Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants
Abstract Background The receptor-binding domain (RBD) variants of SARS-CoV-2 could impair antibody-mediated neutralization of the virus by host immunity; thus, prospective surveillance of antibody escape mutants and understanding the evolution of RBD are urgently needed. Methods Using the single B c...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | Genome Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13073-021-00985-w |
| _version_ | 1818890721683308544 |
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| author | Chunyan Yi Xiaoyu Sun Yixiao Lin Chenjian Gu Longfei Ding Xiao Lu Zhuo Yang Yaguang Zhang Liyan Ma Wangpeng Gu Aidong Qu Xu Zhou Xiuling Li Jianqing Xu Zhiyang Ling Youhua Xie Hongzhou Lu Bing Sun |
| author_facet | Chunyan Yi Xiaoyu Sun Yixiao Lin Chenjian Gu Longfei Ding Xiao Lu Zhuo Yang Yaguang Zhang Liyan Ma Wangpeng Gu Aidong Qu Xu Zhou Xiuling Li Jianqing Xu Zhiyang Ling Youhua Xie Hongzhou Lu Bing Sun |
| author_sort | Chunyan Yi |
| collection | DOAJ |
| description | Abstract Background The receptor-binding domain (RBD) variants of SARS-CoV-2 could impair antibody-mediated neutralization of the virus by host immunity; thus, prospective surveillance of antibody escape mutants and understanding the evolution of RBD are urgently needed. Methods Using the single B cell cloning technology, we isolated and characterized 93 RBD-specific antibodies from the memory B cells of four COVID-19 convalescent individuals in the early stage of the pandemic. Then, global RBD alanine scanning with a panel of 19 selected neutralizing antibodies (NAbs), including several broadly reactive NAbs, was performed. Furthermore, we assessed the impact of single natural mutation or co-mutations of concern at key positions of RBD on the neutralization escape and ACE2 binding function by recombinant proteins and pseudoviruses. Results Thirty-three amino acid positions within four independent antigenic sites (1 to 4) of RBD were identified as valuable indicators of antigenic changes in the RBD. The comprehensive escape mutation map not only confirms the widely circulating strains carrying important immune escape RBD mutations such as K417N, E484K, and L452R, but also facilitates the discovery of new immune escape-enabling mutations such as F486L, N450K, F490S, and R346S. Of note, these escape mutations could not affect the ACE2 binding affinity of RBD, among which L452R even enhanced binding. Furthermore, we showed that RBD co-mutations K417N, E484K, and N501Y present in B.1.351 appear more resistant to NAbs and human convalescent plasma from the early stage of the pandemic, possibly due to an additive effect. Conversely, double mutations E484Q and L452R present in B.1.617.1 variant show partial antibody evasion with no evidence for an additive effect. Conclusions Our study provides a global view of the determinants for neutralizing antibody recognition, antigenic conservation, and RBD conformation. The in-depth escape maps may have value for prospective surveillance of SARS-CoV-2 immune escape variants. Special attention should be paid to the accumulation of co-mutations at distinct major antigenic sites. Finally, the new broadly reactive NAbs described here represent new potential opportunities for the prevention and treatment of COVID-19. |
| first_indexed | 2024-12-19T17:29:25Z |
| format | Article |
| id | doaj.art-abd6694f3c9440cb879d9d5eacd4c115 |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-12-19T17:29:25Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-abd6694f3c9440cb879d9d5eacd4c1152022-12-21T20:12:29ZengBMCGenome Medicine1756-994X2021-10-0113111710.1186/s13073-021-00985-wComprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variantsChunyan Yi0Xiaoyu Sun1Yixiao Lin2Chenjian Gu3Longfei Ding4Xiao Lu5Zhuo Yang6Yaguang Zhang7Liyan Ma8Wangpeng Gu9Aidong Qu10Xu Zhou11Xiuling Li12Jianqing Xu13Zhiyang Ling14Youhua Xie15Hongzhou Lu16Bing Sun17State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghai Public Health Clinical Center, Shanghai Medical College, Fudan UniversityKey Laboratory of Medical Molecular Virology (MOE/MOH), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Medical College, Fudan UniversityShanghai Public Health Clinical Center, Shanghai Medical College, Fudan UniversityState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghai Institute of Biological Products Co., LtdShanghai Institute of Biological Products Co., LtdShanghai Institute of Biological Products Co., LtdShanghai Public Health Clinical Center, Shanghai Medical College, Fudan UniversityState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesKey Laboratory of Medical Molecular Virology (MOE/MOH), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Medical College, Fudan UniversityShanghai Public Health Clinical Center, Shanghai Medical College, Fudan UniversityState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesAbstract Background The receptor-binding domain (RBD) variants of SARS-CoV-2 could impair antibody-mediated neutralization of the virus by host immunity; thus, prospective surveillance of antibody escape mutants and understanding the evolution of RBD are urgently needed. Methods Using the single B cell cloning technology, we isolated and characterized 93 RBD-specific antibodies from the memory B cells of four COVID-19 convalescent individuals in the early stage of the pandemic. Then, global RBD alanine scanning with a panel of 19 selected neutralizing antibodies (NAbs), including several broadly reactive NAbs, was performed. Furthermore, we assessed the impact of single natural mutation or co-mutations of concern at key positions of RBD on the neutralization escape and ACE2 binding function by recombinant proteins and pseudoviruses. Results Thirty-three amino acid positions within four independent antigenic sites (1 to 4) of RBD were identified as valuable indicators of antigenic changes in the RBD. The comprehensive escape mutation map not only confirms the widely circulating strains carrying important immune escape RBD mutations such as K417N, E484K, and L452R, but also facilitates the discovery of new immune escape-enabling mutations such as F486L, N450K, F490S, and R346S. Of note, these escape mutations could not affect the ACE2 binding affinity of RBD, among which L452R even enhanced binding. Furthermore, we showed that RBD co-mutations K417N, E484K, and N501Y present in B.1.351 appear more resistant to NAbs and human convalescent plasma from the early stage of the pandemic, possibly due to an additive effect. Conversely, double mutations E484Q and L452R present in B.1.617.1 variant show partial antibody evasion with no evidence for an additive effect. Conclusions Our study provides a global view of the determinants for neutralizing antibody recognition, antigenic conservation, and RBD conformation. The in-depth escape maps may have value for prospective surveillance of SARS-CoV-2 immune escape variants. Special attention should be paid to the accumulation of co-mutations at distinct major antigenic sites. Finally, the new broadly reactive NAbs described here represent new potential opportunities for the prevention and treatment of COVID-19.https://doi.org/10.1186/s13073-021-00985-wSARS-CoV-2Neutralizing antibodiesRBD antigenic sitsEscape variants |
| spellingShingle | Chunyan Yi Xiaoyu Sun Yixiao Lin Chenjian Gu Longfei Ding Xiao Lu Zhuo Yang Yaguang Zhang Liyan Ma Wangpeng Gu Aidong Qu Xu Zhou Xiuling Li Jianqing Xu Zhiyang Ling Youhua Xie Hongzhou Lu Bing Sun Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants Genome Medicine SARS-CoV-2 Neutralizing antibodies RBD antigenic sits Escape variants |
| title | Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants |
| title_full | Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants |
| title_fullStr | Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants |
| title_full_unstemmed | Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants |
| title_short | Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants |
| title_sort | comprehensive mapping of binding hot spots of sars cov 2 rbd specific neutralizing antibodies for tracking immune escape variants |
| topic | SARS-CoV-2 Neutralizing antibodies RBD antigenic sits Escape variants |
| url | https://doi.org/10.1186/s13073-021-00985-w |
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