Genetic heterogeneity of porcine and ruminant pestiviruses mainly isolated in Japan.

The genetic variability of porcine and ruminant pestiviruses was studied by comparative nucleotide sequence analysis of 73 isolates (42 porcine and 31 ruminant), including 65 Japanese isolates (35 porcine and 30 ruminant). The 5'-untranslated region (UTR) amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) was determined by direct sequencing and phylogenetic analysis was performed from the nucleotide sequence data. Most porcine isolates were divided into two major subgroups, classical swine fever virus (CSFV) subgroup 1 (CSFV-1, represented by Brecia strain) and subgroup 2 (CSFV-2, represented by Alfort strain). However, the Japanese Kanagawa/74, Okinawa/86, Okinawa/86-2 and Thai CBR/93 strains were the most distinct variants and these were assigned to another new disparate subgroup, CSFV-3 (represented by p97 strain). Most ruminant isolates were classified as the bovine viral diarrhoea virus (BVDV) genotype-I (BVDV-I) and subdivided into two subgroups, BVDV-Ia (represented by the NADL strain) and Ib (represented by the Osloss strain). Two bovine isolates (MS-1 and SY-89) and a contaminating strain (V/FLL) from an ovine cell line were classified as BVDV genotype-II (BVDV-II) on genetic characteristics. These data suggested that the detection and phylogenetic analysis of 5'-UTRs are useful for the rapid characterization of field isolates.