Mutational pathways in early HIV infection: novel guide to immunologic analyses

描述（由申请人提供）：缺乏对保护相关关系的理解可能在于，至少部分原因是，历史上病毒与宿主的相互作用没有被交互式地研究过，而是专注于方程的单面。本研究的假设是建立在自然HIV-1感染中的病毒突变途径受到病毒体内进化空间的限制，以及给定宿主内的病毒进化空间受到免疫反应和病毒适应性之间动态平衡的限制的假设之上。我们假设，全面评估HIV-1感染早期的病毒突变途径可能有助于制定特定的免疫学问题，从而对病毒特异性免疫反应进行彻底的相互作用分析，并有可能更好地了解HIV的发病机制。应用Gag突变沿HIV-1感染时间线直接映射的新方法，病毒动力学模式将被评估，特别关注不同类型病毒突变之间的时间和关系，并将转化为一系列特定的免疫学假设，揭示病毒-宿主相互作用的机制。目的1：鉴定和表征HIV-1C Gag突变途径。利用具有估计血清转化时间的前瞻性样本集，并应用单基因组扩增/测序和超深度测序（在一个子集中），绘制HIV-1C Gag病毒突变的出现时间、优势和完整性（或短暂性/缺失）。目的2：设计一系列免疫学相关假设，关注免疫反应与病毒突变途径之间的动态相互作用。具体的免疫学问题将基于实际的突变途径来解决，因此，将改进现有的评估原发性HIV感染中病毒特异性T细胞反应的方法，并将有助于在未来的研究中探索免疫保护的相关性和机制。提出的研究将揭示宿主-病毒相互作用的早期进化动力学，并可能实现更好的免疫原设计。

DESCRIPTION (provided by applicant): The lack of understanding of the correlates of protection may lie, at least partially, in the fact that historically virus-host interactions have not been studied interactively, but rather by focusing on a single side of the equation. The hypothesis of this study is built on the assumptions that viral mutational pathways in natural HIV-1 infection are restricted by the viral in vivo evolutionary space, and that viral evolutionary space within a given host is confined by a dynamic balance between immune responses and viral fitness. We hypothesize that comprehensive assessment of viral mutational pathways in the early phase of HIV-1 infection may help in formulating specific immunologic questions leading to thorough interactive analysis of virus-specific immune responses, and is likely to result in better understanding of HIV pathogenesis. Applying a novel approach of direct mapping of Gag mutations along the time line of HIV-1 infection, patterns of viral dynamics will be assessed with a particular focus on timing and relationships between different types of viral mutations, and will be translated to a series of specific immunologic hypotheses revealing the mechanisms of virus-host interactions. Aim 1: To identify and characterize HIV-1C Gag mutational pathways. To map time of appearance, dominance, and completeness (or transiency/loss) of viral mutations in HIV-1C Gag by utilizing prospective sample sets with estimated time of seroconversion and applying single-genome amplification/sequencing and ultra-deep sequencing (in a subset). Aim 2: To design a series of immunologically relevant hypotheses focusing on the dynamic interactions between immune responses and viral mutational pathways. The specific immunologic questions will be addressed based on actual mutational pathways, and therefore, will improve existing methods of assessing virus-specific T cell responses in primary HIV infection, and will help to explore correlates and mechanisms of immune protection in future studies. The proposed study will reveal early evolutionary dynamics of host-virus interactions, and will likely enable better immunogen design. PUBLIC HEALTH RELEVANCE: The lack of understanding of the correlates of protection may lie, at least partially, in the fact that historically virus-host interactions have not been studied interactively, but rather by focusing on a single side of the equation. The study will apply a novel approach of direct mapping of Gag mutations along the time line of HIV-1 infection, and will asses patterns of viral dynamics with a particular focus on timing and relationships between different types of viral mutations. Results will be translated to a series of specific immunologic hypotheses revealing the mechanisms of virus-host interactions.