Phylogenetic analysis of bovine viral diarrhea viruses using five different genetic regions

Phylogenetic analysis of the five different regions (5′ non-coding region (5′NCR), Npro, E2, NS3 and NS5B–3′NCR) of 48 Japanese and reported bovine viral diarrhea virus (BVDV) genomes was performed. Japanese BVDVs were segregated into BVDV1 subdivided into six subgroups and BVDV2. One isolate, So CP/75, isolated in 1975 and previously proposed as subgroup 1e according to its 5′NCR sequence, was quite unique and formed an independent lineage in the tree of any region. Another isolate, 190CP, obtained from an experimental mucosal disease case was classified as subgroup 1e, defined by Becher et al. in the 5′NCR, Npro and E2 regions, whereas it was classified as subgroup 1a in the NS5B–3′NCR region. The genomic sequences of the American isolates ILLC and ILLNC obtained from the GenBank database were assigned into subgroup 1b in the 5′NCR, Npro, E2 and NS5B–3′NCR regions, whereas they were assigned into subgroup 1a in the NS3 region, suggesting that recombination between the virus strains classified into different subgroups had occurred in an animal. These findings suggest that phylogenetic analysis of several genetic regions is useful for the further characterization of field BVDV isolates.