Despite adherence to antiretroviral therapy (ART), low levels of plasma virus persist in most individuals with HIV-1. In a small subset of these individuals, this non-suppressible viremia is detected by routine clinical testing (plasma HIV-1 RNA >20 copies/ml) and has been shown to be of clonal cellular origin. The mechanisms by which these virions escape immune clearance is not defined, but reduced binding and neutralization of their surface envelope protein (Env) by antibodies (Abs) may contribute. To assess this possibility, we measured the monoclonal antibody (mAb) sensitivity of HIV-1 Env in plasma virus from 4 well-characterized individuals on ART with non-suppressible viremia. Thirty-two env plasma sequences were used to produce pseudovirus for neutralization assays with both autologous plasma and a panel of 15 recombinant antibodies that targeted different regions of HIV-1 Env protein. We found that autologous plasma had no neutralizing activity against the pseudoviruses consistent with persistence of viremia. In general, the Envs from the non-suppressible plasma virus were also less sensitive to mAb neutralization compared controls: tier 1 (6535), tier 2 (TRO11) or tier 3 (PVO) subtype B envs , although variability across Envs was evident. Two Env protein variants from one donor, R-09_A8 and R-09_C2, were less sensitive to VRC01 likely due to an additional N-glycan site at a VRC01 contact site and longer V5 regions. Most of the donor Envs were sensitive to at least two of three V3-glycan mAbs except for variant C-03_A6, which showed reduced sensitivity to all three. The CD4 binding site mAb 3BNC117 and the Gp41-specific mAb 10E8 neutralized pseudoviruses from all donors, indicating the potential for clearance of persistent viremia in these individuals studied.

Author summary: In a fraction of individuals on suppressive antiretroviral therapy (ART), episodes of persistent low-level viremia can be observed that is not attributed to ineffective ART and/or non-adherence. Previously in three individuals, we have shown that this viremia results from large HIV-1 infected T cell clones harboring replication-competent proviruses. The factor(s) that allow these infectious virions to be detected and not cleared by the immune system is unknown, suggesting that these virions can evade humoral responses. Using single genome sequencing, we amplified the env from plasma derived virions from these individuals, cloned env -containing amplicons into an expression vector to produce pseudo viruses, which we tested against either their autologous contemporaneous autologous immunoglobulins (Ig) or a panel of 15 recombinant monoclonal antibodies. The results revealed that these pseudovirus were not neutralized by their autologous Igs and exhibited complex pseudovirus-specific susceptibility profiles for the monoclonal antibodies they were tested against. Collectively, our findings suggest that despite resistance to autologous Ig, likely combinations of monoclonal antibodies will be needed to clear this persistent viremia.

尽管患者坚持接受抗逆转录病毒治疗（ART），大多数感染HIV-1的个体中仍存在低水平的血浆病毒。在一小部分这些个体中，通过常规临床检测可以发现非抑制性病毒血症（血浆中的HIV-1 RNA >20拷贝/ml），并且已经证明这种非抑制性病毒血症是由克隆细胞起源引起的。这些病毒逃避免疫清除的机制尚不清楚，但抗体会减少它们表面包膜蛋白（Env）的结合和中和作用可能是原因之一。为了评估这一可能性，我们测量了来自4名在ART治疗下具有非抑制性病毒血症的个体中血浆病毒HIV-1 Env的单克隆抗体（mAb）敏感性。使用32个env血浆序列来产生假病毒，并用自体血浆和一组针对HIV-1 Env蛋白不同区域的15种重组抗体进行中和试验。我们发现，自体血浆对这些假病毒没有中和活性，这与持续存在的病毒血症一致。总的来说，来自非抑制性血浆病毒的Env通常也比对照（包括Tier 1的6535、Tier 2的TRO11或Tier 3的PVO亚型B env）更不敏感于mAb中和作用，尽管不同Env之间存在差异。一名供体来源的两个Env蛋白变体R-09_A8和R-09_C2对VRC01的敏感性降低，可能是由于在VRC01结合位点上多出了一个N-糖基化位点以及更长的V5区域。大多数供体的Env都对三种V3-glycan mAbs中的至少两种敏感，但变体C-03_A6显示出对这三者的中和敏感度降低。CD4结合位点mAb 3BNC117和Gp41特异性mAb 10E8可以中和所有供体的假病毒，表明清除这些个体中的持续性病毒血症是可能的。

作者总结： 在一小部分接受抑制性抗逆转录病毒治疗（ART）的人群中，可观察到持续低水平的病毒血症，这一现象不能归因于不充分的ART或非依从性。之前我们在三名患者中已经证明这种病毒血症是由携带复制功能完整的HIV-1前病毒的大T细胞克隆引起的。允许这些感染病毒被检测出且未被免疫系统清除的因素尚不清楚，这表明这些病毒能够逃避体液反应。使用单基因组测序技术，我们从这些个体的血浆中扩增了env，将含env的扩增片段克隆到表达载体中以产生假病毒，并测试了它们对自体当代免疫球蛋白（Ig）或一组15种重组单克隆抗体的敏感性。结果显示，这些假病毒未被其相应的自体Igs中和，并且在与所测试的单克隆抗体相互作用时表现出复杂的伪型特异性敏感度模式。总的来说，我们的发现表明尽管存在对自体Ig的抵抗力，但很可能需要多种mAb组合来清除这种持续性病毒血症。