Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape

• Published in: Nature communications Vol. 13; no. 1; pp. 4958 - 12
• Main Authors: Zhao, Zhennan, Zhou, Jingya, Tian, Mingxiong, Huang, Min, Liu, Sheng, Xie, Yufeng, Han, Pu, Bai, Chongzhi, Han, Pengcheng, Zheng, Anqi, Fu, Lutang, Gao, Yuanzhu, Peng, Qi, Li, Ying, Chai, Yan, Zhang, Zengyuan, Zhao, Xin, Song, Hao, Qi, Jianxun, Wang, Qihui, Wang, Peiyi, Gao, George F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.08.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/1; 101/28; 631/326/596/4130; 631/45/612/1256; 631/535/1258/1259; 82/103; 82/29; 82/80; 82/83; ACE2; Angiotensin-Converting Enzyme 2; Antibodies, Monoclonal - genetics; Antibodies, Neutralizing - genetics; Binding; Conformation; COVID-19; Epitopes; Humanities and Social Sciences; Humans; Monoclonal antibodies; multidisciplinary; Mutagenesis; Mutation; Receptors, Virus - metabolism; SARS-CoV-2 - genetics; Science; Science (multidisciplinary); Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus; Stability
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-32665-7

Omicron SARS-CoV-2 is rapidly spreading worldwide. To delineate the impact of emerging mutations on spike’s properties, we performed systematic structural analyses on apo Omicron spike and its complexes with human ACE2 or S309 neutralizing antibody (NAb) by cryo-EM. The Omicron spike preferentially adopts the one-RBD-up conformation both before and after ACE2 binding, which is in sharp contrast to the orchestrated conformational changes to create more up-RBDs upon ACE2 binding as observed in the prototype and other four variants of concern (VOCs). Furthermore, we found that S371L, S373P and S375F substitutions enhance the stability of the one-RBD-up conformation to prevent exposing more up-RBDs triggered by ACE2 binding. The increased stability of the one-RBD-up conformation restricts the accessibility of S304 NAb, which targets a cryptic epitope in the closed conformation, thus facilitating the immune evasion by Omicron. These results expand our understanding of Omicron spike’s conformation, receptor binding and antibody evasion mechanism. The SARS-CoV-2 Omicron variant spreads rapidly. Here the authors show that Omicron S preferentially adopts the one-RBD-up conformation, which leads to a non-RBM-binding monoclonal antibody escape. Mutagenesis reveals that S371L, S373P and S375F substitutions enhance the conformational stability.