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Rao X, Zhao R, Tong Z, Guo S, Peng W, Liu K, Li S, Wu L, Tong J, Chai Y, Han P, Wang F, Jia P, Li Z, Zhao X, Li D, Zhang R, Zhang X, Zou W, Li W, Wang Q, Gao GF, Wu Y, Dai L, Gao F. Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2314193120. [PMID: 38109549 PMCID: PMC10756187 DOI: 10.1073/pnas.2314193120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/20/2023] Open
Abstract
Currently, monoclonal antibodies (MAbs) targeting the SARS-CoV-2 receptor binding domain (RBD) of spike (S) protein are classified into seven classes based on their binding epitopes. However, most of these antibodies are seriously impaired by SARS-CoV-2 Omicron and its subvariants, especially the recent BQ.1.1, XBB and its derivatives. Identification of broadly neutralizing MAbs against currently circulating variants is imperative. In this study, we identified a "breathing" cryptic epitope in the S protein, named as RBD-8. Two human MAbs, BIOLS56 and IMCAS74, were isolated recognizing this epitope with broad neutralization abilities against tested sarbecoviruses, including SARS-CoV, pangolin-origin coronaviruses, and all the SARS-CoV-2 variants tested (Omicron BA.4/BA.5, BQ.1.1, and XBB subvariants). Searching through the literature, some more RBD-8 MAbs were defined. More importantly, BIOLS56 rescues the immune-evaded antibody, RBD-5 MAb IMCAS-L4.65, by making a bispecific MAb, to neutralize BQ.1 and BQ.1.1, thereby producing an MAb to cover all the currently circulating Omicron subvariants. Structural analysis reveals that the neutralization effect of RBD-8 antibodies depends on the extent of epitope exposure, which is affected by the angle of antibody binding and the number of up-RBDs induced by angiotensin-converting enzyme 2 binding. This cryptic epitope which recognizes non- receptor binding motif (non-RBM) provides guidance for the development of universal therapeutic antibodies and vaccines against COVID-19.
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Affiliation(s)
- Xia Rao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
- Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Runchu Zhao
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- Institute of Physical Science and Information, Anhui University, Hefei230039, China
| | - Zhou Tong
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- Shanxi Academy of Advanced Research and Innovation, Taiyuan030032, China
| | - Shuxin Guo
- Faculty of Health Sciences, University of Macau, Macau Special Administrative Region999078, China
| | - Weiyu Peng
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen518038, China
| | - Kefang Liu
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Shihua Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Lili Wu
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Jianyu Tong
- Shanxi Academy of Advanced Research and Innovation, Taiyuan030032, China
| | - Yan Chai
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Pu Han
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Feiran Wang
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei230026, China
| | - Peng Jia
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Zhaohui Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Xin Zhao
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Dedong Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Rong Zhang
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
- Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning530004, China
| | - Xue Zhang
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
| | - Weiwei Zou
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
| | - Weiwei Li
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Qihui Wang
- University of Chinese Academy of Sciences, Beijing100049, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - George Fu Gao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
- Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing100101, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Yan Wu
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
| | - Lianpan Dai
- University of Chinese Academy of Sciences, Beijing100049, China
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Feng Gao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
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