Santos André F A, Lengruber Renan B, Soares Esmeralda A, Jere Abhay, Sprinz Eduardo, Martinez Ana M B, Silveira Jussara, Sion Fernando S, Pathak Vinay K, Soares Marcelo A
Laboratório de Virologia Humana, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
PLoS One. 2008 Mar 12;3(3):e1781. doi: 10.1371/journal.pone.0001781.
Although extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H) is poorly understood.
We wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI.
This is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.
尽管已有大量关于HIV逆转录酶前400个氨基酸的耐药信息，但抗逆转录病毒治疗对Pol蛋白C端结构域（拇指区、连接区和核糖核酸酶H区）的影响仍知之甚少。
我们旨在对HIV-1 M组亚型和重组体中逆转录酶C端结构域的保守区域进行特征分析。此外，我们希望鉴定HIV-1逆转录酶C端结构域中与核苷类逆转录酶抑制剂（NRTI）相关的突变。我们对巴西临床病毒分离株的118个核糖核酸酶H结构域进行了测序，并分析了从公共HIV序列数据库收集的510个拇指区和连接区结构域序列以及450个核糖核酸酶H结构域序列，同时分析了它们的治疗状态和病史。对未接受过治疗和接受过NRTI治疗的数据集进行组内和组间保守性比较，并使用Fisher精确检验确定差异。发现M组变体中三分之一的逆转录酶C端残基是保守的。在仅接受过NRTI治疗的分离株中发现了三个突变。在B亚型中，连接区的九个突变和核糖核酸酶H的六个突变与NRTI治疗相关。其中一些突变位于接触核酸的氨基酸残基处或附近，或靠近核糖核酸酶H活性位点。本文指出的几个残基最近与NRTI暴露有关或增加了对NRTI的耐药性。
这是首次对一个大型序列数据集进行全面的基因型分析，该数据集描述了体内HIV-1逆转录酶C端结构域中与NRTI相关的突变。对逆转录酶C端结构域保守性的研究结果可能为针对这些区域的更合理药物设计方案铺平道路。
