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Zhang X, Wu J, Luo Y, Wang Y, Wu Y, Xu X, Zhang Y, Kong R, Chi Y, Sun Y, Chen S, He Q, Zhu F, Zhou Z. CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses. Brief Bioinform 2024; 25:bbae183. [PMID: 38653491 PMCID: PMC11036340 DOI: 10.1093/bib/bbae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/24/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Coronaviruses have threatened humans repeatedly, especially COVID-19 caused by SARS-CoV-2, which has posed a substantial threat to global public health. SARS-CoV-2 continuously evolves through random mutation, resulting in a significant decrease in the efficacy of existing vaccines and neutralizing antibody drugs. It is critical to assess immune escape caused by viral mutations and develop broad-spectrum vaccines and neutralizing antibodies targeting conserved epitopes. Thus, we constructed CovEpiAb, a comprehensive database and analysis resource of human coronavirus (HCoVs) immune epitopes and antibodies. CovEpiAb contains information on over 60 000 experimentally validated epitopes and over 12 000 antibodies for HCoVs and SARS-CoV-2 variants. The database is unique in (1) classifying and annotating cross-reactive epitopes from different viruses and variants; (2) providing molecular and experimental interaction profiles of antibodies, including structure-based binding sites and around 70 000 data on binding affinity and neutralizing activity; (3) providing virological characteristics of current and past circulating SARS-CoV-2 variants and in vitro activity of various therapeutics; and (4) offering site-level annotations of key functional features, including antibody binding, immunological epitopes, SARS-CoV-2 mutations and conservation across HCoVs. In addition, we developed an integrated pipeline for epitope prediction named COVEP, which is available from the webpage of CovEpiAb. CovEpiAb is freely accessible at https://pgx.zju.edu.cn/covepiab/.
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Affiliation(s)
- Xue Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - JingCheng Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Luo
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yilin Wang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yujie Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobin Xu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yufang Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruiying Kong
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 310058, China
- ZJU-UoE Institute, Zhejiang University, Haining 314400, China
| | - Yisheng Sun
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Shuqing Chen
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiaojun He
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Innovation Institute for Artificial Intelligence in Medicine, Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou 310018, China
| | - Feng Zhu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Innovation Institute for Artificial Intelligence in Medicine, Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou 310018, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 310058, China
| | - Zhan Zhou
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Innovation Institute for Artificial Intelligence in Medicine, Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou 310018, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 310058, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
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Guo L, Lin S, Chen Z, Cao Y, He B, Lu G. Targetable elements in SARS-CoV-2 S2 subunit for the design of pan-coronavirus fusion inhibitors and vaccines. Signal Transduct Target Ther 2023; 8:197. [PMID: 37164987 PMCID: PMC10170451 DOI: 10.1038/s41392-023-01472-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/12/2023] Open
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused devastating impacts on the public health and the global economy. Rapid viral antigenic evolution has led to the continual generation of new variants. Of special note is the recently expanding Omicron subvariants that are capable of immune evasion from most of the existing neutralizing antibodies (nAbs). This has posed new challenges for the prevention and treatment of COVID-19. Therefore, exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In sharp contrast to the massive accumulation of mutations within the SARS-CoV-2 receptor-binding domain (RBD), the S2 fusion subunit has remained highly conserved among variants. Hence, S2-based therapeutics may provide effective cross-protection against new SARS-CoV-2 variants. Here, we summarize the most recently developed broad-spectrum fusion inhibitors (e.g., nAbs, peptides, proteins, and small-molecule compounds) and candidate vaccines targeting the conserved elements in SARS-CoV-2 S2 subunit. The main focus includes all the targetable S2 elements, namely, the fusion peptide, stem helix, and heptad repeats 1 and 2 (HR1-HR2) bundle. Moreover, we provide a detailed summary of the characteristics and action-mechanisms for each class of cross-reactive fusion inhibitors, which should guide and promote future design of S2-based inhibitors and vaccines against new coronaviruses.
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Affiliation(s)
- Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Yang X, Chi H, Wu M, Wang Z, Lang Q, Han Q, Wang X, Liu X, Li Y, Wang X, Huang N, Bi J, Liang H, Gao Y, Zhao Y, Feng N, Yang S, Wang T, Xia X, Ge L. Discovery and characterization of SARS-CoV-2 reactive and neutralizing antibodies from humanized CAMouseHG mice through rapid hybridoma screening and high-throughput single-cell V(D)J sequencing. Front Immunol 2022; 13:992787. [PMID: 36211410 PMCID: PMC9545174 DOI: 10.3389/fimmu.2022.992787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
The coronavirus disease 2019 pandemic has caused more than 532 million infections and 6.3 million deaths to date. The reactive and neutralizing fully human antibodies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective detection tools and therapeutic measures. During SARS-CoV-2 infection, a large number of SARS-CoV-2 reactive and neutralizing antibodies will be produced. Most SARS-CoV-2 reactive and neutralizing fully human antibodies are isolated from human and frequently encoded by convergent heavy-chain variable genes. However, SARS-CoV-2 viruses can mutate rapidly during replication and the resistant variants of neutralizing antibodies easily survive and evade the immune response, especially in the face of such focused antibody responses in humans. Therefore, additional tools are needed to develop different kinds of fully human antibodies to compensate for current deficiency. In this study, we utilized antibody humanized CAMouseHG mice to develop a rapid antibody discovery method and examine the antibody repertoire of SARS-CoV-2 RBD-reactive hybridoma cells derived from CAMouseHG mice by using high-throughput single-cell V(D)J sequencing analysis. CAMouseHG mice were immunized by 28-day rapid immunization method. After electrofusion and semi-solid medium screening on day 12 post-electrofusion, 171 hybridoma clones were generated based on the results of SARS-CoV-2 RBD binding activity assay. A rather obvious preferential usage of IGHV6-1 family was found in these hybridoma clones derived from CAMouseHG mice, which was significantly different from the antibodies found in patients with COVID-19. After further virus neutralization screening and antibody competition assays, we generated a noncompeting two-antibody cocktail, which showed a potent prophylactic protective efficacy against SARS-CoV-2 in cynomolgus macaques. These results indicate that humanized CAMouseHG mice not only provide a valuable platform to obtain fully human reactive and neutralizing antibodies but also have a different antibody repertoire from humans. Thus, humanized CAMouseHG mice can be used as a good complementary tool in discovery of fully human therapeutic and diagnostic antibodies.
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Affiliation(s)
- Xi Yang
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
| | - Hang Chi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Meng Wu
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
| | - Zhenshan Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Qiaoli Lang
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
| | - Qiuxue Han
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China
| | - Xinyue Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Xueqin Liu
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
| | - Yuanguo Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiwen Wang
- Food and Drug Inspection Laboratory, Administration for Drug and Instrument Supervision and Inspection, Beijing, China
| | - Nan Huang
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
| | - Jinhao Bi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
| | - Hao Liang
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- *Correspondence: Liangpeng Ge, ; Tiecheng Wang, ; Xianzhu Xia,
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- *Correspondence: Liangpeng Ge, ; Tiecheng Wang, ; Xianzhu Xia,
| | - Liangpeng Ge
- Institute of Bioengineering, ChongQing Academy of Animal Sciences, Chongqing, China
- *Correspondence: Liangpeng Ge, ; Tiecheng Wang, ; Xianzhu Xia,
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