Abstract

Objectives

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.

Methods

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).

Results

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).

Conclusions

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.

中文翻译：

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用于分析 HIV 耐药性和病毒载量的高通量下一代测序方法的性能。

摘要

目标

评估基于全基因组下一代测序 (NGS) 的 HIV 耐药性检测高通量研究检测的性能，该检测也可量化 HIV 病毒载量。

方法

血浆样本 ( n  =  145) 来自 HIV 阳性 MSM (HPTN 078)。使用临床分析（ViroSeq HIV-1 基因分型系统和 Abbott RealTime HIV-1 病毒载量分析）和基于全基因组 NGS (veSEQ-HIV) 的研究分析对样本进行了分析。

结果

HIV 蛋白酶和逆转录酶序列 ( n  =  142) 和整合酶序列 ( n  = 138) 是使用 ViroSeq 获得的。使用 veSEQ-HIV 获得了 142 个样品中的 100 个（70.4%）来自所有三个区域的序列；病毒载量较高的样本获得的结果更频繁（93.5% 的样本为 >5000 拷贝/mL；26 个样本为 1000-5000 拷贝/mL 为 50.0%；23 个样本<1000 拷贝/mL 为 0%）。对于具有两种方法结果的样品，使用 ViroSeq 在 33 个样品中检测到耐药性突变 (DRM)，使用 veSEQ-HIV 在 42 个样品中检测到耐药性突变 (DRM)（检测阈值：5.0%）。总共检测到 146 个主要 DRM；两种方法均检测到 107 种，仅通过 veSEQ-HIV 检测到 37 种（频率范围：5.0%–30.6%），仅通过 ViroSeq 检测到 2 种。veSEQ-HIV 估计的 HIV 病毒载量与 Abbott RealTime 病毒载量测定的结果密切相关 ( R ² = 0.85; n  =  142）。

结论

与基于群体测序的方法相比，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 DRM 是准确的，并且检测到的突变水平较低。veSEQ-HIV 方法还提供了 HIV 病毒载量数据。