Intrahost HIV population dynamics in CNS and other tissues

描述(申请人提供)：艾滋病毒在宿主内产生复杂的遗传群体，并在抗逆转录病毒治疗下在各种细胞类型和组织中保持潜伏，这是治疗治愈的障碍。然而，对于不同组织中潜伏的病毒库的相对大小，如中枢神经系统(CNS)，人们知之甚少，更不知道不同组织中病毒亚群之间随着时间的推移进行交换的情况。深度测序技术允许对这些人群进行广泛采样。以前的研究一直受到中枢神经系统病毒多样性样本有限的阻碍，因为他们只研究了单个或偶尔多个稀疏时间点。设计可行的病毒根除战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。为了解决这些知识差距，我们将应用最新开发的技术，数字聚合酶链式反应(DPCR)和超深度测序(UDS)，来量化组织储存库的大小和脑脊液细胞以及培养上清和外周血单核细胞和血浆的纵向样本中病毒亚群的动态。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，以支撑观察。随着时间的推移，我们将对来自CNS和血液的病毒种群序列应用系统发育学方法来评估种群动态。研究样本包括一组独特的、密集连续抽样的10名艾滋病毒受试者，他们正在接受抗逆转录病毒(ART)治疗的中断或在继续抗逆转录病毒治疗的情况下病毒反弹。该项目将产生大约120万个病毒序列。将对这些进行分析，以描绘CNS病毒库如何与其他病毒亚群动态相互作用，并有助于病毒的多样化和致病性。该项目还将测量中枢神经系统病毒库的大小。在消除人类受试者的身份后，病毒序列将酌情张贴在公共科学数据资源实用程序上，为该项目生成的软件将公开提供。

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.