Species characterization in the genus Pestivirus according to palindromic nucleotide substitutions in the 5′-untranslated region
Species characterization in the genus Pestivirus according to palindromic nucleotide substitutions in the 5′-untranslated region
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DOI：
10.1016/j.jviromet.2011.04.004
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发表时间：
2011-06-01
影响因子：
3.1
通讯作者：
Harasawa, Ryo
中科院分区：
文献类型：
--
作者：
Giangaspero, Massimo;Harasawa, Ryo
通过对534株瘟病毒的分析，发现瘟病毒基因组5 '端非翻译区（UTR）的3个可变位点（V1、V2和V3）上的回文核苷酸替换（PNS）可用于瘟病毒的分类学分离。在定性和定量二级结构特征的基础上，在属内鉴定了种，确定了种分离物之间的遗传距离，澄清了边界和多相关序列，并对显示出意外基因组序列的瘟病毒株进行了表征和聚类。已经确定了九个基因组：牛病毒性腹泻病毒1型（BVDV-1）、牛病毒性腹泻病毒2型（BVDV-2）、边境病病毒（BDV）和猪瘟病毒（CSFV）种属和试验种属叉角羚、长颈鹿、牛病毒性腹泻病毒3型（BVDV-3）（HoBi组），边界病病毒2（BDV-2）回文位置已经根据识别低可变位置（LVP）的核苷酸碱基对的变化来表征，所述低可变位置包括碱基-对存在于少于80%的属中。单菌株序列或遗传组之间的分歧的确定很容易通过比较从对齐的二级结构的碱基配对组合。这提供了明确的信息，如物种内的异质性水平，物种之间的相关性，或促进特定菌株的表征和聚类。BVDV-1和BDV种属具有异质性，显示分离株位于种属的边界上。在BVDV-2种属内，鉴别出两个主要基因组，两组菌株显示出共同的序列特征（多相关菌株）。通过定量分析可以正确分配它们。CSFV与BDV的亲缘关系也很明显。此外，在这种情况下，模糊的菌株序列可以聚类在物种中显示最低的divergence.In结论，建议的分类程序是基于只有在5 '-UTR的战略和高度保守的基因组区域的评估此外，定量分析程序的应用允许更好地确定物种之间的关系。(C)2011爱思唯尔有限公司版权所有。
The palindromic nucleotide substitutions (PNS) at the three variable loci (V1, V2 and V3) in the 5'-untranslated region (UTR) of the Pestivirus genome have been considered for taxonomical segregation of the species, through the evaluation of 534 strains. On the basis of qualitative and quantitative secondary structure characteristics, species have been identified within the genus, determining genetic distances between species isolates, clarifying borderline and multirelated sequences, and characterizing and clustering the Pestivirus strains showing unexpected genomic sequences. Nine genomic groups have been identified: the species Bovine viral diarrhea virus 1 (BVDV-1), Bovine viral diarrhea virus 2 (BVDV-2), Border disease virus (BDV) and Classical swine fever virus (CSFV) and the tentative species Pronghorn, Giraffe, Bovine viral diarrhea virus 3 (BVDV-3) (HoBi group), Border disease virus 2 (BDV-2) (Italian small ruminant isolates) and Bungowannah.Palindromic positions have been characterized according to changes in nucleotide base-pairs identifying low variable positions (LVP) including base-pairs present in less than 80% of the genus. The determination of divergence between single strain sequences or genetic groups was obtained easily by comparing base-pairing combinations from aligned secondary structures. This provided clear information such as the level of heterogeneity within a species, the relatedness between species, or facilitating the characterization and clustering of specific strains. The BVDV-1 and BDV species resulted heterogeneous, showing isolates located on a borderline in the species. Within the BVDV-2 species, two main genogroups were identified, with strains showing common sequence characteristics to both groups (multirelated strains). They could be allocated correctly by quantitative analysis. Similarly, the relation between CSFV and BDV species appeared very clearly. Also in this case, ambiguous strain sequences could be clustered in the species showing the lowest divergence values.In conclusion, the proposed taxonomical procedure is based on the evaluation of only the strategic and highly conserved genome regions in the 5'-UTR Furthermore, the application of quantitative analytical procedure allowed for a better determination of relation among species. (C) 2011 Elsevier B.V. All rights reserved.