Abstract: The rapid expansion of access to antiretroviral therapy (ART) has led to the emergence of multi-class drug resistance (MDR) in people living with HIV (PLWH). However, the viral evolutionary dynamics of the development of MDR has not been well documented. For this study, plasma and peripheral blood mononuclear cells (PBMC) were longitudinally collected at different time points from a PLWH who suffered several periods of ART failure. Next generation sequencing (NGS) was used to analyze the distribution and percent of drug resistance mutations in PBMC and plasma. The results showed the gradual replacement of the wild type protease and integrase genotype by protease inhibitors (PI) and integrase strand transfer inhibitor (INSTI) drug resistant mutations when patient’s ART regimen was changed – driving the increase of genetic variability in HIV DNA. Sampling for this study was initiated after the patient was first diagnosed with ART failure, five years after ART treatment was first initiated. By that time, mutants resistant to the reverse transcriptase inhibitor nevirapine (NVP) had already replaced almost 100% of wild type. After the introduction of the protease inhibitor lopinavir/ritonavir (LPV/r) to the patient’s ART, resistant protease inhibitor (PI) mutants developed slowly. After one month, none were found in PMBC DNA; after sixteen months, less than 20% were mutants; and after three years (two months prior to the patient’s death) PI mutants were still under 50%. However, integrase strand transfer inhibitor (INSTI) mutations evolved much more quickly, replacing approximately 75% of the wild genotype in HIV DNA one year after addition of the integrase inhibitor raltegravir to the patient’s ART, and almost 100% after two years. In summary, our dataset provides the first analysis of the distribution and percent of drug resistance mutations in PBMC and plasma during the development of a four-class drug resistant HIV-1 CRF01_AE virion. The study also showed that months before drug resistant mutants could be found in plasma, NGS identified them in HIV DNA, demonstrating that this can be a very effective tool for early detection of the development of drug resistance.

Keywords: multi-class drug resistance, HIV, CRF01_AE, ART, NGS, HIV DNA


中文翻译：

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感染 HIV-1 CRF01_AE 的个体中多类耐药性的患者体内发展

摘要：抗逆转录病毒疗法 (ART) 的快速普及导致 HIV 感染者 (PLWH) 出现多类耐药性 (MDR)。然而，MDR 发展的病毒进化动力学还没有得到很好的记录。在这项研究中，我们在不同时间点从一名遭受多次 ART 失败的 PLWH 纵向收集血浆和外周血单核细胞 (PBMC)。下一代测序（NGS）用于分析PBMC和血浆中耐药突变的分布和百分比。结果表明，当患者的 ART 方案改变时，蛋白酶抑制剂 (PI) 和整合酶链转移抑制剂 (INSTI) 耐药突变逐渐取代了野生型蛋白酶和整合酶基因型，从而推动了 HIV DNA 遗传变异性的增加。本研究的采样是在患者首次被诊断为 ART 失败后，即首次开始 ART 治疗五年后开始的。到那时，对逆转录酶抑制剂奈韦拉平 (NVP) 具有抗性的突变体已经取代了几乎 100% 的野生型。在将蛋白酶抑制剂洛匹那韦/利托那韦 (LPV/r) 引入患者的 ART 后，耐药蛋白酶抑制剂 (PI) 突变体发展缓慢。一个月后，在 PMBC DNA 中没有发现；16 个月后，不到 20% 是突变体；三年后（患者死亡前两个月），PI 突变体仍低于 50%。然而，整合酶链转移抑制剂（INSTI）突变进化得更快，在将整合酶抑制剂拉替拉韦添加到患者的 ART 一年后，替换了 HIV DNA 中大约 75% 的野生基因型，两年后几乎 100%。总之，我们的数据集首次分析了在四类耐药 HIV-1 CRF01_AE 病毒体开发过程中 PBMC 和血浆中耐药突变的分布和百分比。该研究还表明，在血浆中发现耐药突变体的几个月前，NGS 在 HIV DNA 中鉴定了它们，这表明这可以成为早期检测耐药性发展的非常有效的工具。我们的数据集首次分析了四类耐药 HIV-1 CRF01_AE 病毒体开发过程中 PBMC 和血浆中耐药突变的分布和百分比。该研究还表明，在血浆中发现耐药突变体的几个月前，NGS 在 HIV DNA 中鉴定了它们，这表明这可以成为早期检测耐药性发展的非常有效的工具。我们的数据集首次分析了四类耐药 HIV-1 CRF01_AE 病毒体开发过程中 PBMC 和血浆中耐药突变的分布和百分比。该研究还表明，在血浆中发现耐药突变体的几个月前，NGS 在 HIV DNA 中鉴定了它们，这表明这可以成为早期检测耐药性发展的非常有效的工具。

关键词：多类耐药性，HIV，CRF01_AE，ART，NGS，HIV DNA