Intrahost HIV population dynamics in CNS and other tissues

描述（由申请人提供）：艾滋病毒在宿主体内产生复杂的遗传群体，并在抗逆转录病毒治疗下潜伏在多种细胞类型和组织中，这是治疗性治愈的障碍。然而，人们对不同组织（如中枢神经系统（CNS））中潜伏病毒库的相对大小知之甚少，对不同组织中病毒亚群之间随时间的交换就更少了。深度测序技术允许对这些种群进行广泛采样。由于对中枢神经系统中病毒多样性的采样有限，以及他们只研究单个或偶尔多个稀疏时间点，先前的研究受到了阻碍。设计可行的病毒根除策略将需要以更高的分辨率表征中枢神经系统病毒库及其种群动态。为了解决这些知识上的空白，我们将应用最近开发的技术，数字PCR （dPCR）和超深度测序（UDS），来量化组织库大小和病毒亚群的动态，存档的脑脊液细胞和上清、外周血单核细胞和血浆的纵向样本。在这里，我们将评估抗逆转录病毒治疗中断后发生的病毒亚群相互作用，这提供了稳态病毒和细胞动力学的实质性扰动，以固定观察结果。随着时间的推移，我们将应用系统发育方法对来自中枢神经系统和血液的病毒种群序列进行评估，以评估种群动态。该研究样本包括一个独特的、密集的连续抽样组，由10名接受抗逆转录病毒（ART）治疗中断或面对持续抗逆转录病毒治疗时病毒反弹的HIV+受试者组成。该项目将产生大约120万个病毒序列。将对这些进行分析，以描述中枢神经系统病毒库如何与其他病毒亚群动态相互作用，并有助于病毒多样化和致病性。该项目还将测量中枢神经系统病毒库的大小。在人类受试者去识别后，病毒序列将酌情发布在公共科学数据资源公用事业上，为本项目生成的软件将向公众开放。

DESCRIPTION (provided by applicant): HIV creates complex genetic populations within a host, and remains latent in a variety of cell types and tissues under antiretroviral therapy, representing a barrier to therapeutic cure. Yet little is known about the relative sizes of latent viral reservoirs in different tissues such as the central nervous system (CNS), and even less about exchange between viral subpopulations in different tissues over time. Deep sequencing technologies allow extensive sampling of these populations. Previous studies have been hampered by limited sampling of viral diversity in the CNS and because they studied only single or occasionally multiple, sparse time points. Designing workable viral eradication strategies will require a characterizing the CNS viral reservoir and its population dynamics with higher resolution. To address these gaps in knowledge, we will apply recently developed techniques, digital PCR (dPCR) and ultra deep sequencing (UDS), to quantify tissue reservoir size and the dynamics of viral subpopulations in archived, longitudinal samples of cerebrospinal fluid cells and supernatant and peripheral blood mononuclear cells and plasma. Here we will evaluate viral subpopulation interactions occurring after antiretroviral treatment interruption, which provides a substantial perturbation of steady state viral and cellular dynamics to anchor the observations. We will apply phylogenetic methods to viral population sequences from CNS and blood over time to assess population dynamics. The study sample comprises a unique, densely serially sampled group of 10 HIV+ subjects undergoing antiretroviral (ART) treatment interruption or viral rebound in the face of continued ART. The project will generate approximately 1.2 million viral sequences. These will be analyzed to delineate how the CNS viral reservoir interacts dynamically with other viral subpopulations and contributes to viral diversification and pathogenicity. The project also will measure the size of CNS viral reservoirs. After de-identification of human subjects, viral sequences will be posted as appropriate on public scientific data resource utilities and software generated for this project will be made publicly available.