David Bergman

Background: Throughout the Americas, Lyssavirus rabies (RV) perpetuates as multiple variants among bat and mesocarnivore species. Interspecific RV spillover occurs on occasion, but clusters and viral host shifts are rare. The spillover and host shift of a big brown bat (Eptesicus fuscus) RV variant Ef-W1 into mesocarnivores was reported previously on several occasions during 2001-2009 in Flagstaff, Arizona, USA, and controlled through rabies vaccination of target wildlife. During autumn 2021, a new cluster of Ef-W1 RV cases infecting striped skunks (Mephitis mephitis) was detected from United States Department of Agriculture enhanced rabies surveillance in Flagstaff. The number of Ef-W1 RV spillover cases within a short timeframe suggested the potential for transmission between skunks and an emerging host shift. Materials and Methods: Whole and partial RV genomic sequencing was performed to evaluate the phylogenetic relationships of the 2021-2023 Ef-W1 cases infecting striped skunks with earlier outbreaks. Additionally, realtime reverse-transcriptase PCR (rtRT-PCR) was used to opportunistically compare viral RNA loads in brain and salivary gland tissues of naturally infected skunks. Results: Genomic RV sequencing revealed that the origin of the 2021-2023 epizootic of Ef-W1 RV was distinct from the multiple outbreaks detected from 2001-2009. Naturally infected skunks with the Ef-W1 RV showed greater viral RNA loads in the brain, but equivalent viral RNA loads in the mandibular salivary glands, compared to an opportunistic sample of skunks naturally infected with a South-Central skunk RV from northern Colorado, USA. Conclusion: Considering a high risk for onward transmission and spread of the Ef-W1 RV in Flagstaff, public outreach, enhanced rabies surveillance, and control efforts, focused on education, sample characterization, and vaccination, have been ongoing since 2021 to mitigate and prevent the spread and establishment of Ef-W1 RV in mesocarnivores.

Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated by United States Department of Agriculture, Animal and Plant Health Inspection Service and State Natural Resources Agencies to quantify the outbreak dynamics of SARS-CoV-2 in North American white-tailed deer (Odocoileus virginianus; WTD) throughout its range in the United States. Local epidemics in WTD were well approximated by a single-outbreak peak followed by fade out. Outbreaks peaked early in the northeast and mid-Atlantic. Local effective reproduction ratios of SARS-CoV-2 were between 1 and 2.5. Ten percent of variability in peak prevalence was explained by human infection pressure. This, together with the similar peak infection prevalence times across many counties and single-peak outbreak dynamics followed by fade out, suggest that widespread transmission via human-to-deer spillover may have been an important driver of the patterns and persistence. We provide a framework for inferring population-level epidemiological processes through joint analysis of many sparsely observed local outbreaks (landscape-scale surveillance data) and linking epidemiological parameters to ecological risk factors. The framework combines mechanistic and statistical models that can identify and track local outbreaks in long-term infection surveillance monitoring data.

It is not possible to systematically screen the environment for rabies virus (RABV) using current approaches. We sought to determine under what conditions RABV is detectable from feces and other accessible samples from infected wildlife to broaden the number of biological samples that could be used to test for RABV. We employed a recently-developed quantitative RT-PCR assay called the "LN34 panlyssavirus real-time RT-PCR assay", which is highly sensitive and specific for all variants of RABV. We harvested and tested brain tissue, fecal, and/or mouth swab samples from 25 confirmed RABV positive bats of six species. To determine if rabies RNA lasts in feces sufficiently long post-defecation to use it as a surveillance tool, we tested fecal samples from 10 bats at the time of sample collection and after 24 hours of exposure to ambient conditions, with an additional test on six bats out to 72 hours. To assess whether we could pool fecal pellets and still detect a positive, we generated dilutions of known positives at 1:1, 1:10, 1:50, and 1:200. For six individuals for which matched brain, mouth swab, and fecal samples were tested, results were positive for 100%, 67%, and 67%, respectively. For the first time test to 24 hours, 63% of feces that were positive at time 0 were still positive after 24 hours, and 50% of samples at 72 hours were positive across all three replicates. Pooling tests revealed that fecal positives were detected at 1:10 dilution, but not at 1:50 or 1:200. Our preliminary results suggest that fecal samples hold promise for a rapid and non-invasive environmental screening system.

Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated by United States Department of Agriculture, Animal and Plant Health Inspection Service and state natural resources agencies to quantify outbreak dynamics of SARS-CoV-2 in North American white-tailed deer (Odocoileus virginianus; WTD) throughout its range in the United States. Local epidemics in WTD were well approximated by a single outbreak peak followed by fade out. Outbreaks peaked earliest in the northeast and mid-Atlantic. Local effective reproduction ratios of SARS-CoV-2 were between 1 and 2.5. Ten percent of variability in peak prevalence was explained by human infection pressure. This, together with the similar peak infection prevalence times across many counties and single-peak outbreak dynamics followed by fade out, suggest that widespread transmission via human-to-deer spillover may have been an important driver of the patterns and persistence. We provide a framework for inferring population-level epidemiological processes through joint analysis of many sparsely-observed local outbreaks (landscape scale surveillance data) and linking epidemiological parameters to ecological risk factors. The framework combines mechanistic and statistical models that can identify and track local outbreaks in long-term infection surveillance monitoring data.

Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated
by United States Department of Agriculture, Animal and Plant Health Inspection Service and state natural resources agencies to quantify outbreak dynamics of SARS-CoV-2 in North American white-tailed deer
(Odocoileus virginianus; WTD) throughout its range in the United States. Local epidemics in WTD were well approximated by a single outbreak peak followed by fade out. Outbreaks peaked earliest in the northeast and mid-Atlantic. Local effective reproduction numbers of SARS-CoV-2 were between 1 and 2.5. Ten percent of variability in peak prevalence was explained by human infection pressure. This, together with the
similar peak infection prevalence times across many counties and single-peak outbreak dynamics followed by fade out, suggest that widespread transmission via human-to-deer spillover may have been an important
driver of the patterns and persistence. We provide a framework for inferring population-level epidemiological processes through joint analysis of many sparsely-observed local outbreaks (landscape scale surveillance data) and linking epidemiological parameters to ecological risk factors. The framework combines mechanistic and statistical models that can identify and track local outbreaks in long-term infection surveillance monitoring data.

America, canine rabies has been nearly eliminated due to effective vaccination programs and the major rabies reservoirs are now bats and mesocarnivores (Gilbert 2018; Velasco-Villa et al. 2017). Rabies virus variants typically circulate within reservoir populations, with cross-species transmission to non-reservoir species during outbreaks. Cross-species transmission typically leads to dead-end infections, but more rarely host-shift events may occur in which the virus adapts to the new host and is maintained in that host through time (Badrane and Tordo 2001). For example, three independent host-shifts occurred between 2001 and 2009 and again in 2021-2023 in Flagstaff, Arizona, when striped skunks (Mephitis mephitis) and gray foxes (Urocyon cinereoargenteus) became infected with rabies variants associated with the big brown bat (Eptesicus fuscus) (Leslie et al. 2006; Kuzmin et al. 2012). Cross-species

Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated by
United States Department of Agriculture, Animal and Plant Health Inspection Service and state natural resources agencies to quantify infection of SARS-CoV-2 in North American white-tailed deer (Odocoileus
virginianus; WTD) using a hierarchical epidemiological model in the eastern half of the United States. Our model found that male deer had higher positivity than female deer, and positivity was higher in counties
with higher human population density or deer habitat. Estimated SARS-CoV-2 local epidemiological reproduction numbers were between 1 and 2.5 in most well-sampled counties, with local epidemics in WTD
peaking earlier in the northeast and mid-Atlantic relative to the Midwest and Southeast. Similar peak infection prevalence times across many counties provided indirect evidence for widespread transmission via
human-to-deer spillover, while the widespread high estimates of local epidemiological reproduction number suggested that sustained deer-to-deer transmission is also probable. The model estimated 10% of infected
WTD were infected due to human infection pressure.

Broad-scale data show SARS-CoV-2 occurrence in white-tailed deer throughout much of their range in the conterminous United States and reinforce findings of substantial SARS-CoV-2 infection and exposure. Results shed light on both current infections and prior exposure, with prevalence decreasing over time and seroprevalence increasing.

Recovery of the endangered Mount Graham red squirrel (MGRS) will likely be long and challenging. Its limited habitat, isolation to Pinaleño Mountain range, and demographic characteristics restrict its ability to rebound quickly from threats that impact both the squirrel and its habitat. Currently, threats to the MGRS include habitat degradation and loss through high-severity wildfire, fire suppression activities, insect outbreaks, climate change, and human development, and predation, as well as competition with Abert's squirrels. The most recent wildfire in 2017 impacted over 48,000 acres of already reduced habitat. A critical first step is to protect and manage the remaining population of the MGRS and its habitat. Management includes but is not limited to maintaining and improving the spruce-fir and mixed conifer biomes, while balancing the need to reduce risk of catastrophic wildfire with the needs of the squirrel. The U.S. Department of Agriculture, Animal and Plant Health Inspection Service Wildlife Services is conducting an Abert's Squirrel Removal Project at the request of the Arizona Game and Fish Department and the U.S. Fish and Wildlife Service (USFWS), in collaboration with a team of Mount Graham red squirrel experts and managers, to reduce the number of Abert's squirrels in historical MGRS habitat throughout the Pinaleño Mountains to assist in meeting the needs of the USFWS' 2011 MGRS draft recovery plan. Abert's squirrel removals are conducted monthly to minimize competition with MGRS.

Gray foxes (Urocyon cinereoargenteus) are considered a widespread and common species in the southwestern United States, although little is known about their spatial ecology that can inform rabies management strategies. We used data acquired from very high frequency and global positioning system satellite collars on gray foxes in the White Mountains and Pinaleno Mountains of Arizona to assess habitat use, movement patterns, and home range requirements. We present preliminary results from adult gray foxes (n = 3) from a larger study aimed at understanding gray fox space use for zoonotic disease management in the state. Average home range size was 3.78 – 2.74 km2 (SD) and gray foxes used ponderosa pine forests across both study sites, with individuals also selecting for this vegetation community at the home range scale.

Interspecific interactions among mesocarnivores can influence community dynamics and resource partitioning. Insights into these interactions can enhance understanding of local ecological processes that have impacts on pathogen transmission, such as the rabies lyssavirus. Host species ecology can provide an important baseline for disease management strategies especially in biologically diverse ecosystems and heterogeneous landscapes. We used a mesocarnivore guild native to the southwestern United States, a regional rabies
hotspot, that are prone to rabies outbreaks as our study system. Gray foxes (Urocyon cinereoargenteus), striped skunks (Mephitis mephitis), bobcats (Lynx rufus), and coyotes (Canis latrans) share large portions of their geographic ranges and can compete for resources, occupy similar niches, and influence population dynamics of each other. We deployed 80 cameras across two mountain ranges in Arizona, stratified by vegetation type. We used two-stage modeling to gain insight into species occurrence and co-occurrence patterns. There was strong evidence for the effects of elevation, season, and temperature impacting
detection probability of all four species, with understory height and canopy cover also influencing gray foxes and skunks. For all four mesocarnivores, a second stage multi-species co-occurrence model better explained patterns of detection than the single-species occurrence model. These four species are influencing the space use of each other and are likely competing for resources seasonally. We did not observe spatial partitioning between these competitors, likely due to an abundance of cover and food resources in the biologically diverse system we studied. From our results we can draw inferences on community dynamics to inform rabies management in a regional hotspot. Understanding environmental factors in disease hotspots can provide useful information to develop more reliable early-warning systems for viral outbreaks. We recommend that disease management focus on delivering oral vaccine baits onto the landscape when natural food resources are less abundant, specifically during the two drier seasons in Arizona (pre-monsoon spring and autumn) to maximize
intake by all mesocarnivores.

Coyote (Canis latrans) attacks on humans, once thought to be rare, have increased in frequency over the past decade. In Arizona, the number of wildlife human encounters has increased as our urban environments have expanded into the coyote's natural environment. Coyotes have learned to utilize drip irrigation, pet food, household refuse, and pets as prey. The problem of potential coyote

Broad-scale data show SARS-CoV-2 occurrence in white-tailed deer throughout much of their range in the conterminous United States and reinforce findings of considerable SARS-CoV-2 infection and exposure. Results shed light on both current infections and prior exposure, with prevalence decreasing over time and seroprevalence increasing.