Wildlife reservoirs of SARS-CoV-2 may enable viral adaptation and spillback from animals to humans. In North America, there is evidence of unsustained spillover of SARS-CoV-2 from humans to white-tailed deer ( Odocoileus virginianus ), but no evidence of transmission from deer to humans. Through a biosurveillance program in Ontario, Canada we identified a new and highly divergent lineage of SARS-CoV-2 in white-tailed deer. This lineage is the most divergent SARS-CoV-2 lineage identified to date, with 76 consensus mutations (including 37 previously associated with non-human animal hosts) and signatures of considerable evolution and transmission within wildlife. Phylogenetic analysis also revealed an epidemiologically linked human case. Together, our findings represent the first clear evidence of sustained evolution of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.

Chytridiomycosis, caused by the fungi Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, is associated with massive amphibian mortality events worldwide and with some species’ extinctions. Previous ecological niche models suggest that B. dendrobatidis is not well‐suited to northern, temperate climates, but these predictions have often relied on datasets in which northern latitudes are underrepresented. Recent northern detections of B. dendrobatidis suggest that these models may have underestimated the suitability of higher latitudes for this fungus. We used qPCR to test for B. dendrobatidis in 1,041 non‐invasive epithelial swab samples from 18 species of amphibians collected across 735,345 km² in Ontario and Akimiski Island (Nunavut), Canada. We detected the pathogen in 113 samples (10.9%) from 11 species. Only one specimen exhibited potential clinical signs of disease. We used these data to produce six Species Distribution Models of B. dendrobatidis, which classified half of the study area as potential habitat for the fungus. We also tested each sample for B. salamandrivorans, an emerging pathogen that is causing alarming declines in European salamanders, but is not yet detected in North America. We did not detect B. salamandrivorans in any of the samples, providing a baseline for future surveillance. We assessed the potential risk of future introduction by comparing salamander richness to temperature‐dependent mortality, predicted by a previous exposure study. Areas with the highest species diversity and predicted mortality risk extended 60,530 km² across southern Ontario, highlighting the potential threat B. salamandrivorans poses to northern Nearctic amphibians. Preventing initial introduction will require coordinated, transboundary regulation of trade in amphibians (including frogs that can carry and disperse B. salamandrivorans), and surveillance of the pathways of introduction (e.g., water and wildlife). Our results can inform surveillance for both pathogens and efforts to mitigate the spread of chytridiomycosis through wild populations.

White-tailed deer are susceptible to SARS-CoV-2 and represent a highly important species for surveillance. Nasal swabs and retropharyngeal lymph nodes from white-tailed deer (n=258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and transcriptomics to further characterize infection and investigate host response to infection. We detected Delta SARS-CoV-2 (AY.44) in deer from the Estrie region; sequences clustered with human sequences from GISAID collected in October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 encoding a truncated protein were detected. Host expression patterns in SARS-CoV-2 infected deer were associated with the innate immune response, including signalling pathways related to anti-viral, pro- and anti-inflammatory signalling, and host damage. Our findings provide preliminary insights of host response to SARS-CoV-2 infection in deer and underscores the importance of ongoing surveillance of key wildlife species for SARS-CoV-2.

Despite proactive measures to prevent raccoon rabies entering Canada from the United States, several incursions of this disease have occurred. The largest outbreak, first reported in December 2015 in the city of Hamilton, Ontario, has resulted in the reporting of 449 animal cases as of December 31, 2018. Initial phylogenetic studies on the index case suggested that this outbreak was not due to local cross-border spread from the Niagara region of the United States where raccoon rabies has persisted for several years. Phylogenetic analysis of whole genome sequences of a viral collection from the Hamilton area and several US states indicates that a long-distance translocation of a diseased animal from southeastern New York State was responsible for this incursion. The role of the skunk as a potential secondary host supporting persistence and / or spread of the virus is also examined. Distinct variants of rabies virus are harbored by several wildlife species across North America. The variant associated with the raccoon host is especially problematic given its rapid spread throughout the eastern seaboard of the United States over the second half of the 20^th century and the high population density of this species in urban habitats that raises the potential for disease spread to both companion animals and their owners. Accordingly, extensive efforts to control raccoon rabies have been undertaken at many jurisdictional levels. This study uses current methods of genome analysis to explore the origins of a raccoon rabies outbreak in and around the city of Hamilton, Ontario, Canada, located close to the border with western New York state. In contrast to previous Canadian outbreaks of raccoon rabies, which were due to cross-border spread of the virus, this study demonstrates that the incursion into the Hamilton area was the result of a long-distance animal translocation from south-eastern New York. The implications of this event for strategies to control raccoon rabies are discussed.

Following an incursion of the mid-Atlantic raccoon variant of the rabies virus into southern Ontario, Canada, in late 2015, the direct rapid immunohistochemical test for rabies (dRIT) was employed on a large scale to establish the outbreak perimeter and to diagnose specific cases to inform rabies control management actions. In a 17-month period, 5800 wildlife carcasses were tested using the dRIT, of which 307 were identified as rabid. When compared with the gold standard fluorescent antibody test (FAT), the dRIT was found to have a sensitivity of 100% and a specificity of 98.2%. Positive and negative test agreement was shown to be 98.3% and 99.1%, respectively, with an overall test agreement of 98.8%. The average cost to test a sample was $3.13 CAD for materials, and hands-on technical time to complete the test is estimated at 0.55 h. The dRIT procedure was found to be accurate, fast, inexpensive, easy to learn and perform, and an excellent tool for monitoring the progression of a wildlife rabies incursion.

The largest outbreak of raccoon rabies in Canada was first reported in Hamilton, Ontario, in 2015 following a probable translocation event from the United States. We used a spatially-explicit agent-based model to evaluate the effectiveness of provincial control programs in an urban-centric outbreak if control interventions were used until 2025, 2020, or never used. Calibration tests suggested that a seroprevalence of protective rabies antibodies 2.1 times higher than that inferred from seroprevalence in program assessments was required in simulations to replicate observed raccoon rabies cases. Our simulation results showed that if control interventions with an adjusted seroprevalence were used until 2025 or 2020, the probability of rabies elimination due to control intervention use was 49.2% and 42.1%, respectively. However, if controls were never used, the probability that initial rabies cases failed to establish a sustained outbreak was only 18.2%. In simulations where rabies was not successfully eliminated, using control interventions until 2025 resulted in 67% fewer new infections compared to only applying controls until 2020 and in 90% fewer new infections compared to no control intervention use. However, the model likely underestimated rabies elimination rates since we did not adjust for adaptive control strategies in response to changes in rabies distributions and case numbers, as well as extending control interventions past 2025. Our agent-based model offers a cost-effective strategy to evaluate approaches to rabies control applications.