Genome comparison of a novel classical swine fever virus isolated in China in 2004 with other CSFV strains
Genome comparison of a novel classical swine fever virus isolated in China in 2004 with other CSFV strains
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2004年中国分离的新型猪瘟病毒与其他猪瘟病毒株的基因组比较
DOI：
10.1007/s11262-005-0048-2
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发表时间：
2006-10-01
期刊：
影响因子：
1.6
通讯作者：
Qian, Ping
中科院分区：
文献类型：
--
作者：
Li, Xiangmin;Xu, Zhuofei;Qian, Ping
从河南省猪圈中分离到的新型猪瘟病毒SWH/CA/2004的基因组长度为12296个核苷酸（nt）。它由373-nt的5‘端非翻译区（NTR）、11697-nt的编码3898个氨基酸的多蛋白（aa）的开放阅读框（ORF）和226-nt的3’-NTR组成。对SWH/CA/2004分离株（GenBank登录：DQ127910）与其他已知CSFV分离株进行基因组比较分析。SWH/CA/2004与其他报道菌株对应片段在核苷酸水平上的同源性为80.4 ~ 99.8%，在氨基酸水平上的同源性为89.5 ~ 99.8%。从进化角度看，分离株SWH/CA/2004与高毒力分离株cF114/CA/2001亲缘关系密切，两两距离为0.013；与中毒力分离株GXWZ02/CA/2003亲缘关系较远，两两距离为0.170。构建了全基因组及以下区域E-rns、E1、E2和基于ns5b的邻居连接（NJ）方法的系统发育树，并根据毒力、中毒力和高毒力大致划分为不同的遗传组，而其他基于区域的NJ树在这些遗传组之间表现出序列保守性。这四个基因组区域可能构成不同猪瘟分离株遗传分型的重要标准。基于这些分析，推断分离株SWH/CA/2004属于高毒力分离株群。然而，SWH/CA/2004在3'-NTR中也含有14-U缺失，这是无毒分离株的特征。这些分析构成了基于基因组不同区域的脑脊液系统发育的综合研究，并可能为未来的分子流行病学研究提供基础，以确定毒株暴发并触发实施适当的控制措施。
The genome of a novel classical swine fever virus (CSFV), SWH/CA/2004, isolated from a hog pen in Henan Province, central China, is 12296 nucleotides (nt) in length. It is composed of a 373-nt 5' terminal non-translated region (NTR), a 11697-nt open reading frame (ORF) encoding a polyprotein of 3898 amino acids (aa), and a 226-nt 3'-NTR. Genome comparison of the SWH/CA/2004 isolate (GenBank Accession: DQ127910) with other known CSFV isolates was performed and analyzed. Corresponding segments from SWH/CA/2004 and other reported strains shared 80.4-99.8% identity at the nucleotide level and 89.5-99.8% identity at the amino acid level. From an evolutionary point of view, isolate SWH/CA/2004 is closely related to the highly virulent isolate cF114/CA/2001, with a pairwise distance of 0.013; and distantly related to the moderately virulent isolate GXWZ02/CA/2003, with pairwise distance 0.170. The phylogenetic trees of the full-length genome and the following region E-rns, E1, E2, and NS5B-based neighbor-joining (NJ) method were constructed and approximately divided into different genetic groups according to avirulence, moderate virulence and high virulence, while other region-based NJ trees demonstrated sequence conservation between these groups. The four genomic regions may constitute important criteria for genetic typing of diverse CSFV isolates. Based on these analyses, isolate SWH/CA/2004 was deduced to belong to the highly virulent isolate group. However, SWH/CA/2004 also contains a 14-U deletion in the 3'-NTR that is characteristic of avirulent isolates. These analyses constitute a comprehensive study of the phylogenetics of CSF based on distinct regions of the genome and may provide the basis for future molecular epidemiology research to identify virulent strain outbreaks and trigger implementation of appropriate control measures.