Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens

A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.

HIV疫苗研发面临的核心挑战之一，在于筛选出可诱导广谱中和抗体（broadly neutralizing antibodies，bNAbs）的免疫原。尽管目前在bNAbs的分离与表征领域已取得显著进展，但其所识别的表位普遍免疫原性较弱。因此，截至当前所有研发的候选疫苗，均未能诱导出针对HIV包膜蛋白（envelope protein，Env）的令人满意的中和抗体水平。针对免疫原性低下这一难题，一种可行策略是基于从罕见个体中获取的包膜（envelope，env）基因构建疫苗，这类个体被称为精英中和者（elite neutralizers，ENs），其曾携带可诱导bNAbs形成的特定序列。从这类个体中筛选得到的Env蛋白，可能具备尚未被阐明的罕见结构特征，能够增强bNAbs所识别表位的免疫原性。本研究描述了从一名产生了异常广谱且强效bNAbs的EN体内回收env基因的过程。由于缺乏纵向样本，我们结合单时间点采集的血浆与前病毒序列，以推断系统发育树（phylogenetic tree）。通过将祖先重建（ancestral reconstruction）数据与病毒中和数据相结合，我们得以在该个体体内演化出的海量病毒准种中进行筛选，识别出那些似乎定义了“从中和敏感Env向EN血浆中出现的中和抵抗Env”转变的节点对应的包膜序列。来自这些节点的合成基因在感染性实验中具备功能活性，且可被bNAbs有效中和，有望为HIV疫苗研发提供一类全新的免疫原来源。