GENETIC-HETEROGENEITY OF INDIAN FIELD ISOLATES OF FOOT-AND-MOUTH-DISEASE VIRUS SEROTYPE O AS REVEALED BY PARTIAL SEQUENCING OF ID GENE

The sequence of 165 nucleotides at the 3' end of the 1D gene, determin ed from RT-PCR amplified cDNA fragments, of 25 type O strains isolated from different parts/regions of India during 1987-1995 and the vaccin e strain (R2/75) currently in use in India were subjected to phylogene tic analysis. One isolate from the neighbouring country Nepal was also included in the study. The virus/field strains showed high degree of genetic heterogeneity among themselves with % divergence in nucleotide sequence ranging from 1.2 co 19.4%. The Indian strains were much away (13.3-20.6%) from the exotic type O strains of 01BFS, 01K, and 01Camp os. The type O strains analyzed were classified into three genotypes b asing on level of divergence observed in nucleotide sequence. The type O vaccine virus (R2/75) was > 7% divergent (7.3-15.2%) from the field strains which revealed significant (> 5%) genetic heterogeneity betwe en the two. The phylogenetic analysis identified three distinct lineag es, viz., (i) lineage 1 represented by the exotic strains, (ii) lineag e 2 represented by 25 of the held strains which clustered into seven s ubgroups/sublines (2a-2g), and (iii) lineage 3 represented by a unique field isolate which shared the branching/origin with the vaccine stra in. The lineage 2 which comprised of 25 of the 26 type O field strains analyzed, was placed almost at equidistance from the lineages 1 and 3 in the phylogenetic tree. The vaccine strain was closer to the viruse s in lineage 2. Though there was no specific distribution pattern of s equences in different geographical regions of India, the viruses/ sequ ences in subgroup 2f appeared to be restricted to the southern states. Comparison of deduced amino acid sequence in the immunodominant regio ns 133-160 and 200-208 of the 1D gene product (VP1) showed that the tw o viruses in lineage 3 had unique amino acid residues at the positions 138 (D), 139 (G), 144 (I), and 158 (A) compared to rest of the strain s including the exotic ones. Comparison of amino acid residues at crit ical positions 144, 148, 149, 151, 153, 154, and 208 revealed similari ty between the type O strains analyzed. The virus strains showed varia tion (V/L/I) at position 144. One field strain showed replacement from Q(149) --> E and another from P-208 --> L. Thus, the study revealed t hat the type O FMD virus populations circulating in India and causing disease outbreaks are genetically much heterogeneous but related at th e immunodominant region of VP1 polypeptide, and there are more than on e genetically distinct virus populations in almost every region of the country which is possible due to unrestricted animal movement in the country. The involvement of vaccine virus in disease outbreaks was rul ed out as the field strains (excluding the one in lineage 3) were phyl ogenetically distinct from it. (C) 1998 Elsevier Science B.V. All righ ts reserved.