Evidence of homologous recombination in canine distemper virus, a non-segmented negative sense RNA virus

Canine distemper virus (CDV) is a major pathogen of dogs that belongs to the genus Morbillivirus of the family Paramyxoviridae. It has a non-segmented single-stranded negative sense RNA genome and can cause severe disease in dogs and wild carnivores. Although homologous recombination has been demonstrated in many members of Paramyxoviridae, for CDV, these events are rarely reported. To detect possible recombination events, all the complete CDV genomes available in GenBank up to August 2014 were screened using distinct algorithms to detect genetic conversions and incongruent phylogenies. Eight putative recombinant viruses derived from different CDV genotypes and also from different hosts were detected. The breakpoints of the recombinant strains were located mainly on the fusion and the hemagglutinin glycoproteins. Our work reinforces that homologous recombination is a frequent phenomena in morbillivirus populations under natural replication and suggests that CDV vaccine strains can play an important role in shaping the evolution of this virus.