Genetic diversity of foot-and-mouth disease virus serotype O in Pakistan and Afghanistan, 1997-2009

► Sequencing of the foot-and-mouth disease virus VP1 coding region from samples collected in Pakistan and Afghanistan revealed the presence of least three different lineages within the ME-SA (Middle East South Asia) topotype. ► The PanAsia lineage is currently dominant in the area. ► Both PanAsia-II and a new sublineage termed PanAsia-III are co-circulating. ► The PanAsia-III sublineage has unique amino acid signature residues. ► The rate of evolution of the PanAsia-II and PanAsia-III sublineages are similar.