猪瘟病毒编码区基因选择压力及重组分析

Analysis of selection pressure and recombination in coding-region of classical swine fever virus

为了更全面地探究选择压力和基因重组对猪瘟病毒基因组全编码区进化的影响，本研究通过生物信息学软件包PAML 4.5中的codeml程序和RDP 3.44中的6种重组检测算法，对采集时间1994~2010年，涵盖3个基因型中的6个基因亚型，遍布11个国家的50株猪瘟病毒（CSFV）基因组全编码区进行了选择压力及重组分析. 结果显示编码区基因所编码的全部12个蛋白质的选择压力测度参数ω均低于1，表明CSFV所承受选择压力的总体趋势为净化选择，其中NS3，NS4A和NS4B蛋白所承受的净化选择压力较大；而Npro，Erns，E1，E2和NS5A蛋白含有正选择位点，存在较大的正选择压力，表明猪瘟病毒的适应性进化与宿主免疫应答有关. 重组分析的结果共检测出4株重组毒株，其中3株为新发现，分别为HCLV/99，ALD和SWH，其重组区域所涉及的基因组主要编码与猪瘟病毒免疫和病毒毒力相关的蛋白，且重组的确改变了重组株所在的进化树分支；而蛋白NS3，NS4A和NS4B的编码区均没有发现重组痕迹，其遗传距离较短，进化程度较低，这些结果表明重组可能改变猪瘟病毒毒力，并影响猪瘟病毒的遗传进化. 由此可见，猪瘟病毒针对宿主免疫系统的选择压力而产生的突变和重组推动了病毒编码区基因的进化. 本研究为疫苗靶标的研究与日渐趋于复杂的猪瘟病毒流行病学研究提供了理论基础.

We detected the selection pressure and recombination of all 50 strains Classical Swine Fever Virus （CSFV） available complete coding region, based on the maximum likelihood estimation and six algorithms within Recombinant Detect Program 3.44, to provide the first complete overview of the evolution of CSFV. The results showed the overall ω （nonsynonymous/synonymous） of 12 proteins under one-radio model were all lower than 1, indicating that the selection pressure of CSFV was subject to strong purifying selection. Among the 12 proteins, NS3, NS4A and NS4B proteins underwent the stronger purifying selection; meanwhile Npro, Erns, E1, E2 and NS5A proteins were detected the positive selection sites, underwent the stonger positive selection, indicating that the adaptive evolution of CSFV were related to the host immune response. Furthermore, 4 putative recombination virus strains, and the newly found HCLV/99, ALD and SWH, were detected in 50 sample sequences by recombination analysis. The proteins related to the genome recombination were involved in the immunity and virulence of CSFV, and the recombination changed the phylogenetic tree branch of recombination strain. However, the recombination loci were detected in most proteins except NS3, NS4A and NS4B proteins which processed the shorter genetic distance. Our research suggested that the mutation and recombination under the selection pressure of the host immune system promoted the evolution of coding region in CSFV. These studies would provide the foundation for vaccine targets and the more and more complex situation of CSFV epidemiological research.