Department of Microbiology, St John's Medical College and Hospital, Bangalore, India.
J Antimicrob Chemother. 2013 Sep;68(9):2003-6. doi: 10.1093/jac/dkt138. Epub 2013 Apr 30.
Genotypic tropism testing (GTT) of HIV is increasingly used prior to the initiation of CCR5 antagonist therapy in HIV-infected individuals. Normally performed on plasma-derived virus, the test is challenging when performed in patients with suppressed viraemia. We aimed to evaluate the performance of cell-associated proviral DNA against plasma-derived viral RNA as the genetic material for GTT in an Indian clinical setting.
From 52 HIV-1-infected individuals, the env V3 region was successfully amplified and sequenced from both proviral DNA and plasma RNA paired samples having a viral load >2500 copies/mL (n = 42) and from proviral DNA only in 10 antiretroviral therapy (ART)-experienced patients with a viral load <500 copies/mL. GTT was performed using the Geno2Pheno algorithm with the interpretative false positive rate (FPR) cut-off of 10%.
Among paired samples, 40 of 42 patients harboured subtype C strains. Plasma RNA tropism prediction revealed X4 tropism in 4 of 42 (9.5%). A high concordance of 97.6% in tropism prediction was noted in simultaneous RNA/DNA samples (38 R5 and 3 X4). Discordance was observed in one sample showing R5 tropism in proviral DNA and X4 tropism in plasma RNA. Comparison of Geno2Pheno FPRs in both the plasma and proviral compartments showed good correlation (overall, r = 0.87; ART-naive patients, r = 0.79; ART-failing patients, r = 0.97). GTT was successfully performed in all 10 whole blood DNA samples having a viral load <500 copies/mL, all showing R5 tropism.
High concordance in tropism prediction from proviral DNA and plasma-viral RNA suggests that prediction of viral tropism using proviral DNA is accurate and feasible in resource-limited clinical settings, particularly in patients with low or suppressed viraemia.
在开始使用 CCR5 拮抗剂治疗 HIV 感染个体之前，越来越多地对 HIV 进行基因嗜性测试（GTT）。该测试通常在血浆衍生的病毒上进行，当在病毒血症受抑制的患者中进行时，具有挑战性。我们旨在评估细胞相关前病毒 DNA 相对于血浆衍生的病毒 RNA 作为 GTT 的遗传物质在印度临床环境中的性能。
从 52 名 HIV-1 感染个体中，成功地从具有病毒载量> 2500 拷贝/ml 的配对的前病毒 DNA 和血浆 RNA 样本（n = 42）和仅在 10 名接受抗逆转录病毒治疗（ART）的经验丰富的病毒载量<500 拷贝/ml 的患者的前病毒 DNA 中成功扩增和测序了 env V3 区域。使用 Geno2Pheno 算法进行 GTT，解释性假阳性率（FPR）截断值为 10%。
在配对样本中，42 名患者中有 40 名携带 C 型亚株。血浆 RNA 嗜性预测显示 42 名患者中有 4 名（9.5%）为 X4 嗜性。同时 RNA/DNA 样本中观察到 97.6%的高一致性（38 例 R5 和 3 例 X4）。在一个样本中观察到了嗜性不一致，该样本在前病毒 DNA 中显示 R5 嗜性，而在血浆 RNA 中显示 X4 嗜性。比较两种血浆和前病毒区的 Geno2Pheno FPR 显示出良好的相关性（总体而言，r = 0.87；ART 初治患者，r = 0.79；ART 失败患者，r = 0.97）。在病毒载量<500 拷贝/ml 的所有 10 个全血 DNA 样本中均成功进行了 GTT，均显示 R5 嗜性。
前病毒 DNA 和血浆病毒 RNA 中的嗜性预测具有高度一致性，这表明在前病毒 DNA 中使用病毒嗜性预测在资源有限的临床环境中是准确和可行的，特别是在病毒血症低或受抑制的患者中。
