Sequence analysis of the RNA polymerase gene of foot-and-mouth disease virus serotype asia1

The complete nucleotide (nt.) sequence of the RNA polymerase (3D) gene and 81 nt. in the 3'-untranslated region of foot-and-mouth disease virus (FMDV) serotype Asia1 (IND63/72) was determined and compared with the sequence of other FMDV serotypes. The 3D genomic region was 1410 nt. long encoding 470 amino acids with an inframe stop codon (TAA) at nt. position 1411-1413. Th e deduced amino acid sequence of the protein showed 8 conserved motifs as r eported in other picornaviruses, 2 of which are 100% identical across the s erotypes. Antigenic regions in the polymerase protein were predicted and fo und to be located at the N-terminus of the protein. The phylogenetic analys is showed that the FMD viruses were segregated into different clusters base d on geographical origin; the Asia1 virus did not cluster tightly with any of the geographical groups.