Partial sequence analysis of VP1 of Indian isolates of foot-and-mouth disease virus type Asia-1

Nucleotide sequence of 3' end of VP1 (1D region) was determined using RT-PCR amplified DNA of 31 foot and mouth disease virus (FMDV) type Asia-1 field isolates originating from 11 different geographically distinct states of India during the period 1987-2000. These field strains exhibited an average of 7.5% divergence among them and were found to be divergent from the Indian vaccine strains Asia-1 WBN 117/85, IND 8/79, and IND 63/72, by an average 5.9, 14.8, and 7.4% divergence, respectively. Phylogenetic analysis of these 31 field isolates including 3 of the vaccine strains of India and sequences of 22 Indian field isolates obtained from the GenBank revealed that all the Indian FMDV type Asia-1 isolates belonged to a single genotype comprising of two distinct lineages (Lineages A and B). All the field isolates under study belonged to the Lineage-B comprising 8 different clusters, which also includes the vaccine strains WBN-117/85 and IND 8/79. Surprisingly, another vaccine strain IND 63/72 formed Lineage-A. Phylogenetic analysis of sequences of another 23 exotic type Asia-1 isolates from 15 different countries obtained from the GenBank along with the 56 Indian isolates revealed the existence of three distinct genotypes. The prototype strain Asia-1 PAK 1/54 belongs to a separate genotype. Two strains from India along with one strain each from China and Russia belongs to another genotype. The third genotype is formed by the remaining isolates including all the 31 isolates from the present study and exotic viruses from 14 other different countries. Comparison of deduced amino acid (aa) sequence indicated that majority of the mutations were found within two distinct regions corresponding to amino acid positions 130-160 and 193-211. The motif at aa positions 138-141 in vaccine strains WBN 117/85, IND 8/79 and in all the field isolates was ETTS/P; however, the same motif in IND 63/72 was TQPT. The motif 153-156 in majority of Indian isolates including vaccine strains WBN 117/85 and IND 8/79 was LSGQ/R whereas the same motif seen in IND 63/72 was VSNR. The study revealed that the FMDV type Asia-1 isolates circulating in the country are not highly heterogeneous, but showed considerable genetic variations. Certain mutations were also observed in the residues, which have been proved to be contributing to the formation of neutralizing epitopes. In neutralization studies employing polyclonal antisera, type Asia-1 WBN 117/85 revealed broader serological spectrum than other vaccine strains of India used in this study.