我国南方四省HIV-1 CRF01_AE流行毒株基因特征研究

发布时间：2018-02-22 08:45

本文关键词： CRF01_AE 流行簇遗传特征　出处：《苏州大学》2009年硕士论文　论文类型：学位论文

【摘要】： 目的:分析我国南方四省HIV-1感染者中流行的CRF01_AE毒株的遗传特征。方法:从广东、广西、江西和湖南2006年新报告HIV-1感染者的血浆样本中提取病毒RNA,用逆转录/巢式PCR方法扩增gag和env基因片段,对获得的核酸序列以及拼接的gagenv序列构建Neighbor-Joining进化树,确定主要的流行簇,并对CRF01_AE不同流行簇毒株进行分析;运用VESPA(Viral Epidemiology Signature Pattern Analysis)、Entropy、Consensus Maker等软件分析不同的流行簇毒株遗传变异特征;并且利用BEAST(Bayesian Evolutionary Analysis by Sampling Trees)软件估算我国南方四省CRF01_AE主要流行簇毒株的流行起始时间和平均进化速率。结果:从四个省获得的CRF01_AE毒株感染病例210例,主要通过异性性接触(130/210,61.9%)和静脉注射吸毒(61/210,29.1%)感染。利用不同基因区序列以及gagenv序列分别进行系统进化树分析,发现我国南方四省的CRF01_AE毒株形成两个主要的流行簇,其中,流行簇I包含123例样本,流行簇II包含57例样本,其它33例样本的序列散在分布于两个流行簇之间。流行簇I与流行簇II的人群分布组成存在显著差异。VESPA和共享序列分析特征性氨基酸结果显示,两个流行簇毒株在gag基因片段的发现3个特征性氨基酸位点,env基因片段存在10个特征性氨基酸位点。在13个特征性氨基酸位点中,有8个位点的氨基酸存在极性差异,主要表现为在流行簇I内为疏水氨基酸,在流行簇II毒株相应的位点为亲水氨基酸。核苷酸遗传多样性分析结果显示,两个流行簇毒株在gag基因片段上42个位点的核苷酸多态性存在显著差异,env基因片段40个位点的核苷酸多态性存在差异。流行簇I相对独立,未发现与之相关的已知国际流行毒株,其最近祖先株形成时间为13.0年,平均进化速率为6.72×10~(-3)替换/位点/年;而流行簇II毒株与来自越南的不同年代的多条序列混杂在一起,流行起始时间稍早于流行簇I,平均进化速率为12.25×10~(-3)替换/位点/年。结论:本研究通过Neighbour-Joining系统进化树Interior Branch Test检验方法和gagenv拼接序列构建系统进化树两种方法的结合,发现南方四省的210例CRF01_AE感染者中存在两个主要的流行簇。流行簇I毒株具有较低的遗传多样性和较慢的进化速率,最近共同祖先株形成时间稍晚于流行簇II,而且流行簇I相对独立,未发现与之直接相关的国际参考毒株,是我国南方四省CRF01_AE的优势毒株。而流行簇II毒株与越南不同年代的CRF01_AE毒株存在多次相互传播过程,其组成毒株更加复杂。
[Abstract]:Objective: to analyze the genetic characteristics of CRF01_AE strains in four provinces of southern China. Methods: viral RNAs were extracted from plasma samples from Guangdong, Guangxi, Jiangxi and Hunan provinces in 2006, and gag and env gene fragments were amplified by reverse transcription / nested PCR. The nucleic acid sequence and the spliced gagenv sequence were used to construct the Neighbor-Joining evolutionary tree, to identify the main epidemic clusters, and to analyze the different strains of CRF01_AE, and to analyze the genetic variation of the different strains by using VESPA(Viral Epidemiology Signature Pattern Analysis EntropyConsensus Maker and other softwares, such as VESPA(Viral Epidemiology Signature Pattern Analysis, EntropyConsensus Maker and so on. The BEAST(Bayesian Evolutionary Analysis by Sampling trees software was used to estimate the onset time and the average evolutionary rate of the main CRF01_AE strains in the four provinces of southern China. Results: 210 cases of CRF01_AE virus infection were obtained from four provinces, mainly through heterosexual contact (130 / 210 / 61.9) and intravenous drug use (61 / 210 / 29.1). Phylogenetic tree analysis was carried out using different gene sequences and gagenv sequences, respectively. It was found that there were two main epidemic clusters of CRF01_AE strains in four provinces of southern China. Among them, epidemic cluster I contained 123 samples and epidemic cluster II consisted of 57 samples. The sequence of the other 33 samples was scattered between two epidemic clusters. There were significant differences in population distribution between epidemic cluster I and cluster II. VESPA and shared sequence analysis showed that there were significant differences in population distribution between the two groups, and the results of shared sequence analysis showed that there were significant differences in population distribution between the two groups. There were 10 characteristic amino acid loci in three characteristic amino acid loci and 8 amino acid polar differences among 13 characteristic amino acid loci. It was mainly expressed as hydrophobic amino acids in epidemic cluster I and hydrophilic amino acids in epidemic cluster II strains. The results of nucleotide genetic diversity analysis showed that, There were significant differences in nucleotide polymorphisms of 42 loci in the gag gene fragments between the two strains, and there were significant differences in the nucleotide polymorphisms of 40 loci in the gag gene fragments, and the epidemic cluster I was relatively independent. There was no known international epidemic strain associated with it, its most recent ancestor strain was formed at 13.0 years and the average evolutionary rate was 6.72 脳 10 ~ (-3)) substitution / locus / year, while the epidemic cluster II strain was mixed with multiple sequences of different ages from Vietnam. The onset time of epidemic was earlier than that of epidemic cluster I, and the average evolutionary rate was 12.25 脳 10 ~ (-3)) substitution / site / year. Conclusion: this study combines Neighbour-Joining phylogenetic tree Interior Branch Test test with gagenv splicing sequence to construct phylogenetic tree. It was found that there were two main epidemic clusters in 210 cases of CRF01_AE infection in four southern provinces, and the epidemic cluster I strain had lower genetic diversity and slower rate of evolution. Recently, the common ancestor strain was formed later than the epidemic cluster II, and the epidemic cluster I was relatively independent, and no international reference strain directly related to it was found. It is the dominant strain of CRF01_AE in four southern provinces of China, and the epidemic cluster II virus strain has multiple transmission processes with CRF01_AE strain of Vietnam in different ages, and its constituent strains are more complicated.
【学位授予单位】：苏州大学
【学位级别】：硕士
【学位授予年份】：2009
【分类号】：R181.3

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