一株HIV-1 01_AE/07_BC独特重组病毒近全长基因组分析

Near full-length genomic sequence analysis of an HIV-1 01_AE/07_BC unique recombinant form virus

目的对在深圳发现的一例gag和env基因片段亚型不一致的HIV感染者样本进行近全长基因组扩增和序列分析,以了解其重组特征并分析可能的来源。方法利用近末端稀释法分两段扩增病毒近全长基因组并测定序列,使用Sim Plot 3.5软件分析全长基因组序列中的重组断点,并采用分片段构建进化树的方法确认重组断点。对长度超过300 bp的片段与相应亚型的全部近全长基因组序列构建进化树,分析亲本毒株可能的来源。结果经扩增测序获得1条长度为8 975 bp的HIV-1近全长基因组序列。断点分析结果表明该序列由CRF01_AE和CRF07_BC重组而成,重组断点相应于HXB2的位置分别为1 185、1 817、8 782、9 043和9 216,其中片段Ⅰ、Ⅲ、Ⅴ来源于CRF01_AE毒株,片段Ⅱ、Ⅳ、Ⅵ来源于CRF07_BC毒株。亲本毒株来源分析表明,与片段Ⅱ成簇的CRF07_BC序列主要来自北方男男同性传播人群,Bootstrap值为74%,片段Ⅲ与CRF01_AE的簇5病毒成簇,其中多数序列来自北方男男同性传播人群,Bootstrap值为100%。结论本文获得了一株CRF01_AE和CRF07_BC重组形成的独特型重组病毒,其亲本病毒与我国北方男男同性恋人群流行的毒株同源,有可能来源于深圳本地性传播人群中流行的病毒。

Objective To understand the genetic characteristics and analyze the possible source for parents strains, weamplified the near full-length genome of a HIV positive sample with discordant genotypes for gag and env fragments collectedin Shenzhen, and performed the phylogenetic analysis. Methods Two overlapping segments of HIV-1 genome were amplifiedby near- endpoint dilution method, and the products were sequenced directly. The breakpoints of genome were determinedusing Sim Plot 3.5 and confirmed by the phylogenetic trees for segments. To determine the possible population source for theparents strains, the phylogenetic trees were reconstructed using all available near full-length genomic sequences downloadfrom Los Alamos HIV sequence database for the segments with length over 300 bp. Results We obtained a nearly full-lengthgenome sequence with length of 8 975 bp, which was the recombinant of CRF01_AE and CRF07_BC. The breakpoints siteswere 1 185, 1 817, 8 782, 9 043, 9 216 corresponding to HXB2. The segments I, III, V came from CRF01_AE and segments II,IV, and VI came from CRF07_BC. The phylogenetic tree showed that the segments II and III of GD140095 were clustered withthe CRF07_BC and CRF01_AE sequences respectively, which was prevalent in MSM in northern China,and Bootstrap valuewere 74% and 100%,respectively. Conclusion A unique recombinant form virus between CRF01_AE and CRF07_BC wereamplified and characterized. The parents＇ viruses were homologous with the HIV- 1 strains prevalent in MSM in northernChina and they may originate from the local HIV-1 viruses in sexual transmission population in Shenzhen.