Genetic targets for the detection and identification of Venezuelan equine encephalitis viruses

Rt-PCR probes targeted to different gene sequences of VEE (Venezuelan equine encephalitis) virus strain TC-83 were assessed for their sensitivity, specificity and non-specific cross-reactivity. A generic VEE virus amplimer (VNSP4F2/VNSP4R2), targeted against nsP4 was identified, which was sensitive (detected at least 10 pfu) and robust (worked over a wide range of salt concentrations and annealing temperatures). An E2 amplimer designed against TC-83, (VE2F/VE2R), identified VEE strains TRD (1AB), P676 (1C), 3880 (1D) Everglades (2) vRNA whilst a second E2 primer pair designed against strain 68U201, (68UF/68UR), identified all the remaining VEE viruses in the sere-complex. This would suggest that the VEE virus E2 gene can be sub-divided at the genetic level into two separate groups making it a useful target for differentiation of sero-subtypes 1 and 2 from the other VEE virus subtype. Using a panel of amplimers targeted to different VEE genes and strains it was possible to distinguish between most of the serotypes, but most importantly, we were able to detect the epizootic strains TRD and P676 as well as other VEE viruses implicated in human disease (sero-subtypes 1D and 1E).