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Classification and identification of pestivirus RNA based on secondary structures

基于二级结构的瘟病毒RNA分类与鉴定

基本信息

批准号：
09660316
负责人：
HARASAWA Ryo
金额：
$ 1.54万
依托单位：
The University of Tokyo
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
1997
资助国家：
日本
起止时间：
1997 至 1998
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-09660316/
关键词：
Pestivirus

项目摘要

Twenty cell lines of various animal origin were examined for the presence of pestivirus contamination by the reverse transcription-polymerase chain reaction, and 15 (75%) cell lines were found to be positive. The RT-PCR products of the 5' untranslated region (UTR) of pestivirus genome were sequenced and subjected to genotyping. A phylogenetic tree among pestiviruses constructed by analyzing the 5'-UTR indicated that the genetic relatedness between border disease virus (BDV) and hog cholera virus (HCV) is much closer than those between genotypes of bovine diarrhea virus (BVDV). This suggests that BDV, BVDV and HCV are host variants within a single species, which can be distinguished by comparison of secondary structures at three variable locations in the 5'-UTR.Stem-loop structures at three variable regions in the 5'-UTR render genotyping of the contaminated pestiviruses. Bovine cell lines tested were all contaminated with any of genotypes I, II or III of BVDV.Cell lines of canine, feli … More ne and primate origin were contaminated with genotype II of BVDV.Cell line ChlEs of caprine origin was contaminated with BDV.Thus a simple and practical method for pestivirus genotyping based on analysis of the secondary structures in the 5'-UTR was developed. Three stable stem-loop structures, V1, V2 and V3, predicted by computer in the 5'-UTR, included strictly conserved consensus base-pairings which are shared by all the genotypes of pestivirus or are characteristic to each genotype of pestivirus. On the basis of the palindromic nucleotide substitution at the secondary structural level, six genotypes have been identified among pestivirus strains, irrespective of the cytopathic and non-cytopathic biotypes. They are genotypes Ia, Ib, Ic and II in bovine viral diarrhea virus, genotype III in border disease virus, and genotype IV in classical swine fever virus. The stable stem-loop structures, which were maintained by palindromic nucleotide substitutions in the stem region, may represent references for the classification and identification of pestivirus species and/or genotypes. Less

通过逆转录-聚合酶链反应检查了20种不同动物来源的细胞系是否存在瘟病毒污染，发现15种（75%）细胞系呈阳性。对瘟病毒基因组5'非翻译区（UTR）的RT-PCR产物进行测序和基因分型。通过分析5 '-UTR构建的瘟病毒系统发育树表明，边界病病毒（BDV）与猪瘟病毒（HCV）之间的亲缘关系远比牛腹泻病毒（BVDV）基因型之间的亲缘关系近。这表明BDV、BVDV和HCV是同一种内的宿主变异体，其可以通过比较5 '-UTR中三个可变位置处的二级结构来区分。5'-UTR中三个可变区处的茎环结构对污染的瘟病毒进行基因分型。检测的牛细胞系均被BVDV基因型I、II或III中的任一种污染。 ...更多信息本研究建立了一种简单实用的基于5 '-UTR二级结构分析的瘟病毒基因分型方法。在5 '-UTR中，通过计算机预测的三个稳定的茎-环结构，V1，V2和V3，包括严格保守的共有碱基配对，其为所有瘟病毒基因型所共有或为每个瘟病毒基因型所特有。在二级结构水平上的回文核苷酸取代的基础上，已经在瘟病毒株中鉴定出6种基因型，而不考虑致细胞病变和非致细胞病变的生物型。它们分别是牛病毒性腹泻病毒的Ia、Ib、Ic和II基因型，边界病病毒的III基因型和猪瘟病毒的IV基因型。茎区回文核苷酸取代所维持的稳定茎环结构可作为瘟病毒种和/或基因型分类和鉴定的参考。少