Structural analysis of the untranslated reglons of Classical swine fever virus genome, and its application ot differential diagnosis

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Classical swine fever virus (CSFV), a causative agent of swine fever or hog cholera, is a species, along with Border disease virus (BDV), Bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, of the genus Pestivirus within the family Flaviviridae. The CSFV genome is a single-stranded positive sense RNA which is bracketed by untranslated regions (UTR) at the 5' and 3' ends. Sixteen clinical strains of CSFV isolated in Japan were subjected to analyses of utcleotide sequence variations in the 5' end and NS5B regions of the genome. These isolates were divided into three genovars, CSFV-1, CSFV-2, and CSFV-3, based on palindromic nucleotide substitutions (PNS) at the three variable loci in the 5'-UTR.Phylogenetic trees constructed from nucleotide sequences in the 5'-UTR and NS5B gene indicated that the CSFV strains were divided into three clusters I, II and III.CSFV strains included in the clusters I, II and III were identical to those in the CSFV-1, CSFV-2 and CSFV-3 genovars, respectively. Thus, the Japanese isolates of CSFV were found to be included in the group II (CSFV-2) as well as in the group I (CSFV-1). The Kanagawa/74 strain, along with the Okinawa/86 strain, was classified into the third cluster, CSFV-3. Secondary structures predicted at the three variable regions in the 5'-UTR showed typical PNS which were useful for classification or typing of CSFV.The identification of genetic variations based on PNS in the genome of CSFV strains within limited geographic area like an island such as Japan might improve our understandings of CSFV evolution and epizootiology, and might provide genetic markers for biological differences, such as in virulence.