Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades.
This study deals with a comparative analysis of complete genome sequences of twenty-one serotype Asia 1 foot-and-mouth disease (FMD) field viruses isolated over a period of two decades from India, two vaccine strains and seven exotic sequences. The Indian viruses could be grouped in to three distinct lineages at the entire coding region, evolving independently probably under differential selection pressure as evident from the lineage-specific signatures identified. This comparison revealed 80% of amino acids at the polyprotein region to be invariant. Twenty-one residues in L, 3A and P1 region were identified to be under positive selection of which some are antigenically critical. Analysis at functionally crucial motifs, receptor contact residues, polyprotein cleavage sites and at putative T-cell epitopes expands the knowledge beyond other serotypes. Antigenic site II in betaB-betaC loop of VP2 was highly unstable suggesting its exposure to extreme immune pressure. A single cross-over at the L proteinase region in an isolate from buffalo, also featuring an extensive deletion at the 5' untranslated region (UTR), reflects the role of intraserotypic genetic recombination in natural evolution. The likely biological relevance of deletions/insertions observed at UTRs, VP1 and 3A could not be deduced. Altogether, a substantial amount of data raised on full length genomes of type Asia 1 virus adds value to the FMD virus genomics.
Foot-and-Mouth Disease, Indian Veterinary Research Institute Campus, Mukteswar-Kumaon, Nainital 263138, Uttarakhand, India.
Jajati K
JK
Mohapatra
Aniket
A
Sanyal
Divakar
D
Hemadri
Chakradhar
C
Tosh
Subhajit
S
Biswas
Nick J
NJ
Knowles
Thaha J
TJ
Rasool
Santanu K
SK
Bandyopadhyay
Bramhadev
B
Pattnaik
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D000956:Antigens, Viral / Q000235:genetics / Q000276:immunology; D001483:Base Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005536:Foot-and-Mouth Disease / Q000453:epidemiology* / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000145:classification* / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification; D016679:Genome, Viral; D005838:Genotype; D007194:India / Q000453:epidemiology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D017385:Sequence Homology; D012703:Serotyping; D014764:Viral Proteins / Q000235:genetics / Q000276:immunology
D000956:Antigens, Viral; D012367:RNA, Viral; D014764:Viral Proteins