Detection and genotyping of bovine diarrhea virus by reverse transcription-polymerase chain amplification of the 5′ untranslated region

A reverse-transcription polymerase chain reaction (RT-PCR) was developed to differentiate the bovine diarrhea virus (BVDV) from other pestiviruses, and to determine the genotype of the BVDV isolates. For this purpose, primer pairs were selected in the 5′ untranslated region (5′UTR). The primers B(E) and B(2) were located in highly conserved regions and were pestivirus-specific. Two primer pairs named B(3)B(4) and B(5)B(6) were specific of BVDV genotypes I and II, respectively. With this technique, an amplification product of the expected size was obtained with either the B(3)B(4) or the B(5)B(6) primer pairs for the 107 BVDV isolates tested but not for BDV or CSFV. For some isolates that were grouped in the genotype II, sequence analysis of the PCR fragments confirmed their classification into this genotype.