Direct typing and molecular evolutionary analysis of field samples of foot-and-mouth disease virus collected in Viet Nam between 2006 and 2007

In this study, we used universal or duplex serotype-specific (O and Asia 1) RT-PCR to analyze clinical field samples of foot-and-mouth disease virus (FMDV) or virus isolates collected in Viet Nam between 2006 and 2007. We found viral serotypes O and Asia 1 circulating concurrently during this period. Direct sequencing of type-specific RT-PCR products revealed the existence of three different topotypes of serotype O: Southeast Asia (SEA), Middle East-South Asia (ME-SA), and Cathay. Of these, SEA was most prevalent during the period. All samples of serotype Asia 1 belonged to genetic group V. Based on the rooted maximum likelihood phylogenetic trees inferred from the VP1 region, new lineages in topotype SEA were originating from Viet Nam, and group V strains of Asia 1 have undergone fewer passages from the common ancestor, compared with other genetic groups. The co-circulation of different types of FMDV may complicate the individual or population genomic structures of FMDV and make conventional multiplex diagnostic methods and phylogenetic analyses with relevant evolutionary models essential in Viet Nam.