Characterization of Non-subtype B HIV-1 Reservoirs and its Association with Longitudinal Clinical Outcomes

项目摘要 目前的艾滋病毒抗逆转录病毒治疗成功地控制了病毒复制， 从致命的疾病到可控的慢性病然而，尽管抑制病毒复制期间， 研究表明，潜伏的病毒库仍然是可检测的，这助长了病毒反弹。 当抗病毒抑制治疗中断时。这些病毒库几乎是立即建立起来的 当HIV不可逆地将其病毒基因组整合到人类DNA中时，病毒宿主非常 持久，不易受目前可用的抗逆转录病毒药物的治疗效果的影响， 对最近的实验性治疗方法难治。艾滋病毒感染的另一个特点是， 病毒准种的宿主内基因型多样性。除了与碱基替换相关的遗传多样性之外， 突变，从慢性感染患者中回收的病毒DNA基因组池， 抑制性治疗通常含有高频率基因组截短和/或高度突变的、非复制的 病毒DNA基因组。在这些患者中只有一小部分前病毒基因组是基因组完整的 并且在没有治疗的情况下可能导致生产性病毒复制和病毒学反弹。此外，委员会认为， 已经证明，用基因组完整和基因组缺陷的前病毒感染的HIV感染细胞， 克隆扩展，作为HIV持续存在的机制。然而，我们目前对艾滋病毒的理解 储存库几乎完全来自对一种称为B亚型HIV-1的毒株的研究， 病毒亚型影响第一世界国家，但只占全球流行病的10%。相反，非B型艾滋病毒- 1亚型主要分布在撒哈拉以南非洲等地区，那里的疾病负担是全球最高的。 剩下的90%的其他HIV-1亚型感染是否在储存库大小上存在差异， 和组合物。为了解决这个问题，我们将利用以前NIH资助的现有生物库， 乌干达艾滋病毒队列（UARTO），其中包含10年来纵向收集的12360份血细胞样本 来自500名主要为A1和D亚型的HIV-1感染者。我们将使用三个尖端的 技术（1）FLIP-seq，获得近全长HIV-1 DNA基因组图谱，（2）MIP-seq，共捕获HIV- 1整合位点和病毒基因组，和（3）和完整的前病毒DNA测定（IPDA），以纵向测量 储层的衰减/膨胀率。这三种技术都使我们能够专注于罕见的完整病毒DNA 基因组是艾滋病毒治疗策略的目标。在子类型之间，我们将比较储层特征 包括绝对基因组完整库大小、克隆扩增程度、整合位点分布、病毒 启动子基因型和纵向衰变/扩增动力学。我们将进一步调查人口统计学， 与基因组完整病毒相关的临床和宿主因素。总的来说，我们的目标是找出差异，或缺乏 的差异，艾滋病毒-1亚型之间的水库，以告知艾滋病毒治愈的研究工作，是否治愈策略 应该是亚型特异性的

PROJECT SUMMARY Current HIV antiretroviral treatment successfully controls viral replication and has transformed HIV-infection from a fatal illness to a manageable chronic condition. However, despite suppression of viral replication during treatment, studies have shown that pools of latent viral reservoirs remain detectable, which fuel viral rebound when antiviral suppression treatment is interrupted. These viral reservoirs are established almost immediately upon infection when HIV irreversibly integrates its viral genome into human DNA. Viral reservoirs are extremely durable, not susceptible to therapeutic effects of currently available antiretroviral agents, and have been refractory to recent experimental treatment approaches. HIV infection is also characterized by a high level of intrahost genotypic diversity of viral quasispecies. In addition to genetic diversity associated base substitution mutations, pools of viral DNA genomes recovered from chronically-infected patients under prolonged suppressive therapy often contain high frequencies of genome-truncated and/or hypermutated, non-replication- competent viral DNA genomes. Only a small fraction of proviral genomes in these patients are genome-intact and may lead to productive viral replication and virologic rebound in the absence of treatment. Furthermore, HIV-infected cells infected with both genome-intact and genome-defective proviruses have been shown to clonally expand, serving as a mechanism of HIV persistence. However, our current understanding of HIV reservoirs has been derived almost exclusively from studies on a strain called subtype B HIV-1, the predominate viral subtype affecting first-world nations but only makes up 10% of the global epidemic. In contrast, non-B HIV- 1 subtypes predominate regions such as sub-Saharan Africa where disease burden is the highest globally. Questions remain on whether the remaining 90% of infections by other HIV-1 subtypes differ in reservoir sizes and compositions. To address this question, we will leverage an existing biobank of a previously NIH-funded Ugandan HIV cohort (UARTO), which houses 12360 blood cell samples collected longitudinally over ten years from 500 predominantly subtype A1 and D HIV-1-infected individuals. We will use three cutting-edge technologies (1) FLIP-seq to obtain near-full-length HIV-1 DNA genomes profiles, (2) MIP-seq to co-capture HIV- 1 integration sites and viral genome, and (3) and the Intact Proviral DNA Assay (IPDA) to longitudinally measure the decay/expansion rate of the reservoir. All three technologies allow us to focus on the rare intact viral DNA genomes that is the target for HIV cure strategies. Across subtypes, we will compare reservoir characteristics including absolute genome-intact reservoir sizes, extent of clonal expansion, integration site profiles, viral promoter genotypes, and longitudinal decay/expansion dynamics. We will further investigate demographic, clinical and host factors associated with genome-intact viruses. Overall, we aim identify differences, or the lack of differences, between HIV-1 subtype reservoirs to inform HIV cure research effort on whether a cure strategy should be subtype-specific.