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Processes Underlying Rabies Virus Incursions across US-Canada Border as Revealed by Whole-Genome Phylogeography - PubMed

Processes Underlying Rabies Virus Incursions across US-Canada Border as Revealed by Whole-Genome Phylogeography

Hannah Trewby et al. Emerg Infect Dis. 2017 Sep.

Abstract

Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen's spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has invaded large areas of eastern North America. Although expansion into Canada has been largely prevented through vaccination along the US border, several outbreaks have occurred in Canada. Applying phylogeographic approaches to 289 RRV whole-genome sequences derived from isolates collected in Canada and adjacent US states, we examined the processes underlying these outbreaks. RRV incursions were attributable predominantly to systematic virus leakage of local strains across areas along the border where vaccination has been conducted but also to single stochastic events such as long-distance translocations. These results demonstrate the utility of phylogeographic analysis of pathogen genomes for understanding transboundary outbreaks.

Keywords: Canada; United States; phylogeography; rabies; raccoon rabies virus; spatial epidemiology; transboundary outbreaks; viruses; whole-genome sequencing; wildlife disease; zoonoses.

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Figures

Figure 1
Figure 1

Time-scaled maximum clade credibility phylogeny of sequenced genomes of raccoon-specific variant of rabies virus, US–Canada border. Branches are colored by inferred geographic region. Samples belonging to Canada lineages are labeled by province and year of first sample, as is backflow of infection from Canada into Vermont. Black diamonds indicate nodes with >90% posterior support. HPD, highest posterior density; NB, New Brunswick; ON, Ontario; QC, Quebec.

Figure 2
Figure 2

Distribution of coalescent times for raccoon-specific variant of rabies virus near the US–Canada border, clade I (A) and clade III (B). Gray histograms give the distribution of coalescent times for each US sample in the clade, and colored bars and labels indicate the coalescent times for the most recent common ancestor of each Canada lineage in the specified clade. Gray dashed lines indicate the 95th percentiles of the coalescent times for virus from the United States. ON, Ontario; QC, Quebec.

Figure 3
Figure 3

Locations of sequenced samples from Canada outbreaks of raccoon-specific variant of rabies virus infection in western Ontario (n = 1), eastern Ontario (n = 56), Quebec (n = 51), and New Brunswick (n = 32); and from the United States within 75 km of the border in western New York (n = 23), northwestern New York (n = 29, including 5 samples into clade I, indicated by squares), and Vermont (n = 64, including 2 samples from New York that grouped within this clade, indicated by squares); and from throughout Maine (n = 33). Map generated by using ggmap package (20). NB, New Brunswick; ON, Ontario; QC, Quebec.

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