Molecular phylogeny of leader proteinase gene of type A of Foot-and-mouth disease virus from India.
We previously demonstrated the presence of three genotypes (IV, VI and VII) of type A (subtype A22) of Foot-and-mouth disease virus (FMDV) in India based on 1D gene sequence analysis. In the present study, the leader proteinase (L(pro)) gene sequences of 35 type A FMDV field isolates sampled over a period of 24 years (1977-2000) have been analyzed. Maximum-likelihood (ML) phylogenetic analysis revealed four distinct genetic lineages (A-D), indicating high divergence in L gene of type A FMDV. Lineages A and D correspond to the earlier genotypes IV, and VII, respectively. The genotype VI isolates were divided into two separate lineages (B and C) in the tree with high confidence values (96-99%). One isolate (IND 21/90) showed incongruous grouping between the (1D and L) gene-based analyses, which could be due to intergenotypic recombination. The ML molecular clock hypothesis was easily rejected on the data set studied indicating the absence of clock-like evolution in the L gene. ML codon-substitution models identified positive selection in the amino acid site 194 of C-terminal extension of the Lb(pro) with high posterior probability (>99%). The catalytic triad of the L(pro) at C-51, H-148 and D-163 were conserved across all the Indian isolates studied. Finally, amino acid differences between the lineages have been discussed briefly.
Tosh
C
C
Project Directorate on Foot-and-Mouth Disease, IVRI Campus, Mukteswar-Kumaon, India. tosh64@email.com
Mittal
M
M
Sanyal
A
A
Hemadri
D
D
Bandyopadhyay
S K
SK
D000595:Amino Acid Sequence; D000818:Animals; D002020:Buffaloes; D002417:Cattle; D002418:Cattle Diseases / Q000821:virology*; D002460:Cell Line; D006224:Cricetinae; D010450:Endopeptidases / Q000737:chemistry / Q000235:genetics*; D005536:Foot-and-Mouth Disease / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics*; D007194:India; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
D010450:Endopeptidases; C088747:leader proteinase, foot-and-mouth disease virus