Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA.
Department of Virology, Harvard Medical School, Boston, Massachusetts, USA.
J Virol. 2024 Mar 19;98(3):e0172023. doi: 10.1128/jvi.01720-23. Epub 2024 Feb 27.
The rational design of HIV-1 immunogens to trigger the development of broadly neutralizing antibodies (bNAbs) requires understanding the viral evolutionary pathways influencing this process. An acute HIV-1-infected individual exhibiting >50% plasma neutralization breadth developed neutralizing antibody specificities against the CD4-binding site (CD4bs) and V1V2 regions of Env gp120. Comparison of pseudoviruses derived from early and late autologous sequences demonstrated the development of >2 log resistance to VRC13 but not to other CD4bs-specific bNAbs. Mapping studies indicated that the V3 and CD4-binding loops of Env gp120 contributed significantly to developing resistance to the autologous neutralizing response and that the CD4-binding loop (CD4BL) specifically was responsible for the developing resistance to VRC13. Tracking viral evolution during the development of this cross-neutralizing CD4bs response identified amino acid substitutions arising at only 4 of 11 known VRC13 contact sites (K282, T283, K421, and V471). However, each of these mutations was external to the V3 and CD4BL regions conferring resistance to VRC13 and was transient in nature. Rather, complete resistance to VRC13 was achieved through the cooperative expression of a cluster of single amino acid changes within and immediately adjacent to the CD4BL, including a T359I substitution, exchange of a potential -linked glycosylation (PNLG) site to residue S362 from N363, and a P369L substitution. Collectively, our data characterize complex HIV-1 evolution in an individual developing resistance to a VRC13-like neutralizing antibody response and identify novel VRC13-associated escape mutations that may be important to inducing VRC13-like bNAbs for lineage-based immunogens.IMPORTANCEThe pursuit of eliciting broadly neutralizing antibodies (bNAbs) through vaccination and their use as therapeutics remains a significant focus in the effort to eradicate HIV-1. Key to our understanding of this approach is a more extensive understanding of bNAb contact sites and susceptible escape mutations in HIV-1 envelope (). We identified a broad neutralizer exhibiting VRC13-like responses, a non-germline restricted class of CD4-binding site antibody distinct from the well-studied VRC01-class. Through longitudinal envelope sequencing and Env-pseudotyped neutralization assays, we characterized a complex escape pathway requiring the cooperative evolution of four amino acid changes to confer complete resistance to VRC13. This suggests that VRC13-class bNAbs may be refractory to rapid escape and attractive for therapeutic applications. Furthermore, the identification of longitudinal viral changes concomitant with the development of neutralization breadth may help identify the viral intermediates needed for the maturation of VRC13-like responses and the design of lineage-based immunogens.
HIV-1 免疫原的理性设计，以引发广泛中和抗体（bNAb）的产生，需要了解影响这一过程的病毒进化途径。在急性 HIV-1 感染个体中，表现出 >50%的血浆中和广度，会产生针对 Env gp120 的 CD4 结合位点（CD4bs）和 V1V2 区域的中和抗体特异性。比较源自早期和晚期自体序列的假病毒表明，对 VRC13 的抗性发展>2 个对数，但对其他 CD4bs 特异性 bNAb 没有抗性。作图研究表明，Env gp120 的 V3 和 CD4 结合环对产生对自体中和反应的抗性有显著贡献，而 CD4 结合环（CD4BL）特异性负责产生对 VRC13 的抗性。在这种交叉中和 CD4bs 反应的发展过程中追踪病毒进化，仅在 11 个已知 VRC13 接触位点中的 4 个（K282、T283、K421 和 V471）出现氨基酸取代。然而，这些突变中的每一个都在 V3 和 CD4BL 区域之外，对 VRC13 产生抗性，并且本质上是短暂的。通过在 CD4BL 内和紧邻的位置表达一组单个氨基酸变化，包括 T359I 取代、将潜在的 -连接糖基化（PNLG）位点从 N363 交换到 S362，以及 P369L 取代，完全抵抗 VRC13。总的来说，我们的数据描绘了个体中对 VRC13 样中和抗体反应产生抗性的复杂 HIV-1 进化，并确定了新的 VRC13 相关逃逸突变，这些突变可能对诱导基于谱系的免疫原的 VRC13 样 bNAb 很重要。
重要性
通过接种疫苗诱导广泛中和抗体（bNAb）并将其用作治疗剂仍然是消除 HIV-1 的重要焦点。我们对这种方法的理解的关键是更广泛地了解 HIV-1 包膜（）中的 bNAb 接触位点和易感性逃逸突变。我们鉴定了一种具有 VRC13 样反应的广谱中和剂，这是一种非种系限制的 CD4 结合位点抗体，与研究得很好的 VRC01 类不同。通过纵向包膜测序和 Env 假型中和测定，我们描述了一种复杂的逃逸途径，需要四个氨基酸变化的协同进化才能完全抵抗 VRC13。这表明 VRC13 类 bNAb 可能对快速逃逸具有抗性，并且适合治疗应用。此外，与中和广度发展同时发生的纵向病毒变化的鉴定，可能有助于确定 VRC13 样反应成熟和基于谱系的免疫原设计所需的病毒中间体。
