Meixenberger Karolin, Yousef Kaveh Pouran, Somogyi Sybille, Fiedler Stefan, Bartmeyer Barbara, von Kleist Max, Kücherer Claudia
HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany.
Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
J Int AIDS Soc. 2014 Nov 2;17(4 Suppl 3):19746. doi: 10.7448/IAS.17.4.19746. eCollection 2014.
The aim of our study was to analyze the occurrence and evolution of HIV-1 integrase polymorphisms during the HIV-1 epidemic in Germany prior to the introduction of the first integrase inhibitor raltegravir in 2007.
Plasma samples from drug-naïve HIV-1 infected individuals newly diagnosed between 1986 and 2006 were used to determine PCR-based population sequences of the HIV-1 integrase (amino acids 1-278). The HIV-1 subtype was determined using the REGA HIV-1 subtyping tool. We calculated the frequency of amino acids at each position of the HIV-1 integrase in 337 subtype B strains for the time periods 1986-1989, 1991-1994, 1995-1998, 1999-2002, and 2003-2006. Positions were defined as polymorphic if amino acid variation was >1% in any period. Logistic regression was used to identify trends in amino acid variation over time. Resistance-associated mutations were identified according to the IAS 2013 list and the HIVdb, ANRS and GRADE algorithms.
Overall, 56.8% (158/278) amino acid positions were polymorphic and 15.8% (25/158) of these positions exhibited a significant trend in amino acid variation over time. Proportionately, most polymorphic positions (63.3%, 31/49) were detected in the N-terminal zinc finger domain of the HIV-1 integrase. Motifs and residues essential for HIV-1 integrase activity were little polymorphic, but within the minimal non-specific DNA binding region I220-D270 up to 18.1% amino acid variation was noticed, including four positions with significant amino acid variation over time (S230, D232, D256, A265). No major resistance mutations were identified, and minor resistance mutations were rarely observed without trend over time. E157Q considered by HIVdb, ANRS, and GRADE algorithms was the most frequent resistance-associated polymorphism with an overall prevalence of 2.4%.
Detailed knowledge of the evolutionary variation of HIV-1 integrase polymorphisms is important to understand the development of resistance in the presence of the drug. Our results will contribute to define the relevance of integrase polymorphisms in HIV-strains resistant to integrase inhibitors and to improve resistance interpretation algorithms.
我们研究的目的是分析在2007年第一种整合酶抑制剂拉替拉韦引入德国之前，HIV-1疫情期间HIV-1整合酶多态性的发生和演变情况。
使用1986年至2006年间新诊断的未接受过抗逆转录病毒治疗的HIV-1感染个体的血浆样本，通过聚合酶链反应（PCR）确定HIV-1整合酶（氨基酸1-278）的群体序列。使用REGA HIV-1亚型分型工具确定HIV-1亚型。我们计算了1986 - 1989年、1991 - 1994年、1995 - 1998年、1999 - 2002年和2003 - 2006年期间337株B亚型毒株中HIV-1整合酶每个位置氨基酸的频率。如果在任何时间段内氨基酸变异>1%，则该位置被定义为多态性位置。使用逻辑回归来确定氨基酸变异随时间的趋势。根据国际艾滋病协会（IAS）2013年列表以及HIVdb、法国国家艾滋病研究机构（ANRS）和全球抗药性和治疗效果评估（GRADE）算法来鉴定耐药相关突变。
总体而言，56.8%（158/278）的氨基酸位置是多态性的，其中15.8%（25/158）的位置在氨基酸变异上呈现出随时间的显著趋势。按比例计算，大多数多态性位置（63.3%，31/49）在HIV-1整合酶的N端锌指结构域中被检测到。对于HIV-1整合酶活性至关重要的基序和残基多态性较小，但在最小非特异性DNA结合区域I220 - D270内，观察到高达18.1%的氨基酸变异，包括四个随时间有显著氨基酸变异的位置（S230、D232、D256、A265）。未鉴定出主要耐药突变，并且很少观察到无随时间变化趋势的次要耐药突变。根据HIVdb、ANRS和GRADE算法被认定的E157Q是最常见的耐药相关多态性，总体流行率为2.4%。
详细了解HIV-1整合酶多态性的进化变异对于理解在药物存在情况下耐药性的发展很重要。我们的结果将有助于确定整合酶多态性在对整合酶抑制剂耐药的HIV毒株中的相关性，并改进耐药性解释算法。
