Genetic characterization of a caprine Pestivirus as the first member of a putative novel pestivirus subgroup

Currently, the genus Pestivirus comprises four approved species, namely bovine viral diarrhoea viruses 1 and 2 (BVDV-1, BVDV-2), classical swine fever virus and border disease virus (BDV). Recently, three major genotypes have been identified within the species BDV and termed as subgroups BDV-1, BDV-2 and BDV-3. Here, an isolate from animals in a herd showing BD-like syndromes, which occurred in central Italy was analysed. A reverse transcriptase polymerase chain reaction was performed using primers that specifically amplify a fragment of the 5'-non-coding region (5'-NCR) from BDV. Both the 5'-NCR fragment and the entire N-pro gene were sequenced and used for genetic typing. The 5'-NCR sequence revealed that the newly isolated Pestivirus could be allocated to the BDV species. Interestingly, the N-pro sequence of this virus isolate significantly differed from all the ovine pestiviruses previously described, providing evidence for the presence of an additional subgroup within the species BDV.