CRF01_AE/CRF07_BC重组毒株近似全长基因组序列和系统进化分析

Phylogenetic analysis and sequencing of approximate full-length genome of CRF01_AE/CRF07_BC recombinant strains

目的鉴定我国深圳地区人类免疫缺陷病毒-Ⅰ型(HIV-1)新型二代毒株(CRF01_AE/CRF07_BC),了解重组毒株的流行特征及新型重组模式。方法对深圳市2011-2016年新确诊的未接受抗逆转录病毒治疗的HIV-1感染者血浆样本进行近似全长基因组扩增和测序,选取第一代重组毒株作为母本的第二代独特重组毒株作为研究对象;获得的近似全长基因组序列使用Quality Control工具进行质量检测和基因型初步分析,基于近似全长序列使用最大似然法构建系统进化树;随后使用jpHMM和RIP工具进行重组断点分析,并构建Neighbor-Joining系统进化树验证重组断点,并对来自不同母本的重组片段进行同源性分析。结果从我国深圳地区HIV-1感染者中发现了两种新型二代独特重组毒株(CRF01_AE/CRF07_BC):LS13810和LS4017并获得其近似全长基因组序列;其中LS13810近似全长基因组以CRF01_AE为骨架,分别在病毒的pol和tat区插入两个来自于CRF07_BC的片段;而LS4017近似全长基因组的5′半分子来源于CRF07_BC,而3′半分子主要来源于CRF01_AE,3′半分子的gp120区插入了部分CRF07_BC片段。结论深圳市已经出现了完全由一代重组毒株重组形成的第二代独特重组毒株,重组毒株正在向更加复杂的形式演变,当地乃至我国均亟需建立能准确监测重组毒株发生和流行情况的分子监测策略,以应对毒株重组模式变化和重组毒株流行为HIV-1感染的精准防控和诊断、治疗带来的挑战。

OBJECTIVE To identify the novel second-generation human immunodeficiency virus-1(HIV-1)strains(CRF01_AE/CRF07_BC)in Shenzhen,China,and understand the prevalence characteristics and novel recombination patterns of the recombinant strains.METHODS The approximate full-length genomes were amplified and sequenced for the plasma samples of the patients who were newly diagnosed with HIV-1 infection and did not receive antiretroviral therapy in Shenzhen from 2011 to 2016.Second-generation unique recombinants with first-generation recombinants as the parent strains were selected as the research objects.The obtained approximate full-length genome sequences were subjected to quality control and preliminary subtyping analysis by using the Quality Control tool,and a maximum likelihood systematic evolutionary tree was constructed based on the approximate full-length genome sequence,jpHMM and RIP tools were used for recombination breakpoint analysis,a Neighbor-Joining systematic evolutionary tree was constructed to verify the recombination breakpoint,and homology analysis was performed for the recombination fragments from different parent strains.RESULTS Two novel second-generation unique recombinants(CRF01_AE/CRF07_BC):LS13810 and LS4017 were discovered among the patients with HIV-1 infection in Shenzhen,China,and their approximate full-length genome sequences were obtained.The approximate full-length genome of LS13810 had CRF01_AE as the backbone and inserted two fragments from CRF07_BC in the pol and tat genes,respectively.The 5′half of the approximate full-length genome of LS4017 originated from CRF07_BC,while the 3′half mainly originated from CRF01_AE,and a small segment of CRF07_BC was inserted into the gp120 region of the 3′half.CONCLUSION A unique second-generation recombinant strain,completely formed by the first-generation recombinant strain,has emerged in Shenzhen,China.The recombinant strains are evolving into more complex forms,and it is urgent for local and even national authorities to establish molecular monitoring strategies that can accurately monitor the occurrence and prevalence of recombinant strains so as to cope with the challenges that are brought by changes in the recombination patterns of the strains and the precise prevention,control,diagnosis and treatment of the prevalent HIV-1 infection.