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

项目总结 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，并将艾滋病毒感染从 一种致命的疾病到一种可控制的慢性病。然而，尽管病毒复制在 在治疗方面，研究表明，潜伏的病毒库仍然可被检测到，这助长了病毒的反弹 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 一旦感染，当艾滋病毒不可逆转地将其病毒基因组整合到人类DNA中时。病毒库是极其重要的 耐用，对目前可用的抗逆转录病毒药物的治疗效果不敏感，并已 对最近的实验性治疗方法难以奏效。艾滋病毒感染的特征也是高水平的 病毒准种的寄主内基因多样性。除了与遗传多样性相关的碱基替换 从长期感染的慢性感染患者中恢复的突变和病毒DNA基因组池 抑制疗法通常包含基因组截断和/或超突变、非复制的高频率- 有能力的病毒DNA基因组。这些患者中只有一小部分前病毒基因组是基因组完整的 在没有治疗的情况下，可能会导致病毒的高效复制和病毒学反弹。此外， 感染了基因组完整和基因组缺陷前病毒的HIV感染细胞被证明 克隆性扩张，作为艾滋病毒持续存在的机制。然而，我们目前对艾滋病毒的理解 水库几乎完全来自对一种名为B亚型HIV-1的毒株的研究，这种毒株是主要的 影响第一世界国家的病毒亚型只占全球疫情的10%。相比之下，非B型艾滋病毒- 1亚型在全球疾病负担最高的撒哈拉以南非洲等地区占主导地位。 其他HIV-1亚型感染的其余90%的人是否在宿主大小上存在差异仍是个问题 和作曲。为了解决这个问题，我们将利用之前由NIH资助的现有生物库 乌干达艾滋病毒队列(UARTO)，其中包括十年来纵向收集的12360个血细胞样本 来自500名主要是A1和D亚型HIV-1感染者。我们将使用三个尖端技术 技术(1)Flip-SEQ获得接近全长的HIV-1 DNA基因组图谱，(2)MIP-SEQ共同捕获HIV-1 1整合位点和病毒基因组，以及(3)和完整的前病毒DNA分析(IPDA)进行纵向测量 储集层的衰变/膨胀率。所有这三项技术都让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。跨子类型，我们将比较储集层特征 包括绝对基因组完整的储存库大小、克隆扩张程度、整合位点分布、病毒 启动子基因类型，以及纵向衰变/扩张动力学。我们将进一步调查人口统计， 与基因组完整的病毒相关的临床和宿主因素。总体而言，我们的目标是找出差异或不足 的差异，HIV-1亚型储备库之间的差异，以告知HIV治愈研究的努力是否有治愈策略 应该是特定于子类型的。

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.