Development and evaluation of Reverse Transcription-Polymer-ase Chain Reaction (RT-PCR) assay for differentiation of Foot and Mouth Disease virus serotype O lineages circulating in India

Foot and mouth disease (FMD) is endemic in India and among the three prevalent serotypes (O, A and Asial), serotype O causes majority of the FMD incidences. Phylogenetic analysis based on the VP1 coding region sequences of FMD serotype O viruses from India has revealed the circulation of two major genetic lineages (Ind2001 and Pan Asia) in recent years. Timely determination of lineage in circulation is essential for effective implementation of FMD control. In present study, a rapid and simple lineage PCR assay to differen-tiate present genetic lineages of serotype O viruses was developed and evaluated. Stretches of lineage specific signature residues were identified and primers were designed. The lineage differentiating PCR assay can be very useful for preliminary identification of serotype O lineages circulating in the country before proceeding with sequencing of VP1 coding region for confirmation, which is time consuming.