title: Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario.
abstract: Raccoon rabies remains a serious public health problem throughout much of the eastern seaboard of North America due to the urban nature of the reservoir host and the many challenges inherent in multi-jurisdictional efforts to administer co-ordinated and comprehensive wildlife rabies control programmes. Better understanding of the mechanisms of spread of rabies virus can play a significant role in guiding such control efforts. To facilitate a detailed molecular epidemiological study of raccoon rabies virus movements across eastern North America, we developed a methodology to efficiently determine whole genome sequences of hundreds of viral samples. The workflow combines the generation of a limited number of overlapping amplicons covering the complete viral genome and use of high throughput sequencing technology. The value of this approach is demonstrated through a retrospective phylogenetic analysis of an outbreak of raccoon rabies which occurred in the province of Ontario between 1999 and 2005. As demonstrated by the number of single nucleotide polymorphisms detected, whole genome sequence data were far more effective than single gene sequences in discriminating between samples and this facilitated the generation of more robust and informative phylogenies that yielded insights into the spatio-temporal pattern of viral spread. With minor modification this approach could be applied to other rabies virus variants thereby facilitating greatly improved phylogenetic inference and thus better understanding of the spread of this serious zoonotic disease. Such information will inform the most appropriate strategies for rabies control in wildlife reservoirs.
authors.affiliation: Animal Health Microbiology Research, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada. Electronic address: susan.nadin-davis@inspection.gc.ca.
authors.forename: Susan A
authors.initials: SA
authors.lastname: Nadin-Davis
authors.affiliation: Animal Health Microbiology Research, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada. Electronic address: adam.colville@inspection.gc.ca.
authors.forename: Adam
authors.initials: A
authors.lastname: Colville
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK. Electronic address: hannah.trewby@glasgow.ac.uk.
authors.forename: Hannah
authors.initials: H
authors.lastname: Trewby
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK. Electronic address: roman.biek@glasgow.ac.uk.
authors.forename: Roman
authors.initials: R
authors.lastname: Biek
authors.affiliation: Department of Biology, Emory University, Atlanta, GA 30322, United States. Electronic address: lreal@emory.edu.
authors.forename: Leslie
authors.initials: L
authors.lastname: Real
mesh_terms: D000818:Animals; D004196:Disease Outbreaks; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D009864:Ontario / Q000453:epidemiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011818:Rabies / Q000453:epidemiology / Q000635:transmission / Q000662:veterinary* / Q000821:virology; D011820:Rabies virus / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D011821:Raccoons / Q000821:virology*; D012189:Retrospective Studies; D015047:Zoonoses / Q000453:epidemiology* / Q000635:transmission / Q000821:virology
keywords: Illumina next generation sequencing; Molecular epidemiology; Raccoon rabies virus; Viral phylogeny