台灣豬瘟病毒之親緣演化樹分析Phylogenetic analysis of classical swine fever virus in Taiwan
潘居祥； 鍾明華；黃天祥；劉信孚；林士鈺；賴秀穗
將1989 至 2003 年收集到的158 個豬瘟病例針對Erns 及E2 封套醣蛋白基因，以RT -PCR增幅此兩區間並進行核酸定序及親緣演化樹分析。雖然兩者出現類似的樹形圖，但Erns 比E2具有更好的區別效果。親緣演化樹分析結果顯示，115個田間分離株歸屬於2.1亞群，又可進一步區分為2.1a 及2.1b，且此兩亞群都被認為是外來型病毒株，其餘的43個田間分離株屬於3.4亞群，被認為是本土型病毒株。2.1a 亞群病毒株最早發現於1994年，且於1995年以後成為田間優勢族群，然而3.4 亞群病毒株盛行於1994 年以前，但自1996 年以後就無法從田間分離到。過去十餘年，我們戲劇性地看到台灣田間流行的豬瘟病毒從3.4亞群轉變成2.1a 亞群，但不是從本土型病毒株的基因突變所造成。從基因庫資料分析發現，2.1a 亞群與德國分離株Paderborn 及寮國分離株L67 最相近，然而2.1b 亞群與中國廣西省分離株最為相近。另針對完整的封套醣蛋白Erns 、E1 及E2 以樹形圖分析27 個豬瘟病毒核酸序列，結果發現此區間相較於全長的開放讀碼區(ORF)更具有良好的區別效果。
Two envelope glycoprotein (Erns and E2) regions of the classical swine fever virus (CSFV) were amplified by RT-PCR and sequenced directly from 158 specimens collected between 1989 and 2003 in Taiwan. Phylogenetic analysis of the two regions revealed a similar tree topology and the Erns region provided better discrimination than the E2 region. One hundred and fifteen isolates out of the 158 isolates were clustered within subgroup 2.1 (further classified as 2.1a and 2.1b) and 2.2, which were considered to be likely of the introduced strains, whereas the remaining 43 isolates were clustered within subgroup 3.4 and were considered to be of the endemic strains. The subgroup 2.1a viruses were first detected in 1994 and predominated from 1995 onwards. However, subgroup 3.4 viruses were prevalent in the early years, not being isolated after 1996. We have observed a dramatic switch in genotype from subgroup 3.4 to 2.1a. The subgroup 2.1a isolates are closely related to the Paderborn and Lao isolates, whereas 2.1b isolates have a close relationship to the Chinese Guangxi isolates. The phylogenetic tree of 27 CSFV sequences based on the complete envelope glycoprotein gene (Erns–E2) displayed better resolution than that based on the complete open reading frame.
年份：西元 2004 年
期別：第 40 期
Classical swine fever (CSF), previously referred to as hog cholera, is a significant infectious disease of swine caused by classical swine fever virus (CSFV).The causative agent of CSFV belongs to the genus Pestivirus within the family Flaviviridae [21]. The genome of CSFV consists of a positive-stranded RNA approximately 12.3 kb in length, and comprises a single large open reading frame (ORF) spanning 11,694 nucleotides that encode a polyprotein composed of 3,898 amino acids [20]. The polyprotein is proteolytically processed to produce both structural and nonstructural polypeptides [25]. The viral proteins are arranged in the following order (from the N to the C terminal): Npro, C, Erns, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A and NS5B. The structural proteins represented by the capsid protein, C and three envelope glycoproteins, Erns, E1 and E2, while the remaining proteins are presumably nonstructural proteins [21]. Three glycoproteins are associated with the envelope of the virion [32].　　Phylogenetic analysis of different regions of the viral genome pertaining to the molecular discrimination of CSFV isolates has previously been reported. The regions analyzed include the 5_NTR [6, 7, 10, 18, 27, 28], E2 [18, 19, 33], NS5B [3], 5_NTR and E2 [1, 8], 5_NTR, E2 and NS5B [18, 24], 5_NTR and NS5B [9], E1/E2 [17, 37], E2 and NS5B [34, 35], 5_NTR, E2/NS2 and NS2 [29], 3_NTR [2, 36], and the complete open reading frame (ORF) [22]. Three regions of the CSFV genome (5_NTR, E2 and NS5B) have been widely sequenced and used in genetic analyses to investigate the diversity among isolates.Atentative assignment of world isolates of CSFV by genotyping has been divided it into three groups with three or four subgroups: 1.1, 1.2, 1.3; 2.1, 2.2, 2.3; 3.1, 3.2, 3.3, 3.4 [24].　　Molecular epidemiological analyses of CSFV isolates distributed in the world are a useful to trace the geographic origins of CSFV and to understand how they spread.A large epidemic of CSF outbreaks occurred in the European Community at the beginning of 1997. The disease presumably spread to the Netherlands, Italy, Spain, and eventually to Belgium [8]. Sequence analysis based on 5_NTR and E1/E2 regions revealed that the isolates of the Dutch outbreaks of 1997–1998 were closely linked to a small CSF outbreak at Paderborn, Germany in 1996 [37]. Analysis of the E2 and partial 5_NTR sequence data showed that the Paderborn isolate (subgroup 2.1) triggered the Dutch outbreak [22].　　Records of CSF in Taiwan date back to 1938 during occupancy by Japan. In an effort to control this highly contagious disease, the live attenuated lapinized hog cholera vaccine strain (LPC) has been widely used in the field since 1958. Vaccination significantly decreased the rate of occurrence. However sporadic outbreaks were still reported every year. The aim of thisworkwas to analyze the phylogenetic relationship of CSFV isolates collected in Taiwan between 1989 and 2003.