Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.
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DOI：
10.1371/journal.ppat.1002529
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发表时间：
2012
期刊：
影响因子：
6.7
通讯作者：
Allen TM
中科院分区：
文献类型：
--
作者：
Henn MR;Boutwell CL;Charlebois P;Lennon NJ;Power KA;Macalalad AR;Berlin AM;Malboeuf CM;Ryan EM;Gnerre S;Zody MC;Erlich RL;Green LM;Berical A;Wang Y;Casali M;Streeck H;Bloom AK;Dudek T;Tully D;Newman R;Axten KL;Gladden AD;Battis L;Kemper M;Zeng Q;Shea TP;Gujja S;Zedlack C;Gasser O;Brander C;Hess C;Günthard HF;Brumme ZL;Brumme CJ;Bazner S;Rychert J;Tinsley JP;Mayer KH;Rosenberg E;Pereyra F;Levin JZ;Young SK;Jessen H;Altfeld M;Birren BW;Walker BD;Allen TM
深度测序技术通过提供一种快速和经济有效的方法来敏感地表征快速进化的病毒准种，有可能改变对高度可变的病毒病原体的研究。在这里，我们报告了一个高通量的HIV-1全基因组深度测序平台，它结合了454焦磷酸测序与新的组装和变异检测算法。在一项研究中，我们将这些基因数据与详细的免疫学分析相结合，以全面评估HIV-1感染急性期的病毒进化和免疫逃逸。大多数早期的低频率突变代表了病毒对宿主CD8+T细胞反应的适应性，这证明了在病毒血症高峰期的早期下降期间发生了强大的免疫选择压力。能够识别这些低频逃逸变异体的CD8+T细胞反应与更有效的次级HLA锚逃逸突变的选择和进化是一致的。在整个病毒基因组中也观察到了频繁的，在某些情况下，传播的突变迅速逆转。当位于限制性CD8表位时，这些低频回复突变足以启动对这些表位的从头反应，再次说明免疫反应识别和响应低频变异的能力。更重要的是，病毒从最主要的免疫优势CD8+T细胞反应中迅速逃逸的同时，本研究对象的初始病毒载量下降处于停滞状态，这表明维持有效的、主要的CD8反应与早期病毒血症的减少程度之间存在潜在的联系。我们的结论是，免疫优势的CD8+T细胞反应对HIV-1复制的早期控制可能受到常规测序方法检测不到的快速、低频病毒适应的显著影响，这值得进一步研究。这些数据支持疫苗诱导的CD8+T细胞反应针对病毒更高限制区域的迫切需要，以确保维持免疫优势的CD8反应和早期病毒血症的持续下降。HIV-1和其他高度可变的病原体快速突变以逃避疫苗诱导的免疫反应的能力是开发针对这些高度持久的病原体的有效疫苗的主要障碍。将下一代或深度测序技术应用于宿主病原体的研究，可以显著提高我们对这些病原体颠覆宿主免疫的机制的理解，并有助于开发新的疫苗和治疗方法。在这里，我们开发了一种454深度测序方法，能够灵敏地检测整个HIV-1基因组中的低频病毒变异。当应用于HIV-1感染的急性期时，我们观察到大多数早期、低频率的突变代表了病毒对宿主细胞免疫反应的适应，这是在病毒载量高峰下降的早期发展出强大宿主免疫的证据。然而，病毒快速逃脱最主要的免疫反应与失去这种最初的病毒控制有关，这表明针对病毒更保守区域的免疫反应的重要性。这些数据提供了对颠覆宿主免疫反应控制早期HIV-1复制能力的早期进化事件的更多了解，为设计更有效的疫苗策略提供了重要的见解。
Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms. In one subject we combined these genetic data with detailed immunological analyses to comprehensively evaluate viral evolution and immune escape during the acute phase of HIV-1 infection. The majority of early, low frequency mutations represented viral adaptation to host CD8+ T cell responses, evidence of strong immune selection pressure occurring during the early decline from peak viremia. CD8+ T cell responses capable of recognizing these low frequency escape variants coincided with the selection and evolution of more effective secondary HLA-anchor escape mutations. Frequent, and in some cases rapid, reversion of transmitted mutations was also observed across the viral genome. When located within restricted CD8 epitopes these low frequency reverting mutations were sufficient to prime de novo responses to these epitopes, again illustrating the capacity of the immune response to recognize and respond to low frequency variants. More importantly, rapid viral escape from the most immunodominant CD8+ T cell responses coincided with plateauing of the initial viral load decline in this subject, suggestive of a potential link between maintenance of effective, dominant CD8 responses and the degree of early viremia reduction. We conclude that the early control of HIV-1 replication by immunodominant CD8+ T cell responses may be substantially influenced by rapid, low frequency viral adaptations not detected by conventional sequencing approaches, which warrants further investigation. These data support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia. The ability of HIV-1 and other highly variable pathogens to rapidly mutate to escape vaccine-induced immune responses represents a major hurdle to the development of effective vaccines to these highly persistent pathogens. Application of next-generation or deep sequencing technologies to the study of host pathogens could significantly improve our understanding of the mechanisms by which these pathogens subvert host immunity, and aid in the development of novel vaccines and therapeutics. Here, we developed a 454 deep sequencing approach to enable the sensitive detection of low-frequency viral variants across the entire HIV-1 genome. When applied to the acute phase of HIV-1 infection we observed that the majority of early, low frequency mutations represented viral adaptations to host cellular immune responses, evidence of strong host immunity developing during the early decline of peak viral load. Rapid viral escape from the most dominant immune responses however correlated with loss of this initial viral control, suggestive of the importance of mounting immune responses against more conserved regions of the virus. These data provide a greater understanding of the early evolutionary events subverting the ability of host immune responses to control early HIV-1 replication, yielding important insight into the design of more effective vaccine strategies.
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