title: Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India.
abstract: Foot-and-mouth disease virus (FMDV) serotype Asia1 was first reported in India in 1951, where three major genetic lineages (B, C and D) of this serotype have been described until now. In this study, the capsid protein coding region of serotype Asia1 viruses (n = 99) from India were analyzed, giving importance to the viruses circulating since 2007. All of the isolates (n = 50) recovered during 2007-2013 were found to group within the re-emerging cluster of lineage C (designated as sublineage C(R)). The evolutionary rate of sublineage C(R) was estimated to be slightly higher than that of the serotype as a whole, and the time of the most recent common ancestor for this cluster was estimated to be approximately 2001. In comparison to the older isolates of lineage C (1993-2001), the re-emerging viruses showed variation at eight amino acid positions, including substitutions at the antigenically critical residues VP279 and VP2131. However, no direct correlation was found between sequence variations and antigenic relationships. The number of codons under positive selection and the nature of the selection pressure varied widely among the structural proteins, implying a heterogeneous pattern of evolution in serotype Asia1. While episodic diversifying selection appears to play a major role in shaping the evolution of VP1 and VP3, selection pressure acting on codons of VP2 is largely pervasive. Further, episodic positive selection appears to be responsible for the early diversification of lineage C. Recombination events identified in the structural protein coding region indicates its probable role in adaptive evolution of serotype Asia1 viruses.
authors.affiliation: ICAR-Project Directorate on Foot and Mouth Disease, Mukteswar-Kumaon, Nainital, 263 138, Uttarakhand, India, saranvirol@gmail.com.
authors.forename: Saravanan
authors.initials: S
authors.lastname: Subramaniam
authors.forename: Jajati K
authors.initials: JK
authors.lastname: Mohapatra
authors.forename: Biswajit
authors.initials: B
authors.lastname: Das
authors.forename: Gaurav K
authors.initials: GK
authors.lastname: Sharma
authors.forename: Jitendra K
authors.initials: JK
authors.lastname: Biswal
authors.forename: Sonalika
authors.initials: S
authors.lastname: Mahajan
authors.forename: Jyoti
authors.initials: J
authors.lastname: Misri
authors.forename: Bana B
authors.initials: BB
authors.lastname: Dash
authors.forename: Bramhadev
authors.initials: B
authors.lastname: Pattnaik
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001208:Asia / Q000453:epidemiology; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics*; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology / Q000821:virology*; D019143:Evolution, Molecular; D005536:Foot-and-Mouth Disease / Q000453:epidemiology / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D014644:Genetic Variation; D007194:India / Q000453:epidemiology; D016366:Open Reading Frames; D010802:Phylogeny; D012641:Selection, Genetic; D016415:Sequence Alignment; D065288:Serogroup
chemical_list: D036022:Capsid Proteins