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

经典猪瘟病毒（CSFV）是猪瘟或猪瘟的病原体，与边境病病毒（BDV）、牛病毒性腹泻病毒1 （BVDV-1）和BVDV-2一起属于黄病毒科鼠疫病毒属。猪瘟病毒基因组是一种单链阳性RNA，在5‘和3’端被未翻译区（UTR）包围。对日本分离的16株CSFV临床毒株进行了基因组5′端和NS5B区核苷酸序列变异分析。根据5'-UTR中三个可变位点的回文核苷酸替换（PNS），将这些分离株分为CSFV-1、CSFV-2和CSFV-3三个基因型。根据5′-UTR和NS5B基因的核苷酸序列构建的系统进化树显示，该猪瘟病毒可分为3个集群I、II和III。聚类ⅰ、ⅱ和ⅲ的猪瘟毒株分别与猪瘟ⅰ、ⅱ和ⅲ基因型相同。因此，发现日本分离的猪瘟病毒既属于II组（CSFV-2），也属于I组（CSFV-1）。神奈川/74株与冲绳/86株被归为第三类CSFV-3。在5'-UTR的三个可变区域预测的二级结构显示典型的PNS，这对猪瘟的分类或分型有用。基于PNS的猪瘟病毒基因组遗传变异鉴定可能会提高我们对猪瘟病毒进化和流行病学的理解，并可能为诸如毒力等生物学差异提供遗传标记。

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.