The nucleotide sequence of the 5′-untranslated region of bovine viral diarrhoea virus: its use as a probe in rapid detection of bovine viral diarrhoea viruses and border disease viruses

A 289 bp cDNA fragment from the 5'-untranslated region (UTR) of 16 bovine viral diarrhoea virus (BVDV) isolates was amplified by reverse transcription and polymerase chain reaction, and sequenced by dideoxy DNA sequencing. The sequence showed greater than 90% homology between the isolates and BVDV NADL in this region, and greater than 97% homology within a 72 base sub-region (nt 314-386). The 289 bp fragment was then used as a probe for rapid detection of BVDV and border disease virus (BDV) from cell culture samples by dot-blot hybridization. This probe hybridized to 100% of BVDV isolates (n = 78) and 100% of BDV isolates (n = 9), but not to the uninfected BT cells or other bovine infectious agents. A shorter probe from the more conserved sub-region also was tested for hybridization with some of the isolates, and the results were similar to those using the longer probe. These results suggest that the 5'-UTR is highly conserved among BVDV and BDV isolates, and may be used as a potential probe for rapid detection of BVDV and BDV in clinical and cell culture samples from cattle and sheep.