Genetic and evolutionary analysis of a new Asia-4 lineage and naturally recombinant canine distemper virus strains from Thailand

Canine distemper virus (CDV), a pathogen causing fatal disease in a wide range of carnivores, can be classified into several geographically-related lineages. It is unclear how genetic recombination contributed to the evolution and emergence of the novel CDV strains and the evolutions of these strains are not fully yet investigated. In this study, the complete genome sequences of eight CDV viruses, isolated from domestic dogs in Thailand, were investigated. Interestingly, most of the identified CDV strains (CDV1-3, -5, -8 TH/2014) clustered as a novel Asia-4 lineage, while the CDV4, -6, -7 TH/2014 belonged to the Asia-1 lineage. Recombination analysis revealed that the CDV4 TH/2014 is a putative recombinant virus from the Asia-1 and America-2 parent viruses. In contrast, no recombination events were detected in the Asia-4 lineage, indicating that it is a distinctive lineage. Evolutionary analysis suggested that the CDV Asia-4 lineage had emerged since 1924 and shared common ancestor with the America-2 lineage. Pressure analysis revealed that CDV nucleotides were under negative selection pressure for its rapid adaptation. These findings demonstrate the evolution of CDV Asia-4 lineage and identified the Asia-1 recombination event. The information regarding genetic diversity of CDVs is essential for further CDV’s research and monitoring.