兔病毒性出血症病毒YL株衣壳蛋白(VP60)基因的克隆和生物信息学分析

Cloning and Bioinformatics Analyzing for Capsid Protein (VP60) Gene of Rabbit Hemorrhagic Disease Virus YL Strain

应用RT-PCR方法从兔出血症病毒(RHDV)西北分离株YL株中克隆出衣壳蛋白VP60基因并测序,YL株是中国西北地区首株被测序的RHDV,测序结果显示VP60基因全长1 740 bp,编码579个氨基酸,测序结果在GenBank中注册(登录号为DQ530363)。从GenBank下载全部已发表的40株RHDV序列,运用生物信息学软件分析,构建系统进化树和氨基酸序列同源性表,结果表明,世界不同地区RHDV分离株基因序列虽然非常保守,达到90%以上,但可以分为5个基因群,并且基因型和地域性没有必然联系,中国的分离株除了WX84株外,其它均处于第V基因群,该基因群内近年分离出的中国4个不同大地区(西北、华东、东北、西南)的RHDV毒株与NJ85株遗传距离很近,很可能都来自同一毒株NJ85。同时,对4个不同大地区的近年的4个代表性分离株的二级结构、抗原性进行了预测分析,结果显示二级结构有一定差异,但抗原性相同,这与RHDV只有一个血清型的看法相一致。

The capsid protein VP60 gene of rabbit hemorrhagic disease virus（RHDV）YL Strain was cloned by RT-PCR and then sequenced. YL Strain was the first RHDV strain being sequenced in the Northwest of China. The results showed that the nucleotide sequence of VP60 gene was 1740nt in length and encoding a protein of 580 aa. The sequence had been submitted to GenBank （the accession number is DQ530363）. We downloaded all other 39 sequences of published RHDV isolates from GenBank and then constructed phylogenetic tree and drawn homology and divergence form by bioinformatics software. The results indicated that the VP60 gene of RHDV was very conservative, and the homology of the nucleotide among different isolates exceeded 90%, but they can be divided into 5 gene groups. The gene group and region had negative connection. All Chinese RHDV isolates belonged to the Ⅴ gene group eccept WX84 Strain. In this group, the hereditary distance between the strains isolated in recent years and NJ85 Strain was very close. The RHDV strains of China isolated in recent years probably come from the same strain NJ85. Meanwhile, the secondary structure and antigenic index of four strains from different areas of China were predicted and analyzed. The results revealed that there were certain differences in secondary structure, but the antigenicity was identical.