A RT-PCR assay for the rapid recognition of border disease virus.

A reverse transcription--polymerase chain reaction (RT-PCR) method was developed for the specific detection of border disease virus (BDV), using the primers PBD1 and PBD2 flanking a 225 bp DNA fragment, selected from the 5'noncoding region of the pestivirus genome. In tests on 70 pestiviruses it was shown to be BDV-specific. A closed, one-tube nested RT-PCR method employing general pestivirus outer primers (324 and 326), and the same BDV-specific inner primers (PBD1 and PBD2) in conjunction with a BDV-specific fluorogenic TaqMan probe also detected only BDV and was more sensitive. BDV-specific RT-PCR was used in combination with a PCR specific for bovine viral diarrhoea virus type 2 (BVDV2) to ascertain whether virus stocks contained mixtures of BDV and BVDV2. It was shown that the ovine pestivirus strains 175375 and 59386 were originally BDV, but after subculture had become contaminated with BVDV2. This explains a previously reported discrepancy in the genetic typing of 59386. Although the BDV-specific RT-PCR can also detect BDV in clinical samples, the assay is likely to be most useful for the rapid typing of laboratory pestivirus strains.