Detection and characterization of foot-and-mouth disease virus in sub-Saharan Africa.

Genomic amplification of the VP1 gene of SAT-type foot-and-mouth disease virus (FMDV) was performed with published and novel oligonucleotide primers. The primer pair with the highest SAT-type recognition (67%) was identified and selected for optimization. Modifications to primers significantly improved SAT-type detection (100%), broadened the recognition range to European (A, O and C) and Asian (Asia-1) serotypes and improved test sensitivity. In addition to being able to confirm the presence of FMDV in a clinical specimen within 6 h of receipt, the PCR product, which is amenable to nucleotide sequencing, enables genetic characterization of viruses into serotype and topotype within 48 h. VP1 gene sequence analysis of isolates from seven African countries and representative of five of the six serotypes occurring on the continent, revealed that SAT-types have the highest levels of intratypic variation. Intratypic variation for the SAT-types ranged from 34-40.4% on nucleotide level, and from 24.1-27.5% on amino acid level. In addition, the methodology presented here was shown to be useful for determining the origin and tracing the course of epizootics in both wild and domestic cloven-hoofed animals.