On Aug. 25th, 2021, the joint research group of Junyu Xiao and Xiaoliang Xie from the Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking-Tsinghua Center for Life Sciences(CLS), the School of Life Sciences jointly published a paper, entitled “Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants” in Cell Research. This paper analyzed a series of fully humanized neutralizing antibodies targeting the B.1.351 spike protein’s combination strategies and responses to the Delta mutant based on structural information.

　　As the SARS-CoV-2 variants spread worldwide, mutant strains continue to emerge. The World Health Organization has successively defined mutant strains as "Variant of Concern (VOCs)". To name a few, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta). The spread of these variants has brought influential challenges to the global anti-epidemic work and defines it urgent to screen for highly active neutralizing antibodies against these new variants.

　　In the previous studies, Xiaoliang Xie's team discovered a set of monoclonal antibodies that can effectively neutralize the B.1.351 mutant by analyzing the immune responses of long-term convalescents and vaccine recipients to the B.1.351 mutant (Cao et al., Cell Research 31:732-741, 2021). This work further analyzes the molecular mechanism and pairing of these neutralizing antibodies.

　　Through the pseudovirus neutralization experiment, it was found that the two antibodies of BD-812 and BD-836 had very high activity, and the neutralization of the B.1.351 pseudovirus was close to the pM level. High-resolution single-particle cryo-electron microscopy (cryo-EM) studies have shown that BD-812 and BD-836 bind to the left and right shoulders of the spike protein’s receptor-binding domain (RBD) of the B.1.351 mutant strain, respectively. BD-812 and BD-836 have binding epitopes that do not interfere with each other and can directly hinder the binding of RBD to the ACE2 receptor. It is particularly essential that the binding of BD-812 and BD-836 to RBD is not affected by the two mutation sites of L452R and T478K in the Delta mutant, and the pseudovirus experiments also show that they can effectively neutralize the B.1.617.2 variant.

　　The work also analyzes how other antibodies target the B.1.351 spike protein. The combination of BD-821 and BD-771 is very similar to the BD-812/BD-836 mentioned above binding mode, and both also have potent neutralizing activity against the Delta mutant. However, BD-821 covered a smaller RBD interface than BD-812, explaining its weaker neutralizing activity. BD-813 binds to the back of the RBD and can directly block the binding to ACE2 and maintains activity against the Delta mutant. BD-744, BD-667, and BD-804 bind to the “chest” of RBD and do not overlap the binding epitope of ACE2, but the epitopes of these antibodies all involve the Leu452 site, and the Delta mutant had a harrowing escape against them. The L452R mutation in the Delta mutant would render many neutralizing antibodies targeting this region ineffective.

　　In conclusion, this study systematically analyzed a series of fully humanized neutralizing antibodies targeting the B.1.351 spike protein and their combination strategies and responses to the Delta mutant based on structural information. In particular, the BD-812/BD-836 antibody combination from long-term convalescents performed very well, showing pM-level activity against the B.1.617.1 and B.1.617.2 variants, and is expected to become a candidate drug for SARS-CoV-2 VOCs.

　　Dr. Shuo Du, Ph.D. candidates Pulan Liu and Zhiying Zhang are the co-first authors of this paper. Prof. Junyu Xiao, Prof. Xiaoliang Xie and Dr. Yunlong Cao are the co-corresponding authors. The Youchun Wang Group and Weijin Huang Group from the National Institutes for Food and Drug Control (NIFDC) provided strong support for the pseudovirus neutralization experiment. The research was supported by the State Key Laboratory of Protein and Plant Gene Research, the National key research and development plan, the National Natural Science Foundation of China, and the Qidong Industrial Innovation Fund of the School of Life Sciences, Peking University.

　　DOI: https://doi.org/10.1038/s41422-021-00555-0