Nucleotide sequence of the bovine viral diarrhoea virus Osloss strain: comparison with related viruses and identification of specific DNA probes in the 5' untranslated region

The nucleotide sequence of the cytopathic Osloss isolate of bovine viral diarrhoea virus (BVDV) was deduced from overlapping cDNA clones and from PCR products. The Osloss genome is an RNA molecule of positive polarity containing 12480 nucleotides and having the capacity to code for a polyprotein of 3975 amino acids. The presence of the previously described internal stop codon in this viral sequence was disproved after direct sequencing of the appropriate PCR-amplified fragment. Except for the previously reported insertion of a sequence coding for a ubiquitin-like protein, the viral genome shares great similarity with those of three other strains of the pestivirus genus. Computer-assisted sequence analyses and comparisons of known pestiviral genomic sequences led us to identify selected PCR primers in the 5' untranslated region. These primers were used successfully to amplify 18 distinct pestivirus isolates and potential DNA probes were noted from the deduced sequences. The possible use of a well conserved 26 base fragment as a diagnostic probe was confirmed in hybridization experiments. The 5' untranslated region was further studied and compared with those of other members of the Flaviviridae family, which includes the flaviviruses and the hepatitis C virus group. These sequence analyses support the possibility of discrimination amongst the closely related ruminant pestiviruses, border disease virus and BVDV.