Project 2 - Identification of the source of viral rebound using SIV proviral genome analysis

摘要 制定成功策略以延迟并最终防止病毒反弹的关键 在治疗中断时，确定病毒反弹的来源和机制。正在进行 关于反跳来源的争论包括：1）CD 4 + T细胞或组织巨噬细胞 是反弹的主要来源，2）淋巴细胞中正在进行的复制周期是否 组织有助于反弹，3）HIV-1感染是否可以主动驱动克隆扩张 通过整合到增殖相关的基因中。我们在此提议探索 这些问题在SIV模型的合作研究中使用了我们开发的新技术， 组利用HIV-1前病毒的全长单基因组测序，我们最近发现， 患者细胞中的绝大多数（>95%）HIV-1前病毒是有缺陷的。这一发现 这大大复杂化了对诸如反弹病毒血症的来源、 治疗期间持续的病毒进化，以及克隆扩增在病毒持久性中的作用。在 初步研究表明，大多数SIV前病毒也是有缺陷的。通过关注 那些没有缺陷的前病毒，我们将能够更好地了解细胞来源， 病毒反弹，并解决有关治疗期间持续病毒复制的争议 以及通过受感染细胞的增殖来扩大储库。这些研究将在 与霍普金斯的同事合作，他们将采用其他新的检测方法来检测复制能力 本申请中描述的经处理猕猴队列中的SIV。这些研究 应该能为病毒反弹的来源提供新的见解。

Abstract The key to developing successful strategies to delay and ultimately prevent viral rebound upon treatment interruption is to identify the source and mechanisms of viral rebound. Ongoing debates regarding the source of rebound include 1) whether CD4+ T cells or tissue macrophages are the dominant source of rebound, 2) whether ongoing cycles of replication in the lymphoid tissue contribute to rebound, 3) whether HIV-1 infection may actively drive the clonal expansion of infected cells through integration into proliferation-related genes. We propose here to explore these issues in collaborative studies in the SIV model using a new technology developed by our group. Using full length, single genome sequencing of HIV-1 proviruses, we have recently shown that the vast majority (>95%) of HIV-1 proviruses in patient cells are defective. This discovery greatly complicates analysis of issues such as the source of rebound viremia, the possibility of ongoing viral evolution during treatment, and the role of clonal expansion in viral persistence. In preliminary studies, we have shown that most SIV proviruses are also defective. By focusing on those proviruses that are not defective, we will be able to better understand the cellular sources of viral rebound and to address controversies regarding ongoing viral replication during treatment and reservoir expansion through proliferation of infected cells. This studies will be carried out in conjunction with Hopkins colleagues who will employ other novel assays for replication-competent SIV in the cohorts of treated macaques described in the application. Together these studies should provide new insights into the sources of viral rebound.