Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
Nat Commun. 2023 Jul 13;14(1):4186. doi: 10.1038/s41467-023-39837-z.
Most proviruses persisting in people living with HIV (PWH) on antiretroviral therapy (ART) are defective. However, rarer intact proviruses almost always reinitiate viral rebound if ART stops. Therefore, assessing therapies to prevent viral rebound hinges on specifically quantifying intact proviruses. We evaluated the same samples from 10 male PWH on ART using the two-probe intact proviral DNA assay (IPDA) and near full length (nfl) Q4PCR. Both assays admitted similar ratios of intact to total HIV DNA, but IPDA found ~40-fold more intact proviruses. Neither assay suggested defective proviruses decay over 10 years. However, the mean intact half-lives were different: 108 months for IPDA and 65 months for Q4PCR. To reconcile this difference, we modeled additional longitudinal IPDA data and showed that decelerating intact decay could arise from very long-lived intact proviruses and/or misclassified defective proviruses: slowly decaying defective proviruses that are intact in IPDA probe locations (estimated up to 5%, in agreement with sequence library based predictions). The model also demonstrates how misclassification can lead to underestimated efficacy of therapies that exclusively reduce intact proviruses. We conclude that sensitive multi-probe assays combined with specific nfl-verified assays would be optimal to document absolute and changing levels of intact HIV proviruses.
大多数在接受抗逆转录病毒疗法 (ART) 的艾滋病毒感染者 (PWH) 体内持续存在的前病毒都是有缺陷的。然而，如果停止 ART，罕见的完整前病毒几乎总是会重新引发病毒反弹。因此，评估预防病毒反弹的治疗方法取决于对完整前病毒的具体定量。我们使用两探针完整前病毒 DNA 检测法 (IPDA) 和近乎全长 (nfl) Q4PCR 评估了来自 10 名接受 ART 的男性 PWH 的相同样本。两种检测方法都承认了类似的完整前病毒与总 HIV DNA 的比例，但 IPDA 发现了大约 40 倍更多的完整前病毒。两种检测方法都没有表明缺陷前病毒在 10 年内衰减。然而，完整前病毒的平均半衰期不同：IPDA 为 108 个月，Q4PCR 为 65 个月。为了调和这一差异，我们对额外的纵向 IPDA 数据进行了建模，并表明完整前病毒衰减的减缓可能源于非常长寿的完整前病毒和/或分类错误的缺陷前病毒：在 IPDA 探针位置上缓慢衰减的完整缺陷前病毒（估计高达 5%，与基于序列库的预测一致）。该模型还展示了错误分类如何导致对专门减少完整前病毒的治疗方法的疗效估计不足。我们得出结论，敏感的多探针检测法与特定的 nfl 验证检测法相结合，将是记录完整 HIV 前病毒的绝对和变化水平的最佳方法。
