Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
Department of Global Health, University of Washington, Seattle, WA, United States of America.
PLoS Pathog. 2020 Feb 5;16(2):e1008286. doi: 10.1371/journal.ppat.1008286. eCollection 2020 Feb.
A reservoir of HIV-infected cells that persists despite suppressive antiretroviral therapy (ART) is the source of viral rebound upon ART cessation and the major barrier to a cure. Understanding reservoir seeding dynamics will help identify the best timing for HIV cure strategies. Here we characterize reservoir seeding using longitudinal samples from before and after ART initiation in individuals who sequentially became infected with genetically distinct HIV variants (superinfected). We previously identified cases of superinfection in a cohort of Kenyan women, and the dates of both initial infection and superinfection were determined. Six women, superinfected 0.2-5.2 years after initial infection, were subsequently treated with ART 5.4-18.0 years after initial infection. We performed next-generation sequencing of HIV gag and env RNA from plasma collected during acute infection as well as every ~2 years thereafter until ART initiation, and of HIV DNA from PBMCs collected 0.9-4.8 years after viral suppression on ART. We assessed phylogenetic relationships between HIV DNA reservoir sequences and longitudinal plasma RNA sequences prior to ART, to determine proportions of initial and superinfecting variants in the reservoir. The proportions of initial and superinfection lineage variants present in the HIV DNA reservoir were most similar to the proportions present in HIV RNA immediately prior to ART initiation. Phylogenetic analysis confirmed that the majority of HIV DNA reservoir sequences had the smallest pairwise distance to RNA sequences from timepoints closest to ART initiation. Our data suggest that while reservoir cells are created throughout pre-ART infection, the majority of HIV-infected cells that persist during ART entered the reservoir near the time of ART initiation. We estimate the half-life of pre-ART DNA reservoir sequences to be ~25 months, which is shorter than estimated reservoir decay rates during suppressive ART, implying continual decay and reseeding of the reservoir up to the point of ART initiation.
尽管有抑制性抗逆转录病毒疗法（ART），但仍存在感染 HIV 的细胞库，这是 ART 停止后病毒反弹的源头，也是治愈的主要障碍。了解储存库播种动力学将有助于确定治愈 HIV 的最佳时机。在这里，我们使用在开始接受 ART 之前和之后从个体中获得的纵向样本来描述储存库播种情况，这些个体先后感染了具有遗传上不同的 HIV 变体（超级感染）。我们之前在肯尼亚女性队列中发现了超级感染的病例，并确定了初始感染和超级感染的日期。在最初感染后 0.2-5.2 年发生超级感染的 6 名女性，在最初感染后 5.4-18.0 年随后接受了 ART 治疗。我们对急性感染期间采集的血浆中 HIV gag 和 env RNA 以及在开始接受 ART 后每 ~2 年采集的 HIV DNA 进行了下一代测序，以及在开始接受 ART 抑制病毒后 0.9-4.8 年采集的 PBMCs 中的 HIV DNA。我们评估了在开始接受 ART 之前，HIV DNA 储存库序列与纵向血浆 RNA 序列之间的系统发育关系，以确定储存库中初始和超级感染变体的比例。在开始接受 ART 之前，HIV DNA 储存库中存在的初始和超级感染谱系变体的比例与 HIV RNA 中存在的比例最相似。系统发育分析证实，大多数 HIV DNA 储存库序列与最接近开始接受 ART 时间点的 RNA 序列具有最小的成对距离。我们的数据表明，尽管在接受 ART 之前的感染过程中会产生储存库细胞，但在接受 ART 期间持续存在的大多数感染 HIV 的细胞是在接受 ART 启动时进入储存库的。我们估计，接受 ART 前 DNA 储存库序列的半衰期约为 25 个月，比在抑制性 ART 期间估计的储存库衰减率短，这意味着在开始接受 ART 之前，储存库不断衰减和重新播种。
