Evidence of two co-circulating genetic lineages of canine distemper virus in South America

► Genetic diversity in the full-length H gene sequence permits the identification of different canine distemper virus (CDV) lineages. ► Two co-circulating lineages were detected in South America: the Europe 1 lineage and a new South America 2 lineage. ► South America 2 lineage may be a lineage circulating in wild populations in South American countries. ► South American CDV strain showed high amino-acid divergence in comparison with the vaccine strains.