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Historically, the genus pestivirus was believed to contain three species of viruses; bovine viral diarrhea virus (BVDV), border disease virus (BDV) and classical swine fever virus (CSFV). However, based on limited sequence analysis of a small number of pestiviral isolates from domestic livestock, evidence has recently emerged indicating that at least four distinct genotypes exist. In an attempt to gain a better understanding of the degree of viral variation among ruminant pestiviruses, the entire structural gene coding region of an ovine pestivirus. BD31, genome encompassing 3358 nucleotides was cloned and sequenced. Sequence analysis revealed that BD31 shares less than 71% nucleotide similarity with other pestiviruses, suggesting, that BD31 is distinct from BVDV, CSFV as well as other ovine and bovine pestiviruses currently referred to as BVDV type II. Based on this data, BD31 is the first North American pestivirus isolate that falls under the category true BDV. Results from the analysis of the nucleotide sequence of the E0-E1 coding region of six additional ruminant pestiviruses identified the existence of three distinct virus genotypes in North America. Thus, among ruminent pestiviruses, bovine isolates can be grouped into two genotypes, namely types 1 and 4, whereas ovine isolates fall into genotypes 1, 3 and 4.

Viruses that comprise the Pestivirus genus cause significant losses to the livestock industry. Based on sequence analysis, currently 4 distinct genotypes are identified of which 3 infect cattle and sheep. Distinguishing between bovine and ovine isolates by serological tests has often been difficult because of a high degree of cross reactivity. In this study, a nested polymerase chain reaction (PCR) assay was developed to identify and distinguish between bovine viral diarrhea virus (BVDV) type I, BVDV type II, as well as border disease virus (BDV) genotypes. Consensus oligonucleotide primers were designed to amplify a 826-bp product from any of the 3 pestivirus types in a reverse transcription-PCR (RT-PCR). This product was subjected to a second round of nested PCR with type-specific primers which yielded DNA products of unique size characteristic for each pestivirus genotype. Using this assay, we were able to rapidly characterize several viral isolates and determine that all 3 genotypes can be found among ovine isolates.

Border disease virus (BDV) of sheep, an important ovine pathogen, is serologically related to the two other well characterized members of the Pestivirus genus of the Flaviviridae family, namely bovine viral diarrhea virus (BVDV) and hog cholera virus (HoCV). To determine its genetic relationship to BVDV and HoCV, the genome of BDV strain, BD-78 encompassing the 5' untranslated region (UTR) and structural gene coding region was molecularly cloned and the nucleotide sequence determined. The sequenced region of 3,567 nucleotides contained one open reading frame encoding 1063 amino acids. The nucleotide and amino acid sequences of BD-78 were compared with those of two BVDV strains NADL and SD-1, and the Alfort and Brescia strains of HoCV. The overall nucleotide sequence homologies of the region sequenced of BD-78 are 68.3% with BVDV-NADL, 67.8% with BVDV-SD-1, 69.0% with HoCV-Brescia, and 65.8% with HoCV-Alfort. The overall amino acid sequence homologies of BD-78 are 76.1% with NADL, 76.5% with SD-1, 74.2% with Brescia, and 72.9% with Alfort. The most conserved nucleotide and amino acid sequences between BD-78 and the other pestivirueses are in the 5' UTR and the capsid protein coding region (p14), where as the most divergent sequences are in the E2 coding region. These findings suggest that BDV is a unique virus in the Pestivirus genus.