Phylogenetic and genotypic characteristics of the foot-and-mouth disease virus from outbreaks in southern Vietnam, 2019

In 2019, multiple FMD outbreaks occurred in swine farms vaccinated against FMDV in southern Vietnam. This study investigated the genotypic characteristics of FMDV strains from these outbreaks. Seven samples were collected from pigs exhibiting FMD clinical signs. All FMDV-positive samples were amplified and sequenced for the gene encoding the VP1. Results were analyzed and compared with sequences of reference strains and vaccine strains on GenBank. Phylogenetic analysis showed that all seven field isolates belonged to serotype O, topotype SEA/Mya-98. These strains shared high homology with strains from Vietnam (2018), Korea, and China, but low homology with vaccine strains. Moreover, 21 amino acid substitutions were found in the VP1 protein of the FMDV field strains, many of which were crucial antigenic determinants involved in the neutralization of FMDV. These findings suggest that the current vaccine may not be effective against the emerging FMDV strains in southern Vietnam. •Foot-and-Mouth Disease virus (FMDV) infection was prevalent in swine farms.•FMDV was identified in farms that had been immunized against CSFV.•The VP1 of FMDV strains circulating and vaccine strains differ in their antigenicity.•Antigenic changes in the VP1 of FMDV strains may give a plausible explanation for the present vaccination efforts' failures.