Population-based sequencing of the V3 region of env for predicting the coreceptor usage of human immunodeficiency virus type 1 quasispecies
Population-based sequencing of the V3 region of env for predicting the coreceptor usage of human immunodeficiency virus type 1 quasispecies
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DOI：
10.1128/jcm.02090-06
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发表时间：
2007-05-01
影响因子：
9.4
通讯作者：
Izopet, Jacques
中科院分区：
文献类型：
--
作者：
Delobel, Pierre;Nugeyre, Marie-Therese;Izopet, Jacques
基于基因型群体的方法可能比表型重组测定更快、更便宜，用于确定患者样本中人类免疫缺陷病毒 1 型 (HIV-1) 辅助受体的使用情况，但其临床使用需要良好的基因型-表型相关性以及与克隆分析的一致性。我们通过对 26 名感染 B 亚型 HIV-1 的患者的 V1 至 V3 env PCR 产物进行克隆分析来评估这些要求。我们使用所得的分子克隆集（所有分子克隆均使用单循环重组病毒表型进入测定进行测序和表征）来重新评估基因型-表型相关性。结合先前描述的 V3 基因型的 11/25 和净电荷规则改进了 HIV-1 辅助受体使用的预测。我们还评估了基于群体和克隆分析的一致性，以预测 HIV-1 准种的辅助受体使用。我们基于群体的重组表型测定和 V3 直接测序对于检测病毒群体中次要物种的存在具有相似的敏感性，并且两者都与克隆分析具有良好的相关性。通过结合两个简单的基因型规则获得改进的基因型-表型相关性以及与克隆分析的良好一致性表明V3的直接测序是基于群体的重组表型测定的有价值的替代方案。
Genotypic population-based methods could be faster and less expensive than phenotypic recombinant assays for determining human immunodeficiency virus type 1 (HIV-1) coreceptor usage in patient samples, but their clinical use requires good genotype-phenotype correlation and concordance with clonal analyses. We have assessed these requirements by clonal analysis of the V1 to V3 env PCR products of 26 patients infected with subtype B HIV-1. We used the resulting set of molecular clones, all sequenced and characterized using a single-cycle recombinant virus phenotypic entry assay, to reevaluate genotype-phenotype correlations. Combining the previously described 11/25 and net charge rules for the V3 genotype improved the prediction of HIV-1 coreceptor usage. We also evaluated the concordance of population-based and clonal analyses for predicting the coreceptor usage of HIV-1 quasispecies. Our population-based recombinant phenotypic assay and direct sequencing of V3 were similarly sensitive for detecting the presence of minor species in the virus population, and both correlated well with clonal analysis. The improved genotype-phenotype correlation obtained by combining two simple genotypic rules and the good concordance with clonal analyses suggest that direct sequencing of V3 is a valuable alternative to population-based recombinant phenotypic assays.