Virologic Failures on Initial Boosted-PI Regimen Infrequently Possess Low-Level Variants with Major PI Resistance Mutations by Ultra-Deep Sequencing

BackgroundIt is unknown whether HIV-positive patients experiencing virologic failure (VF) on boosted-PI (PI/r) regimens without drug resistant mutations (DRM) by standard genotyping harbor low-level PI resistant variants. CASTLE compared the efficacy of atazanavir/ritonavir (ATV/r) with lopinavir/ritonavir (LPV/r), each in combination with TVD in ARV-naïve subjects. ObjectiveTo determine if VF on an initial PI/r-based regimen possess low-level resistant variants that may affect a subsequent PI-containing regimen. Methods/ResultsPatients experiencing VF on a Tenofovir/Emtricitabine+PI/r regimen were evaluated by ultra deep sequencing (UDS) for mutations classified/weighted by Stanford HIVdb. Samples were evaluated for variants to 0.4% levels. 36 VF subjects were evaluated by UDS; 24 had UDS for PI and RT DRMs. Of these 24, 19 (79.2%) had any DRM by UDS. The most common UDS-detected DRM were NRTI in 18 subjects: M184V/I (11), TAMs(7) & K65R(4); PI DRMs were detected in 9 subjects: M46I/V(5), F53L(2), I50V(1), D30N(1), and N88S(1). The remaining 12 subjects, all with VLs12 for ATV or LPV: N88S (at 0.43% level-mutational load 1,828) in 1 subject on ATV; I50V (0.44%-mutational load 110) and L76V (0.52%-mutational load 20) in 1 subject each, both on LPV. All VF samples remained phenotypically susceptible to the treatment PI/r. ConclusionAmong persons experiencing VF without PI DRMs with standard genotyping on an initial PI/r regimen, low-level variants possessing major PI DRMs were present in a minority of cases, occurred in isolation, and did not result in phenotypic resistance. NRTI DRMs were detected in a high proportion of subjects. These data suggest that PIs may remain effective in subjects experiencing VF on a PI/r-based regimen when PI DRMs are not detected by standard or UDS genotyping.【背景】目前尚不明确，接受增强型蛋白酶抑制剂（boosted protease inhibitor, PI/r）方案治疗后出现病毒学失败（virologic failure, VF）且经标准基因分型未检出药物耐药突变（drug resistant mutations, DRM）的HIV阳性患者，是否携带低水平PI类耐药变异株。CASTLE试验对比了阿扎那韦/利托那韦（ATV/r）与洛匹那韦/利托那韦（LPV/r）分别联合TVD在初治抗反转录病毒受试者中的疗效。 【研究目的】旨在明确初始基于PI/r方案治疗后出现病毒学失败的患者，是否存在可能影响后续含PI类药物方案的低水平耐药变异株。 【方法与结果】对接受替诺福韦/恩曲他滨+PI/r方案治疗后出现病毒学失败的患者，采用超深度测序（ultra deep sequencing, UDS），依据斯坦福HIV数据库（Stanford HIVdb）对突变进行分类与权重赋值。本研究对变异株的检测灵敏度可达0.4%的检出限。共纳入36例病毒学失败受试者接受UDS检测，其中24例同时针对PI与逆转录酶（RT）耐药突变开展UDS检测。此24例受试者中，19例（79.2%）经UDS检出至少1种耐药突变。UDS检出的最常见耐药突变为核苷类反转录酶抑制剂（nucleoside reverse transcriptase inhibitor, NRTI）相关突变，共18例受试者：M184V/I（11例）、胸腺嘧啶类似物突变（thymidine analog mutations, TAMs，7例）与K65R（4例）；PI类相关耐药突变则在9例受试者中检出：M46I/V（5例）、F53L（2例）、I50V（1例）、D30N（1例）及N88S（1例）。其余12例受试者均接受ATV或LPV治疗，其中1例接受ATV治疗的受试者检出N88S突变（检出比例0.43%，突变负荷1828）；2例分别接受LPV治疗的受试者各检出I50V（0.44%，突变负荷110）与L76V（0.52%，突变负荷20）突变。所有病毒学失败样本对治疗用PI/r均表现为表型敏感。 【结论】对于初始接受PI/r方案治疗、经标准基因分型未检出PI类相关耐药突变但出现病毒学失败的患者，携带主要PI类耐药突变的低水平变异株仅在少数病例中检出，且以孤立突变形式存在，未导致表型耐药。核苷类反转录酶抑制剂耐药突变在高比例受试者中可被检出。本研究数据提示，若经标准基因分型或超深度测序未检出PI类相关耐药突变，那么PI类药物对于接受PI/r方案治疗后出现病毒学失败的患者仍可能保持临床有效性。