Detection of Inferred CCR5-and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing
Detection of Inferred CCR5-and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing
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DOI：
10.1371/journal.ppat.1002106
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发表时间：
2011-06-01
期刊：
影响因子：
6.7
通讯作者：
van't Wout, Angelique B.
中科院分区：
文献类型：
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作者：
Bunnik, Evelien M.;Swenson, Luke C.;van't Wout, Angelique B.
使用CXCR 4的人类免疫缺陷病毒1型（HIV-1）变异体的出现与加速疾病进展相关。使用CXCR 4的变体被认为是从使用CCR 5的变体进化而来的，但由于过渡中间体变体通常存在的频率极低，因此很难研究该过程中涉及的动力学和突变途径，因此对其了解甚少。在这里，我们结合基于V3的辅助受体预测工具PSSMNSI/SI和geno 2 pheno（[辅助受体]）对病毒包膜的V3环进行了超深度测序，以检测从CCR 5到CXCR 4使用过渡期间的HIV-1变体。我们分析了PBMC和血清样本获得8个HIV-1感染的个人在三个月的时间间隔长达一年前的第一个表型检测CXCR 4-使用MT-2检测变异。每个样本生成3，482至10，521个读数。在所有个体中，在MT-2检测中使用CXCR 4的变异体的表型检测之前至少3个月，检测到预测的使用CXCR 4的HIV-1的V3序列。随后使用最小生成树对这些V3序列的遗传关系进行分析，发现辅助受体使用的转变遵循涉及连续中间变体的逐步突变途径，与主要预测的CCR 5和CXCR 4使用变体相比，这些中间变体通常以相对较低的频率存在。此外，我们观察到个体之间在预测的CXCR 4使用变体的数量、主要预测的CCR 5使用变体之间的多样性以及存在或不存在具有不一致表型预测的中间变体方面的差异。这些结果首次详细描述了自然HIV-1感染中从CCR 5使用过渡到CXCR 4使用期间V3的突变途径。
The emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants is associated with accelerated disease progression. CXCR4-using variants are believed to evolve from CCR5-using variants, but due to the extremely low frequency at which transitional intermediate variants are often present, the kinetics and mutational pathways involved in this process have been difficult to study and are therefore poorly understood. Here, we used ultra-deep sequencing of the V3 loop of the viral envelope in combination with the V3-based coreceptor prediction tools PSSMNSI/SI and geno2pheno([coreceptor]) to detect HIV-1 variants during the transition from CCR5- to CXCR4-usage. We analyzed PBMC and serum samples obtained from eight HIV-1-infected individuals at three-month intervals up to one year prior to the first phenotypic detection of CXCR4-using variants in the MT-2 assay. Between 3,482 and 10,521 reads were generated from each sample. In all individuals, V3 sequences of predicted CXCR4-using HIV-1 were detected at least three months prior to phenotypic detection of CXCR4-using variants in the MT-2 assay. Subsequent analysis of the genetic relationships of these V3 sequences using minimum spanning trees revealed that the transition in coreceptor usage followed a stepwise mutational pathway involving sequential intermediate variants, which were generally present at relatively low frequencies compared to the major predicted CCR5-and CXCR4-using variants. In addition, we observed differences between individuals with respect to the number of predicted CXCR4-using variants, the diversity among major predicted CCR5-using variants, and the presence or absence of intermediate variants with discordant phenotype predictions. These results provide the first detailed description of the mutational pathways in V3 during the transition from CCR5-to CXCR4-usage in natural HIV-1 infection.