by the lack of systematic and routine surveillance of their hosts and vectors. In this review, we: (1) outline animal health impacts of BT and EHD in the USA; (2) describe current knowledge of the distribution and abundance of BT and EHD and their vectors in the USA; and (3) highlight the importance of disease (BT and EHD) and vector surveillance for ruminant populations.

A Survey of Tick Surveillance and Control Practices in the United States.

Tickborne diseases are an increasing public health threat in the United States. Prevention and diagnosis of tickborne diseases are improved by access to current and accurate information on where medically important ticks and their associated human and veterinary pathogens are present, their local abundance or prevalence, and when ticks are actively seeking hosts. The true extent of tick and tickborne pathogen expansion is poorly defined, in part because of a lack of nationally standardized tick surveillance. We surveyed 140 vector-borne disease professionals working in state, county, and local public health and vector control agencies to assess their 1) tick surveillance program objectives, 2) pathogen testing methods, 3) tick control practices, 4) data communication strategies, and 5) barriers to program development and operation. Fewer than half of respondents reported that their jurisdiction was engaged in routine, active tick surveillance, but nearly two-thirds reported engaging in passive tick surveillance. Detection of tick presence was the most commonly stated current surveillance objective (76.2%). Most of the programs currently supporting tick pathogen testing were in the Northeast (70.8%), Upper and Central Midwest (64.3%), and the West (71.4%) regions. The most common pathogens screened for were Rickettsia spp. (Rickettsiales: Rickettsiaceae) and bacterial and viral agents transmitted by Ixodes (Acari: Ixodidae) ticks. Only 12% of respondents indicated their jurisdiction directly conducts or otherwise financially supports tick control. Responses indicated that their ability to expand the capacity of tick surveillance and control programs was impeded by inconsistent funding, limited infrastructure, guidance on best practices, and institutional capacity to perform these functions.

Comparing Contributions of Passive and Active Tick Collection Methods to Determine Establishment of Ticks of Public Health Concern Within Illinois.

In Illinois, between 1990 and 2017, tick-borne diseases in humans increased 10-fold, yet we have insufficient information on when and where people are exposed to vector ticks (Ixodida: Ixodidae). The aims of our research were to compare contributions of passive and active tick collection methods in determining establishment of ticks of public health concern and obtain information on tick distributions within Illinois. We used three surveillance strategies within the Illinois Tick Inventory Collaboration Network to gather information about the ticks of public health concern: 1) passive collection (voluntary submission by the public); 2) systematic collection (biweekly active surveillance); and 3) special collections (active collections in locations of special interest). Of collected adult and nymphal ticks, 436 were from passive collections, 142 from systematic collections, and 1,270 from special collections. Tick species distribution status changed in 36 counties. Our data provide noteworthy updates to distribution maps for use by public health agencies to develop prevention and control strategies. Additionally, the program built a network of collaborations and partnerships to support future tick surveillance efforts within Illinois and highlighted how the combination of the three surveillance strategies can be used to determine geographic spread of ticks, pinpoint locations in need of more surveillance, and help with long-term efforts that support phenology studies.

Spatial analysis of chronic wasting disease in free-ranging white-tailed deer (Odocoileus virginianus) in Illinois, 2008-2019.

Understanding the geographic distribution and clustering of chronic wasting disease (CWD) among free-ranging white-tailed deer (Odocoileus virginianus) populations can inform disease management practices. We used a retrospective analysis of surveillance data to evaluate CWD's spatial and temporal dynamics within 16 CWD-infected northern Illinois counties. Of 42,541 deer samples collected and tested for CWD from recreational hunter harvest between 2008 and 2019, we recorded 359 (0.84%) CWD-positive samples. We observed variability in CWD cases over time and space. By county, the median CWD-positive proportion was 0.84%, varying from a minimum of 0.14% in McHenry County to a maximum of 6.28% in Boone County. Across years, there were differences among CWD-positive proportions with a median of 0.90%, ranging from a minimum of 0.27% in 2012 to a maximum of 1.60% in 2019. We used a retrospective discrete Poisson scan statistic model to evaluate the space-time clustering of CWD-positive deer. We identified a statistically significant (p < .001) primary cluster C1 (area = 23.59 km2 ; RR = 10.48), occurring from 2010 to 2015 in the north-central part of the study area, and a secondary cluster C2, occurring from 2014 to 2019 (area = 9.27 km2 ; RR = 3.88) in the north-west of the study area. Detected CWD-positive space-time clusters suggest that the risk of CWD is not random. Space-time clusters of CWD can be used to evaluate the effectiveness of the Illinois CWD management programme. The area surrounding the older C1 cluster has undergone longer and more intense CWD management compared with C2. Currently, the older C1 cluster is no longer as high risk compared with the newer cluster C2, suggesting that management efforts in C2 should be increased. However, all CWD clusters should be targeted with surveillance, prevention and management programmes, including reducing deer densities to limit further spread of CWD.

Food Safety Considerations Related to the Consumption and Handling of Game Meat in North America.

Emerging foodborne pathogens present a threat to public health. It is now recognized that several foodborne pathogens originate from wildlife as demonstrated by recent global disease outbreaks. Zoonotic spillover events are closely related to the ubiquity of parasitic, bacterial, and viral pathogens present within human and animal populations and their surrounding environment. Foodborne diseases have economic and international trade impacts, incentivizing effective wildlife disease management. In North America, there are no food safety standards for handling and consumption of free-ranging game meat. Game meat consumption continues to rise in North America; however, this growing practice could place recreational hunters and game meat consumers at increased risk of foodborne diseases. Recreational hunters should follow effective game meat food hygiene practices from harvest to storage and consumption. Here, we provide a synthesis review that evaluates the ecological and epidemiological drivers of foodborne disease risk in North American hunter populations that are associated with the harvest and consumption of terrestrial mammal game meat. We anticipate this work could serve as a foundation of preventive measures that mitigate foodborne disease transmission between free-ranging mammalian and human populations.

Prion Protein Gene (PRNP) Sequences Suggest Differing Vulnerability to Chronic Wasting Disease for Florida Key Deer (Odocoileus virginianus clavium) and Columbian White-Tailed Deer (O. v. leucurus).

Chronic wasting disease (CWD) is a fatal, highly transmissible spongiform encephalopathy caused by an infectious prion protein. CWD is spreading across North American cervids. Studies of the prion protein gene (PRNP) in white-tailed deer (WTD; Odocoileus virginianus) have identified non-synonymous substitutions associated with reduced CWD frequency. Because CWD is spreading rapidly geographically, it may impact cervids of conservation concern. Here, we examined the genetic vulnerability to CWD of 2 subspecies of WTD: the endangered Florida Key deer (O. v. clavium) and the threatened Columbian WTD (O. v. leucurus). In Key deer (n = 48), we identified 3 haplotypes formed by 5 polymorphisms, of which 2 were non-synonymous. The polymorphism c.574G>A, unique to Key deer (29 of 96 chromosomes), encodes a non-synonymous substitution from valine to isoleucine at codon 192. In 91 of 96 chromosomes, Key deer carried c.286G>A (G96S), previously associated with substantially reduced susceptibility to CWD. Key deer may be less genetically susceptible to CWD than many mainland WTD populations. In Columbian WTD (n = 13), 2 haplotypes separated by one synonymous substitution (c.438C>T) were identified. All of the Columbian WTD carried alleles that in other mainland populations are associated with relatively high susceptibility to CWD. While larger sampling is needed, future management plans should consider that Columbian WTD are likely to be genetically more vulnerable to CWD than many other WTD populations. Finally, we suggest that genetic vulnerability to CWD be assessed by sequencing PRNP across other endangered cervids, both wild and in captive breeding facilities.

Association of chronic wasting disease susceptibility with prion protein variation in white-tailed deer (Odocoileus virginianus).

Chronic wasting disease (CWD) is caused by prions, infectious proteinaceous particles, PrPCWD. We sequenced the PRNP gene of 2,899 white-tailed deer (WTD) from Illinois and southern Wisconsin, finding 38 haplotypes. Haplotypes A, B, D, E, G and 9 others encoded Q95G96S100N103A123Q226, designated 'PrP variant A.' Haplotype C and 4 other haplotypes encoded PrP 'variant C' (Q95S96S100N103A123Q226). Haplotype F and two other haplotypes encoded PrP 'variant F' (H95G96S100N103A123Q226). The association of CWD with encoded PrP variants was examined in 2,537 tested WTD from counties with CWD. Relative to PrP variant A, CWD susceptibility was lower in deer with PrP variant C (OR = 0.26, p < 0.001), and even lower in deer with PrP variant F (OR = 0.10, p < 0.0001). Susceptibility to CWD was highest in deer with both chromosomes encoding PrP variant A, lower with one copy encoding PrP variant A (OR = 0.25, p < 0.0001) and lowest in deer without PrP variant A (OR = 0.07, p < 0.0001). There appeared to be incomplete dominance for haplotypes encoding PrP variant C in reducing CWD susceptibility. Deer with both chromosomes encoding PrP variant F (FF) or one encoding PrP variant C and the other F (CF) were all CWD negative. Our results suggest that an increased population frequency of PrP variants C or F and a reduced frequency of PrP variant A may reduce the risk of CWD infection. Understanding the population and geographic distribution of PRNP polymorphisms may be a useful tool in CWD management.