Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
J Antimicrob Chemother. 2020 Dec 1;75(12):3510-3516. doi: 10.1093/jac/dkaa352.
To evaluate the performance of a high-throughput research assay for HIV drug resistance testing based on whole genome next-generation sequencing (NGS) that also quantifies HIV viral load.
Plasma samples (n = 145) were obtained from HIV-positive MSM (HPTN 078). Samples were analysed using clinical assays (the ViroSeq HIV-1 Genotyping System and the Abbott RealTime HIV-1 Viral Load assay) and a research assay based on whole-genome NGS (veSEQ-HIV).
HIV protease and reverse transcriptase sequences (n = 142) and integrase sequences (n = 138) were obtained using ViroSeq. Sequences from all three regions were obtained for 100 (70.4%) of the 142 samples using veSEQ-HIV; results were obtained more frequently for samples with higher viral loads (93.5% for 93 samples with >5000 copies/mL; 50.0% for 26 samples with 1000-5000 copies/mL; 0% for 23 samples with <1000 copies/mL). For samples with results from both methods, drug resistance mutations (DRMs) were detected in 33 samples using ViroSeq and 42 samples using veSEQ-HIV (detection threshold: 5.0%). Overall, 146 major DRMs were detected; 107 were detected by both methods, 37 were detected by veSEQ-HIV only (frequency range: 5.0%-30.6%) and two were detected by ViroSeq only. HIV viral loads estimated by veSEQ-HIV strongly correlated with results from the Abbott RealTime Viral Load assay (R2 = 0.85; n = 142).
The NGS-based veSEQ-HIV method provided results for most samples with higher viral loads, was accurate for detecting major DRMs, and detected mutations at lower levels compared with a method based on population sequencing. The veSEQ-HIV method also provided HIV viral load data.
评估一种基于高通量全基因组下一代测序（NGS）的 HIV 耐药性检测研究检测方法的性能，该方法还可定量 HIV 病毒载量。
从 HIV 阳性男男性行为者（HPTN 078）中获得血浆样本（n=145）。使用临床检测方法（ViroSeq HIV-1 基因分型系统和 Abbott RealTime HIV-1 病毒载量检测）和基于全基因组 NGS 的研究检测方法（veSEQ-HIV）对样本进行分析。
使用 ViroSeq 获得了 HIV 蛋白酶和逆转录酶序列（n=142）和整合酶序列（n=138）。使用 veSEQ-HIV 获得了 142 个样本中 100 个（70.4%）的所有三个区域的序列；对于病毒载量较高的样本，结果获得的频率更高（93.5%的 93 个样本病毒载量>5000 拷贝/ml；50.0%的 26 个样本病毒载量为 1000-5000 拷贝/ml；23 个样本病毒载量<1000 拷贝/ml，检测结果均为 0%）。对于两种方法均有结果的样本，使用 ViroSeq 检测到 33 个样本存在耐药相关突变（DRMs），使用 veSEQ-HIV 检测到 42 个样本存在耐药相关突变（检测阈值：5.0%）。总体上，检测到 146 种主要 DRMs；107 种由两种方法检测到，37 种由 veSEQ-HIV 检测到（频率范围：5.0%-30.6%），2 种由 ViroSeq 检测到。veSEQ-HIV 检测到的 HIV 病毒载量与 Abbott RealTime 病毒载量检测结果高度相关（R2=0.85；n=142）。
基于 NGS 的 veSEQ-HIV 方法为大多数病毒载量较高的样本提供了结果，对于检测主要 DRMs 是准确的，与基于群体测序的方法相比，能够检测到更低水平的突变。veSEQ-HIV 方法还提供了 HIV 病毒载量数据。
