NUCLEOTIDE-SEQUENCE OF THE BOVINE VIRAL DIARRHEA 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 vir al diarrhoea virus (BVDV) was deduced from overlapping cDNA clones and from PCR products. The Osloss genome is an RNA molecule of positive p olarity containing 12480 nucleotides and having the capacity to code f or a polyprotein of 3975 amino acids. The presence of the previously d escribed internal stop codon in this viral sequence was disproved afte r direct sequencing of the appropriate PCR-amplified fragment. Except for the previously reported insertion of a sequence coding for a ubiqu itin-like protein, the viral genome shares great similarity with those of three other strains of the pestivirus genus. Computer-assisted seq uence analyses and comparisons of known pestiviral genomic sequences l ed 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 sequenc es. The possible use of a well conserved 26 base fragment as a diagnos tic probe was confirmed in hybridization experiments. The 5' untransla ted region was further studied and compared with those of other member s of the Flaviviridae family, which includes the flaviviruses and the hepatitis C virus group. These sequence analyses support the possibili ty of discrimination amongst the closely related ruminant pestiviruses , border disease virus and BVDV.