Comparative sequence analysis of representative foot-and-mouth disease virus genomes from Southeast Asia

Foot-and-mouth disease (FMD) is endemic in mainland Southeast Asia where up to seven genetically distinct viral lineages co-circulate (O/SEA/Mya-98, O/SEA/Cam-94, O/ME-SA/PanAsia, O/ME-SA/PanAsia-2, O/CATHAY, A/ASIA/Sea-97, and serotype Asia 1). The aim of this study was to analyse the sequence variability between representative complete genomes for these seven lineages. The genome sequences varied from 8130 to 8192 nucleotides in length and shared nucleotide identities ranging from 91.8 to 78.9%. Broad-scale differences such as block and codon deletions observed in these genomes paralleled features that have been reported previously for other FMDV sequences from Southeast Asia. Comparison between these sequences revealed the presence of 2501 variant sites which were more evident in regions encoding surface capsid proteins (VP2, VP3 and VP1) compared to regions encoding non-structural proteins. Specific comparisons between closely related O/ME-SA sequences showed that the distribution of variant sites was focussed particularly at the 5' end of the genome indicating that recombination may have occurred during the evolution of the O/ME-SA/PanAsia-2 lineage. These sequences provide insights into the evolutionary mechanisms by which new lineages generate genetic and antigenic novelty in the region and will form the basis of studies to define the spatio-temporal epidemiology of FMDV.