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We describe the pathology of natural infection with highly pathogenic avian influenza A(H5N1) virus of Eurasian lineage Goose/Guangdong clade 2.3.4.4b in 67 wild terrestrial mammals throughout the United States during April 1‒July 21, 2022. Affected mammals include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals showed primarily neurologic signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.

In the continental US, four terrestrial mammalian species are reservoirs for seven antigenic rabies virus variants. Cross species transmission (CST) occurs when a rabies virus variant causes disease in non-reservoir species. This study analyzed national surveillance data for rabies in terrestrial mammals. The CST rate was defined as: number of rabid non-reservoir animals/number of rabid reservoir animals. CST rates were analyzed for trend. Clusters of high CST rate counties were evaluated using space-time scanning statistics. The number of counties reporting a raccoon variant CST rate >1.0 increased from 75 in 1992 to 187 in 2011; counties with skunk variant CST rates >1.0 remained unchanged during the same period. As of 2011, for every rabid raccoon reported within the raccoon variant region, there were 0.73 cases of this variant reported in non-reservoir animals. Skunks were the most common non-reservoir animal reported with the raccoon rabies variant. Domestic animals were the most common non-reservoir animal diagnosed with a skunk rabies virus variant (n = 1,601). Cross species transmission rates increased fastest among domestic animals. Cross species transmission of rabies virus variants into non-reservoir animals increases the risk of human exposures and threatens current advances toward rabies control. Cross species transmission in raccoon rabies enzootic regions increased dramatically during the study period. Pet owners should vaccinate their dogs and cats to ensure against CST, particularly in regions with active foci of rabies circulation. Clusters of high CST activity represent areas for further study to better understand interspecies disease transmission dynamics. Each CST event has the potential to result in a rabies virus adapted for sustained transmission in a new species; therefore further understanding of the dynamics of CST may help in early detection or prevention of the emergence of new terrestrial rabies virus variants.

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data.

People and wildlife are living in an increasingly urban world, replete with unprecedented human densities, sprawling built environments, and altered landscapes. Such anthropogenic pressures can affect multiple processes within an ecological community, from spatial patterns to interspecific interactions. We tested two competing hypotheses, human shields vs. human competitors, to characterize how humans affect the carnivore community using multispecies occupancy models. From 2017 to 2020, we conducted the first camera survey of city parks in Detroit, Michigan, and collected spatial occurrence data of the local native carnivore community. Our 12,106–trap night survey captured detection data for coyotes (Canis latrans), red foxes (Vulpes vulpes), raccoons (Procyon lotor), and striped skunks (Mephitis mephitis). Overall occupancy varied across species (Ψcoyote = 0.40, Ψraccoon = 0.54, Ψred fox = 0.19, Ψstriped skunk = 0.09). Contrary to expectations, humans did not significantly affect individual occupancy for these urban carnivores. However, co-occurrence between coyote and skunk increased with human activity. The observed positive spatial association between an apex and subordinate pair supports the human shield hypothesis. Our findings demonstrate how urban carnivores can exploit spatial refugia and coexist with humans in the cityscape.

Babesia species are intraerythrocytic protozoan parasites that infect a variety of hosts. The goal of this study was to evaluate the piroplasm species present in skunks in various states in the United States and determine whether there was any geographic variation. Spleen, whole blood, or blood on filter paper were received from Pennsylvania, Kentucky, North Carolina, South Carolina, Georgia, Missouri, Louisiana, Texas, Kansas, and California, and were tested for Babesia sp. We tested four species of skunks including striped skunk ( Mephitis mephitis, n  = 72), eastern spotted skunk ( Spilogale putorius, n  = 28), western spotted skunk ( Spilogale gracilis, n  = 15), and hog-nosed skunk ( Conepatus leuconotus, n  = 11). A PCR assay targeting the 18S rRNA region and cox1 region were used to determine if skunks were infected with piroplasms and for phylogenetic analyses. A total of 48.4% (61/126) of skunks tested positive for a Babesia species. Both the 18S and cox1 analysis supported a skunk-specific Babesia microti -like sp. of carnivores as well as a species in the B. microti complex that is phylogenetically unique from both B. microti of humans and the B. microti- like sp. of carnivores. In the 18S analysis, there was a third species of Babesia in hog-nosed skunks in the western piroplasm group. This study shows that at least three species of piroplasms occur in skunk species in the United States and further highlights the importance of phylogenetic analyses and the use of multiple gene targets when studying piroplasms. Les espèces de Babesia sont des protozoaires parasites intraérythrocytaires qui infectent divers hôtes. Le but de cette étude était d’évaluer les espèces de piroplasmes présentes chez les mouffettes dans divers états des États-Unis et de déterminer s’il existait une variation géographique. Des rates, du sang total ou du sang sur papier filtre ont été reçus de Pennsylvanie, du Kentucky, de Caroline du Nord, de Caroline du Sud, de Géorgie, du Missouri, de Louisiane, du Texas, du Kansas et de Californie, et ont été testés pour Babesia sp. Nous avons testé quatre espèces de mouffettes, dont la mouffette rayée ( Mephitis mephitis , n  = 72), la mouffette tachetée de l’Est ( Spilogale putorius , n  = 28), la mouffette tachetée de l’Ouest ( Spilogale gracilis , n  = 15) et la mouffette à nez plat ( Conepatus leuconotus, n  = 11). Un test PCR ciblant la région de l’ARNr 18S et la région cox1 a été utilisé pour déterminer si les mouffettes étaient infectées par des piroplasmes et pour des analyses phylogénétiques. Au total, 48,4 % (61/126) des mouffettes ont été testées positives pour une espèce de Babesia . Les analyses du 18S et du cox1 ont toutes deux confirmé une espèce de type Babesia microti de carnivores spécifique aux mouffettes ainsi qu’une espèce du complexe B. microti qui est phylogénétiquement unique à la fois par rapport à B. microti de l’homme et à l’espèce des carnivores. Dans l’analyse 18S, il y avait une troisième espèce de Babesia chez les mouffettes à nez plat du groupe des piroplasmes de l’ouest. Cette étude montre qu’au moins trois espèces de piroplasmes sont présentes chez les espèces de mouffettes aux États-Unis et souligne en outre l’importance des analyses phylogénétiques et de l’utilisation de plusieurs cibles génétiques lors de l’étude des piroplasmes.

Purpose At least thirty species of wild carnivores have been recorded harboring Bartonella , and one of the most common pathogenic species infecting them is Bartonella rochalimae , which can cause endocarditis in humans and dogs. This bacterium can infect various mammals including wild carnivores, as well as ectoparasitic vectors such as fleas and ticks. Here we report the presence of B. rochalimae , in a Pulex simulans flea collected from a Mephitis macroura skunk in the municipality of Santa Cruz in Sonora, Mexico. Methods Fleas were collected from a M. macroura in Sonora, Mexico, in October 2019. They were identified to species level and subsequently tested for the presence of Bartonella using molecular tools including conventional PCR, sequencing, and phylogenetic analysis. Results A total of 10 P. simulans fleas (one male, nine females) were collected from the M. macroura skunk. The PCR and phylogenetic analysis indicated a prevalence of 10% (1/10) and a sequence clustered with the clade of B. rochalimae . Conclusions We confirmed the presence of B. rochalimae in a P. simulans flea collected from a M. macroura skunk in the area of Santa Cruz, Sonora, Mexico. Based on our results and previous studies in northern Mexico, which are consistent, it is necessary to continue monitoring Bartonella in M. macroura skunks and their fleas, since they could be important reservoirs of this bacterium in northern Mexico.

Intraguild interactions influence the structure and local dynamics of carnivore mammals’ assemblages. The potential effects of these interactions are often determined by the body size of competing members and may result in negative relationships in their abundance and, ultimately, lead to species exclusion or coexistence. The relative importance of interspecific interactions along with landscape characteristics in determining population patterns of understudied and threatened sympatric small carnivores, such as skunks, remains poorly documented. Therefore, we assessed the spatiotemporal variation in the abundance of American hog-nosed skunks Conepatus leuconotus and pygmy spotted skunks Spilogale pygmaea and the effect of interspecific interactions, resource availability, and habitat complexity on their local abundance in areas with the deciduous tropical forest south of the Mexican Pacific slope. We used presence-absence data for skunk species from three camera-trapping surveys between 2018 and 2020 in combination with Royle-Nichols occupancy models fitted in a Bayesian framework to estimate abundance, incorporating the effects of covariates related to the factors evaluated. We analyzed the relationship between the abundances of skunks using Bayesian Generalized Linear Models. Both skunk species showed significant differences in their abundances between seasons and between study sites. Overall, pygmy skunks were more abundant than hog-nosed skunks. We found negative relationships among the relative abundances of skunks during the dry seasons, but no evidence that local abundance is governed by the competitive dominance of the larger species. Patterns of skunk abundance were better explained by prey availability and other predictors related to habitat complexity, rather than interspecific interactions, since these models showed the highest predictive accuracies and strong positive and negative relationships. Our study highlights the underlying factors that determine the local abundance of these understudied and threatened small carnivores, allowing us to better understand the mechanisms that govern their coexistence for effective management and conservation of species in seasonal environments.

The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the present study we reconstructed spatiotemporal spread of SCSK in the whole territory of its circulation using a combination of Bayesian methods. The analysis based on 241 glycoprotein gene sequences demonstrated that SCSK is much more divergent phylogenetically than was appreciated previously. According to our analyses the SCSK originated in the territory of Texas ~170 years ago, and spread geographically during the following decades. The wavefront velocity in the northward direction was significantly greater than in the eastward and westward directions. Rivers (except the Mississippi River and Rio Grande River) did not constitute significant barriers for epizootic spread, in contrast to deserts and mountains. The mean dispersal rate of skunk rabies was lower than that of the raccoon and fox rabies. Viral lineages circulate in their areas with limited evidence of geographic spread during decades. However, spatiotemporal reconstruction shows that after a long period of stability the dispersal rate and wavefront velocity of SCSK are increasing. Our results indicate that there is a need to develop control measures for SCSK, and suggest how such measure can be implemented most efficiently. Our approach can be extrapolated to other rabies reservoirs and used as a tool for investigation of epizootic patterns and planning interventions towards disease elimination.

•58% (18/31) of skunks presented ONRAB® baits had detectable rabies antibody by week 7 post-vaccination.•100% (25/25) of skunks administered ONRAB® per os had detectable rabies antibody by week 7 post-vaccination.•All 10 control skunks succumbed to experimental rabies virus infection.•81% (25/31) of skunks in the ONRAB® bait group survived rabies challenge.•100% (23/23) of skunks administered ONRAB® per os survived rabies challenge. Skunks are one of the most important rabies vector species in North America due to their wide geographic distribution, high susceptibility to the rabies virus, and tendency to inhabit areas around human dwellings and domestic animals. Oral vaccination is a cost-effective, socially acceptable technique often used to control rabies in terrestrial wildlife; however, control of rabies in skunks has proven especially challenging due to the lack of a vaccine effective by the oral route in this species. In this study, we examined the antibody response of captive striped skunks (Mephitis mephitis) to ONRAB® and tested the protection afforded by the vaccine against rabies virus. Thirty-one skunks were each offered one ONRAB® vaccine bait, 25 skunks were administered ONRAB® via direct instillation into the oral cavity (DIOC) and ten controls received no vaccine. A blood sample was collected from controls and vaccinates 6 weeks prior to treatment, and then 5 and 7 weeks post-vaccination (PV). A competitive ELISA was used to detect rabies antibody (RAb). Pre-vaccination sera for all skunks, and sera for all controls throughout the serology study, were negative for RAb. Fifty-eight percent (18/31) of skunks in the bait group and 100% (25/25) of skunks that received ONRAB® DIOC had detectable RAb by 7 week PV. All 10 controls succumbed to experimental rabies infection. In the group of skunks administered ONRAB® DIOC, 100% (23/23) survived challenge 247 days PV. Survival of skunks presented ONRAB® baits was 81% (25/31). In the bait group, all 18 skunks that had detectable RAb by 7 week PV survived challenge. Seven additional skunks without detectable RAb prior to week 7 PV also survived. Lack of any remarkable pathology in study animals, together with positive serology and challenge results, supports that ONRAB® is a safe and effective oral rabies vaccine for use in skunks.

In nature, rabies virus (RABV; genus Lyssavirus, family Rhabdoviridae) represents an assemblage of phylogenetic lineages, associated with specific mammalian host species. Although it is generally accepted that RABV evolved originally in bats and further shifted to carnivores, mechanisms of such host shifts are poorly understood, and examples are rarely present in surveillance data. Outbreaks in carnivores caused by a RABV variant, associated with big brown bats, occurred repeatedly during 2001-2009 in the Flagstaff area of Arizona. After each outbreak, extensive control campaigns were undertaken, with no reports of further rabies cases in carnivores for the next several years. However, questions remained whether all outbreaks were caused by a single introduction and further perpetuation of bat RABV in carnivore populations, or each outbreak was caused by an independent introduction of a bat virus. Another question of concern was related to adaptive changes in the RABV genome associated with host shifts. To address these questions, we sequenced and analyzed 66 complete and 20 nearly complete RABV genomes, including those from the Flagstaff area and other similar outbreaks in carnivores, caused by bat RABVs, and representatives of the major RABV lineages circulating in North America and worldwide. Phylogenetic analysis demonstrated that each Flagstaff outbreak was caused by an independent introduction of bat RABV into populations of carnivores. Positive selection analysis confirmed the absence of post-shift changes in RABV genes. In contrast, convergent evolution analysis demonstrated several amino acids in the N, P, G and L proteins, which might be significant for pre-adaptation of bat viruses to cause effective infection in carnivores. The substitution S/T₂₄₂ in the viral glycoprotein is of particular merit, as a similar substitution was suggested for pathogenicity of Nishigahara RABV strain. Roles of the amino acid changes, detected in our study, require additional investigations, using reverse genetics and other approaches.