Sequencing and genetic analysis of the VP1 gene of type A FMDV strains isolated in Ha Noi City and Ha Tinh province in 2013

Abstract

Epidemiological characterization studies based on molecular analyses and decoding of VP1 gene of the foot and mouth disease virus (FMDV) strains circulating in the world showed that FMDV type A was classified into 10 major genotypes (I–X). In this study, VP1 gene sequences of the three FMD virus strains (isolated in Ha Noi and Ha Tinh in 2013) signing A/VN/HN15/2013, A/VN/HN16/2013, and A/VN/HT21/2013 were analyzed. The result of phylogenetic analysis revealed that all of three type A FMD virus strains in this study belonged to genotype IX, a common genotype circulating in the recent years in Viet Nam. The result of analyzing nucleotide (nt) and amino acid (aa) sequences of these virus strains also indicated that similarity and identity levels of their nt and aa sequences were very high, reaching 100%. However, these similarity levels comparing with those of the other Vietnamese type A FMD virus strains in GenBank were lower, which were 89.7 – 91.5% (for nt) and 90.9 – 94.9% (for aa).