利用下一代测序技术在大型国际队列中检测到的传播性 HIV-1 耐药性：来自抗逆转录病毒治疗时机选择（START）研究的结果。
Transmitted HIV-1 drug resistance in a large international cohort using next-generation sequencing: results from the Strategic Timing of Antiretroviral Treatment (START) study.
机构信息
Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA.
Institute for Global Health, UCL, London, UK.
出版信息
HIV Med. 2021 May;22(5):360-371. doi: 10.1111/hiv.13038. Epub 2020 Dec 25.
OBJECTIVES
The aim of this analysis was to characterize transmitted drug resistance (TDR) in Strategic Timing of Antiretroviral Treatment (START) study participants by next-generation sequencing (NGS), a sensitive assay capable of detecting low-frequency variants.
METHODS
Stored plasma from participants with entry HIV RNA > 1000 copies/mL were analysed by NGS (Illumina MiSeq). TDR was based on the WHO 2009 surveillance definition with the addition of reverse transcriptase (RT) mutations T215N and E138K, and integrase strand transfer inhibitor (INSTI) surveillance mutations (Stanford HIVdb). Drug resistance mutations (DRMs) detected at three thresholds are reported: > 2%, 5% and 20% of the viral population.
RESULTS
Between 2009 and 2013, START enrolled 4684 antiretroviral therapy (ART)-naïve individuals in 35 countries. Baseline NGS data at study entry were available for 2902 participants. Overall prevalence rates of TDR using a detection threshold of 2%/5%/20% were 9.2%/5.6%/3.2% for nucleoside reverse transcriptase inhibitors (NRTIs), 9.2%/6.6%/4.9% for non-NRTIs, 11.4%/5.5%/2.4% for protease inhibitors (PIs) and 3.5%/1.6%/0.1% for INSTI DRMs and varied by geographic region. Using the 2% detection threshold, individual DRMs with the highest prevalence were: PI M46IL (5.5%), RT K103NS (3.5%), RT G190ASE (3.1%), T215ISCDVEN (2.5%), RT M41L (2.2%), RT K219QENR (1.7%) and PI D30N (1.6%). INSTI DRMs were detected almost exclusively below the 20% detection threshold, most commonly Y143H (0.4%), Q148R (0.4%) and T66I (0.4%).
CONCLUSIONS
Use of NGS in this study population resulted in the detection of a large proportion of low-level variants which would not have been detected by traditional Sanger sequencing. Global surveillance studies utilizing NGS should provide a more comprehensive assessment of TDR prevalence in different regions of the world.
目的
本分析旨在通过下一代测序（NGS）对开始抗逆转录病毒治疗（START）研究参与者的传播耐药性（TDR）进行特征描述，NGS 是一种能够检测低频变异的灵敏检测方法。
方法
采用 NGS（Illumina MiSeq）分析具有入组 HIV RNA>1000 拷贝/ml 的参与者的储存血浆。根据世界卫生组织 2009 年监测定义，加上逆转录酶（RT）突变 T215N 和 E138K，以及整合酶链转移抑制剂（INSTI）监测突变（斯坦福 HIVdb）来确定 TDR。报告三种检测阈值下检测到的耐药突变（DRMs）：病毒群的>2%、5%和 20%。
结果
2009 年至 2013 年，START 在 35 个国家招募了 4684 名未接受过抗逆转录病毒治疗（ART）的个体。2902 名参与者在研究入组时可获得基线 NGS 数据。使用检测阈值 2%/5%/20%时，核苷逆转录酶抑制剂（NRTIs）的 TDR 总体流行率分别为 9.2%/5.6%/3.2%，非核苷逆转录酶抑制剂（NNRTIs）为 9.2%/6.6%/4.9%，蛋白酶抑制剂（PI）为 11.4%/5.5%/2.4%，INSTI DRMs 为 3.5%/1.6%/0.1%，且按地理位置不同而有所差异。使用 2%的检测阈值，流行率最高的个体 DRM 为：PI M46IL（5.5%）、RT K103NS（3.5%）、RT G190ASE（3.1%）、T215ISCDVEN（2.5%）、RT M41L（2.2%）、RT K219QENR（1.7%）和 PI D30N（1.6%）。INSTI DRMs 几乎仅在 20%的检测阈值以下检测到，最常见的是 Y143H（0.4%）、Q148R（0.4%）和 T66I（0.4%）。
结论
本研究人群中使用 NGS 检测到了很大比例的低频变异，这些变异用传统的 Sanger 测序无法检测到。利用 NGS 进行的全球监测研究应该能够更全面地评估世界不同地区的 TDR 流行率。
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