Department of Pathology, Stanford University School of Medicine, Stanford, California.
Clinical Virology Laboratory, Stanford Health Care, Stanford, California.
J Mol Diagn. 2019 Nov;21(6):961-970. doi: 10.1016/j.jmoldx.2019.06.003. Epub 2019 Aug 2.
Genotypic antiretroviral drug resistance testing is a critical component of the global efforts to control the HIV-1 epidemic. This study investigates the semiautomated, next-generation sequencing (NGS)-based Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay in a prospective cohort of HIV-1-infected patients. Two-hundred sixty-nine samples were successfully sequenced by both NGS and Sanger sequencing. Among the 261 protease/reverse transcriptase (PR/RT) sequences, a mean of 0.37 drug resistance mutations were identified by both Sanger and NGS, 0.08 by NGS alone, and 0.03 by Sanger alone. Among the 50 integrase sequences, a mean of 0.3 drug resistance mutations were detected by both Sanger and NGS, and 0.08 by NGS alone. NGS estimated higher levels of drug resistance to one or more antiretroviral drugs for 6.5% of PR/RT sequences and 4.0% of integrase sequences, whereas Sanger estimated higher levels of drug resistance for 3.8% of PR/RT sequences. Although the samples successfully sequenced by the Sentosa SQ HIV Genotyping Assay demonstrated similar predicted resistance compared with Sanger, 44% of Sentosa runs failed quality control requiring 17 additional runs. This semi-automated NGS-based assay may aid in HIV-1 genotypic drug resistance testing, though numerous quality control issues were observed when this platform was used in a clinical laboratory setting. With additional refinement, the Sentosa SQ HIV-1 Genotyping Assay may contribute to the global efforts to control HIV-1.
基因型抗逆转录病毒药物耐药性检测是控制 HIV-1 流行的全球努力的重要组成部分。本研究调查了前瞻性 HIV-1 感染患者队列中半自动、基于下一代测序（NGS）的 Vela Diagnostics Sentosa SQ HIV-1 基因分型检测。成功对 269 个样本进行了 NGS 和 Sanger 测序。在 261 个蛋白酶/逆转录酶（PR/RT）序列中，通过 Sanger 和 NGS 均鉴定出平均 0.37 个耐药突变，通过 NGS 单独鉴定出 0.08 个，通过 Sanger 单独鉴定出 0.03 个。在 50 个整合酶序列中，通过 Sanger 和 NGS 均检测到平均 0.3 个耐药突变，通过 NGS 单独检测到 0.08 个。NGS 估计对一种或多种抗逆转录病毒药物的耐药水平高于 PR/RT 序列的 6.5%和整合酶序列的 4.0%，而 Sanger 估计 PR/RT 序列的耐药水平高于 3.8%。虽然 Sentosa SQ HIV 基因分型检测成功测序的样本与 Sanger 相比显示出相似的预测耐药性，但 44%的 Sentosa 运行失败需要 17 个额外的运行来进行质量控制。这种半自动的基于 NGS 的检测方法可能有助于 HIV-1 基因型药物耐药性检测，尽管在临床实验室环境中使用该平台时观察到了许多质量控制问题。随着进一步改进，Sentosa SQ HIV-1 基因分型检测可能有助于控制 HIV-1 的全球努力。
