Predicting the odds of chronic wasting disease with Habitat Risk software.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) across the US and Canada as well as to Scandinavia and South Korea. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies have employed epidemiological models to understand long-term environmental risk. However, continued rapid spread of CWD into new regions of the continent has underscored the need for extension of these models into broader tools applicable for wide use by wildlife agencies. Additionally, efforts to semi-automate models will facilitate access of technical scientific methods to broader users. We introduce software (Habitat Risk) designed to link a previously published epidemiological model with spatially referenced environmental and disease testing data to enable agency personnel to make up-to-date, localized, data-driven predictions regarding the odds of CWD detection in surrounding areas after an outbreak is discovered. Habitat Risk requires pre-processing publicly available environmental datasets and standardization of disease testing (surveillance) data, after which an autonomous computational workflow terminates in a user interface that displays an interactive map of disease risk. We demonstrated the use of the Habitat Risk software with surveillance data of white-tailed deer from Tennessee, USA.

Predicting chronic wasting disease in white-tailed deer at the county scale using machine learning.

Continued spread of chronic wasting disease (CWD) through wild cervid herds negatively impacts populations, erodes wildlife conservation, drains resource dollars, and challenges wildlife management agencies. Risk factors for CWD have been investigated at state scales, but a regional model to predict locations of new infections can guide increasingly efficient surveillance efforts. We predicted CWD incidence by county using CWD surveillance data depicting white-tailed deer (Odocoileus virginianus) in 16 eastern and midwestern US states. We predicted the binary outcome of CWD-status using four machine learning models, utilized five-fold cross-validation and grid search to pinpoint the best model, then compared model predictions against the subsequent year of surveillance data. Cross validation revealed that the Light Boosting Gradient model was the most reliable predictor given the regional data. The predictive model could be helpful for surveillance planning. Predictions of false positives emphasize areas that warrant targeted CWD surveillance because of similar conditions with counties known to harbor CWD. However, disagreements in positives and negatives between the CWD Prediction Web App predictions and the on-the-ground surveillance data one year later underscore the need for state wildlife agency professionals to use a layered modeling approach to ensure robust surveillance planning. The CWD Prediction Web App is at https://cwd-predict.streamlit.app/ .

White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern.

The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability to transmit from deer to deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. Here, we present a comprehensive cross-sectional study assessing the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September to December 2020, n = 2,700) and 2021 (Season 2, September to December 2021, n = 2,762) were tested by SARS-CoV-2 real-time RT-PCR (rRT-PCR). SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence of multiple SARS-CoV-2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD. Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses. Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans. Thus, implementation of continuous surveillance programs to monitor SARS-CoV-2 dynamics in WTD is warranted, and measures to minimize virus transmission between humans and animals are urgently needed.

OCCURRENCE OF MANGE IN AMERICAN BLACK BEARS (URSUS AMERICANUS) IN NEW YORK STATE, USA.

Mange, a parasitic skin disease caused by various species of mites, is found in free-ranging wildlife populations and has been increasingly reported in American black bears (Ursus americanus) over the last decade in New York State (NYS), USA. Our goal was to describe the geographic, seasonal, and demographic factors associated with mange in this species in NYS. Our retrospective study used historic, opportunistic data from diagnostic necropsy records and visual sighting reports collected by the NYS Wildlife Health Program from 2009 to 2018. We used chi-square tests for independence and odds ratios to examine whether geographic location, year, season, sex, age, and reason for laboratory submission were associated with mange in bears. We used maps and seasonal analysis to investigate emerging patterns. We confirmed increased black bear mange reports in recent years. Necropsy data revealed more bears submitted to the laboratory because of mange, mainly caused by Sarcoptes scabiei; females were more likely than males to present with sarcoptic mange. We found that cases of mange in the Northern Zone were widely disseminated throughout the region, whereas cases in the Southern Zone were concentrated in two areas along the Pennsylvania border. Seasonally, mange cases showed peaks occurring in late spring to early summer and in fall. Our results were on the basis of available data; a comprehensive statewide surveillance program would be useful to better understand the apparent increase in mange and its potential impact on both the welfare of individual animals and the population of black bears in NYS. Additional research on the timing of transmission dynamics associated with females in winter dens may be helpful to wildlife managers to identify strategies to mitigate deleterious spread of the disease in black bears.

Prevalence of anticoagulant rodenticide exposure in red-tailed hawks (Buteo jamaicensis) and utility of clotting time assays to detect coagulopathy.

Anticoagulant rodenticides (ARs) continue to be used across the United States as a method for controlling pest rodent species. As a consequence, wild birds of prey are exposed to these toxicants by eating poisoned prey items. ARs prevent the hepatic recycling of vitamin K and thereby impede the post-translational processing of coagulation factors II, VII, IX, and X that are required for procoagulant complex assembly. Through this mechanism of action, ARs cause hemorrhage and death in their target species. Various studies have documented the persistence of these contaminants in birds of prey but few have attempted to use affordable and accessible diagnostic tests to diagnose coagulopathy in free-ranging birds of prey. In our study free-ranging red-tailed hawks were found to be exposed to difethialone and brodifacoum. Eleven of sixteen (68%) livers tested for AR exposure had detectable residues. Difethialone was found in 1/16 (6%), and brodifacoum was detected in 10/16 (62%) liver samples that were tested for rodenticide residues. Difethialone was found at a concentration of 0.18 ug/g wet weight and brodifacoum concentrations ranged from 0.003-0.234 ug/g wet weight. Two out of 34 (6%) RTHA assessed for blood rodenticide had brodifacoum in serum with measured concentrations of 0.003 and 0.006 ug/g. The range of clotting times in the prothrombin time (PT) and Russell's viper venom time assays for control RTHA were 16.7 to 39.7 s and 11.5 to 91.8 s, respectively. One study bird was diagnosed with clinical AR intoxication with a brodifacoum levels in blood of 0.006 and 0.234 ug/g wet weight in blood and liver respectively, a packed cell volume (PCV) of 19%, and PT and RVVT times of >180 s. No correlation was found between PT and RVVT in the control or free-range RTHA, and there was no relationship found between the presence of liver anticoagulant residues and clotting times in the PT and RVVT.

Species, causes, and outcomes of wildlife rehabilitation in New York State.

Wildlife rehabilitation is a publicly popular practice, though not without controversy. State wildlife agencies frequently debate the ecological impact of rehabilitation. By analyzing case records, we can clarify and quantify the causes for rehabilitation, species involved, and treatment outcomes. This data would aid regulatory agencies and rehabilitators in making informed decisions, as well as gaining insight into causes of species mortality. In New York State, the Department of Environmental Conservation (NYSDEC) has licensed rehabilitators since 1980 and annual reporting is required. In this study, we analyzed 58,185 individual wildlife cases that were attended by New York rehabilitators between 2012 and 2014. These encompassed 30,182 (51.9%) birds, 25,447 (43.7%) mammals, 2,421 (4.2%) reptiles, and 75 (0.1%) amphibians. We identified patterns among taxonomic representation, reasons for presentation to a rehabilitation center, and animal disposition. Major causes of presentation were trauma (n = 22,156; 38.1%) and orphaning (n = 21,679; 37.3%), with habitat loss (n = 3,937; 6.8%), infectious disease (n = 1,824; 3.1%), and poisoning or toxin exposure (n = 806; 1.4%) playing lesser roles. The overall release rate for animals receiving care was 50.2% while 45.3% died or were euthanized during the rehabilitation process. A relatively small number (0.3%) were permanently non-releasable and placed in captivity; 4.1% had unknown outcomes. A comparable evaluation in 1989 revealed that wildlife submissions have increased (annual mean 12,583 vs 19,395), and are accompanied by a significant improvement in release (50.2% in the study period vs 44.4% in 1989) (χ2(1) = 90.43, p < 0.0001). In this manuscript, we aim to describe the rehabilitator community in New York State, and present the causes and outcomes for rehabilitation over a three-year period.

Atypical Dermatophytosis in 12 North American Porcupines (Erethizon dorsatum) from the Northeastern United States 2010-2017.

Twelve wild North American porcupines (Erethizon dorsatum) out of a total of 44 of this species examined in an 8-year period were diagnosed with dermatopathies while being cared for at two wildlife rehabilitation clinics. Biopsy and necropsy were performed on seven and five animals, respectively. Atypical dermatophytosis was diagnosed in all cases. Lesions consisted of diffuse severe epidermal hyperkeratosis and mild hyperplasia with mild lymphoplasmacytic dermatitis and no folliculitis. Dermatophytes were noted histologically as hyphae and spores in hair shafts, and follicular and epidermal keratin. Trichophyton sp. was grown in 5/6 animals where culture was performed, with a molecular diagnosis of Arthroderma benhamiae/Trichophyton mentagrophytes in these five cases. Metagenomic analysis of formalin-fixed paraffin-embedded tissue samples from three cases identified fungi from 17 orders in phyla Basidiomycota and Ascomycota. Alteration of therapy from ketaconazole, which was unsuccessful in four out of five early cases, to terbinafine or nitraconazole led to the resolution of disease and recovery to release in four subsequent animals. In all, six animals were euthanized or died due to dermatopathy, no cases resolved spontaneously, and six cases were resolved with therapy. The work we present demonstrates an atypical lesion and anatomical distribution due to dermatophytosis in a series of free-ranging wild porcupines and the successful development of novel techniques for extracting and sequencing nucleic acids from fungus in archival formalin-fixed paraffin-embedded animal tissue.

Infection of eight mesocarnivores in New Hampshire and Vermont with a distinct clade of canine distemper virus in 2016-2017.

Three fishers (Martes pennanti), 2 gray foxes (Urocyon cinereoargenteus), 1 mink (Neovison vison), 1 skunk (Mephitis mephitis), and 1 raccoon (Procyon lotor), from Vermont and New Hampshire, had lesions on autopsy consistent with canine distemper virus (CDV) infections diagnosed in a 12-mo period in 2016-2017. Lesions of CDV infection were most commonly noted in the lungs (8 of 8 animals), urothelium (5 of 8), biliary tract (5 of 8), gastrointestinal tract (4 of 7), and brain (4 of 6). Splenic lesions were seen in 3 animals. The diagnosis was confirmed via immunohistochemistry and virus isolation. Viral genotyping indicated that all 8 animals were infected with a distinct clade of CDV that has only been reported in wildlife in New England, and this clade of viruses is distinct from vaccine strains. During the 12 mo when these cases occurred, no other CDV clade was identified in any other wildlife or domesticated animal submitted from the 2 states.

Necrotizing Enteritis in Nesting Adult Eastern Bluebirds (Sialia sialis) in New York State, USA.

Increased mortalities of adult Eastern Bluebirds, Sialia sialis, breeding in artificial nesting boxes were recorded in New York State, US. A total of 46 dead bluebirds were reported from 23 sites between early April and mid-August 2017. The maximum distance between sites was over 600 km. A total of 27 carcasses were available for postmortem examination. The most common cause of death was necrotizing enteritis, found in 56% (9/16) of birds that could be examined histopathologically. Lesions consisted of foci of hypereosinophilic debris and inflammation rich in Gram-negative bacteria. Aerobic and anaerobic culture of intestines from 4/8 birds with necrotizing enteritis yielded no growth. Plagiorhynchus cylindraceus acanthocephalids were often (6/9, 67%) but not invariably present in affected birds. Occasional incidental lesions included foreign-body microgranulomas in the wall of the ventriculus and intravascular nematodiasis at the base of the heart. The cause of sporadic outbreaks of necrotizing enteritis in breeding bluebirds remains undetermined and warrants further investigation.