广西一株HIV-1 CRF01_AE/CRF07_BC独特重组毒株的鉴定

Identification of a HIV-1 CRF01_AE/CRF07_BC unique recombinant form in Guangxi

目的对一条不能明确亚型的HIV-1近似全长基因组序列进行分析,确定毒株的重组特征及可能来源。方法利用近末端稀释法分两段进行HIV-1近似全长基因组的扩增,获取序列后使用SimPlot软件分析近似全长基因组序列的重组模式及断点,采用分片段构建ML进化树的方法确认重组断点准确性,绘制重组病毒的基因镶嵌模式图。对各基因片段与相应亚型的全部近似全长基因组序列构建ML进化树,推测其亲本毒株可能来源。结果扩增及测序后,获得一条长度为8943 bp(HXB2:649~9599)的HIV-1近似全长基因组序列。断点分析表明,该序列的重组模式是以CRF01AE为骨架插入CRF07BC片段,其中片段Ⅰ、Ⅲ和Ⅴ来自CRF01AE毒株,片段Ⅱ和Ⅳ来自CRF07BC毒株,4个重组断点相对应于HXB2的位置分别为3957、4224、5560和5899。亲本毒株来源分析表明,与片段Ⅰ、Ⅲ和Ⅴ成簇的CRF01AE序列主要来自东南亚国家如泰国、老挝、越南。片段Ⅱ和Ⅳ则与我国西南地区吸毒人群中的CRF07BC序列聚集。结论获得一株由CRF01AE和CRF07BC重组形成的HIV-1独特重组毒株,其亲本病毒中的CRF01AE可能与东南亚国家的毒株同源,而CRF07BC可能来自我国西南地区的吸毒人群。

Objective We analyzed the near full-length genome of an HIV-positive sample with an undetermined subtype to determine the recombinant characteristics and possible source of the parental virus.Methods The near fulllength genome of HIV-1 was amplified in two overlapping segments by the near-terminal dilution method.The positive products were sequenced directly to obtain genomic sequences.The recombinant patterns and breakpoints of the near fulllength genome were determined using the SimPlot software and confirmed by the maximum likelihood phylogenetic trees for segments.The mosaic structures of the genome were drawn.To determine the possible source of the parental virus,the maximum likelihood phylogenetic trees were reconstructed using all available near full-length genomic sequences download from Los Alamos HIV sequence database for each segment.Results After amplification and sequencing,we obtained a near full-length genome with a length of 8943 bp(HXB2:649-9599).The breakpoints analysis showed that the genome kept the CRF01AE parental backbone with two CRF07BC segments inserted.The segmentsⅠ,ⅢandⅤcame from CRF01AE,and segmentsⅡandⅣcame from CRF07BC.Four breakpoints were 3957,4224,5560,and 5899 corresponding to HXB2.The phylogenetic tree showed that the segmentsⅠ,ⅢandⅤwere clustered with CRF01AE sequences from southeast Asian countries such as Thailand,Laos,and Vietnam,while segmentⅡandⅣwere clustered with CRF07BC sequences from injection drug users in southwest China.Conclusion A HIV-1 unique recombinant form between CRF01AE and CRF07BC was obtained.The parental virus of CRF01AE might be homologous with the HIV-1 prevalent in Southeast Asian countries,while CRF07BC might come from injection drug users in southwest China.