我国HIV-1主要流行地区B'亚型与CRF07_BC重组毒株遗传变异分析
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摘要
我国中部地区河南及其周边省份的既往献浆员人群(former plasma donations，FPDs)和西南西北地区的静脉吸毒人群(intravenous drug users，IDUs)是我国HIV传播过程中主要的高危人群。我国正面临着HIV-1通过多种传播方式由高危人群向普通人群扩散的危机。为了解我国HIV-1毒株的流行状况，我们于2003年8月至2005年9月分别在河南、山西、四川和新疆等地采集了508份HIV-1阳性样本，经巢式PCR扩增及纯化、测序，得到的序列通过GCG软件包和国际HIV分子生物学网站提供的在线分析工具对得到的序列进行了基因型、遗传多样性，氨基酸序列、抗原表位、N-糖基化位点以及辅助受体进行了分析。在本研究中我们分析了gp120、gag、nef和tat基因的全长序列，主要结果如下：1)遗传多样性。河南和山西地区的既往献浆人群中流行的HIV-1毒株的主要亚型为B’亚型，在四川和新疆的静脉吸毒人群中流行的HIV-1毒株为CRF07_BC重组模式。B’亚型与CRF07_BC毒株中C3区段的遗传多样性高于其他保守区；河南和山西地区B’亚型毒株中V1，V4区的差异显著；B’亚型毒株gag基因变异较大的区段是P17区段，CRF07_BC毒株中则为P1P6区段。2)特征性氨基酸。我们对B’亚型毒株的gp120，gag和tat基因以及CRF07_BC重组毒株的gp120，gag，tat和nef基因的地区性特异性氨基酸位点进行了确认。3)V3环顶端四肽和N-糖基化位点以及辅助受体结合位点的变化。B’亚型毒株V3环顶端四肽存在6种不同的基序，GPGQ占43.59％，而CRF07_BC重组毒株V3环顶端四肽存在着4种类型，GPGQ所占比例为96.06％。B’亚型毒株V3环N-糖基化位点的丢失率高于CRF07_BC。在B’亚型毒株中，可能使用CCR5作为辅助受体的占14.1％，在CRF07_BC亚型毒株中，可能使用CCR5作为辅助受体的占86.7％。4)抗原表位。河南和山西地区B’亚型毒株与中和表位的完全一致率较低，与CTL抗原表位的完全一致率较高。5)P6区段缺失。在新疆地区CRF07_BC病毒P6区段的中部区域出现了高频率的1-13个氨基酸的缺失，在CD4+和病毒载量方面，有缺失和没有缺失的毒株之间没有明显的区别。
由上述结果，我们可以得出以下结论：1)不同亚型的毒株在不同的高危人群中持续传播，导致HIV-1毒株在特定的高危人群中特异性的流行趋势。相同亚型毒株的遗传多样性与特定地区毒株的流行时间相关。C3区段在保守区段中变异程度最高，V3区段在可变区段中最保守。2)不同地区流行的具有独特特点的毒株可能是由于特异性的祖先株产生的奠基者效应导致的，还可能是由于传播过程很少出现省与省之间毒株的交叉传播。3)与CRF07_BC重组毒株相比，B’亚型毒株由于V3环的多样性和N-糖基化位点的丢失率较高，B’亚型毒株可能会受到更强有力的免疫压力作用。4)我国B’亚型毒株与已知中和抗体表位的一致性较低，与已知CTL抗原表位的一致性较高。5)CRF07_BC重组毒株Gag基因P6区段1-13个氨基酸的缺失对病毒复制能力和病毒载量的影响不明显。
Former plasma donors (FPDs) who live in Henan and contiguous provinces ofcentral China and injecting drug users (IDUs) in provinces in southwest and northwestChina represent the major hig-risk populations for HIV prevalence all over the country.China is facing the crisis that HIV is spreading from high risk population to commonpopulation by several transmission pathways. To characterize current HIV-1prevalence, we collected 508 HIV-1 sero-positive blood samples from Henan, Shanxi, Sichuan and Xinjiang provinces between August 2003 to September 2005 andsequences were successfully obtained by nested-PCR and subsequent auto-sequencing.GCG software package and online sequence analysis tools were used to editsequences and analyze genotype, genetic distance, amino acid sequences, antigenepitopes, N-linked glycosylation sites and coreceptor. In this paper, we analyzed thefull-length gp120, gag, nef and tat. We observed: 1) Genetic diversity. Thailand B isthe major strain circulating in FPDs in Henan and Shanxi provinces whereasCRF07_BC strain is predominantly circulating in IDUs in Sichuan and Xinjiangprovinces. The analysis of genetic distances revealed that C3 regions of B' clade andCRFO7_BC are more variable than other conservative regions; there is significantdifference in V1 and V4 regions between B' strains from Henan and from Shanxiprovinces; the genetic distance culminates in P17 region in B' strains derived Gagwhereas P1P6 represents the most variable region in CRF07_BC gag gene. 2)Characteristics in amino acid sequences. Regional specific amino acid motifs wereidentified in gp120, gag and tat of B' strains and gp120, gag, nef and tat ofCRF07_BC strains. 3) Variation at the tip, N-linked glycosites of V3 loop andcoreceptor binding sites. 6 different motifs were defined at the tip of B' derived V3loop, among those GPGQ accounts for 43.59％cases, whereas 4 motifs co-exist at thetip of CRF07_BC V3 loop and 96.06％cases contain GPGQ sequences. The losingrate of N-linked glycosites is higher at V3 loop in B' subtype strains than CRF07_BC. 14.1％B' strains and 86.7％CRF07_BC strains contain CCR5 motif. 4) Antigenepitopes. The sequences at CTL epitopes are more consistent in B' strains than that atneutralization epitopes. 5) Deletion in P6. A deletion of 1-13 amino acids wasfrequently observed at the central region of p6 in CRF07_BC derived Gag, and nosignificant differences in CD4~+ counts and virus loads were observed betweensubjects infected by viral strains with/without this deletion.
From those results above, we concluded: 1) Different HIV-1 clades areconsistently circulating in different big-risk populations and thereby resulted insegregated HIV-1 strain specific prevalence. C3 is the most variable region amongconservative regions of B' and CRF07_BC strains. 2) The regional HIV-1 prevalencemay be initiated by regional specific ancestor viral strain, inter-province exchange ofviral strains was rare. 3) B' clade may undertake more immune pressure thanCRF07_BC, which resulted in more variations at the tip and N-linked glycosites ofV3 loop. 4) The antigen epitopes of B' genotype strains in China are more identical toknown CTL epitopes than to neutralization epitope, 5) The deletion of 1-13 aminoacids in gag P6 region of CRF07_BC strains has little influence to viral replicationand fitness.
由上述结果，我们可以得出以下结论：1)不同亚型的毒株在不同的高危人群中持续传播，导致HIV-1毒株在特定的高危人群中特异性的流行趋势。相同亚型毒株的遗传多样性与特定地区毒株的流行时间相关。C3区段在保守区段中变异程度最高，V3区段在可变区段中最保守。2)不同地区流行的具有独特特点的毒株可能是由于特异性的祖先株产生的奠基者效应导致的，还可能是由于传播过程很少出现省与省之间毒株的交叉传播。3)与CRF07_BC重组毒株相比，B’亚型毒株由于V3环的多样性和N-糖基化位点的丢失率较高，B’亚型毒株可能会受到更强有力的免疫压力作用。4)我国B’亚型毒株与已知中和抗体表位的一致性较低，与已知CTL抗原表位的一致性较高。5)CRF07_BC重组毒株Gag基因P6区段1-13个氨基酸的缺失对病毒复制能力和病毒载量的影响不明显。
Former plasma donors (FPDs) who live in Henan and contiguous provinces ofcentral China and injecting drug users (IDUs) in provinces in southwest and northwestChina represent the major hig-risk populations for HIV prevalence all over the country.China is facing the crisis that HIV is spreading from high risk population to commonpopulation by several transmission pathways. To characterize current HIV-1prevalence, we collected 508 HIV-1 sero-positive blood samples from Henan, Shanxi, Sichuan and Xinjiang provinces between August 2003 to September 2005 andsequences were successfully obtained by nested-PCR and subsequent auto-sequencing.GCG software package and online sequence analysis tools were used to editsequences and analyze genotype, genetic distance, amino acid sequences, antigenepitopes, N-linked glycosylation sites and coreceptor. In this paper, we analyzed thefull-length gp120, gag, nef and tat. We observed: 1) Genetic diversity. Thailand B isthe major strain circulating in FPDs in Henan and Shanxi provinces whereasCRF07_BC strain is predominantly circulating in IDUs in Sichuan and Xinjiangprovinces. The analysis of genetic distances revealed that C3 regions of B' clade andCRFO7_BC are more variable than other conservative regions; there is significantdifference in V1 and V4 regions between B' strains from Henan and from Shanxiprovinces; the genetic distance culminates in P17 region in B' strains derived Gagwhereas P1P6 represents the most variable region in CRF07_BC gag gene. 2)Characteristics in amino acid sequences. Regional specific amino acid motifs wereidentified in gp120, gag and tat of B' strains and gp120, gag, nef and tat ofCRF07_BC strains. 3) Variation at the tip, N-linked glycosites of V3 loop andcoreceptor binding sites. 6 different motifs were defined at the tip of B' derived V3loop, among those GPGQ accounts for 43.59％cases, whereas 4 motifs co-exist at thetip of CRF07_BC V3 loop and 96.06％cases contain GPGQ sequences. The losingrate of N-linked glycosites is higher at V3 loop in B' subtype strains than CRF07_BC. 14.1％B' strains and 86.7％CRF07_BC strains contain CCR5 motif. 4) Antigenepitopes. The sequences at CTL epitopes are more consistent in B' strains than that atneutralization epitopes. 5) Deletion in P6. A deletion of 1-13 amino acids wasfrequently observed at the central region of p6 in CRF07_BC derived Gag, and nosignificant differences in CD4~+ counts and virus loads were observed betweensubjects infected by viral strains with/without this deletion.
From those results above, we concluded: 1) Different HIV-1 clades areconsistently circulating in different big-risk populations and thereby resulted insegregated HIV-1 strain specific prevalence. C3 is the most variable region amongconservative regions of B' and CRF07_BC strains. 2) The regional HIV-1 prevalencemay be initiated by regional specific ancestor viral strain, inter-province exchange ofviral strains was rare. 3) B' clade may undertake more immune pressure thanCRF07_BC, which resulted in more variations at the tip and N-linked glycosites ofV3 loop. 4) The antigen epitopes of B' genotype strains in China are more identical toknown CTL epitopes than to neutralization epitope, 5) The deletion of 1-13 aminoacids in gag P6 region of CRF07_BC strains has little influence to viral replicationand fitness.
引文
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