Smyth Redmond P, Schlub Timothy E, Grimm Andrew J, Waugh Caryll, Ellenberg Paula, Chopra Abha, Mallal Simon, Cromer Deborah, Mak Johnson, Davenport Miles P
Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia.
J Virol. 2014 Mar;88(5):2891-902. doi: 10.1128/JVI.03014-13. Epub 2013 Dec 26.
HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified full-length HIV-1 genome and high-throughput sequence analysis to study recombination in gag and pol in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies.
The ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in gag and pol and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of viral dynamics and evolution, which will be useful for the design of robust antiretroviral therapies.
HIV-1感染的特征是快速产生基因多样性，这有助于病毒逃避免疫选择和抗逆转录病毒治疗。尽管重组在病毒多样性和进化中起关键作用，但对于影响高度相似基因组之间重组的基因组因素却知之甚少。在本研究中，我们使用经过最小修饰的全长HIV-1基因组和高通量序列分析来研究T细胞中gag和pol基因的重组。我们发现，在多个重组热点处重组更易发生，这些热点处的重组频率比相应的冷点高六倍。有趣的是，这些热点出现在HIV-1基因组的重要特征附近，但不在蛋白酶抑制剂或逆转录酶抑制剂耐药性突变位点的紧邻区域。我们表明，五个献血者的重组热点和冷点是一致的，并且与共受体介导的进入无关。最后，我们检查了常见的实验混杂因素，发现这些因素并不会驱动重组热点的位置。这是第一项在具有强大统计能力且紧密反映HIV-1准种之间自然重组事件的条件下，确定两个相似病毒基因组之间重组热点位置的研究。
HIV-1逃避免疫系统和抗逆转录病毒治疗的能力取决于病毒准种内的基因多样性。逆转录病毒重组是一种重要机制，有助于产生和维持这种基因多样性，但对于HIV-1基因组内重组率如何变化却知之甚少。我们测量了gag和pol基因的重组率，并确定了重组热点和冷点，表明重组并非随机发生，而是取决于潜在的基因序列。这些重组热点和冷点的强度和位置可用于改进病毒动力学和进化模型，这将有助于设计有效的抗逆转录病毒疗法。
