Sequence and phylogenetic analysis of the L and VP1 genes of foot-and-mouth disease virus serotype Asia1.
Most of the molecular epidemiological studies of foot-and-mouth disease virus (FMDV) are based on comparison of VP1 gene sequence. In this report, we determine the nucleotide (nt) sequence of the L (603 nt) and VP1 (633 nt) genes of 27 FMDV serotype Asia 1 isolates recovered from different outbreaks in India, and compared with each other and the vaccine strain, IND 63/72, used in the country. Independent phylogenetic analyses on both the aligned gene sequences identified two major lineages (designated A & B) in the Asia 1 isolates. Both L- and VP1-based trees were congruent with respect to the major branching pattern of the isolates. The lineage A is represented by the isolates of 1986-2000 including the vaccine strain IND 63/72, whereas, lineage B appeared to be dominant and responsible for most of the recent outbreaks. A correlation was observed between the clustering of the isolates in the phylogenetic tree and the amino acid changes at many of the positions in VP1 as well as in L protein. The annual rate of evolution in L and VP1 genes was found similar and estimated to be 4.0 x 10(-3) and 3.8 x 10(-3) substitutions per nucleotide, respectively. Our result, largely from the congruence in phylogenetic trees and the rate of evolution in both the genes, suggests the possibility for the use of L gene sequence in phylogenetic comparison of FMDV.
Mohapatra
Jajati Kesari
JK
Project Directorate on FMD Indian Veterinary Research Institute Campus, Mukteswar-Kumaon, Nainital 263 138, India
Sanyal
Aniket
A
Hemadri
Divakar
D
Tosh
Chakradhar
C
Sabarinath
G P
GP
Venkataramanan
Ramamurthy
R
D000595:Amino Acid Sequence; D001208:Asia / Q000453:epidemiology; D036022:Capsid Proteins / Q000235:genetics*; D005536:Foot-and-Mouth Disease / Q000453:epidemiology / Q000821:virology; D029544:Foot-and-Mouth Disease Virus / Q000145:classification* / Q000235:genetics; D005814:Genes, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012703:Serotyping
D036022:Capsid Proteins