Evolutionary dynamics of foot-and-mouth disease virus O/ME-SA/Ind2001 lineage

•Phylogenetic analysis of Ind2001 lineage revealed two major splits and three sub-lineages.•The mean nucleotide substitution rate was calculated to be 6.338×10−3.•Intra-epidemic antigenic diversity was evident.•Periodic emergence and re-emergence of Ind2001 and PanAsia lineage. Foot-and-mouth disease (FMD) virus serotype O Ind2001 lineage within the Middle East–South Asia topotype is the major cause of recent FMD incidences in India. A sub-lineage of Ind2001 caused severe outbreaks in the southern region of the country during 2013 and also reported for the first time from Libya. In this study, we conducted a detailed evolutionary analysis of Ind2001 lineage. Phylogenetic analysis of Ind2001 lineage based on maximum likelihood method revealed two major splits and three sub-lineages. The mean nucleotide substitution rate for this lineage was calculated to be 6.338×10−3substitutions/site/year (s/s/y), which is similar to those of PanAsian sub-lineages. Evolutionary time scale analysis indicated that the Ind2001 lineage might have originated in 1989. The sub-lineage Ind2001d that caused 2013 outbreaks seems to be relatively more divergent genetically from other Ind2001 sub-lineages. Seven codons in the VP1 region of Ind2001 were found to be under positive selection. Four out of 24 recent Ind2001 strains tested in 2D-MNT had antigenic relationship value of