Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences.
Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences.
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DOI：
10.1186/1297-9716-43-50
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发表时间：
2012-06-07
影响因子：
4.4
通讯作者：
Becher P
中科院分区：
文献类型：
--
作者：
Postel A;Schmeiser S;Bernau J;Meindl-Boehmer A;Pridotkas G;Dirbakova Z;Mojzis M;Becher P
分子流行病学已被证明是控制猪瘟（CSF）的重要工具，在过去二十年中，其使用显着增加。系统发生分析是病毒追踪的先决条件，因此可以实施更有效的控制措施。到目前为止，5 ′ NTR（150个核苷酸，nt）和E2基因（190个核苷酸）的片段经常被用于系统发育分析。短序列长度代表了区分密切相关分离株以及拟定CSFV组和亚组的置信水平的限制因素。在这项研究中，我们使用了一组33个CSFV分离株，以确定病毒基因组5 ′末端三分之一内3508-3510 nt区域的核苷酸序列。包括来自GenBank数据库的22个额外序列，基因组的不同区域，包括以前使用的短5 ′ NTR和E2片段以及编码单个病毒蛋白Npro、C、Erns、E1和E2的基因组区域，比较了变异性和系统发育分析的适用性。全长E2编码序列（1119 nt）被证明是最适合可靠的和统计学上显着的同源性和分析显示的结果一样好，获得了更长的整个5 ′ NTR-E2序列。因此，欧盟和OIE CSF参考实验室推荐了这一策略，因为它为CSFV分子流行病学提供了坚实和改进的基础。最后，这种方法的力量说明了密切相关的猪瘟病毒株最近在立陶宛爆发的系统发育分析。
Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins Npro, C, Erns, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.
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影响因子：
3.8
作者：
Lowings, P;Ibata, G;Paton, D
通讯作者：
Paton, D
影响因子：
14.9
作者：
DEVEREUX, J;HAEBERLI, P;SMITHIES, O
通讯作者：
SMITHIES, O
影响因子：
3.3
作者：
Blome, Sandra;Grotha, Inga;Greiser-Wilke, Irene
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Greiser-Wilke, Irene
树突镜：大型系统发育树的互动观众。
影响因子：
3
作者：
Huson, Daniel H.;Richter, Daniel C.;Rausch, Christian;Dezulian, Tobias;Franz, Markus;Rupp, Regula
通讯作者：
Rupp, Regula
影响因子：
5.8
作者：
Milne, Iain;Lindner, Dominik;Bayer, Micha;Husmeier, Dirk;McGuire, Grainne;Marshall, David F.;Wright, Frank
通讯作者：
Wright, Frank