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

描述(由申请人提供)：对保护的相关性缺乏了解，可能至少部分是因为历史上没有交互地研究病毒与宿主的相互作用，而是侧重于等式的单一方面。这项研究的假设建立在这样的假设之上，即自然感染HIV-1中的病毒变异路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合度之间的动态平衡的限制。我们假设，在HIV-1感染的早期阶段，对病毒突变途径的全面评估可能有助于制定特定的免疫学问题，导致对病毒特异性免疫反应的彻底交互分析，并可能导致对HIV发病机制的更好理解。应用一种沿着HIV-1感染时间线直接绘制Gag突变的新方法，将特别关注不同类型病毒突变之间的时间和关系来评估病毒动力学模式，并将转化为一系列揭示病毒与宿主相互作用机制的特定免疫学假说。目的1：鉴定和鉴定HIV-1C Gag突变途径。通过应用单基因组扩增/测序和超深度测序(在一个子集中)，利用具有估计的血清转换时间的预期样本集，绘制HIV-1C Gag中病毒突变出现的时间、显性和完整性(或瞬时/丢失)。目的2：设计一系列免疫学相关假说，重点研究免疫反应和病毒变异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，将改进现有的评估初次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。这项拟议的研究将揭示宿主-病毒相互作用的早期进化动力学，并可能使更好的免疫原设计成为可能。 公共卫生相关性：对保护的相关性缺乏了解，可能至少部分是因为历史上没有交互地研究病毒与宿主的相互作用，而是侧重于等式的单一方面。这项研究将应用一种新的方法，沿着HIV-1感染的时间线直接绘制Gag突变的图谱，并将评估病毒动力学的模式，特别关注不同类型的病毒突变之间的时间和关系。结果将被转化为一系列特定的免疫学假说，揭示病毒与宿主相互作用的机制。

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.