本文關(guān)鍵詞： CRF01_AE 流行簇 遺傳特征　出處：《蘇州大學(xué)》2009年碩士論文　論文類型：學(xué)位論文

【摘要】： 目的:分析我國南方四省HIV-1感染者中流行的CRF01_AE毒株的遺傳特征。 方法:從廣東、廣西、江西和湖南2006年新報(bào)告HIV-1感染者的血漿樣本中提取病毒RNA,用逆轉(zhuǎn)錄/巢式PCR方法擴(kuò)增gag和env基因片段,對獲得的核酸序列以及拼接的gagenv序列構(gòu)建Neighbor-Joining進(jìn)化樹,確定主要的流行簇,并對CRF01_AE不同流行簇毒株進(jìn)行分析;運(yùn)用VESPA(Viral Epidemiology Signature Pattern Analysis)、Entropy、Consensus Maker等軟件分析不同的流行簇毒株遺傳變異特征;并且利用BEAST(Bayesian Evolutionary Analysis by Sampling Trees)軟件估算我國南方四省CRF01_AE主要流行簇毒株的流行起始時(shí)間和平均進(jìn)化速率。 結(jié)果:從四個(gè)省獲得的CRF01_AE毒株感染病例210例,主要通過異性性接觸(130/210,61.9%)和靜脈注射吸毒(61/210,29.1%)感染。利用不同基因區(qū)序列以及gagenv序列分別進(jìn)行系統(tǒng)進(jìn)化樹分析,發(fā)現(xiàn)我國南方四省的CRF01_AE毒株形成兩個(gè)主要的流行簇,其中,流行簇I包含123例樣本,流行簇II包含57例樣本,其它33例樣本的序列散在分布于兩個(gè)流行簇之間。流行簇I與流行簇II的人群分布組成存在顯著差異。VESPA和共享序列分析特征性氨基酸結(jié)果顯示,兩個(gè)流行簇毒株在gag基因片段的發(fā)現(xiàn)3個(gè)特征性氨基酸位點(diǎn),env基因片段存在10個(gè)特征性氨基酸位點(diǎn)。在13個(gè)特征性氨基酸位點(diǎn)中,有8個(gè)位點(diǎn)的氨基酸存在極性差異,主要表現(xiàn)為在流行簇I內(nèi)為疏水氨基酸,在流行簇II毒株相應(yīng)的位點(diǎn)為親水氨基酸。核苷酸遺傳多樣性分析結(jié)果顯示,兩個(gè)流行簇毒株在gag基因片段上42個(gè)位點(diǎn)的核苷酸多態(tài)性存在顯著差異,env基因片段40個(gè)位點(diǎn)的核苷酸多態(tài)性存在差異。流行簇I相對獨(dú)立,未發(fā)現(xiàn)與之相關(guān)的已知國際流行毒株,其最近祖先株形成時(shí)間為13.0年,平均進(jìn)化速率為6.72×10~(-3)替換/位點(diǎn)/年;而流行簇II毒株與來自越南的不同年代的多條序列混雜在一起,流行起始時(shí)間稍早于流行簇I,平均進(jìn)化速率為12.25×10~(-3)替換/位點(diǎn)/年。 結(jié)論:本研究通過Neighbour-Joining系統(tǒng)進(jìn)化樹Interior Branch Test檢驗(yàn)方法和gagenv拼接序列構(gòu)建系統(tǒng)進(jìn)化樹兩種方法的結(jié)合,發(fā)現(xiàn)南方四省的210例CRF01_AE感染者中存在兩個(gè)主要的流行簇。流行簇I毒株具有較低的遺傳多樣性和較慢的進(jìn)化速率,最近共同祖先株形成時(shí)間稍晚于流行簇II,而且流行簇I相對獨(dú)立,未發(fā)現(xiàn)與之直接相關(guān)的國際參考毒株,是我國南方四省CRF01_AE的優(yōu)勢毒株。而流行簇II毒株與越南不同年代的CRF01_AE毒株存在多次相互傳播過程,其組成毒株更加復(fù)雜。
[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.
【學(xué)位授予單位】：蘇州大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2009
【分類號(hào)】：R181.3

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1 程春林;我國南方四省HIV-1 CRF01_AE流行毒株基因特征研究[D];蘇州大學(xué);2009年

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本文編號(hào)：1524001