Uncovering a conserved vulnerability site in SARS-CoV-2 by a human antibody

An essential step for SARS-CoV-2 infection is the attachment to the host cell receptor by its Spike receptor-binding domain (RBD). Most of the existing RBD-targeting neutralizing antibodies block the receptor-binding motif (RBM), a mutable region with the potential to generate neutralization escape mutants. Here, we isolated and structurally characterized a non-RBM-targeting monoclonal antibody (FD20) from convalescent patients. FD20 engages the RBD at an epitope distal to the RBM with a KD of 5.6 nM, neutralizes SARS-CoV-2 including the current Variants of Concern such as B.1.1.7, B.1.351, P.1, and B.1.617.2 (Delta), displays modest cross-reactivity against SARS-CoV, and reduces viral replication in hamsters. The epitope coincides with a predicted 'ideal' vulnerability site with high functional and structural constraints. Mutation of the residues of the conserved epitope variably affects FD20-binding but confers little or no resistance to neutralization. Finally, in vitro mode-of-action characterization and negative-stain electron microscopy suggests a neutralization mechanism by which FD20 destructs the Spike. Our results reveal a conserved vulnerability site in the SARS-CoV-2 Spike for the development of potential antiviral drugs.

新型冠状病毒（Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2）感染的关键步骤之一，是通过其刺突蛋白受体结合结构域（Receptor-binding Domain, RBD）与宿主细胞受体结合。现有绝大多数靶向RBD的中和抗体会阻断受体结合基序（Receptor-binding Motif, RBM）——这是一段易发生突变、可产生中和逃逸突变株的区域。本研究从康复期患者体内分离得到一株非靶向RBM的单克隆抗体（FD20），并完成了其结构表征。FD20与RBD结合的表位位于RBM远端区域，解离常数（Dissociation Constant, KD）为5.6 nM；该抗体可中和包括当前主流关切变异株在内的SARS-CoV-2，具体包括B.1.1.7、B.1.351、P.1及B.1.617.2（德尔塔Delta）；同时对严重急性呼吸综合征冠状病毒（SARS-CoV）展现出轻度交叉反应活性，并可在仓鼠体内抑制病毒复制。该表位与一个被预测为"理想"的病毒脆弱位点高度契合，该位点具有严格的功能与结构约束性。保守表位残基的突变会不同程度影响FD20与抗原的结合，但几乎无法赋予病毒中和逃逸抗性。最后，体外作用模式表征及负染电子显微镜（Negative-stain Electron Microscopy）实验结果显示，FD20通过破坏刺突蛋白的方式发挥中和作用。本研究结果揭示了SARS-CoV-2刺突蛋白上一处保守的脆弱位点，可为潜在抗病毒药物的研发提供关键靶点。