Chen Xi, Zou Xiaobai, He Jianmei, Zheng Jun, Chiarella Jennifer, Kozal Michael J
Hunan Provincial Center for Disease Control and Prevention, Changsha, China.
Yale School of Medicine, New Haven, United States of America.
PLoS One. 2016 Feb 19;11(2):e0149215. doi: 10.1371/journal.pone.0149215. eCollection 2016.
Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF).
29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels.
DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×10(4) c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1-4% and 24 (60%) at levels of 5-19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS.
DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.
确定经历病毒学失败（VF）的接受抗逆转录病毒治疗（ART）患者中低水平和高水平HIV耐药突变（DRM）的流行情况。
对来自湖南省18个县的29例经历VF的受试者进行评估，通过Sanger测序（SS）和深度测序（DS）检测DRM的流行情况（斯坦福DRM算法值≥15，包括低、中和高水平耐药），检测频率水平为1%。
对29例接受ART治疗的受试者的样本进行了DS检测；病毒载量中位数为4.95×10(4) c/ml；82.76%为CRF01_AE亚型。DS检测到58个DRM，SS检测到18个DRM。在DS检测到的58个突变中，40个频率水平<20%（26个非核苷类逆转录酶抑制剂突变、12个核苷类逆转录酶抑制剂突变和2个蛋白酶抑制剂突变），其中95.00%（(38/40)）的突变通过标准基因分型未检测到。在这40个低水平DRM中，16个（40%）频率水平为1 - 4%，24个（60%）频率水平为5 - 19%。SS检测到DS检测出的17个（88.24%）频率水平≥20%的DRM中的15个。与DS检测到DRM相关的唯一变量是ART依从性（过去7天内漏服剂量）；所有报告在过去7天内漏服一剂的患者DS检测到有DRM。
对主要感染AE亚型的接受治疗受试者的VF样本进行DS检测，经常能识别出算法值≥15的斯坦福HIV数据库核苷类逆转录酶抑制剂和非核苷类逆转录酶抑制剂耐药突变。在接受抗逆转录病毒治疗受试者来源的VF标本中，DS检测到的低频耐药变异通常会被标准基因分型遗漏。
