McGill University AIDS Centre, Lady Davis Institute of Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
Antimicrob Agents Chemother. 2013 Oct;57(10):4681-8. doi: 10.1128/AAC.01029-13. Epub 2013 Jul 15.
E138K, a G→A mutation in HIV-1 reverse transcriptase (RT), is preferentially selected by etravirine (ETR) and rilpivirine over other substitutions at position E138 that offer greater drug resistance. We hypothesized that there was a mutational bias for the E138K substitution and designed an allele-specific PCR to monitor the emergence of E138A/G/K/Q/R/V during ETR selection experiments. We also performed competition experiments using mutated viruses and quantified the prevalence of E138 minority species in drug-naive patients. E138K, as well as E138G, consistently emerged first during ETR selection experiments, followed by E138A and E138Q; E138R was never selected. Surprisingly, E138K was identified as a tiny minority in 23% of drug-naive subtype B patients, a result confirmed by ultradeep sequencing (UDS). This result could reflect a low fitness cost of E138K; however, E138K was one of the least fit substitutions at codon E138, even after taking into account the deoxynucleoside triphosphate pools of the cells used in competition experiments. Further UDS analysis revealed other minority species in a pattern consistent with the mutational bias of HIV RT. There was no evidence of APOBEC3-hypermutation in these selection experiments or in patients. Our results confirm the mutational bias of HIV-1 in patients and highlight the importance of G→A mutations in HIV-1 drug resistance evolution.
E138K，HIV-1 逆转录酶（RT）中的 G→A 突变，在 ETR 和 rilpivirine 中比位置 E138 中的其他突变更优先选择，这些突变提供了更大的耐药性。我们假设存在 E138K 取代的突变偏向性，并设计了等位基因特异性 PCR 来监测 ETR 选择实验中 E138A/G/K/Q/R/V 的出现。我们还使用突变病毒进行了竞争实验，并量化了在未经药物治疗的患者中 E138 少数物种的流行率。E138K 和 E138G 在 ETR 选择实验中始终首先出现，其次是 E138A 和 E138Q；E138R 从未被选择。令人惊讶的是，在 23%的未经药物治疗的 B 亚型患者中，E138K 被鉴定为少数，这一结果通过超深度测序（UDS）得到证实。这一结果可能反映了 E138K 的低适应性成本；然而，E138K 是 E138 密码子中适应能力最差的取代之一，即使考虑到竞争实验中细胞的脱氧核苷三磷酸池也是如此。进一步的 UDS 分析揭示了其他少数物种的存在模式与 HIV RT 的突变偏向性一致。在这些选择实验或患者中没有证据表明 APOBEC3 超突变。我们的结果证实了 HIV-1 在患者中的突变偏向性，并强调了 HIV-1 耐药性进化中 G→A 突变的重要性。
