Phylogenetic analysis of West Nile virus in Quebec, Canada, 2004–2016: Co-circulation of distinct variants harbouring conserved amino acid motifs in North America

West Nile virus (WNV) was introduced for the first time in the western hemisphere in 1999 in New York City. In 2002, a phenotype-modifying mutation (Env-V159A) defined the first North American genotype WN02. So far, three genotypes has been described in North America but little is known about WNV evolution in Canada. We report the phylogenetic characterization of twenty-six WNV genomes isolated from mosquitoes in the province of Quebec. WNV strains found in Quebec are phylogenetically related to American strains collected in northern and southern regions. We also noted the presence of two robust monophyletic groups of isolates characterized by distinct conserved amino acid motifs. These emerging genotypes were detected for several years in different ecosystems. These results highlight the need for the maintenance of a nationwide surveillance to follow the dispersion of emergent WNV genotypes.