An internal duplication in the 5' noncoding region of strain H: a bovine viral diarrhoea virus (BVDV) isolated from pigs.

A pig pestivirus isolate, strain H, was characterized by using reverse transcription-PCR (RT-PCR) and direct sequencing of the amplicons. A duplication of 74 nucleotides was found at the 5' terminus of the 5' noncoding (NC) region, which was also found in RNA isolates from tonsils from two other pigs from the same farm. When the duplication was omitted, the 5' NC region showed 97.8% similarity to bovine viral diarrhoea virus (BVDV) strain Korevaar and 94% to BVDV strain Osloss. Furthermore, the rearrangement of the 5' NC region of strain H was maintained after passaging in different cell lines and is not common for ruminant-like pestivirus isolated from pigs. Phylogenetic analysis based on the deduced amino acid sequence of the E2 gene of strain H confirmed the findings of the 5' NC region and show that this strain belongs to the BVDVIb subgroup. These results show for the first time rearrangements in the 5' NC region of a pestivirus.