Origins of the arctic fox variant rabies viruses responsible for recent cases of the disease in southern Ontario

Low levels of genetic differentiation and structure in red fox populations in Eastern Canada and implications for Arctic fox rabies propagation potential

Rabies is a lethal zoonosis present in most parts of the world which can be transmitted to humans through the bite from an infected mammalian reservoir host. The Arctic rabies virus variant (ARVV) persists mainly in populations of Arctic foxes (Vulpes lagopus), and to a lesser extent in red fox populations (Vulpes vulpes). Red foxes are thought to be responsible for sporadic southward movement waves of the ARVV outside the enzootic area of northern Canada. In this study, we wanted to investigate whether red foxes displayed notable levels of genetic structure across the Quebec-Labrador Peninsula, which includes portions of the provinces of Quebec and Newfoundland-Labrador in Canada, and is a region with a history of southward ARVV movement waves. We combined two datasets that were collected and genotyped using different protocols, totalling 675 red fox individuals across the whole region and genotyped across 13 microsatellite markers. We found two genetic clusters across the region, reflecting a latitudinal gradient, and characterized by low genetic differentiation. We also observed weak but significant isolation by distance, which seems to be marginally more important for females than for males. These findings suggest a general lack of resistance to movement in red fox populations across the Quebec-Labrador Peninsula, regardless of sex. Implications of these findings include additional support for the hypothesis of long-distance southward ARVV propagation through its red fox reservoir host.

Long-term satellite tracking reveals patterns of long-distance dispersal in juvenile and adult Arctic foxes (Vulpes lagopus)

Long-distance dispersal plays a key role in species distribution and persistence. However, its movement metrics and ecological implications may differ whether it is undertaken by juveniles (natal dispersal) or adults (breeding dispersal). We investigated the influence of life stage on long-distance dispersal in the Arctic fox, an important tundra predator. We fitted 170 individuals with satellite collars during a 13-year study on Bylot Island (Nunavut, Canada), and analysed the tracks of 10 juveniles and 27 adults engaging in long-distance dispersal across the Canadian High Arctic. This behaviour was much more common than expected, especially in juveniles (62.5%, adults: 19.4%). Emigration of juveniles occurred mainly at the end of summer while departure of adults was not synchronized. Juveniles travelled for longer periods and over longer cumulative distances than adults, but spent similar proportions of their time travelling on sea ice versus land. Successful immigration occurred mostly in late spring and was similar for juveniles and adults (30% versus 37%). Our results reveal how life stage influences key aspects of long-distance dispersal in a highly mobile canid. This new knowledge is critical to understand the circumpolar genetic structure of the species, and how Arctic foxes can spread zoonoses across vast geographical areas.

Long-term satellite tracking reveals patterns of long-distance dispersal in juvenile and adult Arctic foxes (Vulpes lagopus)

Long-distance dispersal plays a key role in species distribution and persistence. However, its movement metrics and ecological implications may differ whether it is undertaken by juveniles (natal dispersal) or adults (breeding dispersal). We investigated the influence of life stage on long-distance dispersal in the Arctic fox, an important tundra predator. We fitted 170 individuals with satellite collars during a 13-year study on Bylot Island (Nunavut, Canada), and analysed the tracks of 10 juveniles and 27 adults engaging in long-distance dispersal across the Canadian High Arctic. This behaviour was much more common than expected, especially in juveniles (62.5%, adults: 19.4%). Emigration of juveniles occurred mainly at the end of summer while departure of adults was not synchronized. Juveniles travelled for longer periods and over longer cumulative distances than adults, but spent similar proportions of their time travelling on sea ice versus land. Successful immigration occurred mostly in late spring and was similar for juveniles and adults (30% versus 37%). Our results reveal how life stage influences key aspects of long-distance dispersal in a highly mobile canid. This new knowledge is critical to understand the circumpolar genetic structure of the species, and how Arctic foxes can spread zoonoses across vast geographical areas.

Long-term satellite tracking reveals patterns of long-distance dispersal in juvenile and adult Arctic foxes (Vulpes lagopus)

Long-distance dispersal plays a key role in species distribution and persistence. However, its movement metrics and ecological implications may differ whether it is undertaken by juveniles (natal dispersal) or adults (breeding dispersal). We investigated the influence of life stage on long-distance dispersal in the Arctic fox, an important tundra predator. We fitted 170 individuals with satellite collars during a 13-year study on Bylot Island (Nunavut, Canada), and analysed the tracks of 10 juveniles and 27 adults engaging in long-distance dispersal across the Canadian High Arctic. This behaviour was much more common than expected, especially in juveniles (62.5%, adults: 19.4%). Emigration of juveniles occurred mainly at the end of summer while departure of adults was not synchronized. Juveniles travelled for longer periods and over longer cumulative distances than adults, but spent similar proportions of their time travelling on sea ice versus land. Successful immigration occurred mostly in late spring and was similar for juveniles and adults (30% versus 37%). Our results reveal how life stage influences key aspects of long-distance dispersal in a highly mobile canid. This new knowledge is critical to understand the circumpolar genetic structure of the species, and how Arctic foxes can spread zoonoses across vast geographical areas.

Genetic Diversity, Evolutionary Dynamics, and Pathogenicity of Ferret Badger Rabies Virus Variants in Mainland China, 2008–2018

In contrast to dog-associated human rabies cases decline year by year due to the rabies vaccination coverage rates increase in China, ferret badger (FB, Melogale moschata)-associated human rabies cases emerged in the 1990s, and are now an increasingly recognized problem in southeast China. To investigate epidemiology, temporal evolution dynamics, transmission characterization, and pathogenicity of FB-associated rabies viruses (RABVs), from 2008 to 2018, we collected 3,622 FB brain samples in Jiangxi and Zhejiang Province, and detected 112 RABV isolates. Four FB-related lineages were identified by phylogenetic analysis (lineages A–D), the estimated Times to Most Recent Common Ancestor were 1941, 1990, 1937, and 1997 for lineages A–D, respectively. Furthermore, although no FB-associated human rabies case has been reported there apart from Wuyuan area, FB-RABV isolates are mainly distributed in Jiangxi Province. Pathogenicity of FB-RABVs was assessed using peripheral inoculation in mice and in beagles with masseter muscles, mortality-rates ranging from 20 to 100% in mice and 0 to 20% in beagles in the groups infected with the various isolates. Screening of sera from humans with FB bites and no post-exposure prophylaxis to rabies revealed that five of nine were positive for neutralizing antibodies of RABV. All the results above indicated that FB-RABV variants caused a lesser pathogenicity in mice, beagles, and even humans. Vaccination in mice suggests that inactivated vaccine or recombinant subunit vaccine products can be used to control FB-associated rabies, however, oral vaccines for stray dogs and wildlife need to be developed and licensed in China urgently.

Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses.

The ecological niche of reported rabies cases in Canada is similar to Alaska

The ecology of rabies in the circumpolar North is still not well understood. We use machine learning, a geographic information system and data explicit in time and space obtained for reported rabies cases and predictors in Canada to develop an ecological niche model for the distribution of reported rabies cases in the American north (Alaska and Canada). The ecological niche model based on reported rabies cases in Canada predicted reported rabies cases in Alaska, suggesting a rather robust inference and even similar drivers on a continental scale. As found in Alaska, proximity to human infrastructure—specifically along the coast—was a strong predictor in the detection of rabies cases in Canada. Also, this finding highlights the need for a more systematic landscape sampling for rabies infection model predictions to better understand and tackle the ecology of this important zoonotic disease on a landscape scale at some distance from human infrastructure in wilderness areas.

The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes)

Populations are exposed to different types and strains of pathogens across heterogeneous landscapes, where local interactions between host and pathogen may present reciprocal selective forces leading to correlated patterns of spatial genetic structure. Understanding these coevolutionary patterns provides insight into mechanisms of disease spread and maintenance. Arctic rabies (AR) is a lethal disease with viral variants that occupy distinct geographic distributions across North America and Europe. Red fox (Vulpes vulpes) are a highly susceptible AR host, whose range overlaps both geographically distinct AR strains and regions where AR is absent. It is unclear if genetic structure exists among red fox populations relative to the presence/absence of AR or the spatial distribution of AR variants. Acquiring these data may enhance our understanding of the role of red fox in AR maintenance/spread and inform disease control strategies. Using a genotyping-by-sequencing assay targeting 116 genomic regions of immunogenetic relevance, we screened for sequence variation among red fox populations from Alaska and an outgroup from Ontario, including areas with different AR variants, and regions where the disease was absent. Presumed neutral SNP data from the assay found negligible levels of neutral genetic structure among Alaskan populations. The immunogenetically-associated data identified 30 outlier SNPs supporting weak to moderate genetic structure between regions with and without AR in Alaska. The outliers included SNPs with the potential to cause missense mutations within several toll-like receptor genes that have been associated with AR outcome. In contrast, there was a lack of genetic structure between regions with different AR variants. Combined, we interpret these data to suggest red fox populations respond differently to the presence of AR, but not AR variants. This research increases our understanding of AR dynamics in the Arctic, where host/disease patterns are undergoing flux in a rapidly changing Arctic landscape, including the continued northward expansion of red fox into regions previously predominated by the arctic fox (Vulpes lagopus).

Relationships between fox populations and rabies virus spread in northern Canada

Rabies spreads in both Arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) throughout the Canadian Arctic but limited wildlife disease surveillance, due to the extensive landmass of the Canadian north and its small widely scattered human population, undermines our knowledge of disease transmission patterns. This study has explored genetic population structure in both the rabies virus and its fox hosts to better understand factors that impact rabies spread. Phylogenetic analysis of 278 samples of the Arctic lineage of rabies virus recovered over 40 years identified four sub-lineages, A1 to A4. The A1 lineage has been restricted to southern regions of the Canadian province of Ontario. The A2 lineage, which predominates in Siberia, has also spread to northern Alaska while the A4 lineage was recovered from southern Alaska only. The A3 sub-lineage, which was also found in northern Alaska, has been responsible for virtually all cases across northern Canada and Greenland, where it further differentiated into 18 groups which have systematically evolved from a common predecessor since 1975. In areas of Arctic and red fox sympatry, viral groups appear to circulate in both hosts, but both mitochondrial DNA control region sequences and 9-locus microsatellite genotypes revealed contrasting phylogeographic patterns for the two fox species. Among 157 Arctic foxes, 33 mitochondrial control region haplotypes were identified but little genetic structure differentiating localities was detected. Among 162 red foxes, 18 control region haplotypes delineated three groups which discriminated among the Churchill region of Manitoba, northern Quebec and Labrador populations, and the coastal Labrador locality of Cartwright. Microsatellite analyses demonstrated some genetic heterogeneity among sampling localities of Arctic foxes but no obvious pattern, while two or three clusters of red foxes suggested some admixture between the Churchill and Quebec-Labrador regions but uniqueness of the Cartwright group. The limited population structure of Arctic foxes is consistent with the rapid spread of rabies virus subtypes throughout the north, while red fox population substructure suggests that disease spread in this host moves most readily down certain independent corridors such as the northeastern coast of Canada and the central interior. Interestingly the evidence suggests that these red fox populations have limited capacity to maintain the virus over the long term, but they may contribute to viral persistence in areas of red and Arctic fox sympatry.

Serological Responses of Raccoons and Striped Skunks to Ontario Rabies Vaccine Bait in West Virginia during 2012-2016

Since the 1990s, oral rabies vaccination (ORV) has been used successfully to halt the westward spread of the raccoon rabies virus (RV) variant from the eastern continental USA. Elimination of raccoon RV from the eastern USA has proven challenging across targeted raccoon (Procyon lotor) and striped skunk (Mephitis mephitis) populations impacted by raccoon RV. Field trial evaluations of the Ontario Rabies Vaccine Bait (ONRAB) were initiated to expand ORV products available to meet the rabies management goal of raccoon RV elimination. This study describes the continuation of a 2011 trial in West Virginia. Our objective was to evaluate raccoon and skunk response to ORV occurring in West Virginia for an additional two years (2012–2013) at 75 baits/km² followed by three years (2014–2016) of evaluation at 300 baits/km². We measured the change in rabies virus-neutralizing antibody (RVNA) seroprevalence in targeted wildlife populations by comparing levels pre- and post-ORV during each year of study. The increase in bait density from 75/km² to 300/km² corresponded to an increase in average post-ORV seroprevalence for raccoon and skunk populations. Raccoon population RVNA levels increased from 53% (300/565, 95% CI: 50–57%) to 82.0% (596/727, 95% CI: 79–85%) during this study, and skunk population RVNA levels increased from 11% (8/72, 95% CI: 6–20%) to 39% (51/130, 95% CI: 31–48%). The RVNA seroprevalence pre-ORV demonstrated an increasing trend across study years for both bait densities and species, indicating that multiple years of ORV may be necessary to achieve and maintain RVNA seroprevalence in target wildlife populations for the control and elimination of raccoon RV in the eastern USA.

Update on lyssaviruses and rabies: will past progress play as prologue in the near term towards future elimination?

Rabies is an ancient, much-feared, and neglected infectious disease. Caused by pathogens in the family Rhabdoviridae, genus Lyssavirus, and distributed globally, this viral zoonosis results in tens of thousands of human fatalities and millions of exposures annually. All mammals are believed susceptible, but only certain taxa act as reservoirs. Dependence upon direct routing to, replication within, and passage from the central nervous system serves as a basic viral strategy for perpetuation. By a combination of stealth and subversion, lyssaviruses are quintessential neurotropic agents and cause an acute, progressive encephalitis. No treatment exists, so prevention is the key. Although not a disease considered for eradication, something of a modern rebirth has been occurring within the field as of late with regard to detection, prevention, and management as well as applied research. For example, within the past decade, new lyssaviruses have been characterized; sensitive and specific diagnostics have been optimized; pure, potent, safe, and efficacious human biologics have improved human prophylaxis; regional efforts have controlled canine rabies by mass immunization; wildlife rabies has been controlled by oral rabies vaccination over large geographic areas in Europe and North America; and debate has resumed over the controversial topic of therapy. Based upon such progress to date, there are certain expectations for the next 10 years. These include pathogen discovery, to uncover additional lyssaviruses in the Old World; laboratory-based surveillance enhancement by simplified, rapid testing; anti-viral drug appearance, based upon an improved appreciation of viral pathobiology and host response; and improvements to canine rabies elimination regionally throughout Africa, Asia, and the Americas by application of the best technical, organizational, economic, and socio-political practices. Significantly, anticipated Gavi support will enable improved access of human rabies vaccines in lesser developed countries at a national level, with integrated bite management, dose-sparing regimens, and a 1 week vaccination schedule.