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.

Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease.

Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.

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/ .

NOVEL REPORT OF THE EUROPEAN VARIANT OF ECHINOCOCCUS MULTILOCULARIS IN COYOTES (CANIS LATRANS) IN NEW YORK STATE.

Echinococcus multilocularis is a zoonotic cestode that can infect wildlife, domestic animals, and humans. In humans, infection with the larval stage of the parasite causes the disease alveolar echinococcosis, which can be fatal if left untreated. Surveillance for the parasite in New York State occurred during the 2021-2022 coyote (Canis latrans) hunting season. Fecal samples and the gastrointestinal tracts (GIT) from 43 coyote carcasses were collected from hunters and trappers across 8 counties. Fecal samples were screened for E. multilocularis DNA using a multiplex PCR. Three samples tested positive for E. multilocularis DNA. Subsequently, adult cestodes were collected from GIT samples using the sedimentation, filtration, and counting technique. Phylogenetic analysis of DNA sequences from the nad2 and cob genes from individual worms indicated these New York sequences cluster with E. multilocularis sequences from Europe. This is the first report of adult E. multilocularis cestodes in New York State, as well as the first detection of the European haplotype of E. multilocularis in wildlife in the northeastern United States.

Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease.

Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.

Infection and tissue distribution of highly pathogenic avian influenza A type H5N1 (clade 2.3.4.4b) in red fox kits (Vulpes vulpes).

Avian influenza H5N1 is a highly pathogenic virus that primarily affects birds. However, it can also infect other animal species, including mammals. We report the infection of nine juvenile red foxes (Vulpes vulpes) with Highly Pathogenic Avian Influenza A type H5N1 (Clade 2.3.4.4b) in the spring of 2022 in the central, western, and northern regions of New York, USA. The foxes displayed neurologic signs, and examination of brain and lung tissue revealed lesions, with brain lesions ranging from moderate to severe meningoencephalitis. Analysis of tissue tropism using RT-PCR methods showed a comparatively lower Ct value in the brain, which was confirmed by in situ hybridization targeting Influenza A RNA. The viral RNA labelling was highly clustered and overlapped the brain lesions, observed in neurons, and grey matter. Whole viral genome sequences obtained from the affected foxes were subjected to phylogenetic and mutation analysis to determine influenza A clade, host specificity, and potential occurrence of viral reassortment. Infections in red foxes likely occurred due to preying on infected wild birds and are unlikely due to transmission between foxes or other mammals.

How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species.

Restoration of depleted populations is an important method in biological conservation. Reintroduction strategies frequently aim to restore stable, increasing, self-sustaining populations. Knowledge of asymptotic system dynamics may provide advantage in selecting reintroduction strategies. We introduce interactive software that is designed to identify strategies for release of females that are immediately aligned with stable population dynamics from species represented by 2-, 3-, 4-, and 5-stage life history strategies. The software allows managers to input a matrix of interest, the desired number of breeding females, and the desired management timeline, and calls upon stable population theory to give release strategies that are in concert with both stable population status and the management goals. We demonstrate how the software can aid in assessing various strategies ahead of a hypothetical restoration. For the purpose of demonstration of the tool only, we use published vital rates of an ungulate species, but remark that the selection of species for demonstration is not central to the use of this tool. Adaption of this tool to real-life restorations of any 2-, 3-, 4-, or 5-stage iteroparous species may aid in understanding how to minimize undesirable recovery complications that may naturally arise from transient population dynamics. The software is freely available at: https//cwhl.vet.cornell.edu/tools/stapopd.

LEPTOSPIROSIS IN URBAN AND SUBURBAN AMERICAN BLACK BEARS ( URSUS AMERICANUS) IN WESTERN NORTH CAROLINA, USA.

American black bear ( Ursus americanus) populations in North Carolina, US have recovered significantly in recent decades and now occupy much of western North Carolina, including urban-suburban areas. We used the black bear as a potential sentinel for leptospirosis, a bacterial zoonotic disease caused by Leptospira spp., which is maintained by domestic and wild mammals. We determined whether Leptospira spp. were present across a gradient of housing densities in the urban and suburban black bear population in and around Asheville, North Carolina using serologic and molecular surveys. We collected blood from captured black bears ( n=94) and kidneys and bladders from carcasses ( n=19). We tested a total of 96 (47 females, 47 males, and 2 unknown) serum samples by microscopic agglutination test (MAT) and had positive results (titer >1:100) for L. kirschneri serovar Grippotyphosa (L. Grippotyphosa) in 4 females (8%) and 5 males (10%). No other serovars showed elevated titers in MAT. We tested a total of 125 samples using PCR ( n=96 serum, n=20 kidney, and n=9 bladders) and obtained positive results from one serum (1%), one kidney (5%), and one bladder (11%). The presence of Leptospira spp. in black bears occupying an urban and suburban landscape may indicate a more extensive occurrence of the bacteria among animals in the study region because black bears are the top carnivore in that ecosystem. Potential threats of widespread contamination during natural events such as flood or drought must be considered.

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.

MORTALITY TRENDS IN NORTHERN SEA OTTERS ( ENHYDRA LUTRIS KENYONI) COLLECTED FROM THE COASTS OF WASHINGTON AND OREGON, USA (2002-15).

During 2002-15 we examined the causes of mortality in a population of northern sea otters ( Enhydra lutris kenyoni). Beachcast sea otters were collected primarily from the US coast of Washington. Although there are no permanent sea otter residents in Oregon, several beachcast otters were collected from the Oregon coast. Infectious diseases were the primary cause of death (56%) for otters we examined. Sarcocystosis was the leading infectious cause of death (54%) and was observed throughout the study period. Some infectious diseases, such as morbilliviral encephalitis and leptospirosis, were documented for a limited number of years and then not detected again despite continued testing for these pathogens in necropsied animals. Trauma was the second most common cause of death (14%) during the study period. The continued stable growth of the Washington population of otters suggests they are able to tolerate current mortality rates.

Snake fungal disease: an emerging threat to wild snakes.

Since 2006, there has been a marked increase in the number of reports of severe and often fatal fungal skin infections in wild snakes in the eastern USA. The emerging condition, referred to as snake fungal disease (SFD), was initially documented in rattlesnakes, where the infections were believed to pose a risk to the viability of affected populations. The disease is caused by Ophidiomyces ophiodiicola, a fungus recently split from a complex of fungi long referred to as the Chrysosporium anamorph of Nannizziopsis vriesii (CANV). Here we review the current state of knowledge about O. ophiodiicola and SFD. In addition, we provide original findings which demonstrate that O. ophiodiicola is widely distributed in eastern North America, has a broad host range, is the predominant cause of fungal skin infections in wild snakes and often causes mild infections in snakes emerging from hibernation. This new information, together with what is already available in the scientific literature, advances our knowledge of the cause, pathogenesis and ecology of SFD. However, additional research is necessary to elucidate the factors driving the emergence of this disease and develop strategies to mitigate its impacts.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Tonsillar biopsy test for chronic wasting disease: Two sampling approaches in mule deer and white-tailed deer.

Preclinical antemortem testing of deer (Odocoileus spp.) for chronic wasting disease (CWD) can be important for determining prevalence rates and removing infected individuals from wild populations. Because samples with high numbers of tonsillar follicles are likely to provide earlier detection of CWD than samples with fewer follicles, the method of obtaining follicular samples may be critical when investigating disease prevalence. Between January 2003 and January 2005, white-tailed deer (O. virginianus) in southeast and southwest Minnesota and white-tailed and mule deer (O. hemionus) in Wind Cave National Park, South Dakota, were sampled using dorso-lateral and ventral-medial approaches for collecting tonsillar follicles. We obtained significantly more follicles using a dorso-lateral (median number of follicles = 19) rather than a ventral-medial (median number of follicles = 5.5) approach. No differences were observed in collection of tonsillar follicles that were related to sex, age class, or species of deer. We recommend the dorso-lateral approach for assessing CWD prevalence in deer populations.

A review of episodes of zinc phosphide toxicosis in wild geese (Branta spp.) in Oregon (2004-2011).

Epizootic mortality in several geese species, including cackling geese (Branta hutchinsii) and Canada geese (Branta canadensis), has been recognized in the Willamette Valley of Oregon for over a decade. Birds are generally found dead on a body of water or are occasionally observed displaying neurologic clinical signs such as an inability to raise or control the head prior to death. Investigation of these epizootic mortality events has revealed the etiology to be accidental poisoning with the rodenticide zinc phosphide (Zn(3)P(2)). Gross and histologic changes are restricted to acute pulmonary congestion and edema, sometimes accompanied by distension of the upper alimentary tract by fresh grass. Geese are unusually susceptible to this pesticide; when combined with an epidemiologic confluence of depredation of specific agricultural crops by rodents and seasonal avian migration pathways, epizootic toxicosis may occur. Diagnosis requires a high index of suspicion, appropriate sample collection and handling, plus specific test calibration for this toxicant. Interagency cooperation, education of farmers regarding pesticide use, and enforcement of regulations has been successful in greatly decreasing these mortality events since 2009.

Pathogen exposure and blood chemistry in the Washington, USA population of northern sea otters (Enhydra lutris kenyoni).

Northern sea otters (Enhydra lutris kenyoni) from Washington State, United States were evaluated in 2011 to determine health status and pathogen exposure. Antibodies to Brucella spp. (10%) and influenza A virus (23%) were detected for the first time in this population in 2011. Changes in clinical pathology values (serum chemistries), exposure to pathogens, and overall health of the population over the last decade were assessed by comparing 2011 data to the data collected on this population in 2001-2002. Several serum chemistry parameters were different between study years and sexes but were not clinically significant. The odds of canine distemper virus exposure were higher for otters sampled in 2001-2002 (80%) compared to 2011 (10%); likelihood of exposure significantly increased with age. Prevalence of exposure to Sarcocystis neurona was also higher in 2001-2002 (29%) than in 2011 (0%), but because testing methods varied between study years the results were not directly comparable. Exposure to Leptospira spp. was only observed in 2001-2002. Odds of Toxoplasma gondii exposure were higher for otters sampled in 2011 (97%) than otters in 2001-2002 (58%). Substantial levels of domoic acid (n = 2) and saxitoxin (n = 2) were found in urine or fecal samples from animals sampled in 2011. No evidence of calicivirus or Coxiella burnetii exposure in the Washington population of northern sea otters was found in either 2001-2002 or 2011. Changes in exposure status from 2001-2002 to 2011 suggest that the Washington sea otter population may be dealing with new disease threats (e.g., influenza) while also increasing their susceptibility to diseases that may be highly pathogenic in naïve individuals (e.g., canine distemper).

Surveillance of Wildlife Diseases: Lessons from the West Nile Virus Outbreak.

The West Nile virus outbreak of 1999 revealed many weaknesses in this country's ability to respond to disease threats that cross species lines. There were issues of poor communication among human, domestic animal, and wildlife health agencies that delayed diagnosis; a lack of diagnostic capacity of wildlife agencies at the state level; the exclusion of captive wildlife from any surveillance efforts; an inability to visualize the geospatial relationship between the human and avian outbreaks in a timely manner; and marked disparities of funding levels across agencies. Wildlife has played an important role in recent emerging infectious diseases, and it is clear that a One Health approach will be necessary to respond to future threats. The question is, are we any better prepared to recognize and respond to a wildlife-related emerging infectious disease than we were 14 years ago? Have the lessons of WNV been learned?

Expansion of an exotic species and concomitant disease outbreaks: pigeon paramyxovirus in free-ranging Eurasian collared doves.

Eurasian collared doves (Streptopelia decaocto) have expanded their range across the United States since their introduction several decades ago. Recent mortality events in Eurasian collared doves in Arizona and Montana, USA, during the winter of 2009-2010 were the result of pigeon paramyxovirus (PPMV), a novel disease agent. The first instance of mortality by this emerging infectious disease in this species occurred in Florida in 2001 with subsequent disease events in 2006 and 2008. Full diagnostic necropsies were performed on carcasses from the three states. PPMV was identified by RT-PCR and virus isolation and was sequenced to the VIb genotype of avian paramyxovirus-1 (APMV). Other APMVs are common in a variety of free-ranging birds, but concern is warranted because of the potential for commingling of this species with native birds, virus evolution, and threats to domestic poultry. Improved surveillance for wildlife mortality events and efforts to prevent introduction of non-native animals could reduce the threat of introducing new pathogens.