一种基因型 HIV-1 前病毒 DNA 核心受体嗜性测定法：在病毒血症患者中的特征。
A genotypic HIV-1 proviral DNA coreceptor tropism assay: characterization in viremic subjects.
机构信息
Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA.
University of California, Davis, School of Medicine, Davis, CA, USA.
出版信息
AIDS Res Ther. 2014 May 21;11:14. doi: 10.1186/1742-6405-11-14. eCollection 2014.
BACKGROUND
HIV-1 coreceptor tropism testing is used to evaluate eligibility for CCR5 antagonist therapy. However, HIV-1 RNA-based tests are not suitable for virologically suppressed patients, therefore the use of proviral DNA tropism testing has been investigated. We describe a novel proviral DNA-based genotypic tropism assay and compare its performance to that of a sensitive HIV-1 RNA-based genotypic test.
METHODS
Tropism was determined using HIV-1 plasma RNA and proviral DNA from 42 paired samples from patients with plasma viral loads ≥1000 HIV-1 RNA copies/mL. Proviral DNA sample types included whole blood, separated peripheral blood mononuclear cells resuspended in phosphate-buffered saline and peripheral blood mononuclear cells resuspended in spun plasma. The HIV-1 envelope V3 region was PCR-amplified, sequenced in triplicate, and analyzed for tropism with the geno2pheno algorithm using a 10% false-positive rate (FPR).
RESULTS
Amplicons were obtained from proviral DNA and plasma RNA in 41/42 samples. Tropism predictions were highly concordant (93%-98%) between proviral DNA and plasma RNA, regardless of the proviral DNA isolation method. Non-R5 proviral DNA results were obtained for 100% of patients with detectable non-R5 plasma HIV-1 RNA results. Geno2pheno FPRs for proviral DNA and plasma RNA were highly correlated (Spearman rho = 0.86).
CONCLUSIONS
Our findings demonstrate that proviral DNA tropism determinations from whole blood or peripheral blood mononuclear cells were highly concordant with plasma HIV-1 RNA tropism determinations. This assay may be useful for screening virologically suppressed patients for CCR5-antagonist eligibility and for research purposes.
背景
HIV-1 核心受体嗜性测试用于评估 CCR5 拮抗剂治疗的资格。然而，基于 HIV-1 RNA 的测试不适合病毒学抑制的患者，因此已经研究了使用前病毒 DNA 嗜性测试。我们描述了一种新的基于前病毒 DNA 的基因型嗜性测定法，并将其性能与敏感的 HIV-1 RNA 基于基因型的测试进行了比较。
方法
使用来自 42 对具有血浆病毒载量≥1000 HIV-1 RNA 拷贝/ml 的患者的血浆 RNA 和前病毒 DNA 来确定嗜性。前病毒 DNA 样本类型包括全血、悬浮在磷酸盐缓冲盐水（phosphate-buffered saline）中的分离外周血单核细胞（peripheral blood mononuclear cells）和悬浮在旋转血浆中的外周血单核细胞。PCR 扩增 HIV-1 包膜 V3 区，重复三管测序，并使用 geno2pheno 算法（使用 10%假阳性率（FPR））分析嗜性。
结果
在 42 个样本中的 41 个样本中获得了扩增子。无论前病毒 DNA 分离方法如何，前病毒 DNA 和血浆 RNA 之间的嗜性预测高度一致（93%-98%）。对于可检测到的非 R5 血浆 HIV-1 RNA 结果的 100%患者，获得了非 R5 前病毒 DNA 结果。前病毒 DNA 和血浆 RNA 的 geno2pheno FPR 高度相关（Spearman rho=0.86）。
结论
我们的研究结果表明，来自全血或外周血单核细胞的前病毒 DNA 嗜性测定与血浆 HIV-1 RNA 嗜性测定高度一致。该测定法可能有助于筛选病毒学抑制患者是否有 CCR5 拮抗剂治疗的资格，以及用于研究目的。
Zotero 插件