Evaluation of primers for PCR amplification of RNA polymerase gene sequences of foot-and-mouth disease virus

Eight oligonucleotide primers in 7 different combinations were used to amplify 3D gene sequences of foot-and-mouth disease virus (FMDV) by reverse transcription-polymerase chain reaction (RT-PCR). Six of the primers were designed at this laboratory. All the primer combinations could specifically amplify 3D gene sequences of FMDV serotypes O, A, and C. The largest fragment amplified was of 1393 bp and the smallest was of 208 bp in size. The 1393 bp fragment included sequences from the preceeding P18 region of FMDV genome. The second largest fragment of 734 bp included sequences from the 3'-extracistronic region of viral genome. The remaining fragments were amplified either from the 3'- or 5'-half of the 3D gene. Specific amplification of the entire 3D gene in fragments of different size showed sequence conservation in the 3D genomic region of FMDV and usefulness of the primers reported in detecting inapparent or persistent FMDV infection in susceptible animals by RT-PCR.